moorhen 0.0.1

package/baby-gru/monomers/a/A.cif

@@ -0,0 +1,271 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+A     A       "ADENOSINE-5'-MONOPHOSPHATE"     RNA     35     23     .     
+#
+data_comp_A
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+A       OP3     O       OP      -1      22.184      9.416       -6.467      
+A       P       P       P       0       23.061      10.073      -7.517      
+A       OP1     O       O       0       22.426      10.079      -8.894      
+A       OP2     O       OP      -1      24.478      9.532       -7.523      
+A       "O5'"   O       O2      0       23.184      11.622      -7.081      
+A       "C5'"   C       CH2     0       23.997      12.510      -7.889      
+A       "C4'"   C       CH1     0       23.959      13.900      -7.302      
+A       "O4'"   O       O2      0       24.489      13.865      -5.952      
+A       "C3'"   C       CH1     0       24.795      14.957      -8.033      
+A       "O3'"   O       OH1     0       24.040      15.590      -9.060      
+A       "C2'"   C       CH1     0       25.162      15.917      -6.899      
+A       "O2'"   O       OH1     0       24.142      16.849      -6.609      
+A       "C1'"   C       CH1     0       25.367      14.950      -5.735      
+A       N9      N       NR5     0       26.737      14.457      -5.612      
+A       C8      C       CR15    0       27.206      13.184      -5.839      
+A       N7      N       NRD5    0       28.493      13.056      -5.636      
+A       C5      C       CR56    0       28.908      14.321      -5.248      
+A       C6      C       CR6     0       30.172      14.840      -4.890      
+A       N6      N       NH2     0       31.287      14.114      -4.866      
+A       N1      N       NRD6    0       30.240      16.155      -4.553      
+A       C2      C       CR16    0       29.111      16.881      -4.579      
+A       N3      N       NRD6    0       27.874      16.499      -4.898      
+A       C4      C       CR56    0       27.833      15.193      -5.227      
+A       "H5'"   H       H       0       23.653      12.531      -8.815      
+A       "H5''"  H       H       0       24.931      12.185      -7.909      
+A       "H4'"   H       H       0       23.023      14.194      -7.269      
+A       "H3'"   H       H       0       25.613      14.544      -8.414      
+A       "HO3'"  H       H       0       24.512      16.204      -9.407      
+A       "H2'"   H       H       0       26.008      16.394      -7.110      
+A       "HO2'"  H       H       0       24.469      17.486      -6.152      
+A       "H1'"   H       H       0       25.116      15.407      -4.901      
+A       H8      H       H       0       26.656      12.471      -6.115      
+A       H61     H       H       0       31.972      14.381      -4.386      
+A       H62     H       H       0       31.333      13.371      -5.331      
+A       H2      H       H       0       29.207      17.789      -4.337      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+A       OP3           P      SINGLE       n     1.517  0.0192     1.517  0.0192
+A         P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+A         P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+A         P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+A     "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+A     "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+A     "C4'"       "O4'"      SINGLE       n     1.451  0.0100     1.451  0.0100
+A     "C4'"       "C3'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+A     "O4'"       "C1'"      SINGLE       n     1.409  0.0100     1.409  0.0100
+A     "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+A     "C3'"       "C2'"      SINGLE       n     1.531  0.0100     1.531  0.0100
+A     "C2'"       "O2'"      SINGLE       n     1.411  0.0100     1.411  0.0100
+A     "C2'"       "C1'"      SINGLE       n     1.525  0.0100     1.525  0.0100
+A     "C1'"          N9      SINGLE       n     1.458  0.0100     1.458  0.0100
+A        N9          C8      SINGLE       y     1.372  0.0100     1.372  0.0100
+A        N9          C4      SINGLE       y     1.374  0.0101     1.374  0.0101
+A        C8          N7      DOUBLE       y     1.310  0.0100     1.310  0.0100
+A        N7          C5      SINGLE       y     1.388  0.0100     1.388  0.0100
+A        C5          C6      SINGLE       y     1.408  0.0100     1.408  0.0100
+A        C5          C4      DOUBLE       y     1.381  0.0100     1.381  0.0100
+A        C6          N6      SINGLE       n     1.330  0.0100     1.330  0.0100
+A        C6          N1      DOUBLE       y     1.354  0.0100     1.354  0.0100
+A        N1          C2      SINGLE       y     1.339  0.0100     1.339  0.0100
+A        C2          N3      DOUBLE       y     1.330  0.0100     1.330  0.0100
+A        N3          C4      SINGLE       y     1.343  0.0100     1.343  0.0100
+A     "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+A     "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+A     "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+A     "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+A     "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+A     "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.994  0.0200
+A     "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+A     "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.984  0.0200
+A        C8          H8      SINGLE       n     1.082  0.0130     0.942  0.0170
+A        N6         H61      SINGLE       n     1.016  0.0100     0.877  0.0200
+A        N6         H62      SINGLE       n     1.016  0.0100     0.877  0.0200
+A        C2          H2      SINGLE       n     1.082  0.0130     0.945  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+A       OP3           P         OP1     112.864    1.69
+A       OP3           P         OP2     112.864    1.69
+A       OP3           P       "O5'"     105.808    2.07
+A       OP1           P         OP2     112.864    1.69
+A       OP1           P       "O5'"     105.808    2.07
+A       OP2           P       "O5'"     105.808    2.07
+A         P       "O5'"       "C5'"     118.783    1.50
+A     "O5'"       "C5'"       "C4'"     109.342    1.50
+A     "O5'"       "C5'"       "H5'"     109.845    1.50
+A     "O5'"       "C5'"      "H5''"     109.845    1.50
+A     "C4'"       "C5'"       "H5'"     109.624    1.50
+A     "C4'"       "C5'"      "H5''"     109.624    1.50
+A     "H5'"       "C5'"      "H5''"     108.472    1.50
+A     "C5'"       "C4'"       "O4'"     109.123    1.50
+A     "C5'"       "C4'"       "C3'"     116.008    1.52
+A     "C5'"       "C4'"       "H4'"     108.268    1.50
+A     "O4'"       "C4'"       "C3'"     105.388    1.50
+A     "O4'"       "C4'"       "H4'"     108.947    1.50
+A     "C3'"       "C4'"       "H4'"     109.363    1.86
+A     "C4'"       "O4'"       "C1'"     109.903    1.50
+A     "C4'"       "C3'"       "O3'"     111.281    2.46
+A     "C4'"       "C3'"       "C2'"     102.602    1.50
+A     "C4'"       "C3'"       "H3'"     110.452    2.54
+A     "O3'"       "C3'"       "C2'"     111.581    2.83
+A     "O3'"       "C3'"       "H3'"     110.380    1.67
+A     "C2'"       "C3'"       "H3'"     110.504    1.75
+A     "C3'"       "O3'"      "HO3'"     108.744    3.00
+A     "C3'"       "C2'"       "O2'"     112.782    2.45
+A     "C3'"       "C2'"       "C1'"     101.239    1.50
+A     "C3'"       "C2'"       "H2'"     110.596    1.51
+A     "O2'"       "C2'"       "C1'"     111.715    2.69
+A     "O2'"       "C2'"       "H2'"     110.448    1.97
+A     "C1'"       "C2'"       "H2'"     110.636    1.70
+A     "C2'"       "O2'"      "HO2'"     109.103    2.13
+A     "O4'"       "C1'"       "C2'"     106.047    1.50
+A     "O4'"       "C1'"          N9     108.477    1.50
+A     "O4'"       "C1'"       "H1'"     109.807    1.50
+A     "C2'"       "C1'"          N9     113.824    1.50
+A     "C2'"       "C1'"       "H1'"     109.015    1.50
+A        N9       "C1'"       "H1'"     109.561    1.50
+A     "C1'"          N9          C8     126.848    1.91
+A     "C1'"          N9          C4     127.459    1.80
+A        C8          N9          C4     105.693    1.50
+A        N9          C8          N7     113.469    1.50
+A        N9          C8          H8     123.206    1.50
+A        N7          C8          H8     123.326    1.50
+A        C8          N7          C5     104.739    1.50
+A        N7          C5          C6     132.250    1.50
+A        N7          C5          C4     110.483    1.50
+A        C6          C5          C4     117.267    1.50
+A        C5          C6          N6     123.792    1.50
+A        C5          C6          N1     117.409    1.50
+A        N6          C6          N1     118.799    1.50
+A        C6          N6         H61     119.723    1.50
+A        C6          N6         H62     119.723    1.50
+A       H61          N6         H62     120.554    1.88
+A        C6          N1          C2     118.521    1.50
+A        N1          C2          N3     129.332    1.50
+A        N1          C2          H2     115.313    1.50
+A        N3          C2          H2     115.355    1.50
+A        C2          N3          C4     110.982    1.50
+A        N9          C4          C5     105.616    1.50
+A        N9          C4          N3     127.895    1.50
+A        C5          C4          N3     126.489    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+A       C2e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+A       C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+A       C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+A       C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+A       C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+A       C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+A       C3e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+A       C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+A       C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+A       C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+A       C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+A       C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+A       alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+A       beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+A       epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+A       gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+A       sp3_sp3_52      "C3'"     "C2'"     "O2'"     "HO2'"    180.000       10.00     3     
+A              const_14          N7          C8          N9       "C1'"     180.000    10.0     2
+A              const_26          C5          C4          N9       "C1'"     180.000    10.0     2
+A              const_17          N9          C8          N7          C5       0.000    10.0     2
+A              const_20          C6          C5          N7          C8     180.000    10.0     2
+A       const_sp2_sp2_4          N7          C5          C6          N6       0.000     5.0     2
+A              const_21          N9          C4          C5          N7       0.000    10.0     2
+A             sp2_sp2_1          C5          C6          N6         H61     180.000     5.0     2
+A       const_sp2_sp2_6          N6          C6          N1          C2     180.000     5.0     2
+A       const_sp2_sp2_7          N3          C2          N1          C6       0.000     5.0     2
+A       const_sp2_sp2_9          N1          C2          N3          C4       0.000     5.0     2
+A              const_12          N9          C4          N3          C2     180.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+A  chir_1    P    "O5'"    OP3    OP2    both
+A  chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+A  chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+A  chir_4    "C2'"    "O2'"    "C1'"    "C3'"    negative
+A  chir_5    "C1'"    "O4'"    N9    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+A  plan-1       "C1'"   0.020
+A  plan-1          C2   0.020
+A  plan-1          C4   0.020
+A  plan-1          C5   0.020
+A  plan-1          C6   0.020
+A  plan-1          C8   0.020
+A  plan-1          H2   0.020
+A  plan-1          H8   0.020
+A  plan-1          N1   0.020
+A  plan-1          N3   0.020
+A  plan-1          N6   0.020
+A  plan-1          N7   0.020
+A  plan-1          N9   0.020
+A  plan-2          C6   0.020
+A  plan-2         H61   0.020
+A  plan-2         H62   0.020
+A  plan-2          N6   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+A           SMILES              ACDLabs 10.04                                                                                                                       O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
+A SMILES_CANONICAL               CACTVS 3.341                                                                                                   Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
+A           SMILES               CACTVS 3.341                                                                                                         Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
+A SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                               c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
+A           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                                 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
+A            InChI                InChI  1.03 InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
+A         InChIKey                InChI  1.03                                                                                                                                    UDMBCSSLTHHNCD-KQYNXXCUSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+A   acedrg               243         "dictionary generator"                  
+A   acedrg_database      11          "data source"                           
+A   rdkit                2017.03.2   "Chemoinformatics tool"
+A   refmac5              5.8.0238    "optimization tool"                     

package/baby-gru/monomers/a/ALA.cif

@@ -0,0 +1,164 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ALA ALA ALANINE peptide 13 6 .
+
+data_comp_ALA
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ALA N N NT3 1 2.468 26.274 12.957
+ALA CA C CH1 0 1.178 26.922 13.361
+ALA C C C 0 1.439 28.343 13.878
+ALA O O O 0 2.486 28.630 14.460
+ALA CB C CH3 0 0.480 26.082 14.404
+ALA OXT O OC -1 0.604 29.234 13.722
+ALA H H H 0 2.921 25.868 13.764
+ALA H2 H H 0 3.058 26.917 12.554
+ALA H3 H H 0 2.282 25.582 12.318
+ALA HA H H 0 0.598 26.983 12.566
+ALA HB3 H H 0 1.017 26.056 15.214
+ALA HB2 H H 0 0.361 25.178 14.067
+ALA HB1 H H 0 -0.389 26.468 14.605
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+ALA N n/a CA START
+ALA H N . .
+ALA H2 N . .
+ALA H3 N . .
+ALA CA N C .
+ALA HA CA . .
+ALA CB CA HB3 .
+ALA HB1 CB . .
+ALA HB2 CB . .
+ALA HB3 CB . .
+ALA C CA . END
+ALA O C . .
+ALA OXT C . .
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+ALA N CA SINGLE n 1.482 0.0101 1.482 0.0101
+ALA CA C SINGLE n 1.533 0.0100 1.533 0.0100
+ALA CA CB SINGLE n 1.509 0.0143 1.509 0.0143
+ALA C O DOUBLE n 1.247 0.0187 1.247 0.0187
+ALA C OXT SINGLE n 1.247 0.0187 1.247 0.0187
+ALA N H SINGLE n 1.036 0.0160 0.911 0.0200
+ALA N H2 SINGLE n 1.036 0.0160 0.911 0.0200
+ALA N H3 SINGLE n 1.036 0.0160 0.911 0.0200
+ALA CA HA SINGLE n 1.089 0.0100 0.986 0.0200
+ALA CB HB3 SINGLE n 1.089 0.0100 0.972 0.0152
+ALA CB HB2 SINGLE n 1.089 0.0100 0.972 0.0152
+ALA CB HB1 SINGLE n 1.089 0.0100 0.972 0.0152
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+ALA CA N H 109.643 1.50
+ALA CA N H2 109.643 1.50
+ALA CA N H3 109.643 1.50
+ALA H N H2 109.028 2.41
+ALA H N H3 109.028 2.41
+ALA H2 N H3 109.028 2.41
+ALA N CA C 109.627 1.50
+ALA N CA CB 109.912 1.50
+ALA N CA HA 108.529 1.50
+ALA C CA CB 111.490 1.50
+ALA C CA HA 108.541 1.50
+ALA CB CA HA 108.878 1.50
+ALA CA C O 117.159 1.57
+ALA CA C OXT 117.159 1.57
+ALA O C OXT 125.683 1.50
+ALA CA CB HB3 109.546 1.50
+ALA CA CB HB2 109.546 1.50
+ALA CA CB HB1 109.546 1.50
+ALA HB3 CB HB2 109.386 1.50
+ALA HB3 CB HB1 109.386 1.50
+ALA HB2 CB HB1 109.386 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+ALA hh1 N CA CB HB3 60.000 10.0 3
+ALA sp3_sp3_1 C CA N H 180.000 10.0 3
+ALA sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+ALA chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+ALA plan-1 C 0.020
+ALA plan-1 CA 0.020
+ALA plan-1 O 0.020
+ALA plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+ALA SMILES ACDLabs 10.04 O=C(O)C(N)C
+ALA SMILES_CANONICAL CACTVS 3.341 C[C@H](N)C(O)=O
+ALA SMILES CACTVS 3.341 C[CH](N)C(O)=O
+ALA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@@H](C(=O)O)N
+ALA SMILES "OpenEye OEToolkits" 1.5.0 CC(C(=O)O)N
+ALA InChI InChI 1.03 InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1
+ALA InChIKey InChI 1.03 QNAYBMKLOCPYGJ-REOHCLBHSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+ALA acedrg 243 "dictionary generator"
+ALA acedrg_database 11 "data source"
+ALA rdkit 2017.03.2 "Chemoinformatics tool"
+ALA refmac5 5.8.0238 "optimization tool"

package/baby-gru/monomers/a/ARG.cif

@@ -0,0 +1,252 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ARG ARG ARGININE peptide 27 12 .
+
+data_comp_ARG
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ARG N N NT3 1 69.985 15.005 89.950
+ARG CA C CH1 0 70.216 14.541 91.355
+ARG C C C 0 71.708 14.259 91.564
+ARG O O O 0 72.388 13.743 90.676
+ARG CB C CH2 0 69.385 13.289 91.658
+ARG CG C CH2 0 67.879 13.507 91.601
+ARG CD C CH2 0 67.094 12.291 92.059
+ARG NE N NC1 0 67.243 11.140 91.175
+ARG CZ C C 0 66.685 9.948 91.378
+ARG NH1 N NC2 0 65.981 9.717 92.472
+ARG NH2 N NC2 1 66.835 8.986 90.484
+ARG OXT O OC -1 72.264 14.541 92.626
+ARG H H H 0 70.044 14.217 89.320
+ARG H2 H H 0 70.646 15.658 89.704
+ARG H3 H H 0 69.116 15.405 89.879
+ARG HA H H 0 69.942 15.262 91.969
+ARG HB3 H H 0 69.622 12.968 92.552
+ARG HB2 H H 0 69.627 12.591 91.014
+ARG HG3 H H 0 67.619 13.723 90.680
+ARG HG2 H H 0 67.641 14.271 92.169
+ARG HD3 H H 0 66.144 12.528 92.116
+ARG HD2 H H 0 67.392 12.041 92.960
+ARG HE H H 0 67.731 11.239 90.459
+ARG HH11 H H 0 65.222 10.145 92.604
+ARG HH12 H H 0 66.271 9.135 93.067
+ARG HH21 H H 0 67.581 8.926 90.023
+ARG HH22 H H 0 66.187 8.406 90.354
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+ARG N n/a CA START
+ARG H N . .
+ARG H2 N . .
+ARG H3 N . .
+ARG CA N C .
+ARG HA CA . .
+ARG CB CA CG .
+ARG HB3 CB . .
+ARG HB2 CB . .
+ARG CG CB CD .
+ARG HG3 CG . .
+ARG HG2 CG . .
+ARG CD CG NE .
+ARG HD3 CD . .
+ARG HD2 CD . .
+ARG NE CD CZ .
+ARG HE NE . .
+ARG CZ NE NH2 .
+ARG NH1 CZ HH12 .
+ARG HH11 NH1 . .
+ARG HH12 NH1 . .
+ARG NH2 CZ HH22 .
+ARG HH21 NH2 . .
+ARG HH22 NH2 . .
+ARG C CA . END
+ARG O C . .
+ARG OXT C . .
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+ARG N CA SINGLE n 1.488 0.0100 1.488 0.0100
+ARG CA C SINGLE n 1.533 0.0100 1.533 0.0100
+ARG CA CB SINGLE n 1.532 0.0100 1.532 0.0100
+ARG C O DOUBLE n 1.247 0.0187 1.247 0.0187
+ARG C OXT SINGLE n 1.247 0.0187 1.247 0.0187
+ARG CB CG SINGLE n 1.522 0.0100 1.522 0.0100
+ARG CG CD SINGLE n 1.517 0.0143 1.517 0.0143
+ARG CD NE SINGLE n 1.456 0.0136 1.456 0.0136
+ARG NE CZ SINGLE n 1.328 0.0112 1.328 0.0112
+ARG CZ NH1 SINGLE n 1.321 0.0100 1.321 0.0100
+ARG CZ NH2 DOUBLE n 1.322 0.0100 1.322 0.0100
+ARG N H SINGLE n 1.036 0.0160 0.911 0.0200
+ARG N H2 SINGLE n 1.036 0.0160 0.911 0.0200
+ARG N H3 SINGLE n 1.036 0.0160 0.911 0.0200
+ARG CA HA SINGLE n 1.089 0.0100 0.985 0.0200
+ARG CB HB3 SINGLE n 1.089 0.0100 0.980 0.0160
+ARG CB HB2 SINGLE n 1.089 0.0100 0.980 0.0160
+ARG CG HG3 SINGLE n 1.089 0.0100 0.981 0.0160
+ARG CG HG2 SINGLE n 1.089 0.0100 0.981 0.0160
+ARG CD HD3 SINGLE n 1.089 0.0100 0.981 0.0152
+ARG CD HD2 SINGLE n 1.089 0.0100 0.981 0.0152
+ARG NE HE SINGLE n 1.016 0.0100 0.872 0.0200
+ARG NH1 HH11 SINGLE n 1.016 0.0100 0.881 0.0200
+ARG NH1 HH12 SINGLE n 1.016 0.0100 0.881 0.0200
+ARG NH2 HH21 SINGLE n 1.016 0.0100 0.879 0.0200
+ARG NH2 HH22 SINGLE n 1.016 0.0100 0.879 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+ARG CA N H 110.062 1.93
+ARG CA N H2 110.062 1.93
+ARG CA N H3 110.062 1.93
+ARG H N H2 109.028 2.41
+ARG H N H3 109.028 2.41
+ARG H2 N H3 109.028 2.41
+ARG N CA C 109.241 1.50
+ARG N CA CB 110.374 1.62
+ARG N CA HA 108.487 1.50
+ARG C CA CB 111.037 2.40
+ARG C CA HA 108.824 1.50
+ARG CB CA HA 108.967 1.50
+ARG CA C O 117.124 1.50
+ARG CA C OXT 117.124 1.50
+ARG O C OXT 125.752 1.50
+ARG CA CB CG 114.117 1.50
+ARG CA CB HB3 108.549 1.50
+ARG CA CB HB2 108.549 1.50
+ARG CG CB HB3 108.775 1.50
+ARG CG CB HB2 108.775 1.50
+ARG HB3 CB HB2 107.844 1.50
+ARG CB CG CD 112.387 3.00
+ARG CB CG HG3 109.262 1.50
+ARG CB CG HG2 109.262 1.50
+ARG CD CG HG3 108.956 1.50
+ARG CD CG HG2 108.956 1.50
+ARG HG3 CG HG2 107.927 1.57
+ARG CG CD NE 112.382 2.90
+ARG CG CD HD3 109.197 1.51
+ARG CG CD HD2 109.197 1.51
+ARG NE CD HD3 109.183 1.50
+ARG NE CD HD2 109.183 1.50
+ARG HD3 CD HD2 107.877 1.50
+ARG CD NE CZ 124.510 1.50
+ARG CD NE HE 117.883 1.50
+ARG CZ NE HE 117.606 1.50
+ARG NE CZ NH1 120.052 1.50
+ARG NE CZ NH2 120.052 1.50
+ARG NH1 CZ NH2 119.896 1.50
+ARG CZ NH1 HH11 119.855 2.01
+ARG CZ NH1 HH12 119.855 2.01
+ARG HH11 NH1 HH12 120.290 2.09
+ARG CZ NH2 HH21 119.855 2.01
+ARG CZ NH2 HH22 119.855 2.01
+ARG HH21 NH2 HH22 120.290 2.09
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+ARG chi1 N CA CB CG -60.000 10.0 3
+ARG chi2 CA CB CG CD 180.000 10.0 3
+ARG chi3 CB CG CD NE -60.000 10.0 3
+ARG chi4 CG CD NE CZ 180.000 10.0 6
+ARG chi5 CD NE CZ NH2 180.000 5.0 2
+ARG hh1 NE CZ NH1 HH12 180.000 5.0 2
+ARG hh2 NE CZ NH2 HH22 0.000 5.0 2
+ARG sp3_sp3_1 C CA N H 180.000 10.0 3
+ARG sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+ARG chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+ARG plan-1 C 0.020
+ARG plan-1 CA 0.020
+ARG plan-1 O 0.020
+ARG plan-1 OXT 0.020
+ARG plan-2 CD 0.020
+ARG plan-2 CZ 0.020
+ARG plan-2 HE 0.020
+ARG plan-2 NE 0.020
+ARG plan-3 CZ 0.020
+ARG plan-3 NE 0.020
+ARG plan-3 NH1 0.020
+ARG plan-3 NH2 0.020
+ARG plan-4 CZ 0.020
+ARG plan-4 HH11 0.020
+ARG plan-4 HH12 0.020
+ARG plan-4 NH1 0.020
+ARG plan-5 CZ 0.020
+ARG plan-5 HH21 0.020
+ARG plan-5 HH22 0.020
+ARG plan-5 NH2 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+ARG SMILES ACDLabs 10.04 O=C(O)C(N)CCCN\C(=[NH2+])N
+ARG SMILES_CANONICAL CACTVS 3.341 N[C@@H](CCCNC(N)=[NH2+])C(O)=O
+ARG SMILES CACTVS 3.341 N[CH](CCCNC(N)=[NH2+])C(O)=O
+ARG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N
+ARG SMILES "OpenEye OEToolkits" 1.5.0 C(CC(C(=O)O)N)CNC(=[NH2+])N
+ARG InChI InChI 1.03 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1
+ARG InChIKey InChI 1.03 ODKSFYDXXFIFQN-BYPYZUCNSA-O
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+ARG acedrg 243 "dictionary generator"
+ARG acedrg_database 11 "data source"
+ARG rdkit 2017.03.2 "Chemoinformatics tool"
+ARG refmac5 5.8.0238 "optimization tool"