# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:35:33 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(cc1c2ccc(Cl)cc2)c3ccc(cc3)C4(CCCC4)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
 6HH  6HH  '1-{4-[6-amino-5-(4-chlorophenyl)pyridin-3-yl]phenyl}cyclopentane-1-carboxylic acid'  ligand  49  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6HH
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
 6HH  C4   C   CR16  0  -0.275   3.3610   1.0501   0.5872
 6HH  N2   N   NH2   0  -0.828  -4.0778   3.1629  -0.0852
 6HH  C7   C   CR6   0  -0.002  -0.3362   1.4325  -0.0502
 6HH  C6   C   CR6   0   0.074   1.0320   0.8916  -0.0493
 6HH  C9   C   CR6   0  -0.037  -2.7423   1.1364  -0.0084
 6HH  C13  C   CR16  0  -0.307  -4.9185   0.4209   1.0106
 6HH  C20  C   CH2   0  -0.442   6.0187  -2.6679   1.1088
 6HH  C21  C   CH2   0  -0.437   5.4005  -3.1086  -0.2122
 6HH  C8   C   CR16  0  -0.245  -1.4646   0.6105  -0.0067
 6HH  C18  C   CT    0  -0.243   5.0837  -0.6842  -0.0033
 6HH  C16  C   CR16  0  -0.195  -5.0892  -1.7202  -0.7484
 6HH  C19  C   CH2   0  -0.428   5.3116  -1.3444   1.3860
 6HH  C1   C   CR16  0  -0.300   1.3366  -0.3023  -0.7005
 6HH  C2   C   CR16  0  -0.311   2.6292  -0.8074  -0.7120
 6HH  C3   C   CR6   0   0.164   3.6694  -0.1351  -0.0808
 6HH  C5   C   CR16  0  -0.306   2.0730   1.5558   0.6032
 6HH  C10  C   CR6   0   0.404  -2.8642   2.5449  -0.0792
 6HH  N1   N   N     0  -0.445  -1.7953   3.3361  -0.1184
 6HH  C11  C   CR16  0  -0.108  -0.5858   2.7979  -0.0981
 6HH  C12  C   CR6   0   0.057  -3.9148   0.2410   0.0572
 6HH  C14  C   CR16  0  -0.193  -5.9944  -0.4487   1.0907
 6HH  C15  C   CR6   0  -0.052  -6.0706  -1.5148   0.2079
 6HH  C17  C   CR16  0  -0.305  -4.0202  -0.8403  -0.8173
 6HH  CL1  CL  CL    0  -0.127  -7.4124  -2.6064   0.3041
 6HH  C22  C   CH2   0  -0.472   5.4095  -1.8192  -1.0259
 6HH  C23  C   C     0   0.549   6.0770   0.4318  -0.2725
 6HH  O1   O   O     0  -0.429   7.0218   0.7157   0.4201
 6HH  O2   O   OH1   0  -0.588   5.8136   1.0458  -1.4210
 6HH  H3   H   HCR6  0   0.253   4.1320   1.5898   1.1263
 6HH  H7   H   HNH2  0   0.395  -4.8784   2.6464  -0.4099
 6HH  H8   H   HNH2  0   0.387  -4.0711   4.1310  -0.3628
 6HH  H9   H   HCR6  0   0.273  -4.8580   1.2414   1.7136
 6HH  H16  H   HCH2  0   0.239   5.8851  -3.3891   1.9159
 6HH  H15  H   HCH2  0   0.224   7.0935  -2.5117   0.9821
 6HH  H18  H   HCH2  0   0.241   5.9497  -3.9117  -0.7050
 6HH  H17  H   HCH2  0   0.225   4.3771  -3.4599  -0.0495
 6HH  H5   H   HCR6  0   0.263  -1.3452  -0.4645   0.0665
 6HH  H11  H   HCR6  0   0.282  -5.1559  -2.5509  -1.4376
 6HH  H14  H   HCH2  0   0.243   4.3401  -1.5495   1.8391
 6HH  H13  H   HCH2  0   0.249   5.8533  -0.6948   2.0720
 6HH  H1   H   HCR6  0   0.251   0.5615  -0.8434  -1.2295
 6HH  H2   H   HCR6  0   0.252   2.8100  -1.7391  -1.2316
 6HH  H4   H   HCR6  0   0.252   1.8758   2.4701   1.1489
 6HH  H6   H   HCR6  0   0.257   0.2399   3.5006  -0.1470
 6HH  H10  H   HCR6  0   0.283  -6.7599  -0.2983   1.8396
 6HH  H12  H   HCR6  0   0.266  -3.2628  -0.9954  -1.5752
 6HH  H19  H   HCH2  0   0.260   6.4163  -1.6800  -1.4292
 6HH  H20  H   HCH2  0   0.256   4.7404  -1.8234  -1.8851
 6HH  H21  H   HOH1  0   0.481   6.4869   1.7196  -1.5977

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
 6HH  CL1  C15  single    1.732  0.020  1.732
 6HH  C15  C16  aromatic  1.386  0.020  1.386
 6HH  C15  C14  aromatic  1.386  0.020  1.386
 6HH  C16  C17  aromatic  1.386  0.020  1.386
 6HH  C14  C13  aromatic  1.386  0.020  1.386
 6HH  C17  C12  aromatic  1.395  0.020  1.395
 6HH  N2   C10  single    1.362  0.020  1.362
 6HH  C13  C12  aromatic  1.396  0.020  1.396
 6HH  C12  C9   single    1.477  0.020  1.477
 6HH  C10  C9   aromatic  1.416  0.020  1.416
 6HH  C10  N1   aromatic  1.330  0.020  1.330
 6HH  C9   C8   aromatic  1.382  0.020  1.382
 6HH  N1   C11  aromatic  1.324  0.020  1.324
 6HH  C8   C7   aromatic  1.397  0.020  1.397
 6HH  C11  C7   aromatic  1.389  0.020  1.389
 6HH  C7   C6   single    1.471  0.020  1.471
 6HH  C6   C5   aromatic  1.397  0.020  1.397
 6HH  C6   C1   aromatic  1.394  0.020  1.394
 6HH  C5   C4   aromatic  1.384  0.020  1.384
 6HH  C4   C3   aromatic  1.395  0.020  1.395
 6HH  C1   C2   aromatic  1.388  0.020  1.388
 6HH  C3   C2   aromatic  1.390  0.020  1.390
 6HH  C3   C18  single    1.519  0.020  1.519
 6HH  C22  C18  single    1.562  0.020  1.562
 6HH  C22  C21  single    1.525  0.020  1.525
 6HH  C18  C19  single    1.555  0.020  1.555
 6HH  C18  C23  single    1.518  0.020  1.518
 6HH  C19  C20  single    1.526  0.020  1.526
 6HH  C21  C20  single    1.524  0.020  1.524
 6HH  C23  O1   double    1.205  0.020  1.205
 6HH  C23  O2   single    1.329  0.020  1.329
 6HH  C4   H3   single    0.930  0.020  1.080
 6HH  N2   H7   single    0.890  0.020  1.040
 6HH  N2   H8   single    0.890  0.020  1.040
 6HH  C13  H9   single    0.930  0.020  1.080
 6HH  C20  H16  single    0.970  0.020  1.090
 6HH  C20  H15  single    0.970  0.020  1.090
 6HH  C21  H18  single    0.970  0.020  1.090
 6HH  C21  H17  single    0.970  0.020  1.090
 6HH  C8   H5   single    0.930  0.020  1.080
 6HH  C16  H11  single    0.930  0.020  1.080
 6HH  C19  H14  single    0.970  0.020  1.090
 6HH  C19  H13  single    0.970  0.020  1.090
 6HH  C1   H1   single    0.930  0.020  1.080
 6HH  C2   H2   single    0.930  0.020  1.080
 6HH  C5   H4   single    0.930  0.020  1.080
 6HH  C11  H6   single    0.930  0.020  1.080
 6HH  C14  H10  single    0.930  0.020  1.080
 6HH  C17  H12  single    0.930  0.020  1.080
 6HH  C22  H19  single    0.970  0.020  1.090
 6HH  C22  H20  single    0.970  0.020  1.090
 6HH  O2   H21  single    0.850  0.020  0.980

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
 6HH  H3   C4   C5   118.30  3.000
 6HH  H3   C4   C3   120.24  3.000
 6HH  C5   C4   C3   121.45  3.000
 6HH  H8   N2   H7   114.18  3.000
 6HH  H8   N2   C10  115.56  3.000
 6HH  H7   N2   C10  118.51  3.000
 6HH  C11  C7   C8   115.75  3.000
 6HH  C11  C7   C6   121.91  3.000
 6HH  C8   C7   C6   122.34  3.000
 6HH  C5   C6   C1   117.57  3.000
 6HH  C1   C6   C7   121.19  3.000
 6HH  C5   C6   C7   121.24  3.000
 6HH  C12  C9   C10  122.49  3.000
 6HH  C10  C9   C8   117.29  3.000
 6HH  C12  C9   C8   120.22  3.000
 6HH  H9   C13  C14  118.80  3.000
 6HH  H9   C13  C12  120.07  3.000
 6HH  C14  C13  C12  121.12  3.000
 6HH  H15  C20  H16  107.50  3.000
 6HH  H15  C20  C19  110.65  3.000
 6HH  H16  C20  C19  112.48  3.000
 6HH  H15  C20  C21  109.85  3.000
 6HH  H16  C20  C21  113.62  3.000
 6HH  C19  C20  C21  102.73  3.000
 6HH  H17  C21  H18  107.57  3.000
 6HH  H17  C21  C22  110.87  3.000
 6HH  H18  C21  C22  112.24  3.000
 6HH  H17  C21  C20  110.08  3.000
 6HH  H18  C21  C20  113.61  3.000
 6HH  C22  C21  C20  102.46  3.000
 6HH  H5   C8   C9   118.64  3.000
 6HH  H5   C8   C7   119.79  3.000
 6HH  C9   C8   C7   121.53  3.000
 6HH  C23  C18  C22  106.35  3.000
 6HH  C23  C18  C3   109.53  3.000
 6HH  C22  C18  C3   115.05  3.000
 6HH  C23  C18  C19  112.00  3.000
 6HH  C22  C18  C19  104.23  3.000
 6HH  C3   C18  C19  109.60  3.000
 6HH  H11  C16  C17  120.23  3.000
 6HH  H11  C16  C15  120.67  3.000
 6HH  C17  C16  C15  119.10  3.000
 6HH  H13  C19  H14  107.06  3.000
 6HH  H13  C19  C18  112.48  3.000
 6HH  H14  C19  C18  108.68  3.000
 6HH  H13  C19  C20  113.66  3.000
 6HH  H14  C19  C20  108.96  3.000
 6HH  C18  C19  C20  105.90  3.000
 6HH  H1   C1   C2   118.73  3.000
 6HH  H1   C1   C6   119.98  3.000
 6HH  C2   C1   C6   121.28  3.000
 6HH  H2   C2   C3   120.63  3.000
 6HH  H2   C2   C1   118.23  3.000
 6HH  C3   C2   C1   121.14  3.000
 6HH  C2   C3   C18  123.02  3.000
 6HH  C18  C3   C4   119.24  3.000
 6HH  C2   C3   C4   117.58  3.000
 6HH  H4   C5   C6   120.08  3.000
 6HH  H4   C5   C4   118.94  3.000
 6HH  C6   C5   C4   120.97  3.000
 6HH  N1   C10  C9   121.60  3.000
 6HH  N1   C10  N2   116.48  3.000
 6HH  C9   C10  N2   121.90  3.000
 6HH  C11  N1   C10  119.46  3.000
 6HH  H6   C11  N1   115.54  3.000
 6HH  H6   C11  C7   120.09  3.000
 6HH  N1   C11  C7   124.36  3.000
 6HH  C17  C12  C13  118.28  3.000
 6HH  C13  C12  C9   121.54  3.000
 6HH  C17  C12  C9   120.15  3.000
 6HH  H10  C14  C15  120.60  3.000
 6HH  H10  C14  C13  120.16  3.000
 6HH  C15  C14  C13  119.24  3.000
 6HH  CL1  C15  C14  119.46  3.000
 6HH  C14  C15  C16  120.97  3.000
 6HH  CL1  C15  C16  119.57  3.000
 6HH  H12  C17  C12  119.81  3.000
 6HH  H12  C17  C16  118.91  3.000
 6HH  C12  C17  C16  121.28  3.000
 6HH  H20  C22  H19  105.98  3.000
 6HH  H20  C22  C18  113.02  3.000
 6HH  H19  C22  C18  109.94  3.000
 6HH  H20  C22  C21  114.47  3.000
 6HH  H19  C22  C21  108.05  3.000
 6HH  C18  C22  C21  105.30  3.000
 6HH  O2   C23  O1   122.90  3.000
 6HH  O2   C23  C18  111.31  3.000
 6HH  O1   C23  C18  125.74  3.000
 6HH  H21  O2   C23  109.96  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
 6HH  CONST_01  C7   C6   C5   C4   180.00   0.0  0
 6HH  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 6HH  CONST_03  C1   C2   C3   C4     0.00   0.0  0
 6HH  CONST_04  C12  C9   C8   C7   180.00   0.0  0
 6HH  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 6HH  CONST_06  C10  N1   C11  C7     0.00   0.0  0
 6HH  CONST_07  C2   C1   C6   C7   180.00   0.0  0
 6HH  CONST_08  C9   C8   C7   C6   180.00   0.0  0
 6HH  CONST_09  N1   C11  C7   C6   180.00   0.0  0
 6HH  CONST_10  C3   C4   C5   C6     0.00   0.0  0
 6HH  CONST_11  C3   C2   C1   C6     0.00   0.0  0
 6HH  CONST_12  C16  C17  C12  C9   180.00   0.0  0
 6HH  CONST_13  C14  C13  C12  C9   180.00   0.0  0
 6HH  CONST_14  C11  N1   C10  C9     0.00   0.0  0
 6HH  CONST_15  C11  C7   C8   C9     0.00   0.0  0
 6HH  CONST_16  C16  C15  C14  C13    0.00   0.0  0
 6HH  CONST_17  C16  C17  C12  C13    0.00   0.0  0
 6HH  CONST_21  N1   C10  C9   C8     0.00   0.0  0
 6HH  CONST_22  N1   C11  C7   C8     0.00   0.0  0
 6HH  CONST_26  C5   C6   C1   C2     0.00   0.0  0
 6HH  CONST_27  C5   C4   C3   C2     0.00   0.0  0
 6HH  CONST_30  C12  C9   C10  N1   180.00   0.0  0
 6HH  CONST_31  C15  C16  C17  C12    0.00   0.0  0
 6HH  CONST_32  C15  C14  C13  C12    0.00   0.0  0
 6HH  CONST_33  C17  C16  C15  C14    0.00   0.0  0
 6HH  CONST_34  C17  C12  C13  C14    0.00   0.0  0
 6HH  CONST_35  C5   C4   C3   C18  180.00   0.0  0
 6HH  CONST_36  C1   C2   C3   C18  180.00   0.0  0
 6HH  CONST_37  C12  C9   C10  N2     0.00   0.0  0
 6HH  CONST_38  C8   C9   C10  N2   180.00   0.0  0
 6HH  CONST_39  C11  N1   C10  N2   180.00   0.0  0
 6HH  CONST_40  CL1  C15  C14  C13  180.00   0.0  0
 6HH  CONST_41  CL1  C15  C16  C17  180.00   0.0  0
 6HH  CONST_42  H2   C2   C3   C4   180.00   0.0  0
 6HH  CONST_43  H4   C5   C6   C7     0.00   0.0  0
 6HH  CONST_44  H1   C1   C6   C7     0.00   0.0  0
 6HH  CONST_45  H5   C8   C7   C6     0.00   0.0  0
 6HH  CONST_46  H6   C11  C7   C6     0.00   0.0  0
 6HH  CONST_47  H3   C4   C5   C6   180.00   0.0  0
 6HH  CONST_48  H12  C17  C12  C9     0.00   0.0  0
 6HH  CONST_49  H9   C13  C12  C9     0.00   0.0  0
 6HH  CONST_50  H10  C14  C15  C16  180.00   0.0  0
 6HH  CONST_51  H11  C16  C17  C12  180.00   0.0  0
 6HH  CONST_53  H8   N2   C10  C9   180.00   0.0  0
 6HH  CONST_54  H21  O2   C23  C18  180.00   0.0  0
 6HH  Var_01    C18  C22  C21  C20  -37.22  30.0  1
 6HH  Var_02    C18  C19  C20  C21  -34.66  30.0  1
 6HH  Var_03    C22  C21  C20  C19   44.33  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
 6HH  chir_01  C18  C22  C19  C3  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
 6HH  plan-1  C4   0.020
 6HH  plan-1  C7   0.020
 6HH  plan-1  C6   0.020
 6HH  plan-1  C18  0.020
 6HH  plan-1  C1   0.020
 6HH  plan-1  C2   0.020
 6HH  plan-1  C3   0.020
 6HH  plan-1  C5   0.020
 6HH  plan-1  H3   0.020
 6HH  plan-1  H1   0.020
 6HH  plan-1  H2   0.020
 6HH  plan-1  H4   0.020
 6HH  plan-2  N2   0.020
 6HH  plan-2  C7   0.020
 6HH  plan-2  C6   0.020
 6HH  plan-2  C9   0.020
 6HH  plan-2  C8   0.020
 6HH  plan-2  C10  0.020
 6HH  plan-2  N1   0.020
 6HH  plan-2  C11  0.020
 6HH  plan-2  C12  0.020
 6HH  plan-2  H5   0.020
 6HH  plan-2  H6   0.020
 6HH  plan-3  C9   0.020
 6HH  plan-3  C13  0.020
 6HH  plan-3  C16  0.020
 6HH  plan-3  C12  0.020
 6HH  plan-3  C14  0.020
 6HH  plan-3  C15  0.020
 6HH  plan-3  C17  0.020
 6HH  plan-3  CL1  0.020
 6HH  plan-3  H9   0.020
 6HH  plan-3  H11  0.020
 6HH  plan-3  H10  0.020
 6HH  plan-3  H12  0.020
 6HH  plan-4  N2   0.020
 6HH  plan-4  C10  0.020
 6HH  plan-4  H7   0.020
 6HH  plan-4  H8   0.020
 6HH  plan-5  C18  0.020
 6HH  plan-5  C23  0.020
 6HH  plan-5  O1   0.020
 6HH  plan-5  O2   0.020
 6HH  plan-5  H21  0.020

