moorhen 0.0.1

package/baby-gru/monomers/l/LYS.cif

@@ -0,0 +1,228 @@
+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
+LYS LYS LYSINE peptide 25 10 .
+
+data_comp_LYS
+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
+LYS N N NT3 1 38.134 40.603 -3.577
+LYS CA C CH1 0 39.079 39.656 -4.250
+LYS C C C 0 38.446 39.121 -5.542
+LYS O O O 0 37.236 39.206 -5.758
+LYS CB C CH2 0 39.474 38.516 -3.303
+LYS CG C CH2 0 38.326 37.709 -2.705
+LYS CD C CH2 0 38.793 36.584 -1.805
+LYS CE C CH2 0 37.658 35.737 -1.267
+LYS NZ N NT3 1 36.721 36.512 -0.417
+LYS OXT O OC -1 39.143 38.584 -6.404
+LYS H H H 0 38.459 40.795 -2.640
+LYS H2 H H 0 37.251 40.226 -3.535
+LYS H3 H H 0 38.102 41.424 -4.074
+LYS HA H H 0 39.892 40.158 -4.490
+LYS HB3 H H 0 39.997 38.898 -2.567
+LYS HB2 H H 0 40.059 37.901 -3.792
+LYS HG3 H H 0 37.789 37.330 -3.432
+LYS HG2 H H 0 37.751 38.313 -2.189
+LYS HD3 H H 0 39.290 36.966 -1.049
+LYS HD2 H H 0 39.407 36.008 -2.307
+LYS HE3 H H 0 38.025 35.001 -0.740
+LYS HE2 H H 0 37.160 35.351 -2.012
+LYS HZ1 H H 0 37.148 37.219 -0.039
+LYS HZ2 H H 0 36.394 35.982 0.242
+LYS HZ3 H H 0 36.030 36.817 -0.920
+
+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
+LYS N n/a CA START
+LYS H N . .
+LYS H2 N . .
+LYS H3 N . .
+LYS CA N C .
+LYS HA CA . .
+LYS CB CA CG .
+LYS HB3 CB . .
+LYS HB2 CB . .
+LYS CG CB CD .
+LYS HG3 CG . .
+LYS HG2 CG . .
+LYS CD CG CE .
+LYS HD3 CD . .
+LYS HD2 CD . .
+LYS CE CD NZ .
+LYS HE3 CE . .
+LYS HE2 CE . .
+LYS NZ CE HZ3 .
+LYS HZ1 NZ . .
+LYS HZ2 NZ . .
+LYS HZ3 NZ . .
+LYS C CA . END
+LYS O C . .
+LYS 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
+LYS N CA SINGLE n 1.488 0.0100 1.488 0.0100
+LYS CA C SINGLE n 1.533 0.0100 1.533 0.0100
+LYS CA CB SINGLE n 1.532 0.0100 1.532 0.0100
+LYS C O DOUBLE n 1.247 0.0187 1.247 0.0187
+LYS C OXT SINGLE n 1.247 0.0187 1.247 0.0187
+LYS CB CG SINGLE n 1.523 0.0114 1.523 0.0114
+LYS CG CD SINGLE n 1.514 0.0200 1.514 0.0200
+LYS CD CE SINGLE n 1.514 0.0111 1.514 0.0111
+LYS CE NZ SINGLE n 1.482 0.0123 1.482 0.0123
+LYS N H SINGLE n 1.036 0.0160 0.911 0.0200
+LYS N H2 SINGLE n 1.036 0.0160 0.911 0.0200
+LYS N H3 SINGLE n 1.036 0.0160 0.911 0.0200
+LYS CA HA SINGLE n 1.089 0.0100 0.985 0.0200
+LYS CB HB3 SINGLE n 1.089 0.0100 0.980 0.0160
+LYS CB HB2 SINGLE n 1.089 0.0100 0.980 0.0160
+LYS CG HG3 SINGLE n 1.089 0.0100 0.981 0.0163
+LYS CG HG2 SINGLE n 1.089 0.0100 0.981 0.0163
+LYS CD HD3 SINGLE n 1.089 0.0100 0.981 0.0160
+LYS CD HD2 SINGLE n 1.089 0.0100 0.981 0.0160
+LYS CE HE3 SINGLE n 1.089 0.0100 0.976 0.0165
+LYS CE HE2 SINGLE n 1.089 0.0100 0.976 0.0165
+LYS NZ HZ1 SINGLE n 1.036 0.0160 0.907 0.0200
+LYS NZ HZ2 SINGLE n 1.036 0.0160 0.907 0.0200
+LYS NZ HZ3 SINGLE n 1.036 0.0160 0.907 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
+LYS CA N H 110.062 1.93
+LYS CA N H2 110.062 1.93
+LYS CA N H3 110.062 1.93
+LYS H N H2 109.028 2.41
+LYS H N H3 109.028 2.41
+LYS H2 N H3 109.028 2.41
+LYS N CA C 109.241 1.50
+LYS N CA CB 110.374 1.62
+LYS N CA HA 108.487 1.50
+LYS C CA CB 111.037 2.40
+LYS C CA HA 108.824 1.50
+LYS CB CA HA 108.967 1.50
+LYS CA C O 117.124 1.50
+LYS CA C OXT 117.124 1.50
+LYS O C OXT 125.752 1.50
+LYS CA CB CG 115.311 1.56
+LYS CA CB HB3 108.549 1.50
+LYS CA CB HB2 108.549 1.50
+LYS CG CB HB3 108.650 1.50
+LYS CG CB HB2 108.650 1.50
+LYS HB3 CB HB2 107.844 1.50
+LYS CB CG CD 113.328 2.00
+LYS CB CG HG3 108.601 1.50
+LYS CB CG HG2 108.601 1.50
+LYS CD CG HG3 108.806 1.50
+LYS CD CG HG2 108.806 1.50
+LYS HG3 CG HG2 107.646 1.50
+LYS CG CD CE 113.073 1.98
+LYS CG CD HD3 109.041 1.50
+LYS CG CD HD2 109.041 1.50
+LYS CE CD HD3 108.889 1.50
+LYS CE CD HD2 108.889 1.50
+LYS HD3 CD HD2 107.927 1.57
+LYS CD CE NZ 111.734 1.84
+LYS CD CE HE3 109.576 1.50
+LYS CD CE HE2 109.576 1.50
+LYS NZ CE HE3 108.989 1.50
+LYS NZ CE HE2 108.989 1.50
+LYS HE3 CE HE2 108.067 1.50
+LYS CE NZ HZ1 109.775 1.81
+LYS CE NZ HZ2 109.775 1.81
+LYS CE NZ HZ3 109.775 1.81
+LYS HZ1 NZ HZ2 109.021 2.83
+LYS HZ1 NZ HZ3 109.021 2.83
+LYS HZ2 NZ HZ3 109.021 2.83
+
+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
+LYS chi1 N CA CB CG 60.000 10.0 3
+LYS chi2 CA CB CG CD 180.000 10.0 3
+LYS chi3 CB CG CD CE 180.000 10.0 3
+LYS chi4 CG CD CE NZ -60.000 10.0 3
+LYS hh1 CD CE NZ HZ3 180.000 10.0 3
+LYS sp3_sp3_1 C CA N H 180.000 10.0 3
+LYS 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
+LYS 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
+LYS plan-1 C 0.020
+LYS plan-1 CA 0.020
+LYS plan-1 O 0.020
+LYS 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
+LYS SMILES ACDLabs 10.04 O=C(O)C(N)CCCC[NH3+]
+LYS SMILES_CANONICAL CACTVS 3.341 N[C@@H](CCCC[NH3+])C(O)=O
+LYS SMILES CACTVS 3.341 N[CH](CCCC[NH3+])C(O)=O
+LYS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CC[NH3+])C[C@@H](C(=O)O)N
+LYS SMILES "OpenEye OEToolkits" 1.5.0 C(CC[NH3+])CC(C(=O)O)N
+LYS InChI InChI 1.03 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
+LYS InChIKey InChI 1.03 KDXKERNSBIXSRK-YFKPBYRVSA-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
+LYS acedrg 243 "dictionary generator"
+LYS acedrg_database 11 "data source"
+LYS rdkit 2017.03.2 "Chemoinformatics tool"
+LYS refmac5 5.8.0238 "optimization tool"

package/baby-gru/monomers/m/MET.cif

@@ -0,0 +1,201 @@
+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
+MET MET METHIONINE peptide 20 9 .
+
+data_comp_MET
+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
+MET N N NT3 1 16.037 15.646 51.828
+MET CA C CH1 0 15.071 16.764 51.610
+MET C C C 0 13.643 16.205 51.599
+MET O O O 0 12.690 16.897 51.959
+MET CB C CH2 0 15.363 17.484 50.287
+MET CG C CH2 0 16.318 18.656 50.431
+MET SD S S2 0 17.944 18.169 51.065
+MET CE C CH3 0 18.820 17.872 49.530
+MET OXT O OC -1 13.412 15.053 51.231
+MET H H H 0 16.981 15.997 51.742
+MET H2 H H 0 15.894 14.957 51.174
+MET H3 H H 0 15.912 15.283 52.708
+MET HA H H 0 15.157 17.399 52.358
+MET HB3 H H 0 14.521 17.810 49.907
+MET HB2 H H 0 15.743 16.840 49.657
+MET HG3 H H 0 15.926 19.317 51.041
+MET HG2 H H 0 16.435 19.085 49.557
+MET HE3 H H 0 19.747 17.685 49.721
+MET HE2 H H 0 18.758 18.654 48.968
+MET HE1 H H 0 18.426 17.117 49.077
+
+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
+MET N CA SINGLE n 1.488 0.0100 1.488 0.0100
+MET CA C SINGLE n 1.533 0.0100 1.533 0.0100
+MET CA CB SINGLE n 1.532 0.0100 1.532 0.0100
+MET C O DOUBLE n 1.247 0.0187 1.247 0.0187
+MET C OXT SINGLE n 1.247 0.0187 1.247 0.0187
+MET CB CG SINGLE n 1.517 0.0200 1.517 0.0200
+MET CG SD SINGLE n 1.811 0.0200 1.811 0.0200
+MET SD CE SINGLE n 1.792 0.0100 1.792 0.0100
+MET N H SINGLE n 1.036 0.0160 0.911 0.0200
+MET N H2 SINGLE n 1.036 0.0160 0.911 0.0200
+MET N H3 SINGLE n 1.036 0.0160 0.911 0.0200
+MET CA HA SINGLE n 1.089 0.0100 0.985 0.0200
+MET CB HB3 SINGLE n 1.089 0.0100 0.978 0.0200
+MET CB HB2 SINGLE n 1.089 0.0100 0.978 0.0200
+MET CG HG3 SINGLE n 1.089 0.0100 0.981 0.0122
+MET CG HG2 SINGLE n 1.089 0.0100 0.981 0.0122
+MET CE HE3 SINGLE n 1.089 0.0100 0.965 0.0170
+MET CE HE2 SINGLE n 1.089 0.0100 0.965 0.0170
+MET CE HE1 SINGLE n 1.089 0.0100 0.965 0.0170
+
+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
+MET N n/a CA START
+MET H N . .
+MET H2 N . .
+MET H3 N . .
+MET CA N C .
+MET HA CA . .
+MET CB CA CG .
+MET HB3 CB . .
+MET HB2 CB . .
+MET CG CB SD .
+MET HG3 CG . .
+MET HG2 CG . .
+MET SD CG CE .
+MET CE SD HE3 .
+MET HE1 CE . .
+MET HE2 CE . .
+MET HE3 CE . .
+MET C CA . END
+MET O C . .
+MET OXT C . .
+
+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
+MET CA N H 110.062 1.93
+MET CA N H2 110.062 1.93
+MET CA N H3 110.062 1.93
+MET H N H2 109.028 2.41
+MET H N H3 109.028 2.41
+MET H2 N H3 109.028 2.41
+MET N CA C 109.241 1.50
+MET N CA CB 110.906 1.50
+MET N CA HA 108.487 1.50
+MET C CA CB 109.344 1.50
+MET C CA HA 108.824 1.50
+MET CB CA HA 109.670 1.50
+MET CA C O 117.124 1.50
+MET CA C OXT 117.124 1.50
+MET O C OXT 125.752 1.50
+MET CA CB CG 113.476 1.50
+MET CA CB HB3 108.666 1.50
+MET CA CB HB2 108.666 1.50
+MET CG CB HB3 108.955 1.50
+MET CG CB HB2 108.955 1.50
+MET HB3 CB HB2 107.698 1.50
+MET CB CG SD 112.576 2.44
+MET CB CG HG3 109.206 1.50
+MET CB CG HG2 109.206 1.50
+MET SD CG HG3 108.861 1.50
+MET SD CG HG2 108.861 1.50
+MET HG3 CG HG2 107.939 1.50
+MET CG SD CE 100.595 1.50
+MET SD CE HE3 109.425 1.50
+MET SD CE HE2 109.425 1.50
+MET SD CE HE1 109.425 1.50
+MET HE3 CE HE2 109.509 1.50
+MET HE3 CE HE1 109.509 1.50
+MET HE2 CE HE1 109.509 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
+MET chi1 N CA CB CG -90.000 10.0 3
+MET chi2 CA CB CG SD 60.000 10.0 3
+MET chi3 CB CG SD CE 90.000 10.0 3
+MET hh1 CG SD CE HE3 180.000 10.0 3
+MET sp3_sp3_1 C CA N H 180.000 10.0 3
+MET 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
+MET 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
+MET plan-1 C 0.020
+MET plan-1 CA 0.020
+MET plan-1 O 0.020
+MET 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
+MET SMILES ACDLabs 10.04 O=C(O)C(N)CCSC
+MET SMILES_CANONICAL CACTVS 3.341 CSCC[C@H](N)C(O)=O
+MET SMILES CACTVS 3.341 CSCC[CH](N)C(O)=O
+MET SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CSCC[C@@H](C(=O)O)N
+MET SMILES "OpenEye OEToolkits" 1.5.0 CSCCC(C(=O)O)N
+MET InChI InChI 1.03 InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
+MET InChIKey InChI 1.03 FFEARJCKVFRZRR-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
+MET acedrg 243 "dictionary generator"
+MET acedrg_database 11 "data source"
+MET rdkit 2017.03.2 "Chemoinformatics tool"
+MET refmac5 5.8.0238 "optimization tool"

package/baby-gru/monomers/m/MSE.cif

@@ -0,0 +1,201 @@
+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
+MSE MSE SELENOMETHIONINE peptide 20 9 .
+
+data_comp_MSE
+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
+MSE N N NT3 1 10.980 -7.344 20.020
+MSE CA C CH1 0 10.215 -8.538 19.563
+MSE C C C 0 8.775 -8.458 20.089
+MSE O O O 0 8.605 -7.967 21.223
+MSE OXT O OC -1 7.876 -8.895 19.344
+MSE CB C CH2 0 10.896 -9.824 20.043
+MSE CG C CH2 0 12.189 -10.151 19.325
+MSE SE SE SE 0 12.850 -11.935 19.808
+MSE CE C CH3 0 13.628 -11.498 21.557
+MSE H H H 0 11.808 -7.339 19.642
+MSE H2 H H 0 11.069 -7.358 20.927
+MSE H3 H H 0 10.544 -6.581 19.779
+MSE HA H H 0 10.192 -8.533 18.579
+MSE HB2 H H 0 10.295 -10.556 19.923
+MSE HB3 H H 0 11.082 -9.746 20.975
+MSE HG2 H H 0 12.870 -9.483 19.555
+MSE HG3 H H 0 12.044 -10.114 18.355
+MSE HE1 H H 0 14.013 -12.298 21.947
+MSE HE2 H H 0 12.935 -11.153 22.141
+MSE HE3 H H 0 14.320 -10.828 21.443
+
+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
+MSE N n/a CA START
+MSE H N . .
+MSE H2 N . .
+MSE H3 N . .
+MSE CA N C .
+MSE HA CA . .
+MSE CB CA CG .
+MSE HB2 CB . .
+MSE HB3 CB . .
+MSE CG CB SE .
+MSE HG2 CG . .
+MSE HG3 CG . .
+MSE SE CG CE .
+MSE CE SE HE1 .
+MSE HE3 CE . .
+MSE HE2 CE . .
+MSE HE1 CE . .
+MSE C CA . END
+MSE O C . .
+MSE 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
+MSE N CA SINGLE n 1.488 0.0100 1.488 0.0100
+MSE CA C SINGLE n 1.533 0.0100 1.533 0.0100
+MSE CA CB SINGLE n 1.532 0.0100 1.532 0.0100
+MSE C O DOUBLE n 1.247 0.0187 1.247 0.0187
+MSE C OXT SINGLE n 1.247 0.0187 1.247 0.0187
+MSE CB CG SINGLE n 1.514 0.0200 1.514 0.0200
+MSE CG SE SINGLE n 1.963 0.0200 1.963 0.0200
+MSE SE CE SINGLE n 1.963 0.0200 1.963 0.0200
+MSE N H SINGLE n 1.036 0.0160 0.911 0.0200
+MSE N H2 SINGLE n 1.036 0.0160 0.911 0.0200
+MSE N H3 SINGLE n 1.036 0.0160 0.911 0.0200
+MSE CA HA SINGLE n 1.089 0.0100 0.985 0.0200
+MSE CB HB2 SINGLE n 1.089 0.0100 0.954 0.0200
+MSE CB HB3 SINGLE n 1.089 0.0100 0.954 0.0200
+MSE CG HG2 SINGLE n 1.089 0.0100 0.981 0.0167
+MSE CG HG3 SINGLE n 1.089 0.0100 0.981 0.0167
+MSE CE HE1 SINGLE n 1.089 0.0100 0.970 0.0162
+MSE CE HE2 SINGLE n 1.089 0.0100 0.970 0.0162
+MSE CE HE3 SINGLE n 1.089 0.0100 0.970 0.0162
+
+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
+MSE CA N H 110.062 1.93
+MSE CA N H2 110.062 1.93
+MSE CA N H3 110.062 1.93
+MSE H N H2 109.028 2.41
+MSE H N H3 109.028 2.41
+MSE H2 N H3 109.028 2.41
+MSE N CA C 109.241 1.50
+MSE N CA CB 110.245 1.51
+MSE N CA HA 108.487 1.50
+MSE C CA CB 110.728 2.07
+MSE C CA HA 108.824 1.50
+MSE CB CA HA 109.207 1.50
+MSE CA C O 117.124 1.50
+MSE CA C OXT 117.124 1.50
+MSE O C OXT 125.752 1.50
+MSE CA CB CG 113.897 1.50
+MSE CA CB HB2 108.567 1.50
+MSE CA CB HB3 108.567 1.50
+MSE CG CB HB2 108.056 1.50
+MSE CG CB HB3 108.056 1.50
+MSE HB2 CB HB3 107.715 1.50
+MSE CB CG SE 111.593 3.00
+MSE CB CG HG2 109.535 1.63
+MSE CB CG HG3 109.535 1.63
+MSE SE CG HG2 109.134 1.50
+MSE SE CG HG3 109.134 1.50
+MSE HG2 CG HG3 108.011 1.50
+MSE CG SE CE 98.689 1.50
+MSE SE CE HE1 109.134 1.50
+MSE SE CE HE2 109.134 1.50
+MSE SE CE HE3 109.134 1.50
+MSE HE1 CE HE2 109.290 1.50
+MSE HE1 CE HE3 109.290 1.50
+MSE HE2 CE HE3 109.290 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
+MSE sp3_sp3_1 C CA N H 180.000 10.0 3
+MSE sp2_sp3_1 O C CA N 0.000 10.0 6
+MSE sp3_sp3_10 N CA CB CG 180.000 10.0 3
+MSE sp3_sp3_19 CA CB CG SE 180.000 10.0 3
+MSE sp3_sp3_28 CB CG SE CE 180.000 10.0 3
+MSE sp3_sp3_31 HE1 CE SE CG 180.000 10.0 3
+
+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
+MSE 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
+MSE plan-1 C 0.020
+MSE plan-1 CA 0.020
+MSE plan-1 O 0.020
+MSE 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
+MSE SMILES ACDLabs 10.04 O=C(O)C(N)CC[Se]C
+MSE SMILES_CANONICAL CACTVS 3.341 C[Se]CC[C@H](N)C(O)=O
+MSE SMILES CACTVS 3.341 C[Se]CC[CH](N)C(O)=O
+MSE SMILES_CANONICAL ""OpenEye OEToolkits" 1.5.0 C[Se]CC[C@@H](C(=O)O)N
+MSE SMILES ""OpenEye OEToolkits" 1.5.0 C[Se]CCC(C(=O)O)N
+MSE InChI InChI 1.03 InChI=1S/C5H11NO2Se/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
+MSE InChIKey InChI 1.03 RJFAYQIBOAGBLC-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
+MSE acedrg 243 ""dictionary generator"
+MSE acedrg_database 11 ""data source"
+MSE rdkit 2017.03.2 ""Chemoinformatics tool"
+MSE refmac5 5.8.0238 ""optimization tool"

package/baby-gru/monomers/n/NA.cif

@@ -0,0 +1,30 @@
+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
+NA NA 'SODIUM ION                          ' NON-POLYMER 1 1 .
+
+data_comp_NA
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+NA NA NA NA 1.000 0.000 0.000 0.000
+
+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
+NA NA n/a . END