# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:34:02 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: (3aR,4R,7S,7aS)-2-(4-nitronaphthalen-1-yl)hexahydro-1H-4,7-ethanoisoindole-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc(N2C(=O)[C@H]3C4CCC(CC4)[C@H]3C2=O)c5ccccc15
#
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
 HYQ  HYQ  (3aR,4R,7S,7aS)-2-(4-nitronaphthalen-1-yl)hexahydro-1H-4,7-ethanoisoindole-1,3(2H)-dione  ligand  44  26  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HYQ
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
 HYQ  C1    C  CR15   0  -0.391  -2.9084  -0.9397   0.8248
 HYQ  C4    C  CR5    0   0.563  -1.4601  -0.7770   1.2052
 HYQ  O10   O  O      0  -0.406  -0.9835  -0.6861   2.3067
 HYQ  N9    N  NR5    0  -0.672  -0.7101  -0.7435   0.0374
 HYQ  C14   C  CR6    0   0.322   0.7040  -0.6972   0.0287
 HYQ  C16   C  CR16   0  -0.287   1.3970  -1.8727   0.0539
 HYQ  C19   C  CR16   0  -0.286   2.7981  -1.8582   0.0477
 HYQ  C20   C  CR6    0   0.200   3.4600  -0.6637   0.0407
 HYQ  N23   N  N      1   0.325   4.9134  -0.7361   0.1089
 HYQ  O26   O  O     -1  -0.368   5.4846   0.0240   0.8540
 HYQ  O25   O  O      0  -0.363   5.4625  -1.5773  -0.5602
 HYQ  C17   C  CR66   0   0.111   2.7912   0.5884  -0.0053
 HYQ  C21   C  CR16   0  -0.287   3.4363   1.8458  -0.0950
 HYQ  C24   C  CR16   0  -0.239   2.7071   3.0005  -0.1642
 HYQ  C22   C  CR16   0  -0.240   1.3015   2.9682  -0.1407
 HYQ  C18   C  CR16   0  -0.310   0.6494   1.7706  -0.0712
 HYQ  C15   C  CR66   0   0.115   1.3674   0.5552  -0.0127
 HYQ  C6    C  CR5    0   0.563  -1.4735  -0.8554  -1.1174
 HYQ  O13   O  O      0  -0.405  -1.0093  -0.8395  -2.2276
 HYQ  C2    C  CR15   0  -0.391  -2.9173  -0.9899  -0.7103
 HYQ  C5    C  CH1    0  -0.251  -3.8133   0.1222  -1.2694
 HYQ  C12   C  CH2    0  -0.437  -5.2267  -0.1140  -0.7321
 HYQ  C8    C  CH2    0  -0.438  -5.2186  -0.0685   0.8139
 HYQ  C3    C  CH1    0  -0.251  -3.8008   0.2052   1.3200
 HYQ  C7    C  CH2    0  -0.462  -3.3150   1.5388   0.7518
 HYQ  C11   C  CH2    0  -0.463  -3.3205   1.4886  -0.7927
 HYQ  H1    H  HCR5   0   0.320  -3.2554  -1.8821   1.2585
 HYQ  H16   H  HCR6   0   0.293   0.8710  -2.8169   0.0838
 HYQ  H19   H  HCR6   0   0.308   3.3382  -2.7937   0.0774
 HYQ  H21   H  HCR6   0   0.266   4.5120   1.9155  -0.1227
 HYQ  H24   H  HCR6   0   0.275   3.2204   3.9496  -0.2395
 HYQ  H22   H  HCR6   0   0.275   0.7382   3.8901  -0.1884
 HYQ  H18   H  HCR6   0   0.239  -0.4313   1.7547  -0.0686
 HYQ  H2    H  HCR5   0   0.320  -3.2713  -1.9577  -1.0771
 HYQ  H5    H  HCH1   0   0.254  -3.8122   0.0786  -2.3600
 HYQ  H121  H  HCH2   0   0.240  -5.6023  -1.0754  -1.0893
 HYQ  H122  H  HCH2   0   0.242  -5.8926   0.6499  -1.1379
 HYQ  H81   H  HCH2   0   0.240  -5.5839  -1.0091   1.2317
 HYQ  H82   H  HCH2   0   0.242  -5.8852   0.7139   1.1818
 HYQ  H3    H  HCH1   0   0.254  -3.7876   0.2328   2.4110
 HYQ  H71   H  HCH2   0   0.255  -3.9685   2.3345   1.1141
 HYQ  H72   H  HCH2   0   0.234  -2.3222   1.7812   1.1417
 HYQ  H111  H  HCH2   0   0.234  -2.3298   1.7039  -1.2040
 HYQ  H112  H  HCH2   0   0.255  -3.9745   2.2609  -1.2015

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
 HYQ  C1   C4    single    1.506  0.020  1.506
 HYQ  C1   C2    single    1.536  0.020  1.536
 HYQ  C1   C3    single    1.534  0.020  1.534
 HYQ  C1   H1    single    0.970  0.020  1.090
 HYQ  C4   O10   double    1.204  0.020  1.204
 HYQ  C4   N9    single    1.388  0.020  1.388
 HYQ  N9   C14   single    1.415  0.020  1.415
 HYQ  N9   C6    single    1.389  0.020  1.389
 HYQ  C14  C16   aromatic  1.365  0.020  1.365
 HYQ  C14  C15   aromatic  1.418  0.020  1.418
 HYQ  C16  C19   aromatic  1.401  0.020  1.401
 HYQ  C16  H16   single    0.930  0.020  1.080
 HYQ  C19  C20   aromatic  1.366  0.020  1.366
 HYQ  C19  H19   single    0.930  0.020  1.080
 HYQ  C20  N23   single    1.457  0.020  1.457
 HYQ  C20  C17   aromatic  1.420  0.020  1.420
 HYQ  N23  O26   single    1.208  0.020  1.208
 HYQ  N23  O25   double    1.207  0.020  1.207
 HYQ  C17  C21   aromatic  1.416  0.020  1.416
 HYQ  C17  C15   aromatic  1.424  0.020  1.424
 HYQ  C21  C24   aromatic  1.367  0.020  1.367
 HYQ  C21  H21   single    0.930  0.020  1.080
 HYQ  C24  C22   aromatic  1.406  0.020  1.406
 HYQ  C24  H24   single    0.930  0.020  1.080
 HYQ  C22  C18   aromatic  1.365  0.020  1.365
 HYQ  C22  H22   single    0.930  0.020  1.080
 HYQ  C18  C15   aromatic  1.413  0.020  1.413
 HYQ  C18  H18   single    0.930  0.020  1.080
 HYQ  C6   O13   double    1.204  0.020  1.204
 HYQ  C6   C2    single    1.506  0.020  1.506
 HYQ  C2   C5    single    1.534  0.020  1.534
 HYQ  C2   H2    single    0.970  0.020  1.090
 HYQ  C5   C12   single    1.530  0.020  1.530
 HYQ  C5   C11   single    1.529  0.020  1.529
 HYQ  C5   H5    single    0.970  0.020  1.090
 HYQ  C12  C8    single    1.547  0.020  1.547
 HYQ  C12  H121  single    0.970  0.020  1.090
 HYQ  C12  H122  single    0.970  0.020  1.090
 HYQ  C8   C3    single    1.530  0.020  1.530
 HYQ  C8   H81   single    0.970  0.020  1.090
 HYQ  C8   H82   single    0.970  0.020  1.090
 HYQ  C3   C7    single    1.529  0.020  1.529
 HYQ  C3   H3    single    0.970  0.020  1.090
 HYQ  C7   C11   single    1.545  0.020  1.545
 HYQ  C7   H71   single    0.970  0.020  1.090
 HYQ  C7   H72   single    0.970  0.020  1.090
 HYQ  C11  H111  single    0.970  0.020  1.090
 HYQ  C11  H112  single    0.970  0.020  1.090

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
 HYQ  H1    C1   C3    109.30  3.000
 HYQ  H1    C1   C2    111.48  3.000
 HYQ  C3    C1   C2    110.11  3.000
 HYQ  H1    C1   C4    107.33  3.000
 HYQ  C3    C1   C4    113.41  3.000
 HYQ  C2    C1   C4    105.16  3.000
 HYQ  N9    C4   O10   123.65  3.000
 HYQ  N9    C4   C1    108.04  3.000
 HYQ  O10   C4   C1    128.32  3.000
 HYQ  C6    N9   C14   123.16  3.000
 HYQ  C6    N9   C4    113.61  3.000
 HYQ  C14   N9   C4    123.09  3.000
 HYQ  C15   C14  C16   121.58  3.000
 HYQ  C15   C14  N9    119.79  3.000
 HYQ  C16   C14  N9    118.63  3.000
 HYQ  H16   C16  C19   119.71  3.000
 HYQ  H16   C16  C14   120.37  3.000
 HYQ  C19   C16  C14   119.92  3.000
 HYQ  H19   C19  C20   121.00  3.000
 HYQ  H19   C19  C16   119.39  3.000
 HYQ  C20   C19  C16   119.59  3.000
 HYQ  C17   C20  N23   121.01  3.000
 HYQ  C17   C20  C19   122.89  3.000
 HYQ  N23   C20  C19   116.10  3.000
 HYQ  O25   N23  O26   124.43  3.000
 HYQ  O25   N23  C20   117.55  3.000
 HYQ  O26   N23  C20   117.99  3.000
 HYQ  C15   C17  C21   118.41  3.000
 HYQ  C15   C17  C20   116.77  3.000
 HYQ  C21   C17  C20   124.77  3.000
 HYQ  H21   C21  C24   118.43  3.000
 HYQ  H21   C21  C17   120.90  3.000
 HYQ  C24   C21  C17   120.67  3.000
 HYQ  H24   C24  C22   119.71  3.000
 HYQ  H24   C24  C21   119.44  3.000
 HYQ  C22   C24  C21   120.85  3.000
 HYQ  H22   C22  C18   120.07  3.000
 HYQ  H22   C22  C24   120.03  3.000
 HYQ  C18   C22  C24   119.90  3.000
 HYQ  H18   C18  C15   119.69  3.000
 HYQ  H18   C18  C22   119.39  3.000
 HYQ  C15   C18  C22   120.92  3.000
 HYQ  C18   C15  C17   119.22  3.000
 HYQ  C18   C15  C14   121.55  3.000
 HYQ  C17   C15  C14   119.23  3.000
 HYQ  C2    C6   O13   128.34  3.000
 HYQ  C2    C6   N9    108.03  3.000
 HYQ  O13   C6   N9    123.64  3.000
 HYQ  H2    C2   C5    109.29  3.000
 HYQ  H2    C2   C6    107.38  3.000
 HYQ  C5    C2   C6    113.38  3.000
 HYQ  H2    C2   C1    111.47  3.000
 HYQ  C5    C2   C1    110.12  3.000
 HYQ  C6    C2   C1    105.17  3.000
 HYQ  H5    C5   C11   110.30  3.000
 HYQ  H5    C5   C12   110.22  3.000
 HYQ  C11   C5   C12   109.04  3.000
 HYQ  H5    C5   C2    109.55  3.000
 HYQ  C11   C5   C2    110.25  3.000
 HYQ  C12   C5   C2    107.44  3.000
 HYQ  H122  C12  H121  106.54  3.000
 HYQ  H122  C12  C8    110.75  3.000
 HYQ  H121  C12  C8    110.77  3.000
 HYQ  H122  C12  C5    108.95  3.000
 HYQ  H121  C12  C5    109.79  3.000
 HYQ  C8    C12  C5    109.97  3.000
 HYQ  H82   C8   H81   106.50  3.000
 HYQ  H82   C8   C3    109.03  3.000
 HYQ  H81   C8   C3    109.73  3.000
 HYQ  H82   C8   C12   110.78  3.000
 HYQ  H81   C8   C12   110.81  3.000
 HYQ  C3    C8   C12   109.92  3.000
 HYQ  H3    C3   C7    110.22  3.000
 HYQ  H3    C3   C8    110.27  3.000
 HYQ  C7    C3   C8    109.12  3.000
 HYQ  H3    C3   C1    109.54  3.000
 HYQ  C7    C3   C1    110.26  3.000
 HYQ  C8    C3   C1    107.38  3.000
 HYQ  H72   C7   H71   105.29  3.000
 HYQ  H72   C7   C11   111.51  3.000
 HYQ  H71   C7   C11   110.69  3.000
 HYQ  H72   C7   C3    110.44  3.000
 HYQ  H71   C7   C3    108.80  3.000
 HYQ  C11   C7   C3    110.00  3.000
 HYQ  H112  C11  H111  105.23  3.000
 HYQ  H112  C11  C7    110.70  3.000
 HYQ  H111  C11  C7    111.48  3.000
 HYQ  H112  C11  C5    108.81  3.000
 HYQ  H111  C11  C5    110.52  3.000
 HYQ  C7    C11  C5    109.99  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
 HYQ  CONST_01  C20  C19  C16  C14    0.00   0.0  0
 HYQ  CONST_02  C20  C17  C15  C14    0.00   0.0  0
 HYQ  CONST_03  C21  C17  C15  C14  180.00   0.0  0
 HYQ  CONST_04  C22  C18  C15  C14  180.00   0.0  0
 HYQ  CONST_05  C17  C15  C14  C16    0.00   0.0  0
 HYQ  CONST_06  C18  C15  C14  C16  180.00   0.0  0
 HYQ  CONST_07  C17  C20  C19  C16    0.00   0.0  0
 HYQ  CONST_08  C15  C14  C16  C19    0.00   0.0  0
 HYQ  CONST_09  C21  C17  C20  C19  180.00   0.0  0
 HYQ  CONST_10  C15  C17  C20  C19    0.00   0.0  0
 HYQ  CONST_11  C24  C21  C17  C20  180.00   0.0  0
 HYQ  CONST_12  C18  C15  C17  C20  180.00   0.0  0
 HYQ  CONST_13  C22  C24  C21  C17    0.00   0.0  0
 HYQ  CONST_14  C22  C18  C15  C17    0.00   0.0  0
 HYQ  CONST_15  C18  C15  C17  C21    0.00   0.0  0
 HYQ  CONST_16  C18  C22  C24  C21    0.00   0.0  0
 HYQ  CONST_17  C15  C17  C21  C24    0.00   0.0  0
 HYQ  CONST_18  C15  C18  C22  C24    0.00   0.0  0
 HYQ  CONST_19  C19  C16  C14  N9   180.00   0.0  0
 HYQ  CONST_20  C17  C15  C14  N9   180.00   0.0  0
 HYQ  CONST_21  C18  C15  C14  N9     0.00   0.0  0
 HYQ  CONST_22  C14  N9   C4   C1   180.00   0.0  0
 HYQ  CONST_23  C6   N9   C4   C1     0.00   0.0  0
 HYQ  CONST_24  N23  C20  C19  C16  180.00   0.0  0
 HYQ  CONST_25  C21  C17  C20  N23    0.00   0.0  0
 HYQ  CONST_26  C15  C17  C20  N23  180.00   0.0  0
 HYQ  CONST_27  C14  N9   C4   O10    0.00   0.0  0
 HYQ  CONST_28  C6   N9   C4   O10  180.00   0.0  0
 HYQ  CONST_29  H16  C16  C14  N9     0.00   0.0  0
 HYQ  CONST_30  H19  C19  C16  C14  180.00   0.0  0
 HYQ  CONST_31  H18  C18  C15  C14    0.00   0.0  0
 HYQ  CONST_32  H21  C21  C17  C20    0.00   0.0  0
 HYQ  CONST_33  H24  C24  C21  C17  180.00   0.0  0
 HYQ  CONST_34  H22  C22  C24  C21  180.00   0.0  0
 HYQ  Var_01    C16  C14  N9   C4    88.16  30.0  2
 HYQ  Var_02    C2   C6   N9   C4    -0.36  30.0  1
 HYQ  Var_03    C3   C8   C12  C5     0.27  30.0  1
 HYQ  Var_04    C3   C7   C11  C5     0.14  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
 HYQ  chir_01  C1  C4   C2   C3  positiv
 HYQ  chir_02  C2  C1   C6   C5  positiv
 HYQ  chir_03  C5  C11  C12  C2  positiv
 HYQ  chir_04  C3  C7   C8   C1  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
 HYQ  plan-1  N9   0.020
 HYQ  plan-1  C14  0.020
 HYQ  plan-1  C16  0.020
 HYQ  plan-1  C19  0.020
 HYQ  plan-1  C20  0.020
 HYQ  plan-1  N23  0.020
 HYQ  plan-1  C17  0.020
 HYQ  plan-1  C21  0.020
 HYQ  plan-1  C24  0.020
 HYQ  plan-1  C22  0.020
 HYQ  plan-1  C18  0.020
 HYQ  plan-1  C15  0.020
 HYQ  plan-1  H16  0.020
 HYQ  plan-1  H19  0.020
 HYQ  plan-1  H21  0.020
 HYQ  plan-1  H24  0.020
 HYQ  plan-1  H22  0.020
 HYQ  plan-1  H18  0.020
 HYQ  plan-2  C20  0.020
 HYQ  plan-2  N23  0.020
 HYQ  plan-2  O26  0.020
 HYQ  plan-2  O25  0.020
 HYQ  plan-3  N9   0.020
 HYQ  plan-3  C6   0.020
 HYQ  plan-3  O13  0.020
 HYQ  plan-3  C2   0.020
 HYQ  plan-4  C1   0.020
 HYQ  plan-4  C4   0.020
 HYQ  plan-4  O10  0.020
 HYQ  plan-4  N9   0.020
 HYQ  plan-4  C14  0.020
 HYQ  plan-4  C6   0.020

