# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 19:02:49 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 2-chloro-5-(3-chlorophenyl)-6-{[(R)-(4-cyanophenyl)(1-methyl-1H-imidazol-5-yl)methoxy]methyl}pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cncc1[C@H](OCc2nc(Cl)c(cc2c3cccc(Cl)c3)C#N)c4ccc(cc4)C#N
#
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
 2C5  2C5  2-chloro-5-(3-chlorophenyl)-6-{[(R)-(4-cyanophenyl)(1-methyl-1H-imidazol-5-yl)methoxy]methyl}pyridine-3-carbonitrile  ligand  50  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2C5
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
 2C5  O2    O   O2    0  -0.488  -0.8030   0.3532   0.2852
 2C5  C38   C   CH1   0  -0.033  -2.0524   0.3262   0.9272
 2C5  C40   C   CR6   0   0.061  -3.1203   0.1000  -0.1250
 2C5  C43   C   CR16  0  -0.250  -4.4445  -0.0266   0.2923
 2C5  C44   C   CR16  0  -0.228  -5.4574  -0.2446  -0.6202
 2C5  C45   C   CR6   0  -0.007  -5.1485  -0.3361  -1.9784
 2C5  C46   C   CR16  0  -0.220  -3.8298  -0.2120  -2.4061
 2C5  C47   C   CR16  0  -0.307  -2.8215   0.0017  -1.4796
 2C5  C52   C   CR16  0  -0.216   1.5755  -4.6055   0.7943
 2C5  C53   C   CR6   0  -0.023   2.7853  -4.0058   1.1070
 2C5  CL1   CL  CL    0  -0.121   4.0247  -4.9370   1.8792
 2C5  C65   C   CSP   0   0.056  -6.1878  -0.5591  -2.9301
 2C5  C7    C   CR16  0  -0.250   3.0276  -2.6729   0.8183
 2C5  N1    N   NS    0  -0.252  -7.0269  -0.7459  -3.6975
 2C5  C2    C   CR16  0  -0.246   0.5944  -3.8431   0.1773
 2C5  C3    C   CR6   0   0.005   2.0352  -1.9136   0.2034
 2C5  C4    C   CR16  0  -0.274   0.8163  -2.5071  -0.1189
 2C5  C1    C   CH2   0  -0.226   0.3047   0.3796   1.1566
 2C5  N3    N   N     0  -0.448  -2.8315   3.0019   3.3681
 2C5  C10   C   CR15  0  -0.234  -2.6721   1.6889   3.0433
 2C5  C12   C   CR5   0   0.271  -2.3101   1.5587   1.7307
 2C5  N4    N   NR5   0  -0.442  -2.2434   2.8404   1.2449
 2C5  C5    C   CR15  0   0.084  -2.5589   3.6589   2.2690
 2C5  C15   C   CH3   0  -0.531  -1.8263   3.2704  -0.0736
 2C5  N2    N   N     0  -0.388   1.7678   1.8217  -0.0583
 2C5  C11   C   CR6   0   0.229   1.5153   0.5608   0.2885
 2C5  C13   C   CR6   0   0.017   2.3144  -0.5029  -0.1379
 2C5  C14   C   CR16  0  -0.134   3.4231  -0.1962  -0.9187
 2C5  C17   C   CR6   0   0.014   3.6816   1.1202  -1.2714
 2C5  C6    C   CR6   0   0.158   2.7942   2.0947  -0.8106
 2C5  C9    C   CSP   0   0.048   4.8048   1.4537  -2.0785
 2C5  N5    N   NS    0  -0.221   5.7210   1.7104  -2.7264
 2C5  CL2   CL  CL    0  -0.053   3.0516   3.7426  -1.2334
 2C5  HC38  H   HCH1  0   0.273  -2.1028  -0.5173   1.6335
 2C5  HC43  H   HCR6  0   0.271  -4.6898   0.0465   1.3446
 2C5  HC44  H   HCR6  0   0.283  -6.4811  -0.3440  -0.2857
 2C5  HC46  H   HCR6  0   0.282  -3.5915  -0.2822  -3.4588
 2C5  HC47  H   HCR6  0   0.275  -1.8034   0.0949  -1.8288
 2C5  HC52  H   HCR6  0   0.286   1.4005  -5.6471   1.0259
 2C5  HC7   H   HCR6  0   0.287   3.9757  -2.2228   1.0831
 2C5  HC2   H   HCR6  0   0.276  -0.3516  -4.3001  -0.0800
 2C5  HC4   H   HCR6  0   0.269   0.0460  -1.9339  -0.6165
 2C5  HC11  H   HCH2  0   0.259   0.2464   1.2225   1.8532
 2C5  HC12  H   HCH2  0   0.249   0.3671  -0.5399   1.7486
 2C5  HC10  H   HCR5  0   0.261  -2.8284   0.8939   3.7579
 2C5  HC5   H   HCR5  0   0.281  -2.5709   4.7328   2.1534
 2C5  H151  H   HCH3  0   0.263  -0.7669   3.0763  -0.2275
 2C5  H152  H   HCH3  0   0.258  -2.3962   2.7605  -0.8467
 2C5  H153  H   HCH3  0   0.267  -2.0074   4.3380  -0.1629
 2C5  HC14  H   HCR6  0   0.307   4.0792  -0.9826  -1.2680

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
 2C5  O2   C38   single    1.405  0.020  1.405
 2C5  O2   C1    single    1.410  0.020  1.410
 2C5  C38  C40   single    1.516  0.020  1.516
 2C5  C38  C12   single    1.494  0.020  1.494
 2C5  C38  HC38  single    0.970  0.020  1.090
 2C5  C40  C43   aromatic  1.394  0.020  1.394
 2C5  C40  C47   aromatic  1.391  0.020  1.391
 2C5  C43  C44   aromatic  1.381  0.020  1.381
 2C5  C43  HC43  single    0.930  0.020  1.080
 2C5  C44  C45   aromatic  1.396  0.020  1.396
 2C5  C44  HC44  single    0.930  0.020  1.080
 2C5  C45  C46   aromatic  1.392  0.020  1.392
 2C5  C45  C65   single    1.427  0.020  1.427
 2C5  C46  C47   aromatic  1.386  0.020  1.386
 2C5  C46  HC46  single    0.930  0.020  1.080
 2C5  C47  HC47  single    0.930  0.020  1.080
 2C5  C52  C53   aromatic  1.386  0.020  1.386
 2C5  C52  C2    aromatic  1.387  0.020  1.387
 2C5  C52  HC52  single    0.930  0.020  1.080
 2C5  C53  CL1   single    1.732  0.020  1.732
 2C5  C53  C7    aromatic  1.385  0.020  1.385
 2C5  C65  N1    triple    1.152  0.020  1.152
 2C5  C7   C3    aromatic  1.393  0.020  1.393
 2C5  C7   HC7   single    0.930  0.020  1.080
 2C5  C2   C4    aromatic  1.386  0.020  1.386
 2C5  C2   HC2   single    0.930  0.020  1.080
 2C5  C3   C4    aromatic  1.393  0.020  1.393
 2C5  C3   C13   single    1.478  0.020  1.478
 2C5  C4   HC4   single    0.930  0.020  1.080
 2C5  C1   C11   single    1.501  0.020  1.501
 2C5  C1   HC11  single    0.970  0.020  1.090
 2C5  C1   HC12  single    0.970  0.020  1.090
 2C5  N3   C10   aromatic  1.362  0.020  1.362
 2C5  N3   C5    aromatic  1.309  0.020  1.309
 2C5  C10  C12   aromatic  1.368  0.020  1.368
 2C5  C10  HC10  single    0.930  0.020  1.080
 2C5  C12  N4    aromatic  1.372  0.020  1.372
 2C5  N4   C5    aromatic  1.348  0.020  1.348
 2C5  N4   C15   single    1.448  0.020  1.448
 2C5  C5   HC5   single    0.930  0.020  1.080
 2C5  C15  H151  single    0.970  0.020  1.090
 2C5  C15  H152  single    0.970  0.020  1.090
 2C5  C15  H153  single    0.970  0.020  1.090
 2C5  N2   C11   aromatic  1.332  0.020  1.332
 2C5  N2   C6    aromatic  1.302  0.020  1.302
 2C5  C11  C13   aromatic  1.397  0.020  1.397
 2C5  C13  C14   aromatic  1.390  0.020  1.390
 2C5  C14  C17   aromatic  1.387  0.020  1.387
 2C5  C14  HC14  single    0.930  0.020  1.080
 2C5  C17  C6    aromatic  1.396  0.020  1.396
 2C5  C17  C9    single    1.423  0.020  1.423
 2C5  C6   CL2   single    1.721  0.020  1.721
 2C5  C9   N5    triple    1.151  0.020  1.151

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
 2C5  C1    O2   C38   114.63  3.000
 2C5  HC38  C38  C12   106.21  3.000
 2C5  HC38  C38  C40   107.37  3.000
 2C5  C12   C38  C40   112.02  3.000
 2C5  HC38  C38  O2    110.39  3.000
 2C5  C12   C38  O2    112.54  3.000
 2C5  C40   C38  O2    108.19  3.000
 2C5  C47   C40  C43   119.29  3.000
 2C5  C47   C40  C38   122.35  3.000
 2C5  C43   C40  C38   118.35  3.000
 2C5  HC43  C43  C44   119.12  3.000
 2C5  HC43  C43  C40   119.99  3.000
 2C5  C44   C43  C40   120.89  3.000
 2C5  HC44  C44  C45   120.29  3.000
 2C5  HC44  C44  C43   120.30  3.000
 2C5  C45   C44  C43   119.41  3.000
 2C5  C65   C45  C46   119.94  3.000
 2C5  C65   C45  C44   119.87  3.000
 2C5  C46   C45  C44   120.18  3.000
 2C5  HC46  C46  C47   120.02  3.000
 2C5  HC46  C46  C45   120.13  3.000
 2C5  C47   C46  C45   119.84  3.000
 2C5  HC47  C47  C46   118.87  3.000
 2C5  HC47  C47  C40   120.75  3.000
 2C5  C46   C47  C40   120.38  3.000
 2C5  HC52  C52  C2    120.67  3.000
 2C5  HC52  C52  C53   120.65  3.000
 2C5  C2    C52  C53   118.68  3.000
 2C5  C7    C53  CL1   119.02  3.000
 2C5  C7    C53  C52   121.47  3.000
 2C5  CL1   C53  C52   119.51  3.000
 2C5  N1    C65  C45   180.00  3.000
 2C5  HC7   C7   C3    120.36  3.000
 2C5  HC7   C7   C53   120.16  3.000
 2C5  C3    C7   C53   119.47  3.000
 2C5  HC2   C2   C4    119.76  3.000
 2C5  HC2   C2   C52   119.48  3.000
 2C5  C4    C2   C52   120.76  3.000
 2C5  C13   C3   C4    121.22  3.000
 2C5  C13   C3   C7    119.19  3.000
 2C5  C4    C3   C7    119.55  3.000
 2C5  HC4   C4   C3    120.25  3.000
 2C5  HC4   C4   C2    119.67  3.000
 2C5  C3    C4   C2    120.07  3.000
 2C5  HC12  C1   HC11  107.78  3.000
 2C5  HC12  C1   C11   111.60  3.000
 2C5  HC11  C1   C11   108.54  3.000
 2C5  HC12  C1   O2    111.29  3.000
 2C5  HC11  C1   O2    111.46  3.000
 2C5  C11   C1   O2    106.18  3.000
 2C5  C5    N3   C10   105.02  3.000
 2C5  HC10  C10  C12   127.09  3.000
 2C5  HC10  C10  N3    122.33  3.000
 2C5  C12   C10  N3    110.58  3.000
 2C5  N4    C12  C10   105.29  3.000
 2C5  N4    C12  C38   124.87  3.000
 2C5  C10   C12  C38   129.82  3.000
 2C5  C15   N4   C5    125.35  3.000
 2C5  C15   N4   C12   127.85  3.000
 2C5  C5    N4   C12   106.66  3.000
 2C5  HC5   C5   N4    121.65  3.000
 2C5  HC5   C5   N3    125.90  3.000
 2C5  N4    C5   N3    112.44  3.000
 2C5  H153  C15  H152  108.36  3.000
 2C5  H153  C15  H151  109.03  3.000
 2C5  H152  C15  H151  109.03  3.000
 2C5  H153  C15  N4    108.57  3.000
 2C5  H152  C15  N4    110.92  3.000
 2C5  H151  C15  N4    110.87  3.000
 2C5  C6    N2   C11   119.91  3.000
 2C5  C13   C11  N2    122.20  3.000
 2C5  C13   C11  C1    123.09  3.000
 2C5  N2    C11  C1    114.70  3.000
 2C5  C14   C13  C11   117.35  3.000
 2C5  C14   C13  C3    119.40  3.000
 2C5  C11   C13  C3    123.25  3.000
 2C5  HC14  C14  C17   119.64  3.000
 2C5  HC14  C14  C13   120.30  3.000
 2C5  C17   C14  C13   120.05  3.000
 2C5  C9    C17  C6    121.69  3.000
 2C5  C9    C17  C14   120.92  3.000
 2C5  C6    C17  C14   117.39  3.000
 2C5  CL2   C6   C17   119.49  3.000
 2C5  CL2   C6   N2    117.45  3.000
 2C5  C17   C6   N2    123.06  3.000
 2C5  N5    C9   C17   180.00  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
 2C5  CONST_01  C45   C44  C43  C40     0.00   0.0  0
 2C5  CONST_02  C45   C46  C47  C40     0.00   0.0  0
 2C5  CONST_03  C46   C47  C40  C43     0.00   0.0  0
 2C5  CONST_04  C46   C45  C44  C43     0.00   0.0  0
 2C5  CONST_05  C47   C40  C43  C44     0.00   0.0  0
 2C5  CONST_06  C47   C46  C45  C44     0.00   0.0  0
 2C5  CONST_07  C3    C7   C53  C52     0.00   0.0  0
 2C5  CONST_08  C3    C4   C2   C52     0.00   0.0  0
 2C5  CONST_09  C4    C2   C52  C53     0.00   0.0  0
 2C5  CONST_10  C4    C3   C7   C53     0.00   0.0  0
 2C5  CONST_11  C13   C3   C7   C53   180.00   0.0  0
 2C5  CONST_12  C2    C52  C53  C7      0.00   0.0  0
 2C5  CONST_13  C2    C4   C3   C7      0.00   0.0  0
 2C5  CONST_16  C13   C3   C4   C2    180.00   0.0  0
 2C5  CONST_17  N2    C11  C13  C3    180.00   0.0  0
 2C5  CONST_18  C17   C14  C13  C3    180.00   0.0  0
 2C5  CONST_21  N4    C12  C10  N3      0.00   0.0  0
 2C5  CONST_22  C12   N4   C5   N3      0.00   0.0  0
 2C5  CONST_23  N4    C5   N3   C10     0.00   0.0  0
 2C5  CONST_24  C5    N4   C12  C10     0.00   0.0  0
 2C5  CONST_25  C5    N3   C10  C12     0.00   0.0  0
 2C5  CONST_26  C14   C13  C11  N2      0.00   0.0  0
 2C5  CONST_27  C14   C17  C6   N2      0.00   0.0  0
 2C5  CONST_28  C17   C6   N2   C11     0.00   0.0  0
 2C5  CONST_29  C17   C14  C13  C11     0.00   0.0  0
 2C5  CONST_30  C6    N2   C11  C13     0.00   0.0  0
 2C5  CONST_31  C6    C17  C14  C13     0.00   0.0  0
 2C5  CONST_32  C44   C43  C40  C38   180.00   0.0  0
 2C5  CONST_33  C46   C47  C40  C38   180.00   0.0  0
 2C5  CONST_34  N3    C10  C12  C38   180.00   0.0  0
 2C5  CONST_35  C5    N4   C12  C38   180.00   0.0  0
 2C5  CONST_36  C65   C45  C44  C43   180.00   0.0  0
 2C5  CONST_37  C65   C45  C46  C47   180.00   0.0  0
 2C5  CONST_38  C2    C52  C53  CL1   180.00   0.0  0
 2C5  CONST_39  C3    C7   C53  CL1   180.00   0.0  0
 2C5  CONST_40  C1    C11  C13  C3      0.00   0.0  0
 2C5  CONST_41  C6    N2   C11  C1    180.00   0.0  0
 2C5  CONST_42  C14   C13  C11  C1    180.00   0.0  0
 2C5  CONST_43  C15   N4   C5   N3    180.00   0.0  0
 2C5  CONST_44  C15   N4   C12  C10   180.00   0.0  0
 2C5  CONST_45  C9    C17  C6   N2    180.00   0.0  0
 2C5  CONST_46  CL2   C6   N2   C11   180.00   0.0  0
 2C5  CONST_47  C9    C17  C14  C13   180.00   0.0  0
 2C5  CONST_48  CL2   C6   C17  C14   180.00   0.0  0
 2C5  CONST_49  HC44  C44  C43  C40   180.00   0.0  0
 2C5  CONST_50  HC46  C46  C47  C40   180.00   0.0  0
 2C5  CONST_51  HC47  C47  C40  C43   180.00   0.0  0
 2C5  CONST_52  HC43  C43  C44  C45   180.00   0.0  0
 2C5  CONST_53  HC7   C7   C53  C52   180.00   0.0  0
 2C5  CONST_54  HC4   C4   C2   C52   180.00   0.0  0
 2C5  CONST_55  HC2   C2   C52  C53   180.00   0.0  0
 2C5  CONST_56  HC52  C52  C53  C7    180.00   0.0  0
 2C5  CONST_57  HC14  C14  C13  C3      0.00   0.0  0
 2C5  CONST_58  HC5   C5   N3   C10   180.00   0.0  0
 2C5  CONST_59  HC10  C10  C12  N4    180.00   0.0  0
 2C5  Var_01    N2    C11  C1   O2     82.71  30.0  2
 2C5  Var_02    H151  C15  N4   C12   -67.04  30.0  2
 2C5  Var_03    C11   C1   O2   C38  -173.80  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
 2C5  chir_01  C38  O2  C40  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
 2C5  plan-1  C38   0.020
 2C5  plan-1  N3    0.020
 2C5  plan-1  C10   0.020
 2C5  plan-1  C12   0.020
 2C5  plan-1  N4    0.020
 2C5  plan-1  C5    0.020
 2C5  plan-1  C15   0.020
 2C5  plan-1  HC10  0.020
 2C5  plan-1  HC5   0.020
 2C5  plan-2  C38   0.020
 2C5  plan-2  C40   0.020
 2C5  plan-2  C43   0.020
 2C5  plan-2  C44   0.020
 2C5  plan-2  C45   0.020
 2C5  plan-2  C46   0.020
 2C5  plan-2  C47   0.020
 2C5  plan-2  C65   0.020
 2C5  plan-2  N1    0.020
 2C5  plan-2  HC43  0.020
 2C5  plan-2  HC44  0.020
 2C5  plan-2  HC46  0.020
 2C5  plan-2  HC47  0.020
 2C5  plan-3  C52   0.020
 2C5  plan-3  C53   0.020
 2C5  plan-3  CL1   0.020
 2C5  plan-3  C7    0.020
 2C5  plan-3  C2    0.020
 2C5  plan-3  C3    0.020
 2C5  plan-3  C4    0.020
 2C5  plan-3  C13   0.020
 2C5  plan-3  HC52  0.020
 2C5  plan-3  HC7   0.020
 2C5  plan-3  HC2   0.020
 2C5  plan-3  HC4   0.020
 2C5  plan-4  C3    0.020
 2C5  plan-4  C1    0.020
 2C5  plan-4  N2    0.020
 2C5  plan-4  C11   0.020
 2C5  plan-4  C13   0.020
 2C5  plan-4  C14   0.020
 2C5  plan-4  C17   0.020
 2C5  plan-4  C6    0.020
 2C5  plan-4  C9    0.020
 2C5  plan-4  N5    0.020
 2C5  plan-4  CL2   0.020
 2C5  plan-4  HC14  0.020

