# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:22:53 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: (2~{S})-1-[2,4-bis(chloranyl)-3-[[2-methyl-4-(trifluoromethyl)quinolin-8-yl]oxymethyl]phenyl]carbonyl-~{N}-methyl-pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@@H]1CCCN1C(=O)c2ccc(Cl)c(COc3cccc4c(cc(C)nc34)C(F)(F)F)c2Cl
#
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
 LK8  LK8  (2~{S})-1-[2,4-bis(chloranyl)-3-[[2-methyl-4-(trifluoromethyl)quinolin-8-yl]oxymethyl]phenyl]carbonyl-~{N}-methyl-pyrrolidine-2-carboxamide  ligand  58  36  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LK8
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
 LK8  C3   C   CR66  0   0.086  14.4354  -22.9448  13.6280
 LK8  C5   C   CR16  0  -0.402  13.2598  -22.4455  11.5662
 LK8  C7   C   CR6   0  -0.110  13.2884  -23.2504  15.7191
 LK8  C11  C   CT    0   1.075  12.0491  -23.3014  16.5665
 LK8  C8   C   CR16  0  -0.391  14.5055  -23.4570  16.2946
 LK8  O34  O   O     0  -0.497  21.6224  -26.0933   5.4241
 LK8  C33  C   C     0   0.539  20.8445  -25.8850   6.3443
 LK8  N35  N   NH1   0  -0.617  19.5229  -26.0517   6.2376
 LK8  C36  C   CH3   0  -0.512  18.8907  -26.4642   5.0068
 LK8  C32  C   CR15  0  -0.157  21.3673  -25.5066   7.7219
 LK8  C31  C   CH2   0  -0.481  21.5807  -26.7433   8.6064
 LK8  C30  C   CH2   0  -0.471  21.3944  -26.1997  10.0179
 LK8  C29  C   CH2   0  -0.275  20.2397  -25.2212   9.8566
 LK8  N28  N   NR5   0  -0.483  20.4608  -24.6829   8.5130
 LK8  O27  O   O     0  -0.458  20.5054  -23.0136   7.0045
 LK8  C20  C   CR6   0   0.055  19.3240  -22.6016   9.0086
 LK8  C19  C   CR6   0  -0.170  17.9697  -22.8075   9.2383
 LK8  CL1  CL  CL    0  -0.102  17.2027  -24.1526   8.4570
 LK8  C21  C   CR16  0  -0.316  19.9442  -21.5134   9.6062
 LK8  C22  C   CR16  0  -0.168  19.2380  -20.6681  10.4413
 LK8  C23  C   CR6   0  -0.129  17.8917  -20.9049  10.6574
 LK8  CL2  CL  CL    0  -0.097  17.0338  -19.8290  11.7015
 LK8  C18  C   CR6   0   0.293  17.2156  -21.9665  10.0553
 LK8  C17  C   CH2   0  -0.267  15.7549  -22.1726  10.3241
 LK8  C4   C   CR6   0   0.369  14.4429  -22.6645  12.2270
 LK8  C6   C   CR16  0  -0.229  12.0449  -22.4926  12.2721
 LK8  C1   C   CR16  0  -0.367  11.9987  -22.7511  13.6132
 LK8  N10  N   N     0  -0.420  15.6283  -23.1586  14.2204
 LK8  C9   C   CR6   0   0.239  15.6773  -23.4064  15.4990
 LK8  C2   C   CR66  0   0.123  13.2012  -22.9817  14.3227
 LK8  F14  F   F     0  -0.315  11.3863  -22.1379  16.5384
 LK8  F12  F   F     0  -0.294  12.3172  -23.5625  17.8463
 LK8  F13  F   F     0  -0.315  11.2014  -24.2487  16.1460
 LK8  H1   H   HCR6  0   0.296  13.2340  -22.2437  10.5041
 LK8  H2   H   HCH3  0   0.255  17.8064  -23.5832  15.4036
 LK8  H3   H   HCH3  0   0.257  17.1986  -22.9030  16.9201
 LK8  H4   H   HCH3  0   0.257  17.0414  -24.6231  16.6159
 LK8  H5   H   HCR6  0   0.283  14.6083  -23.6590  17.3517
 LK8  H6   H   HNH1  0   0.390  18.9400  -25.8548   7.0332
 LK8  H7   H   HCH3  0   0.250  17.8234  -26.5606   5.1831
 LK8  H8   H   HCH3  0   0.239  19.0422  -25.7332   4.2119
 LK8  H9   H   HCH3  0   0.240  19.2703  -27.4272   4.6657
 LK8  H10  H   HCR5  0   0.285  22.3137  -24.9792   7.5722
 LK8  H11  H   HCH2  0   0.252  20.8196  -27.4983   8.3950
 LK8  H12  H   HCH2  0   0.272  22.5569  -27.1931   8.4374
 LK8  H13  H   HCH2  0   0.263  21.1767  -26.9782  10.7472
 LK8  H14  H   HCH2  0   0.249  22.2912  -25.6702  10.3447
 LK8  H15  H   HCH2  0   0.270  20.2469  -24.4313  10.6055
 LK8  H16  H   HCH2  0   0.249  19.2778  -25.7368   9.9112
 LK8  H17  H   HCR6  0   0.289  20.9957  -21.3301   9.4293
 LK8  H18  H   HCR6  0   0.295  19.7307  -19.8315  10.9158
 LK8  H19  H   HCH2  0   0.260  15.2209  -21.2247  10.2026
 LK8  H20  H   HCH2  0   0.263  15.3117  -22.8846   9.6261
 LK8  H21  H   HCR6  0   0.271  11.1251  -22.3182  11.7300
 LK8  H22  H   HCR6  0   0.255  11.0368  -22.7772  14.1020
 LK8  C15  C   CH3   0  -0.735  17.0084  -23.6418  16.1397
 LK8  O16  O   O2    0  -0.439  15.6545  -22.6413  11.6566
 LK8  C26  C   C     0   0.500  20.1369  -23.4550   8.0812

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
 LK8  C36  N35  single    1.444  0.020  1.444
 LK8  N35  C33  single    1.336  0.020  1.336
 LK8  O34  C33  double    1.223  0.020  1.223
 LK8  O27  C26  double    1.221  0.020  1.221
 LK8  C33  C32  single    1.521  0.020  1.521
 LK8  C26  N28  single    1.341  0.020  1.341
 LK8  C26  C20  single    1.500  0.020  1.500
 LK8  C32  N28  single    1.458  0.020  1.458
 LK8  C32  C31  single    1.535  0.020  1.535
 LK8  N28  C29  single    1.464  0.020  1.464
 LK8  C20  C21  aromatic  1.388  0.020  1.388
 LK8  C20  C19  aromatic  1.389  0.020  1.389
 LK8  C21  C22  aromatic  1.382  0.020  1.382
 LK8  CL1  C19  single    1.734  0.020  1.734
 LK8  C31  C30  single    1.524  0.020  1.524
 LK8  C19  C18  aromatic  1.394  0.020  1.394
 LK8  C22  C23  aromatic  1.384  0.020  1.384
 LK8  C18  C23  aromatic  1.395  0.020  1.395
 LK8  C18  C17  single    1.499  0.020  1.499
 LK8  C29  C30  single    1.522  0.020  1.522
 LK8  C23  CL2  single    1.727  0.020  1.727
 LK8  C17  O16  single    1.416  0.020  1.416
 LK8  O16  C4   single    1.339  0.020  1.339
 LK8  C5   C4   aromatic  1.373  0.020  1.373
 LK8  C5   C6   aromatic  1.406  0.020  1.406
 LK8  C4   C3   aromatic  1.429  0.020  1.429
 LK8  C6   C1   aromatic  1.367  0.020  1.367
 LK8  C3   N10  aromatic  1.349  0.020  1.349
 LK8  C3   C2   aromatic  1.417  0.020  1.417
 LK8  C1   C2   aromatic  1.415  0.020  1.415
 LK8  N10  C9   aromatic  1.303  0.020  1.303
 LK8  C2   C7   aromatic  1.425  0.020  1.425
 LK8  C9   C15  single    1.496  0.020  1.496
 LK8  C9   C8   aromatic  1.417  0.020  1.417
 LK8  F13  C11  single    1.339  0.020  1.339
 LK8  C7   C8   aromatic  1.362  0.020  1.362
 LK8  C7   C11  single    1.502  0.020  1.502
 LK8  C11  F14  single    1.339  0.020  1.339
 LK8  C11  F12  single    1.333  0.020  1.333
 LK8  C5   H1   single    0.930  0.020  1.080
 LK8  C15  H2   single    0.970  0.020  1.090
 LK8  C15  H3   single    0.970  0.020  1.090
 LK8  C15  H4   single    0.970  0.020  1.090
 LK8  C8   H5   single    0.930  0.020  1.080
 LK8  N35  H6   single    0.860  0.020  1.020
 LK8  C36  H7   single    0.970  0.020  1.090
 LK8  C36  H8   single    0.970  0.020  1.090
 LK8  C36  H9   single    0.970  0.020  1.090
 LK8  C32  H10  single    0.970  0.020  1.090
 LK8  C31  H11  single    0.970  0.020  1.090
 LK8  C31  H12  single    0.970  0.020  1.090
 LK8  C30  H13  single    0.970  0.020  1.090
 LK8  C30  H14  single    0.970  0.020  1.090
 LK8  C29  H15  single    0.970  0.020  1.090
 LK8  C29  H16  single    0.970  0.020  1.090
 LK8  C21  H17  single    0.930  0.020  1.080
 LK8  C22  H18  single    0.930  0.020  1.080
 LK8  C17  H19  single    0.970  0.020  1.090
 LK8  C17  H20  single    0.970  0.020  1.090
 LK8  C6   H21  single    0.930  0.020  1.080
 LK8  C1   H22  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
 LK8  C2   C3   N10  123.43  3.000
 LK8  C2   C3   C4   119.38  3.000
 LK8  N10  C3   C4   117.20  3.000
 LK8  H1   C5   C6   118.61  3.000
 LK8  H1   C5   C4   121.54  3.000
 LK8  C6   C5   C4   119.86  3.000
 LK8  C2   C7   C8   119.83  3.000
 LK8  C8   C7   C11  119.58  3.000
 LK8  C2   C7   C11  120.59  3.000
 LK8  F13  C11  F12  106.87  3.000
 LK8  F12  C11  F14  106.84  3.000
 LK8  F13  C11  F14  107.14  3.000
 LK8  F12  C11  C7   112.47  3.000
 LK8  F14  C11  C7   111.53  3.000
 LK8  F13  C11  C7   111.66  3.000
 LK8  H5   C8   C9   118.49  3.000
 LK8  H5   C8   C7   121.76  3.000
 LK8  C9   C8   C7   119.75  3.000
 LK8  C32  C33  N35  116.31  3.000
 LK8  C32  C33  O34  120.34  3.000
 LK8  N35  C33  O34  123.22  3.000
 LK8  H6   N35  C36  118.45  3.000
 LK8  H6   N35  C33  119.06  3.000
 LK8  C36  N35  C33  122.46  3.000
 LK8  H9   C36  H8   108.41  3.000
 LK8  H9   C36  H7   108.34  3.000
 LK8  H8   C36  H7   108.32  3.000
 LK8  H9   C36  N35  111.51  3.000
 LK8  H8   C36  N35  111.65  3.000
 LK8  H7   C36  N35  108.50  3.000
 LK8  H10  C32  N28  109.87  3.000
 LK8  H10  C32  C31  110.30  3.000
 LK8  N28  C32  C31  103.23  3.000
 LK8  H10  C32  C33  107.06  3.000
 LK8  C31  C32  C33  111.66  3.000
 LK8  N28  C32  C33  114.72  3.000
 LK8  H12  C31  H11  108.01  3.000
 LK8  H12  C31  C30  113.64  3.000
 LK8  H11  C31  C30  109.91  3.000
 LK8  H12  C31  C32  111.60  3.000
 LK8  H11  C31  C32  110.38  3.000
 LK8  C30  C31  C32  103.25  3.000
 LK8  H14  C30  H13  108.09  3.000
 LK8  H14  C30  C29  110.07  3.000
 LK8  H13  C30  C29  112.28  3.000
 LK8  H14  C30  C31  110.48  3.000
 LK8  H13  C30  C31  112.94  3.000
 LK8  C29  C30  C31  102.94  3.000
 LK8  H16  C29  H15  108.29  3.000
 LK8  H16  C29  N28  110.62  3.000
 LK8  H15  C29  N28  111.31  3.000
 LK8  H16  C29  C30  111.05  3.000
 LK8  H15  C29  C30  112.87  3.000
 LK8  N28  C29  C30  102.65  3.000
 LK8  C26  N28  C29  126.55  3.000
 LK8  C29  N28  C32  112.58  3.000
 LK8  C26  N28  C32  119.52  3.000
 LK8  C21  C20  C19  118.74  3.000
 LK8  C19  C20  C26  123.12  3.000
 LK8  C21  C20  C26  118.05  3.000
 LK8  C18  C19  CL1  119.51  3.000
 LK8  C18  C19  C20  122.34  3.000
 LK8  CL1  C19  C20  118.15  3.000
 LK8  H17  C21  C22  119.45  3.000
 LK8  H17  C21  C20  119.79  3.000
 LK8  C22  C21  C20  120.76  3.000
 LK8  H18  C22  C23  120.49  3.000
 LK8  H18  C22  C21  120.38  3.000
 LK8  C23  C22  C21  119.12  3.000
 LK8  C18  C23  CL2  119.61  3.000
 LK8  CL2  C23  C22  118.09  3.000
 LK8  C18  C23  C22  122.29  3.000
 LK8  C17  C18  C23  119.95  3.000
 LK8  C17  C18  C19  123.31  3.000
 LK8  C23  C18  C19  116.73  3.000
 LK8  H20  C17  H19  107.21  3.000
 LK8  H20  C17  O16  110.93  3.000
 LK8  H19  C17  O16  110.88  3.000
 LK8  H20  C17  C18  111.76  3.000
 LK8  H19  C17  C18  109.65  3.000
 LK8  O16  C17  C18  106.46  3.000
 LK8  O16  C4   C5   124.89  3.000
 LK8  C5   C4   C3   119.92  3.000
 LK8  O16  C4   C3   115.20  3.000
 LK8  H21  C6   C1   119.57  3.000
 LK8  H21  C6   C5   118.54  3.000
 LK8  C1   C6   C5   121.89  3.000
 LK8  H22  C1   C2   121.76  3.000
 LK8  H22  C1   C6   118.63  3.000
 LK8  C2   C1   C6   119.61  3.000
 LK8  C9   N10  C3   119.62  3.000
 LK8  N10  C9   C8   121.77  3.000
 LK8  C8   C9   C15  119.32  3.000
 LK8  N10  C9   C15  118.91  3.000
 LK8  C1   C2   C7   125.04  3.000
 LK8  C7   C2   C3   115.61  3.000
 LK8  C1   C2   C3   119.35  3.000
 LK8  H4   C15  H3   106.94  3.000
 LK8  H4   C15  H2   108.77  3.000
 LK8  H3   C15  H2   108.64  3.000
 LK8  H4   C15  C9   110.81  3.000
 LK8  H3   C15  C9   110.79  3.000
 LK8  H2   C15  C9   110.78  3.000
 LK8  C4   O16  C17  118.07  3.000
 LK8  C20  C26  O27  120.22  3.000
 LK8  C20  C26  N28  116.93  3.000
 LK8  O27  C26  N28  122.82  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
 LK8  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 LK8  CONST_02  C8   C9   N10  C3      0.00   0.0  0
 LK8  CONST_03  C6   C1   C2   C3      0.00   0.0  0
 LK8  CONST_04  C8   C7   C2   C3      0.00   0.0  0
 LK8  CONST_05  N10  C3   C4   C5    180.00   0.0  0
 LK8  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 LK8  CONST_07  C2   C1   C6   C5      0.00   0.0  0
 LK8  CONST_08  C4   C3   C2   C7    180.00   0.0  0
 LK8  CONST_09  N10  C3   C2   C7      0.00   0.0  0
 LK8  CONST_10  C6   C1   C2   C7    180.00   0.0  0
 LK8  CONST_11  N10  C9   C8   C7      0.00   0.0  0
 LK8  CONST_12  C1   C2   C7   C8    180.00   0.0  0
 LK8  CONST_13  C23  C22  C21  C20     0.00   0.0  0
 LK8  CONST_14  C23  C18  C19  C20     0.00   0.0  0
 LK8  CONST_15  C22  C21  C20  C19     0.00   0.0  0
 LK8  CONST_16  C22  C23  C18  C19     0.00   0.0  0
 LK8  CONST_17  C18  C19  C20  C21     0.00   0.0  0
 LK8  CONST_18  C18  C23  C22  C21     0.00   0.0  0
 LK8  CONST_19  C1   C6   C5   C4      0.00   0.0  0
 LK8  CONST_20  C9   N10  C3   C4    180.00   0.0  0
 LK8  CONST_21  C1   C2   C3   C4      0.00   0.0  0
 LK8  CONST_22  N10  C3   C2   C1    180.00   0.0  0
 LK8  CONST_23  C2   C3   N10  C9      0.00   0.0  0
 LK8  CONST_24  C2   C7   C8   C9      0.00   0.0  0
 LK8  CONST_25  C15  C9   N10  C3    180.00   0.0  0
 LK8  CONST_26  C11  C7   C2   C3    180.00   0.0  0
 LK8  CONST_27  C15  C9   C8   C7    180.00   0.0  0
 LK8  CONST_28  C1   C2   C7   C11     0.00   0.0  0
 LK8  CONST_29  C9   C8   C7   C11   180.00   0.0  0
 LK8  CONST_30  C22  C21  C20  C26   180.00   0.0  0
 LK8  CONST_31  C18  C19  C20  C26   180.00   0.0  0
 LK8  CONST_32  C17  C18  C19  C20   180.00   0.0  0
 LK8  CONST_33  CL2  C23  C18  C19   180.00   0.0  0
 LK8  CONST_34  C21  C20  C19  CL1   180.00   0.0  0
 LK8  CONST_35  C23  C18  C19  CL1   180.00   0.0  0
 LK8  CONST_36  CL2  C23  C22  C21   180.00   0.0  0
 LK8  CONST_37  C17  C18  C23  C22   180.00   0.0  0
 LK8  CONST_38  C6   C5   C4   O16   180.00   0.0  0
 LK8  CONST_39  N10  C3   C4   O16     0.00   0.0  0
 LK8  CONST_40  C2   C3   C4   O16   180.00   0.0  0
 LK8  CONST_41  C20  C26  N28  C32   180.00   0.0  0
 LK8  CONST_42  C20  C26  N28  C29     0.00   0.0  0
 LK8  CONST_43  H1   C5   C4   C3    180.00   0.0  0
 LK8  CONST_44  H22  C1   C2   C3    180.00   0.0  0
 LK8  CONST_45  H18  C22  C21  C20   180.00   0.0  0
 LK8  CONST_46  H17  C21  C20  C19   180.00   0.0  0
 LK8  CONST_47  H21  C6   C5   C4    180.00   0.0  0
 LK8  CONST_48  H5   C8   C9   N10   180.00   0.0  0
 LK8  CONST_49  O27  C26  N28  C32     0.00   0.0  0
 LK8  CONST_50  O27  C26  N28  C29   180.00   0.0  0
 LK8  CONST_51  C32  C33  N35  C36   180.00   0.0  0
 LK8  CONST_52  H6   N35  C33  C32     0.00   0.0  0
 LK8  CONST_53  C36  N35  C33  O34     0.00   0.0  0
 LK8  Var_01    C30  C29  N28  C32    17.02  30.0  1
 LK8  Var_02    C29  C30  C31  C32    39.16  30.0  1
 LK8  Var_03    N28  C29  C30  C31   -34.23  30.0  1
 LK8  Var_04    C21  C20  C26  N28   109.17  30.0  2
 LK8  Var_05    F13  C11  C7   C8   -120.39  30.0  2
 LK8  Var_06    O16  C17  C18  C19   107.02  30.0  2
 LK8  Var_07    H2   C15  C9   C8    179.30  30.0  2
 LK8  Var_08    H7   C36  N35  C33   178.09  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
 LK8  chir_01  C32  C33  N28  C31  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
 LK8  plan-1  C20  0.020
 LK8  plan-1  C19  0.020
 LK8  plan-1  CL1  0.020
 LK8  plan-1  C21  0.020
 LK8  plan-1  C22  0.020
 LK8  plan-1  C23  0.020
 LK8  plan-1  CL2  0.020
 LK8  plan-1  C18  0.020
 LK8  plan-1  C17  0.020
 LK8  plan-1  H17  0.020
 LK8  plan-1  H18  0.020
 LK8  plan-1  C26  0.020
 LK8  plan-2  C3   0.020
 LK8  plan-2  C5   0.020
 LK8  plan-2  C7   0.020
 LK8  plan-2  C11  0.020
 LK8  plan-2  C8   0.020
 LK8  plan-2  C4   0.020
 LK8  plan-2  C6   0.020
 LK8  plan-2  C1   0.020
 LK8  plan-2  N10  0.020
 LK8  plan-2  C9   0.020
 LK8  plan-2  C2   0.020
 LK8  plan-2  H1   0.020
 LK8  plan-2  H5   0.020
 LK8  plan-2  H21  0.020
 LK8  plan-2  H22  0.020
 LK8  plan-2  C15  0.020
 LK8  plan-2  O16  0.020
 LK8  plan-3  C32  0.020
 LK8  plan-3  C29  0.020
 LK8  plan-3  N28  0.020
 LK8  plan-3  O27  0.020
 LK8  plan-3  C20  0.020
 LK8  plan-3  C26  0.020
 LK8  plan-4  O34  0.020
 LK8  plan-4  C33  0.020
 LK8  plan-4  N35  0.020
 LK8  plan-4  C36  0.020
 LK8  plan-4  C32  0.020
 LK8  plan-4  H6   0.020

