# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 07:14:12 2022
#   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  38  21  .  2022-03-18  2022-03-18
;
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   0.057  25.6656  13.8684  48.8106
 G0C  C5   C  CR6    0   0.001  24.9033  12.8986  49.4826
 G0C  C6   C  CR16   0  -0.162  23.9060  13.3357  50.3367
 G0C  N1   N  N      0  -0.400  23.6277  14.6145  50.5606
 G0C  C3   C  CR6    0   0.250  25.3665  15.2130  49.0484
 G0C  OP1  O  OP    -1  -0.881  28.2928   9.4385  49.8867
 G0C  P    P  P      0   1.245  26.9264   9.4853  49.2203
 G0C  OP2  O  OP    -1  -0.891  25.9053   8.4733  49.7270
 G0C  OP3  O  O      0  -0.881  26.9542   9.6336  47.6976
 G0C  OP4  O  O2     0  -0.653  26.3384  11.0063  49.7928
 G0C  C5A  C  CH2    0  -0.230  25.1067  11.4185  49.2796
 G0C  C2   C  CR6    0   0.117  24.3312  15.5457  49.9398
 G0C  C2A  C  CH3    0  -0.787  23.9911  16.9824  50.2105
 G0C  O3   O  OH1    0  -0.600  26.0838  16.1671  48.4338
 G0C  C4A  C  C1     0  -0.122  26.7576  13.4298  47.9193
 G0C  N    N  N      0  -0.334  27.1331  14.0863  46.9058
 G0C  CA   C  CH2    0  -0.279  28.2267  13.5944  46.1007
 G0C  CB   C  CH2    0  -0.497  29.0145  12.3820  46.5816
 G0C  CG   C  CH2    0  -0.570  30.1697  12.0426  45.6504
 G0C  SD   S  S2     0  -0.047  31.4966  13.2830  45.5892
 G0C  CE   C  CH3    0  -0.767  32.2266  13.0651  47.2278
 G0C  H1   H  HCR6   0   0.247  23.2958  12.6116  50.8674
 G0C  H4   H  HCH2   0   0.197  24.2683  10.8953  49.7619
 G0C  H5   H  HCH2   0   0.185  25.0237  11.1987  48.2065
 G0C  H6   H  HCH3   0   0.270  23.1623  17.0363  50.9121
 G0C  H7   H  HCH3   0   0.255  24.8278  17.5331  50.6498
 G0C  H8   H  HCH3   0   0.257  23.6906  17.5126  49.3029
 G0C  H9   H  HOH1   0   0.482  25.8454  17.0412  48.7625
 G0C  H10  H  H      0   0.258  27.2055  12.4796  48.2043
 G0C  H11  H  HCH2   0   0.227  28.9125  14.4358  45.9597
 G0C  H12  H  HCH2   0   0.252  28.3706  11.5006  46.6551
 G0C  H13  H  HCH2   0   0.270  29.8176  11.9423  44.6211
 G0C  H14  H  HCH2   0   0.274  30.6137  11.0850  45.9284
 G0C  H15  H  HCH3   0   0.272  33.0785  13.7391  47.2975
 G0C  H16  H  HCH3   0   0.261  31.5248  13.3153  48.0214
 G0C  H17  H  HCH3   0   0.259  32.5783  12.0433  47.3657
 G0C  H18  H  HCH2   0   0.231  27.8225  13.3928  45.1019
 G0C  H19  H  HCH2   0   0.234  29.3971  12.5557  47.5921

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    1.522  0.020  1.522
 G0C  CA   CB   single    1.524  0.020  1.524
 G0C  CA   N    single    1.444  0.020  1.444
 G0C  SD   CE   single    1.807  0.020  1.807
 G0C  N    C4A  double    1.265  0.020  1.265
 G0C  C4A  C4   single    1.476  0.020  1.476
 G0C  OP3  P    deloc     1.530  0.020  1.530
 G0C  O3   C3   single    1.343  0.020  1.343
 G0C  C4   C3   aromatic  1.398  0.020  1.398
 G0C  C4   C5   aromatic  1.405  0.020  1.405
 G0C  C3   C2   aromatic  1.406  0.020  1.406
 G0C  C5A  C5   single    1.508  0.020  1.508
 G0C  C5A  OP4  single    1.397  0.020  1.397
 G0C  C5   C6   aromatic  1.384  0.020  1.384
 G0C  P    OP2  deloc     1.524  0.020  1.524
 G0C  P    OP4  single    1.728  0.020  1.728
 G0C  P    OP1  deloc     1.521  0.020  1.521
 G0C  C2   C2A  single    1.501  0.020  1.501
 G0C  C2   N1   aromatic  1.322  0.020  1.322
 G0C  C6   N1   aromatic  1.328  0.020  1.328
 G0C  C6   H1   single    0.930  0.020  1.080
 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   123.15  3.000
 G0C  C3   C4   C5   117.81  3.000
 G0C  C4A  C4   C5   119.02  3.000
 G0C  C5A  C5   C6   119.36  3.000
 G0C  C6   C5   C4   117.92  3.000
 G0C  C5A  C5   C4   122.70  3.000
 G0C  H1   C6   N1   116.24  3.000
 G0C  H1   C6   C5   119.75  3.000
 G0C  N1   C6   C5   124.01  3.000
 G0C  C2   N1   C6   119.19  3.000
 G0C  O3   C3   C2   121.03  3.000
 G0C  C2   C3   C4   119.54  3.000
 G0C  O3   C3   C4   119.43  3.000
 G0C  OP4  P    OP3  104.51  3.000
 G0C  OP4  P    OP2  104.26  3.000
 G0C  OP3  P    OP2  114.04  3.000
 G0C  OP4  P    OP1  100.81  3.000
 G0C  OP2  P    OP1  115.84  3.000
 G0C  OP3  P    OP1  115.00  3.000
 G0C  C5A  OP4  P    115.98  3.000
 G0C  H5   C5A  H4   105.99  3.000
 G0C  H5   C5A  OP4  111.50  3.000
 G0C  H4   C5A  OP4  111.77  3.000
 G0C  H5   C5A  C5   108.53  3.000
 G0C  H4   C5A  C5   107.77  3.000
 G0C  OP4  C5A  C5   111.06  3.000
 G0C  C2A  C2   C3   120.51  3.000
 G0C  C2A  C2   N1   117.97  3.000
 G0C  C3   C2   N1   121.53  3.000
 G0C  H8   C2A  H7   107.43  3.000
 G0C  H8   C2A  H6   107.58  3.000
 G0C  H7   C2A  H6   107.40  3.000
 G0C  H8   C2A  C2   112.13  3.000
 G0C  H7   C2A  C2   112.40  3.000
 G0C  H6   C2A  C2   109.67  3.000
 G0C  H9   O3   C3   110.87  3.000
 G0C  H10  C4A  N    122.74  3.000
 G0C  H10  C4A  C4   113.93  3.000
 G0C  N    C4A  C4   123.32  3.000
 G0C  CA   N    C4A  119.65  3.000
 G0C  H18  CA   H11  104.78  3.000
 G0C  H18  CA   CB   109.38  3.000
 G0C  H11  CA   CB   109.17  3.000
 G0C  H18  CA   N    106.94  3.000
 G0C  H11  CA   N    106.52  3.000
 G0C  CB   CA   N    119.11  3.000
 G0C  H19  CB   H12  105.76  3.000
 G0C  H19  CB   CG   109.57  3.000
 G0C  H12  CB   CG   107.95  3.000
 G0C  H19  CB   CA   110.24  3.000
 G0C  H12  CB   CA   110.97  3.000
 G0C  CG   CB   CA   112.13  3.000
 G0C  H14  CG   H13  106.89  3.000
 G0C  H14  CG   SD   108.08  3.000
 G0C  H13  CG   SD   105.44  3.000
 G0C  H14  CG   CB   110.40  3.000
 G0C  H13  CG   CB   110.63  3.000
 G0C  SD   CG   CB   114.99  3.000
 G0C  CE   SD   CG   100.49  3.000
 G0C  H17  CE   H16  109.36  3.000
 G0C  H17  CE   H15  108.66  3.000
 G0C  H16  CE   H15  108.39  3.000
 G0C  H17  CE   SD   111.00  3.000
 G0C  H16  CE   SD   111.90  3.000
 G0C  H15  CE   SD   107.43  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     68.08  30.0  3
 G0C  Var_02    N    C4A  C4  C5    150.58  30.0  3
 G0C  Var_03    H6   C2A  C2  N1     -0.50  30.0  2
 G0C  Var_04    CB   CA   N   C4A    -7.23  30.0  2
 G0C  Var_05    CG   CB   CA  N    -177.18  30.0  3
 G0C  Var_06    SD   CG   CB  CA     66.45  30.0  2
 G0C  Var_07    H15  CE   SD  CG    177.59  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

