# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 15:16:55 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-({[(1R)-6-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2[C@@H](CCCc2c1)CNc3cnccc3C(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
 9FJ  9FJ  '3-({[(1R)-6-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid'  ligand  42  23  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9FJ
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
 9FJ  O9   O  O      0  -0.598  -3.3797  -1.7752  -1.2189
 9FJ  C7   C  C      0   0.442  -4.3604  -1.0813  -0.8512
 9FJ  O8   O  OC    -1  -0.574  -5.5553  -1.3685  -1.0231
 9FJ  C6   C  CR6    0  -0.134  -4.0597   0.2268  -0.1351
 9FJ  C5   C  CR16   0  -0.343  -5.1089   1.0364   0.2739
 9FJ  C4   C  CR16   0  -0.123  -4.8718   2.2366   0.9241
 9FJ  N3   N  N      0  -0.386  -3.6410   2.6658   1.1828
 9FJ  C2   C  CR16   0  -0.194  -2.6196   1.9170   0.8068
 9FJ  C1   C  CR6    0   0.297  -2.7446   0.6767   0.1439
 9FJ  N10  N  NH1    0  -0.716  -1.6589  -0.0470  -0.2056
 9FJ  C11  C  CH2    0  -0.244  -0.2978   0.3497   0.0260
 9FJ  C12  C  CH1    0  -0.344   0.6585  -0.7680  -0.3999
 9FJ  C17  C  CR6    0   0.092   2.1023  -0.3145  -0.2730
 9FJ  C18  C  CR16   0  -0.293   2.5125   0.8700  -0.8796
 9FJ  C19  C  CR16   0  -0.386   3.8145   1.3426  -0.7995
 9FJ  C20  C  CR6    0   0.379   4.7609   0.6040  -0.0945
 9FJ  O22  O  O2     0  -0.475   6.0525   0.9623   0.0576
 9FJ  C23  C  CH3    0  -0.436   6.4877   2.1714  -0.5293
 9FJ  C21  C  CR16   0  -0.398   4.3769  -0.5997   0.4884
 9FJ  C16  C  CR6    0   0.073   3.0710  -1.0673   0.4042
 9FJ  C15  C  CH2    0  -0.503   2.7344  -2.3999   1.0205
 9FJ  C14  C  CH2    0  -0.446   1.5194  -3.0276   0.3588
 9FJ  C13  C  CH2    0  -0.433   0.3617  -2.0457   0.3921
 9FJ  H2   H  HCR6   0   0.250  -6.1254   0.7222   0.0801
 9FJ  H3   H  HCR6   0   0.241  -5.6930   2.8689   1.2423
 9FJ  H4   H  HCR6   0   0.256  -1.6336   2.3076   1.0345
 9FJ  H5   H  HNH1   0   0.405  -1.8889  -0.8973  -0.7138
 9FJ  H6   H  HCH2   0   0.232  -0.0663   1.2761  -0.5128
 9FJ  H7   H  HCH2   0   0.221  -0.1269   0.5624   1.0896
 9FJ  H8   H  HCH1   0   0.249   0.4735  -0.9739  -1.4627
 9FJ  H9   H  HCR6   0   0.251   1.8011   1.4549  -1.4507
 9FJ  H10  H  HCR6   0   0.273   4.0663   2.2721  -1.2915
 9FJ  H11  H  HCH3   0   0.226   6.3785   2.1625  -1.6171
 9FJ  H12  H  HCH3   0   0.226   5.9509   3.0366  -0.1311
 9FJ  H13  H  HCH3   0   0.258   7.5426   2.2722  -0.2865
 9FJ  H14  H  HCR6   0   0.249   5.1204  -1.1897   1.0134
 9FJ  H15  H  HCH2   0   0.247   3.6013  -3.0609   0.9531
 9FJ  H16  H  HCH2   0   0.242   2.5354  -2.2704   2.0899
 9FJ  H17  H  HCH2   0   0.222   1.7556  -3.3002  -0.6745
 9FJ  H18  H  HCH2   0   0.237   1.2461  -3.9508   0.8732
 9FJ  H19  H  HCH2   0   0.220   0.1533  -1.7842   1.4358
 9FJ  H20  H  HCH2   0   0.237  -0.5455  -2.5163   0.0087

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
 9FJ  C23  O22  single    1.413  0.020  1.413
 9FJ  C19  C18  aromatic  1.387  0.020  1.387
 9FJ  C19  C20  aromatic  1.392  0.020  1.392
 9FJ  C18  C17  aromatic  1.393  0.020  1.393
 9FJ  O22  C20  single    1.349  0.020  1.349
 9FJ  C20  C21  aromatic  1.391  0.020  1.391
 9FJ  C17  C12  single    1.519  0.020  1.519
 9FJ  C17  C16  aromatic  1.401  0.020  1.401
 9FJ  C12  C11  single    1.531  0.020  1.531
 9FJ  C12  C13  single    1.532  0.020  1.532
 9FJ  C21  C16  aromatic  1.390  0.020  1.390
 9FJ  C11  N10  single    1.437  0.020  1.437
 9FJ  C16  C15  single    1.506  0.020  1.506
 9FJ  N10  C1   single    1.351  0.020  1.351
 9FJ  C14  C13  single    1.518  0.020  1.518
 9FJ  C14  C15  single    1.519  0.020  1.519
 9FJ  C1   C2   aromatic  1.412  0.020  1.412
 9FJ  C1   C6   aromatic  1.418  0.020  1.418
 9FJ  C2   N3   aromatic  1.321  0.020  1.321
 9FJ  N3   C4   aromatic  1.329  0.020  1.329
 9FJ  C6   C7   single    1.521  0.020  1.521
 9FJ  C6   C5   aromatic  1.387  0.020  1.387
 9FJ  C7   O9   deloc     1.256  0.020  1.256
 9FJ  C7   O8   deloc     1.241  0.020  1.241
 9FJ  C4   C5   aromatic  1.385  0.020  1.385
 9FJ  C5   H2   single    0.930  0.020  1.080
 9FJ  C4   H3   single    0.930  0.020  1.080
 9FJ  C2   H4   single    0.930  0.020  1.080
 9FJ  N10  H5   single    0.860  0.020  1.020
 9FJ  C11  H6   single    0.970  0.020  1.090
 9FJ  C11  H7   single    0.970  0.020  1.090
 9FJ  C12  H8   single    0.970  0.020  1.090
 9FJ  C18  H9   single    0.930  0.020  1.080
 9FJ  C19  H10  single    0.930  0.020  1.080
 9FJ  C23  H11  single    0.970  0.020  1.090
 9FJ  C23  H12  single    0.970  0.020  1.090
 9FJ  C23  H13  single    0.970  0.020  1.090
 9FJ  C21  H14  single    0.930  0.020  1.080
 9FJ  C15  H15  single    0.970  0.020  1.090
 9FJ  C15  H16  single    0.970  0.020  1.090
 9FJ  C14  H17  single    0.970  0.020  1.090
 9FJ  C14  H18  single    0.970  0.020  1.090
 9FJ  C13  H19  single    0.970  0.020  1.090
 9FJ  C13  H20  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
 9FJ  C6   C7   O8   117.04  3.000
 9FJ  O8   C7   O9   125.68  3.000
 9FJ  C6   C7   O9   117.28  3.000
 9FJ  C1   C6   C5   117.29  3.000
 9FJ  C5   C6   C7   119.42  3.000
 9FJ  C1   C6   C7   123.29  3.000
 9FJ  H2   C5   C4   119.78  3.000
 9FJ  H2   C5   C6   119.25  3.000
 9FJ  C4   C5   C6   120.97  3.000
 9FJ  H3   C4   N3   117.13  3.000
 9FJ  H3   C4   C5   120.88  3.000
 9FJ  N3   C4   C5   121.98  3.000
 9FJ  C2   N3   C4   118.53  3.000
 9FJ  H4   C2   C1   119.69  3.000
 9FJ  H4   C2   N3   116.04  3.000
 9FJ  C1   C2   N3   124.27  3.000
 9FJ  N10  C1   C2   121.40  3.000
 9FJ  C2   C1   C6   116.95  3.000
 9FJ  N10  C1   C6   121.65  3.000
 9FJ  H5   N10  C11  121.72  3.000
 9FJ  H5   N10  C1   113.30  3.000
 9FJ  C11  N10  C1   124.88  3.000
 9FJ  H7   C11  H6   106.23  3.000
 9FJ  H7   C11  C12  108.28  3.000
 9FJ  H6   C11  C12  110.37  3.000
 9FJ  H7   C11  N10  110.92  3.000
 9FJ  H6   C11  N10  110.74  3.000
 9FJ  C12  C11  N10  110.20  3.000
 9FJ  H8   C12  C13  108.13  3.000
 9FJ  H8   C12  C17  107.27  3.000
 9FJ  C13  C12  C17  112.95  3.000
 9FJ  H8   C12  C11  107.51  3.000
 9FJ  C13  C12  C11  110.11  3.000
 9FJ  C17  C12  C11  110.64  3.000
 9FJ  C16  C17  C18  117.63  3.000
 9FJ  C16  C17  C12  122.49  3.000
 9FJ  C18  C17  C12  119.84  3.000
 9FJ  H9   C18  C19  117.56  3.000
 9FJ  H9   C18  C17  119.69  3.000
 9FJ  C19  C18  C17  122.75  3.000
 9FJ  H10  C19  C20  121.88  3.000
 9FJ  H10  C19  C18  119.01  3.000
 9FJ  C20  C19  C18  119.11  3.000
 9FJ  C21  C20  O22  116.53  3.000
 9FJ  C21  C20  C19  118.91  3.000
 9FJ  O22  C20  C19  124.55  3.000
 9FJ  C23  O22  C20  118.38  3.000
 9FJ  H13  C23  H12  108.77  3.000
 9FJ  H13  C23  H11  108.65  3.000
 9FJ  H12  C23  H11  108.65  3.000
 9FJ  H13  C23  O22  106.58  3.000
 9FJ  H12  C23  O22  112.01  3.000
 9FJ  H11  C23  O22  112.06  3.000
 9FJ  H14  C21  C16  119.37  3.000
 9FJ  H14  C21  C20  118.96  3.000
 9FJ  C16  C21  C20  121.67  3.000
 9FJ  C15  C16  C21  118.87  3.000
 9FJ  C15  C16  C17  121.23  3.000
 9FJ  C21  C16  C17  119.88  3.000
 9FJ  H16  C15  H15  106.02  3.000
 9FJ  H16  C15  C14  109.19  3.000
 9FJ  H15  C15  C14  110.97  3.000
 9FJ  H16  C15  C16  109.60  3.000
 9FJ  H15  C15  C16  109.44  3.000
 9FJ  C14  C15  C16  111.47  3.000
 9FJ  H18  C14  H17  106.76  3.000
 9FJ  H18  C14  C13  110.22  3.000
 9FJ  H17  C14  C13  110.26  3.000
 9FJ  H18  C14  C15  110.15  3.000
 9FJ  H17  C14  C15  109.97  3.000
 9FJ  C13  C14  C15  109.45  3.000
 9FJ  H20  C13  H19  106.22  3.000
 9FJ  H20  C13  C14  110.32  3.000
 9FJ  H19  C13  C14  108.67  3.000
 9FJ  H20  C13  C12  109.81  3.000
 9FJ  H19  C13  C12  109.28  3.000
 9FJ  C14  C13  C12  112.34  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
 9FJ  CONST_01  N3   C2   C1   C6     0.00   0.0  0
 9FJ  CONST_02  N3   C4   C5   C6     0.00   0.0  0
 9FJ  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 9FJ  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 9FJ  CONST_05  C1   C2   N3   C4     0.00   0.0  0
 9FJ  CONST_06  C1   C6   C5   C4     0.00   0.0  0
 9FJ  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 9FJ  CONST_08  C20  C21  C16  C17    0.00   0.0  0
 9FJ  CONST_09  C21  C20  C19  C18    0.00   0.0  0
 9FJ  CONST_10  C21  C16  C17  C18    0.00   0.0  0
 9FJ  CONST_11  C16  C17  C18  C19    0.00   0.0  0
 9FJ  CONST_12  C16  C21  C20  C19    0.00   0.0  0
 9FJ  CONST_13  C2   C1   C6   C7   180.00   0.0  0
 9FJ  CONST_14  C4   C5   C6   C7   180.00   0.0  0
 9FJ  CONST_15  N10  C1   C6   C5   180.00   0.0  0
 9FJ  CONST_16  N10  C1   C2   N3   180.00   0.0  0
 9FJ  CONST_17  O22  C20  C19  C18  180.00   0.0  0
 9FJ  CONST_18  C16  C21  C20  O22  180.00   0.0  0
 9FJ  CONST_19  H4   C2   C1   C6   180.00   0.0  0
 9FJ  CONST_20  H3   C4   C5   C6   180.00   0.0  0
 9FJ  CONST_21  H2   C5   C4   N3   180.00   0.0  0
 9FJ  CONST_22  H9   C18  C17  C12    0.00   0.0  0
 9FJ  CONST_23  H10  C19  C18  C17  180.00   0.0  0
 9FJ  CONST_24  H14  C21  C16  C17  180.00   0.0  0
 9FJ  CONST_25  C11  N10  C1   C6   180.00   0.0  0
 9FJ  CONST_26  C11  N10  C1   C2     0.00   0.0  0
 9FJ  CONST_27  H5   N10  C1   C6     0.00   0.0  0
 9FJ  Var_01    C15  C14  C13  C12   62.63  30.0  1
 9FJ  Var_02    C14  C15  C16  C17   23.24  30.0  1
 9FJ  Var_03    C13  C14  C15  C16  -54.09  30.0  1
 9FJ  Var_04    C1   C6   C7   O9    -0.84  30.0  3
 9FJ  Var_05    C12  C11  N10  C1   175.44  30.0  2
 9FJ  Var_06    C21  C20  O22  C23  179.42  30.0  2
 9FJ  Var_07    H11  C23  O22  C20  -61.55  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
 9FJ  chir_01  C12  C17  C11  C13  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
 9FJ  plan-1  C7   0.020
 9FJ  plan-1  C6   0.020
 9FJ  plan-1  C5   0.020
 9FJ  plan-1  C4   0.020
 9FJ  plan-1  N3   0.020
 9FJ  plan-1  C2   0.020
 9FJ  plan-1  C1   0.020
 9FJ  plan-1  N10  0.020
 9FJ  plan-1  H2   0.020
 9FJ  plan-1  H3   0.020
 9FJ  plan-1  H4   0.020
 9FJ  plan-2  C12  0.020
 9FJ  plan-2  C17  0.020
 9FJ  plan-2  C18  0.020
 9FJ  plan-2  C19  0.020
 9FJ  plan-2  C20  0.020
 9FJ  plan-2  O22  0.020
 9FJ  plan-2  C21  0.020
 9FJ  plan-2  C16  0.020
 9FJ  plan-2  C15  0.020
 9FJ  plan-2  H9   0.020
 9FJ  plan-2  H10  0.020
 9FJ  plan-2  H14  0.020
 9FJ  plan-3  C1   0.020
 9FJ  plan-3  N10  0.020
 9FJ  plan-3  C11  0.020
 9FJ  plan-3  H5   0.020
 9FJ  plan-4  O9   0.020
 9FJ  plan-4  C7   0.020
 9FJ  plan-4  O8   0.020
 9FJ  plan-4  C6   0.020

