# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 11:40:35 2021
#   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  53  28  .  2022-03-29  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.662   8.2502  18.6758  -19.1935
 HSI  C56   C   CH2   0  -0.416   8.8203  19.7388  -20.1221
 HSI  C52   C   CH2   0  -0.430   9.2770  19.1686  -21.4574
 HSI  C48   C   CH2   0  -0.446   9.8377  20.2258  -22.4077
 HSI  C44   C   CH2   0  -0.427  10.5503  19.6671  -23.6451
 HSI  C40   C   CH2   0  -0.462  12.0516  19.4051  -23.5051
 HSI  C9    C   CH1   0  -0.387  12.4399  18.2994  -22.4926
 HSI  C5    C   CH2   0  -0.602  12.6954  18.8811  -21.0950
 HSI  C3    C   C     0   0.556  12.7531  17.8609  -19.9921
 HSI  O1    O   OH1   0  -0.587  13.4998  16.8133  -20.3225
 HSI  O4    O   O     0  -0.438  12.2090  17.9744  -18.9224
 HSI  C11   C   C     0   0.412  13.5814  17.4505  -23.0319
 HSI  O12   O   O     0  -0.388  13.3454  16.3784  -23.5460
 HSI  C13   C   CR6   0  -0.021  14.9941  17.9261  -22.9586
 HSI  C14   C   CR16  0  -0.280  15.3462  19.2740  -23.0014
 HSI  C16   C   CR16  0  -0.280  16.6740  19.6613  -22.9693
 HSI  C18   C   CR6   0  -0.113  17.6847  18.7019  -22.8712
 HSI  C25   C   CSP   0   0.153  19.0479  19.0972  -22.8136
 HSI  C26   C   CSP   0   0.146  20.2058  19.4362  -22.7628
 HSI  C27   C   CR6   0  -0.107  21.5669  19.8390  -22.6988
 HSI  C28   C   CR16  0  -0.297  22.5824  18.8887  -22.5551
 HSI  C30   C   CR16  0  -0.202  23.9080  19.2795  -22.4890
 HSI  C32   C   CR6   0  -0.043  24.2219  20.6288  -22.5679
 HSI  CL1   CL  CL    0  -0.116  25.8778  21.1211  -22.4856
 HSI  C33   C   CR16  0  -0.201  23.2320  21.5902  -22.7117
 HSI  C35   C   CR16  0  -0.298  21.9083  21.1928  -22.7767
 HSI  C19   C   CR16  0  -0.284  17.3351  17.3473  -22.8273
 HSI  C21   C   CR16  0  -0.259  16.0082  16.9695  -22.8839
 HSI  H601  H   HCH3  0   0.225   7.9448  19.1001  -18.2364
 HSI  H602  H   HCH3  0   0.215   7.3769  18.1914  -19.6346
 HSI  H603  H   HCH3  0   0.217   8.9908  17.8998  -18.9909
 HSI  H561  H   HCH2  0   0.212   8.0750  20.5218  -20.2926
 HSI  H562  H   HCH2  0   0.210   9.6686  20.2294  -19.6340
 HSI  H521  H   HCH2  0   0.214  10.0123  18.3822  -21.2700
 HSI  H522  H   HCH2  0   0.222   8.4383  18.6643  -21.9491
 HSI  H481  H   HCH2  0   0.233   9.0055  20.8559  -22.7336
 HSI  H482  H   HCH2  0   0.213  10.5153  20.8999  -21.8711
 HSI  H441  H   HCH2  0   0.225  10.0503  18.7508  -23.9756
 HSI  H442  H   HCH2  0   0.238  10.4384  20.3799  -24.4657
 HSI  H401  H   HCH2  0   0.256  12.4289  19.1405  -24.4964
 HSI  H402  H   HCH2  0   0.240  12.5460  20.3430  -23.2355
 HSI  H9    H   HCH1  0   0.276  11.5983  17.6033  -22.4334
 HSI  H51   H   HCH2  0   0.301  13.6329  19.4451  -21.0740
 HSI  H52   H   HCH2  0   0.294  11.9157  19.5973  -20.8445
 HSI  HO1   H   HOH1  0   0.485  13.5333  16.1770  -19.5918
 HSI  H14   H   HCR6  0   0.271  14.5929  20.0443  -23.0840
 HSI  H16   H   HCR6  0   0.269  16.9297  20.7111  -23.0168
 HSI  H28   H   HCR6  0   0.274  22.3331  17.8379  -22.4941
 HSI  H30   H   HCR6  0   0.288  24.6878  18.5390  -22.3777
 HSI  H33   H   HCR6  0   0.288  23.4871  22.6393  -22.7728
 HSI  H35   H   HCR6  0   0.274  21.1324  21.9379  -22.8878
 HSI  H19   H   HCR6  0   0.268  18.1094  16.5962  -22.7508
 HSI  H21   H   HCR6  0   0.269  15.7576  15.9176  -22.8524

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    1.522  0.020  1.522
 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    1.522  0.020  1.522
 HSI  C56  H561  single    0.970  0.020  1.090
 HSI  C56  H562  single    0.970  0.020  1.090
 HSI  C52  C48   single    1.528  0.020  1.528
 HSI  C52  H521  single    0.970  0.020  1.090
 HSI  C52  H522  single    0.970  0.020  1.090
 HSI  C48  C44   single    1.533  0.020  1.533
 HSI  C48  H481  single    0.970  0.020  1.090
 HSI  C48  H482  single    0.970  0.020  1.090
 HSI  C44  C40   single    1.530  0.020  1.530
 HSI  C44  H441  single    0.970  0.020  1.090
 HSI  C44  H442  single    0.970  0.020  1.090
 HSI  C40  C9    single    1.549  0.020  1.549
 HSI  C40  H401  single    0.970  0.020  1.090
 HSI  C40  H402  single    0.970  0.020  1.090
 HSI  C9   C11   single    1.521  0.020  1.521
 HSI  C9   C5    single    1.535  0.020  1.535
 HSI  C9   H9    single    0.970  0.020  1.090
 HSI  C5   C3    single    1.503  0.020  1.503
 HSI  C5   H51   single    0.970  0.020  1.090
 HSI  C5   H52   single    0.970  0.020  1.090
 HSI  C3   O1    single    1.328  0.020  1.328
 HSI  C3   O4    double    1.205  0.020  1.205
 HSI  O1   HO1   single    0.850  0.020  0.980
 HSI  C11  O12   double    1.212  0.020  1.212
 HSI  C11  C13   single    1.492  0.020  1.492
 HSI  C13  C21   aromatic  1.396  0.020  1.396
 HSI  C13  C14   aromatic  1.394  0.020  1.394
 HSI  C14  C16   aromatic  1.383  0.020  1.383
 HSI  C14  H14   single    0.930  0.020  1.080
 HSI  C16  C18   aromatic  1.397  0.020  1.397
 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  1.388  0.020  1.388
 HSI  C30  H30   single    0.930  0.020  1.080
 HSI  C32  C33   aromatic  1.387  0.020  1.387
 HSI  C32  CL1   single    1.729  0.020  1.729
 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  1.381  0.020  1.381
 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  107.59  3.000
 HSI  H603  C60  H601  107.68  3.000
 HSI  H602  C60  H601  107.65  3.000
 HSI  H603  C60  C56   110.82  3.000
 HSI  H602  C60  C56   111.29  3.000
 HSI  H601  C60  C56   111.63  3.000
 HSI  H562  C56  H561  106.06  3.000
 HSI  H562  C56  C52   109.06  3.000
 HSI  H561  C56  C52   109.62  3.000
 HSI  H562  C56  C60   109.34  3.000
 HSI  H561  C56  C60   109.85  3.000
 HSI  C52   C56  C60   112.70  3.000
 HSI  H522  C52  H521  105.12  3.000
 HSI  H522  C52  C48   108.68  3.000
 HSI  H521  C52  C48   110.95  3.000
 HSI  H522  C52  C56   109.67  3.000
 HSI  H521  C52  C56   108.73  3.000
 HSI  C48   C52  C56   113.36  3.000
 HSI  H482  C48  H481  105.19  3.000
 HSI  H482  C48  C44   109.38  3.000
 HSI  H481  C48  C44   108.85  3.000
 HSI  H482  C48  C52   110.36  3.000
 HSI  H481  C48  C52   107.74  3.000
 HSI  C44   C48  C52   114.86  3.000
 HSI  H442  C44  H441  105.81  3.000
 HSI  H442  C44  C40   106.31  3.000
 HSI  H441  C44  C40   109.41  3.000
 HSI  H442  C44  C48   108.71  3.000
 HSI  H441  C44  C48   109.65  3.000
 HSI  C40   C44  C48   116.39  3.000
 HSI  H402  C40  H401  105.96  3.000
 HSI  H402  C40  C9    109.74  3.000
 HSI  H401  C40  C9    109.48  3.000
 HSI  H402  C40  C44   108.60  3.000
 HSI  H401  C40  C44   107.28  3.000
 HSI  C9    C40  C44   115.34  3.000
 HSI  H9    C9   C11   103.97  3.000
 HSI  H9    C9   C5    108.66  3.000
 HSI  C11   C9   C5    114.15  3.000
 HSI  H9    C9   C40   107.27  3.000
 HSI  C5    C9   C40   111.49  3.000
 HSI  C11   C9   C40   110.78  3.000
 HSI  H52   C5   H51   105.68  3.000
 HSI  H52   C5   C3    107.78  3.000
 HSI  H51   C5   C3    107.63  3.000
 HSI  H52   C5   C9    109.86  3.000
 HSI  H51   C5   C9    110.81  3.000
 HSI  C3    C5   C9    114.65  3.000
 HSI  O4    C3   O1    123.28  3.000
 HSI  O4    C3   C5    124.74  3.000
 HSI  O1    C3   C5    111.98  3.000
 HSI  HO1   O1   C3    110.46  3.000
 HSI  C13   C11  O12   119.15  3.000
 HSI  C13   C11  C9    121.00  3.000
 HSI  O12   C11  C9    119.85  3.000
 HSI  C21   C13  C14   118.74  3.000
 HSI  C14   C13  C11   123.08  3.000
 HSI  C21   C13  C11   118.15  3.000
 HSI  H14   C14  C16   118.12  3.000
 HSI  H14   C14  C13   121.04  3.000
 HSI  C16   C14  C13   120.82  3.000
 HSI  H16   C16  C18   119.91  3.000
 HSI  H16   C16  C14   119.84  3.000
 HSI  C18   C16  C14   120.25  3.000
 HSI  C19   C18  C25   120.52  3.000
 HSI  C25   C18  C16   120.40  3.000
 HSI  C19   C18  C16   119.09  3.000
 HSI  C26   C25  C18   180.00  3.000
 HSI  C27   C26  C25   180.00  3.000
 HSI  C35   C27  C28   119.11  3.000
 HSI  C28   C27  C26   120.51  3.000
 HSI  C35   C27  C26   120.38  3.000
 HSI  H28   C28  C30   119.51  3.000
 HSI  H28   C28  C27   119.92  3.000
 HSI  C30   C28  C27   120.58  3.000
 HSI  H30   C30  C32   120.58  3.000
 HSI  H30   C30  C28   120.16  3.000
 HSI  C32   C30  C28   119.26  3.000
 HSI  C33   C32  CL1   119.39  3.000
 HSI  CL1   C32  C30   119.39  3.000
 HSI  C33   C32  C30   121.22  3.000
 HSI  H33   C33  C35   120.11  3.000
 HSI  H33   C33  C32   120.65  3.000
 HSI  C35   C33  C32   119.24  3.000
 HSI  H35   C35  C33   119.56  3.000
 HSI  H35   C35  C27   119.85  3.000
 HSI  C33   C35  C27   120.60  3.000
 HSI  H19   C19  C21   120.06  3.000
 HSI  H19   C19  C18   119.70  3.000
 HSI  C21   C19  C18   120.24  3.000
 HSI  H21   C21  C19   119.18  3.000
 HSI  H21   C21  C13   119.97  3.000
 HSI  C19   C21  C13   120.84  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  CONST_29  HO1   O1   C3   C5   180.00   0.0  0
 HSI  Var_01    C21   C13  C11  C9   151.69  30.0  2
 HSI  Var_02    C48   C52  C56  C60  179.35  30.0  3
 HSI  Var_03    C44   C48  C52  C56  168.84  30.0  3
 HSI  Var_04    C40   C44  C48  C52  -89.84  30.0  3
 HSI  Var_05    C9    C40  C44  C48   65.07  30.0  3
 HSI  Var_06    O1    C3   C5   C9    45.78  30.0  3
 HSI  Var_07    H601  C60  C56  C52  179.01  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
 HSI  plan-4  HO1  0.020

