# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 23:06:23 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (3R)-3-(4-methyl-1,3-dioxo-1,3-dihydro-2H-pyrrolo[3,4-c]quinolin-2-yl)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@H](CC(O)=O)N1C(=O)c2c(C)nc3ccccc3c2C1=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
 QQ3  QQ3  '(3R)-3-(4-methyl-1,3-dioxo-1,3-dihydro-2H-pyrrolo[3,4-c]quinolin-2-yl)hexanoic acid'  ligand  41  24  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QQ3
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
 QQ3  C8    C  CH3    0  -0.660   3.6565   3.3455   2.3054
 QQ3  C7    C  CH2    0  -0.425   2.7950   2.1327   1.9802
 QQ3  C6    C  CH2    0  -0.404   3.3773   1.3035   0.8425
 QQ3  C5    C  CH1    0  -0.098   2.6101   0.0173   0.5436
 QQ3  C12   C  CH2    0  -0.600   3.2724  -0.8040  -0.5580
 QQ3  C18   C  C      0   0.420   2.5290  -2.0746  -1.0130
 QQ3  O4    O  OC    -1  -0.624   3.0329  -2.6656  -1.9896
 QQ3  O3    O  O      0  -0.590   1.5109  -2.4188  -0.3817
 QQ3  N1    N  NR5    0  -0.590   1.2012   0.2772   0.2580
 QQ3  C4    C  CR5    0   0.580   0.7241   0.8433  -0.9065
 QQ3  O1    O  O      0  -0.407   1.3917   1.3685  -1.7637
 QQ3  C3    C  CR56   0  -0.173  -0.7500   0.6766  -0.8803
 QQ3  C10   C  CR6    0   0.203  -1.7405   1.0867  -1.7985
 QQ3  C14   C  CH3    0  -0.729  -1.4073   1.8323  -3.0493
 QQ3  N2    N  N      0  -0.463  -2.9964   0.8071  -1.5514
 QQ3  C11   C  CR66   0   0.191  -3.3521   0.1364  -0.4289
 QQ3  C15   C  CR16   0  -0.287  -4.7244  -0.1332  -0.2286
 QQ3  C17   C  CR16   0  -0.250  -5.1396  -0.8053   0.8881
 QQ3  C16   C  CR16   0  -0.245  -4.2093  -1.2393   1.8561
 QQ3  C13   C  CR16   0  -0.334  -2.8726  -0.9972   1.6958
 QQ3  C9    C  CR66   0   0.054  -2.4169  -0.3054   0.5511
 QQ3  C1    C  CR56   0   0.104  -1.0811   0.0037   0.2565
 QQ3  C2    C  CR5    0   0.598   0.1781  -0.2629   1.0127
 QQ3  O2    O  O      0  -0.402   0.2883  -0.7941   2.0876
 QQ3  H81C  H  HCH3   0   0.217   4.6606   3.0483   2.6129
 QQ3  H82C  H  HCH3   0   0.217   3.7584   3.9989   1.4369
 QQ3  H83C  H  HCH3   0   0.227   3.2251   3.9366   3.1141
 QQ3  H71C  H  HCH2   0   0.215   2.6872   1.5064   2.8711
 QQ3  H72C  H  HCH2   0   0.216   1.7872   2.4677   1.7201
 QQ3  H61C  H  HCH2   0   0.223   3.4550   1.9138  -0.0614
 QQ3  H62C  H  HCH2   0   0.227   4.4001   1.0108   1.0994
 QQ3  H5    H  HCH1   0   0.255   2.5987  -0.5812   1.4557
 QQ3  H121  H  HCH2   0   0.235   3.4796  -0.1815  -1.4318
 QQ3  H122  H  HCH2   0   0.249   4.2554  -1.1056  -0.1806
 QQ3  H141  H  HCH3   0   0.258  -0.7465   1.2480  -3.6900
 QQ3  H142  H  HCH3   0   0.254  -2.3171   2.0612  -3.5991
 QQ3  H143  H  HCH3   0   0.258  -0.8888   2.7645  -2.8235
 QQ3  H15   H  HCR6   0   0.269  -5.4312   0.2029  -0.9760
 QQ3  H17   H  HCR6   0   0.271  -6.1922  -1.0076   1.0356
 QQ3  H16   H  HCR6   0   0.271  -4.5601  -1.7679   2.7321
 QQ3  H13   H  HCR6   0   0.267  -2.1640  -1.3313   2.4396

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
 QQ3  C8   C7    single    1.523  0.020  1.523
 QQ3  C7   C6    single    1.523  0.020  1.523
 QQ3  C6   C5    single    1.527  0.020  1.527
 QQ3  C5   C12   single    1.525  0.020  1.525
 QQ3  C5   N1    single    1.461  0.020  1.461
 QQ3  C12  C18   single    1.541  0.020  1.541
 QQ3  C18  O4    deloc     1.248  0.020  1.248
 QQ3  C18  O3    deloc     1.246  0.020  1.246
 QQ3  N1   C4    single    1.380  0.020  1.380
 QQ3  N1   C2    single    1.381  0.020  1.381
 QQ3  C4   O1    double    1.207  0.020  1.207
 QQ3  C4   C3    single    1.484  0.020  1.484
 QQ3  C3   C10   aromatic  1.412  0.020  1.412
 QQ3  C3   C1    aromatic  1.362  0.020  1.362
 QQ3  C10  C14   single    1.494  0.020  1.494
 QQ3  C10  N2    aromatic  1.310  0.020  1.310
 QQ3  N2   C11   aromatic  1.355  0.020  1.355
 QQ3  C11  C15   aromatic  1.413  0.020  1.413
 QQ3  C11  C9    aromatic  1.425  0.020  1.425
 QQ3  C15  C17   aromatic  1.368  0.020  1.368
 QQ3  C17  C16   aromatic  1.411  0.020  1.411
 QQ3  C16  C13   aromatic  1.368  0.020  1.368
 QQ3  C13  C9    aromatic  1.413  0.020  1.413
 QQ3  C9   C1    aromatic  1.402  0.020  1.402
 QQ3  C1   C2    single    1.493  0.020  1.493
 QQ3  C2   O2    double    1.204  0.020  1.204
 QQ3  C8   H81C  single    0.970  0.020  1.090
 QQ3  C8   H82C  single    0.970  0.020  1.090
 QQ3  C8   H83C  single    0.970  0.020  1.090
 QQ3  C7   H71C  single    0.970  0.020  1.090
 QQ3  C7   H72C  single    0.970  0.020  1.090
 QQ3  C6   H61C  single    0.970  0.020  1.090
 QQ3  C6   H62C  single    0.970  0.020  1.090
 QQ3  C5   H5    single    0.970  0.020  1.090
 QQ3  C12  H121  single    0.970  0.020  1.090
 QQ3  C12  H122  single    0.970  0.020  1.090
 QQ3  C14  H141  single    0.970  0.020  1.090
 QQ3  C14  H142  single    0.970  0.020  1.090
 QQ3  C14  H143  single    0.970  0.020  1.090
 QQ3  C15  H15   single    0.930  0.020  1.080
 QQ3  C17  H17   single    0.930  0.020  1.080
 QQ3  C16  H16   single    0.930  0.020  1.080
 QQ3  C13  H13   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
 QQ3  H83C  C8   H82C  107.61  3.000
 QQ3  H83C  C8   H81C  107.61  3.000
 QQ3  H82C  C8   H81C  107.53  3.000
 QQ3  H83C  C8   C7    111.48  3.000
 QQ3  H82C  C8   C7    111.08  3.000
 QQ3  H81C  C8   C7    111.34  3.000
 QQ3  H72C  C7   H71C  106.15  3.000
 QQ3  H72C  C7   C6    109.96  3.000
 QQ3  H71C  C7   C6    109.52  3.000
 QQ3  H72C  C7   C8    109.16  3.000
 QQ3  H71C  C7   C8    109.74  3.000
 QQ3  C6    C7   C8    112.13  3.000
 QQ3  H62C  C6   H61C  106.08  3.000
 QQ3  H62C  C6   C5    106.87  3.000
 QQ3  H61C  C6   C5    110.12  3.000
 QQ3  H62C  C6   C7    109.12  3.000
 QQ3  H61C  C6   C7    109.92  3.000
 QQ3  C5    C6   C7    114.37  3.000
 QQ3  H5    C5   N1    104.54  3.000
 QQ3  H5    C5   C12   108.24  3.000
 QQ3  N1    C5   C12   111.92  3.000
 QQ3  H5    C5   C6    107.68  3.000
 QQ3  N1    C5   C6    111.89  3.000
 QQ3  C12   C5   C6    112.13  3.000
 QQ3  H122  C12  H121  105.20  3.000
 QQ3  H122  C12  C18   107.92  3.000
 QQ3  H121  C12  C18   108.98  3.000
 QQ3  H122  C12  C5    106.80  3.000
 QQ3  H121  C12  C5    110.68  3.000
 QQ3  C18   C12  C5    116.60  3.000
 QQ3  O3    C18  O4    126.55  3.000
 QQ3  O3    C18  C12   118.18  3.000
 QQ3  O4    C18  C12   115.27  3.000
 QQ3  C2    N1   C4    111.43  3.000
 QQ3  C2    N1   C5    122.54  3.000
 QQ3  C4    N1   C5    124.86  3.000
 QQ3  C3    C4   O1    127.67  3.000
 QQ3  C3    C4   N1    106.41  3.000
 QQ3  O1    C4   N1    125.92  3.000
 QQ3  C1    C3   C10   121.06  3.000
 QQ3  C1    C3   C4    108.16  3.000
 QQ3  C10   C3   C4    130.78  3.000
 QQ3  N2    C10  C14   118.57  3.000
 QQ3  N2    C10  C3    119.21  3.000
 QQ3  C14   C10  C3    122.22  3.000
 QQ3  H143  C14  H142  108.82  3.000
 QQ3  H143  C14  H141  106.96  3.000
 QQ3  H142  C14  H141  108.83  3.000
 QQ3  H143  C14  C10   111.07  3.000
 QQ3  H142  C14  C10   109.99  3.000
 QQ3  H141  C14  C10   111.08  3.000
 QQ3  C11   N2   C10   120.89  3.000
 QQ3  C9    C11  C15   118.74  3.000
 QQ3  C9    C11  N2    123.43  3.000
 QQ3  C15   C11  N2    117.83  3.000
 QQ3  H15   C15  C17   121.21  3.000
 QQ3  H15   C15  C11   118.50  3.000
 QQ3  C17   C15  C11   120.29  3.000
 QQ3  H17   C17  C16   119.37  3.000
 QQ3  H17   C17  C15   119.90  3.000
 QQ3  C16   C17  C15   120.73  3.000
 QQ3  H16   C16  C13   119.89  3.000
 QQ3  H16   C16  C17   119.48  3.000
 QQ3  C13   C16  C17   120.63  3.000
 QQ3  H13   C13  C9    119.85  3.000
 QQ3  H13   C13  C16   120.37  3.000
 QQ3  C9    C13  C16   119.78  3.000
 QQ3  C1    C9   C13   125.82  3.000
 QQ3  C1    C9   C11   114.35  3.000
 QQ3  C13   C9   C11   119.83  3.000
 QQ3  C2    C1   C9    131.12  3.000
 QQ3  C2    C1   C3    107.82  3.000
 QQ3  C9    C1   C3    121.05  3.000
 QQ3  O2    C2   C1    127.46  3.000
 QQ3  O2    C2   N1    126.34  3.000
 QQ3  C1    C2   N1    106.15  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
 QQ3  CONST_01  C11   N2   C10  C3     0.00   0.0  0
 QQ3  CONST_02  C11   C9   C1   C3     0.00   0.0  0
 QQ3  CONST_03  C13   C9   C1   C3   180.00   0.0  0
 QQ3  CONST_04  C9    C1   C3   C10    0.00   0.0  0
 QQ3  CONST_05  C15   C11  N2   C10  180.00   0.0  0
 QQ3  CONST_06  C9    C11  N2   C10    0.00   0.0  0
 QQ3  CONST_07  C1    C3   C10  N2     0.00   0.0  0
 QQ3  CONST_08  C17   C15  C11  N2   180.00   0.0  0
 QQ3  CONST_09  C13   C9   C11  N2   180.00   0.0  0
 QQ3  CONST_10  C1    C9   C11  N2     0.00   0.0  0
 QQ3  CONST_11  C16   C17  C15  C11    0.00   0.0  0
 QQ3  CONST_12  C16   C13  C9   C11    0.00   0.0  0
 QQ3  CONST_13  C13   C9   C11  C15    0.00   0.0  0
 QQ3  CONST_14  C1    C9   C11  C15  180.00   0.0  0
 QQ3  CONST_15  C13   C16  C17  C15    0.00   0.0  0
 QQ3  CONST_16  C9    C11  C15  C17    0.00   0.0  0
 QQ3  CONST_17  C9    C13  C16  C17    0.00   0.0  0
 QQ3  CONST_18  C1    C9   C13  C16  180.00   0.0  0
 QQ3  CONST_19  C2    N1   C4   C3     0.00   0.0  0
 QQ3  CONST_20  C14   C10  C3   C4     0.00   0.0  0
 QQ3  CONST_21  C1    C3   C10  C14  180.00   0.0  0
 QQ3  CONST_22  C11   N2   C10  C14  180.00   0.0  0
 QQ3  CONST_23  C3    C4   N1   C5   180.00   0.0  0
 QQ3  CONST_24  C2    N1   C4   O1   180.00   0.0  0
 QQ3  CONST_25  H15   C15  C11  N2     0.00   0.0  0
 QQ3  CONST_26  H17   C17  C15  C11  180.00   0.0  0
 QQ3  CONST_27  H13   C13  C9   C11  180.00   0.0  0
 QQ3  CONST_28  H16   C16  C17  C15  180.00   0.0  0
 QQ3  CONST_29  O1    C4   N1   C5     0.00   0.0  0
 QQ3  Var_01    H141  C14  C10  C3    60.34  30.0  2
 QQ3  Var_02    C5    C6   C7   C8   175.63  30.0  3
 QQ3  Var_03    O4    C18  C12  C5   174.22  30.0  3
 QQ3  Var_04    H81C  C8   C7   C6   -60.38  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 QQ3  chir_01  C5  C6  C12  N1  positiv

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
 QQ3  plan-1  C5   0.020
 QQ3  plan-1  N1   0.020
 QQ3  plan-1  C4   0.020
 QQ3  plan-1  O1   0.020
 QQ3  plan-1  C3   0.020
 QQ3  plan-1  C10  0.020
 QQ3  plan-1  C14  0.020
 QQ3  plan-1  N2   0.020
 QQ3  plan-1  C11  0.020
 QQ3  plan-1  C15  0.020
 QQ3  plan-1  C17  0.020
 QQ3  plan-1  C16  0.020
 QQ3  plan-1  C13  0.020
 QQ3  plan-1  C9   0.020
 QQ3  plan-1  C1   0.020
 QQ3  plan-1  C2   0.020
 QQ3  plan-1  O2   0.020
 QQ3  plan-1  H15  0.020
 QQ3  plan-1  H17  0.020
 QQ3  plan-1  H16  0.020
 QQ3  plan-1  H13  0.020
 QQ3  plan-2  C12  0.020
 QQ3  plan-2  C18  0.020
 QQ3  plan-2  O4   0.020
 QQ3  plan-2  O3   0.020

