# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 06:06:18 2021
#   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  42  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_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   0.095  27.7644  -13.2241  -4.2388
 G0F  C5   C  CR6   0  -0.016  28.4995  -12.0819  -3.9171
 G0F  C6   C  CR16  0  -0.129  29.7491  -12.2376  -3.3384
 G0F  N1   N  N     0  -0.410  30.2933  -13.4173  -3.0770
 G0F  C3   C  CR6   0   0.256  28.3542  -14.4576  -3.9751
 G0F  OP1  O  O     0  -0.691  25.0770   -9.3757  -4.4180
 G0F  P    P  P     0   1.460  25.9646   -9.2474  -3.2437
 G0F  OP2  O  OH1   0  -0.728  25.2634   -9.2765  -1.8136
 G0F  OP3  O  OH1   0  -0.738  26.8451   -7.9210  -3.1664
 G0F  OP4  O  O2    0  -0.583  27.0718  -10.3853  -3.0744
 G0F  C5A  C  CH2   0  -0.300  27.9670  -10.7044  -4.1547
 G0F  C2   C  CR6   0   0.135  29.6239  -14.5192  -3.3828
 G0F  C2A  C  CH3   0  -0.785  30.2678  -15.8406  -3.0869
 G0F  O3   O  OH1   0  -0.623  27.6665  -15.5662  -4.3141
 G0F  C4A  C  CH2   0  -0.372  26.4196  -13.1586  -4.9145
 G0F  N    N  NH1   0  -0.598  26.5876  -13.2655  -6.3561
 G0F  CA   C  CH2   0  -0.274  25.3396  -13.1119  -7.0907
 G0F  CB   C  CH2   0  -0.435  25.0237  -11.6510  -7.3777
 G0F  CG   C  CH2   0  -0.570  23.7322  -11.4679  -8.1615
 G0F  SD   S  S2    0  -0.050  22.2132  -11.8920  -7.2593
 G0F  CE   C  CH3   0  -0.779  22.0805  -10.4725  -6.1489
 G0F  H1   H  HCR6  0   0.257  30.3387  -11.3639  -3.0784
 G0F  H2   H  HOH1  0   0.502  24.5138   -9.8831  -1.7477
 G0F  H3   H  HOH1  0   0.501  26.4271   -7.1414  -3.5553
 G0F  H4   H  HCH2  0   0.270  28.7836   -9.9800  -4.1669
 G0F  H5   H  HCH2  0   0.258  27.4504  -10.6450  -5.1158
 G0F  H6   H  HCH3  0   0.272  31.2159  -15.6832  -2.5782
 G0F  H7   H  HCH3  0   0.258  29.6459  -16.4684  -2.4438
 G0F  H8   H  HCH3  0   0.260  30.4738  -16.4070  -3.9991
 G0F  H9   H  HOH1  0   0.487  28.1666  -16.3662  -4.1199
 G0F  H10  H  HCH2  0   0.249  25.9370  -12.2086  -4.6871
 G0F  H11  H  HCH2  0   0.197  24.4912  -13.5806  -6.5712
 G0F  H12  H  HCH2  0   0.228  25.4464  -13.6366  -8.0434
 G0F  H13  H  HCH2  0   0.230  25.8406  -11.2302  -7.9718
 G0F  H14  H  HCH2  0   0.245  24.9913  -11.0674  -6.4536
 G0F  H15  H  HCH2  0   0.267  23.7322  -12.1105  -9.0455
 G0F  H16  H  HCH2  0   0.272  23.6371  -10.4404  -8.5180
 G0F  H17  H  HCH3  0   0.270  21.1506  -10.5807  -5.5930
 G0F  H18  H  HCH3  0   0.270  22.9057  -10.4261  -5.4419
 G0F  H19  H  HCH3  0   0.256  22.0400   -9.5418  -6.7143
 G0F  H20  H  HCH2  0   0.231  25.7559  -13.9319  -4.5043
 G0F  H21  H  HNH1  0   0.354  26.9758  -14.1764  -6.5648

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    1.817  0.020  1.817
 G0F  CG   CB   single    1.522  0.020  1.522
 G0F  SD   CE   single    1.807  0.020  1.807
 G0F  CA   CB   single    1.522  0.020  1.522
 G0F  CA   N    single    1.456  0.020  1.456
 G0F  N    C4A  single    1.455  0.020  1.455
 G0F  C4A  C4   single    1.507  0.020  1.507
 G0F  OP1  P    double    1.478  0.020  1.478
 G0F  O3   C3   single    1.348  0.020  1.348
 G0F  C4   C3   aromatic  1.392  0.020  1.392
 G0F  C4   C5   aromatic  1.396  0.020  1.396
 G0F  C3   C2   aromatic  1.402  0.020  1.402
 G0F  C5A  C5   single    1.496  0.020  1.496
 G0F  C5A  OP4  single    1.439  0.020  1.439
 G0F  C5   C6   aromatic  1.386  0.020  1.386
 G0F  P    OP3  single    1.594  0.020  1.594
 G0F  P    OP4  single    1.597  0.020  1.597
 G0F  P    OP2  single    1.593  0.020  1.593
 G0F  C2   C2A  single    1.499  0.020  1.499
 G0F  C2   N1   aromatic  1.325  0.020  1.325
 G0F  C6   N1   aromatic  1.325  0.020  1.325
 G0F  C6   H1   single    0.930  0.020  1.080
 G0F  OP2  H2   single    0.850  0.020  0.980
 G0F  OP3  H3   single    0.850  0.020  0.980
 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   120.10  3.000
 G0F  C3   C4   C5   117.27  3.000
 G0F  C4A  C4   C5   122.54  3.000
 G0F  C5A  C5   C6   119.39  3.000
 G0F  C6   C5   C4   118.63  3.000
 G0F  C5A  C5   C4   121.97  3.000
 G0F  H1   C6   N1   116.50  3.000
 G0F  H1   C6   C5   119.96  3.000
 G0F  N1   C6   C5   123.55  3.000
 G0F  C2   N1   C6   119.16  3.000
 G0F  O3   C3   C2   122.14  3.000
 G0F  C2   C3   C4   120.15  3.000
 G0F  O3   C3   C4   117.70  3.000
 G0F  OP4  P    OP3  101.82  3.000
 G0F  OP4  P    OP2  101.36  3.000
 G0F  OP3  P    OP2  102.40  3.000
 G0F  OP2  P    OP1  116.58  3.000
 G0F  OP4  P    OP1  116.04  3.000
 G0F  OP3  P    OP1  116.27  3.000
 G0F  H2   OP2  P    114.46  3.000
 G0F  H3   OP3  P    114.39  3.000
 G0F  C5A  OP4  P    120.65  3.000
 G0F  H5   C5A  H4   107.93  3.000
 G0F  H5   C5A  OP4  110.74  3.000
 G0F  H4   C5A  OP4  109.06  3.000
 G0F  H5   C5A  C5   110.98  3.000
 G0F  H4   C5A  C5   110.28  3.000
 G0F  OP4  C5A  C5   107.84  3.000
 G0F  C2A  C2   C3   120.71  3.000
 G0F  C2A  C2   N1   118.06  3.000
 G0F  C3   C2   N1   121.22  3.000
 G0F  H8   C2A  H7   107.50  3.000
 G0F  H8   C2A  H6   107.52  3.000
 G0F  H7   C2A  H6   107.70  3.000
 G0F  H8   C2A  C2   111.89  3.000
 G0F  H7   C2A  C2   112.21  3.000
 G0F  H6   C2A  C2   109.82  3.000
 G0F  H9   O3   C3   111.56  3.000
 G0F  H20  C4A  H10  105.56  3.000
 G0F  H20  C4A  N    112.83  3.000
 G0F  H10  C4A  N    108.78  3.000
 G0F  H20  C4A  C4   109.95  3.000
 G0F  H10  C4A  C4   109.86  3.000
 G0F  N    C4A  C4   109.76  3.000
 G0F  H21  N    CA   108.64  3.000
 G0F  H21  N    C4A  108.34  3.000
 G0F  CA   N    C4A  113.14  3.000
 G0F  H12  CA   H11  106.41  3.000
 G0F  H12  CA   CB   108.47  3.000
 G0F  H11  CA   CB   109.76  3.000
 G0F  H12  CA   N    107.78  3.000
 G0F  H11  CA   N    112.20  3.000
 G0F  CB   CA   N    111.98  3.000
 G0F  H14  CB   H13  106.00  3.000
 G0F  H14  CB   CG   110.24  3.000
 G0F  H13  CB   CG   107.92  3.000
 G0F  H14  CB   CA   111.04  3.000
 G0F  H13  CB   CA   108.45  3.000
 G0F  CG   CB   CA   112.88  3.000
 G0F  H16  CG   H15  106.82  3.000
 G0F  H16  CG   SD   108.00  3.000
 G0F  H15  CG   SD   105.33  3.000
 G0F  H16  CG   CB   110.82  3.000
 G0F  H15  CG   CB   110.24  3.000
 G0F  SD   CG   CB   115.19  3.000
 G0F  CE   SD   CG   100.55  3.000
 G0F  H19  CE   H18  109.21  3.000
 G0F  H19  CE   H17  108.55  3.000
 G0F  H18  CE   H17  108.68  3.000
 G0F  H19  CE   SD   110.78  3.000
 G0F  H18  CE   SD   112.16  3.000
 G0F  H17  CE   SD   107.36  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     80.35  30.0  2
 G0F  Var_02    N    C4A  C4   C5     93.31  30.0  2
 G0F  Var_03    H6   C2A  C2   N1      3.80  30.0  2
 G0F  Var_04    CA   N    C4A  C4   -175.75  30.0  1
 G0F  Var_05    CB   CA   N    C4A    86.32  30.0  2
 G0F  Var_06    CG   CB   CA   N     179.23  30.0  3
 G0F  Var_07    SD   CG   CB   CA     68.20  30.0  2
 G0F  Var_08    H17  CE   SD   CG    176.08  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

