# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 18:31:17 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 5-{5-[1-(oxetan-3-yl)piperidin-4-yl]-1-(propan-2-yl)-1H-pyrazol-3-yl}-3-(trifluoromethyl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1nc(cc1C2CCN(CC2)C3COC3)c4cnc(N)c(c4)C(F)(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
 9FV  9FV  5-{5-[1-(oxetan-3-yl)piperidin-4-yl]-1-(propan-2-yl)-1H-pyrazol-3-yl}-3-(trifluoromethyl)pyridin-2-amine  ligand  55  29  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9FV
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
 9FV  C14  C  CR16  0  -0.102  -2.5072   1.8800  -0.6498
 9FV  C5   C  CR5   0   0.522   1.2127  -0.4634  -0.5030
 9FV  C6   C  CR15  0  -0.619   0.2916   0.5630  -0.5537
 9FV  C11  C  CR6   0  -0.334  -4.6497   0.4183   0.1301
 9FV  C7   C  CR5   0   0.298  -0.9580  -0.0578  -0.3743
 9FV  C9   C  CR6   0  -0.048  -2.2853   0.5496  -0.3192
 9FV  C10  C  CR16  0  -0.217  -3.4071  -0.1785   0.0719
 9FV  C12  C  CR6   0   0.459  -4.7585   1.7881  -0.2098
 9FV  C3   C  CH3   0  -0.646   0.6484  -3.5108   1.2070
 9FV  C1   C  CH3   0  -0.644   0.3916  -3.8370  -1.2874
 9FV  N4   N  NR5   0  -0.334   0.4965  -1.5942  -0.3081
 9FV  N8   N  N     0  -0.317  -0.8096  -1.3638  -0.2303
 9FV  N13  N  N     0  -0.447  -3.6855   2.4763  -0.5957
 9FV  N15  N  NH2   0  -0.831  -5.9334   2.4665  -0.2171
 9FV  C16  C  CT    0   1.073  -5.8495  -0.3766   0.5219
 9FV  F17  F  F     0  -0.321  -6.4751   0.1452   1.5940
 9FV  F18  F  F     0  -0.314  -6.7659  -0.4218  -0.4581
 9FV  F19  F  F     0  -0.297  -5.5501  -1.6390   0.8313
 9FV  C20  C  CH1   0  -0.386   2.7049  -0.4080  -0.5584
 9FV  C21  C  CH2   0  -0.417   3.2016   0.7468  -1.4252
 9FV  C22  C  CH2   0  -0.289   4.7201   0.8185  -1.4057
 9FV  N23  N  NT    0  -0.426   5.2155   0.9669  -0.0478
 9FV  C24  C  CH2   0  -0.298   4.8228  -0.1592   0.7798
 9FV  C25  C  CH2   0  -0.412   3.3074  -0.2761   0.8448
 9FV  C26  C  C     0  -0.189   6.6059   1.3231  -0.0001
 9FV  C27  C  C     0  -0.148   7.2248   1.6879   1.3557
 9FV  O28  O  O     0  -0.515   8.2843   0.7400   1.1793
 9FV  C29  C  C     0  -0.156   7.7341   0.2663  -0.0572
 9FV  H1   H  HCR6  0   0.261  -1.6837   2.5065  -0.9784
 9FV  H2   H  HCR5  0   0.260   0.5002   1.6114  -0.6899
 9FV  H3   H  HCR6  0   0.272  -3.2879  -1.2222   0.3305
 9FV  H4   H  HCH3  0   0.234  -0.4282  -3.5636   1.3682
 9FV  H5   H  HCH3  0   0.236   1.0571  -4.5152   1.3155
 9FV  H6   H  HCH3  0   0.237   1.0850  -2.8859   1.9867
 9FV  H7   H  HCH3  0   0.238   0.6549  -3.4480  -2.2712
 9FV  H8   H  HCH3  0   0.236   0.7915  -4.8477  -1.2084
 9FV  H9   H  HCH3  0   0.233  -0.6942  -3.8957  -1.2168
 9FV  H10  H  HCH1  0   0.260   2.0504  -2.9323  -0.2975
 9FV  H11  H  HNH2  0   0.396  -6.6999   2.1768   0.3650
 9FV  H12  H  HNH2  0   0.395  -5.8529   3.4657  -0.3158
 9FV  H13  H  HCH1  0   0.254   3.0860  -1.3353  -1.0041
 9FV  H14  H  HCH2  0   0.244   2.8566   0.6260  -2.4542
 9FV  H15  H  HCH2  0   0.227   2.7990   1.6936  -1.0547
 9FV  H16  H  HCH2  0   0.198   5.1338  -0.0784  -1.8993
 9FV  H17  H  HCH2  0   0.242   5.0492   1.6783  -1.9931
 9FV  H19  H  HCH2  0   0.199   5.2374  -1.1109   0.4078
 9FV  H20  H  HCH2  0   0.249   5.2072  -0.0248   1.7922
 9FV  H21  H  HCH2  0   0.230   2.8907   0.6094   1.3329
 9FV  H22  H  HCH2  0   0.240   3.0425  -1.1376   1.4622
 9FV  H23  H  H     0   0.264   6.7623   2.1133  -0.7366
 9FV  H24  H  H     0   0.225   7.5896   2.7150   1.4423
 9FV  H25  H  H     0   0.215   6.6055   1.4695   2.2309
 9FV  H26  H  H     0   0.212   7.4096  -0.7772   0.0027
 9FV  H27  H  H     0   0.221   8.4343   0.3636  -0.8912
 9FV  C2   C  CH1   0  -0.122   0.9678  -2.9684  -0.1784

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
 9FV  C29  C26  single    1.547  0.020  1.547
 9FV  C29  O28  single    1.434  0.020  1.434
 9FV  C24  C25  single    1.521  0.020  1.521
 9FV  C24  N23  single    1.452  0.020  1.452
 9FV  C1   C2   single    1.522  0.020  1.522
 9FV  C26  N23  single    1.436  0.020  1.436
 9FV  C26  C27  single    1.534  0.020  1.534
 9FV  C25  C20  single    1.533  0.020  1.533
 9FV  O28  C27  single    1.433  0.020  1.433
 9FV  N23  C22  single    1.453  0.020  1.453
 9FV  C20  C5   single    1.494  0.020  1.494
 9FV  C20  C21  single    1.527  0.020  1.527
 9FV  C2   N4   single    1.459  0.020  1.459
 9FV  C2   C3   single    1.522  0.020  1.522
 9FV  C22  C21  single    1.520  0.020  1.520
 9FV  C5   N4   aromatic  1.353  0.020  1.353
 9FV  C5   C6   aromatic  1.380  0.020  1.380
 9FV  N4   N8   aromatic  1.329  0.020  1.329
 9FV  C6   C7   aromatic  1.407  0.020  1.407
 9FV  N8   C7   aromatic  1.322  0.020  1.322
 9FV  C7   C9   single    1.461  0.020  1.461
 9FV  C9   C14  aromatic  1.389  0.020  1.389
 9FV  C9   C10  aromatic  1.393  0.020  1.393
 9FV  C14  N13  aromatic  1.322  0.020  1.322
 9FV  C10  C11  aromatic  1.380  0.020  1.380
 9FV  N13  C12  aromatic  1.332  0.020  1.332
 9FV  C11  C12  aromatic  1.416  0.020  1.416
 9FV  C11  C16  single    1.492  0.020  1.492
 9FV  C12  N15  single    1.357  0.020  1.357
 9FV  F17  C16  single    1.347  0.020  1.347
 9FV  F18  C16  single    1.342  0.020  1.342
 9FV  C16  F19  single    1.334  0.020  1.334
 9FV  C14  H1   single    0.930  0.020  1.080
 9FV  C6   H2   single    0.930  0.020  1.080
 9FV  C10  H3   single    0.930  0.020  1.080
 9FV  C3   H4   single    0.970  0.020  1.090
 9FV  C3   H5   single    0.970  0.020  1.090
 9FV  C3   H6   single    0.970  0.020  1.090
 9FV  C1   H7   single    0.970  0.020  1.090
 9FV  C1   H8   single    0.970  0.020  1.090
 9FV  C1   H9   single    0.970  0.020  1.090
 9FV  C2   H10  single    0.970  0.020  1.090
 9FV  N15  H11  single    0.890  0.020  1.040
 9FV  N15  H12  single    0.890  0.020  1.040
 9FV  C20  H13  single    0.970  0.020  1.090
 9FV  C21  H14  single    0.970  0.020  1.090
 9FV  C21  H15  single    0.970  0.020  1.090
 9FV  C22  H16  single    0.970  0.020  1.090
 9FV  C22  H17  single    0.970  0.020  1.090
 9FV  C24  H19  single    0.970  0.020  1.090
 9FV  C24  H20  single    0.970  0.020  1.090
 9FV  C25  H21  single    0.970  0.020  1.090
 9FV  C25  H22  single    0.970  0.020  1.090
 9FV  C26  H23  single    0.970  0.020  1.090
 9FV  C27  H24  single    0.970  0.020  1.090
 9FV  C27  H25  single    0.970  0.020  1.090
 9FV  C29  H26  single    0.970  0.020  1.090
 9FV  C29  H27  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
 9FV  H1   C14  N13  115.35  3.000
 9FV  H1   C14  C9   120.25  3.000
 9FV  N13  C14  C9   124.40  3.000
 9FV  C20  C5   N4   124.41  3.000
 9FV  N4   C5   C6   105.88  3.000
 9FV  C20  C5   C6   129.61  3.000
 9FV  H2   C6   C7   128.12  3.000
 9FV  H2   C6   C5   126.81  3.000
 9FV  C7   C6   C5   105.07  3.000
 9FV  C16  C11  C12  121.12  3.000
 9FV  C16  C11  C10  120.33  3.000
 9FV  C12  C11  C10  118.54  3.000
 9FV  N8   C7   C9   120.57  3.000
 9FV  C9   C7   C6   128.94  3.000
 9FV  N8   C7   C6   110.49  3.000
 9FV  C10  C9   C7   121.66  3.000
 9FV  C10  C9   C14  116.03  3.000
 9FV  C7   C9   C14  122.32  3.000
 9FV  H3   C10  C9   118.84  3.000
 9FV  H3   C10  C11  120.43  3.000
 9FV  C9   C10  C11  120.72  3.000
 9FV  N15  C12  N13  115.96  3.000
 9FV  N15  C12  C11  123.49  3.000
 9FV  N13  C12  C11  120.51  3.000
 9FV  H6   C3   H5   107.87  3.000
 9FV  H6   C3   H4   108.51  3.000
 9FV  H5   C3   H4   108.13  3.000
 9FV  H6   C3   C2   111.26  3.000
 9FV  H5   C3   C2   109.90  3.000
 9FV  H4   C3   C2   111.05  3.000
 9FV  H9   C1   H8   108.11  3.000
 9FV  H9   C1   H7   108.56  3.000
 9FV  H8   C1   H7   107.93  3.000
 9FV  H9   C1   C2   111.15  3.000
 9FV  H8   C1   C2   109.73  3.000
 9FV  H7   C1   C2   111.26  3.000
 9FV  N8   N4   C2   118.41  3.000
 9FV  N8   N4   C5   112.58  3.000
 9FV  C2   N4   C5   129.01  3.000
 9FV  N4   N8   C7   105.98  3.000
 9FV  C12  N13  C14  119.80  3.000
 9FV  H12  N15  H11  113.81  3.000
 9FV  H12  N15  C12  115.29  3.000
 9FV  H11  N15  C12  120.87  3.000
 9FV  F19  C16  F18  106.90  3.000
 9FV  F19  C16  F17  106.64  3.000
 9FV  F18  C16  F17  106.09  3.000
 9FV  F19  C16  C11  112.62  3.000
 9FV  F18  C16  C11  112.04  3.000
 9FV  F17  C16  C11  112.11  3.000
 9FV  H13  C20  C25  107.94  3.000
 9FV  H13  C20  C21  107.19  3.000
 9FV  C25  C20  C21  109.07  3.000
 9FV  H13  C20  C5   109.31  3.000
 9FV  C21  C20  C5   111.96  3.000
 9FV  C25  C20  C5   111.21  3.000
 9FV  H15  C21  H14  107.38  3.000
 9FV  H15  C21  C22  108.82  3.000
 9FV  H14  C21  C22  109.44  3.000
 9FV  H15  C21  C20  110.04  3.000
 9FV  H14  C21  C20  110.39  3.000
 9FV  C22  C21  C20  110.69  3.000
 9FV  H17  C22  H16  106.63  3.000
 9FV  H17  C22  N23  108.63  3.000
 9FV  H16  C22  N23  111.90  3.000
 9FV  H17  C22  C21  109.34  3.000
 9FV  H16  C22  C21  109.28  3.000
 9FV  N23  C22  C21  110.94  3.000
 9FV  C26  N23  C24  115.81  3.000
 9FV  C26  N23  C22  112.74  3.000
 9FV  C24  N23  C22  111.18  3.000
 9FV  H20  C24  H19  106.67  3.000
 9FV  H20  C24  C25  108.71  3.000
 9FV  H19  C24  C25  108.82  3.000
 9FV  H20  C24  N23  109.76  3.000
 9FV  H19  C24  N23  112.05  3.000
 9FV  C25  C24  N23  110.70  3.000
 9FV  H22  C25  H21  107.10  3.000
 9FV  H22  C25  C24  109.04  3.000
 9FV  H21  C25  C24  109.66  3.000
 9FV  H22  C25  C20  110.74  3.000
 9FV  H21  C25  C20  109.18  3.000
 9FV  C24  C25  C20  111.04  3.000
 9FV  H23  C26  C29  111.42  3.000
 9FV  H23  C26  C27  111.48  3.000
 9FV  C29  C26  C27   84.31  3.000
 9FV  H23  C26  N23  107.21  3.000
 9FV  C27  C26  N23  118.61  3.000
 9FV  C29  C26  N23  122.38  3.000
 9FV  H25  C27  H24  108.24  3.000
 9FV  H25  C27  O28  112.65  3.000
 9FV  H24  C27  O28  112.61  3.000
 9FV  H25  C27  C26  115.53  3.000
 9FV  H24  C27  C26  115.34  3.000
 9FV  O28  C27  C26   91.84  3.000
 9FV  C29  O28  C27   92.35  3.000
 9FV  H27  C29  H26  108.46  3.000
 9FV  H27  C29  O28  112.50  3.000
 9FV  H26  C29  O28  112.43  3.000
 9FV  H27  C29  C26  115.75  3.000
 9FV  H26  C29  C26  115.66  3.000
 9FV  O28  C29  C26   91.28  3.000
 9FV  H10  C2   N4   106.26  3.000
 9FV  H10  C2   C1   108.38  3.000
 9FV  N4   C2   C1   110.52  3.000
 9FV  H10  C2   C3   108.65  3.000
 9FV  N4   C2   C3   110.43  3.000
 9FV  C1   C2   C3   112.37  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
 9FV  CONST_01  C6   C7   C9   C14     0.00   0.0  0
 9FV  CONST_02  N8   C7   C9   C14   180.00   0.0  0
 9FV  CONST_03  C11  C10  C9   C14     0.00   0.0  0
 9FV  CONST_04  C11  C12  N13  C14     0.00   0.0  0
 9FV  CONST_05  C7   N8   N4   C5      0.00   0.0  0
 9FV  CONST_06  N8   C7   C6   C5      0.00   0.0  0
 9FV  CONST_07  C9   C7   C6   C5    180.00   0.0  0
 9FV  CONST_08  N8   N4   C5   C6      0.00   0.0  0
 9FV  CONST_09  N4   N8   C7   C6      0.00   0.0  0
 9FV  CONST_10  C10  C9   C7   C6    180.00   0.0  0
 9FV  CONST_11  C7   C9   C10  C11   180.00   0.0  0
 9FV  CONST_12  N4   C5   C6   C7      0.00   0.0  0
 9FV  CONST_13  N13  C14  C9   C7    180.00   0.0  0
 9FV  CONST_14  N4   N8   C7   C9    180.00   0.0  0
 9FV  CONST_15  C12  N13  C14  C9      0.00   0.0  0
 9FV  CONST_16  C12  C11  C10  C9      0.00   0.0  0
 9FV  CONST_17  N8   C7   C9   C10     0.00   0.0  0
 9FV  CONST_18  N13  C14  C9   C10     0.00   0.0  0
 9FV  CONST_19  N13  C12  C11  C10     0.00   0.0  0
 9FV  CONST_20  C20  C5   C6   C7    180.00   0.0  0
 9FV  CONST_21  C20  C5   N4   N8    180.00   0.0  0
 9FV  CONST_22  N15  C12  N13  C14   180.00   0.0  0
 9FV  CONST_23  C2   N4   C5   C6    180.00   0.0  0
 9FV  CONST_24  C2   N4   N8   C7    180.00   0.0  0
 9FV  CONST_25  C16  C11  C10  C9    180.00   0.0  0
 9FV  CONST_26  N15  C12  C11  C10   180.00   0.0  0
 9FV  CONST_27  C20  C5   N4   C2      0.00   0.0  0
 9FV  CONST_28  C16  C11  C12  N13   180.00   0.0  0
 9FV  CONST_29  H3   C10  C9   C14   180.00   0.0  0
 9FV  CONST_30  H1   C14  C9   C7      0.00   0.0  0
 9FV  CONST_31  H2   C6   C7   C9      0.00   0.0  0
 9FV  CONST_33  H12  N15  C12  C11   180.00   0.0  0
 9FV  Var_01    N23  C24  C25  C20    56.98  30.0  1
 9FV  Var_02    N23  C22  C21  C20   -57.57  30.0  1
 9FV  Var_03    C24  N23  C22  C21    60.52  30.0  1
 9FV  Var_04    C25  C24  N23  C22   -60.06  30.0  1
 9FV  Var_05    H26  C29  O28  C27  -114.92  30.0  1
 9FV  Var_06    H24  C27  O28  C29  -122.15  30.0  1
 9FV  Var_07    C1   C2   N4   C5   -118.92  30.0  2
 9FV  Var_08    F17  C16  C11  C10   122.49  30.0  2
 9FV  Var_09    H7   C1   C2   N4     57.77  30.0  3
 9FV  Var_10    H4   C3   C2   N4     63.82  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
 9FV  chir_01  C20  C25  C5   C21  negativ
 9FV  chir_02  C26  N23  C29  C27  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
 9FV  plan-1  C5   0.020
 9FV  plan-1  C6   0.020
 9FV  plan-1  C7   0.020
 9FV  plan-1  C9   0.020
 9FV  plan-1  N4   0.020
 9FV  plan-1  N8   0.020
 9FV  plan-1  C20  0.020
 9FV  plan-1  H2   0.020
 9FV  plan-1  C2   0.020
 9FV  plan-2  C14  0.020
 9FV  plan-2  C11  0.020
 9FV  plan-2  C7   0.020
 9FV  plan-2  C9   0.020
 9FV  plan-2  C10  0.020
 9FV  plan-2  C12  0.020
 9FV  plan-2  N13  0.020
 9FV  plan-2  N15  0.020
 9FV  plan-2  C16  0.020
 9FV  plan-2  H1   0.020
 9FV  plan-2  H3   0.020
 9FV  plan-3  C12  0.020
 9FV  plan-3  N15  0.020
 9FV  plan-3  H11  0.020
 9FV  plan-3  H12  0.020

