# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 02:40:44 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 7,8-dimethyl-2,4-dioxo-10-(3-phenylpropyl)-1,2,3,4-tetrahydrobenzo[g]pteridin-10-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2nc3C(=O)NC(=O)Nc3[n+](CCCc4ccccc4)c2cc1C
#
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
 GZ4  GZ4  7,8-dimethyl-2,4-dioxo-10-(3-phenylpropyl)-1,2,3,4-tetrahydrobenzo[g]pteridin-10-ium  ligand  48  27  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GZ4
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
 GZ4  C4   C  CR66  0  -0.034  -2.5291  -1.2633   0.2710
 GZ4  C5   C  CR66  0   0.794  -1.2709  -1.2655  -0.3852
 GZ4  C6   C  CR6   0   0.714  -1.1744  -3.6817  -0.2745
 GZ4  N1   N  NR16  0  -0.776  -0.6560  -2.4368  -0.6183
 GZ4  C7   C  CR6   0   0.589  -3.1553  -2.5535   0.6471
 GZ4  C8   C  CR66  0   0.467  -1.3584   1.0789  -0.4209
 GZ4  N2   N  NR16  0  -0.724  -2.4012  -3.6573   0.3330
 GZ4  C9   C  CR16  0  -0.366  -0.8125   2.3319  -0.6966
 GZ4  C10  C  CR6   0   0.103  -1.4894   3.4848  -0.3514
 GZ4  C11  C  CH3   0  -0.736  -0.8781   4.8136  -0.6512
 GZ4  N3   N  NR6   1  -0.551  -0.7330  -0.1057  -0.7567
 GZ4  C13  C  CH2   0  -0.445   1.7346  -0.0394  -0.5273
 GZ4  C14  C  CH2   0  -0.522   3.0479   0.0608  -1.3025
 GZ4  C15  C  CR6   0   0.133   4.2251   0.1060  -0.3682
 GZ4  O1   O  O     0  -0.384  -4.2295  -2.6304   1.1825
 GZ4  N    N  N     0  -0.336  -3.1636  -0.1712   0.5541
 GZ4  O    O  O     0  -0.412  -0.5661  -4.6909  -0.5072
 GZ4  C3   C  CR66  0   0.206  -2.6079   1.0045   0.2377
 GZ4  C2   C  CR16  0  -0.346  -3.2858   2.1908   0.5781
 GZ4  C1   C  CR6   0   0.089  -2.7569   3.4201   0.2942
 GZ4  C    C  CH3   0  -0.736  -3.4889   4.6746   0.6511
 GZ4  C20  C  CR16  0  -0.310   4.9210  -1.0543  -0.0392
 GZ4  C19  C  CR16  0  -0.239   5.9847  -1.0162   0.8533
 GZ4  C18  C  CR16  0  -0.271   6.3654   0.1868   1.4328
 GZ4  C17  C  CR16  0  -0.239   5.6767   1.3503   1.1129
 GZ4  C16  C  CR16  0  -0.304   4.6153   1.3077   0.2193
 GZ4  H4   H  HNR6  0   0.468   0.2535  -2.4794  -1.0605
 GZ4  H5   H  HNR6  0   0.453  -2.7894  -4.5637   0.5702
 GZ4  H6   H  HCR6  0   0.293   0.1533   2.4346  -1.1681
 GZ4  H8   H  HCH3  0   0.266  -1.5582   5.4321  -1.2391
 GZ4  H7   H  HCH3  0   0.269  -0.6712   5.3605   0.2711
 GZ4  H9   H  HCH3  0   0.269   0.0552   4.7129  -1.2004
 GZ4  H10  H  HCH2  0   0.320   0.5878  -0.9307  -2.1568
 GZ4  H11  H  HCH2  0   0.329   0.5323   0.7885  -2.1407
 GZ4  H12  H  HCH2  0   0.271   1.6369   0.8120   0.1507
 GZ4  H13  H  HCH2  0   0.267   1.7452  -0.9345   0.1003
 GZ4  H15  H  HCH2  0   0.262   3.1392  -0.7930  -1.9783
 GZ4  H14  H  HCH2  0   0.261   3.0332   0.9577  -1.9275
 GZ4  H3   H  HCR6  0   0.290  -4.2409   2.0938   1.0781
 GZ4  H2   H  HCH3  0   0.258  -2.8713   5.3385   1.2571
 GZ4  H1   H  HCH3  0   0.262  -3.7720   5.2312  -0.2448
 GZ4  H    H  HCH3  0   0.267  -4.3963   4.4532   1.2090
 GZ4  H20  H  HCR6  0   0.248   4.6312  -1.9972  -0.4888
 GZ4  H19  H  HCR6  0   0.255   6.5181  -1.9273   1.0929
 GZ4  H18  H  HCR6  0   0.255   7.1953   0.2185   2.1266
 GZ4  H17  H  HCR6  0   0.255   5.9676   2.2932   1.5579
 GZ4  H16  H  HCR6  0   0.247   4.0860   2.2211  -0.0279
 GZ4  C12  C  CH2   0  -0.429   0.5497  -0.0757  -1.4829

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
 GZ4  C    C1   single    1.496  0.020  1.496
 GZ4  C1   C2   aromatic  1.368  0.020  1.368
 GZ4  C1   C10  aromatic  1.424  0.020  1.424
 GZ4  C11  C10  single    1.493  0.020  1.493
 GZ4  C2   C3   aromatic  1.408  0.020  1.408
 GZ4  C10  C9   aromatic  1.381  0.020  1.381
 GZ4  C3   N    aromatic  1.338  0.020  1.338
 GZ4  C3   C8   aromatic  1.414  0.020  1.414
 GZ4  C9   C8   aromatic  1.394  0.020  1.394
 GZ4  N    C4   aromatic  1.294  0.020  1.294
 GZ4  C8   N3   aromatic  1.381  0.020  1.381
 GZ4  C18  C17  aromatic  1.389  0.020  1.389
 GZ4  C18  C19  aromatic  1.388  0.020  1.388
 GZ4  C17  C16  aromatic  1.388  0.020  1.388
 GZ4  O1   C7   double    1.203  0.020  1.203
 GZ4  C4   C7   single    1.483  0.020  1.483
 GZ4  C4   C5   aromatic  1.419  0.020  1.419
 GZ4  C19  C20  aromatic  1.389  0.020  1.389
 GZ4  C7   N2   single    1.373  0.020  1.373
 GZ4  N3   C5   aromatic  1.331  0.020  1.331
 GZ4  N3   C12  single    1.474  0.020  1.474
 GZ4  C16  C15  aromatic  1.393  0.020  1.393
 GZ4  C5   N1   single    1.343  0.020  1.343
 GZ4  C20  C15  aromatic  1.392  0.020  1.392
 GZ4  C12  C13  single    1.523  0.020  1.523
 GZ4  C15  C14  single    1.504  0.020  1.504
 GZ4  N2   C6   single    1.369  0.020  1.369
 GZ4  C13  C14  single    1.528  0.020  1.528
 GZ4  N1   C6   single    1.392  0.020  1.392
 GZ4  C6   O    double    1.201  0.020  1.201
 GZ4  N1   H4   single    0.860  0.020  1.020
 GZ4  N2   H5   single    0.860  0.020  1.020
 GZ4  C9   H6   single    0.930  0.020  1.080
 GZ4  C11  H8   single    0.970  0.020  1.090
 GZ4  C11  H7   single    0.970  0.020  1.090
 GZ4  C11  H9   single    0.970  0.020  1.090
 GZ4  C12  H10  single    0.970  0.020  1.090
 GZ4  C12  H11  single    0.970  0.020  1.090
 GZ4  C13  H12  single    0.970  0.020  1.090
 GZ4  C13  H13  single    0.970  0.020  1.090
 GZ4  C14  H15  single    0.970  0.020  1.090
 GZ4  C14  H14  single    0.970  0.020  1.090
 GZ4  C2   H3   single    0.930  0.020  1.080
 GZ4  C    H2   single    0.970  0.020  1.090
 GZ4  C    H1   single    0.970  0.020  1.090
 GZ4  C    H    single    0.970  0.020  1.090
 GZ4  C20  H20  single    0.930  0.020  1.080
 GZ4  C19  H19  single    0.930  0.020  1.080
 GZ4  C18  H18  single    0.930  0.020  1.080
 GZ4  C17  H17  single    0.930  0.020  1.080
 GZ4  C16  H16  single    0.930  0.020  1.080

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
 GZ4  N    C4   C7   118.15  3.000
 GZ4  C7   C4   C5   119.37  3.000
 GZ4  N    C4   C5   122.48  3.000
 GZ4  N3   C5   N1   121.75  3.000
 GZ4  N1   C5   C4   119.18  3.000
 GZ4  N3   C5   C4   119.07  3.000
 GZ4  O    C6   N2   123.69  3.000
 GZ4  O    C6   N1   121.01  3.000
 GZ4  N2   C6   N1   115.30  3.000
 GZ4  H4   N1   C6   113.89  3.000
 GZ4  H4   N1   C5   121.59  3.000
 GZ4  C6   N1   C5   124.51  3.000
 GZ4  O1   C7   N2   122.75  3.000
 GZ4  N2   C7   C4   114.18  3.000
 GZ4  O1   C7   C4   123.08  3.000
 GZ4  C3   C8   N3   117.92  3.000
 GZ4  N3   C8   C9   123.05  3.000
 GZ4  C3   C8   C9   119.03  3.000
 GZ4  H5   N2   C7   117.04  3.000
 GZ4  H5   N2   C6   115.52  3.000
 GZ4  C7   N2   C6   127.44  3.000
 GZ4  H6   C9   C10  117.92  3.000
 GZ4  H6   C9   C8   121.47  3.000
 GZ4  C10  C9   C8   120.60  3.000
 GZ4  C1   C10  C11  119.73  3.000
 GZ4  C11  C10  C9   119.49  3.000
 GZ4  C1   C10  C9   120.78  3.000
 GZ4  H9   C11  H7   108.07  3.000
 GZ4  H9   C11  H8   108.38  3.000
 GZ4  H7   C11  H8   106.81  3.000
 GZ4  H9   C11  C10  111.74  3.000
 GZ4  H7   C11  C10  110.71  3.000
 GZ4  H8   C11  C10  110.95  3.000
 GZ4  C12  N3   C8   119.76  3.000
 GZ4  C12  N3   C5   120.44  3.000
 GZ4  C8   N3   C5   119.76  3.000
 GZ4  H13  C13  H12  106.42  3.000
 GZ4  H13  C13  C14  109.67  3.000
 GZ4  H12  C13  C14  109.90  3.000
 GZ4  H13  C13  C12  110.38  3.000
 GZ4  H12  C13  C12  109.78  3.000
 GZ4  C14  C13  C12  110.60  3.000
 GZ4  H14  C14  H15  106.77  3.000
 GZ4  H14  C14  C15  109.95  3.000
 GZ4  H15  C14  C15  110.03  3.000
 GZ4  H14  C14  C13  109.40  3.000
 GZ4  H15  C14  C13  109.53  3.000
 GZ4  C15  C14  C13  111.07  3.000
 GZ4  C16  C15  C20  118.63  3.000
 GZ4  C20  C15  C14  120.87  3.000
 GZ4  C16  C15  C14  120.48  3.000
 GZ4  C3   N    C4   119.08  3.000
 GZ4  C2   C3   N    118.88  3.000
 GZ4  N    C3   C8   121.54  3.000
 GZ4  C2   C3   C8   119.57  3.000
 GZ4  H3   C2   C1   121.17  3.000
 GZ4  H3   C2   C3   117.45  3.000
 GZ4  C1   C2   C3   121.38  3.000
 GZ4  C    C1   C2   120.99  3.000
 GZ4  C2   C1   C10  118.63  3.000
 GZ4  C    C1   C10  120.38  3.000
 GZ4  H    C    H1   107.96  3.000
 GZ4  H    C    H2   108.14  3.000
 GZ4  H1   C    H2   107.00  3.000
 GZ4  H    C    C1   111.09  3.000
 GZ4  H1   C    C1   111.01  3.000
 GZ4  H2   C    C1   111.47  3.000
 GZ4  H20  C20  C19  119.67  3.000
 GZ4  H20  C20  C15  119.56  3.000
 GZ4  C19  C20  C15  120.78  3.000
 GZ4  H19  C19  C18  120.11  3.000
 GZ4  H19  C19  C20  119.76  3.000
 GZ4  C18  C19  C20  120.12  3.000
 GZ4  H18  C18  C17  120.21  3.000
 GZ4  H18  C18  C19  120.21  3.000
 GZ4  C17  C18  C19  119.57  3.000
 GZ4  H17  C17  C16  119.79  3.000
 GZ4  H17  C17  C18  120.11  3.000
 GZ4  C16  C17  C18  120.10  3.000
 GZ4  H16  C16  C17  119.61  3.000
 GZ4  H16  C16  C15  119.58  3.000
 GZ4  C17  C16  C15  120.80  3.000
 GZ4  H11  C12  H10  104.50  3.000
 GZ4  H11  C12  C13  111.93  3.000
 GZ4  H10  C12  C13  112.31  3.000
 GZ4  H11  C12  N3   107.49  3.000
 GZ4  H10  C12  N3   108.62  3.000
 GZ4  C13  C12  N3   111.61  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
 GZ4  CONST_01  C2   C3   N    C4    180.00   0.0  0
 GZ4  CONST_02  C8   C3   N    C4      0.00   0.0  0
 GZ4  CONST_03  C8   N3   C5   C4      0.00   0.0  0
 GZ4  CONST_04  C3   N    C4   C5      0.00   0.0  0
 GZ4  CONST_05  C3   C8   N3   C5      0.00   0.0  0
 GZ4  CONST_06  C9   C8   N3   C5    180.00   0.0  0
 GZ4  CONST_07  C1   C2   C3   C8      0.00   0.0  0
 GZ4  CONST_08  C1   C10  C9   C8      0.00   0.0  0
 GZ4  CONST_09  C2   C1   C10  C9      0.00   0.0  0
 GZ4  CONST_10  C2   C3   C8   C9      0.00   0.0  0
 GZ4  CONST_11  N    C3   C8   C9    180.00   0.0  0
 GZ4  CONST_12  C3   C2   C1   C10     0.00   0.0  0
 GZ4  CONST_13  C3   C8   C9   C10     0.00   0.0  0
 GZ4  CONST_14  N3   C8   C9   C10   180.00   0.0  0
 GZ4  CONST_15  C2   C3   C8   N3    180.00   0.0  0
 GZ4  CONST_16  N    C3   C8   N3      0.00   0.0  0
 GZ4  CONST_17  N    C4   C5   N3      0.00   0.0  0
 GZ4  CONST_18  C18  C17  C16  C15     0.00   0.0  0
 GZ4  CONST_19  C18  C19  C20  C15     0.00   0.0  0
 GZ4  CONST_20  C1   C2   C3   N     180.00   0.0  0
 GZ4  CONST_21  C17  C18  C19  C20     0.00   0.0  0
 GZ4  CONST_22  C17  C16  C15  C20     0.00   0.0  0
 GZ4  CONST_23  C16  C17  C18  C19     0.00   0.0  0
 GZ4  CONST_24  C16  C15  C20  C19     0.00   0.0  0
 GZ4  CONST_25  C6   N2   C7   C4      0.00   0.0  0
 GZ4  CONST_26  N2   C6   N1   C5      0.00   0.0  0
 GZ4  CONST_27  C7   N2   C6   N1      0.00   0.0  0
 GZ4  CONST_28  C12  N3   C5   C4    180.00   0.0  0
 GZ4  CONST_29  C12  N3   C5   N1      0.00   0.0  0
 GZ4  CONST_30  C11  C10  C9   C8    180.00   0.0  0
 GZ4  CONST_31  C    C1   C10  C9    180.00   0.0  0
 GZ4  CONST_32  C12  N3   C8   C9      0.00   0.0  0
 GZ4  CONST_33  C2   C1   C10  C11   180.00   0.0  0
 GZ4  CONST_34  C3   C8   N3   C12   180.00   0.0  0
 GZ4  CONST_35  C17  C16  C15  C14   180.00   0.0  0
 GZ4  CONST_36  C19  C20  C15  C14   180.00   0.0  0
 GZ4  CONST_37  C    C1   C2   C3    180.00   0.0  0
 GZ4  CONST_38  O    C6   N1   C5    180.00   0.0  0
 GZ4  CONST_39  O1   C7   N2   C6    180.00   0.0  0
 GZ4  CONST_40  O    C6   N2   C7    180.00   0.0  0
 GZ4  CONST_41  H3   C2   C3   C8    180.00   0.0  0
 GZ4  CONST_42  H6   C9   C8   N3      0.00   0.0  0
 GZ4  CONST_43  H17  C17  C16  C15   180.00   0.0  0
 GZ4  CONST_44  H19  C19  C20  C15   180.00   0.0  0
 GZ4  CONST_45  H18  C18  C19  C20   180.00   0.0  0
 GZ4  CONST_46  H16  C16  C15  C20   180.00   0.0  0
 GZ4  CONST_47  H20  C20  C19  C18   180.00   0.0  0
 GZ4  CONST_48  H5   N2   C7   C4    180.00   0.0  0
 GZ4  CONST_49  H4   N1   C6   N2    180.00   0.0  0
 GZ4  Var_01    C13  C12  N3   C5    -88.10  30.0  2
 GZ4  Var_02    C16  C15  C14  C13   -82.92  30.0  2
 GZ4  Var_03    H8   C11  C10  C9    125.16  30.0  2
 GZ4  Var_04    H2   C    C1   C10   -54.61  30.0  2
 GZ4  Var_05    C15  C14  C13  C12   179.65  30.0  3
 GZ4  Var_06    C14  C13  C12  N3   -177.21  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
 GZ4  plan-1  C14  0.020
 GZ4  plan-1  C15  0.020
 GZ4  plan-1  C20  0.020
 GZ4  plan-1  C19  0.020
 GZ4  plan-1  C18  0.020
 GZ4  plan-1  C17  0.020
 GZ4  plan-1  C16  0.020
 GZ4  plan-1  H20  0.020
 GZ4  plan-1  H19  0.020
 GZ4  plan-1  H18  0.020
 GZ4  plan-1  H17  0.020
 GZ4  plan-1  H16  0.020
 GZ4  plan-2  C4   0.020
 GZ4  plan-2  C5   0.020
 GZ4  plan-2  C6   0.020
 GZ4  plan-2  N1   0.020
 GZ4  plan-2  C7   0.020
 GZ4  plan-2  C8   0.020
 GZ4  plan-2  N2   0.020
 GZ4  plan-2  C9   0.020
 GZ4  plan-2  C10  0.020
 GZ4  plan-2  C11  0.020
 GZ4  plan-2  N3   0.020
 GZ4  plan-2  O1   0.020
 GZ4  plan-2  N    0.020
 GZ4  plan-2  O    0.020
 GZ4  plan-2  C3   0.020
 GZ4  plan-2  C2   0.020
 GZ4  plan-2  C1   0.020
 GZ4  plan-2  C    0.020
 GZ4  plan-2  H4   0.020
 GZ4  plan-2  H5   0.020
 GZ4  plan-2  H6   0.020
 GZ4  plan-2  H3   0.020
 GZ4  plan-2  C12  0.020

