# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 04:43:30 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  52  31  .  2021-08-05  2021-08-05  
;
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   0.477   3.9732  -0.7415  -0.5718
 5VC  C14  C   CR16  0  -0.385   3.9219  -2.1293  -0.7277
 5VC  C15  C   CR16  0  -0.140   2.7317  -2.6684  -1.1808
 5VC  C16  C   CR16  0  -0.374   1.6480  -1.8465  -1.4578
 5VC  C11  C   CR6   0   0.279   1.8013  -0.4793  -1.2717
 5VC  C21  C   CR15  0   0.017   7.9670  -1.8384   0.7421
 5VC  C27  C   CR16  0  -0.243  -7.5124   0.9308   0.6441
 5VC  O23  O   O2    0  -0.488  -3.5777  -0.3336   0.3190
 5VC  C24  C   CR6   0   0.264  -4.8151   0.1638   0.4364
 5VC  C25  C   CR6   0   0.529  -5.8498  -0.7288   0.1461
 5VC  C26  C   CR6   0  -0.230  -7.1735  -0.3565   0.2487
 5VC  C18  C   CR5   0   0.318   6.2949  -0.5029   0.2699
 5VC  N22  N   N     0  -0.446   6.6829  -1.7376   0.2788
 5VC  S19  S   S2    0   0.189   7.4888   0.6366   0.8332
 5VC  C20  C   CR15  0  -0.528   8.5730  -0.6819   1.0900
 5VC  N17  N   NH1   0  -0.734   5.0792  -0.0388  -0.1253
 5VC  C10  C   CH2   0  -0.496   0.6779   0.4840  -1.5177
 5VC  C1   C   CT    0  -0.242   0.3200   1.3265  -0.2748
 5VC  C7   C   C     0   0.610   1.4630   2.2735   0.0700
 5VC  O8   O   OH1   0  -0.599   1.8298   3.0199  -0.9664
 5VC  O9   O   O     0  -0.441   1.9433   2.4107   1.1677
 5VC  C2   C   CH2   0  -0.431   0.0143   0.4383   0.9380
 5VC  C3   C   CH2   0  -0.463  -1.2510  -0.3938   0.7584
 5VC  C4   C   CH1   0   0.048  -2.4402   0.5113   0.4960
 5VC  F30  F   F     0  -0.292  -5.5355  -1.9688  -0.2352
 5VC  CL3  CL  CL    0  -0.091  -8.3922  -1.5164  -0.1262
 5VC  C28  C   CR16  0  -0.264  -6.4940   1.8219   0.9306
 5VC  C29  C   CR16  0  -0.361  -5.1573   1.4537   0.8299
 5VC  C5   C   CH2   0  -0.489  -2.2017   1.3850  -0.7267
 5VC  C6   C   CH2   0  -0.430  -0.9196   2.2006  -0.5744
 5VC  N12  N   N     0  -0.475   2.9419   0.0477  -0.8440
 5VC  H1   H   HCR6  0   0.292   4.7723  -2.7511  -0.5009
 5VC  H2   H   HCR6  0   0.272   2.6503  -3.7395  -1.3125
 5VC  H3   H   HCR6  0   0.260   0.7086  -2.2537  -1.8059
 5VC  H5   H   HCR6  0   0.285  -8.5504   1.2207   0.7236
 5VC  H6   H   HCR5  0   0.306   9.5672  -0.5254   1.4752
 5VC  H7   H   HNH1  0   0.414   4.9207   0.9571  -0.0755
 5VC  H8   H   HCH2  0   0.274   0.9384   1.1465  -2.3464
 5VC  H9   H   HCH2  0   0.265  -0.1993  -0.0695  -1.8518
 5VC  H10  H   HOH1  0   0.476   2.5321   3.6293  -0.6962
 5VC  H11  H   HCH2  0   0.254   0.8559  -0.2228   1.1535
 5VC  H12  H   HCH2  0   0.243  -0.1078   1.0703   1.8210
 5VC  H13  H   HCH2  0   0.233  -1.1401  -1.1094  -0.0616
 5VC  H14  H   HCH2  0   0.256  -1.4236  -0.9790   1.6643
 5VC  H15  H   HCH1  0   0.231  -2.5841   1.1457   1.3802
 5VC  H16  H   HCR6  0   0.275  -6.7405   2.8287   1.2383
 5VC  H17  H   HCR6  0   0.292  -4.3960   2.1847   1.0627
 5VC  H18  H   HCH2  0   0.245  -2.1610   0.7535  -1.6184
 5VC  H19  H   HCH2  0   0.261  -3.0313   2.0797  -0.8803
 5VC  H20  H   HCH2  0   0.248  -1.0557   2.9133   0.2460
 5VC  H21  H   HCH2  0   0.259  -0.7636   2.7936  -1.4770
 5VC  H4   H   HCR5  0   0.273   8.4286  -2.8132   0.8081

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  1.391  0.020  1.391
 5VC  C25  C24  aromatic  1.397  0.020  1.397
 5VC  C25  F30  single    1.335  0.020  1.335
 5VC  N22  C18  aromatic  1.294  0.020  1.294
 5VC  C20  S19  aromatic  1.726  0.020  1.726
 5VC  C24  O23  single    1.339  0.020  1.339
 5VC  C18  S19  aromatic  1.744  0.020  1.744
 5VC  C18  N17  single    1.360  0.020  1.360
 5VC  N17  C13  single    1.384  0.020  1.384
 5VC  O23  C4   single    1.428  0.020  1.428
 5VC  C5   C4   single    1.522  0.020  1.522
 5VC  C5   C6   single    1.527  0.020  1.527
 5VC  C4   C3   single    1.517  0.020  1.517
 5VC  C6   C1   single    1.546  0.020  1.546
 5VC  C13  N12  aromatic  1.327  0.020  1.327
 5VC  C13  C14  aromatic  1.397  0.020  1.397
 5VC  N12  C11  aromatic  1.327  0.020  1.327
 5VC  C14  C15  aromatic  1.383  0.020  1.383
 5VC  O9   C7   double    1.206  0.020  1.206
 5VC  C3   C2   single    1.525  0.020  1.525
 5VC  C11  C10  single    1.500  0.020  1.500
 5VC  C11  C16  aromatic  1.388  0.020  1.388
 5VC  C1   C2   single    1.534  0.020  1.534
 5VC  C1   C10  single    1.544  0.020  1.544
 5VC  C1   C7   single    1.524  0.020  1.524
 5VC  C15  C16  aromatic  1.388  0.020  1.388
 5VC  C7   O8   single    1.329  0.020  1.329
 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  O8   H10  single    0.850  0.020  0.980
 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  112.66  3.000
 5VC  N12  C13  C14  122.64  3.000
 5VC  N17  C13  C14  124.71  3.000
 5VC  H1   C14  C15  121.55  3.000
 5VC  H1   C14  C13  121.37  3.000
 5VC  C15  C14  C13  117.08  3.000
 5VC  H2   C15  C16  120.20  3.000
 5VC  H2   C15  C14  119.37  3.000
 5VC  C16  C15  C14  120.43  3.000
 5VC  H3   C16  C11  120.65  3.000
 5VC  H3   C16  C15  121.30  3.000
 5VC  C11  C16  C15  118.04  3.000
 5VC  N12  C11  C10  116.20  3.000
 5VC  C10  C11  C16  121.85  3.000
 5VC  N12  C11  C16  121.94  3.000
 5VC  H4   C21  C20  124.39  3.000
 5VC  H4   C21  N22  119.20  3.000
 5VC  C20  C21  N22  116.41  3.000
 5VC  H5   C27  C28  121.28  3.000
 5VC  H5   C27  C26  120.26  3.000
 5VC  C28  C27  C26  118.46  3.000
 5VC  C4   O23  C24  120.37  3.000
 5VC  C29  C24  C25  117.97  3.000
 5VC  C25  C24  O23  115.40  3.000
 5VC  C29  C24  O23  126.62  3.000
 5VC  F30  C25  C26  119.88  3.000
 5VC  F30  C25  C24  118.59  3.000
 5VC  C26  C25  C24  121.54  3.000
 5VC  CL3  C26  C25  118.74  3.000
 5VC  C25  C26  C27  120.38  3.000
 5VC  CL3  C26  C27  120.87  3.000
 5VC  N17  C18  S19  118.88  3.000
 5VC  N17  C18  N22  126.55  3.000
 5VC  S19  C18  N22  114.58  3.000
 5VC  C18  N22  C21  110.72  3.000
 5VC  C20  S19  C18   88.79  3.000
 5VC  H6   C20  S19  121.44  3.000
 5VC  H6   C20  C21  129.06  3.000
 5VC  S19  C20  C21  109.50  3.000
 5VC  H7   N17  C18  117.56  3.000
 5VC  H7   N17  C13  113.03  3.000
 5VC  C18  N17  C13  129.40  3.000
 5VC  H9   C10  H8   105.51  3.000
 5VC  H9   C10  C1   109.72  3.000
 5VC  H8   C10  C1   109.57  3.000
 5VC  H9   C10  C11  109.08  3.000
 5VC  H8   C10  C11  109.59  3.000
 5VC  C1   C10  C11  113.08  3.000
 5VC  C6   C1   C2   108.71  3.000
 5VC  C2   C1   C7   109.29  3.000
 5VC  C6   C1   C7   107.09  3.000
 5VC  C7   C1   C10  110.33  3.000
 5VC  C2   C1   C10  111.52  3.000
 5VC  C6   C1   C10  109.78  3.000
 5VC  O9   C7   O8   122.41  3.000
 5VC  O8   C7   C1   112.31  3.000
 5VC  O9   C7   C1   125.13  3.000
 5VC  H10  O8   C7   109.64  3.000
 5VC  H12  C2   H11  106.08  3.000
 5VC  H12  C2   C3   108.54  3.000
 5VC  H11  C2   C3   109.41  3.000
 5VC  H12  C2   C1   109.05  3.000
 5VC  H11  C2   C1   110.67  3.000
 5VC  C3   C2   C1   112.84  3.000
 5VC  H14  C3   H13  106.69  3.000
 5VC  H14  C3   C4   109.83  3.000
 5VC  H13  C3   C4   109.87  3.000
 5VC  H14  C3   C2   109.01  3.000
 5VC  H13  C3   C2   111.17  3.000
 5VC  C4   C3   C2   110.19  3.000
 5VC  H15  C4   C5   109.63  3.000
 5VC  H15  C4   C3   107.95  3.000
 5VC  C5   C4   C3   111.02  3.000
 5VC  H15  C4   O23  109.72  3.000
 5VC  C3   C4   O23  107.02  3.000
 5VC  C5   C4   O23  111.41  3.000
 5VC  H16  C28  C29  119.11  3.000
 5VC  H16  C28  C27  119.40  3.000
 5VC  C29  C28  C27  121.49  3.000
 5VC  H17  C29  C28  118.85  3.000
 5VC  H17  C29  C24  120.98  3.000
 5VC  C28  C29  C24  120.17  3.000
 5VC  H19  C5   H18  106.30  3.000
 5VC  H19  C5   C6   108.17  3.000
 5VC  H18  C5   C6   111.01  3.000
 5VC  H19  C5   C4   111.03  3.000
 5VC  H18  C5   C4   109.24  3.000
 5VC  C6   C5   C4   110.98  3.000
 5VC  H21  C6   H20  106.49  3.000
 5VC  H21  C6   C5   109.13  3.000
 5VC  H20  C6   C5   108.53  3.000
 5VC  H21  C6   C1   110.67  3.000
 5VC  H20  C6   C1   108.81  3.000
 5VC  C5   C6   C1   112.98  3.000
 5VC  C11  N12  C13  119.86  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  CONST_38  H10  O8   C7   C1   180.00   0.0  0
 5VC  Var_01    C4   C5   C6   C1    54.88  30.0  1
 5VC  Var_02    C4   C3   C2   C1   -57.88  30.0  1
 5VC  Var_03    N22  C18  N17  C13    1.72  30.0  2
 5VC  Var_04    C18  N17  C13  C14   -1.42  30.0  2
 5VC  Var_05    C1   C10  C11  C16  121.90  30.0  2
 5VC  Var_06    C29  C24  O23  C4    -5.46  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  H5   0.020
 5VC  plan-3  H16  0.020
 5VC  plan-3  H17  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
 5VC  plan-4  H10  0.020

