# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 12:57:52 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (3R)-N-[3-(7-methoxy-3,4-dihydroquinolin-1(2H)-yl)propyl]-3-methyl-2-oxo-1,2,3,4-tetrahydroquinoxaline-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2CCCN(CCCNC(=O)c3cccc4NC(=O)[C@@H](C)Nc34)c2c1
#
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
 2O4  2O4  (3R)-N-[3-(7-methoxy-3,4-dihydroquinolin-1(2H)-yl)propyl]-3-methyl-2-oxo-1,2,3,4-tetrahydroquinoxaline-5-carboxamide  ligand  58  30  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2O4
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
 2O4  C4   C  CR16  0  -0.335  -5.1289   1.1909  -2.2158
 2O4  C14  C  CH2   0  -0.482   6.4851   2.3306   0.6545
 2O4  C5   C  CR16  0  -0.268  -3.9201   1.8777  -2.2442
 2O4  C6   C  CR16  0  -0.322  -2.9847   1.6488  -1.2555
 2O4  C11  C  CH2   0  -0.322   2.6371   0.8000   1.7634
 2O4  C7   C  CR6   0  -0.128  -3.2259   0.7367  -0.2219
 2O4  C8   C  C     0   0.555  -2.1990   0.4807   0.8235
 2O4  C10  C  CH2   0  -0.483   1.4712   1.0157   0.8006
 2O4  C12  C  CH2   0  -0.275   4.2580   2.6425   1.6969
 2O4  C13  C  CH2   0  -0.476   5.3022   3.2739   0.7991
 2O4  N1   N  NH1   0  -0.652  -0.9199   0.6613   0.4602
 2O4  N2   N  NT    0  -0.534   3.8966   1.3021   1.2693
 2O4  C3   C  CR6   0   0.352  -5.3983   0.3083  -1.1891
 2O4  N3   N  NH1   0  -0.676  -4.8647  -0.7716   0.8363
 2O4  C2   C  C     0   0.521  -6.8993  -1.3961  -0.3057
 2O4  N    N  NH1   0  -0.721  -6.6331  -0.3356  -1.1026
 2O4  C22  C  CR6   0   0.302  -4.4656   0.0761  -0.1612
 2O4  C1   C  CH1   0  -0.251  -5.7100  -1.8944   0.4915
 2O4  C    C  CH3   0  -0.660  -4.9857  -2.9958  -0.2866
 2O4  O1   O  O     0  -0.510  -2.5021   0.1188   1.9603
 2O4  C20  C  CR6   0   0.415   4.7148   0.5429   0.4743
 2O4  C19  C  CR16  0  -0.473   4.3026  -0.7024  -0.0171
 2O4  C18  C  CR6   0   0.387   5.1373  -1.4790  -0.8190
 2O4  O    O  O2    0  -0.479   4.6183  -2.6611  -1.2204
 2O4  C21  C  CH3   0  -0.432   5.4085  -3.4944  -2.0414
 2O4  C17  C  CR16  0  -0.421   6.4031  -1.0245  -1.1662
 2O4  C16  C  CR16  0  -0.309   6.8029   0.2179  -0.6786
 2O4  C15  C  CR6   0   0.007   6.0107   1.0036   0.1342
 2O4  H1   H  HCR6  0   0.275  -5.8733   1.3589  -2.9849
 2O4  H3   H  HCH2  0   0.235   6.9679   2.2114   1.6311
 2O4  H4   H  HCR6  0   0.260  -3.7213   2.5899  -3.0327
 2O4  H5   H  HCR6  0   0.257  -2.0566   2.2053  -1.2761
 2O4  H6   H  HCH2  0   0.261   2.4223   1.3078   2.7075
 2O4  H7   H  HCH2  0   0.246   2.7276  -0.2596   2.0168
 2O4  H10  H  HCH2  0   0.243   1.3490   2.0854   0.6095
 2O4  H11  H  HCH2  0   0.242   1.6937   0.5428  -0.1605
 2O4  H12  H  HCH2  0   0.224   4.6243   2.6241   2.7316
 2O4  H13  H  HCH2  0   0.242   3.3554   3.2589   1.6975
 2O4  H14  H  HCH2  0   0.246   5.6073   4.2273   1.2324
 2O4  H15  H  HCH2  0   0.233   4.8721   3.4877  -0.1830
 2O4  H16  H  HNH1  0   0.406  -0.6985   0.7784  -0.5152
 2O4  H17  H  HNH1  0   0.398  -4.1931  -0.9265   1.5734
 2O4  H18  H  HNH1  0   0.410  -7.3730  -0.0219  -1.7161
 2O4  H19  H  HCH1  0   0.288  -6.0974  -2.3101   1.4218
 2O4  H20  H  HCH3  0   0.251  -4.1366  -3.3568   0.2937
 2O4  H21  H  HCH3  0   0.246  -5.6482  -3.8405  -0.4747
 2O4  H22  H  HCH3  0   0.235  -4.6119  -2.6319  -1.2451
 2O4  H23  H  HCR6  0   0.255   3.3186  -1.0941   0.2034
 2O4  H24  H  HCH3  0   0.224   6.3381  -3.7925  -1.5496
 2O4  H25  H  HCH3  0   0.255   4.8181  -4.3859  -2.2401
 2O4  H26  H  HCH3  0   0.223   5.6545  -3.0179  -2.9942
 2O4  H27  H  HCR6  0   0.263   7.0722  -1.5912  -1.7979
 2O4  H28  H  HCR6  0   0.241   7.7887   0.5832  -0.9450
 2O4  O2   O  O     0  -0.466  -7.9907  -1.9339  -0.2692
 2O4  C9   C  CH2   0  -0.242   0.1833   0.4479   1.3730
 2O4  H2   H  HCH2  0   0.247   7.2408   2.7493  -0.0129
 2O4  H8   H  HCH2  0   0.234   0.3065  -0.6205   1.5804
 2O4  H9   H  HCH2  0   0.241  -0.0446   0.9302   2.3256

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
 2O4  C9   N1   single    1.448  0.020  1.448
 2O4  C9   C10  single    1.519  0.020  1.519
 2O4  N1   C8   single    1.342  0.020  1.342
 2O4  O1   C8   double    1.231  0.020  1.231
 2O4  C8   C7   single    1.488  0.020  1.488
 2O4  C7   C6   aromatic  1.400  0.020  1.400
 2O4  C7   C22  aromatic  1.406  0.020  1.406
 2O4  C1   C    single    1.531  0.020  1.531
 2O4  C1   N3   single    1.447  0.020  1.447
 2O4  C1   C2   single    1.516  0.020  1.516
 2O4  C6   C5   aromatic  1.380  0.020  1.380
 2O4  C10  C11  single    1.527  0.020  1.527
 2O4  C22  N3   single    1.369  0.020  1.369
 2O4  C22  C3   aromatic  1.407  0.020  1.407
 2O4  C5   C4   aromatic  1.391  0.020  1.391
 2O4  C11  N2   single    1.443  0.020  1.443
 2O4  C3   C4   aromatic  1.381  0.020  1.381
 2O4  C3   N    single    1.395  0.020  1.395
 2O4  C2   N    single    1.353  0.020  1.353
 2O4  C2   O2   double    1.217  0.020  1.217
 2O4  C12  N2   single    1.453  0.020  1.453
 2O4  C12  C13  single    1.515  0.020  1.515
 2O4  N2   C20  single    1.370  0.020  1.370
 2O4  C13  C14  single    1.520  0.020  1.520
 2O4  C20  C19  aromatic  1.401  0.020  1.401
 2O4  C20  C15  aromatic  1.417  0.020  1.417
 2O4  C19  C18  aromatic  1.394  0.020  1.394
 2O4  C21  O    single    1.412  0.020  1.412
 2O4  C14  C15  single    1.502  0.020  1.502
 2O4  C15  C16  aromatic  1.380  0.020  1.380
 2O4  C18  O    single    1.352  0.020  1.352
 2O4  C18  C17  aromatic  1.389  0.020  1.389
 2O4  C16  C17  aromatic  1.393  0.020  1.393
 2O4  C4   H1   single    0.930  0.020  1.080
 2O4  C14  H2   single    0.970  0.020  1.090
 2O4  C14  H3   single    0.970  0.020  1.090
 2O4  C5   H4   single    0.930  0.020  1.080
 2O4  C6   H5   single    0.930  0.020  1.080
 2O4  C11  H6   single    0.970  0.020  1.090
 2O4  C11  H7   single    0.970  0.020  1.090
 2O4  C9   H8   single    0.970  0.020  1.090
 2O4  C9   H9   single    0.970  0.020  1.090
 2O4  C10  H10  single    0.970  0.020  1.090
 2O4  C10  H11  single    0.970  0.020  1.090
 2O4  C12  H12  single    0.970  0.020  1.090
 2O4  C12  H13  single    0.970  0.020  1.090
 2O4  C13  H14  single    0.970  0.020  1.090
 2O4  C13  H15  single    0.970  0.020  1.090
 2O4  N1   H16  single    0.860  0.020  1.020
 2O4  N3   H17  single    0.890  0.020  1.040
 2O4  N    H18  single    0.860  0.020  1.020
 2O4  C1   H19  single    0.970  0.020  1.090
 2O4  C    H20  single    0.970  0.020  1.090
 2O4  C    H21  single    0.970  0.020  1.090
 2O4  C    H22  single    0.970  0.020  1.090
 2O4  C19  H23  single    0.930  0.020  1.080
 2O4  C21  H24  single    0.970  0.020  1.090
 2O4  C21  H25  single    0.970  0.020  1.090
 2O4  C21  H26  single    0.970  0.020  1.090
 2O4  C17  H27  single    0.930  0.020  1.080
 2O4  C16  H28  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
 2O4  H1   C4   C3   119.54  3.000
 2O4  H1   C4   C5   120.41  3.000
 2O4  C3   C4   C5   120.04  3.000
 2O4  H3   C14  H2   106.36  3.000
 2O4  H3   C14  C15  110.59  3.000
 2O4  H2   C14  C15  110.22  3.000
 2O4  H3   C14  C13  109.00  3.000
 2O4  H2   C14  C13  111.03  3.000
 2O4  C15  C14  C13  109.60  3.000
 2O4  H4   C5   C6   120.48  3.000
 2O4  H4   C5   C4   120.01  3.000
 2O4  C6   C5   C4   119.51  3.000
 2O4  H5   C6   C7   119.80  3.000
 2O4  H5   C6   C5   118.83  3.000
 2O4  C7   C6   C5   121.36  3.000
 2O4  H7   C11  H6   105.44  3.000
 2O4  H7   C11  N2   110.14  3.000
 2O4  H6   C11  N2   107.79  3.000
 2O4  H7   C11  C10  110.26  3.000
 2O4  H6   C11  C10  109.20  3.000
 2O4  N2   C11  C10  113.66  3.000
 2O4  C22  C7   C8   119.84  3.000
 2O4  C22  C7   C6   119.34  3.000
 2O4  C8   C7   C6   120.81  3.000
 2O4  O1   C8   N1   121.62  3.000
 2O4  O1   C8   C7   121.98  3.000
 2O4  N1   C8   C7   116.40  3.000
 2O4  H11  C10  H10  106.98  3.000
 2O4  H11  C10  C9   109.99  3.000
 2O4  H10  C10  C9   109.67  3.000
 2O4  H11  C10  C11  109.72  3.000
 2O4  H10  C10  C11  109.49  3.000
 2O4  C9   C10  C11  110.90  3.000
 2O4  H13  C12  H12  106.53  3.000
 2O4  H13  C12  N2   108.37  3.000
 2O4  H12  C12  N2   110.18  3.000
 2O4  H13  C12  C13  109.54  3.000
 2O4  H12  C12  C13  109.61  3.000
 2O4  N2   C12  C13  112.43  3.000
 2O4  H15  C13  H14  107.21  3.000
 2O4  H15  C13  C12  110.05  3.000
 2O4  H14  C13  C12  108.76  3.000
 2O4  H15  C13  C14  110.01  3.000
 2O4  H14  C13  C14  111.26  3.000
 2O4  C12  C13  C14  109.52  3.000
 2O4  H16  N1   C9   117.41  3.000
 2O4  H16  N1   C8   119.17  3.000
 2O4  C9   N1   C8   122.40  3.000
 2O4  C20  N2   C12  122.24  3.000
 2O4  C20  N2   C11  121.80  3.000
 2O4  C12  N2   C11  115.94  3.000
 2O4  C22  C3   N    117.72  3.000
 2O4  N    C3   C4   120.92  3.000
 2O4  C22  C3   C4   121.29  3.000
 2O4  H17  N3   C1   116.34  3.000
 2O4  H17  N3   C22  115.68  3.000
 2O4  C1   N3   C22  118.51  3.000
 2O4  C1   C2   N    114.40  3.000
 2O4  N    C2   O2   122.71  3.000
 2O4  C1   C2   O2   122.84  3.000
 2O4  H18  N    C2   117.17  3.000
 2O4  H18  N    C3   117.83  3.000
 2O4  C2   N    C3   124.91  3.000
 2O4  N3   C22  C3   116.19  3.000
 2O4  C3   C22  C7   118.38  3.000
 2O4  N3   C22  C7   125.42  3.000
 2O4  H19  C1   C    109.12  3.000
 2O4  H19  C1   C2   107.18  3.000
 2O4  C    C1   C2   109.90  3.000
 2O4  H19  C1   N3   107.46  3.000
 2O4  C2   C1   N3   109.18  3.000
 2O4  C    C1   N3   113.76  3.000
 2O4  H22  C    H21  108.37  3.000
 2O4  H22  C    H20  108.13  3.000
 2O4  H21  C    H20  107.98  3.000
 2O4  H22  C    C1   111.63  3.000
 2O4  H21  C    C1   110.97  3.000
 2O4  H20  C    C1   109.65  3.000
 2O4  C15  C20  C19  118.30  3.000
 2O4  C15  C20  N2   120.35  3.000
 2O4  C19  C20  N2   121.36  3.000
 2O4  H23  C19  C18  117.40  3.000
 2O4  H23  C19  C20  121.20  3.000
 2O4  C18  C19  C20  121.39  3.000
 2O4  C17  C18  O    124.18  3.000
 2O4  C17  C18  C19  120.47  3.000
 2O4  O    C18  C19  115.34  3.000
 2O4  C21  O    C18  118.29  3.000
 2O4  H26  C21  H25  108.68  3.000
 2O4  H26  C21  H24  108.64  3.000
 2O4  H25  C21  H24  108.68  3.000
 2O4  H26  C21  O    112.06  3.000
 2O4  H25  C21  O    106.63  3.000
 2O4  H24  C21  O    112.04  3.000
 2O4  H27  C17  C16  119.64  3.000
 2O4  H27  C17  C18  122.60  3.000
 2O4  C16  C17  C18  117.77  3.000
 2O4  H28  C16  C15  118.33  3.000
 2O4  H28  C16  C17  118.38  3.000
 2O4  C15  C16  C17  123.29  3.000
 2O4  C16  C15  C20  118.76  3.000
 2O4  C16  C15  C14  121.70  3.000
 2O4  C20  C15  C14  119.54  3.000
 2O4  H9   C9   H8   106.81  3.000
 2O4  H9   C9   N1   109.02  3.000
 2O4  H8   C9   N1   110.41  3.000
 2O4  H9   C9   C10  109.92  3.000
 2O4  H8   C9   C10  109.91  3.000
 2O4  N1   C9   C10  110.69  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
 2O4  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 2O4  CONST_02  C7   C22  C3   C4      0.00   0.0  0
 2O4  CONST_03  C22  C7   C6   C5      0.00   0.0  0
 2O4  CONST_04  C22  C3   C4   C5      0.00   0.0  0
 2O4  CONST_05  C3   C22  C7   C6      0.00   0.0  0
 2O4  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 2O4  CONST_07  C17  C18  C19  C20     0.00   0.0  0
 2O4  CONST_08  C17  C16  C15  C20     0.00   0.0  0
 2O4  CONST_09  C16  C15  C20  C19     0.00   0.0  0
 2O4  CONST_10  C16  C17  C18  C19     0.00   0.0  0
 2O4  CONST_11  C15  C20  C19  C18     0.00   0.0  0
 2O4  CONST_12  C15  C16  C17  C18     0.00   0.0  0
 2O4  CONST_13  C1   C2   N    C3      0.00   0.0  0
 2O4  CONST_14  C8   C7   C6   C5    180.00   0.0  0
 2O4  CONST_15  N3   C22  C7   C8      0.00   0.0  0
 2O4  CONST_16  C3   C22  C7   C8    180.00   0.0  0
 2O4  CONST_17  O    C18  C19  C20   180.00   0.0  0
 2O4  CONST_18  C16  C17  C18  O     180.00   0.0  0
 2O4  CONST_19  O2   C2   N    C3    180.00   0.0  0
 2O4  CONST_20  H5   C6   C5   C4    180.00   0.0  0
 2O4  CONST_21  H28  C16  C15  C14     0.00   0.0  0
 2O4  CONST_22  H1   C4   C5   C6    180.00   0.0  0
 2O4  CONST_23  H4   C5   C6   C7    180.00   0.0  0
 2O4  CONST_24  H23  C19  C20  N2      0.00   0.0  0
 2O4  CONST_25  H27  C17  C18  C19   180.00   0.0  0
 2O4  CONST_26  H18  N    C2   C1    180.00   0.0  0
 2O4  CONST_27  C9   N1   C8   C7    180.00   0.0  0
 2O4  CONST_28  H16  N1   C8   C7      0.00   0.0  0
 2O4  CONST_29  O1   C8   N1   C9      0.00   0.0  0
 2O4  Var_01    C2   N    C3   C4    166.31  30.0  1
 2O4  Var_02    N2   C12  C13  C14   -52.15  30.0  1
 2O4  Var_03    C1   N3   C22  C7   -145.86  30.0  1
 2O4  Var_04    C19  C20  N2   C12  -174.71  30.0  1
 2O4  Var_05    C15  C14  C13  C12    56.30  30.0  1
 2O4  Var_06    C20  N2   C12  C13    21.39  30.0  1
 2O4  Var_07    C20  C15  C14  C13   -31.59  30.0  1
 2O4  Var_08    N1   C8   C7   C6    -27.92  30.0  2
 2O4  Var_09    C12  N2   C11  C10    94.85  30.0  3
 2O4  Var_10    C17  C18  O    C21     0.21  30.0  2
 2O4  Var_11    N2   C11  C10  C9    179.21  30.0  3
 2O4  Var_12    H24  C21  O    C18    60.70  30.0  3
 2O4  Var_13    N1   C9   C10  C11   179.68  30.0  2
 2O4  Var_14    C10  C9   N1   C8   -167.43  30.0  1

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
 2O4  chir_01  C1  C  N3  C2  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
 2O4  plan-1  C4   0.020
 2O4  plan-1  C5   0.020
 2O4  plan-1  C6   0.020
 2O4  plan-1  C7   0.020
 2O4  plan-1  C8   0.020
 2O4  plan-1  C3   0.020
 2O4  plan-1  N3   0.020
 2O4  plan-1  N    0.020
 2O4  plan-1  C22  0.020
 2O4  plan-1  H1   0.020
 2O4  plan-1  H4   0.020
 2O4  plan-1  H5   0.020
 2O4  plan-2  C14  0.020
 2O4  plan-2  N2   0.020
 2O4  plan-2  C20  0.020
 2O4  plan-2  C19  0.020
 2O4  plan-2  C18  0.020
 2O4  plan-2  O    0.020
 2O4  plan-2  C17  0.020
 2O4  plan-2  C16  0.020
 2O4  plan-2  C15  0.020
 2O4  plan-2  H23  0.020
 2O4  plan-2  H27  0.020
 2O4  plan-2  H28  0.020
 2O4  plan-3  C7   0.020
 2O4  plan-3  C8   0.020
 2O4  plan-3  N1   0.020
 2O4  plan-3  O1   0.020
 2O4  plan-3  H16  0.020
 2O4  plan-3  C9   0.020
 2O4  plan-4  C3   0.020
 2O4  plan-4  C2   0.020
 2O4  plan-4  N    0.020
 2O4  plan-4  C1   0.020
 2O4  plan-4  H18  0.020
 2O4  plan-4  O2   0.020

