# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 06:11:23 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 4-(3-chloranyl-2-fluoranyl-phenoxy)-1-[[6-(1,3-thiazol-2-ylamino)pyridin-2-yl]methyl]cyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@]1(CC[C@@H](CC1)Oc2cccc(Cl)c2F)Cc3cccc(Nc4sccn4)n3
#
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
 5VC  5VC  '4-(3-chloranyl-2-fluoranyl-phenoxy)-1-[[6-(1,3-thiazol-2-ylamino)pyridin-2-yl]methyl]cyclohexane-1-carboxylic acid'  ligand  51  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5VC
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
 5VC  C13  C   CR6    0   0.459   4.0887  -0.7120  -0.5217
 5VC  C14  C   CR16   0  -0.384   3.9506  -2.0959  -0.4030
 5VC  C15  C   CR16   0  -0.147   2.6830  -2.6173  -0.5984
 5VC  C16  C   CR16   0  -0.364   1.6189  -1.7784  -0.8892
 5VC  C11  C   CR6    0   0.259   1.8582  -0.4094  -0.9785
 5VC  C21  C   CR15   0   0.016   8.2044  -1.8501   0.3083
 5VC  C27  C   CR16   0  -0.245  -7.6335   0.9588   0.3104
 5VC  O23  O   O2     0  -0.488  -3.6964  -0.3355   0.1940
 5VC  C24  C   CR6    0   0.265  -4.9332   0.1699   0.2461
 5VC  C25  C   CR6    0   0.527  -5.9600  -0.7173  -0.0883
 5VC  C26  C   CR6    0  -0.229  -7.2841  -0.3345  -0.0562
 5VC  C18  C   CR5    0   0.318   6.5280  -0.4992  -0.1062
 5VC  N22  N   N      0  -0.448   6.8605  -1.7382   0.0730
 5VC  S19  S   S2     0   0.184   7.8547   0.6292   0.0025
 5VC  C20  C   CR15   0  -0.529   8.9128  -0.6996   0.3131
 5VC  N17  N   NH1    0  -0.733   5.2828  -0.0232  -0.3646
 5VC  C10  C   CH2    0  -0.490   0.7483   0.5603  -1.2546
 5VC  C1   C   CT     0  -0.213   0.2658   1.3304  -0.0026
 5VC  C7   C   C      0   0.476   1.4018   2.2948   0.4500
 5VC  O8   O   OC    -1  -0.621   1.7219   3.1814  -0.3682
 5VC  O9   O   O      0  -0.599   1.8805   2.1429   1.5894
 5VC  C2   C   CH2    0  -0.422  -0.1508   0.3791   1.1234
 5VC  C3   C   CH2    0  -0.461  -1.4090  -0.4313   0.8180
 5VC  C4   C   CH1    0   0.047  -2.5654   0.4927   0.4871
 5VC  F30  F   F      0  -0.293  -5.6370  -1.9633  -0.4427
 5VC  CL3  CL  CL     0  -0.093  -8.4918  -1.4897  -0.4800
 5VC  C28  C   CR16   0  -0.264  -6.6237   1.8449   0.6395
 5VC  C29  C   CR16   0  -0.364  -5.2865   1.4664   0.6097
 5VC  C5   C   CH2    0  -0.481  -2.2161   1.3969  -0.6844
 5VC  C6   C   CH2    0  -0.428  -0.9487   2.1945  -0.3877
 5VC  N12  N   N      0  -0.454   3.0743   0.0944  -0.8075
 5VC  H1   H   HCR6   0   0.287   4.7931  -2.7282  -0.1757
 5VC  H2   H   HCR6   0   0.266   2.5302  -3.6862  -0.5216
 5VC  H3   H   HCR6   0   0.253   0.6228  -2.1716  -1.0427
 5VC  H6   H   HCR5   0   0.304   9.9680  -0.5522   0.4747
 5VC  H7   H   HNH1   0   0.413   5.1748   0.9750  -0.4703
 5VC  H8   H   HCH2   0   0.245   1.0866   1.2943  -1.9878
 5VC  H9   H   HCH2   0   0.238  -0.0803   0.0167  -1.7120
 5VC  H11  H   HCH2   0   0.232   0.6635  -0.3036   1.3718
 5VC  H12  H   HCH2   0   0.218  -0.3326   0.9682   2.0260
 5VC  H13  H   HCH2   0   0.224  -1.2456  -1.1202  -0.0175
 5VC  H14  H   HCH2   0   0.241  -1.6639  -1.0462   1.6848
 5VC  H15  H   HCH1   0   0.223  -2.7843   1.1007   1.3746
 5VC  H16  H   HCR6   0   0.274  -6.8771   2.8565   0.9254
 5VC  H17  H   HCR6   0   0.292  -4.5317   2.1946   0.8705
 5VC  H18  H   HCH2   0   0.232  -2.0942   0.7832  -1.5820
 5VC  H19  H   HCH2   0   0.247  -3.0312   2.0937  -0.8976
 5VC  H20  H   HCH2   0   0.223  -1.1598   2.8846   0.4380
 5VC  H21  H   HCH2   0   0.233  -0.7046   2.8201  -1.2473
 5VC  H4   H   HCR5   0   0.271   8.6299  -2.8290   0.4768
 5VC  H5   H   HCR6   0   0.284  -8.6721   1.2564   0.3350

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
 5VC  C27  C28  aromatic  1.383  0.020  1.383
 5VC  C27  C26  aromatic  1.389  0.020  1.389
 5VC  CL3  C26  single    1.724  0.020  1.724
 5VC  C28  C29  aromatic  1.390  0.020  1.390
 5VC  C26  C25  aromatic  1.379  0.020  1.379
 5VC  C21  N22  aromatic  1.369  0.020  1.369
 5VC  C21  C20  aromatic  1.351  0.020  1.351
 5VC  C29  C24  aromatic  1.392  0.020  1.392
 5VC  C25  C24  aromatic  1.398  0.020  1.398
 5VC  C25  F30  single    1.335  0.020  1.335
 5VC  N22  C18  aromatic  1.295  0.020  1.295
 5VC  C20  S19  aromatic  1.727  0.020  1.727
 5VC  C24  O23  single    1.337  0.020  1.337
 5VC  C18  S19  aromatic  1.745  0.020  1.745
 5VC  C18  N17  single    1.358  0.020  1.358
 5VC  N17  C13  single    1.387  0.020  1.387
 5VC  O23  C4   single    1.432  0.020  1.432
 5VC  C5   C4   single    1.521  0.020  1.521
 5VC  C5   C6   single    1.527  0.020  1.527
 5VC  C4   C3   single    1.517  0.020  1.517
 5VC  C6   C1   single    1.540  0.020  1.540
 5VC  C13  N12  aromatic  1.327  0.020  1.327
 5VC  C13  C14  aromatic  1.396  0.020  1.396
 5VC  N12  C11  aromatic  1.327  0.020  1.327
 5VC  C14  C15  aromatic  1.385  0.020  1.385
 5VC  O9   C7   deloc     1.245  0.020  1.245
 5VC  C3   C2   single    1.527  0.020  1.527
 5VC  C11  C10  single    1.500  0.020  1.500
 5VC  C11  C16  aromatic  1.393  0.020  1.393
 5VC  C1   C2   single    1.532  0.020  1.532
 5VC  C1   C10  single    1.547  0.020  1.547
 5VC  C1   C7   single    1.557  0.020  1.557
 5VC  C15  C16  aromatic  1.386  0.020  1.386
 5VC  C7   O8   deloc     1.248  0.020  1.248
 5VC  C14  H1   single    0.930  0.020  1.080
 5VC  C15  H2   single    0.930  0.020  1.080
 5VC  C16  H3   single    0.930  0.020  1.080
 5VC  C21  H4   single    0.930  0.020  1.080
 5VC  C27  H5   single    0.930  0.020  1.080
 5VC  C20  H6   single    0.930  0.020  1.080
 5VC  N17  H7   single    0.860  0.020  1.020
 5VC  C10  H8   single    0.970  0.020  1.090
 5VC  C10  H9   single    0.970  0.020  1.090
 5VC  C2   H11  single    0.970  0.020  1.090
 5VC  C2   H12  single    0.970  0.020  1.090
 5VC  C3   H13  single    0.970  0.020  1.090
 5VC  C3   H14  single    0.970  0.020  1.090
 5VC  C4   H15  single    0.970  0.020  1.090
 5VC  C28  H16  single    0.930  0.020  1.080
 5VC  C29  H17  single    0.930  0.020  1.080
 5VC  C5   H18  single    0.970  0.020  1.090
 5VC  C5   H19  single    0.970  0.020  1.090
 5VC  C6   H20  single    0.970  0.020  1.090
 5VC  C6   H21  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
 5VC  N12  C13  N17  112.37  3.000
 5VC  N12  C13  C14  123.04  3.000
 5VC  N17  C13  C14  124.59  3.000
 5VC  H1   C14  C15  121.64  3.000
 5VC  H1   C14  C13  121.49  3.000
 5VC  C15  C14  C13  116.87  3.000
 5VC  H2   C15  C16  120.28  3.000
 5VC  H2   C15  C14  119.41  3.000
 5VC  C16  C15  C14  120.31  3.000
 5VC  H3   C16  C11  120.43  3.000
 5VC  H3   C16  C15  121.12  3.000
 5VC  C11  C16  C15  118.46  3.000
 5VC  N12  C11  C10  117.15  3.000
 5VC  C10  C11  C16  121.35  3.000
 5VC  N12  C11  C16  121.49  3.000
 5VC  H4   C21  C20  124.37  3.000
 5VC  H4   C21  N22  119.17  3.000
 5VC  C20  C21  N22  116.47  3.000
 5VC  H5   C27  C28  121.31  3.000
 5VC  H5   C27  C26  120.28  3.000
 5VC  C28  C27  C26  118.41  3.000
 5VC  C4   O23  C24  120.26  3.000
 5VC  C29  C24  C25  117.85  3.000
 5VC  C25  C24  O23  115.49  3.000
 5VC  C29  C24  O23  126.66  3.000
 5VC  F30  C25  C26  119.85  3.000
 5VC  F30  C25  C24  118.57  3.000
 5VC  C26  C25  C24  121.59  3.000
 5VC  CL3  C26  C25  118.75  3.000
 5VC  C25  C26  C27  120.41  3.000
 5VC  CL3  C26  C27  120.84  3.000
 5VC  N17  C18  S19  118.84  3.000
 5VC  N17  C18  N22  126.66  3.000
 5VC  S19  C18  N22  114.51  3.000
 5VC  C18  N22  C21  110.73  3.000
 5VC  C20  S19  C18   88.82  3.000
 5VC  H6   C20  S19  121.45  3.000
 5VC  H6   C20  C21  129.08  3.000
 5VC  S19  C20  C21  109.47  3.000
 5VC  H7   N17  C18  117.68  3.000
 5VC  H7   N17  C13  112.76  3.000
 5VC  C18  N17  C13  129.55  3.000
 5VC  H9   C10  H8   106.79  3.000
 5VC  H9   C10  C1   110.51  3.000
 5VC  H8   C10  C1   107.80  3.000
 5VC  H9   C10  C11  108.48  3.000
 5VC  H8   C10  C11  109.22  3.000
 5VC  C1   C10  C11  113.81  3.000
 5VC  C6   C1   C2   108.54  3.000
 5VC  C2   C1   C7   111.68  3.000
 5VC  C6   C1   C7   107.49  3.000
 5VC  C7   C1   C10  108.42  3.000
 5VC  C2   C1   C10  111.75  3.000
 5VC  C6   C1   C10  108.84  3.000
 5VC  O9   C7   O8   126.01  3.000
 5VC  O8   C7   C1   115.87  3.000
 5VC  O9   C7   C1   118.09  3.000
 5VC  H12  C2   H11  105.86  3.000
 5VC  H12  C2   C3   108.30  3.000
 5VC  H11  C2   C3   109.16  3.000
 5VC  H12  C2   C1   108.51  3.000
 5VC  H11  C2   C1   110.66  3.000
 5VC  C3   C2   C1   113.99  3.000
 5VC  H14  C3   H13  106.62  3.000
 5VC  H14  C3   C4   109.75  3.000
 5VC  H13  C3   C4   109.30  3.000
 5VC  H14  C3   C2   109.39  3.000
 5VC  H13  C3   C2   111.31  3.000
 5VC  C4   C3   C2   110.39  3.000
 5VC  H15  C4   C5   109.83  3.000
 5VC  H15  C4   C3   108.24  3.000
 5VC  C5   C4   C3   110.81  3.000
 5VC  H15  C4   O23  109.16  3.000
 5VC  C3   C4   O23  107.13  3.000
 5VC  C5   C4   O23  111.57  3.000
 5VC  H16  C28  C29  119.07  3.000
 5VC  H16  C28  C27  119.42  3.000
 5VC  C29  C28  C27  121.51  3.000
 5VC  H17  C29  C28  118.89  3.000
 5VC  H17  C29  C24  120.88  3.000
 5VC  C28  C29  C24  120.22  3.000
 5VC  H19  C5   H18  106.30  3.000
 5VC  H19  C5   C6   108.89  3.000
 5VC  H18  C5   C6   111.10  3.000
 5VC  H19  C5   C4   110.98  3.000
 5VC  H18  C5   C4   108.91  3.000
 5VC  C6   C5   C4   110.59  3.000
 5VC  H21  C6   H20  106.00  3.000
 5VC  H21  C6   C5   109.41  3.000
 5VC  H20  C6   C5   108.38  3.000
 5VC  H21  C6   C1   110.03  3.000
 5VC  H20  C6   C1   108.46  3.000
 5VC  C5   C6   C1   114.23  3.000
 5VC  C11  N12  C13  119.83  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
 5VC  CONST_01  C16  C11  N12  C13    0.00   0.0  0
 5VC  CONST_02  C16  C15  C14  C13    0.00   0.0  0
 5VC  CONST_03  C11  N12  C13  C14    0.00   0.0  0
 5VC  CONST_04  C11  C16  C15  C14    0.00   0.0  0
 5VC  CONST_05  N12  C13  C14  C15    0.00   0.0  0
 5VC  CONST_06  N12  C11  C16  C15    0.00   0.0  0
 5VC  CONST_07  S19  C18  N22  C21    0.00   0.0  0
 5VC  CONST_08  C18  S19  C20  C21    0.00   0.0  0
 5VC  CONST_09  C24  C29  C28  C27    0.00   0.0  0
 5VC  CONST_10  C24  C25  C26  C27    0.00   0.0  0
 5VC  CONST_11  C28  C27  C26  C25    0.00   0.0  0
 5VC  CONST_12  C28  C29  C24  C25    0.00   0.0  0
 5VC  CONST_13  C29  C28  C27  C26    0.00   0.0  0
 5VC  CONST_14  C29  C24  C25  C26    0.00   0.0  0
 5VC  CONST_15  C20  C21  N22  C18    0.00   0.0  0
 5VC  CONST_16  S19  C20  C21  N22    0.00   0.0  0
 5VC  CONST_17  C20  S19  C18  N22    0.00   0.0  0
 5VC  CONST_18  C10  C11  N12  C13  180.00   0.0  0
 5VC  CONST_19  N17  C13  C14  C15  180.00   0.0  0
 5VC  CONST_20  C10  C11  C16  C15  180.00   0.0  0
 5VC  CONST_21  N17  C13  N12  C11  180.00   0.0  0
 5VC  CONST_22  N17  C18  N22  C21  180.00   0.0  0
 5VC  CONST_23  F30  C25  C26  C27  180.00   0.0  0
 5VC  CONST_24  C28  C29  C24  O23  180.00   0.0  0
 5VC  CONST_25  C26  C25  C24  O23  180.00   0.0  0
 5VC  CONST_26  CL3  C26  C25  C24  180.00   0.0  0
 5VC  CONST_27  N17  C18  S19  C20  180.00   0.0  0
 5VC  CONST_28  C29  C24  C25  F30  180.00   0.0  0
 5VC  CONST_29  C28  C27  C26  CL3  180.00   0.0  0
 5VC  CONST_30  H2   C15  C14  C13  180.00   0.0  0
 5VC  CONST_31  H3   C16  C15  C14  180.00   0.0  0
 5VC  CONST_32  H1   C14  C15  C16  180.00   0.0  0
 5VC  CONST_33  H17  C29  C28  C27  180.00   0.0  0
 5VC  CONST_34  H16  C28  C29  C24  180.00   0.0  0
 5VC  CONST_35  H5   C27  C26  C25  180.00   0.0  0
 5VC  CONST_36  H4   C21  N22  C18  180.00   0.0  0
 5VC  CONST_37  H6   C20  S19  C18  180.00   0.0  0
 5VC  Var_01    C4   C5   C6   C1    55.00  30.0  1
 5VC  Var_02    C4   C3   C2   C1   -56.47  30.0  1
 5VC  Var_03    N22  C18  N17  C13   -1.20  30.0  2
 5VC  Var_04    C18  N17  C13  C14    1.64  30.0  2
 5VC  Var_05    C1   C10  C11  C16  102.85  30.0  2
 5VC  Var_06    C29  C24  O23  C4    -2.20  30.0  2

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
 5VC  chir_01  C1  C2   C6  C7  negativ
 5VC  chir_02  C4  O23  C5  C3  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
 5VC  plan-1  C21  0.020
 5VC  plan-1  C18  0.020
 5VC  plan-1  N22  0.020
 5VC  plan-1  S19  0.020
 5VC  plan-1  C20  0.020
 5VC  plan-1  N17  0.020
 5VC  plan-1  H6   0.020
 5VC  plan-1  H4   0.020
 5VC  plan-2  C13  0.020
 5VC  plan-2  C14  0.020
 5VC  plan-2  C15  0.020
 5VC  plan-2  C16  0.020
 5VC  plan-2  C11  0.020
 5VC  plan-2  N17  0.020
 5VC  plan-2  C10  0.020
 5VC  plan-2  N12  0.020
 5VC  plan-2  H1   0.020
 5VC  plan-2  H2   0.020
 5VC  plan-2  H3   0.020
 5VC  plan-3  C27  0.020
 5VC  plan-3  O23  0.020
 5VC  plan-3  C24  0.020
 5VC  plan-3  C25  0.020
 5VC  plan-3  C26  0.020
 5VC  plan-3  F30  0.020
 5VC  plan-3  CL3  0.020
 5VC  plan-3  C28  0.020
 5VC  plan-3  C29  0.020
 5VC  plan-3  H16  0.020
 5VC  plan-3  H17  0.020
 5VC  plan-3  H5   0.020
 5VC  plan-4  C1   0.020
 5VC  plan-4  C7   0.020
 5VC  plan-4  O8   0.020
 5VC  plan-4  O9   0.020

