# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:13:17 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: ~{N}-[(1~{R},6~{R})-6-azanyl-2,2-bis(fluoranyl)cyclohexyl]-5-ethyl-4-[6-(trifluoromethyl)pyrazolo[1,5-a]pyrimidin-3-yl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc(cc1c2cnn3cc(cnc23)C(F)(F)F)C(=O)N[C@@H]4[C@H](N)CCCC4(F)F
#
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
 5RC  5RC  ~{N}-[(1~{R},6~{R})-6-azanyl-2,2-bis(fluoranyl)cyclohexyl]-5-ethyl-4-[6-(trifluoromethyl)pyrazolo[1,5-a]pyrimidin-3-yl]thiophene-2-carboxamide  ligand  52  32  .  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_5RC
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
 5RC  C18  C  CH1   0  -0.234   5.3038  -0.5666   0.4826
 5RC  C16  C  C     0   0.562   2.8892  -0.3477   0.8989
 5RC  C15  C  CH2   0  -0.525  -1.1888   1.3480  -2.1523
 5RC  C19  C  CH1   0  -0.099   6.3296   0.5744   0.4112
 5RC  C20  C  CH2   0  -0.468   6.5727   1.0083  -1.0372
 5RC  C21  C  CH2   0  -0.459   6.9873  -0.1648  -1.9205
 5RC  F30  F  F     0  -0.308  -7.7309  -0.1461  -1.1912
 5RC  C22  C  CH2   0  -0.577   5.9678  -1.3003  -1.8638
 5RC  C23  C  CT    0   0.797   5.7087  -1.7185  -0.4375
 5RC  C11  C  CR15  0  -0.215   0.4419   0.2138   1.0657
 5RC  C12  C  CR5   0  -0.338   1.5974   0.1047   0.3491
 5RC  N1   N  N     0  -0.366  -4.1445   0.8442   1.3750
 5RC  C2   C  CR56  0   0.585  -3.2255   0.3829   0.4434
 5RC  C3   C  CR5   0  -0.242  -1.9911   0.8409   0.8744
 5RC  C4   C  CR15  0  -0.035  -2.2903   1.5395   2.0563
 5RC  N5   N  N     0  -0.287  -3.5779   1.5454   2.3544
 5RC  C6   C  CR16  0   0.113  -5.4576   0.5756   1.2695
 5RC  C7   C  CR6   0  -0.402  -5.8597  -0.1759   0.2101
 5RC  C8   C  CR16  0  -0.036  -4.8792  -0.6338  -0.7142
 5RC  N9   N  N     0  -0.412  -3.6129  -0.3661  -0.6003
 5RC  C10  C  CR5   0   0.210  -0.6710   0.6318   0.2892
 5RC  S13  S  S2    0   0.249   1.3186   0.5025  -1.3037
 5RC  C14  C  CR5   0  -0.252  -0.3410   0.8338  -1.0313
 5RC  N17  N  NH1   0  -0.686   3.9787  -0.1119   0.1328
 5RC  F24  F  F     0  -0.350   6.8377  -2.2953   0.0863
 5RC  O25  O  O     0  -0.469   2.9395  -0.8922   1.9901
 5RC  F26  F  F     0  -0.344   4.7502  -2.6917  -0.3919
 5RC  N27  N  NH2   0  -0.785   5.9212   1.6304   1.3175
 5RC  C28  C  CT    0   1.079  -7.2905  -0.5408   0.0091
 5RC  F29  F  F     0  -0.297  -8.0852   0.0066   0.9298
 5RC  F31  F  F     0  -0.308  -7.4665  -1.8669   0.0643
 5RC  C32  C  CH3   0  -0.653  -1.5696   2.8156  -1.9614
 5RC  H1   H  HCH1  0   0.300   5.2630  -0.9364   1.5083
 5RC  H2   H  HCH2  0   0.256  -0.6583   1.2307  -3.0992
 5RC  H3   H  HCH2  0   0.268  -2.0868   0.7343  -2.2295
 5RC  H4   H  HCH1  0   0.251   7.2705   0.1707   0.7977
 5RC  H5   H  HCH2  0   0.220   5.6729   1.4860  -1.4440
 5RC  H6   H  HCH2  0   0.255   7.3486   1.7768  -1.0481
 5RC  H7   H  HCH2  0   0.255   7.0973   0.1633  -2.9545
 5RC  H8   H  HCH2  0   0.236   7.9683  -0.5315  -1.6076
 5RC  H9   H  HCH2  0   0.250   5.0236  -0.9753  -2.3104
 5RC  H10  H  HCH2  0   0.279   6.3058  -2.1634  -2.4422
 5RC  H11  H  HCR5  0   0.270   0.3797  -0.0051   2.1229
 5RC  H12  H  HCR5  0   0.284  -1.5910   2.0524   2.7000
 5RC  H13  H  HCR6  0   0.340  -6.0984   0.9782   2.0411
 5RC  H14  H  HCR6  0   0.298  -5.1745  -1.2395  -1.5638
 5RC  H15  H  HNH1  0   0.398   3.8758   0.4319  -0.7104
 5RC  H16  H  HNH2  0   0.354   6.6609   2.3189   1.3826
 5RC  H17  H  HNH2  0   0.340   5.1195   2.1228   0.9410
 5RC  H19  H  HCH3  0   0.239  -2.1837   3.1573  -2.7946
 5RC  H20  H  HCH3  0   0.231  -2.1394   2.9627  -1.0442
 5RC  H21  H  HCH3  0   0.230  -0.6829   3.4476  -1.9148

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
 5RC  C21  C20  single    1.526  0.020  1.526
 5RC  C21  C22  single    1.527  0.020  1.527
 5RC  C20  C19  single    1.531  0.020  1.531
 5RC  C19  N27  single    1.450  0.020  1.450
 5RC  C19  C18  single    1.536  0.020  1.536
 5RC  C22  C23  single    1.509  0.020  1.509
 5RC  F24  C23  single    1.372  0.020  1.372
 5RC  C23  C18  single    1.529  0.020  1.529
 5RC  C23  F26  single    1.367  0.020  1.367
 5RC  C18  N17  single    1.444  0.020  1.444
 5RC  F30  C28  single    1.338  0.020  1.338
 5RC  N17  C16  single    1.353  0.020  1.353
 5RC  F29  C28  single    1.334  0.020  1.334
 5RC  C28  F31  single    1.339  0.020  1.339
 5RC  C28  C7   single    1.490  0.020  1.490
 5RC  C8   C7   aromatic  1.423  0.020  1.423
 5RC  C8   N9   aromatic  1.299  0.020  1.299
 5RC  C16  O25  double    1.221  0.020  1.221
 5RC  C16  C12  single    1.475  0.020  1.475
 5RC  C7   C6   aromatic  1.360  0.020  1.360
 5RC  N9   C2   aromatic  1.342  0.020  1.342
 5RC  C11  C12  aromatic  1.364  0.020  1.364
 5RC  C11  C10  aromatic  1.420  0.020  1.420
 5RC  C12  S13  aromatic  1.723  0.020  1.723
 5RC  C2   N1   aromatic  1.387  0.020  1.387
 5RC  C2   C3   aromatic  1.385  0.020  1.385
 5RC  C6   N1   aromatic  1.344  0.020  1.344
 5RC  N1   N5   aromatic  1.331  0.020  1.331
 5RC  C10  C3   single    1.459  0.020  1.459
 5RC  C10  C14  aromatic  1.376  0.020  1.376
 5RC  C3   C4   aromatic  1.405  0.020  1.405
 5RC  S13  C14  aromatic  1.714  0.020  1.714
 5RC  C14  C15  single    1.497  0.020  1.497
 5RC  N5   C4   aromatic  1.322  0.020  1.322
 5RC  C15  C32  single    1.528  0.020  1.528
 5RC  C18  H1   single    0.970  0.020  1.090
 5RC  C15  H2   single    0.970  0.020  1.090
 5RC  C15  H3   single    0.970  0.020  1.090
 5RC  C19  H4   single    0.970  0.020  1.090
 5RC  C20  H5   single    0.970  0.020  1.090
 5RC  C20  H6   single    0.970  0.020  1.090
 5RC  C21  H7   single    0.970  0.020  1.090
 5RC  C21  H8   single    0.970  0.020  1.090
 5RC  C22  H9   single    0.970  0.020  1.090
 5RC  C22  H10  single    0.970  0.020  1.090
 5RC  C11  H11  single    0.930  0.020  1.080
 5RC  C4   H12  single    0.930  0.020  1.080
 5RC  C6   H13  single    0.930  0.020  1.080
 5RC  C8   H14  single    0.930  0.020  1.080
 5RC  N17  H15  single    0.860  0.020  1.020
 5RC  N27  H16  single    0.890  0.020  1.040
 5RC  N27  H17  single    0.890  0.020  1.040
 5RC  C32  H19  single    0.970  0.020  1.090
 5RC  C32  H20  single    0.970  0.020  1.090
 5RC  C32  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
 5RC  H1   C18  N17  107.47  3.000
 5RC  H1   C18  C23  108.68  3.000
 5RC  N17  C18  C23  109.54  3.000
 5RC  H1   C18  C19  108.69  3.000
 5RC  N17  C18  C19  111.58  3.000
 5RC  C23  C18  C19  110.78  3.000
 5RC  O25  C16  N17  123.43  3.000
 5RC  O25  C16  C12  120.41  3.000
 5RC  N17  C16  C12  116.16  3.000
 5RC  H3   C15  H2   106.16  3.000
 5RC  H3   C15  C32  110.13  3.000
 5RC  H2   C15  C32  109.43  3.000
 5RC  H3   C15  C14  109.04  3.000
 5RC  H2   C15  C14  109.73  3.000
 5RC  C32  C15  C14  112.19  3.000
 5RC  H4   C19  N27  106.86  3.000
 5RC  H4   C19  C20  107.58  3.000
 5RC  N27  C19  C20  115.43  3.000
 5RC  H4   C19  C18  106.49  3.000
 5RC  N27  C19  C18  108.89  3.000
 5RC  C20  C19  C18  111.13  3.000
 5RC  H6   C20  H5   105.83  3.000
 5RC  H6   C20  C21  110.00  3.000
 5RC  H5   C20  C21  110.06  3.000
 5RC  H6   C20  C19  108.76  3.000
 5RC  H5   C20  C19  110.12  3.000
 5RC  C21  C20  C19  111.89  3.000
 5RC  H8   C21  H7   106.37  3.000
 5RC  H8   C21  C22  109.82  3.000
 5RC  H7   C21  C22  109.05  3.000
 5RC  H8   C21  C20  109.64  3.000
 5RC  H7   C21  C20  110.18  3.000
 5RC  C22  C21  C20  111.64  3.000
 5RC  H10  C22  H9   106.59  3.000
 5RC  H10  C22  C23  109.55  3.000
 5RC  H9   C22  C23  108.67  3.000
 5RC  H10  C22  C21  111.17  3.000
 5RC  H9   C22  C21  109.89  3.000
 5RC  C23  C22  C21  110.85  3.000
 5RC  F26  C23  F24  105.37  3.000
 5RC  F26  C23  C22  110.45  3.000
 5RC  F24  C23  C22  109.64  3.000
 5RC  F26  C23  C18  109.31  3.000
 5RC  F24  C23  C18  107.76  3.000
 5RC  C22  C23  C18  113.93  3.000
 5RC  H11  C11  C10  123.30  3.000
 5RC  H11  C11  C12  123.10  3.000
 5RC  C10  C11  C12  113.59  3.000
 5RC  S13  C12  C11  110.39  3.000
 5RC  S13  C12  C16  124.77  3.000
 5RC  C11  C12  C16  124.79  3.000
 5RC  C6   N1   N5   125.36  3.000
 5RC  N5   N1   C2   112.78  3.000
 5RC  C6   N1   C2   121.86  3.000
 5RC  N9   C2   C3   133.14  3.000
 5RC  C3   C2   N1   105.74  3.000
 5RC  N9   C2   N1   121.11  3.000
 5RC  C10  C3   C4   126.96  3.000
 5RC  C4   C3   C2   103.67  3.000
 5RC  C10  C3   C2   129.34  3.000
 5RC  H12  C4   N5   119.62  3.000
 5RC  H12  C4   C3   126.83  3.000
 5RC  N5   C4   C3   113.54  3.000
 5RC  C4   N5   N1   104.26  3.000
 5RC  H13  C6   C7   125.93  3.000
 5RC  H13  C6   N1   116.66  3.000
 5RC  C7   C6   N1   117.41  3.000
 5RC  C28  C7   C8   119.68  3.000
 5RC  C8   C7   C6   118.70  3.000
 5RC  C28  C7   C6   121.62  3.000
 5RC  H14  C8   N9   116.69  3.000
 5RC  H14  C8   C7   120.07  3.000
 5RC  N9   C8   C7   123.24  3.000
 5RC  C8   N9   C2   117.68  3.000
 5RC  C14  C10  C3   125.51  3.000
 5RC  C14  C10  C11  112.33  3.000
 5RC  C3   C10  C11  122.14  3.000
 5RC  C14  S13  C12   92.80  3.000
 5RC  S13  C14  C10  110.87  3.000
 5RC  S13  C14  C15  119.72  3.000
 5RC  C10  C14  C15  129.30  3.000
 5RC  H15  N17  C16  119.03  3.000
 5RC  H15  N17  C18  117.77  3.000
 5RC  C16  N17  C18  123.17  3.000
 5RC  H17  N27  H16  105.75  3.000
 5RC  H17  N27  C19  110.14  3.000
 5RC  H16  N27  C19  109.24  3.000
 5RC  F31  C28  F29  107.44  3.000
 5RC  F31  C28  C7   111.30  3.000
 5RC  F29  C28  C7   112.25  3.000
 5RC  C7   C28  F30  111.39  3.000
 5RC  F31  C28  F30  106.61  3.000
 5RC  F29  C28  F30  107.58  3.000
 5RC  H21  C32  H20  108.12  3.000
 5RC  H21  C32  H19  108.02  3.000
 5RC  H20  C32  H19  107.85  3.000
 5RC  H21  C32  C15  111.07  3.000
 5RC  H20  C32  C15  111.41  3.000
 5RC  H19  C32  C15  110.24  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
 5RC  CONST_01  C14  S13  C12  C11     0.00   0.0  0
 5RC  CONST_04  S13  C14  C10  C11     0.00   0.0  0
 5RC  CONST_05  C3   C10  C11  C12   180.00   0.0  0
 5RC  CONST_06  C14  C10  C11  C12     0.00   0.0  0
 5RC  CONST_07  C10  C14  S13  C12     0.00   0.0  0
 5RC  CONST_08  C8   N9   C2   N1      0.00   0.0  0
 5RC  CONST_09  C10  C3   C2   N1    180.00   0.0  0
 5RC  CONST_10  C4   C3   C2   N1      0.00   0.0  0
 5RC  CONST_11  C8   C7   C6   N1      0.00   0.0  0
 5RC  CONST_12  C3   C4   N5   N1      0.00   0.0  0
 5RC  CONST_13  C7   C8   N9   C2      0.00   0.0  0
 5RC  CONST_14  C7   C6   N1   C2      0.00   0.0  0
 5RC  CONST_15  C4   N5   N1   C2      0.00   0.0  0
 5RC  CONST_17  N5   C4   C3   C2      0.00   0.0  0
 5RC  CONST_18  C8   N9   C2   C3    180.00   0.0  0
 5RC  CONST_19  C6   N1   C2   C3    180.00   0.0  0
 5RC  CONST_20  N5   N1   C2   C3      0.00   0.0  0
 5RC  CONST_21  S13  C14  C10  C3    180.00   0.0  0
 5RC  CONST_22  N9   C2   C3   C4    180.00   0.0  0
 5RC  CONST_24  C6   N1   N5   C4    180.00   0.0  0
 5RC  CONST_25  N9   C2   N1   N5    180.00   0.0  0
 5RC  CONST_26  C7   C6   N1   N5    180.00   0.0  0
 5RC  CONST_27  C10  C3   C4   N5    180.00   0.0  0
 5RC  CONST_28  N9   C8   C7   C6      0.00   0.0  0
 5RC  CONST_29  N9   C2   N1   C6      0.00   0.0  0
 5RC  CONST_30  C10  C3   C2   N9      0.00   0.0  0
 5RC  CONST_31  S13  C12  C11  C10     0.00   0.0  0
 5RC  CONST_32  C10  C11  C12  C16   180.00   0.0  0
 5RC  CONST_33  C14  S13  C12  C16   180.00   0.0  0
 5RC  CONST_34  C11  C10  C14  C15   180.00   0.0  0
 5RC  CONST_35  C3   C10  C14  C15     0.00   0.0  0
 5RC  CONST_36  C12  S13  C14  C15   180.00   0.0  0
 5RC  CONST_37  C28  C7   C6   N1    180.00   0.0  0
 5RC  CONST_38  C28  C7   C8   N9    180.00   0.0  0
 5RC  CONST_39  H12  C4   N5   N1    180.00   0.0  0
 5RC  CONST_40  H14  C8   N9   C2    180.00   0.0  0
 5RC  CONST_41  H13  C6   N1   C2    180.00   0.0  0
 5RC  CONST_42  H11  C11  C10  C3      0.00   0.0  0
 5RC  CONST_43  C12  C16  N17  C18   180.00   0.0  0
 5RC  CONST_44  O25  C16  N17  C18     0.00   0.0  0
 5RC  CONST_45  H15  N17  C16  C12     0.00   0.0  0
 5RC  Var_01    C21  C22  C23  C18    53.73  30.0  1
 5RC  Var_02    C22  C21  C20  C19    55.44  30.0  1
 5RC  Var_03    C23  C22  C21  C20   -53.88  30.0  1
 5RC  Var_04    C8   C7   C28  F30   -56.93  30.0  2
 5RC  Var_05    N17  C16  C12  C11  -165.74  30.0  2
 5RC  Var_06    C32  C15  C14  C10    67.18  30.0  2
 5RC  Var_07    H19  C32  C15  C14   179.89  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
 5RC  chir_01  C18  C19  C23  N17  positiv
 5RC  chir_02  C19  N27  C20  C18  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
 5RC  plan-1  C16  0.020
 5RC  plan-1  C15  0.020
 5RC  plan-1  C11  0.020
 5RC  plan-1  C12  0.020
 5RC  plan-1  C3   0.020
 5RC  plan-1  C10  0.020
 5RC  plan-1  S13  0.020
 5RC  plan-1  C14  0.020
 5RC  plan-1  H11  0.020
 5RC  plan-2  N1   0.020
 5RC  plan-2  C2   0.020
 5RC  plan-2  C3   0.020
 5RC  plan-2  C4   0.020
 5RC  plan-2  N5   0.020
 5RC  plan-2  C6   0.020
 5RC  plan-2  C7   0.020
 5RC  plan-2  C8   0.020
 5RC  plan-2  N9   0.020
 5RC  plan-2  C10  0.020
 5RC  plan-2  C28  0.020
 5RC  plan-2  H12  0.020
 5RC  plan-2  H13  0.020
 5RC  plan-2  H14  0.020
 5RC  plan-3  C18  0.020
 5RC  plan-3  C16  0.020
 5RC  plan-3  C12  0.020
 5RC  plan-3  N17  0.020
 5RC  plan-3  O25  0.020
 5RC  plan-3  H15  0.020

