# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:50:01 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: (3R)-3-({4-[(4-chlorophenyl)ethynyl]phenyl}carbonyl)nonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[C@H](CC(O)=O)C(=O)c1ccc(cc1)C#Cc2ccc(Cl)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
 HSI  HSI  '(3R)-3-({4-[(4-chlorophenyl)ethynyl]phenyl}carbonyl)nonanoic acid'  ligand  52  28  .  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_HSI
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
 HSI  C60   C   CH3    0  -0.659   7.7755  18.5080  -19.4812
 HSI  C56   C   CH2    0  -0.416   8.4459  19.6338  -20.2571
 HSI  C52   C   CH2    0  -0.424   9.1953  19.1372  -21.4863
 HSI  C48   C   CH2    0  -0.432   9.8113  20.2669  -22.3088
 HSI  C44   C   CH2    0  -0.426  10.6087  19.8131  -23.5378
 HSI  C40   C   CH2    0  -0.452  12.1101  19.5983  -23.3422
 HSI  C9    C   CH1    0  -0.353  12.4942  18.4888  -22.3337
 HSI  C5    C   CH2    0  -0.603  12.7485  19.0131  -20.9257
 HSI  C3    C   C      0   0.433  13.2188  17.9235  -19.9527
 HSI  O1    O   OC    -1  -0.581  13.7103  16.8994  -20.4791
 HSI  O4    O   O      0  -0.602  13.1016  18.1512  -18.7356
 HSI  C11   C   C      0   0.399  13.6248  17.6394  -22.8867
 HSI  O12   O   O      0  -0.418  13.3790  16.6379  -23.5308
 HSI  C13   C   CR6    0   0.024  15.0518  18.0898  -22.8010
 HSI  C14   C   CR16   0  -0.296  15.4283  19.4294  -22.7647
 HSI  C16   C   CR16   0  -0.277  16.7659  19.7932  -22.7677
 HSI  C18   C   CR6    0  -0.117  17.7623  18.8164  -22.7933
 HSI  C25   C   CSP    0   0.151  19.1372  19.1757  -22.7867
 HSI  C26   C   CSP    0   0.138  20.3096  19.4657  -22.7825
 HSI  C27   C   CR6    0  -0.101  21.6910  19.7996  -22.7776
 HSI  C28   C   CR16   0  -0.298  22.6631  18.7947  -22.7993
 HSI  C30   C   CR16   0  -0.203  24.0093  19.1149  -22.7962
 HSI  C32   C   CR6    0  -0.043  24.3891  20.4489  -22.7713
 HSI  CL1   CL  CL     0  -0.117  26.0705  20.8543  -22.7682
 HSI  C33   C   CR16   0  -0.200  23.4433  21.4636  -22.7491
 HSI  C35   C   CR16   0  -0.300  22.0988  21.1365  -22.7524
 HSI  C19   C   CR16   0  -0.287  17.3871  17.4677  -22.8307
 HSI  C21   C   CR16   0  -0.267  16.0530  17.1178  -22.8472
 HSI  H601  H   HCH3   0   0.224   7.2481  18.8828  -18.6032
 HSI  H602  H   HCH3   0   0.215   7.0487  17.9815  -20.1025
 HSI  H603  H   HCH3   0   0.215   8.5075  17.7744  -19.1384
 HSI  H561  H   HCH2   0   0.208   7.6921  20.3671  -20.5609
 HSI  H562  H   HCH2   0   0.210   9.1417  20.1680  -19.6026
 HSI  H521  H   HCH2   0   0.218   9.9624  18.4264  -21.1672
 HSI  H522  H   HCH2   0   0.212   8.5104  18.5696  -22.1259
 HSI  H481  H   HCH2   0   0.222   8.9949  20.9166  -22.6383
 HSI  H482  H   HCH2   0   0.213  10.4428  20.8925  -21.6692
 HSI  H441  H   HCH2   0   0.217  10.1655  18.8973  -23.9435
 HSI  H442  H   HCH2   0   0.228  10.4988  20.5647  -24.3240
 HSI  H401  H   HCH2   0   0.237  12.5313  19.3718  -24.3266
 HSI  H402  H   HCH2   0   0.227  12.5646  20.5460  -23.0376
 HSI  H9    H   HCH1   0   0.247  11.6543  17.7889  -22.2893
 HSI  H51   H   HCH2   0   0.236  13.4979  19.8119  -20.9366
 HSI  H52   H   HCH2   0   0.246  11.8436  19.4872  -20.5396
 HSI  H14   H   HCR6   0   0.263  14.6853  20.2146  -22.7554
 HSI  H16   H   HCR6   0   0.260  17.0392  20.8399  -22.7509
 HSI  H28   H   HCR6   0   0.271  22.3625  17.7557  -22.8192
 HSI  H30   H   HCR6   0   0.286  24.7537  18.3306  -22.8133
 HSI  H33   H   HCR6   0   0.285  23.7493  22.5007  -22.7295
 HSI  H35   H   HCR6   0   0.271  21.3584  21.9249  -22.7352
 HSI  H19   H   HCR6   0   0.260  18.1498  16.7004  -22.8502
 HSI  H21   H   HCR6   0   0.258  15.7825  16.0711  -22.8829

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
 HSI  C60  C56   single    1.523  0.020  1.523
 HSI  C60  H601  single    0.970  0.020  1.090
 HSI  C60  H602  single    0.970  0.020  1.090
 HSI  C60  H603  single    0.970  0.020  1.090
 HSI  C56  C52   single    1.523  0.020  1.523
 HSI  C56  H561  single    0.970  0.020  1.090
 HSI  C56  H562  single    0.970  0.020  1.090
 HSI  C52  C48   single    1.527  0.020  1.527
 HSI  C52  H521  single    0.970  0.020  1.090
 HSI  C52  H522  single    0.970  0.020  1.090
 HSI  C48  C44   single    1.534  0.020  1.534
 HSI  C48  H481  single    0.970  0.020  1.090
 HSI  C48  H482  single    0.970  0.020  1.090
 HSI  C44  C40   single    1.529  0.020  1.529
 HSI  C44  H441  single    0.970  0.020  1.090
 HSI  C44  H442  single    0.970  0.020  1.090
 HSI  C40  C9    single    1.548  0.020  1.548
 HSI  C40  H401  single    0.970  0.020  1.090
 HSI  C40  H402  single    0.970  0.020  1.090
 HSI  C9   C11   single    1.518  0.020  1.518
 HSI  C9   C5    single    1.524  0.020  1.524
 HSI  C9   H9    single    0.970  0.020  1.090
 HSI  C5   C3    single    1.535  0.020  1.535
 HSI  C5   H51   single    0.970  0.020  1.090
 HSI  C5   H52   single    0.970  0.020  1.090
 HSI  C3   O1    deloc     1.252  0.020  1.252
 HSI  C3   O4    deloc     1.244  0.020  1.244
 HSI  C11  O12   double    1.216  0.020  1.216
 HSI  C11  C13   single    1.499  0.020  1.499
 HSI  C13  C21   aromatic  1.396  0.020  1.396
 HSI  C13  C14   aromatic  1.392  0.020  1.392
 HSI  C14  C16   aromatic  1.386  0.020  1.386
 HSI  C14  H14   single    0.930  0.020  1.080
 HSI  C16  C18   aromatic  1.396  0.020  1.396
 HSI  C16  H16   single    0.930  0.020  1.080
 HSI  C18  C19   aromatic  1.400  0.020  1.400
 HSI  C18  C25   single    1.421  0.020  1.421
 HSI  C25  C26   triple    1.208  0.020  1.208
 HSI  C26  C27   single    1.421  0.020  1.421
 HSI  C27  C35   aromatic  1.398  0.020  1.398
 HSI  C27  C28   aromatic  1.398  0.020  1.398
 HSI  C28  C30   aromatic  1.384  0.020  1.384
 HSI  C28  H28   single    0.930  0.020  1.080
 HSI  C30  C32   aromatic  1.387  0.020  1.387
 HSI  C30  H30   single    0.930  0.020  1.080
 HSI  C32  C33   aromatic  1.387  0.020  1.387
 HSI  C32  CL1   single    1.730  0.020  1.730
 HSI  C33  C35   aromatic  1.384  0.020  1.384
 HSI  C33  H33   single    0.930  0.020  1.080
 HSI  C35  H35   single    0.930  0.020  1.080
 HSI  C19  C21   aromatic  1.379  0.020  1.379
 HSI  C19  H19   single    0.930  0.020  1.080
 HSI  C21  H21   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
 HSI  H603  C60  H602  107.52  3.000
 HSI  H603  C60  H601  107.60  3.000
 HSI  H602  C60  H601  107.58  3.000
 HSI  H603  C60  C56   111.20  3.000
 HSI  H602  C60  C56   111.08  3.000
 HSI  H601  C60  C56   111.66  3.000
 HSI  H562  C56  H561  106.06  3.000
 HSI  H562  C56  C52   109.21  3.000
 HSI  H561  C56  C52   109.47  3.000
 HSI  H562  C56  C60   109.64  3.000
 HSI  H561  C56  C60   109.49  3.000
 HSI  C52   C56  C60   112.76  3.000
 HSI  H522  C52  H521  105.79  3.000
 HSI  H522  C52  C48   108.73  3.000
 HSI  H521  C52  C48   110.80  3.000
 HSI  H522  C52  C56   109.42  3.000
 HSI  H521  C52  C56   108.76  3.000
 HSI  C48   C52  C56   113.08  3.000
 HSI  H482  C48  H481  105.49  3.000
 HSI  H482  C48  C44   109.71  3.000
 HSI  H481  C48  C44   108.80  3.000
 HSI  H482  C48  C52   109.91  3.000
 HSI  H481  C48  C52   107.48  3.000
 HSI  C44   C48  C52   114.99  3.000
 HSI  H442  C44  H441  105.53  3.000
 HSI  H442  C44  C40   106.70  3.000
 HSI  H441  C44  C40   109.10  3.000
 HSI  H442  C44  C48   108.70  3.000
 HSI  H441  C44  C48   109.50  3.000
 HSI  C40   C44  C48   116.71  3.000
 HSI  H402  C40  H401  105.65  3.000
 HSI  H402  C40  C9    109.65  3.000
 HSI  H401  C40  C9    110.01  3.000
 HSI  H402  C40  C44   108.77  3.000
 HSI  H401  C40  C44   106.98  3.000
 HSI  C9    C40  C44   115.32  3.000
 HSI  H9    C9   C11   103.21  3.000
 HSI  H9    C9   C5    108.10  3.000
 HSI  C11   C9   C5    113.87  3.000
 HSI  H9    C9   C40   107.12  3.000
 HSI  C5    C9   C40   113.38  3.000
 HSI  C11   C9   C40   110.39  3.000
 HSI  H52   C5   H51   104.71  3.000
 HSI  H52   C5   C3    109.75  3.000
 HSI  H51   C5   C3    108.32  3.000
 HSI  H52   C5   C9    109.74  3.000
 HSI  H51   C5   C9    110.85  3.000
 HSI  C3    C5   C9    113.12  3.000
 HSI  O4    C3   O1    126.73  3.000
 HSI  O4    C3   C5    117.49  3.000
 HSI  O1    C3   C5    115.76  3.000
 HSI  C13   C11  O12   118.05  3.000
 HSI  C13   C11  C9    121.33  3.000
 HSI  O12   C11  C9    120.21  3.000
 HSI  C21   C13  C14   118.48  3.000
 HSI  C14   C13  C11   123.24  3.000
 HSI  C21   C13  C11   118.14  3.000
 HSI  H14   C14  C16   118.20  3.000
 HSI  H14   C14  C13   120.89  3.000
 HSI  C16   C14  C13   120.90  3.000
 HSI  H16   C16  C18   119.81  3.000
 HSI  H16   C16  C14   119.84  3.000
 HSI  C18   C16  C14   120.35  3.000
 HSI  C19   C18  C25   120.19  3.000
 HSI  C25   C18  C16   120.91  3.000
 HSI  C19   C18  C16   118.90  3.000
 HSI  C26   C25  C18   180.00  3.000
 HSI  C27   C26  C25   180.00  3.000
 HSI  C35   C27  C28   119.00  3.000
 HSI  C28   C27  C26   120.45  3.000
 HSI  C35   C27  C26   120.55  3.000
 HSI  H28   C28  C30   119.51  3.000
 HSI  H28   C28  C27   119.83  3.000
 HSI  C30   C28  C27   120.66  3.000
 HSI  H30   C30  C32   120.62  3.000
 HSI  H30   C30  C28   120.12  3.000
 HSI  C32   C30  C28   119.27  3.000
 HSI  C33   C32  CL1   119.43  3.000
 HSI  CL1   C32  C30   119.44  3.000
 HSI  C33   C32  C30   121.13  3.000
 HSI  H33   C33  C35   120.11  3.000
 HSI  H33   C33  C32   120.58  3.000
 HSI  C35   C33  C32   119.31  3.000
 HSI  H35   C35  C33   119.52  3.000
 HSI  H35   C35  C27   119.85  3.000
 HSI  C33   C35  C27   120.63  3.000
 HSI  H19   C19  C21   120.10  3.000
 HSI  H19   C19  C18   119.64  3.000
 HSI  C21   C19  C18   120.25  3.000
 HSI  H21   C21  C19   119.20  3.000
 HSI  H21   C21  C13   119.70  3.000
 HSI  C19   C21  C13   121.10  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
 HSI  CONST_01  C18   C19  C21  C13    0.00   0.0  0
 HSI  CONST_02  C18   C16  C14  C13    0.00   0.0  0
 HSI  CONST_03  C19   C21  C13  C14    0.00   0.0  0
 HSI  CONST_04  C19   C18  C16  C14    0.00   0.0  0
 HSI  CONST_05  C21   C13  C14  C16    0.00   0.0  0
 HSI  CONST_06  C21   C19  C18  C16    0.00   0.0  0
 HSI  CONST_07  C32   C33  C35  C27    0.00   0.0  0
 HSI  CONST_08  C32   C30  C28  C27    0.00   0.0  0
 HSI  CONST_09  C33   C35  C27  C28    0.00   0.0  0
 HSI  CONST_10  C33   C32  C30  C28    0.00   0.0  0
 HSI  CONST_11  C35   C27  C28  C30    0.00   0.0  0
 HSI  CONST_12  C35   C33  C32  C30    0.00   0.0  0
 HSI  CONST_13  C19   C21  C13  C11  180.00   0.0  0
 HSI  CONST_14  C16   C14  C13  C11  180.00   0.0  0
 HSI  CONST_15  C25   C18  C16  C14  180.00   0.0  0
 HSI  CONST_16  C21   C19  C18  C25  180.00   0.0  0
 HSI  CONST_17  C33   C35  C27  C26  180.00   0.0  0
 HSI  CONST_18  C30   C28  C27  C26  180.00   0.0  0
 HSI  CONST_19  CL1   C32  C30  C28  180.00   0.0  0
 HSI  CONST_20  C35   C33  C32  CL1  180.00   0.0  0
 HSI  CONST_21  H19   C19  C21  C13  180.00   0.0  0
 HSI  CONST_22  H16   C16  C14  C13  180.00   0.0  0
 HSI  CONST_23  H21   C21  C13  C14  180.00   0.0  0
 HSI  CONST_24  H14   C14  C16  C18  180.00   0.0  0
 HSI  CONST_25  H33   C33  C35  C27  180.00   0.0  0
 HSI  CONST_26  H30   C30  C28  C27  180.00   0.0  0
 HSI  CONST_27  H35   C35  C27  C28  180.00   0.0  0
 HSI  CONST_28  H28   C28  C30  C32  180.00   0.0  0
 HSI  Var_01    C21   C13  C11  C9   156.40  30.0  2
 HSI  Var_02    C48   C52  C56  C60  177.10  30.0  3
 HSI  Var_03    C44   C48  C52  C56  178.45  30.0  3
 HSI  Var_04    C40   C44  C48  C52  -92.36  30.0  3
 HSI  Var_05    C9    C40  C44  C48   62.47  30.0  3
 HSI  Var_06    O1    C3   C5   C9    20.66  30.0  3
 HSI  Var_07    H601  C60  C56  C52  179.76  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
 HSI  chir_01  C9  C40  C11  C5  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
 HSI  plan-1  C11  0.020
 HSI  plan-1  C13  0.020
 HSI  plan-1  C14  0.020
 HSI  plan-1  C16  0.020
 HSI  plan-1  C18  0.020
 HSI  plan-1  C25  0.020
 HSI  plan-1  C26  0.020
 HSI  plan-1  C19  0.020
 HSI  plan-1  C21  0.020
 HSI  plan-1  H14  0.020
 HSI  plan-1  H16  0.020
 HSI  plan-1  H19  0.020
 HSI  plan-1  H21  0.020
 HSI  plan-2  C25  0.020
 HSI  plan-2  C26  0.020
 HSI  plan-2  C27  0.020
 HSI  plan-2  C28  0.020
 HSI  plan-2  C30  0.020
 HSI  plan-2  C32  0.020
 HSI  plan-2  CL1  0.020
 HSI  plan-2  C33  0.020
 HSI  plan-2  C35  0.020
 HSI  plan-2  H28  0.020
 HSI  plan-2  H30  0.020
 HSI  plan-2  H33  0.020
 HSI  plan-2  H35  0.020
 HSI  plan-3  C9   0.020
 HSI  plan-3  C11  0.020
 HSI  plan-3  O12  0.020
 HSI  plan-3  C13  0.020
 HSI  plan-4  C5   0.020
 HSI  plan-4  C3   0.020
 HSI  plan-4  O1   0.020
 HSI  plan-4  O4   0.020

