moorhen 0.0.1

package/baby-gru/monomers/p/PHE.cif

@@ -0,0 +1,233 @@
+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
+PHE PHE PHENYLALANINE peptide 23 12 .
+
+data_comp_PHE
+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
+PHE N N NT3 1 3.243 22.325 5.999
+PHE CA C CH1 0 4.243 21.255 5.719
+PHE C C C 0 5.572 21.900 5.306
+PHE O O O 0 5.668 22.539 4.258
+PHE CB C CH2 0 3.717 20.305 4.638
+PHE CG C CR6 0 4.583 19.097 4.377
+PHE CD1 C CR16 0 4.770 18.133 5.361
+PHE CD2 C CR16 0 5.216 18.920 3.151
+PHE CE1 C CR16 0 5.567 17.019 5.125
+PHE CE2 C CR16 0 6.013 17.806 2.917
+PHE CZ C CR16 0 6.188 16.857 3.903
+PHE OXT O OC -1 6.574 21.796 6.014
+PHE H H H 0 3.095 22.874 5.164
+PHE H2 H H 0 3.568 22.893 6.702
+PHE H3 H H 0 2.414 21.925 6.270
+PHE HA H H 0 4.392 20.737 6.550
+PHE HB3 H H 0 3.618 20.812 3.805
+PHE HB2 H H 0 2.825 19.999 4.907
+PHE HD1 H H 0 4.348 18.236 6.199
+PHE HD2 H H 0 5.102 19.564 2.470
+PHE HE1 H H 0 5.684 16.373 5.803
+PHE HE2 H H 0 6.436 17.699 2.079
+PHE HZ H H 0 6.729 16.101 3.743
+
+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
+PHE N n/a CA START
+PHE H N . .
+PHE H2 N . .
+PHE H3 N . .
+PHE CA N C .
+PHE HA CA . .
+PHE CB CA CG .
+PHE HB3 CB . .
+PHE HB2 CB . .
+PHE CG CB CD1 .
+PHE CD1 CG CE1 .
+PHE HD1 CD1 . .
+PHE CE1 CD1 CZ .
+PHE HE1 CE1 . .
+PHE CZ CE1 CE2 .
+PHE HZ CZ . .
+PHE CE2 CZ CD2 .
+PHE HE2 CE2 . .
+PHE CD2 CE2 HD2 .
+PHE HD2 CD2 . .
+PHE C CA . END
+PHE O C . .
+PHE OXT C . .
+PHE CD2 CG . ADD
+
+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
+PHE N CA SINGLE n 1.487 0.0100 1.487 0.0100
+PHE CA C SINGLE n 1.533 0.0100 1.533 0.0100
+PHE CA CB SINGLE n 1.531 0.0100 1.531 0.0100
+PHE C O DOUBLE n 1.247 0.0187 1.247 0.0187
+PHE C OXT SINGLE n 1.247 0.0187 1.247 0.0187
+PHE CB CG SINGLE n 1.508 0.0100 1.508 0.0100
+PHE CG CD1 DOUBLE y 1.385 0.0111 1.385 0.0111
+PHE CG CD2 SINGLE y 1.385 0.0111 1.385 0.0111
+PHE CD1 CE1 SINGLE y 1.386 0.0100 1.386 0.0100
+PHE CD2 CE2 DOUBLE y 1.386 0.0100 1.386 0.0100
+PHE CE1 CZ DOUBLE y 1.376 0.0124 1.376 0.0124
+PHE CE2 CZ SINGLE y 1.376 0.0124 1.376 0.0124
+PHE N H SINGLE n 1.036 0.0160 0.911 0.0200
+PHE N H2 SINGLE n 1.036 0.0160 0.911 0.0200
+PHE N H3 SINGLE n 1.036 0.0160 0.911 0.0200
+PHE CA HA SINGLE n 1.089 0.0100 0.991 0.0200
+PHE CB HB3 SINGLE n 1.089 0.0100 0.980 0.0164
+PHE CB HB2 SINGLE n 1.089 0.0100 0.980 0.0164
+PHE CD1 HD1 SINGLE n 1.082 0.0130 0.944 0.0174
+PHE CD2 HD2 SINGLE n 1.082 0.0130 0.944 0.0174
+PHE CE1 HE1 SINGLE n 1.082 0.0130 0.944 0.0175
+PHE CE2 HE2 SINGLE n 1.082 0.0130 0.944 0.0175
+PHE CZ HZ SINGLE n 1.082 0.0130 0.944 0.0161
+
+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
+PHE CA N H 109.646 1.54
+PHE CA N H2 109.646 1.54
+PHE CA N H3 109.646 1.54
+PHE H N H2 109.028 2.41
+PHE H N H3 109.028 2.41
+PHE H2 N H3 109.028 2.41
+PHE N CA C 109.448 1.50
+PHE N CA CB 110.494 1.50
+PHE N CA HA 108.601 1.50
+PHE C CA CB 111.331 2.53
+PHE C CA HA 108.450 1.50
+PHE CB CA HA 108.690 1.50
+PHE CA C O 117.228 2.13
+PHE CA C OXT 117.228 2.13
+PHE O C OXT 125.543 1.50
+PHE CA CB CG 114.745 1.55
+PHE CA CB HB3 108.434 1.50
+PHE CA CB HB2 108.434 1.50
+PHE CG CB HB3 108.862 1.50
+PHE CG CB HB2 108.862 1.50
+PHE HB3 CB HB2 107.782 1.50
+PHE CB CG CD1 120.970 1.50
+PHE CB CG CD2 120.970 1.50
+PHE CD1 CG CD2 118.060 1.50
+PHE CG CD1 CE1 120.624 1.50
+PHE CG CD1 HD1 119.591 1.50
+PHE CE1 CD1 HD1 119.786 1.50
+PHE CG CD2 CE2 120.624 1.50
+PHE CG CD2 HD2 119.591 1.50
+PHE CE2 CD2 HD2 119.786 1.50
+PHE CD1 CE1 CZ 120.325 1.50
+PHE CD1 CE1 HE1 119.792 1.50
+PHE CZ CE1 HE1 119.883 1.50
+PHE CD2 CE2 CZ 120.325 1.50
+PHE CD2 CE2 HE2 119.792 1.50
+PHE CZ CE2 HE2 119.883 1.50
+PHE CE1 CZ CE2 120.043 1.50
+PHE CE1 CZ HZ 119.979 1.50
+PHE CE2 CZ HZ 119.979 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
+PHE chi1 N CA CB CG 180.000 10.0 3
+PHE chi2 CA CB CG CD1 60.000 10.0 6
+PHE CONST_1 CB CG CD1 CE1 180.000 10.0 2
+PHE CONST_2 CG CD1 CE1 CZ 0.000 10.0 2
+PHE CONST_3 CZ CE2 CD2 CG 0.000 10.0 2
+PHE CONST_4 CD1 CE1 CZ CE2 0.000 10.0 2
+PHE CONST_5 CE1 CZ CE2 CD2 0.000 10.0 2
+PHE sp3_sp3_1 C CA N H 180.000 10.0 3
+PHE const_21 CE2 CD2 CG CD1 0.000 10.0 2
+PHE 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
+PHE 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
+PHE plan-1 CB 0.020
+PHE plan-1 CD1 0.020
+PHE plan-1 CD2 0.020
+PHE plan-1 CE1 0.020
+PHE plan-1 CE2 0.020
+PHE plan-1 CG 0.020
+PHE plan-1 CZ 0.020
+PHE plan-1 HD1 0.020
+PHE plan-1 HD2 0.020
+PHE plan-1 HE1 0.020
+PHE plan-1 HE2 0.020
+PHE plan-1 HZ 0.020
+PHE plan-2 C 0.020
+PHE plan-2 CA 0.020
+PHE plan-2 O 0.020
+PHE plan-2 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
+PHE SMILES ACDLabs 10.04 O=C(O)C(N)Cc1ccccc1
+PHE SMILES_CANONICAL CACTVS 3.341 N[C@@H](Cc1ccccc1)C(O)=O
+PHE SMILES CACTVS 3.341 N[CH](Cc1ccccc1)C(O)=O
+PHE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)C[C@@H](C(=O)O)N
+PHE SMILES "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)CC(C(=O)O)N
+PHE InChI InChI 1.03 InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m0/s1
+PHE InChIKey InChI 1.03 COLNVLDHVKWLRT-QMMMGPOBSA-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
+PHE acedrg 243 "dictionary generator"
+PHE acedrg_database 11 "data source"
+PHE rdkit 2017.03.2 "Chemoinformatics tool"
+PHE refmac5 5.8.0238 "optimization tool"

package/baby-gru/monomers/p/PO4.cif

@@ -0,0 +1,86 @@
+#
+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
+PO4     PO4      "PHOSPHATE ION"     NON-POLYMER     5     5     .     
+#
+data_comp_PO4
+#
+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
+PO4     P       P       P       0       29.978      23.532      13.276      
+PO4     O1      O       O       0       31.126      22.989      14.118      
+PO4     O2      O       OP      -1      30.372      24.882      12.690      
+PO4     O3      O       OP      -1      29.672      22.557      12.145      
+PO4     O4      O       OP      -1      28.741      23.699      14.151      
+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
+PO4           P          O1      DOUBLE       n     1.524  0.0200     1.524  0.0200
+PO4           P          O2      SINGLE       n     1.524  0.0200     1.524  0.0200
+PO4           P          O3      SINGLE       n     1.524  0.0200     1.524  0.0200
+PO4           P          O4      SINGLE       n     1.524  0.0200     1.524  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
+PO4          O1           P          O2     109.461    1.50
+PO4          O1           P          O3     109.461    1.50
+PO4          O1           P          O4     109.461    1.50
+PO4          O2           P          O3     109.461    1.50
+PO4          O2           P          O4     109.461    1.50
+PO4          O3           P          O4     109.461    1.50
+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
+PO4    chir_1    P    O2    O3    O4    both
+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
+PO4           SMILES              ACDLabs 10.04                       "[O-]P([O-])([O-])=O"
+PO4 SMILES_CANONICAL               CACTVS 3.341                     "[O-][P]([O-])([O-])=O"
+PO4           SMILES               CACTVS 3.341                     "[O-][P]([O-])([O-])=O"
+PO4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                       "[O-]P(=O)([O-])[O-]"
+PO4           SMILES "OpenEye OEToolkits" 1.5.0                       "[O-]P(=O)([O-])[O-]"
+PO4            InChI                InChI  1.03 InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
+PO4         InChIKey                InChI  1.03                 NBIIXXVUZAFLBC-UHFFFAOYSA-K
+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
+PO4 acedrg               243         "dictionary generator"                  
+PO4 acedrg_database      11          "data source"                           
+PO4 rdkit                2017.03.2   "Chemoinformatics tool"
+PO4 refmac5              5.8.0238    "optimization tool"                     

package/baby-gru/monomers/p/PRO.cif

@@ -0,0 +1,188 @@
+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
+PRO PRO PROLINE P-peptide 16 8 .
+
+data_comp_PRO
+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
+PRO N N NT1 0 39.073 37.583 83.044
+PRO CA C CH1 0 38.586 38.620 82.115
+PRO C C C 0 37.233 39.220 82.536
+PRO O O O 0 36.343 38.438 82.819
+PRO CB C CH2 0 38.468 37.896 80.764
+PRO CG C CH2 0 38.228 36.459 81.147
+PRO CD C CH2 0 39.062 36.266 82.395
+PRO OXT O OC -1 37.151 40.435 82.556
+PRO H H H 0 38.548 37.515 83.758
+PRO HA H H 0 39.264 39.337 82.043
+PRO HB3 H H 0 39.295 37.986 80.244
+PRO HB2 H H 0 37.720 38.248 80.233
+PRO HG3 H H 0 38.519 35.854 80.435
+PRO HG2 H H 0 37.280 36.300 81.332
+PRO HD3 H H 0 38.664 35.594 82.979
+PRO HD2 H H 0 39.968 35.985 82.168
+
+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
+PRO N n/a CA START
+PRO CA N C .
+PRO HA CA . .
+PRO CB CA CG .
+PRO HB3 CB . .
+PRO HB2 CB . .
+PRO CG CB CD .
+PRO HG3 CG . .
+PRO HG2 CG . .
+PRO CD CG HD2 .
+PRO HD3 CD . .
+PRO HD2 CD . .
+PRO C CA . END
+PRO O C . .
+PRO OXT C . .
+PRO H N . .
+PRO CD N . ADD
+
+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
+PRO N CA SINGLE n 1.468 0.0148 1.468 0.0148
+PRO N CD SINGLE n 1.468 0.0152 1.468 0.0152
+PRO CA C SINGLE n 1.536 0.0100 1.536 0.0100
+PRO CA CB SINGLE n 1.534 0.0126 1.534 0.0126
+PRO C O DOUBLE n 1.218 0.0200 1.218 0.0200
+PRO C OXT SINGLE n 1.218 0.0200 1.218 0.0200
+PRO CB CG SINGLE n 1.508 0.0200 1.508 0.0200
+PRO CG CD SINGLE n 1.515 0.0118 1.515 0.0118
+PRO N H SINGLE n 1.036 0.0160 0.887 0.0200
+PRO CA HA SINGLE n 1.089 0.0100 0.990 0.0121
+PRO CB HB3 SINGLE n 1.089 0.0100 0.981 0.0193
+PRO CB HB2 SINGLE n 1.089 0.0100 0.981 0.0193
+PRO CG HG3 SINGLE n 1.089 0.0100 0.979 0.0132
+PRO CG HG2 SINGLE n 1.089 0.0100 0.979 0.0132
+PRO CD HD3 SINGLE n 1.089 0.0100 0.975 0.0100
+PRO CD HD2 SINGLE n 1.089 0.0100 0.975 0.0100
+
+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
+PRO CA N CD 109.056 3.00
+PRO CA N H 109.307 3.00
+PRO CD N H 106.136 2.25
+PRO N CA C 111.420 2.45
+PRO N CA CB 103.430 2.23
+PRO N CA HA 109.296 1.50
+PRO C CA CB 110.031 2.42
+PRO C CA HA 110.011 1.50
+PRO CB CA HA 109.388 1.50
+PRO CA C O 117.013 1.95
+PRO CA C OXT 117.013 1.95
+PRO O C OXT 125.975 1.50
+PRO CA CB CG 103.507 1.50
+PRO CA CB HB3 111.018 1.50
+PRO CA CB HB2 111.018 1.50
+PRO CG CB HB3 110.886 1.50
+PRO CG CB HB2 110.886 1.50
+PRO HB3 CB HB2 108.922 1.50
+PRO CB CG CD 104.503 1.95
+PRO CB CG HG3 110.864 1.50
+PRO CB CG HG2 110.864 1.50
+PRO CD CG HG3 110.804 1.50
+PRO CD CG HG2 110.804 1.50
+PRO HG3 CG HG2 108.899 1.50
+PRO N CD CG 105.071 2.33
+PRO N CD HD3 110.738 1.50
+PRO N CD HD2 110.738 1.50
+PRO CG CD HD3 110.867 1.50
+PRO CG CD HD2 110.867 1.50
+PRO HD3 CD HD2 108.731 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
+PRO chi1 N CA CB CG 30.000 10.0 3
+PRO chi2 CA CB CG CD -30.000 10.0 3
+PRO chi3 CB CG CD N 30.000 10.0 3
+PRO sp3_sp3_1 CB CA N CD 60.000 10.0 3
+PRO sp3_sp3_34 CG CD N CA 180.000 10.0 3
+PRO 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
+PRO chir_1 CA N C CB positive
+PRO chir_2 N CA CD H both
+
+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
+PRO plan-1 C 0.020
+PRO plan-1 CA 0.020
+PRO plan-1 O 0.020
+PRO 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
+PRO SMILES ACDLabs 10.04 O=C(O)C1NCCC1
+PRO SMILES_CANONICAL CACTVS 3.341 OC(=O)[C@@H]1CCCN1
+PRO SMILES CACTVS 3.341 OC(=O)[CH]1CCCN1
+PRO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1C[C@H](NC1)C(=O)O
+PRO SMILES "OpenEye OEToolkits" 1.5.0 C1CC(NC1)C(=O)O
+PRO InChI InChI 1.03 InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1
+PRO InChIKey InChI 1.03 ONIBWKKTOPOVIA-BYPYZUCNSA-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
+PRO acedrg 243 "dictionary generator"
+PRO acedrg_database 11 "data source"
+PRO rdkit 2017.03.2 "Chemoinformatics tool"
+PRO refmac5 5.8.0238 "optimization tool"

package/baby-gru/monomers/s/SER.cif

@@ -0,0 +1,169 @@
+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
+SER SER SERINE peptide 14 7 .
+
+data_comp_SER
+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
+SER N N NT3 1 88.171 -7.587 -9.891
+SER CA C CH1 0 87.807 -7.240 -11.306
+SER C C C 0 88.531 -5.961 -11.748
+SER O O O 0 88.854 -5.094 -10.935
+SER CB C CH2 0 86.313 -7.100 -11.465
+SER OG O OH1 0 85.652 -8.309 -11.123
+SER OXT O OC -1 88.805 -5.770 -12.932
+SER H H H 0 87.512 -7.174 -9.245
+SER H2 H H 0 89.055 -7.274 -9.678
+SER H3 H H 0 88.150 -8.542 -9.791
+SER HA H H 0 88.114 -7.984 -11.890
+SER HB3 H H 0 86.105 -6.865 -12.397
+SER HB2 H H 0 85.989 -6.373 -10.886
+SER HG H H 0 85.553 -8.334 -10.283
+
+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
+SER N n/a CA START
+SER H N . .
+SER H2 N . .
+SER H3 N . .
+SER CA N C .
+SER HA CA . .
+SER CB CA OG .
+SER HB3 CB . .
+SER HB2 CB . .
+SER OG CB HG .
+SER HG OG . .
+SER C CA . END
+SER O C . .
+SER 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
+SER N CA SINGLE n 1.487 0.0100 1.487 0.0100
+SER CA C SINGLE n 1.533 0.0100 1.533 0.0100
+SER CA CB SINGLE n 1.507 0.0177 1.507 0.0177
+SER C O DOUBLE n 1.247 0.0187 1.247 0.0187
+SER C OXT SINGLE n 1.247 0.0187 1.247 0.0187
+SER CB OG SINGLE n 1.420 0.0140 1.420 0.0140
+SER N H SINGLE n 1.036 0.0160 0.911 0.0200
+SER N H2 SINGLE n 1.036 0.0160 0.911 0.0200
+SER N H3 SINGLE n 1.036 0.0160 0.911 0.0200
+SER CA HA SINGLE n 1.089 0.0100 0.995 0.0200
+SER CB HB3 SINGLE n 1.089 0.0100 0.984 0.0200
+SER CB HB2 SINGLE n 1.089 0.0100 0.984 0.0200
+SER OG HG SINGLE n 0.970 0.0120 0.846 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
+SER CA N H 109.619 1.50
+SER CA N H2 109.619 1.50
+SER CA N H3 109.619 1.50
+SER H N H2 109.028 2.41
+SER H N H3 109.028 2.41
+SER H2 N H3 109.028 2.41
+SER N CA C 109.829 1.50
+SER N CA CB 110.990 1.50
+SER N CA HA 108.049 1.50
+SER C CA CB 111.379 1.50
+SER C CA HA 108.255 1.50
+SER CB CA HA 108.518 1.50
+SER CA C O 117.181 1.50
+SER CA C OXT 117.181 1.50
+SER O C OXT 125.637 1.50
+SER CA CB OG 110.825 1.50
+SER CA CB HB3 109.305 1.50
+SER CA CB HB2 109.305 1.50
+SER OG CB HB3 109.411 1.50
+SER OG CB HB2 109.411 1.50
+SER HB3 CB HB2 108.070 1.50
+SER CB OG HG 108.529 2.94
+
+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
+SER chi1 N CA CB OG -60.000 10.0 3
+SER hh1 CA CB OG HG 90.000 10.0 3
+SER sp3_sp3_1 C CA N H 180.000 10.0 3
+SER 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
+SER 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
+SER plan-1 C 0.020
+SER plan-1 CA 0.020
+SER plan-1 O 0.020
+SER 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
+SER SMILES ACDLabs 10.04 O=C(O)C(N)CO
+SER SMILES_CANONICAL CACTVS 3.341 N[C@@H](CO)C(O)=O
+SER SMILES CACTVS 3.341 N[CH](CO)C(O)=O
+SER SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H](C(=O)O)N)O
+SER SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)N)O
+SER InChI InChI 1.03 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1
+SER InChIKey InChI 1.03 MTCFGRXMJLQNBG-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
+SER acedrg 243 "dictionary generator"
+SER acedrg_database 11 "data source"
+SER rdkit 2017.03.2 "Chemoinformatics tool"
+SER refmac5 5.8.0238 "optimization tool"