# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 22:11:52 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: (2~{S})-2-azanyl-7-(naphthalen-1-ylmethoxy)-3,4-dihydro-1~{H}-naphthalene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1(CCc2ccc(OCc3cccc4ccccc34)cc2C1)C(O)=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
 HNX  HNX  '(2~{S})-2-azanyl-7-(naphthalen-1-ylmethoxy)-3,4-dihydro-1~{H}-naphthalene-2-carboxylic acid'  ligand  46  26  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HNX
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
 HNX  C10  C  CH2    0  -0.518  146.3620  141.2874  133.3968
 HNX  N12  N  NH2    0  -0.802  146.7584  141.1925  136.3672
 HNX  C13  C  CH2    0  -0.219  144.3208  135.2283  134.6389
 HNX  C15  C  CR66   0   0.115  143.5748  132.9776  135.4796
 HNX  C17  C  CR16   0  -0.324  144.0376  130.9449  134.1953
 HNX  C20  C  CR16   0  -0.344  143.0135  133.5731  136.6361
 HNX  C21  C  CR16   0  -0.244  142.3969  132.8131  137.5937
 HNX  C22  C  CR16   0  -0.260  142.3062  131.4154  137.4480
 HNX  C24  C  C      0   0.437  144.7435  142.5636  136.6750
 HNX  C01  C  C1     0  -0.444  144.8476  137.9899  134.5613
 HNX  C02  C  C      0   0.101  145.1733  139.3490  134.5120
 HNX  C03  C  C      0   0.042  145.9374  139.8422  133.4570
 HNX  C04  C  C1     0  -0.278  146.3489  138.9513  132.4631
 HNX  C05  C  C1     0  -0.356  146.0267  137.6100  132.5031
 HNX  C06  C  C      0   0.399  145.2704  137.1184  133.5683
 HNX  C07  C  CH2    0  -0.460  144.6545  140.2579  135.5966
 HNX  C08  C  CT     0  -0.074  145.4734  141.5337  135.7650
 HNX  C09  C  CH2    0  -0.431  145.6042  142.1804  134.3706
 HNX  C14  C  CR6    0   0.031  144.2258  133.7384  134.4640
 HNX  C16  C  CR66   0   0.110  143.4819  131.5676  135.3376
 HNX  C18  C  CR16   0  -0.240  144.6535  131.6952  133.2366
 HNX  C19  C  CR16   0  -0.339  144.7469  133.0963  133.3717
 HNX  C23  C  CR16   0  -0.308  142.8373  130.8097  136.3427
 HNX  O11  O  O2     0  -0.485  145.0039  135.7920  133.5486
 HNX  O25  O  O      0  -0.598  143.5017  142.6197  136.5799
 HNX  O26  O  OC    -1  -0.597  145.4670  143.2903  137.3846
 HNX  H1   H  HCH2   0   0.232  147.4371  141.3501  133.5985
 HNX  H2   H  HCH2   0   0.248  146.2410  141.6653  132.3783
 HNX  H3   H  HNH2   0   0.332  147.3346  140.6733  135.7154
 HNX  H4   H  HNH2   0   0.329  147.2528  142.0496  136.5779
 HNX  H6   H  HCH2   0   0.242  143.3136  135.6567  134.7261
 HNX  H7   H  HCH2   0   0.241  144.8429  135.4559  135.5775
 HNX  H10  H  HCR6   0   0.259  141.9760  133.2897  138.4695
 HNX  H11  H  HCR6   0   0.257  141.8165  130.8253  138.2116
 HNX  H12  H  H      0   0.267  144.2563  137.6407  135.3992
 HNX  H14  H  H      0   0.242  146.9420  139.3217  131.6341
 HNX  H15  H  H      0   0.252  146.3589  136.9379  131.7215
 HNX  H16  H  HCH2   0   0.230  144.6204  139.7124  136.5440
 HNX  H17  H  HCH2   0   0.243  143.6236  140.5322  135.3632
 HNX  H19  H  HCH2   0   0.225  146.1149  143.1444  134.4515
 HNX  H20  H  HCH2   0   0.217  144.6036  142.3855  133.9789
 HNX  H21  H  HCR6   0   0.256  145.0782  131.2209  132.3614
 HNX  H22  H  HCR6   0   0.254  145.2436  133.6574  132.5930
 HNX  H23  H  HCR6   0   0.255  142.7723  129.7348  136.2225
 HNX  H8   H  HCR6   0   0.254  143.9658  129.8686  134.0949
 HNX  H9   H  HCR6   0   0.256  143.0653  134.6446  136.7781

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
 HNX  C10  C03  single    1.508  0.020  1.508
 HNX  C10  C09  single    1.523  0.020  1.523
 HNX  N12  C08  single    1.459  0.020  1.459
 HNX  C13  C14  single    1.503  0.020  1.503
 HNX  C13  O11  single    1.405  0.020  1.405
 HNX  C15  C20  aromatic  1.417  0.020  1.417
 HNX  C15  C14  aromatic  1.426  0.020  1.426
 HNX  C15  C16  aromatic  1.420  0.020  1.420
 HNX  C17  C16  aromatic  1.415  0.020  1.415
 HNX  C17  C18  aromatic  1.364  0.020  1.364
 HNX  C20  C21  aromatic  1.369  0.020  1.369
 HNX  C21  C22  aromatic  1.408  0.020  1.408
 HNX  C22  C23  aromatic  1.368  0.020  1.368
 HNX  C24  C08  single    1.556  0.020  1.556
 HNX  C24  O25  deloc     1.247  0.020  1.247
 HNX  C24  O26  deloc     1.247  0.020  1.247
 HNX  C01  C02  aromatic  1.398  0.020  1.398
 HNX  C01  C06  aromatic  1.387  0.020  1.387
 HNX  C02  C03  aromatic  1.393  0.020  1.393
 HNX  C03  C04  aromatic  1.397  0.020  1.397
 HNX  C04  C05  aromatic  1.380  0.020  1.380
 HNX  C05  C06  aromatic  1.396  0.020  1.396
 HNX  C06  O11  single    1.353  0.020  1.353
 HNX  C07  C08  single    1.525  0.020  1.525
 HNX  C08  C09  single    1.543  0.020  1.543
 HNX  C14  C19  aromatic  1.370  0.020  1.370
 HNX  C16  C23  aromatic  1.414  0.020  1.414
 HNX  C18  C19  aromatic  1.411  0.020  1.411
 HNX  C10  H1   single    0.970  0.020  1.090
 HNX  C10  H2   single    0.970  0.020  1.090
 HNX  N12  H3   single    0.890  0.020  1.040
 HNX  N12  H4   single    0.890  0.020  1.040
 HNX  C13  H6   single    0.970  0.020  1.090
 HNX  C13  H7   single    0.970  0.020  1.090
 HNX  C17  H8   single    0.930  0.020  1.080
 HNX  C20  H9   single    0.930  0.020  1.080
 HNX  C21  H10  single    0.930  0.020  1.080
 HNX  C22  H11  single    0.930  0.020  1.080
 HNX  C01  H12  single    0.930  0.020  1.080
 HNX  C04  H14  single    0.930  0.020  1.080
 HNX  C05  H15  single    0.930  0.020  1.080
 HNX  C07  H16  single    0.970  0.020  1.090
 HNX  C07  H17  single    0.970  0.020  1.090
 HNX  C09  H19  single    0.970  0.020  1.090
 HNX  C09  H20  single    0.970  0.020  1.090
 HNX  C18  H21  single    0.930  0.020  1.080
 HNX  C19  H22  single    0.930  0.020  1.080
 HNX  C23  H23  single    0.930  0.020  1.080
 HNX  C02  C07  single    1.507  0.020  1.507

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
 HNX  H2   C10  H1   105.09  3.000
 HNX  H2   C10  C09  109.75  3.000
 HNX  H1   C10  C09  109.69  3.000
 HNX  H2   C10  C03  109.72  3.000
 HNX  H1   C10  C03  108.90  3.000
 HNX  C09  C10  C03  113.35  3.000
 HNX  H4   N12  H3   106.87  3.000
 HNX  H4   N12  C08  108.55  3.000
 HNX  H3   N12  C08  110.80  3.000
 HNX  H7   C13  H6   106.70  3.000
 HNX  H7   C13  O11  110.44  3.000
 HNX  H6   C13  O11  110.56  3.000
 HNX  H7   C13  C14  109.57  3.000
 HNX  H6   C13  C14  109.76  3.000
 HNX  O11  C13  C14  109.77  3.000
 HNX  C16  C15  C14  119.23  3.000
 HNX  C16  C15  C20  118.23  3.000
 HNX  C14  C15  C20  122.54  3.000
 HNX  H8   C17  C18  120.74  3.000
 HNX  H8   C17  C16  119.08  3.000
 HNX  C18  C17  C16  120.17  3.000
 HNX  H9   C20  C21  118.64  3.000
 HNX  H9   C20  C15  120.29  3.000
 HNX  C21  C20  C15  121.07  3.000
 HNX  H10  C21  C22  119.72  3.000
 HNX  H10  C21  C20  119.79  3.000
 HNX  C22  C21  C20  120.50  3.000
 HNX  H11  C22  C23  120.29  3.000
 HNX  H11  C22  C21  119.82  3.000
 HNX  C23  C22  C21  119.88  3.000
 HNX  O26  C24  O25  126.52  3.000
 HNX  O26  C24  C08  116.51  3.000
 HNX  O25  C24  C08  116.90  3.000
 HNX  H12  C01  C06  121.16  3.000
 HNX  H12  C01  C02  117.88  3.000
 HNX  C06  C01  C02  120.96  3.000
 HNX  C07  C02  C03  121.36  3.000
 HNX  C07  C02  C01  118.72  3.000
 HNX  C03  C02  C01  119.90  3.000
 HNX  C04  C03  C02  118.34  3.000
 HNX  C04  C03  C10  120.01  3.000
 HNX  C02  C03  C10  121.61  3.000
 HNX  H14  C04  C05  118.80  3.000
 HNX  H14  C04  C03  119.16  3.000
 HNX  C05  C04  C03  122.04  3.000
 HNX  H15  C05  C06  119.89  3.000
 HNX  H15  C05  C04  120.71  3.000
 HNX  C06  C05  C04  119.40  3.000
 HNX  O11  C06  C05  116.16  3.000
 HNX  O11  C06  C01  124.49  3.000
 HNX  C05  C06  C01  119.35  3.000
 HNX  H17  C07  H16  106.32  3.000
 HNX  H17  C07  C08  108.68  3.000
 HNX  H16  C07  C08  109.77  3.000
 HNX  H17  C07  C02  108.82  3.000
 HNX  H16  C07  C02  109.48  3.000
 HNX  C08  C07  C02  113.52  3.000
 HNX  C09  C08  C07  107.24  3.000
 HNX  C09  C08  C24  106.91  3.000
 HNX  C07  C08  C24  111.49  3.000
 HNX  C09  C08  N12  113.35  3.000
 HNX  C07  C08  N12  108.83  3.000
 HNX  C24  C08  N12  109.05  3.000
 HNX  H20  C09  H19  106.76  3.000
 HNX  H20  C09  C08  108.94  3.000
 HNX  H19  C09  C08  110.01  3.000
 HNX  H20  C09  C10  109.64  3.000
 HNX  H19  C09  C10  109.37  3.000
 HNX  C08  C09  C10  111.98  3.000
 HNX  C19  C14  C15  119.43  3.000
 HNX  C19  C14  C13  122.23  3.000
 HNX  C15  C14  C13  118.34  3.000
 HNX  C23  C16  C17  121.13  3.000
 HNX  C23  C16  C15  119.39  3.000
 HNX  C17  C16  C15  119.48  3.000
 HNX  H21  C18  C19  119.13  3.000
 HNX  H21  C18  C17  120.29  3.000
 HNX  C19  C18  C17  120.58  3.000
 HNX  H22  C19  C18  118.49  3.000
 HNX  H22  C19  C14  120.40  3.000
 HNX  C18  C19  C14  121.11  3.000
 HNX  H23  C23  C16  118.70  3.000
 HNX  H23  C23  C22  120.38  3.000
 HNX  C16  C23  C22  120.93  3.000
 HNX  C06  O11  C13  118.55  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
 HNX  CONST_01  C22  C21  C20  C15     0.00   0.0  0
 HNX  CONST_02  C18  C19  C14  C15     0.00   0.0  0
 HNX  CONST_03  C18  C17  C16  C15     0.00   0.0  0
 HNX  CONST_04  C22  C23  C16  C15     0.00   0.0  0
 HNX  CONST_05  C20  C15  C16  C17   180.00   0.0  0
 HNX  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 HNX  CONST_07  C22  C23  C16  C17   180.00   0.0  0
 HNX  CONST_08  C14  C19  C18  C17     0.00   0.0  0
 HNX  CONST_09  C19  C14  C15  C20   180.00   0.0  0
 HNX  CONST_10  C23  C16  C15  C20     0.00   0.0  0
 HNX  CONST_11  C23  C22  C21  C20     0.00   0.0  0
 HNX  CONST_12  C14  C15  C20  C21   180.00   0.0  0
 HNX  CONST_13  C16  C15  C20  C21     0.00   0.0  0
 HNX  CONST_14  C16  C23  C22  C21     0.00   0.0  0
 HNX  CONST_15  C04  C03  C02  C01     0.00   0.0  0
 HNX  CONST_16  C04  C05  C06  C01     0.00   0.0  0
 HNX  CONST_17  C05  C06  C01  C02     0.00   0.0  0
 HNX  CONST_18  C05  C04  C03  C02     0.00   0.0  0
 HNX  CONST_19  C06  C01  C02  C03     0.00   0.0  0
 HNX  CONST_20  C06  C05  C04  C03     0.00   0.0  0
 HNX  CONST_21  C23  C16  C15  C14   180.00   0.0  0
 HNX  CONST_22  C19  C14  C15  C16     0.00   0.0  0
 HNX  CONST_23  C19  C18  C17  C16     0.00   0.0  0
 HNX  CONST_24  C23  C16  C17  C18   180.00   0.0  0
 HNX  CONST_25  C20  C15  C14  C13     0.00   0.0  0
 HNX  CONST_26  C16  C15  C14  C13   180.00   0.0  0
 HNX  CONST_27  C18  C19  C14  C13   180.00   0.0  0
 HNX  CONST_28  O11  C06  C01  C02   180.00   0.0  0
 HNX  CONST_29  O11  C06  C05  C04   180.00   0.0  0
 HNX  CONST_30  H14  C04  C03  C10     0.00   0.0  0
 HNX  CONST_31  H10  C21  C20  C15   180.00   0.0  0
 HNX  CONST_32  H22  C19  C14  C15   180.00   0.0  0
 HNX  CONST_33  H8   C17  C16  C15   180.00   0.0  0
 HNX  CONST_34  H23  C23  C16  C15   180.00   0.0  0
 HNX  CONST_35  H11  C22  C21  C20   180.00   0.0  0
 HNX  CONST_36  H9   C20  C21  C22   180.00   0.0  0
 HNX  CONST_37  H15  C05  C06  C01   180.00   0.0  0
 HNX  CONST_38  H12  C01  C02  C03   180.00   0.0  0
 HNX  CONST_39  H21  C18  C19  C14   180.00   0.0  0
 HNX  Var_01    C08  C07  C02  C01   157.38  30.0  1
 HNX  Var_02    C09  C10  C03  C02   -14.37  30.0  1
 HNX  Var_03    C08  C09  C10  C03    44.21  30.0  1
 HNX  Var_04    C01  C06  O11  C13    -3.93  30.0  2
 HNX  Var_05    O11  C13  C14  C15   179.38  30.0  2
 HNX  Var_06    C14  C13  O11  C06  -175.57  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
 HNX  chir_01  C08  C24  C07  C09  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
 HNX  plan-1  C13  0.020
 HNX  plan-1  C15  0.020
 HNX  plan-1  C17  0.020
 HNX  plan-1  C20  0.020
 HNX  plan-1  C21  0.020
 HNX  plan-1  C22  0.020
 HNX  plan-1  C14  0.020
 HNX  plan-1  C16  0.020
 HNX  plan-1  C18  0.020
 HNX  plan-1  C19  0.020
 HNX  plan-1  C23  0.020
 HNX  plan-1  H10  0.020
 HNX  plan-1  H11  0.020
 HNX  plan-1  H21  0.020
 HNX  plan-1  H22  0.020
 HNX  plan-1  H23  0.020
 HNX  plan-1  H8   0.020
 HNX  plan-1  H9   0.020
 HNX  plan-2  C10  0.020
 HNX  plan-2  C01  0.020
 HNX  plan-2  C02  0.020
 HNX  plan-2  C03  0.020
 HNX  plan-2  C04  0.020
 HNX  plan-2  C05  0.020
 HNX  plan-2  C06  0.020
 HNX  plan-2  C07  0.020
 HNX  plan-2  O11  0.020
 HNX  plan-2  H12  0.020
 HNX  plan-2  H14  0.020
 HNX  plan-2  H15  0.020
 HNX  plan-3  C24  0.020
 HNX  plan-3  C08  0.020
 HNX  plan-3  O25  0.020
 HNX  plan-3  O26  0.020

