# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:48:09 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: ethyl (9S)-9-[5-(1H-benzimidazol-2-ylsulfanyl)furan-2-yl]-8-hydroxy-5,6,7,9-tetrahydro-2H-pyrrolo[3,4-b]quinoline-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)c1[nH]cc2[C@H](c3oc(Sc4[nH]c5ccccc5n4)cc3)C6=C(O)CCCC6=Nc12
#
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
 Y3M  Y3M  'ethyl (9S)-9-[5-(1H-benzimidazol-2-ylsulfanyl)furan-2-yl]-8-hydroxy-5,6,7,9-tetrahydro-2H-pyrrolo[3,4-b]quinoline-3-carboxylate'  ligand  56  34  .  2022-07-22  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_Y3M
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
 Y3M  O17   O  O     0  -0.459   3.2760   0.4268   1.7808
 Y3M  C16   C  C     0   0.571   3.2301   0.2673   0.5819
 Y3M  O18   O  O2    0  -0.481   4.0749   0.8488  -0.2721
 Y3M  C19   C  CH2   0  -0.176   5.0573   1.7454   0.2566
 Y3M  C20   C  CH3   0  -0.693   5.8080   2.3469  -0.9067
 Y3M  C7    C  CR5   0   0.137   2.2705  -0.5675  -0.1111
 Y3M  C3    C  CR5   0   0.076   1.2159  -1.3270   0.3855
 Y3M  N6    N  NR15  0  -0.640   2.2538  -0.7146  -1.4748
 Y3M  C5    C  CR15  0  -0.063   1.2403  -1.5212  -1.8473
 Y3M  C4    C  CR5   0   0.054   0.5737  -1.9240  -0.7148
 Y3M  C2    C  CH1   0  -0.508  -0.6964  -2.6989  -0.5488
 Y3M  C8    C  CR6   0  -0.031  -0.8873  -3.0229   0.9239
 Y3M  C13   C  CR6   0   0.345  -1.8294  -3.9243   1.2922
 Y3M  O14   O  OH1   0  -0.592  -2.4911  -4.5736   0.3333
 Y3M  C12   C  C     0  -0.561  -2.1806  -4.2329   2.7118
 Y3M  C11   C  C     0  -0.456  -1.8307  -3.0653   3.6188
 Y3M  C10   C  C     0  -0.525  -0.3925  -2.6442   3.3818
 Y3M  C9    C  CR6   0   0.191  -0.1073  -2.3337   1.9377
 Y3M  N1    N  N     0  -0.458   0.8599  -1.5121   1.7035
 Y3M  C15   C  CR5   0   0.459  -1.8182  -1.8564  -1.0643
 Y3M  O24   O  O     0  -0.394  -2.0689  -0.7315  -0.3726
 Y3M  C23   C  CR5   0   0.146  -2.9613  -0.0084  -1.0783
 Y3M  C22   C  CR15  0  -0.319  -3.3257  -0.6731  -2.2015
 Y3M  C21   C  CR15  0  -0.378  -2.5848  -1.8931  -2.1838
 Y3M  S25   S  S2    0   0.105  -3.4702   1.5109  -0.4220
 Y3M  C26   C  CR5   0   0.263  -1.9106   2.3218  -0.3555
 Y3M  N28   N  N     0  -0.421  -0.8641   2.0309  -1.0651
 Y3M  C29   C  CR56  0   0.153   0.1094   2.8943  -0.6192
 Y3M  C34   C  CR16  0  -0.320   1.4418   3.0198  -1.0075
 Y3M  C33   C  CR16  0  -0.265   2.2052   3.9934  -0.3888
 Y3M  C32   C  CR16  0  -0.279   1.6686   4.8283   0.6022
 Y3M  C31   C  CR16  0  -0.305   0.3493   4.7151   1.0071
 Y3M  C30   C  CR56  0   0.332  -0.4094   3.7346   0.3807
 Y3M  N27   N  NR15  0  -0.693  -1.7132   3.3334   0.5288
 Y3M  H191  H  HCH2  0   0.229   4.5674   2.5235   0.8457
 Y3M  H192  H  HCH2  0   0.236   5.7361   1.2029   0.9185
 Y3M  H201  H  HCH3  0   0.239   6.5620   3.0361  -0.5278
 Y3M  H202  H  HCH3  0   0.239   6.3174   1.5848  -1.4963
 Y3M  H203  H  HCH3  0   0.234   5.1450   2.9072  -1.5671
 Y3M  H6    H  HNR5  0   0.412   2.9117  -0.2943  -2.1101
 Y3M  H5    H  HCR5  0   0.282   1.0555  -1.7424  -2.8864
 Y3M  H2    H  HCH1  0   0.292  -0.6760  -3.6128  -1.1488
 Y3M  H14   H  HOH1  0   0.487  -3.1454  -5.1736   0.7107
 Y3M  H121  H  H     0   0.272  -3.2470  -4.4659   2.7808
 Y3M  H122  H  H     0   0.277  -1.6456  -5.1362   3.0266
 Y3M  H111  H  H     0   0.240  -2.5062  -2.2311   3.4138
 Y3M  H112  H  H     0   0.252  -1.9779  -3.3467   4.6617
 Y3M  H101  H  H     0   0.258  -0.1218  -1.7786   3.9871
 Y3M  H102  H  H     0   0.255   0.2739  -3.4590   3.6896
 Y3M  H21   H  HCR5  0   0.265  -2.5946  -2.6753  -2.9253
 Y3M  H22   H  HCR5  0   0.276  -4.0195  -0.3301  -2.9517
 Y3M  H27   H  HNR5  0   0.424  -2.3820   3.6930   1.1920
 Y3M  H34   H  HCR6  0   0.244   1.8613   2.3742  -1.7675
 Y3M  H33   H  HCR6  0   0.249   3.2412   4.1205  -0.6741
 Y3M  H32   H  HCR6  0   0.255   2.3010   5.5765   1.0617
 Y3M  H31   H  HCR6  0   0.267  -0.0646   5.3556   1.7748

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
 Y3M  O17  C16   double    1.210  0.020  1.210
 Y3M  C16  O18   single    1.335  0.020  1.335
 Y3M  C16  C7    single    1.448  0.020  1.448
 Y3M  O18  C19   single    1.431  0.020  1.431
 Y3M  C19  C20   single    1.510  0.020  1.510
 Y3M  C7   C3    aromatic  1.391  0.020  1.391
 Y3M  C7   N6    aromatic  1.372  0.020  1.372
 Y3M  C3   C4    aromatic  1.407  0.020  1.407
 Y3M  C3   N1    single    1.378  0.020  1.378
 Y3M  N6   C5    aromatic  1.348  0.020  1.348
 Y3M  C5   C4    aromatic  1.374  0.020  1.374
 Y3M  C4   C2    single    1.497  0.020  1.497
 Y3M  C2   C8    single    1.520  0.020  1.520
 Y3M  C2   C15   single    1.495  0.020  1.495
 Y3M  C8   C13   double    1.355  0.020  1.355
 Y3M  C8   C9    single    1.453  0.020  1.453
 Y3M  C13  O14   single    1.334  0.020  1.334
 Y3M  C13  C12   single    1.495  0.020  1.495
 Y3M  C12  C11   single    1.519  0.020  1.519
 Y3M  C11  C10   single    1.517  0.020  1.517
 Y3M  C10  C9    single    1.504  0.020  1.504
 Y3M  C9   N1    double    1.290  0.020  1.290
 Y3M  C15  O24   aromatic  1.344  0.020  1.344
 Y3M  C15  C21   aromatic  1.357  0.020  1.357
 Y3M  O24  C23   aromatic  1.348  0.020  1.348
 Y3M  C23  C22   aromatic  1.355  0.020  1.355
 Y3M  C23  S25   single    1.731  0.020  1.731
 Y3M  C22  C21   aromatic  1.427  0.020  1.427
 Y3M  S25  C26   single    1.759  0.020  1.759
 Y3M  C26  N28   aromatic  1.297  0.020  1.297
 Y3M  C26  N27   aromatic  1.358  0.020  1.358
 Y3M  N28  C29   aromatic  1.376  0.020  1.376
 Y3M  C29  C34   aromatic  1.393  0.020  1.393
 Y3M  C29  C30   aromatic  1.405  0.020  1.405
 Y3M  C34  C33   aromatic  1.383  0.020  1.383
 Y3M  C33  C32   aromatic  1.402  0.020  1.402
 Y3M  C32  C31   aromatic  1.385  0.020  1.385
 Y3M  C31  C30   aromatic  1.389  0.020  1.389
 Y3M  C30  N27   aromatic  1.372  0.020  1.372
 Y3M  C19  H191  single    0.970  0.020  1.090
 Y3M  C19  H192  single    0.970  0.020  1.090
 Y3M  C20  H201  single    0.970  0.020  1.090
 Y3M  C20  H202  single    0.970  0.020  1.090
 Y3M  C20  H203  single    0.970  0.020  1.090
 Y3M  N6   H6    single    0.860  0.020  1.020
 Y3M  C5   H5    single    0.930  0.020  1.080
 Y3M  C2   H2    single    0.970  0.020  1.090
 Y3M  O14  H14   single    0.850  0.020  0.980
 Y3M  C12  H121  single    0.970  0.020  1.090
 Y3M  C12  H122  single    0.970  0.020  1.090
 Y3M  C11  H111  single    0.970  0.020  1.090
 Y3M  C11  H112  single    0.970  0.020  1.090
 Y3M  C10  H101  single    0.970  0.020  1.090
 Y3M  C10  H102  single    0.970  0.020  1.090
 Y3M  C21  H21   single    0.930  0.020  1.080
 Y3M  C22  H22   single    0.930  0.020  1.080
 Y3M  N27  H27   single    0.860  0.020  1.020
 Y3M  C34  H34   single    0.930  0.020  1.080
 Y3M  C33  H33   single    0.930  0.020  1.080
 Y3M  C32  H32   single    0.930  0.020  1.080
 Y3M  C31  H31   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
 Y3M  C7    C16  O18   111.36  3.000
 Y3M  C7    C16  O17   125.10  3.000
 Y3M  O18   C16  O17   123.54  3.000
 Y3M  C19   O18  C16   118.10  3.000
 Y3M  H192  C19  H191  107.81  3.000
 Y3M  H192  C19  C20   110.85  3.000
 Y3M  H191  C19  C20   110.79  3.000
 Y3M  H192  C19  O18   109.83  3.000
 Y3M  H191  C19  O18   109.74  3.000
 Y3M  C20   C19  O18   107.83  3.000
 Y3M  H203  C20  H202  108.41  3.000
 Y3M  H203  C20  H201  107.84  3.000
 Y3M  H202  C20  H201  107.88  3.000
 Y3M  H203  C20  C19   111.66  3.000
 Y3M  H202  C20  C19   111.76  3.000
 Y3M  H201  C20  C19   109.16  3.000
 Y3M  N6    C7   C3    106.68  3.000
 Y3M  N6    C7   C16   123.06  3.000
 Y3M  C3    C7   C16   130.24  3.000
 Y3M  N1    C3   C4    124.97  3.000
 Y3M  N1    C3   C7    127.64  3.000
 Y3M  C4    C3   C7    107.37  3.000
 Y3M  H6    N6   C5    124.55  3.000
 Y3M  H6    N6   C7    125.08  3.000
 Y3M  C5    N6   C7    110.37  3.000
 Y3M  H5    C5   C4    130.60  3.000
 Y3M  H5    C5   N6    121.19  3.000
 Y3M  C4    C5   N6    108.20  3.000
 Y3M  C2    C4   C5    130.88  3.000
 Y3M  C2    C4   C3    121.34  3.000
 Y3M  C5    C4   C3    107.38  3.000
 Y3M  H2    C2   C15   107.21  3.000
 Y3M  H2    C2   C8    110.85  3.000
 Y3M  C15   C2   C8    111.11  3.000
 Y3M  H2    C2   C4    110.85  3.000
 Y3M  C15   C2   C4    107.87  3.000
 Y3M  C8    C2   C4    108.92  3.000
 Y3M  C9    C8   C13   119.95  3.000
 Y3M  C9    C8   C2    120.50  3.000
 Y3M  C13   C8   C2    119.51  3.000
 Y3M  C12   C13  O14   117.76  3.000
 Y3M  C12   C13  C8    123.98  3.000
 Y3M  O14   C13  C8    118.25  3.000
 Y3M  H14   O14  C13   110.98  3.000
 Y3M  H122  C12  H121  106.39  3.000
 Y3M  H122  C12  C11   110.46  3.000
 Y3M  H121  C12  C11   110.52  3.000
 Y3M  H122  C12  C13   109.16  3.000
 Y3M  H121  C12  C13   109.45  3.000
 Y3M  C11   C12  C13   110.75  3.000
 Y3M  H112  C11  H111  107.05  3.000
 Y3M  H112  C11  C10   110.43  3.000
 Y3M  H111  C11  C10   110.16  3.000
 Y3M  H112  C11  C12   109.98  3.000
 Y3M  H111  C11  C12   109.41  3.000
 Y3M  C10   C11  C12   109.78  3.000
 Y3M  H102  C10  H101  106.45  3.000
 Y3M  H102  C10  C9    107.91  3.000
 Y3M  H101  C10  C9    108.78  3.000
 Y3M  H102  C10  C11   109.02  3.000
 Y3M  H101  C10  C11   111.66  3.000
 Y3M  C9    C10  C11   112.76  3.000
 Y3M  N1    C9   C10   116.59  3.000
 Y3M  N1    C9   C8    125.29  3.000
 Y3M  C10   C9   C8    118.04  3.000
 Y3M  C9    N1   C3    116.92  3.000
 Y3M  C21   C15  O24   109.98  3.000
 Y3M  C21   C15  C2    133.87  3.000
 Y3M  O24   C15  C2    115.74  3.000
 Y3M  C23   O24  C15   107.64  3.000
 Y3M  S25   C23  C22   131.73  3.000
 Y3M  S25   C23  O24   117.83  3.000
 Y3M  C22   C23  O24   110.41  3.000
 Y3M  H22   C22  C21   127.93  3.000
 Y3M  H22   C22  C23   126.43  3.000
 Y3M  C21   C22  C23   105.63  3.000
 Y3M  H21   C21  C22   127.37  3.000
 Y3M  H21   C21  C15   126.31  3.000
 Y3M  C22   C21  C15   106.27  3.000
 Y3M  C26   S25  C23    99.11  3.000
 Y3M  N27   C26  N28   113.95  3.000
 Y3M  N27   C26  S25   119.79  3.000
 Y3M  N28   C26  S25   126.24  3.000
 Y3M  C29   N28  C26   104.64  3.000
 Y3M  C30   C29  C34   119.83  3.000
 Y3M  C30   C29  N28   110.16  3.000
 Y3M  C34   C29  N28   130.01  3.000
 Y3M  H34   C34  C33   121.35  3.000
 Y3M  H34   C34  C29   120.85  3.000
 Y3M  C33   C34  C29   117.80  3.000
 Y3M  H33   C33  C32   118.86  3.000
 Y3M  H33   C33  C34   119.54  3.000
 Y3M  C32   C33  C34   121.59  3.000
 Y3M  H32   C32  C31   119.28  3.000
 Y3M  H32   C32  C33   119.22  3.000
 Y3M  C31   C32  C33   121.50  3.000
 Y3M  H31   C31  C30   121.93  3.000
 Y3M  H31   C31  C32   121.57  3.000
 Y3M  C30   C31  C32   116.50  3.000
 Y3M  N27   C30  C31   132.59  3.000
 Y3M  N27   C30  C29   104.64  3.000
 Y3M  C31   C30  C29   122.77  3.000
 Y3M  H27   N27  C30   126.66  3.000
 Y3M  H27   N27  C26   126.70  3.000
 Y3M  C30   N27  C26   106.60  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
 Y3M  CONST_01  C5    C4   C3   C7      0.00   0.0  0
 Y3M  CONST_02  C4    C5   N6   C7      0.00   0.0  0
 Y3M  CONST_03  C5    N6   C7   C3      0.00   0.0  0
 Y3M  CONST_04  N6    C5   C4   C3      0.00   0.0  0
 Y3M  CONST_05  C4    C3   C7   N6      0.00   0.0  0
 Y3M  CONST_06  C22   C23  O24  C15     0.00   0.0  0
 Y3M  CONST_07  C23   C22  C21  C15     0.00   0.0  0
 Y3M  CONST_08  C22   C21  C15  O24     0.00   0.0  0
 Y3M  CONST_09  C21   C22  C23  O24     0.00   0.0  0
 Y3M  CONST_10  C21   C15  O24  C23     0.00   0.0  0
 Y3M  CONST_11  C34   C29  N28  C26   180.00   0.0  0
 Y3M  CONST_12  C30   C29  N28  C26     0.00   0.0  0
 Y3M  CONST_13  C29   C30  N27  C26     0.00   0.0  0
 Y3M  CONST_14  C31   C30  N27  C26   180.00   0.0  0
 Y3M  CONST_15  C30   N27  C26  N28     0.00   0.0  0
 Y3M  CONST_16  C33   C34  C29  N28   180.00   0.0  0
 Y3M  CONST_17  C31   C30  C29  N28   180.00   0.0  0
 Y3M  CONST_18  N27   C30  C29  N28     0.00   0.0  0
 Y3M  CONST_19  N27   C26  N28  C29     0.00   0.0  0
 Y3M  CONST_20  C32   C33  C34  C29     0.00   0.0  0
 Y3M  CONST_21  C32   C31  C30  C29     0.00   0.0  0
 Y3M  CONST_22  C31   C30  C29  C34     0.00   0.0  0
 Y3M  CONST_23  N27   C30  C29  C34   180.00   0.0  0
 Y3M  CONST_24  C31   C32  C33  C34     0.00   0.0  0
 Y3M  CONST_25  C30   C29  C34  C33     0.00   0.0  0
 Y3M  CONST_26  C30   C31  C32  C33     0.00   0.0  0
 Y3M  CONST_27  N27   C30  C31  C32   180.00   0.0  0
 Y3M  CONST_28  C23   O24  C15  C2    180.00   0.0  0
 Y3M  CONST_29  C22   C21  C15  C2    180.00   0.0  0
 Y3M  CONST_30  C4    C3   C7   C16   180.00   0.0  0
 Y3M  CONST_31  N1    C3   C7   C16     0.00   0.0  0
 Y3M  CONST_32  C5    N6   C7   C16   180.00   0.0  0
 Y3M  CONST_33  S25   C23  O24  C15   180.00   0.0  0
 Y3M  CONST_34  S25   C23  C22  C21   180.00   0.0  0
 Y3M  CONST_35  C29   N28  C26  S25   180.00   0.0  0
 Y3M  CONST_36  C30   N27  C26  S25   180.00   0.0  0
 Y3M  CONST_37  H5    C5   N6   C7    180.00   0.0  0
 Y3M  CONST_38  H6    N6   C7   C3    180.00   0.0  0
 Y3M  CONST_39  H21   C21  C15  C2      0.00   0.0  0
 Y3M  CONST_40  H22   C22  C21  C15   180.00   0.0  0
 Y3M  CONST_41  H27   N27  C26  N28   180.00   0.0  0
 Y3M  CONST_42  H34   C34  C29  N28     0.00   0.0  0
 Y3M  CONST_43  H33   C33  C34  C29   180.00   0.0  0
 Y3M  CONST_44  H31   C31  C30  C29   180.00   0.0  0
 Y3M  CONST_45  H32   C32  C33  C34   180.00   0.0  0
 Y3M  Var_01    C8    C9   N1   C3     -3.19  30.0  1
 Y3M  Var_02    C12   C13  C8   C2   -174.65  30.0  1
 Y3M  Var_03    C11   C12  C13  C8     24.23  30.0  1
 Y3M  Var_04    C11   C10  C9   C8    -28.76  30.0  1
 Y3M  Var_05    C10   C11  C12  C13   -51.46  30.0  1
 Y3M  Var_06    C9    C10  C11  C12    54.67  30.0  1
 Y3M  Var_07    N28   C26  S25  C23    22.71  30.0  2
 Y3M  Var_08    C3    C7   C16  O17     1.22  30.0  2
 Y3M  Var_09    C7    C16  O18  C19   177.84  30.0  2
 Y3M  Var_10    C20   C19  O18  C16  -175.63  30.0  3
 Y3M  Var_11    H201  C20  C19  O18   179.90  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
 Y3M  chir_01  C2  C4  C8  C15  negativ

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
 Y3M  plan-1  C2   0.020
 Y3M  plan-1  C15  0.020
 Y3M  plan-1  O24  0.020
 Y3M  plan-1  C23  0.020
 Y3M  plan-1  C22  0.020
 Y3M  plan-1  C21  0.020
 Y3M  plan-1  S25  0.020
 Y3M  plan-1  H21  0.020
 Y3M  plan-1  H22  0.020
 Y3M  plan-2  S25  0.020
 Y3M  plan-2  C26  0.020
 Y3M  plan-2  N28  0.020
 Y3M  plan-2  C29  0.020
 Y3M  plan-2  C34  0.020
 Y3M  plan-2  C33  0.020
 Y3M  plan-2  C32  0.020
 Y3M  plan-2  C31  0.020
 Y3M  plan-2  C30  0.020
 Y3M  plan-2  N27  0.020
 Y3M  plan-2  H27  0.020
 Y3M  plan-2  H34  0.020
 Y3M  plan-2  H33  0.020
 Y3M  plan-2  H32  0.020
 Y3M  plan-2  H31  0.020
 Y3M  plan-3  C16  0.020
 Y3M  plan-3  C7   0.020
 Y3M  plan-3  C3   0.020
 Y3M  plan-3  N6   0.020
 Y3M  plan-3  C5   0.020
 Y3M  plan-3  C4   0.020
 Y3M  plan-3  C2   0.020
 Y3M  plan-3  N1   0.020
 Y3M  plan-3  H6   0.020
 Y3M  plan-3  H5   0.020
 Y3M  plan-4  O17  0.020
 Y3M  plan-4  C16  0.020
 Y3M  plan-4  O18  0.020
 Y3M  plan-4  C7   0.020

