# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 02:28:39 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 7,8-dimethylbenzo[g]pteridine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2nc3NC(=O)NC(=O)c3nc2cc1C
#
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
 LUM  LUM  7,8-dimethylbenzo[g]pteridine-2,4(1H,3H)-dione  ligand  28  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LUM
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
 LUM  N1    N  NR16  0  -0.740   1.4273  -0.0576  -2.3982
 LUM  C2    C  CR6   0   0.681   0.8258  -0.0317  -3.6230
 LUM  C10   C  CR66  0   0.530   0.7609  -0.0352  -1.2019
 LUM  O2    O  OC    0  -0.457   1.4440  -0.0514  -4.6628
 LUM  N3    N  NR16  0  -0.722  -0.5544   0.0185  -3.5947
 LUM  C4    C  CR6   0   0.561  -1.3786   0.0494  -2.4958
 LUM  O4    O  OC    0  -0.412  -2.5819   0.0957  -2.5947
 LUM  C4A   C  CR66  0  -0.028  -0.6557   0.0201  -1.2080
 LUM  N5    N  N     0  -0.377  -1.3422   0.0465  -0.1001
 LUM  C5A   C  CR66  0   0.226  -0.6614   0.0190   1.0550
 LUM  C6    C  CR16  0  -0.361  -1.3559   0.0491   2.2847
 LUM  C9A   C  CR66  0   0.267   0.7575  -0.0398   1.0552
 LUM  C7    C  CR6   0   0.084  -0.6857   0.0207   3.4762
 LUM  C7M   C  CH3   0  -0.736  -1.4328   0.0662   4.7732
 LUM  C8    C  CR6   0   0.090   0.7452  -0.0474   3.4764
 LUM  C8M   C  CH3   0  -0.737   1.4832  -0.0961   4.7771
 LUM  C9    C  CR16  0  -0.370   1.4332  -0.0733   2.2907
 LUM  N10   N  N     0  -0.430   1.4524  -0.0651  -0.0974
 LUM  HN1   H  HNR6  0   0.433   2.4381  -0.0927  -2.3786
 LUM  HN3   H  HNR6  0   0.436  -1.0039   0.0389  -4.5024
 LUM  HC6   H  HCR6  0   0.267  -2.4378   0.0958   2.2588
 LUM  H7M1  H  HCH3  0   0.251  -1.2148  -0.8029   5.3963
 LUM  H7M2  H  HCH3  0   0.252  -1.1635   0.9496   5.3554
 LUM  H7M3  H  HCH3  0   0.259  -2.5078   0.0940   4.6045
 LUM  H8M1  H  HCH3  0   0.254   1.2592   0.7736   5.3975
 LUM  H8M2  H  HCH3  0   0.255   1.2012  -0.9777   5.3560
 LUM  H8M3  H  HCH3  0   0.261   2.5595  -0.1284   4.6197
 LUM  HC9   H  HCR6  0   0.265   2.5152  -0.1204   2.2838

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
 LUM  N1   C2    aromatic  1.365  0.020  1.365
 LUM  N1   C10   aromatic  1.370  0.020  1.370
 LUM  N1   HN1   single    0.860  0.020  1.020
 LUM  C2   O2    double    1.210  0.020  1.210
 LUM  C2   N3    aromatic  1.381  0.020  1.381
 LUM  C10  C4A   aromatic  1.418  0.020  1.418
 LUM  C10  N10   aromatic  1.303  0.020  1.303
 LUM  N3   C4    aromatic  1.374  0.020  1.374
 LUM  N3   HN3   single    0.860  0.020  1.020
 LUM  C4   O4    double    1.208  0.020  1.208
 LUM  C4   C4A   aromatic  1.477  0.020  1.477
 LUM  C4A  N5    aromatic  1.304  0.020  1.304
 LUM  N5   C5A   aromatic  1.341  0.020  1.341
 LUM  C5A  C6    aromatic  1.413  0.020  1.413
 LUM  C5A  C9A   aromatic  1.420  0.020  1.420
 LUM  C6   C7    aromatic  1.367  0.020  1.367
 LUM  C6   HC6   single    0.930  0.020  1.080
 LUM  C9A  C9    aromatic  1.409  0.020  1.409
 LUM  C9A  N10   aromatic  1.346  0.020  1.346
 LUM  C7   C7M   single    1.497  0.020  1.497
 LUM  C7   C8    aromatic  1.433  0.020  1.433
 LUM  C7M  H7M1  single    0.970  0.020  1.090
 LUM  C7M  H7M2  single    0.970  0.020  1.090
 LUM  C7M  H7M3  single    0.970  0.020  1.090
 LUM  C8   C8M   single    1.496  0.020  1.496
 LUM  C8   C9    aromatic  1.371  0.020  1.371
 LUM  C8M  H8M1  single    0.970  0.020  1.090
 LUM  C8M  H8M2  single    0.970  0.020  1.090
 LUM  C8M  H8M3  single    0.970  0.020  1.090
 LUM  C9   HC9   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
 LUM  HN1   N1   C10   118.02  3.000
 LUM  HN1   N1   C2    117.29  3.000
 LUM  C10   N1   C2    124.69  3.000
 LUM  N3    C2   O2    121.92  3.000
 LUM  N3    C2   N1    115.00  3.000
 LUM  O2    C2   N1    123.08  3.000
 LUM  N10   C10  C4A   122.32  3.000
 LUM  N10   C10  N1    118.79  3.000
 LUM  C4A   C10  N1    118.89  3.000
 LUM  HN3   N3   C4    116.74  3.000
 LUM  HN3   N3   C2    115.19  3.000
 LUM  C4    N3   C2    128.06  3.000
 LUM  C4A   C4   O4    124.03  3.000
 LUM  C4A   C4   N3    113.78  3.000
 LUM  O4    C4   N3    122.19  3.000
 LUM  N5    C4A  C4    118.87  3.000
 LUM  N5    C4A  C10   121.55  3.000
 LUM  C4    C4A  C10   119.58  3.000
 LUM  C5A   N5   C4A   117.67  3.000
 LUM  C9A   C5A  C6    119.47  3.000
 LUM  C9A   C5A  N5    120.54  3.000
 LUM  C6    C5A  N5    119.99  3.000
 LUM  HC6   C6   C7    120.75  3.000
 LUM  HC6   C6   C5A   118.11  3.000
 LUM  C7    C6   C5A   121.14  3.000
 LUM  N10   C9A  C9    120.19  3.000
 LUM  N10   C9A  C5A   121.10  3.000
 LUM  C9    C9A  C5A   118.71  3.000
 LUM  C8    C7   C7M   119.98  3.000
 LUM  C8    C7   C6    119.39  3.000
 LUM  C7M   C7   C6    120.63  3.000
 LUM  H7M3  C7M  H7M2  107.79  3.000
 LUM  H7M3  C7M  H7M1  107.83  3.000
 LUM  H7M2  C7M  H7M1  106.89  3.000
 LUM  H7M3  C7M  C7    111.06  3.000
 LUM  H7M2  C7M  C7    111.31  3.000
 LUM  H7M1  C7M  C7    111.75  3.000
 LUM  C9    C8   C8M   120.24  3.000
 LUM  C9    C8   C7    120.13  3.000
 LUM  C8M   C8   C7    119.63  3.000
 LUM  H8M3  C8M  H8M2  107.95  3.000
 LUM  H8M3  C8M  H8M1  107.99  3.000
 LUM  H8M2  C8M  H8M1  106.80  3.000
 LUM  H8M3  C8M  C8    111.29  3.000
 LUM  H8M2  C8M  C8    111.09  3.000
 LUM  H8M1  C8M  C8    111.53  3.000
 LUM  HC9   C9   C8    120.51  3.000
 LUM  HC9   C9   C9A   118.34  3.000
 LUM  C8    C9   C9A   121.15  3.000
 LUM  C9A   N10  C10   116.82  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
 LUM  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 LUM  CONST_02  C4    C4A  C10  N1     0.00   0.0  0
 LUM  CONST_03  N5    C4A  C10  N1   180.00   0.0  0
 LUM  CONST_04  C9A   N10  C10  N1   180.00   0.0  0
 LUM  CONST_05  C4A   C10  N1   C2     0.00   0.0  0
 LUM  CONST_06  N10   C10  N1   C2   180.00   0.0  0
 LUM  CONST_07  C4A   C4   N3   C2     0.00   0.0  0
 LUM  CONST_08  N3    C2   N1   C10    0.00   0.0  0
 LUM  CONST_09  N3    C4   C4A  C10    0.00   0.0  0
 LUM  CONST_10  C5A   N5   C4A  C10    0.00   0.0  0
 LUM  CONST_11  C5A   C9A  N10  C10    0.00   0.0  0
 LUM  CONST_12  C9    C9A  N10  C10  180.00   0.0  0
 LUM  CONST_13  N5    C4A  C4   N3   180.00   0.0  0
 LUM  CONST_14  N10   C10  C4A  C4   180.00   0.0  0
 LUM  CONST_15  C5A   N5   C4A  C4   180.00   0.0  0
 LUM  CONST_16  C9A   N10  C10  C4A    0.00   0.0  0
 LUM  CONST_17  C6    C5A  N5   C4A  180.00   0.0  0
 LUM  CONST_18  C9A   C5A  N5   C4A    0.00   0.0  0
 LUM  CONST_19  N10   C10  C4A  N5     0.00   0.0  0
 LUM  CONST_20  C7    C6   C5A  N5   180.00   0.0  0
 LUM  CONST_21  C9    C9A  C5A  N5   180.00   0.0  0
 LUM  CONST_22  N10   C9A  C5A  N5     0.00   0.0  0
 LUM  CONST_23  C8    C7   C6   C5A    0.00   0.0  0
 LUM  CONST_24  C8    C9   C9A  C5A    0.00   0.0  0
 LUM  CONST_25  C9    C9A  C5A  C6     0.00   0.0  0
 LUM  CONST_26  N10   C9A  C5A  C6   180.00   0.0  0
 LUM  CONST_27  C9    C8   C7   C6     0.00   0.0  0
 LUM  CONST_28  C7    C6   C5A  C9A    0.00   0.0  0
 LUM  CONST_29  C7    C8   C9   C9A    0.00   0.0  0
 LUM  CONST_30  N10   C9A  C9   C8   180.00   0.0  0
 LUM  CONST_31  O4    C4   N3   C2   180.00   0.0  0
 LUM  CONST_32  O2    C2   N1   C10  180.00   0.0  0
 LUM  CONST_33  O4    C4   C4A  C10  180.00   0.0  0
 LUM  CONST_34  C4    N3   C2   O2   180.00   0.0  0
 LUM  CONST_35  N5    C4A  C4   O4     0.00   0.0  0
 LUM  CONST_36  C7M   C7   C6   C5A  180.00   0.0  0
 LUM  CONST_37  C8M   C8   C7   C6   180.00   0.0  0
 LUM  CONST_38  C8M   C8   C9   C9A  180.00   0.0  0
 LUM  CONST_39  C9    C8   C7   C7M  180.00   0.0  0
 LUM  CONST_40  HN3   N3   C2   N1   180.00   0.0  0
 LUM  CONST_41  HN1   N1   C2   N3   180.00   0.0  0
 LUM  CONST_42  HC6   C6   C5A  N5     0.00   0.0  0
 LUM  CONST_43  HC9   C9   C9A  C5A  180.00   0.0  0
 LUM  Var_01    H7M1  C7M  C7   C6   121.97  30.0  2
 LUM  Var_02    H8M1  C8M  C8   C7   -58.36  30.0  2

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
 LUM  plan-1  N1   0.020
 LUM  plan-1  C2   0.020
 LUM  plan-1  C10  0.020
 LUM  plan-1  O2   0.020
 LUM  plan-1  N3   0.020
 LUM  plan-1  C4   0.020
 LUM  plan-1  O4   0.020
 LUM  plan-1  C4A  0.020
 LUM  plan-1  N5   0.020
 LUM  plan-1  C5A  0.020
 LUM  plan-1  C6   0.020
 LUM  plan-1  C9A  0.020
 LUM  plan-1  C7   0.020
 LUM  plan-1  C7M  0.020
 LUM  plan-1  C8   0.020
 LUM  plan-1  C8M  0.020
 LUM  plan-1  C9   0.020
 LUM  plan-1  N10  0.020
 LUM  plan-1  HN1  0.020
 LUM  plan-1  HN3  0.020
 LUM  plan-1  HC6  0.020
 LUM  plan-1  HC9  0.020

