# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:29:11 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: 4-{benzyl[2-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)ethyl]amino}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2N=C3C(=O)NC(=O)N=C3N(CCN(CCCC(O)=O)Cc4ccccc4)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
 GZG  GZG  '4-{benzyl[2-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)ethyl]amino}butanoic acid'  ligand  61  34  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GZG
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
 GZG  C4   C  CH2   0  -0.301  -0.7579   0.0273  -0.7381
 GZG  C5   C  CH2   0  -0.350  -0.1716  -0.2118   0.6480
 GZG  C6   C  CR66  0   0.444   2.1438   0.6316   0.5876
 GZG  C7   C  CR66  0   0.182   3.5279   0.3634   0.5524
 GZG  C8   C  CR66  0  -0.038   3.1582  -1.8751   0.4868
 GZG  C9   C  CR6   0   0.552   3.6782  -3.2605   0.4277
 GZG  C10  C  CR6   0   0.575   1.3152  -3.9690   0.3935
 GZG  C11  C  CR66  0   0.571   1.7263  -1.7086   0.5098
 GZG  C12  C  CR16  0  -0.359   4.4432   1.4299   0.5539
 GZG  C13  C  CR6   0   0.076   4.0267   2.7358   0.5774
 GZG  C14  C  CH3   0  -0.736   5.0147   3.8610   0.5752
 GZG  C15  C  CR6   0   0.096   2.6322   3.0013   0.5969
 GZG  C16  C  CH3   0  -0.746   2.1458   4.4155   0.6040
 GZG  N1   N  NR6   0  -0.568   1.2731  -0.4329   0.6001
 GZG  C19  C  CR6   0   0.079  -2.3489   2.5446  -0.9195
 GZG  O1   O  O     0  -0.445  -6.6425  -1.9142   1.2314
 GZG  C20  C  CR16  0  -0.284  -2.3659   2.8242   0.4465
 GZG  C17  C  CR16  0  -0.373   1.7196   1.9648   0.6046
 GZG  C18  C  CH2   0  -0.333  -2.7670   1.1858  -1.4240
 GZG  O    O  OH1   0  -0.598  -6.5952  -4.0022   0.4541
 GZG  C    C  C     0   0.552  -6.0988  -2.7750   0.5850
 GZG  C1   C  CH2   0  -0.585  -4.8072  -2.6120  -0.1655
 GZG  C2   C  CH2   0  -0.432  -4.1654  -1.2463   0.0113
 GZG  C3   C  CH2   0  -0.272  -2.8628  -1.1599  -0.7715
 GZG  N    N  NT    0  -0.426  -2.1978   0.1221  -0.6234
 GZG  C24  C  CR16  0  -0.312  -1.9527   3.5447  -1.8008
 GZG  C23  C  CR16  0  -0.239  -1.5917   4.8033  -1.3337
 GZG  C22  C  CR16  0  -0.272  -1.6160   5.0739   0.0269
 GZG  C21  C  CR16  0  -0.244  -2.0019   4.0777   0.9169
 GZG  N2   N  N     0  -0.348   4.0014  -0.9012   0.5112
 GZG  N4   N  N     0  -0.543   0.8687  -2.6889   0.4578
 GZG  N3   N  NR16  0  -0.718   2.6940  -4.2009   0.3844
 GZG  O3   O  O     0  -0.425   4.8585  -3.5306   0.4174
 GZG  H1   H  HCH2  0   0.254  -0.3554   0.9552  -1.1507
 GZG  H2   H  HCH2  0   0.245  -0.4437  -0.7707  -1.4236
 GZG  H3   H  HCH2  0   0.281  -0.3777   0.6304   1.3044
 GZG  H4   H  HCH2  0   0.300  -0.6184  -1.0914   1.1033
 GZG  H5   H  HCR6  0   0.274   5.4979   1.1844   0.5318
 GZG  H6   H  HCH3  0   0.252   4.8889   4.5016  -0.2996
 GZG  H7   H  HCH3  0   0.252   4.8972   4.4979   1.4537
 GZG  H8   H  HCH3  0   0.260   6.0360   3.4855   0.5691
 GZG  H9   H  HCH3  0   0.258   2.5160   4.9615  -0.2659
 GZG  H10  H  HCH3  0   0.269   1.0585   4.4688   0.5946
 GZG  H11  H  HCH3  0   0.259   2.5043   4.9491   1.4866
 GZG  H12  H  HCR6  0   0.248  -2.6618   2.0483   1.1417
 GZG  H13  H  HCR6  0   0.274   0.6670   2.2126   0.6134
 GZG  H14  H  HCH2  0   0.256  -3.8563   1.1133  -1.3698
 GZG  H15  H  HCH2  0   0.225  -2.5114   1.0931  -2.4916
 GZG  H16  H  HOH1  0   0.478  -7.4269  -4.0744   0.9456
 GZG  H17  H  HCH2  0   0.278  -4.1230  -3.4046   0.1540
 GZG  H18  H  HCH2  0   0.280  -5.0053  -2.8102  -1.2241
 GZG  H19  H  HCH2  0   0.233  -4.8616  -0.4706  -0.3154
 GZG  H20  H  HCH2  0   0.233  -3.9548  -1.0568   1.0657
 GZG  H21  H  HCH2  0   0.237  -2.1862  -1.9339  -0.3990
 GZG  H22  H  HCH2  0   0.207  -3.0435  -1.4029  -1.8315
 GZG  H24  H  HCR6  0   0.248  -1.9210   3.3384  -2.8646
 GZG  H25  H  HCR6  0   0.253  -1.2860   5.5699  -2.0344
 GZG  H26  H  HCR6  0   0.257  -1.3290   6.0513   0.3931
 GZG  H27  H  HCR6  0   0.254  -2.0205   4.2786   1.9807
 GZG  H28  H  HNR6  0   0.422   2.9843  -5.1706   0.3404
 GZG  O2   O  O     0  -0.468   0.5643  -4.9234   0.3441

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
 GZG  C14  C13  single    1.497  0.020  1.497
 GZG  C13  C12  aromatic  1.371  0.020  1.371
 GZG  C13  C15  aromatic  1.420  0.020  1.420
 GZG  C16  C15  single    1.495  0.020  1.495
 GZG  C12  C7   aromatic  1.405  0.020  1.405
 GZG  C15  C17  aromatic  1.381  0.020  1.381
 GZG  C7   N2   single    1.351  0.020  1.351
 GZG  C7   C6   aromatic  1.410  0.020  1.410
 GZG  C17  C6   aromatic  1.399  0.020  1.399
 GZG  N2   C8   double    1.288  0.020  1.288
 GZG  C6   N1   single    1.375  0.020  1.375
 GZG  O3   C9   double    1.211  0.020  1.211
 GZG  C8   C9   single    1.481  0.020  1.481
 GZG  C8   C11  single    1.442  0.020  1.442
 GZG  C9   N3   single    1.362  0.020  1.362
 GZG  N1   C11  single    1.357  0.020  1.357
 GZG  N1   C5   single    1.462  0.020  1.462
 GZG  C11  N4   double    1.303  0.020  1.303
 GZG  C5   C4   single    1.524  0.020  1.524
 GZG  N3   C10  single    1.398  0.020  1.398
 GZG  C4   N    single    1.448  0.020  1.448
 GZG  N4   C10  single    1.357  0.020  1.357
 GZG  C20  C21  aromatic  1.387  0.020  1.387
 GZG  C20  C19  aromatic  1.394  0.020  1.394
 GZG  C21  C22  aromatic  1.391  0.020  1.391
 GZG  C10  O2   double    1.215  0.020  1.215
 GZG  C18  N    single    1.448  0.020  1.448
 GZG  C18  C19  single    1.508  0.020  1.508
 GZG  C2   C1   single    1.519  0.020  1.519
 GZG  C2   C3   single    1.522  0.020  1.522
 GZG  C1   C    single    1.503  0.020  1.503
 GZG  N    C3   single    1.452  0.020  1.452
 GZG  C19  C24  aromatic  1.391  0.020  1.391
 GZG  C22  C23  aromatic  1.387  0.020  1.387
 GZG  O1   C    double    1.206  0.020  1.206
 GZG  C    O    single    1.330  0.020  1.330
 GZG  C24  C23  aromatic  1.390  0.020  1.390
 GZG  C4   H1   single    0.970  0.020  1.090
 GZG  C4   H2   single    0.970  0.020  1.090
 GZG  C5   H3   single    0.970  0.020  1.090
 GZG  C5   H4   single    0.970  0.020  1.090
 GZG  C12  H5   single    0.930  0.020  1.080
 GZG  C14  H6   single    0.970  0.020  1.090
 GZG  C14  H7   single    0.970  0.020  1.090
 GZG  C14  H8   single    0.970  0.020  1.090
 GZG  C16  H9   single    0.970  0.020  1.090
 GZG  C16  H10  single    0.970  0.020  1.090
 GZG  C16  H11  single    0.970  0.020  1.090
 GZG  C20  H12  single    0.930  0.020  1.080
 GZG  C17  H13  single    0.930  0.020  1.080
 GZG  C18  H14  single    0.970  0.020  1.090
 GZG  C18  H15  single    0.970  0.020  1.090
 GZG  O    H16  single    0.850  0.020  0.980
 GZG  C1   H17  single    0.970  0.020  1.090
 GZG  C1   H18  single    0.970  0.020  1.090
 GZG  C2   H19  single    0.970  0.020  1.090
 GZG  C2   H20  single    0.970  0.020  1.090
 GZG  C3   H21  single    0.970  0.020  1.090
 GZG  C3   H22  single    0.970  0.020  1.090
 GZG  C24  H24  single    0.930  0.020  1.080
 GZG  C23  H25  single    0.930  0.020  1.080
 GZG  C22  H26  single    0.930  0.020  1.080
 GZG  C21  H27  single    0.930  0.020  1.080
 GZG  N3   H28  single    0.860  0.020  1.020

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
 GZG  H2   C4   H1   106.03  3.000
 GZG  H2   C4   N    112.44  3.000
 GZG  H1   C4   N    109.93  3.000
 GZG  H2   C4   C5   110.11  3.000
 GZG  H1   C4   C5   109.58  3.000
 GZG  N    C4   C5   108.72  3.000
 GZG  H4   C5   H3   107.23  3.000
 GZG  H4   C5   N1   107.31  3.000
 GZG  H3   C5   N1   108.91  3.000
 GZG  H4   C5   C4   110.48  3.000
 GZG  H3   C5   C4   110.77  3.000
 GZG  N1   C5   C4   111.96  3.000
 GZG  C17  C6   N1   123.06  3.000
 GZG  N1   C6   C7   118.32  3.000
 GZG  C17  C6   C7   118.62  3.000
 GZG  N2   C7   C12  118.82  3.000
 GZG  N2   C7   C6   121.52  3.000
 GZG  C12  C7   C6   119.66  3.000
 GZG  N2   C8   C11  124.22  3.000
 GZG  C11  C8   C9   117.22  3.000
 GZG  N2   C8   C9   118.56  3.000
 GZG  O3   C9   N3   123.37  3.000
 GZG  N3   C9   C8   113.17  3.000
 GZG  O3   C9   C8   123.45  3.000
 GZG  N3   C10  N4   118.76  3.000
 GZG  N4   C10  O2   122.64  3.000
 GZG  N3   C10  O2   118.60  3.000
 GZG  N4   C11  N1   119.34  3.000
 GZG  N4   C11  C8   124.46  3.000
 GZG  N1   C11  C8   116.19  3.000
 GZG  H5   C12  C13  120.80  3.000
 GZG  H5   C12  C7   117.53  3.000
 GZG  C13  C12  C7   121.67  3.000
 GZG  C15  C13  C14  120.50  3.000
 GZG  C15  C13  C12  118.48  3.000
 GZG  C14  C13  C12  121.02  3.000
 GZG  H8   C14  H7   107.87  3.000
 GZG  H8   C14  H6   107.83  3.000
 GZG  H7   C14  H6   106.87  3.000
 GZG  H8   C14  C13  111.10  3.000
 GZG  H7   C14  C13  111.49  3.000
 GZG  H6   C14  C13  111.48  3.000
 GZG  C17  C15  C16  119.66  3.000
 GZG  C17  C15  C13  120.58  3.000
 GZG  C16  C15  C13  119.76  3.000
 GZG  H11  C16  H10  108.11  3.000
 GZG  H11  C16  H9   106.76  3.000
 GZG  H10  C16  H9   107.90  3.000
 GZG  H11  C16  C15  111.05  3.000
 GZG  H10  C16  C15  111.79  3.000
 GZG  H9   C16  C15  111.03  3.000
 GZG  C11  N1   C6   121.05  3.000
 GZG  C11  N1   C5   118.31  3.000
 GZG  C6   N1   C5   120.58  3.000
 GZG  C24  C19  C18  120.98  3.000
 GZG  C24  C19  C20  118.69  3.000
 GZG  C18  C19  C20  120.32  3.000
 GZG  H12  C20  C21  120.08  3.000
 GZG  H12  C20  C19  119.24  3.000
 GZG  C21  C20  C19  120.68  3.000
 GZG  H13  C17  C15  118.11  3.000
 GZG  H13  C17  C6   120.90  3.000
 GZG  C15  C17  C6   120.98  3.000
 GZG  H15  C18  H14  105.88  3.000
 GZG  H15  C18  N    112.51  3.000
 GZG  H14  C18  N    108.39  3.000
 GZG  H15  C18  C19  109.61  3.000
 GZG  H14  C18  C19  108.63  3.000
 GZG  N    C18  C19  111.59  3.000
 GZG  H16  O    C    109.83  3.000
 GZG  C1   C    O    111.82  3.000
 GZG  O    C    O1   122.89  3.000
 GZG  C1   C    O1   125.30  3.000
 GZG  H18  C1   H17  105.32  3.000
 GZG  H18  C1   C2   110.58  3.000
 GZG  H17  C1   C2   110.66  3.000
 GZG  H18  C1   C    107.92  3.000
 GZG  H17  C1   C    108.24  3.000
 GZG  C2   C1   C    113.73  3.000
 GZG  H20  C2   H19  106.77  3.000
 GZG  H20  C2   C3   108.77  3.000
 GZG  H19  C2   C3   110.57  3.000
 GZG  H20  C2   C1   110.48  3.000
 GZG  H19  C2   C1   109.53  3.000
 GZG  C3   C2   C1   110.65  3.000
 GZG  H22  C3   H21  105.84  3.000
 GZG  H22  C3   N    111.58  3.000
 GZG  H21  C3   N    107.87  3.000
 GZG  H22  C3   C2   109.98  3.000
 GZG  H21  C3   C2   108.31  3.000
 GZG  N    C3   C2   112.93  3.000
 GZG  C3   N    C18  114.35  3.000
 GZG  C3   N    C4   112.94  3.000
 GZG  C18  N    C4   113.28  3.000
 GZG  H24  C24  C23  119.63  3.000
 GZG  H24  C24  C19  119.56  3.000
 GZG  C23  C24  C19  120.81  3.000
 GZG  H25  C23  C22  120.10  3.000
 GZG  H25  C23  C24  119.79  3.000
 GZG  C22  C23  C24  120.10  3.000
 GZG  H26  C22  C21  120.26  3.000
 GZG  H26  C22  C23  120.21  3.000
 GZG  C21  C22  C23  119.52  3.000
 GZG  H27  C21  C22  120.04  3.000
 GZG  H27  C21  C20  119.76  3.000
 GZG  C22  C21  C20  120.20  3.000
 GZG  C8   N2   C7   118.60  3.000
 GZG  C11  N4   C10  119.66  3.000
 GZG  H28  N3   C10  116.21  3.000
 GZG  H28  N3   C9   117.08  3.000
 GZG  C10  N3   C9   126.72  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
 GZG  CONST_01  C13  C12  C7   C6      0.00   0.0  0
 GZG  CONST_02  C13  C15  C17  C6      0.00   0.0  0
 GZG  CONST_03  C15  C13  C12  C7      0.00   0.0  0
 GZG  CONST_04  C15  C17  C6   C7      0.00   0.0  0
 GZG  CONST_05  C17  C15  C13  C12     0.00   0.0  0
 GZG  CONST_06  C17  C6   C7   C12     0.00   0.0  0
 GZG  CONST_07  C22  C21  C20  C19     0.00   0.0  0
 GZG  CONST_08  C22  C23  C24  C19     0.00   0.0  0
 GZG  CONST_09  C23  C22  C21  C20     0.00   0.0  0
 GZG  CONST_10  C23  C24  C19  C20     0.00   0.0  0
 GZG  CONST_11  C21  C20  C19  C24     0.00   0.0  0
 GZG  CONST_12  C21  C22  C23  C24     0.00   0.0  0
 GZG  CONST_13  C8   C11  N1   C6      0.00   0.0  0
 GZG  CONST_14  N4   C11  N1   C6    180.00   0.0  0
 GZG  CONST_15  C10  N3   C9   C8      0.00   0.0  0
 GZG  CONST_16  C10  N4   C11  C8      0.00   0.0  0
 GZG  CONST_17  N4   C10  N3   C9      0.00   0.0  0
 GZG  CONST_18  N1   C11  N4   C10   180.00   0.0  0
 GZG  CONST_19  N3   C10  N4   C11     0.00   0.0  0
 GZG  CONST_20  C16  C15  C17  C6    180.00   0.0  0
 GZG  CONST_21  C14  C13  C12  C7    180.00   0.0  0
 GZG  CONST_22  C16  C15  C13  C12   180.00   0.0  0
 GZG  CONST_23  C17  C15  C13  C14   180.00   0.0  0
 GZG  CONST_24  C21  C20  C19  C18   180.00   0.0  0
 GZG  CONST_25  C23  C24  C19  C18   180.00   0.0  0
 GZG  CONST_26  C8   C11  N1   C5    180.00   0.0  0
 GZG  CONST_27  N4   C11  N1   C5      0.00   0.0  0
 GZG  CONST_28  O2   C10  N3   C9    180.00   0.0  0
 GZG  CONST_29  O3   C9   N3   C10   180.00   0.0  0
 GZG  CONST_30  O2   C10  N4   C11   180.00   0.0  0
 GZG  CONST_31  H5   C12  C7   C6    180.00   0.0  0
 GZG  CONST_32  H13  C17  C6   C7    180.00   0.0  0
 GZG  CONST_33  H27  C21  C20  C19   180.00   0.0  0
 GZG  CONST_34  H25  C23  C24  C19   180.00   0.0  0
 GZG  CONST_35  H26  C22  C21  C20   180.00   0.0  0
 GZG  CONST_36  H24  C24  C19  C20   180.00   0.0  0
 GZG  CONST_37  H12  C20  C19  C24   180.00   0.0  0
 GZG  CONST_38  H28  N3   C9   C8    180.00   0.0  0
 GZG  CONST_39  H16  O    C    O1      0.00   0.0  0
 GZG  Var_01    C6   N1   C5   C4     84.51  30.0  2
 GZG  Var_02    N    C18  C19  C20   -44.21  30.0  2
 GZG  Var_03    H6   C14  C13  C12   119.41  30.0  2
 GZG  Var_04    H9   C16  C15  C13    58.07  30.0  2
 GZG  Var_05    C19  C18  N    C4    -66.86  30.0  2
 GZG  Var_06    N    C4   C5   N1    175.13  30.0  3
 GZG  Var_07    C2   C3   N    C4    150.26  30.0  3
 GZG  Var_08    C18  N    C4   C5    137.61  30.0  3
 GZG  Var_09    C2   C1   C    O1      3.11  30.0  2
 GZG  Var_10    C3   C2   C1   C     179.76  30.0  1
 GZG  Var_11    N    C3   C2   C1   -179.27  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
 GZG  plan-1  C19  0.020
 GZG  plan-1  C20  0.020
 GZG  plan-1  C18  0.020
 GZG  plan-1  C24  0.020
 GZG  plan-1  C23  0.020
 GZG  plan-1  C22  0.020
 GZG  plan-1  C21  0.020
 GZG  plan-1  H12  0.020
 GZG  plan-1  H24  0.020
 GZG  plan-1  H25  0.020
 GZG  plan-1  H26  0.020
 GZG  plan-1  H27  0.020
 GZG  plan-2  C5   0.020
 GZG  plan-2  C6   0.020
 GZG  plan-2  C7   0.020
 GZG  plan-2  C8   0.020
 GZG  plan-2  C9   0.020
 GZG  plan-2  C10  0.020
 GZG  plan-2  C11  0.020
 GZG  plan-2  C12  0.020
 GZG  plan-2  C13  0.020
 GZG  plan-2  C14  0.020
 GZG  plan-2  C15  0.020
 GZG  plan-2  C16  0.020
 GZG  plan-2  N1   0.020
 GZG  plan-2  C17  0.020
 GZG  plan-2  N2   0.020
 GZG  plan-2  N4   0.020
 GZG  plan-2  N3   0.020
 GZG  plan-2  O3   0.020
 GZG  plan-2  H5   0.020
 GZG  plan-2  H13  0.020
 GZG  plan-2  H28  0.020
 GZG  plan-2  O2   0.020
 GZG  plan-3  O1   0.020
 GZG  plan-3  O    0.020
 GZG  plan-3  C    0.020
 GZG  plan-3  C1   0.020
 GZG  plan-3  H16  0.020

