# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:19:21 2021
#   Inital geometry file: a 99 line input string
#   Ligand name: [6-methyl-4-[(~{E})-3-methylsulfanylpropyliminomethyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCCCN=Cc1c(O)c(C)ncc1CO[P](O)(O)=O
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 G0C  G0C  '[6-methyl-4-[(~{E})-3-methylsulfanylpropyliminomethyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate'  ligand  40  21  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G0C
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.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 G0C  C4   C  CR6   0   0.079  25.6648  13.9166  48.7621
 G0C  C5   C  CR6   0   0.004  24.8660  12.9270  49.3542
 G0C  C6   C  CR16  0  -0.135  23.8288  13.3174  50.1807
 G0C  N1   N  N     0  -0.403  23.5519  14.5844  50.4588
 G0C  C3   C  CR6   0   0.259  25.3608  15.2483  49.0548
 G0C  OP1  O  OH1   0  -0.726  28.1215   9.6976  50.7016
 G0C  P    P  P     0   1.458  27.0169   9.7242  49.5542
 G0C  OP2  O  OH1   0  -0.735  26.0212   8.5660  50.0068
 G0C  OP3  O  O     0  -0.701  27.5089   9.6692  48.1628
 G0C  OP4  O  O2    0  -0.585  26.1868  11.0349  49.9422
 G0C  C5A  C  CH2   0  -0.307  25.0875  11.4638  49.1208
 G0C  C2   C  CR6   0   0.128  24.2918  15.5392  49.9224
 G0C  C2A  C  CH3   0  -0.791  23.9604  16.9613  50.2627
 G0C  O3   O  OH1   0  -0.598  26.1052  16.2263  48.5220
 G0C  C4A  C  C1    0  -0.106  26.7858  13.5230  47.8864
 G0C  N    N  N     0  -0.325  27.1891  14.2432  46.9313
 G0C  CA   C  CH2   0  -0.282  28.2884  13.8145  46.1022
 G0C  CB   C  CH2   0  -0.481  28.9685  12.4847  46.3949
 G0C  CG   C  CH2   0  -0.573  30.0951  12.1984  45.4112
 G0C  SD   S  S2    0  -0.043  31.5144  13.3254  45.5389
 G0C  CE   C  CH3   0  -0.770  32.2334  12.7535  47.0950
 G0C  H1   H  HCR6  0   0.262  23.1889  12.5697  50.6377
 G0C  H2   H  HOH1  0   0.502  28.9352  10.1713  50.4842
 G0C  H3   H  HOH1  0   0.502  26.2193   7.6987  49.6284
 G0C  H4   H  HCH2  0   0.276  24.1927  10.9067  49.4044
 G0C  H5   H  HCH2  0   0.261  25.2884  11.2535  48.0678
 G0C  H6   H  HCH3  0   0.276  23.1114  16.9878  50.9410
 G0C  H7   H  HCH3  0   0.260  24.7912  17.4713  50.7572
 G0C  H8   H  HCH3  0   0.264  23.6959  17.5440  49.3767
 G0C  H9   H  HOH1  0   0.487  25.8451  17.0862  48.8720
 G0C  H10  H  H     0   0.235  27.2341  12.5558  48.1182
 G0C  H11  H  HCH2  0   0.239  29.0314  14.6176  46.1323
 G0C  H12  H  HCH2  0   0.252  28.2506  11.6627  46.3302
 G0C  H13  H  HCH2  0   0.274  29.7383  12.2869  44.3826
 G0C  H14  H  HCH2  0   0.277  30.4595  11.1769  45.5339
 G0C  H15  H  HCH3  0   0.275  33.1046  13.3717  47.3034
 G0C  H16  H  HCH3  0   0.260  31.5348  12.8562  47.9239
 G0C  H17  H  HCH3  0   0.261  32.5518  11.7145  47.0188
 G0C  H18  H  HCH2  0   0.237  27.9190  13.8135  45.0707
 G0C  H19  H  HCH2  0   0.234  29.3588  12.4660  47.4165

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.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 G0C  CG   SD   single    1.817  0.020  1.817
 G0C  CG   CB   single    1.523  0.020  1.523
 G0C  CA   CB   single    1.522  0.020  1.522
 G0C  CA   N    single    1.442  0.020  1.442
 G0C  SD   CE   single    1.807  0.020  1.807
 G0C  N    C4A  double    1.262  0.020  1.262
 G0C  C4A  C4   single    1.476  0.020  1.476
 G0C  OP3  P    double    1.477  0.020  1.477
 G0C  O3   C3   single    1.340  0.020  1.340
 G0C  C4   C3   aromatic  1.397  0.020  1.397
 G0C  C4   C5   aromatic  1.403  0.020  1.403
 G0C  C3   C2   aromatic  1.407  0.020  1.407
 G0C  C5A  C5   single    1.498  0.020  1.498
 G0C  C5A  OP4  single    1.438  0.020  1.438
 G0C  C5   C6   aromatic  1.382  0.020  1.382
 G0C  P    OP2  single    1.593  0.020  1.593
 G0C  P    OP4  single    1.599  0.020  1.599
 G0C  P    OP1  single    1.593  0.020  1.593
 G0C  C2   C2A  single    1.499  0.020  1.499
 G0C  C2   N1   aromatic  1.322  0.020  1.322
 G0C  C6   N1   aromatic  1.326  0.020  1.326
 G0C  C6   H1   single    0.930  0.020  1.080
 G0C  OP1  H2   single    0.850  0.020  0.980
 G0C  OP2  H3   single    0.850  0.020  0.980
 G0C  C5A  H4   single    0.970  0.020  1.090
 G0C  C5A  H5   single    0.970  0.020  1.090
 G0C  C2A  H6   single    0.970  0.020  1.090
 G0C  C2A  H7   single    0.970  0.020  1.090
 G0C  C2A  H8   single    0.970  0.020  1.090
 G0C  O3   H9   single    0.850  0.020  0.980
 G0C  C4A  H10  single    0.930  0.020  1.080
 G0C  CA   H11  single    0.970  0.020  1.090
 G0C  CB   H12  single    0.970  0.020  1.090
 G0C  CG   H13  single    0.970  0.020  1.090
 G0C  CG   H14  single    0.970  0.020  1.090
 G0C  CE   H15  single    0.970  0.020  1.090
 G0C  CE   H16  single    0.970  0.020  1.090
 G0C  CE   H17  single    0.970  0.020  1.090
 G0C  CA   H18  single    0.970  0.020  1.090
 G0C  CB   H19  single    0.970  0.020  1.090

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
 G0C  C4A  C4   C3   122.94  3.000
 G0C  C3   C4   C5   117.39  3.000
 G0C  C4A  C4   C5   119.66  3.000
 G0C  C5A  C5   C6   118.68  3.000
 G0C  C6   C5   C4   118.71  3.000
 G0C  C5A  C5   C4   122.61  3.000
 G0C  H1   C6   N1   116.54  3.000
 G0C  H1   C6   C5   119.97  3.000
 G0C  N1   C6   C5   123.49  3.000
 G0C  C2   N1   C6   119.21  3.000
 G0C  O3   C3   C2   121.10  3.000
 G0C  C2   C3   C4   119.44  3.000
 G0C  O3   C3   C4   119.45  3.000
 G0C  H2   OP1  P    114.43  3.000
 G0C  OP4  P    OP3  115.60  3.000
 G0C  OP4  P    OP2  101.68  3.000
 G0C  OP3  P    OP2  116.67  3.000
 G0C  OP4  P    OP1  101.47  3.000
 G0C  OP2  P    OP1  102.51  3.000
 G0C  OP3  P    OP1  116.55  3.000
 G0C  H3   OP2  P    114.40  3.000
 G0C  C5A  OP4  P    120.18  3.000
 G0C  H5   C5A  H4   107.63  3.000
 G0C  H5   C5A  OP4  110.65  3.000
 G0C  H4   C5A  OP4  109.03  3.000
 G0C  H5   C5A  C5   111.43  3.000
 G0C  H4   C5A  C5   109.68  3.000
 G0C  OP4  C5A  C5   108.39  3.000
 G0C  C2A  C2   C3   120.26  3.000
 G0C  C2A  C2   N1   117.99  3.000
 G0C  C3   C2   N1   121.75  3.000
 G0C  H8   C2A  H7   107.57  3.000
 G0C  H8   C2A  H6   107.69  3.000
 G0C  H7   C2A  H6   107.45  3.000
 G0C  H8   C2A  C2   112.04  3.000
 G0C  H7   C2A  C2   112.16  3.000
 G0C  H6   C2A  C2   109.72  3.000
 G0C  H9   O3   C3   110.91  3.000
 G0C  H10  C4A  N    122.36  3.000
 G0C  H10  C4A  C4   114.99  3.000
 G0C  N    C4A  C4   122.64  3.000
 G0C  CA   N    C4A  120.60  3.000
 G0C  H18  CA   H11  104.80  3.000
 G0C  H18  CA   CB   109.32  3.000
 G0C  H11  CA   CB   109.42  3.000
 G0C  H18  CA   N    106.54  3.000
 G0C  H11  CA   N    106.47  3.000
 G0C  CB   CA   N    119.32  3.000
 G0C  H19  CB   H12  106.07  3.000
 G0C  H19  CB   CG   109.64  3.000
 G0C  H12  CB   CG   107.84  3.000
 G0C  H19  CB   CA   110.73  3.000
 G0C  H12  CB   CA   110.62  3.000
 G0C  CG   CB   CA   111.75  3.000
 G0C  H14  CG   H13  106.90  3.000
 G0C  H14  CG   SD   108.17  3.000
 G0C  H13  CG   SD   105.73  3.000
 G0C  H14  CG   CB   110.51  3.000
 G0C  H13  CG   CB   110.57  3.000
 G0C  SD   CG   CB   114.58  3.000
 G0C  CE   SD   CG   100.08  3.000
 G0C  H17  CE   H16  109.32  3.000
 G0C  H17  CE   H15  108.73  3.000
 G0C  H16  CE   H15  108.31  3.000
 G0C  H17  CE   SD   110.98  3.000
 G0C  H16  CE   SD   111.74  3.000
 G0C  H15  CE   SD   107.67  3.000

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
 G0C  CONST_01  N1   C2   C3  C4      0.00   0.0  0
 G0C  CONST_02  N1   C6   C5  C4      0.00   0.0  0
 G0C  CONST_03  C2   C3   C4  C5      0.00   0.0  0
 G0C  CONST_04  C2   N1   C6  C5      0.00   0.0  0
 G0C  CONST_05  C3   C4   C5  C6      0.00   0.0  0
 G0C  CONST_06  C3   C2   N1  C6      0.00   0.0  0
 G0C  CONST_07  C2A  C2   C3  C4    180.00   0.0  0
 G0C  CONST_08  O3   C3   C4  C5    180.00   0.0  0
 G0C  CONST_09  C4A  C4   C5  C6    180.00   0.0  0
 G0C  CONST_10  C2A  C2   N1  C6    180.00   0.0  0
 G0C  CONST_11  O3   C3   C2  N1    180.00   0.0  0
 G0C  CONST_12  C5A  C5   C6  N1    180.00   0.0  0
 G0C  CONST_13  C5A  C5   C4  C3    180.00   0.0  0
 G0C  CONST_14  C4A  C4   C3  C2    180.00   0.0  0
 G0C  CONST_15  H1   C6   C5  C4    180.00   0.0  0
 G0C  Var_01    OP4  C5A  C5  C4     78.91  30.0  2
 G0C  Var_02    N    C4A  C4  C5    150.49  30.0  3
 G0C  Var_03    H6   C2A  C2  N1      0.09  30.0  2
 G0C  Var_04    CB   CA   N   C4A    -0.43  30.0  2
 G0C  Var_05    CG   CB   CA  N     179.55  30.0  3
 G0C  Var_06    SD   CG   CB  CA     66.74  30.0  2
 G0C  Var_07    H15  CE   SD  CG   -179.06  30.0  3

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
 G0C  plan-1  C4   0.020
 G0C  plan-1  C5   0.020
 G0C  plan-1  C6   0.020
 G0C  plan-1  N1   0.020
 G0C  plan-1  C3   0.020
 G0C  plan-1  C5A  0.020
 G0C  plan-1  C2   0.020
 G0C  plan-1  C2A  0.020
 G0C  plan-1  O3   0.020
 G0C  plan-1  C4A  0.020
 G0C  plan-1  H1   0.020
 G0C  plan-2  C4   0.020
 G0C  plan-2  C4A  0.020
 G0C  plan-2  N    0.020
 G0C  plan-2  CA   0.020
 G0C  plan-2  H10  0.020

