# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:11:52 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N-[(1S,2S,3S,4R)-3-hydroxy-1,2,3,4-tetrahydro-1,4-epoxynaphthalen-2-yl]cyclobutanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](NC(=O)C2CCC2)[C@H]3O[C@@H]1c4ccccc34
#
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
 JK7  JK7  N-[(1S,2S,3S,4R)-3-hydroxy-1,2,3,4-tetrahydro-1,4-epoxynaphthalen-2-yl]cyclobutanecarboxamide  ligand  36  19  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JK7
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
 JK7  C10   C  C     0  -0.430   3.9197   0.9618  -0.6515
 JK7  C13   C  CH1   0  -0.162  -2.4996  -1.0968   0.2570
 JK7  C15   C  CR16  0  -0.340  -2.5485   1.5385   0.6033
 JK7  C17   C  CR16  0  -0.256  -0.9349   2.6807  -0.8002
 JK7  O01   O  OH1   0  -0.665  -1.6386  -3.0492   1.4728
 JK7  C02   C  CH1   0   0.062  -1.3543  -1.7329   1.0820
 JK7  C03   C  CH1   0  -0.087  -0.2199  -1.7502   0.0295
 JK7  N04   N  NH1   0  -0.653   0.9348  -1.0098   0.4684
 JK7  C05   C  C     0   0.554   1.9883  -0.7595  -0.3285
 JK7  O06   O  O     0  -0.496   2.0673  -1.1989  -1.4680
 JK7  C07   C  C     0  -0.374   3.0634   0.0947   0.2851
 JK7  C08   C  C     0  -0.456   2.6792   1.3745   1.0621
 JK7  C09   C  C     0  -0.455   3.9110   2.0538   0.4356
 JK7  C11   C  CH1   0  -0.093  -0.9455  -1.1471  -1.2129
 JK7  O12   O  O2    0  -0.477  -2.2611  -1.6570  -1.0314
 JK7  C14   C  CR6   0   0.129  -2.1424   0.3509   0.0335
 JK7  C16   C  CR16  0  -0.257  -1.9367   2.7138   0.1624
 JK7  C18   C  CR16  0  -0.333  -0.5116   1.4706  -1.3532
 JK7  C19   C  CR6   0   0.142  -1.1394   0.3194  -0.9311
 JK7  H101  H  H     0   0.237   4.8821   0.5643  -0.9709
 JK7  H102  H  H     0   0.230   3.3587   1.2700  -1.5352
 JK7  H131  H  HCH1  0   0.270  -3.5057  -1.3132   0.6162
 JK7  H171  H  HCR6  0   0.258  -0.4777   3.6065  -1.1248
 JK7  H011  H  HOH1  0   0.458  -2.2874  -3.0182   2.1834
 JK7  H021  H  HCH1  0   0.240  -1.1004  -1.1092   1.9480
 JK7  H031  H  HCH1  0   0.284   0.0533  -2.7865  -0.1888
 JK7  H041  H  HNH1  0   0.407   0.9130  -0.5862   1.3819
 JK7  H071  H  H     0   0.286   3.7014  -0.5418   0.9071
 JK7  H082  H  H     0   0.236   1.7480   1.8063   0.6882
 JK7  H081  H  H     0   0.243   2.6244   1.3111   2.1489
 JK7  H092  H  H     0   0.231   4.7822   1.9823   1.0877
 JK7  H091  H  H     0   0.235   3.8029   3.0882   0.1110
 JK7  H111  H  HCH1  0   0.262  -0.5384  -1.4343  -2.1778
 JK7  H161  H  HCR6  0   0.257  -2.2467   3.6651   0.5750
 JK7  H181  H  HCR6  0   0.255   0.2809   1.4455  -2.0907
 JK7  H151  H  HCR6  0   0.256  -3.3182   1.5689   1.3643

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
 JK7  C10  C07   single    1.537  0.020  1.537
 JK7  C10  C09   single    1.541  0.020  1.541
 JK7  O06  C05   double    1.224  0.020  1.224
 JK7  C07  C05   single    1.504  0.020  1.504
 JK7  C07  C08   single    1.546  0.020  1.546
 JK7  C05  N04   single    1.344  0.020  1.344
 JK7  C09  C08   single    1.540  0.020  1.540
 JK7  N04  C03   single    1.440  0.020  1.440
 JK7  C03  C11   single    1.560  0.020  1.560
 JK7  C03  C02   single    1.548  0.020  1.548
 JK7  C11  O12   single    1.423  0.020  1.423
 JK7  C11  C19   single    1.506  0.020  1.506
 JK7  O12  C13   single    1.425  0.020  1.425
 JK7  C18  C19   aromatic  1.377  0.020  1.377
 JK7  C18  C17   aromatic  1.396  0.020  1.396
 JK7  O01  C02   single    1.402  0.020  1.402
 JK7  C19  C14   aromatic  1.392  0.020  1.392
 JK7  C02  C13   single    1.548  0.020  1.548
 JK7  C13  C14   single    1.508  0.020  1.508
 JK7  C17  C16   aromatic  1.390  0.020  1.390
 JK7  C14  C15   aromatic  1.378  0.020  1.378
 JK7  C16  C15   aromatic  1.396  0.020  1.396
 JK7  C10  H101  single    0.970  0.020  1.090
 JK7  C10  H102  single    0.970  0.020  1.090
 JK7  C13  H131  single    0.970  0.020  1.090
 JK7  C15  H151  single    0.930  0.020  1.080
 JK7  C17  H171  single    0.930  0.020  1.080
 JK7  O01  H011  single    0.850  0.020  0.980
 JK7  C02  H021  single    0.970  0.020  1.090
 JK7  C03  H031  single    0.970  0.020  1.090
 JK7  N04  H041  single    0.860  0.020  1.020
 JK7  C07  H071  single    0.970  0.020  1.090
 JK7  C08  H082  single    0.970  0.020  1.090
 JK7  C08  H081  single    0.970  0.020  1.090
 JK7  C09  H092  single    0.970  0.020  1.090
 JK7  C09  H091  single    0.970  0.020  1.090
 JK7  C11  H111  single    0.970  0.020  1.090
 JK7  C16  H161  single    0.930  0.020  1.080
 JK7  C18  H181  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
 JK7  H102  C10  H101  108.65  3.000
 JK7  H102  C10  C09   111.61  3.000
 JK7  H101  C10  C09   118.06  3.000
 JK7  H102  C10  C07   111.50  3.000
 JK7  H101  C10  C07   117.72  3.000
 JK7  C09   C10  C07    88.10  3.000
 JK7  H131  C13  C14   117.27  3.000
 JK7  H131  C13  O12   111.99  3.000
 JK7  C14   C13  O12   101.76  3.000
 JK7  H131  C13  C02   115.19  3.000
 JK7  C14   C13  C02   107.35  3.000
 JK7  O12   C13  C02   101.33  3.000
 JK7  H151  C15  C16   120.64  3.000
 JK7  H151  C15  C14   121.61  3.000
 JK7  C16   C15  C14   117.74  3.000
 JK7  H171  C17  C18   119.64  3.000
 JK7  H171  C17  C16   119.46  3.000
 JK7  C18   C17  C16   120.90  3.000
 JK7  H011  O01  C02   108.19  3.000
 JK7  H021  C02  C03   111.93  3.000
 JK7  H021  C02  O01   111.14  3.000
 JK7  C03   C02  O01   109.13  3.000
 JK7  H021  C02  C13   110.99  3.000
 JK7  O01   C02  C13   112.60  3.000
 JK7  C03   C02  C13   100.63  3.000
 JK7  H031  C03  C11   108.87  3.000
 JK7  H031  C03  N04   110.34  3.000
 JK7  C11   C03  N04   114.63  3.000
 JK7  H031  C03  C02   109.24  3.000
 JK7  C11   C03  C02   101.33  3.000
 JK7  N04   C03  C02   112.01  3.000
 JK7  H041  N04  C05   118.44  3.000
 JK7  H041  N04  C03   118.37  3.000
 JK7  C05   N04  C03   122.91  3.000
 JK7  C07   C05  O06   122.52  3.000
 JK7  C07   C05  N04   115.09  3.000
 JK7  O06   C05  N04   122.39  3.000
 JK7  H071  C07  C08   109.91  3.000
 JK7  H071  C07  C05   108.55  3.000
 JK7  C08   C07  C05   119.84  3.000
 JK7  H071  C07  C10   110.46  3.000
 JK7  C08   C07  C10    88.72  3.000
 JK7  C05   C07  C10   118.04  3.000
 JK7  H081  C08  H082  108.75  3.000
 JK7  H081  C08  C09   118.13  3.000
 JK7  H082  C08  C09   111.61  3.000
 JK7  H081  C08  C07   117.74  3.000
 JK7  H082  C08  C07   111.54  3.000
 JK7  C09   C08  C07    87.82  3.000
 JK7  H091  C09  H092  108.65  3.000
 JK7  H091  C09  C08   117.43  3.000
 JK7  H092  C09  C08   111.52  3.000
 JK7  H091  C09  C10   117.59  3.000
 JK7  H092  C09  C10   111.77  3.000
 JK7  C08   C09  C10    88.79  3.000
 JK7  H111  C11  C19   118.17  3.000
 JK7  H111  C11  O12   111.43  3.000
 JK7  C19   C11  O12   101.90  3.000
 JK7  H111  C11  C03   115.53  3.000
 JK7  C19   C11  C03   106.70  3.000
 JK7  O12   C11  C03   100.95  3.000
 JK7  C11   O12  C13    97.43  3.000
 JK7  C19   C14  C15   121.22  3.000
 JK7  C15   C14  C13   134.12  3.000
 JK7  C19   C14  C13   104.58  3.000
 JK7  H161  C16  C17   119.44  3.000
 JK7  H161  C16  C15   119.60  3.000
 JK7  C17   C16  C15   120.96  3.000
 JK7  H181  C18  C19   121.52  3.000
 JK7  H181  C18  C17   120.78  3.000
 JK7  C19   C18  C17   117.70  3.000
 JK7  C18   C19  C14   121.46  3.000
 JK7  C14   C19  C11   104.15  3.000
 JK7  C18   C19  C11   134.25  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
 JK7  CONST_01  C18   C19  C14  C15    0.00   0.0  0
 JK7  CONST_02  C18   C17  C16  C15    0.00   0.0  0
 JK7  CONST_03  C14   C19  C18  C17    0.00   0.0  0
 JK7  CONST_04  C14   C15  C16  C17    0.00   0.0  0
 JK7  CONST_05  C19   C18  C17  C16    0.00   0.0  0
 JK7  CONST_06  C19   C14  C15  C16    0.00   0.0  0
 JK7  CONST_07  H151  C15  C14  C13    0.00   0.0  0
 JK7  CONST_08  H171  C17  C16  C15  180.00   0.0  0
 JK7  CONST_09  H181  C18  C19  C11    0.00   0.0  0
 JK7  CONST_10  H161  C16  C15  C14  180.00   0.0  0
 JK7  CONST_11  C07   C05  N04  C03  180.00   0.0  0
 JK7  CONST_12  O06   C05  N04  C03    0.00   0.0  0
 JK7  CONST_13  H041  N04  C05  C07    0.00   0.0  0
 JK7  Var_01    C07   C08  C09  C10   19.18  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
 JK7  chir_01  C13  O12  C02  C14  negativ
 JK7  chir_02  C02  O01  C13  C03  positiv
 JK7  chir_03  C03  N04  C11  C02  positiv
 JK7  chir_04  C07  C08  C05  C10  negativ
 JK7  chir_05  C11  O12  C03  C19  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
 JK7  plan-1  C03   0.020
 JK7  plan-1  N04   0.020
 JK7  plan-1  C05   0.020
 JK7  plan-1  O06   0.020
 JK7  plan-1  C07   0.020
 JK7  plan-1  H041  0.020
 JK7  plan-2  C13   0.020
 JK7  plan-2  C15   0.020
 JK7  plan-2  C17   0.020
 JK7  plan-2  C11   0.020
 JK7  plan-2  C14   0.020
 JK7  plan-2  C16   0.020
 JK7  plan-2  C18   0.020
 JK7  plan-2  C19   0.020
 JK7  plan-2  H171  0.020
 JK7  plan-2  H161  0.020
 JK7  plan-2  H181  0.020
 JK7  plan-2  H151  0.020

