# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 07:22:18 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (1~{R},2~{R})-2-[7-[[5-chloranyl-3-(trifluoromethyl)pyrazol-1-yl]methyl]-5-oxidanylidene-2-(trifluoromethyl)-[1,3]thiazolo[3,2-a]pyrimidin-3-yl]cyclopropane-1-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cc(Cl)n(CC2=CC(=O)N3C(=N2)SC(=C3[C@@H]4C[C@H]4C#N)C(F)(F)F)n1
#
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
 6RV  6RV  (1~{R},2~{R})-2-[7-[[5-chloranyl-3-(trifluoromethyl)pyrazol-1-yl]methyl]-5-oxidanylidene-2-(trifluoromethyl)-[1,3]thiazolo[3,2-a]pyrimidin-3-yl]cyclopropane-1-carbonitrile  ligand  38  30  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6RV
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
 6RV  C4   C   CR56  0   0.340  -0.5580  -0.1655  -0.1230
 6RV  C6   C   CR6   0   0.608  -1.3132   2.1259  -0.3064
 6RV  C11  C   CT    0   1.094  -3.7077  -2.0548   1.1591
 6RV  C8   C   CR5   0   0.648  -2.8028   0.1999   0.3473
 6RV  C9   C   CR5   0  -0.695  -2.6767  -1.1057   0.6478
 6RV  N3   N   N     0  -0.454   0.6508   0.0674  -0.5055
 6RV  C1   C   CR16  0  -0.484   0.0233   2.3546  -0.7602
 6RV  C2   C   CR6   0   0.277   0.9281   1.3438  -0.8473
 6RV  N5   N   N     0  -0.649  -1.5771   0.7457  -0.0543
 6RV  O7   O   O     0  -0.439  -2.1650   2.9677  -0.1193
 6RV  S10  S   S2    0   0.338  -1.0736  -1.7227   0.4011
 6RV  F12  F   F     0  -0.302  -3.1063  -3.0449   1.8274
 6RV  F13  F   F     0  -0.288  -4.5718  -1.4709   1.9836
 6RV  F14  F   F     0  -0.301  -4.4072  -2.6257   0.1739
 6RV  C15  C   CH1   0  -0.305  -4.0440   1.0013   0.3929
 6RV  C16  C   CH2   0  -0.475  -5.3352   0.4863  -0.1495
 6RV  C17  C   CH1   0  -0.348  -4.5950   1.5602  -0.8928
 6RV  C18  C   CSP   0   0.149  -5.0805   2.9067  -0.8918
 6RV  N19  N   NS    0  -0.274  -5.4873   3.9836  -0.9000
 6RV  C20  C   CH2   0  -0.375   2.3214   1.5914  -1.3568
 6RV  N21  N   NR5   0  -0.286   3.2932   0.7929  -0.6519
 6RV  C22  C   CR5   0   0.368   3.7095   0.9483   0.6219
 6RV  C23  C   CR15  0  -0.490   4.5718  -0.0751   0.9137
 6RV  C24  C   CR5   0   0.019   4.5946  -0.8090  -0.2800
 6RV  N25  N   N     0  -0.271   3.8214  -0.2851  -1.2075
 6RV  C26  C   CT    0   1.074   5.3424  -2.0659  -0.5421
 6RV  F27  F   F     0  -0.304   5.4604  -2.3123  -1.8459
 6RV  F28  F   F     0  -0.309   6.5727  -2.0130  -0.0196
 6RV  F29  F   F     0  -0.314   4.7363  -3.1260   0.0108
 6RV  CL3  CL  CL    0  -0.060   3.1771   2.2399   1.5814
 6RV  H1   H   HCR6  0   0.294   0.2963   3.3729  -0.9983
 6RV  H3   H   HCH1  0   0.339  -4.1224   1.6558   1.2535
 6RV  H4   H   HCH2  0   0.290  -5.3737  -0.4708  -0.6485
 6RV  H5   H   HCH2  0   0.301  -6.2329   0.7581   0.3877
 6RV  H6   H   HCH1  0   0.347  -4.1127   1.2676  -1.8182
 6RV  H7   H   HCH2  0   0.326   2.3817   1.3078  -2.4076
 6RV  H8   H   HCH2  0   0.306   2.5829   2.6466  -1.2863
 6RV  H9   H   HCR5  0   0.304   5.0976  -0.2527   1.8362

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
 6RV  F12  C11  single    1.337  0.020  1.337
 6RV  C16  C15  single    1.492  0.020  1.492
 6RV  C16  C17  single    1.501  0.020  1.501
 6RV  C15  C8   single    1.478  0.020  1.478
 6RV  C15  C17  single    1.506  0.020  1.506
 6RV  F14  C11  single    1.336  0.020  1.336
 6RV  O7   C6   double    1.212  0.020  1.212
 6RV  C11  C9   single    1.492  0.020  1.492
 6RV  C11  F13  single    1.330  0.020  1.330
 6RV  N19  C18  triple    1.151  0.020  1.151
 6RV  C18  C17  single    1.431  0.020  1.431
 6RV  C8   C9   double    1.346  0.020  1.346
 6RV  C8   N5   single    1.401  0.020  1.401
 6RV  C9   S10  single    1.735  0.020  1.735
 6RV  C6   N5   single    1.428  0.020  1.428
 6RV  C6   C1   single    1.430  0.020  1.430
 6RV  N5   C4   single    1.369  0.020  1.369
 6RV  C1   C2   double    1.359  0.020  1.359
 6RV  C4   S10  single    1.722  0.020  1.722
 6RV  C4   N3   double    1.289  0.020  1.289
 6RV  CL3  C22  single    1.695  0.020  1.695
 6RV  C2   N3   single    1.350  0.020  1.350
 6RV  C2   C20  single    1.504  0.020  1.504
 6RV  C20  N21  single    1.442  0.020  1.442
 6RV  C22  N21  aromatic  1.349  0.020  1.349
 6RV  C22  C23  aromatic  1.370  0.020  1.370
 6RV  N21  N25  aromatic  1.323  0.020  1.323
 6RV  C23  C24  aromatic  1.401  0.020  1.401
 6RV  N25  C24  aromatic  1.316  0.020  1.316
 6RV  C24  C26  single    1.486  0.020  1.486
 6RV  F27  C26  single    1.332  0.020  1.332
 6RV  C26  F29  single    1.340  0.020  1.340
 6RV  C26  F28  single    1.338  0.020  1.338
 6RV  C1   H1   single    0.930  0.020  1.080
 6RV  C15  H3   single    0.970  0.020  1.090
 6RV  C16  H4   single    0.970  0.020  1.090
 6RV  C16  H5   single    0.970  0.020  1.090
 6RV  C17  H6   single    0.970  0.020  1.090
 6RV  C20  H7   single    0.970  0.020  1.090
 6RV  C20  H8   single    0.970  0.020  1.090
 6RV  C23  H9   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
 6RV  S10  C4   N5   111.33  3.000
 6RV  S10  C4   N3   122.31  3.000
 6RV  N5   C4   N3   126.35  3.000
 6RV  O7   C6   N5   120.95  3.000
 6RV  N5   C6   C1   112.55  3.000
 6RV  O7   C6   C1   126.50  3.000
 6RV  F14  C11  F13  107.73  3.000
 6RV  F13  C11  F12  107.90  3.000
 6RV  F14  C11  F12  106.71  3.000
 6RV  F13  C11  C9   112.48  3.000
 6RV  F14  C11  C9   112.39  3.000
 6RV  F12  C11  C9   109.36  3.000
 6RV  C15  C8   N5   122.17  3.000
 6RV  N5   C8   C9   111.10  3.000
 6RV  C15  C8   C9   126.72  3.000
 6RV  S10  C9   C8   113.56  3.000
 6RV  S10  C9   C11  117.45  3.000
 6RV  C8   C9   C11  128.98  3.000
 6RV  C2   N3   C4   116.01  3.000
 6RV  H1   C1   C2   121.22  3.000
 6RV  H1   C1   C6   117.17  3.000
 6RV  C2   C1   C6   121.57  3.000
 6RV  C20  C2   C1   121.06  3.000
 6RV  C20  C2   N3   115.57  3.000
 6RV  C1   C2   N3   123.37  3.000
 6RV  C8   N5   C6   126.09  3.000
 6RV  C6   N5   C4   119.81  3.000
 6RV  C8   N5   C4   113.99  3.000
 6RV  C9   S10  C4    89.91  3.000
 6RV  H3   C15  C17  115.29  3.000
 6RV  H3   C15  C16  115.75  3.000
 6RV  C17  C15  C16   60.08  3.000
 6RV  H3   C15  C8   114.37  3.000
 6RV  C17  C15  C8   118.81  3.000
 6RV  C16  C15  C8   121.89  3.000
 6RV  H5   C16  H4   115.01  3.000
 6RV  H5   C16  C17  118.40  3.000
 6RV  H4   C16  C17  115.01  3.000
 6RV  H5   C16  C15  116.82  3.000
 6RV  H4   C16  C15  120.31  3.000
 6RV  C17  C16  C15   60.43  3.000
 6RV  H6   C17  C18  113.92  3.000
 6RV  H6   C17  C16  116.68  3.000
 6RV  C18  C17  C16  120.35  3.000
 6RV  H6   C17  C15  117.77  3.000
 6RV  C18  C17  C15  118.20  3.000
 6RV  C16  C17  C15   59.49  3.000
 6RV  N19  C18  C17  180.00  3.000
 6RV  H8   C20  H7   107.52  3.000
 6RV  H8   C20  N21  110.06  3.000
 6RV  H7   C20  N21  106.85  3.000
 6RV  H8   C20  C2   111.09  3.000
 6RV  H7   C20  C2   109.57  3.000
 6RV  N21  C20  C2   111.57  3.000
 6RV  N25  N21  C22  111.55  3.000
 6RV  N25  N21  C20  121.01  3.000
 6RV  C22  N21  C20  127.28  3.000
 6RV  CL3  C22  C23  130.29  3.000
 6RV  C23  C22  N21  108.02  3.000
 6RV  CL3  C22  N21  121.70  3.000
 6RV  H9   C23  C24  129.46  3.000
 6RV  H9   C23  C22  127.82  3.000
 6RV  C24  C23  C22  102.71  3.000
 6RV  C26  C24  N25  120.53  3.000
 6RV  C26  C24  C23  126.97  3.000
 6RV  N25  C24  C23  112.47  3.000
 6RV  C24  N25  N21  105.25  3.000
 6RV  F29  C26  F28  106.62  3.000
 6RV  F28  C26  F27  107.94  3.000
 6RV  F29  C26  F27  107.31  3.000
 6RV  F28  C26  C24  111.13  3.000
 6RV  F29  C26  C24  111.64  3.000
 6RV  F27  C26  C24  111.95  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
 6RV  CONST_01  C24  C23  C22  N21     0.00   0.0  0
 6RV  CONST_02  C23  C24  N25  N21     0.00   0.0  0
 6RV  CONST_03  C24  N25  N21  C22     0.00   0.0  0
 6RV  CONST_04  N25  C24  C23  C22     0.00   0.0  0
 6RV  CONST_05  N25  N21  C22  C23     0.00   0.0  0
 6RV  CONST_06  C1   C6   N5   C4      0.00   0.0  0
 6RV  CONST_07  S10  C4   N5   C6    180.00   0.0  0
 6RV  CONST_08  N3   C4   N5   C6      0.00   0.0  0
 6RV  CONST_09  C1   C6   N5   C8    180.00   0.0  0
 6RV  CONST_10  S10  C4   N5   C8      0.00   0.0  0
 6RV  CONST_11  N3   C4   N5   C8    180.00   0.0  0
 6RV  CONST_12  N5   C4   N3   C2      0.00   0.0  0
 6RV  CONST_13  S10  C4   N3   C2    180.00   0.0  0
 6RV  CONST_14  C23  C22  N21  C20   180.00   0.0  0
 6RV  CONST_15  C24  N25  N21  C20   180.00   0.0  0
 6RV  CONST_16  C26  C24  N25  N21   180.00   0.0  0
 6RV  CONST_17  C26  C24  C23  C22   180.00   0.0  0
 6RV  CONST_18  CL3  C22  C23  C24   180.00   0.0  0
 6RV  CONST_19  CL3  C22  N21  N25   180.00   0.0  0
 6RV  CONST_20  O7   C6   N5   C4    180.00   0.0  0
 6RV  CONST_21  O7   C6   N5   C8      0.00   0.0  0
 6RV  CONST_22  H9   C23  C22  N21   180.00   0.0  0
 6RV  Var_01    C17  C16  C15  C8   -107.27  30.0  1
 6RV  Var_02    C16  C15  C8   C9    -44.15  30.0  2
 6RV  Var_03    N21  C20  C2   N3    -37.27  30.0  3
 6RV  Var_04    C22  N21  C20  C2    -71.26  30.0  2
 6RV  Var_05    F12  C11  C9   C8   -154.78  30.0  3
 6RV  Var_06    F27  C26  C24  C23  -162.62  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
 6RV  chir_01  C15  C16  C8   C17  both
 6RV  chir_02  C17  C16  C15  C18  both

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
 6RV  plan-1  C20  0.020
 6RV  plan-1  N21  0.020
 6RV  plan-1  C22  0.020
 6RV  plan-1  C23  0.020
 6RV  plan-1  C24  0.020
 6RV  plan-1  N25  0.020
 6RV  plan-1  C26  0.020
 6RV  plan-1  CL3  0.020
 6RV  plan-1  H9   0.020
 6RV  plan-2  C4   0.020
 6RV  plan-2  C6   0.020
 6RV  plan-2  C11  0.020
 6RV  plan-2  C8   0.020
 6RV  plan-2  C9   0.020
 6RV  plan-2  N3   0.020
 6RV  plan-2  C1   0.020
 6RV  plan-2  C2   0.020
 6RV  plan-2  N5   0.020
 6RV  plan-2  O7   0.020
 6RV  plan-2  S10  0.020
 6RV  plan-2  C15  0.020
 6RV  plan-2  C20  0.020
 6RV  plan-2  H1   0.020

