# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 15:38:27 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: (2R)-cyclopentyl{4-[(quinolin-2-yl)methoxy]phenyl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](C1CCCC1)c2ccc(OCc3ccc4ccccc4n3)cc2
#
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
 QY1  QY1  '(2R)-cyclopentyl{4-[(quinolin-2-yl)methoxy]phenyl}acetic acid'  ligand  49  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QY1
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
 QY1  C7   C  CR16   0  -0.293   5.1107   8.2788  64.5268
 QY1  C6   C  CR16   0  -0.295   3.8514  14.3410  62.8084
 QY1  C1   C  CR16   0  -0.253   3.5303   6.6819  63.6401
 QY1  C5   C  CR16   0  -0.315   4.3430  15.5588  60.8271
 QY1  C4   C  CR16   0  -0.181   4.5049   9.0652  60.9519
 QY1  C3   C  CR16   0  -0.311   3.5805   7.2774  62.4087
 QY1  C2   C  CR16   0  -0.255   4.3016   7.1893  64.7068
 QY1  C8   C  CR16   0  -0.337   5.3468  14.6575  60.5105
 QY1  C9   C  CR16   0  -0.340   4.8563  13.4279  62.5126
 QY1  C10  C  CR16   0  -0.305   5.3290  10.1450  60.8260
 QY1  C11  C  CR66   0   0.081   4.4069   8.4028  62.1957
 QY1  C12  C  CR6    0   0.132   3.5676  15.4211  61.9775
 QY1  C13  C  CR66   0   0.195   5.1840   8.9102  63.2651
 QY1  C14  C  CR6    0   0.365   5.6091  13.5791  61.3517
 QY1  C15  C  CR6    0   0.170   6.0634  10.5750  61.9567
 QY1  C16  C  C      0   0.422   2.6027  16.9924  63.6924
 QY1  C17  C  CH2    0  -0.442  -1.2729  16.0826  61.4642
 QY1  C18  C  CH2    0  -0.444  -0.6651  14.9468  60.6183
 QY1  C19  C  CH2    0  -0.436  -0.1080  16.6508  62.3023
 QY1  C20  C  CH2    0  -0.418   0.8398  15.2007  60.6514
 QY1  C21  C  CH1    0  -0.198   1.0839  15.7118  62.0712
 QY1  C22  C  CH2    0  -0.269   7.0245  11.7345  61.8528
 QY1  C23  C  CH1    0  -0.418   2.4429  16.3828  62.2751
 QY1  N24  N  N      0  -0.451   5.9909   9.9883  63.1211
 QY1  O27  O  O2     0  -0.483   6.6035  12.7406  60.9629
 QY1  H1   H  HCR6   0   0.259   5.7058   8.6754  65.3395
 QY1  H2   H  HCR6   0   0.243   3.2775  14.2052  63.7154
 QY1  H3   H  HCR6   0   0.262   2.8976   5.8192  63.8012
 QY1  H4   H  HCR6   0   0.241   4.1571  16.3889  60.1549
 QY1  H5   H  HCR6   0   0.271   3.9261   8.7075  60.1088
 QY1  H6   H  HCR6   0   0.262   2.9904   6.8948  61.5846
 QY1  H7   H  HCR6   0   0.262   4.2503   6.7091  65.6753
 QY1  H8   H  HCR6   0   0.253   5.9337  14.7875  59.6092
 QY1  H9   H  HCR6   0   0.273   5.0268  12.6134  63.2038
 QY1  H10  H  HCR6   0   0.271   5.4230  10.6645  59.8822
 QY1  H13  H  HCH2   0   0.223  -1.0699  14.9124  59.6057
 QY1  H14  H  HCH2   0   0.215  -0.8801  13.9786  61.0775
 QY1  H15  H  HCH2   0   0.212   0.1515  17.6552  61.9537
 QY1  H16  H  HCH2   0   0.224  -0.3545  16.7419  63.3603
 QY1  H17  H  HCH2   0   0.224   1.4256  14.3140  60.4025
 QY1  H18  H  HCH2   0   0.203   1.1094  15.9805  59.9294
 QY1  H19  H  HCH1   0   0.211   1.0050  14.8618  62.7578
 QY1  H20  H  HCH2   0   0.279   7.9739  11.3712  61.4516
 QY1  H21  H  HCH2   0   0.251   7.2247  12.1291  62.8542
 QY1  H22  H  HCH1   0   0.204   2.5099  17.2025  61.5502
 QY1  O25  O  O      0  -0.601   3.1070  18.1302  63.7531
 QY1  H11  H  HCH2   0   0.220  -1.7003  16.8576  60.8257
 QY1  O26  O  OC    -1  -0.600   2.2322  16.2891  64.6555
 QY1  H12  H  HCH2   0   0.222  -2.0869  15.7172  62.0918

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
 QY1  C18  C20  single    1.527  0.020  1.527
 QY1  C18  C17  single    1.541  0.020  1.541
 QY1  C8   C5   aromatic  1.386  0.020  1.386
 QY1  C8   C14  aromatic  1.393  0.020  1.393
 QY1  C20  C21  single    1.529  0.020  1.529
 QY1  C5   C12  aromatic  1.394  0.020  1.394
 QY1  O27  C14  single    1.358  0.020  1.358
 QY1  O27  C22  single    1.408  0.020  1.408
 QY1  C10  C4   aromatic  1.364  0.020  1.364
 QY1  C10  C15  aromatic  1.415  0.020  1.415
 QY1  C4   C11  aromatic  1.413  0.020  1.413
 QY1  C14  C9   aromatic  1.392  0.020  1.392
 QY1  C17  C19  single    1.543  0.020  1.543
 QY1  C12  C23  single    1.509  0.020  1.509
 QY1  C12  C6   aromatic  1.392  0.020  1.392
 QY1  C21  C23  single    1.529  0.020  1.529
 QY1  C21  C19  single    1.535  0.020  1.535
 QY1  C22  C15  single    1.510  0.020  1.510
 QY1  C15  N24  aromatic  1.306  0.020  1.306
 QY1  C23  C16  single    1.551  0.020  1.551
 QY1  C11  C3   aromatic  1.412  0.020  1.412
 QY1  C11  C13  aromatic  1.416  0.020  1.416
 QY1  C9   C6   aromatic  1.390  0.020  1.390
 QY1  C3   C1   aromatic  1.369  0.020  1.369
 QY1  N24  C13  aromatic  1.354  0.020  1.354
 QY1  C13  C7   aromatic  1.413  0.020  1.413
 QY1  C16  O25  deloc     1.246  0.020  1.246
 QY1  C16  O26  deloc     1.249  0.020  1.249
 QY1  C1   C2   aromatic  1.411  0.020  1.411
 QY1  C7   C2   aromatic  1.369  0.020  1.369
 QY1  C7   H1   single    0.930  0.020  1.080
 QY1  C6   H2   single    0.930  0.020  1.080
 QY1  C1   H3   single    0.930  0.020  1.080
 QY1  C5   H4   single    0.930  0.020  1.080
 QY1  C4   H5   single    0.930  0.020  1.080
 QY1  C3   H6   single    0.930  0.020  1.080
 QY1  C2   H7   single    0.930  0.020  1.080
 QY1  C8   H8   single    0.930  0.020  1.080
 QY1  C9   H9   single    0.930  0.020  1.080
 QY1  C10  H10  single    0.930  0.020  1.080
 QY1  C17  H11  single    0.970  0.020  1.090
 QY1  C17  H12  single    0.970  0.020  1.090
 QY1  C18  H13  single    0.970  0.020  1.090
 QY1  C18  H14  single    0.970  0.020  1.090
 QY1  C19  H15  single    0.970  0.020  1.090
 QY1  C19  H16  single    0.970  0.020  1.090
 QY1  C20  H17  single    0.970  0.020  1.090
 QY1  C20  H18  single    0.970  0.020  1.090
 QY1  C21  H19  single    0.970  0.020  1.090
 QY1  C22  H20  single    0.970  0.020  1.090
 QY1  C22  H21  single    0.970  0.020  1.090
 QY1  C23  H22  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
 QY1  H1   C7   C13  118.57  3.000
 QY1  H1   C7   C2   121.17  3.000
 QY1  C13  C7   C2   120.25  3.000
 QY1  H2   C6   C12  119.32  3.000
 QY1  H2   C6   C9   118.66  3.000
 QY1  C12  C6   C9   122.03  3.000
 QY1  H3   C1   C2   119.60  3.000
 QY1  H3   C1   C3   120.15  3.000
 QY1  C2   C1   C3   120.25  3.000
 QY1  H4   C5   C12  119.46  3.000
 QY1  H4   C5   C8   118.72  3.000
 QY1  C12  C5   C8   121.82  3.000
 QY1  H5   C4   C11  119.56  3.000
 QY1  H5   C4   C10  120.80  3.000
 QY1  C11  C4   C10  119.63  3.000
 QY1  H6   C3   C11  119.03  3.000
 QY1  H6   C3   C1   120.71  3.000
 QY1  C11  C3   C1   120.25  3.000
 QY1  H7   C2   C1   119.42  3.000
 QY1  H7   C2   C7   119.93  3.000
 QY1  C1   C2   C7   120.65  3.000
 QY1  H8   C8   C14  119.56  3.000
 QY1  H8   C8   C5   120.30  3.000
 QY1  C14  C8   C5   120.14  3.000
 QY1  H9   C9   C14  121.97  3.000
 QY1  H9   C9   C6   118.22  3.000
 QY1  C14  C9   C6   119.82  3.000
 QY1  H10  C10  C15  120.41  3.000
 QY1  H10  C10  C4   120.89  3.000
 QY1  C15  C10  C4   118.70  3.000
 QY1  C13  C11  C3   119.52  3.000
 QY1  C13  C11  C4   117.31  3.000
 QY1  C3   C11  C4   123.17  3.000
 QY1  C23  C12  C5   120.95  3.000
 QY1  C23  C12  C6   121.92  3.000
 QY1  C5   C12  C6   117.11  3.000
 QY1  N24  C13  C11  122.14  3.000
 QY1  N24  C13  C7   118.80  3.000
 QY1  C11  C13  C7   119.07  3.000
 QY1  O27  C14  C9   124.61  3.000
 QY1  C9   C14  C8   119.08  3.000
 QY1  O27  C14  C8   116.31  3.000
 QY1  N24  C15  C22  116.22  3.000
 QY1  N24  C15  C10  123.17  3.000
 QY1  C22  C15  C10  120.58  3.000
 QY1  O26  C16  O25  126.64  3.000
 QY1  O26  C16  C23  116.92  3.000
 QY1  O25  C16  C23  116.43  3.000
 QY1  H12  C17  H11  106.40  3.000
 QY1  H12  C17  C19  111.97  3.000
 QY1  H11  C17  C19  110.60  3.000
 QY1  H12  C17  C18  111.30  3.000
 QY1  H11  C17  C18  110.90  3.000
 QY1  C19  C17  C18  105.76  3.000
 QY1  H14  C18  H13  106.80  3.000
 QY1  H14  C18  C20  109.40  3.000
 QY1  H13  C18  C20  113.02  3.000
 QY1  H14  C18  C17  110.17  3.000
 QY1  H13  C18  C17  112.73  3.000
 QY1  C20  C18  C17  104.73  3.000
 QY1  H16  C19  H15  106.62  3.000
 QY1  H16  C19  C21  111.89  3.000
 QY1  H15  C19  C21  109.23  3.000
 QY1  H16  C19  C17  112.77  3.000
 QY1  H15  C19  C17  110.12  3.000
 QY1  C21  C19  C17  106.21  3.000
 QY1  H18  C20  H17  107.20  3.000
 QY1  H18  C20  C21  109.55  3.000
 QY1  H17  C20  C21  113.44  3.000
 QY1  H18  C20  C18  110.27  3.000
 QY1  H17  C20  C18  112.89  3.000
 QY1  C21  C20  C18  103.48  3.000
 QY1  H19  C21  C23  108.71  3.000
 QY1  H19  C21  C20  108.13  3.000
 QY1  C23  C21  C20  114.36  3.000
 QY1  H19  C21  C19  108.93  3.000
 QY1  C23  C21  C19  113.68  3.000
 QY1  C20  C21  C19  102.74  3.000
 QY1  H21  C22  H20  107.26  3.000
 QY1  H21  C22  O27  112.05  3.000
 QY1  H20  C22  O27  105.39  3.000
 QY1  H21  C22  C15  109.29  3.000
 QY1  H20  C22  C15  108.84  3.000
 QY1  O27  C22  C15  113.71  3.000
 QY1  H22  C23  C21  107.11  3.000
 QY1  H22  C23  C16  107.70  3.000
 QY1  C21  C23  C16  112.70  3.000
 QY1  H22  C23  C12  107.48  3.000
 QY1  C16  C23  C12  110.72  3.000
 QY1  C21  C23  C12  110.88  3.000
 QY1  C15  N24  C13  119.05  3.000
 QY1  C22  O27  C14  118.65  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
 QY1  CONST_01  C4   C11  C13  C7   180.00   0.0  0
 QY1  CONST_02  C3   C11  C13  C7     0.00   0.0  0
 QY1  CONST_03  C15  N24  C13  C7   180.00   0.0  0
 QY1  CONST_04  C3   C1   C2   C7     0.00   0.0  0
 QY1  CONST_05  C8   C5   C12  C6     0.00   0.0  0
 QY1  CONST_06  C8   C14  C9   C6     0.00   0.0  0
 QY1  CONST_07  C4   C11  C3   C1   180.00   0.0  0
 QY1  CONST_08  C13  C11  C3   C1     0.00   0.0  0
 QY1  CONST_09  C13  C7   C2   C1     0.00   0.0  0
 QY1  CONST_10  C9   C14  C8   C5     0.00   0.0  0
 QY1  CONST_11  C9   C6   C12  C5     0.00   0.0  0
 QY1  CONST_12  N24  C15  C10  C4     0.00   0.0  0
 QY1  CONST_13  N24  C13  C11  C4     0.00   0.0  0
 QY1  CONST_14  C10  C4   C11  C3   180.00   0.0  0
 QY1  CONST_15  N24  C13  C11  C3   180.00   0.0  0
 QY1  CONST_16  C11  C3   C1   C2     0.00   0.0  0
 QY1  CONST_17  C11  C13  C7   C2     0.00   0.0  0
 QY1  CONST_18  N24  C13  C7   C2   180.00   0.0  0
 QY1  CONST_19  C13  C11  C4   C10    0.00   0.0  0
 QY1  CONST_20  C13  N24  C15  C10    0.00   0.0  0
 QY1  CONST_21  C15  C10  C4   C11    0.00   0.0  0
 QY1  CONST_22  C15  N24  C13  C11    0.00   0.0  0
 QY1  CONST_23  C14  C8   C5   C12    0.00   0.0  0
 QY1  CONST_24  C14  C9   C6   C12    0.00   0.0  0
 QY1  CONST_25  O27  C14  C9   C6   180.00   0.0  0
 QY1  CONST_26  O27  C14  C8   C5   180.00   0.0  0
 QY1  CONST_27  C22  C15  C10  C4   180.00   0.0  0
 QY1  CONST_28  C23  C12  C5   C8   180.00   0.0  0
 QY1  CONST_29  C23  C12  C6   C9   180.00   0.0  0
 QY1  CONST_30  C22  C15  N24  C13  180.00   0.0  0
 QY1  CONST_31  H3   C1   C2   C7   180.00   0.0  0
 QY1  CONST_32  H4   C5   C12  C6   180.00   0.0  0
 QY1  CONST_33  H1   C7   C2   C1   180.00   0.0  0
 QY1  CONST_34  H2   C6   C12  C5   180.00   0.0  0
 QY1  CONST_35  H6   C3   C11  C4     0.00   0.0  0
 QY1  CONST_36  H5   C4   C11  C3     0.00   0.0  0
 QY1  CONST_37  H7   C2   C1   C3   180.00   0.0  0
 QY1  CONST_38  H9   C9   C14  C8   180.00   0.0  0
 QY1  CONST_39  H8   C8   C14  C9   180.00   0.0  0
 QY1  CONST_40  H10  C10  C4   C11  180.00   0.0  0
 QY1  Var_01    C21  C20  C18  C17   36.85  30.0  1
 QY1  Var_02    C21  C19  C17  C18   -7.77  30.0  1
 QY1  Var_03    C20  C18  C17  C19  -17.80  30.0  1
 QY1  Var_04    O27  C22  C15  C10   34.74  30.0  2
 QY1  Var_05    C15  C22  O27  C14   75.26  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
 QY1  chir_01  C21  C20  C23  C19  negativ
 QY1  chir_02  C23  C16  C21  C12  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
 QY1  plan-1  C6   0.020
 QY1  plan-1  C5   0.020
 QY1  plan-1  C8   0.020
 QY1  plan-1  C9   0.020
 QY1  plan-1  C12  0.020
 QY1  plan-1  C14  0.020
 QY1  plan-1  C23  0.020
 QY1  plan-1  O27  0.020
 QY1  plan-1  H2   0.020
 QY1  plan-1  H4   0.020
 QY1  plan-1  H8   0.020
 QY1  plan-1  H9   0.020
 QY1  plan-2  C7   0.020
 QY1  plan-2  C1   0.020
 QY1  plan-2  C4   0.020
 QY1  plan-2  C3   0.020
 QY1  plan-2  C2   0.020
 QY1  plan-2  C10  0.020
 QY1  plan-2  C11  0.020
 QY1  plan-2  C13  0.020
 QY1  plan-2  C15  0.020
 QY1  plan-2  C22  0.020
 QY1  plan-2  N24  0.020
 QY1  plan-2  H1   0.020
 QY1  plan-2  H3   0.020
 QY1  plan-2  H5   0.020
 QY1  plan-2  H6   0.020
 QY1  plan-2  H7   0.020
 QY1  plan-2  H10  0.020
 QY1  plan-3  C16  0.020
 QY1  plan-3  C23  0.020
 QY1  plan-3  O25  0.020
 QY1  plan-3  O26  0.020

