# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 14:34:35 2020
#   Inital geometry file: a 163 line input string
#   Ligand name: (3R,4R,5S)-3-(3-chlorophenyl)-4-(4-chlorophenyl)-4-cyano-N-[(3S)-3,4-dihydroxybutyl]-5-(2,2-dimethylpropyl)-D-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C[C@@H]1N[C@H]([C@H](c2cccc(Cl)c2)[C@@]1(C#N)c3ccc(Cl)cc3)C(=O)NCC[C@H](O)CO
#
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
 I09  I09  (3R,4R,5S)-3-(3-chlorophenyl)-4-(4-chlorophenyl)-4-cyano-N-[(3S)-3,4-dihydroxybutyl]-5-(2,2-dimethylpropyl)-D-prolinamide  ligand  68  35  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_I09
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
 I09  C1   C   CH1   0  -0.190  -0.1345   0.0499  -1.6893
 I09  C10  C   C     0   0.575  -1.6091  -0.3331  -1.7155
 I09  N11  N   NH1   0  -0.640  -2.4484   0.6764  -1.9740
 I09  C12  C   CH2   0  -0.238  -3.8917   0.5570  -1.9601
 I09  C13  C   CH2   0  -0.504  -4.5236   1.8663  -1.5102
 I09  C14  C   CH1   0  -0.003  -6.0411   1.7745  -1.3812
 I09  O14  O   OH1   0  -0.663  -6.6559   1.3264  -2.5701
 I09  C15  C   CH2   0  -0.153  -6.6063   3.1051  -0.9125
 I09  O15  O   OH1   0  -0.670  -7.9861   2.9655  -0.6748
 I09  O10  O   O     0  -0.489  -1.9673  -1.4731  -1.4599
 I09  N1   N   NH1   0  -0.580   0.6853  -0.9356  -2.3787
 I09  C2   C   CH1   0  -0.387   0.3397   0.0624  -0.2156
 I09  C21  C   CR6   0   0.215   0.2024   1.3492   0.5461
 I09  C26  C   CR16  0  -0.321   0.4227   2.6000  -0.0247
 I09  C25  C   CR16  0  -0.241   0.3213   3.7514   0.7425
 I09  C22  C   CR16  0  -0.269  -0.1206   1.2771   1.8995
 I09  C23  C   CR6   0  -0.022  -0.2152   2.4349   2.6526
 I09  CL2  CL  CL    0  -0.128  -0.6192   2.3163   4.3346
 I09  C24  C   CR16  0  -0.228   0.0010   3.6823   2.0900
 I09  C3   C   CT    0  -0.260   1.7784  -0.5158  -0.3062
 I09  C37  C   CSP   0   0.128   2.6636   0.5090  -0.8555
 I09  N37  N   NS    0  -0.242   3.3344   1.3155  -1.3279
 I09  C31  C   CR6   0   0.247   2.2976  -1.0526   1.0079
 I09  C32  C   CR16  0  -0.325   3.4503  -0.5630   1.6111
 I09  C33  C   CR16  0  -0.188   3.9018  -1.0724   2.8206
 I09  C36  C   CR16  0  -0.336   1.5981  -2.0728   1.6523
 I09  C35  C   CR16  0  -0.193   2.0355  -2.5932   2.8583
 I09  C34  C   CR6   0  -0.054   3.1897  -2.0864   3.4354
 I09  CL3  CL  CL    0  -0.123   3.7411  -2.7285   4.9458
 I09  C4   C   CH1   0  -0.050   1.5453  -1.5932  -1.4177
 I09  C41  C   CH2   0  -0.427   2.8244  -2.1770  -1.9907
 I09  C42  C   CT    0  -0.082   2.7016  -3.4241  -2.8878
 I09  C45  C   CH3   0  -0.649   1.9984  -3.1102  -4.2095
 I09  C44  C   CH3   0  -0.639   4.1260  -3.8953  -3.1944
 I09  C43  C   CH3   0  -0.654   1.9536  -4.5426  -2.1621
 I09  H1   H   HCH1  0   0.284   0.0089   1.0288  -2.1521
 I09  H2   H   HNH1  0   0.399  -2.0615   1.5655  -2.2486
 I09  H3   H   HCH2  0   0.240  -4.2579   0.2730  -2.9495
 I09  H4   H   HCH2  0   0.242  -4.1626  -0.2450  -1.2726
 I09  H5   H   HCH2  0   0.242  -4.1028   2.1480  -0.5413
 I09  H6   H   HCH2  0   0.235  -4.2614   2.6673  -2.2123
 I09  H7   H   HCH1  0   0.229  -6.2777   1.0148  -0.6277
 I09  H8   H   HOH1  0   0.442  -6.4563   1.9565  -3.2718
 I09  H9   H   HCH2  0   0.198  -6.0657   3.4127  -0.0079
 I09  H10  H   HCH2  0   0.191  -6.4000   3.8679  -1.6785
 I09  H11  H   HOH1  0   0.455  -8.3307   3.8203  -0.4021
 I09  H12  H   HNH1  0   0.366   1.2289  -0.4918  -3.1068
 I09  H14  H   HCH1  0   0.302  -0.2311  -0.6979   0.3241
 I09  H15  H   HCR6  0   0.260   0.6769   2.6971  -1.0716
 I09  H16  H   HCR6  0   0.271   0.4929   4.7171   0.2864
 I09  H17  H   HCR6  0   0.274  -0.3030   0.3151   2.3617
 I09  H18  H   HCR6  0   0.282  -0.0826   4.5808   2.6858
 I09  H19  H   HCR6  0   0.268   4.0243   0.2305   1.1508
 I09  H20  H   HCR6  0   0.285   4.8008  -0.6758   3.2723
 I09  H21  H   HCR6  0   0.272   0.6889  -2.4792   1.2269
 I09  H22  H   HCR6  0   0.286   1.4767  -3.3826   3.3420
 I09  H23  H   HCH1  0   0.258   0.9788  -2.3897  -0.9252
 I09  H24  H   HCH2  0   0.236   3.3660  -1.4000  -2.5428
 I09  H25  H   HCH2  0   0.241   3.4627  -2.4430  -1.1414
 I09  H26  H   HCH3  0   0.217   2.4960  -2.2934  -4.7390
 I09  H27  H   HCH3  0   0.223   2.0181  -3.9836  -4.8643
 I09  H28  H   HCH3  0   0.235   0.9571  -2.8270  -4.0600
 I09  H29  H   HCH3  0   0.223   4.7015  -3.1145  -3.6969
 I09  H30  H   HCH3  0   0.223   4.6617  -4.1688  -2.2825
 I09  H31  H   HCH3  0   0.226   4.1152  -4.7710  -3.8468
 I09  H32  H   HCH3  0   0.230   1.9453  -5.4535  -2.7643
 I09  H33  H   HCH3  0   0.223   2.4259  -4.7814  -1.2065
 I09  H34  H   HCH3  0   0.227   0.9135  -4.2783  -1.9641

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
 I09  C44  C42  single    1.531  0.020  1.531
 I09  C43  C42  single    1.529  0.020  1.529
 I09  C42  C45  single    1.530  0.020  1.530
 I09  C42  C41  single    1.541  0.020  1.541
 I09  C41  C4   single    1.518  0.020  1.518
 I09  CL3  C34  single    1.731  0.020  1.731
 I09  C33  C34  aromatic  1.383  0.020  1.383
 I09  C33  C32  aromatic  1.388  0.020  1.388
 I09  C4   N1   single    1.448  0.020  1.448
 I09  C4   C3   single    1.565  0.020  1.565
 I09  C34  C35  aromatic  1.386  0.020  1.386
 I09  C32  C31  aromatic  1.390  0.020  1.390
 I09  O14  C14  single    1.412  0.020  1.412
 I09  N1   C1   single    1.456  0.020  1.456
 I09  C35  C36  aromatic  1.384  0.020  1.384
 I09  C12  N11  single    1.448  0.020  1.448
 I09  C12  C13  single    1.522  0.020  1.522
 I09  C31  C36  aromatic  1.395  0.020  1.395
 I09  C31  C3   single    1.512  0.020  1.512
 I09  N11  C10  single    1.338  0.020  1.338
 I09  C3   C37  single    1.461  0.020  1.461
 I09  C3   C2   single    1.553  0.020  1.553
 I09  C14  C13  single    1.526  0.020  1.526
 I09  C14  C15  single    1.520  0.020  1.520
 I09  C1   C10  single    1.524  0.020  1.524
 I09  C1   C2   single    1.548  0.020  1.548
 I09  C10  O10  double    1.222  0.020  1.222
 I09  C37  N37  triple    1.150  0.020  1.150
 I09  C2   C21  single    1.502  0.020  1.502
 I09  O15  C15  single    1.407  0.020  1.407
 I09  C21  C22  aromatic  1.393  0.020  1.393
 I09  C21  C26  aromatic  1.392  0.020  1.392
 I09  C22  C23  aromatic  1.384  0.020  1.384
 I09  C26  C25  aromatic  1.387  0.020  1.387
 I09  C23  CL2  single    1.734  0.020  1.734
 I09  C23  C24  aromatic  1.385  0.020  1.385
 I09  C25  C24  aromatic  1.387  0.020  1.387
 I09  C1   H1   single    0.970  0.020  1.090
 I09  N11  H2   single    0.860  0.020  1.020
 I09  C12  H3   single    0.970  0.020  1.090
 I09  C12  H4   single    0.970  0.020  1.090
 I09  C13  H5   single    0.970  0.020  1.090
 I09  C13  H6   single    0.970  0.020  1.090
 I09  C14  H7   single    0.970  0.020  1.090
 I09  O14  H8   single    0.850  0.020  0.980
 I09  C15  H9   single    0.970  0.020  1.090
 I09  C15  H10  single    0.970  0.020  1.090
 I09  O15  H11  single    0.850  0.020  0.980
 I09  N1   H12  single    0.890  0.020  1.040
 I09  C2   H14  single    0.970  0.020  1.090
 I09  C26  H15  single    0.930  0.020  1.080
 I09  C25  H16  single    0.930  0.020  1.080
 I09  C22  H17  single    0.930  0.020  1.080
 I09  C24  H18  single    0.930  0.020  1.080
 I09  C32  H19  single    0.930  0.020  1.080
 I09  C33  H20  single    0.930  0.020  1.080
 I09  C36  H21  single    0.930  0.020  1.080
 I09  C35  H22  single    0.930  0.020  1.080
 I09  C4   H23  single    0.970  0.020  1.090
 I09  C41  H24  single    0.970  0.020  1.090
 I09  C41  H25  single    0.970  0.020  1.090
 I09  C45  H26  single    0.970  0.020  1.090
 I09  C45  H27  single    0.970  0.020  1.090
 I09  C45  H28  single    0.970  0.020  1.090
 I09  C44  H29  single    0.970  0.020  1.090
 I09  C44  H30  single    0.970  0.020  1.090
 I09  C44  H31  single    0.970  0.020  1.090
 I09  C43  H32  single    0.970  0.020  1.090
 I09  C43  H33  single    0.970  0.020  1.090
 I09  C43  H34  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
 I09  H1   C1   C2   110.85  3.000
 I09  H1   C1   N1   109.40  3.000
 I09  C2   C1   N1   106.49  3.000
 I09  H1   C1   C10  110.18  3.000
 I09  C2   C1   C10  108.35  3.000
 I09  N1   C1   C10  111.52  3.000
 I09  O10  C10  N11  124.08  3.000
 I09  O10  C10  C1   120.97  3.000
 I09  N11  C10  C1   114.88  3.000
 I09  H2   N11  C12  117.25  3.000
 I09  H2   N11  C10  118.52  3.000
 I09  C12  N11  C10  124.13  3.000
 I09  H4   C12  H3   107.24  3.000
 I09  H4   C12  C13  110.07  3.000
 I09  H3   C12  C13  110.63  3.000
 I09  H4   C12  N11  108.31  3.000
 I09  H3   C12  N11  110.29  3.000
 I09  C13  C12  N11  110.23  3.000
 I09  H6   C13  H5   106.68  3.000
 I09  H6   C13  C14  109.62  3.000
 I09  H5   C13  C14  108.87  3.000
 I09  H6   C13  C12  109.86  3.000
 I09  H5   C13  C12  108.90  3.000
 I09  C14  C13  C12  112.72  3.000
 I09  H7   C14  C15  108.34  3.000
 I09  H7   C14  O14  105.37  3.000
 I09  C15  C14  O14  112.07  3.000
 I09  H7   C14  C13  108.34  3.000
 I09  C15  C14  C13  110.08  3.000
 I09  O14  C14  C13  112.40  3.000
 I09  H8   O14  C14  108.39  3.000
 I09  H10  C15  H9   106.68  3.000
 I09  H10  C15  O15  111.72  3.000
 I09  H9   C15  O15  111.80  3.000
 I09  H10  C15  C14  108.82  3.000
 I09  H9   C15  C14  108.44  3.000
 I09  O15  C15  C14  109.27  3.000
 I09  H11  O15  C15  108.14  3.000
 I09  H12  N1   C4   110.98  3.000
 I09  H12  N1   C1   110.28  3.000
 I09  C4   N1   C1   109.13  3.000
 I09  H14  C2   C3   104.69  3.000
 I09  H14  C2   C21  107.33  3.000
 I09  C3   C2   C21  115.67  3.000
 I09  H14  C2   C1   107.72  3.000
 I09  C21  C2   C1   117.50  3.000
 I09  C3   C2   C1   103.01  3.000
 I09  C22  C21  C26  118.77  3.000
 I09  C26  C21  C2   123.19  3.000
 I09  C22  C21  C2   118.01  3.000
 I09  H15  C26  C25  118.55  3.000
 I09  H15  C26  C21  120.97  3.000
 I09  C25  C26  C21  120.49  3.000
 I09  H16  C25  C24  119.40  3.000
 I09  H16  C25  C26  119.75  3.000
 I09  C24  C25  C26  120.86  3.000
 I09  H17  C22  C23  119.95  3.000
 I09  H17  C22  C21  119.98  3.000
 I09  C23  C22  C21  120.07  3.000
 I09  C24  C23  CL2  119.47  3.000
 I09  C24  C23  C22  121.43  3.000
 I09  CL2  C23  C22  119.11  3.000
 I09  H18  C24  C23  120.82  3.000
 I09  H18  C24  C25  120.79  3.000
 I09  C23  C24  C25  118.39  3.000
 I09  C4   C3   C31  115.09  3.000
 I09  C31  C3   C37  111.58  3.000
 I09  C4   C3   C37  107.82  3.000
 I09  C37  C3   C2   108.78  3.000
 I09  C31  C3   C2   113.56  3.000
 I09  C4   C3   C2    99.19  3.000
 I09  N37  C37  C3   180.00  3.000
 I09  C36  C31  C32  118.23  3.000
 I09  C36  C31  C3   119.28  3.000
 I09  C32  C31  C3   122.48  3.000
 I09  H19  C32  C33  117.86  3.000
 I09  H19  C32  C31  120.90  3.000
 I09  C33  C32  C31  121.24  3.000
 I09  H20  C33  C34  120.74  3.000
 I09  H20  C33  C32  119.99  3.000
 I09  C34  C33  C32  119.27  3.000
 I09  H21  C36  C35  117.80  3.000
 I09  H21  C36  C31  120.93  3.000
 I09  C35  C36  C31  121.26  3.000
 I09  H22  C35  C34  120.72  3.000
 I09  H22  C35  C36  120.05  3.000
 I09  C34  C35  C36  119.22  3.000
 I09  CL3  C34  C35  119.52  3.000
 I09  C35  C34  C33  120.77  3.000
 I09  CL3  C34  C33  119.71  3.000
 I09  H23  C4   C41  109.03  3.000
 I09  H23  C4   C3   104.97  3.000
 I09  C41  C4   C3   114.02  3.000
 I09  H23  C4   N1   108.77  3.000
 I09  C3   C4   N1   104.31  3.000
 I09  C41  C4   N1   115.13  3.000
 I09  H25  C41  H24  105.95  3.000
 I09  H25  C41  C42  107.54  3.000
 I09  H24  C41  C42  108.65  3.000
 I09  H25  C41  C4   106.96  3.000
 I09  H24  C41  C4   109.49  3.000
 I09  C42  C41  C4   117.62  3.000
 I09  C43  C42  C44  108.97  3.000
 I09  C43  C42  C45  109.60  3.000
 I09  C44  C42  C45  108.52  3.000
 I09  C45  C42  C41  111.94  3.000
 I09  C43  C42  C41  110.78  3.000
 I09  C44  C42  C41  106.94  3.000
 I09  H28  C45  H27  107.91  3.000
 I09  H28  C45  H26  107.90  3.000
 I09  H27  C45  H26  107.40  3.000
 I09  H28  C45  C42  111.97  3.000
 I09  H27  C45  C42  110.23  3.000
 I09  H26  C45  C42  111.26  3.000
 I09  H31  C44  H30  107.62  3.000
 I09  H31  C44  H29  107.68  3.000
 I09  H30  C44  H29  107.74  3.000
 I09  H31  C44  C42  110.92  3.000
 I09  H30  C44  C42  111.47  3.000
 I09  H29  C44  C42  111.24  3.000
 I09  H34  C43  H33  107.83  3.000
 I09  H34  C43  H32  107.14  3.000
 I09  H33  C43  H32  107.66  3.000
 I09  H34  C43  C42  112.04  3.000
 I09  H33  C43  C42  111.33  3.000
 I09  H32  C43  C42  110.62  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
 I09  CONST_01  C24  C23  C22  C21     0.00   0.0  0
 I09  CONST_02  C24  C25  C26  C21     0.00   0.0  0
 I09  CONST_03  C23  C22  C21  C26     0.00   0.0  0
 I09  CONST_04  C23  C24  C25  C26     0.00   0.0  0
 I09  CONST_05  C22  C21  C26  C25     0.00   0.0  0
 I09  CONST_06  C22  C23  C24  C25     0.00   0.0  0
 I09  CONST_07  C34  C33  C32  C31     0.00   0.0  0
 I09  CONST_08  C34  C35  C36  C31     0.00   0.0  0
 I09  CONST_09  C35  C34  C33  C32     0.00   0.0  0
 I09  CONST_10  C35  C36  C31  C32     0.00   0.0  0
 I09  CONST_11  C36  C35  C34  C33     0.00   0.0  0
 I09  CONST_12  C36  C31  C32  C33     0.00   0.0  0
 I09  CONST_13  C23  C22  C21  C2    180.00   0.0  0
 I09  CONST_14  C25  C26  C21  C2    180.00   0.0  0
 I09  CONST_15  C33  C32  C31  C3    180.00   0.0  0
 I09  CONST_16  C35  C36  C31  C3    180.00   0.0  0
 I09  CONST_17  CL2  C23  C22  C21   180.00   0.0  0
 I09  CONST_18  CL2  C23  C24  C25   180.00   0.0  0
 I09  CONST_19  CL3  C34  C33  C32   180.00   0.0  0
 I09  CONST_20  CL3  C34  C35  C36   180.00   0.0  0
 I09  CONST_21  H17  C22  C21  C2      0.00   0.0  0
 I09  CONST_22  H15  C26  C21  C2      0.00   0.0  0
 I09  CONST_23  H16  C25  C26  C21   180.00   0.0  0
 I09  CONST_24  H18  C24  C25  C26   180.00   0.0  0
 I09  CONST_25  H19  C32  C31  C3      0.00   0.0  0
 I09  CONST_26  H21  C36  C31  C3      0.00   0.0  0
 I09  CONST_27  H20  C33  C32  C31   180.00   0.0  0
 I09  CONST_28  H22  C35  C36  C31   180.00   0.0  0
 I09  CONST_29  C12  N11  C10  C1    180.00   0.0  0
 I09  CONST_30  H2   N11  C10  C1      0.00   0.0  0
 I09  CONST_31  O10  C10  N11  C12     0.00   0.0  0
 I09  Var_01    C44  C42  C41  C4   -173.68  30.0  3
 I09  Var_02    C13  C12  N11  C10   147.97  30.0  1
 I09  Var_03    C14  C13  C12  N11  -175.99  30.0  3
 I09  Var_04    H29  C44  C42  C41   -59.08  30.0  3
 I09  Var_05    H32  C43  C42  C41  -174.96  30.0  3
 I09  Var_06    H26  C45  C42  C41    55.12  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
 I09  chir_01  C1   N1   C10  C2   negativ
 I09  chir_02  C14  O14  C13  C15  negativ
 I09  chir_03  C2   C3   C1   C21  positiv
 I09  chir_04  C3   C2   C31  C4   negativ
 I09  chir_05  C4   N1   C41  C3   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
 I09  plan-1  C2   0.020
 I09  plan-1  C21  0.020
 I09  plan-1  C26  0.020
 I09  plan-1  C25  0.020
 I09  plan-1  C22  0.020
 I09  plan-1  C23  0.020
 I09  plan-1  CL2  0.020
 I09  plan-1  C24  0.020
 I09  plan-1  H15  0.020
 I09  plan-1  H16  0.020
 I09  plan-1  H17  0.020
 I09  plan-1  H18  0.020
 I09  plan-2  C3   0.020
 I09  plan-2  C31  0.020
 I09  plan-2  C32  0.020
 I09  plan-2  C33  0.020
 I09  plan-2  C36  0.020
 I09  plan-2  C35  0.020
 I09  plan-2  C34  0.020
 I09  plan-2  CL3  0.020
 I09  plan-2  H19  0.020
 I09  plan-2  H20  0.020
 I09  plan-2  H21  0.020
 I09  plan-2  H22  0.020
 I09  plan-3  C1   0.020
 I09  plan-3  C10  0.020
 I09  plan-3  N11  0.020
 I09  plan-3  C12  0.020
 I09  plan-3  O10  0.020
 I09  plan-3  H2   0.020

