# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 08:02:45 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: [6-methyl-4-[(3-methylsulfanylpropylamino)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCCCNCc1c(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
 G0F  G0F  '[6-methyl-4-[(3-methylsulfanylpropylamino)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate'  ligand  40  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_G0F
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
 G0F  C4   C  CR6    0   0.083  27.7804  -13.1454  -4.2504
 G0F  C5   C  CR6    0  -0.021  28.4417  -12.0481  -3.6931
 G0F  C6   C  CR16   0  -0.158  29.6380  -12.2804  -3.0295
 G0F  N1   N  N      0  -0.408  30.1989  -13.4754  -2.8999
 G0F  C3   C  CR6    0   0.248  28.3740  -14.3977  -4.1036
 G0F  OP1  O  O      0  -0.861  25.4423   -9.3126  -4.9198
 G0F  P    P  P      0   1.251  25.7279   -9.1736  -3.4199
 G0F  OP2  O  OP    -1  -0.880  24.5323   -9.4310  -2.5153
 G0F  OP3  O  OP    -1  -0.890  26.5790   -7.9580  -3.0723
 G0F  OP4  O  O2     0  -0.651  26.7270  -10.5216  -3.0449
 G0F  C5A  C  CH2    0  -0.230  27.9031  -10.6462  -3.7897
 G0F  C2   C  CR6    0   0.126  29.5919  -14.5301  -3.4240
 G0F  C2A  C  CH3    0  -0.782  30.2468  -15.8719  -3.2719
 G0F  O3   O  OH1    0  -0.627  27.7359  -15.4589  -4.6431
 G0F  C4A  C  CH2    0  -0.377  26.4808  -13.0190  -5.0026
 G0F  N    N  NH1    0  -0.600  26.6680  -13.1815  -6.4393
 G0F  CA   C  CH2    0  -0.273  25.4023  -13.1238  -7.1581
 G0F  CB   C  CH2    0  -0.454  24.9624  -11.6949  -7.4525
 G0F  CG   C  CH2    0  -0.569  23.5350  -11.6219  -7.9770
 G0F  SD   S  S2     0  -0.059  22.2597  -11.9943  -6.7341
 G0F  CE   C  CH3    0  -0.790  22.2058  -10.4309  -5.8245
 G0F  H1   H  HCR6   0   0.243  30.1725  -11.4480  -2.5815
 G0F  H4   H  HCH2   0   0.193  28.6825   -9.9545  -3.4380
 G0F  H5   H  HCH2   0   0.185  27.7373  -10.4071  -4.8488
 G0F  H6   H  HCH3   0   0.267  31.1784  -15.7672  -2.7207
 G0F  H7   H  HCH3   0   0.254  29.6178  -16.5798  -2.7257
 G0F  H8   H  HCH3   0   0.253  30.4850  -16.3250  -4.2381
 G0F  H9   H  HOH1   0   0.483  28.2252  -16.2762  -4.4989
 G0F  H10  H  HCH2   0   0.270  26.0523  -12.0371  -4.8165
 G0F  H11  H  HCH2   0   0.187  24.6021  -13.6469  -6.6117
 G0F  H12  H  HCH2   0   0.225  25.5244  -13.6538  -8.1062
 G0F  H13  H  HCH2   0   0.223  25.6292  -11.2699  -8.2094
 G0F  H14  H  HCH2   0   0.262  25.0628  -11.0598  -6.5697
 G0F  H15  H  HCH2   0   0.262  23.3814  -12.3444  -8.7824
 G0F  H16  H  HCH2   0   0.269  23.3193  -10.6361  -8.3931
 G0F  H17  H  HCH3   0   0.263  21.5062  -10.5627  -5.0002
 G0F  H18  H  HCH3   0   0.274  23.1794  -10.1594  -5.4175
 G0F  H19  H  HCH3   0   0.250  21.8412   -9.6247  -6.4607
 G0F  H20  H  HCH2   0   0.207  25.7608  -13.7465  -4.5954
 G0F  H21  H  HNH1   0   0.349  27.0836  -14.0877  -6.6108

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
 G0F  CG   SD   single    1.819  0.020  1.819
 G0F  CG   CB   single    1.522  0.020  1.522
 G0F  SD   CE   single    1.810  0.020  1.810
 G0F  CA   CB   single    1.524  0.020  1.524
 G0F  CA   N    single    1.457  0.020  1.457
 G0F  N    C4A  single    1.458  0.020  1.458
 G0F  C4A  C4   single    1.507  0.020  1.507
 G0F  OP1  P    deloc     1.533  0.020  1.533
 G0F  O3   C3   single    1.351  0.020  1.351
 G0F  C4   C3   aromatic  1.394  0.020  1.394
 G0F  C4   C5   aromatic  1.397  0.020  1.397
 G0F  C3   C2   aromatic  1.401  0.020  1.401
 G0F  C5A  C5   single    1.505  0.020  1.505
 G0F  C5A  OP4  single    1.398  0.020  1.398
 G0F  C5   C6   aromatic  1.388  0.020  1.388
 G0F  P    OP3  deloc     1.524  0.020  1.524
 G0F  P    OP4  single    1.719  0.020  1.719
 G0F  P    OP2  deloc     1.521  0.020  1.521
 G0F  C2   C2A  single    1.501  0.020  1.501
 G0F  C2   N1   aromatic  1.325  0.020  1.325
 G0F  C6   N1   aromatic  1.326  0.020  1.326
 G0F  C6   H1   single    0.930  0.020  1.080
 G0F  C5A  H4   single    0.970  0.020  1.090
 G0F  C5A  H5   single    0.970  0.020  1.090
 G0F  C2A  H6   single    0.970  0.020  1.090
 G0F  C2A  H7   single    0.970  0.020  1.090
 G0F  C2A  H8   single    0.970  0.020  1.090
 G0F  O3   H9   single    0.850  0.020  0.980
 G0F  C4A  H10  single    0.970  0.020  1.090
 G0F  CA   H11  single    0.970  0.020  1.090
 G0F  CA   H12  single    0.970  0.020  1.090
 G0F  CB   H13  single    0.970  0.020  1.090
 G0F  CB   H14  single    0.970  0.020  1.090
 G0F  CG   H15  single    0.970  0.020  1.090
 G0F  CG   H16  single    0.970  0.020  1.090
 G0F  CE   H17  single    0.970  0.020  1.090
 G0F  CE   H18  single    0.970  0.020  1.090
 G0F  CE   H19  single    0.970  0.020  1.090
 G0F  C4A  H20  single    0.970  0.020  1.090
 G0F  N    H21  single    0.890  0.020  1.040

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
 G0F  C4A  C4   C3   119.69  3.000
 G0F  C3   C4   C5   117.52  3.000
 G0F  C4A  C4   C5   122.78  3.000
 G0F  C5A  C5   C6   119.69  3.000
 G0F  C6   C5   C4   117.86  3.000
 G0F  C5A  C5   C4   122.45  3.000
 G0F  H1   C6   N1   116.24  3.000
 G0F  H1   C6   C5   119.56  3.000
 G0F  N1   C6   C5   124.20  3.000
 G0F  C2   N1   C6   119.00  3.000
 G0F  O3   C3   C2   122.02  3.000
 G0F  C2   C3   C4   120.42  3.000
 G0F  O3   C3   C4   117.56  3.000
 G0F  OP4  P    OP3  104.54  3.000
 G0F  OP4  P    OP2  101.21  3.000
 G0F  OP3  P    OP2  115.99  3.000
 G0F  OP2  P    OP1  114.84  3.000
 G0F  OP4  P    OP1  104.51  3.000
 G0F  OP3  P    OP1  113.54  3.000
 G0F  C5A  OP4  P    116.27  3.000
 G0F  H5   C5A  H4   106.17  3.000
 G0F  H5   C5A  OP4  111.56  3.000
 G0F  H4   C5A  OP4  111.71  3.000
 G0F  H5   C5A  C5   108.59  3.000
 G0F  H4   C5A  C5   108.16  3.000
 G0F  OP4  C5A  C5   110.48  3.000
 G0F  C2A  C2   C3   120.87  3.000
 G0F  C2A  C2   N1   118.14  3.000
 G0F  C3   C2   N1   120.99  3.000
 G0F  H8   C2A  H7   107.37  3.000
 G0F  H8   C2A  H6   107.53  3.000
 G0F  H7   C2A  H6   107.58  3.000
 G0F  H8   C2A  C2   112.09  3.000
 G0F  H7   C2A  C2   112.24  3.000
 G0F  H6   C2A  C2   109.82  3.000
 G0F  H9   O3   C3   111.52  3.000
 G0F  H20  C4A  H10  106.00  3.000
 G0F  H20  C4A  N    112.00  3.000
 G0F  H10  C4A  N    108.65  3.000
 G0F  H20  C4A  C4   108.89  3.000
 G0F  H10  C4A  C4   109.28  3.000
 G0F  N    C4A  C4   111.82  3.000
 G0F  H21  N    CA   107.99  3.000
 G0F  H21  N    C4A  108.64  3.000
 G0F  CA   N    C4A  111.73  3.000
 G0F  H12  CA   H11  106.33  3.000
 G0F  H12  CA   CB   108.62  3.000
 G0F  H11  CA   CB   109.36  3.000
 G0F  H12  CA   N    108.17  3.000
 G0F  H11  CA   N    111.58  3.000
 G0F  CB   CA   N    112.54  3.000
 G0F  H14  CB   H13  106.08  3.000
 G0F  H14  CB   CG   109.69  3.000
 G0F  H13  CB   CG   108.32  3.000
 G0F  H14  CB   CA   111.26  3.000
 G0F  H13  CB   CA   108.77  3.000
 G0F  CG   CB   CA   112.47  3.000
 G0F  H16  CG   H15  106.76  3.000
 G0F  H16  CG   SD   107.87  3.000
 G0F  H15  CG   SD   105.64  3.000
 G0F  H16  CG   CB   111.09  3.000
 G0F  H15  CG   CB   110.73  3.000
 G0F  SD   CG   CB   114.33  3.000
 G0F  CE   SD   CG   100.80  3.000
 G0F  H19  CE   H18  109.44  3.000
 G0F  H19  CE   H17  108.45  3.000
 G0F  H18  CE   H17  108.75  3.000
 G0F  H19  CE   SD   110.83  3.000
 G0F  H18  CE   SD   112.11  3.000
 G0F  H17  CE   SD   107.15  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
 G0F  CONST_01  N1   C2   C3   C4      0.00   0.0  0
 G0F  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 G0F  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 G0F  CONST_04  C2   N1   C6   C5      0.00   0.0  0
 G0F  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 G0F  CONST_06  C3   C2   N1   C6      0.00   0.0  0
 G0F  CONST_07  C2A  C2   C3   C4    180.00   0.0  0
 G0F  CONST_08  O3   C3   C4   C5    180.00   0.0  0
 G0F  CONST_09  C4A  C4   C5   C6    180.00   0.0  0
 G0F  CONST_10  C2A  C2   N1   C6    180.00   0.0  0
 G0F  CONST_11  O3   C3   C2   N1    180.00   0.0  0
 G0F  CONST_12  C5A  C5   C6   N1    180.00   0.0  0
 G0F  CONST_13  C5A  C5   C4   C3    180.00   0.0  0
 G0F  CONST_14  C4A  C4   C3   C2    180.00   0.0  0
 G0F  CONST_15  H1   C6   C5   C4    180.00   0.0  0
 G0F  Var_01    OP4  C5A  C5   C4     67.42  30.0  2
 G0F  Var_02    N    C4A  C4   C5    106.26  30.0  2
 G0F  Var_03    H6   C2A  C2   N1     -0.03  30.0  2
 G0F  Var_04    CA   N    C4A  C4    177.22  30.0  1
 G0F  Var_05    CB   CA   N    C4A    83.77  30.0  2
 G0F  Var_06    CG   CB   CA   N    -169.80  30.0  3
 G0F  Var_07    SD   CG   CB   CA     70.65  30.0  2
 G0F  Var_08    H17  CE   SD   CG   -176.46  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
 G0F  plan-1  C4   0.020
 G0F  plan-1  C5   0.020
 G0F  plan-1  C6   0.020
 G0F  plan-1  N1   0.020
 G0F  plan-1  C3   0.020
 G0F  plan-1  C5A  0.020
 G0F  plan-1  C2   0.020
 G0F  plan-1  C2A  0.020
 G0F  plan-1  O3   0.020
 G0F  plan-1  C4A  0.020
 G0F  plan-1  H1   0.020

