# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 02:19:45 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (1S,2R,5S)-5-[3-(trifluoromethyl)-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazin-7(8H)-yl]-2-(2,4,5-trifluorophenyl)cyclohexanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[C@H](CC[C@@H]1c2cc(F)c(F)cc2F)N3CCn4c(C3)nnc4C(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
 417  417  (1S,2R,5S)-5-[3-(trifluoromethyl)-5,6-dihydro[1,2,4]triazolo[4,3-a]pyrazin-7(8H)-yl]-2-(2,4,5-trifluorophenyl)cyclohexanamine  ligand  48  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_417
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
 417  C1    C  CR16  0  -0.559  -7.4439  -0.2417   2.0045
 417  C2    C  CR6   0   0.505  -6.1142  -0.1898   1.6268
 417  C3    C  CR6   0   0.026  -5.0900  -0.7775   2.3521
 417  C4    C  CR16  0  -0.465  -5.4605  -1.4629   3.5078
 417  C5    C  CR6   0   0.408  -6.7779  -1.5348   3.9045
 417  C6    C  CR6   0   0.394  -7.7679  -0.9225   3.1576
 417  C9    C  CH1   0  -0.348  -3.6503  -0.7100   1.9135
 417  C10   C  CH2   0  -0.419  -2.7213  -0.2801   3.0490
 417  C11   C  CH2   0  -0.485  -1.2617  -0.2104   2.6149
 417  C12   C  CH1   0  -0.012  -0.7882  -1.5565   2.0704
 417  C13   C  CH2   0  -0.461  -1.7146  -1.9633   0.9231
 417  C14   C  CH1   0  -0.055  -3.1871  -2.0507   1.3303
 417  N21   N  NT    0  -0.461   0.6019  -1.5233   1.5994
 417  C22   C  CH2   0  -0.337   1.1453  -2.8551   1.3841
 417  C23   C  CH2   0  -0.292   2.3636  -2.7816   0.4852
 417  N24   N  NR5   0  -0.498   3.2682  -1.7846   1.0385
 417  C25   C  CR5   0   0.440   2.8877  -0.8443   1.9240
 417  C26   C  CH2   0  -0.360   1.5011  -0.7761   2.4609
 417  C33   C  CR5   0   0.157   4.5757  -1.5222   0.8126
 417  N34   N  N     0  -0.305   4.9637  -0.5020   1.5178
 417  N35   N  N     0  -0.340   3.8971  -0.0684   2.2205
 417  F36   F  F     0  -0.308  -7.1131  -2.1957   5.0192
 417  F37   F  F     0  -0.307  -5.8237   0.4740   0.4971
 417  N38   N  NH2   0  -0.782  -4.0670  -2.4473   0.2446
 417  C39   C  CT    0   1.079   5.4464  -2.3024  -0.1071
 417  F40   F  F     0  -0.290   6.6623  -1.7767  -0.1635
 417  F41   F  F     0  -0.308   5.5634  -3.5747   0.2919
 417  F42   F  F     0  -0.308   4.9440  -2.3304  -1.3465
 417  F43   F  F     0  -0.303  -9.0386  -0.9933   3.5620
 417  H1    H  HCR6  0   0.310  -8.2121   0.2357   1.4104
 417  H4    H  HCR6  0   0.292  -4.7132  -1.9587   4.1151
 417  H9    H  HCH1  0   0.249  -3.5588   0.0371   1.1179
 417  H101  H  HCH2  0   0.227  -2.8011  -0.9824   3.8848
 417  H102  H  HCH2  0   0.251  -3.0337   0.6936   3.4315
 417  H111  H  HCH2  0   0.231  -1.1306   0.5625   1.8492
 417  H112  H  HCH2  0   0.256  -0.6747   0.0952   3.4826
 417  H12   H  HCH1  0   0.206  -0.8875  -2.2921   2.8890
 417  H131  H  HCH2  0   0.220  -1.6080  -1.2280   0.1168
 417  H132  H  HCH2  0   0.240  -1.4290  -2.9315   0.5051
 417  H14   H  HCH1  0   0.223  -3.2840  -2.8110   2.1164
 417  H221  H  HCH2  0   0.277   0.4161  -3.4883   0.8849
 417  H222  H  HCH2  0   0.237   1.4079  -3.3510   2.3320
 417  H231  H  HCH2  0   0.279   2.8624  -3.7478   0.4416
 417  H232  H  HCH2  0   0.281   2.0801  -2.4842  -0.5239
 417  H261  H  HCH2  0   0.248   1.5092  -1.1500   3.4984
 417  H262  H  HCH2  0   0.291   1.2156   0.2742   2.5034
 417  H381  H  HNH2  0   0.334  -3.9697  -1.7967  -0.5271
 417  H382  H  HNH2  0   0.346  -3.7748  -3.3474  -0.1169

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
 417  C1   C2    aromatic  1.383  0.020  1.383
 417  C1   C6    aromatic  1.378  0.020  1.378
 417  C1   H1    single    0.930  0.020  1.080
 417  C2   F37   single    1.342  0.020  1.342
 417  C2   C3    aromatic  1.386  0.020  1.386
 417  C3   C9    single    1.507  0.020  1.507
 417  C3   C4    aromatic  1.394  0.020  1.394
 417  C4   C5    aromatic  1.378  0.020  1.378
 417  C4   H4    single    0.930  0.020  1.080
 417  C5   C6    aromatic  1.383  0.020  1.383
 417  C5   F36   single    1.339  0.020  1.339
 417  C6   F43   single    1.335  0.020  1.335
 417  C9   C14   single    1.534  0.020  1.534
 417  C9   C10   single    1.529  0.020  1.529
 417  C9   H9    single    0.970  0.020  1.090
 417  C10  C11   single    1.524  0.020  1.524
 417  C10  H101  single    0.970  0.020  1.090
 417  C10  H102  single    0.970  0.020  1.090
 417  C11  C12   single    1.527  0.020  1.527
 417  C11  H111  single    0.970  0.020  1.090
 417  C11  H112  single    0.970  0.020  1.090
 417  C12  C13   single    1.530  0.020  1.530
 417  C12  N21   single    1.468  0.020  1.468
 417  C12  H12   single    0.970  0.020  1.090
 417  C13  C14   single    1.530  0.020  1.530
 417  C13  H131  single    0.970  0.020  1.090
 417  C13  H132  single    0.970  0.020  1.090
 417  C14  N38   single    1.453  0.020  1.453
 417  C14  H14   single    0.970  0.020  1.090
 417  N21  C22   single    1.454  0.020  1.454
 417  N21  C26   single    1.452  0.020  1.452
 417  C22  C23   single    1.516  0.020  1.516
 417  C22  H221  single    0.970  0.020  1.090
 417  C22  H222  single    0.970  0.020  1.090
 417  C23  N24   single    1.456  0.020  1.456
 417  C23  H231  single    0.970  0.020  1.090
 417  C23  H232  single    0.970  0.020  1.090
 417  N24  C33   single    1.353  0.020  1.353
 417  N24  C25   single    1.346  0.020  1.346
 417  C25  N35   double    1.307  0.020  1.307
 417  C25  C26   single    1.489  0.020  1.489
 417  C26  H261  single    0.970  0.020  1.090
 417  C26  H262  single    0.970  0.020  1.090
 417  C33  C39   single    1.488  0.020  1.488
 417  C33  N34   double    1.299  0.020  1.299
 417  N34  N35   single    1.349  0.020  1.349
 417  N38  H381  single    0.890  0.020  1.040
 417  N38  H382  single    0.890  0.020  1.040
 417  C39  F41   single    1.338  0.020  1.338
 417  C39  F40   single    1.326  0.020  1.326
 417  C39  F42   single    1.338  0.020  1.338

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
 417  H1    C1   C6    120.70  3.000
 417  H1    C1   C2    121.06  3.000
 417  C6    C1   C2    118.24  3.000
 417  F37   C2   C3    119.36  3.000
 417  C3    C2   C1    123.48  3.000
 417  F37   C2   C1    117.16  3.000
 417  C9    C3   C4    121.16  3.000
 417  C4    C3   C2    116.49  3.000
 417  C9    C3   C2    122.34  3.000
 417  H4    C4   C5    118.32  3.000
 417  H4    C4   C3    120.44  3.000
 417  C5    C4   C3    121.24  3.000
 417  F36   C5   C6    119.28  3.000
 417  F36   C5   C4    120.33  3.000
 417  C6    C5   C4    120.39  3.000
 417  F43   C6   C5    119.61  3.000
 417  F43   C6   C1    120.23  3.000
 417  C5    C6   C1    120.16  3.000
 417  H9    C9   C14   107.15  3.000
 417  H9    C9   C10   107.28  3.000
 417  C14   C9   C10   110.17  3.000
 417  H9    C9   C3    108.78  3.000
 417  C10   C9   C3    112.16  3.000
 417  C14   C9   C3    111.11  3.000
 417  H102  C10  H101  106.48  3.000
 417  H102  C10  C11   109.45  3.000
 417  H101  C10  C11   108.45  3.000
 417  H102  C10  C9    109.70  3.000
 417  H101  C10  C9    110.03  3.000
 417  C11   C10  C9    112.53  3.000
 417  H112  C11  H111  107.08  3.000
 417  H112  C11  C12   111.32  3.000
 417  H111  C11  C12   109.60  3.000
 417  H112  C11  C10   107.54  3.000
 417  H111  C11  C10   110.23  3.000
 417  C12   C11  C10   110.98  3.000
 417  H12   C12  N21   109.74  3.000
 417  H12   C12  C13   108.92  3.000
 417  N21   C12  C13   109.81  3.000
 417  H12   C12  C11   107.14  3.000
 417  N21   C12  C11   112.83  3.000
 417  C13   C12  C11   108.30  3.000
 417  H132  C13  H131  106.71  3.000
 417  H132  C13  C14   107.62  3.000
 417  H131  C13  C14   109.12  3.000
 417  H132  C13  C12   111.37  3.000
 417  H131  C13  C12   108.32  3.000
 417  C14   C13  C12   113.48  3.000
 417  H14   C14  N38   107.01  3.000
 417  H14   C14  C13   108.36  3.000
 417  N38   C14  C13   113.55  3.000
 417  H14   C14  C9    107.84  3.000
 417  N38   C14  C9    109.87  3.000
 417  C13   C14  C9    109.99  3.000
 417  C26   N21  C22   109.12  3.000
 417  C26   N21  C12   114.06  3.000
 417  C22   N21  C12   112.37  3.000
 417  H222  C22  H221  107.03  3.000
 417  H222  C22  C23   109.91  3.000
 417  H221  C22  C23   107.16  3.000
 417  H222  C22  N21   111.96  3.000
 417  H221  C22  N21   110.53  3.000
 417  C23   C22  N21   110.10  3.000
 417  H232  C23  H231  108.93  3.000
 417  H232  C23  N24   109.08  3.000
 417  H231  C23  N24   109.79  3.000
 417  H232  C23  C22   110.69  3.000
 417  H231  C23  C22   110.44  3.000
 417  N24   C23  C22   107.90  3.000
 417  C33   N24  C25   104.33  3.000
 417  C25   N24  C23   123.55  3.000
 417  C33   N24  C23   132.08  3.000
 417  N35   C25  C26   127.61  3.000
 417  C26   C25  N24   122.17  3.000
 417  N35   C25  N24   110.21  3.000
 417  H262  C26  H261  106.99  3.000
 417  H262  C26  C25   107.60  3.000
 417  H261  C26  C25   108.48  3.000
 417  H262  C26  N21   110.91  3.000
 417  H261  C26  N21   112.84  3.000
 417  C25   C26  N21   109.83  3.000
 417  C39   C33  N34   124.93  3.000
 417  N34   C33  N24   110.50  3.000
 417  C39   C33  N24   124.57  3.000
 417  N35   N34  C33   107.40  3.000
 417  N34   N35  C25   107.55  3.000
 417  H382  N38  H381  105.72  3.000
 417  H382  N38  C14   109.54  3.000
 417  H381  N38  C14   109.60  3.000
 417  F42   C39  F41   106.81  3.000
 417  F42   C39  F40   108.26  3.000
 417  F41   C39  F40   108.02  3.000
 417  F42   C39  C33   111.34  3.000
 417  F40   C39  C33   110.80  3.000
 417  F41   C39  C33   111.44  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
 417  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 417  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 417  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 417  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 417  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 417  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 417  CONST_07  C9   C3   C2   C1   180.00   0.0  0
 417  CONST_08  C9   C3   C4   C5   180.00   0.0  0
 417  CONST_09  N34  C33  N24  C23  180.00   0.0  0
 417  CONST_10  N35  C25  N24  C23  180.00   0.0  0
 417  CONST_11  C26  C25  N24  C23    0.00   0.0  0
 417  CONST_12  N35  N34  C33  N24    0.00   0.0  0
 417  CONST_13  N34  N35  C25  N24    0.00   0.0  0
 417  CONST_14  N34  C33  N24  C25    0.00   0.0  0
 417  CONST_15  C33  N34  N35  C25    0.00   0.0  0
 417  CONST_16  C33  N24  C25  C26  180.00   0.0  0
 417  CONST_17  N34  N35  C25  C26  180.00   0.0  0
 417  CONST_18  N35  C25  N24  C33    0.00   0.0  0
 417  CONST_19  F36  C5   C6   C1   180.00   0.0  0
 417  CONST_20  F43  C6   C1   C2   180.00   0.0  0
 417  CONST_21  F36  C5   C4   C3   180.00   0.0  0
 417  CONST_22  F37  C2   C3   C4   180.00   0.0  0
 417  CONST_23  F43  C6   C5   C4   180.00   0.0  0
 417  CONST_24  F37  C2   C1   C6   180.00   0.0  0
 417  CONST_25  F37  C2   C3   C9     0.00   0.0  0
 417  CONST_26  C39  C33  N24  C23    0.00   0.0  0
 417  CONST_27  C39  C33  N24  C25  180.00   0.0  0
 417  CONST_28  C39  C33  N34  N35  180.00   0.0  0
 417  CONST_29  H4   C4   C3   C2   180.00   0.0  0
 417  CONST_30  H1   C1   C2   C3   180.00   0.0  0
 417  Var_01    C12  C11  C10  C9   -57.65  30.0  1
 417  Var_02    C23  C22  N21  C12  161.09  30.0  1
 417  Var_03    C25  C26  N21  C12  177.97  30.0  1
 417  Var_04    N24  C23  C22  N21   51.45  30.0  1
 417  Var_05    N24  C25  C26  N21  -18.51  30.0  1
 417  Var_06    C33  N24  C23  C22  164.16  30.0  1
 417  Var_07    F41  C39  C33  N24  -62.24  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
 417  chir_01  C9   C3   C14  C10  positiv
 417  chir_02  C12  N21  C13  C11  positiv
 417  chir_03  C14  N38  C9   C13  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
 417  plan-1  C1   0.020
 417  plan-1  C2   0.020
 417  plan-1  C3   0.020
 417  plan-1  C4   0.020
 417  plan-1  C5   0.020
 417  plan-1  C6   0.020
 417  plan-1  C9   0.020
 417  plan-1  F36  0.020
 417  plan-1  F37  0.020
 417  plan-1  F43  0.020
 417  plan-1  H1   0.020
 417  plan-1  H4   0.020
 417  plan-2  C23  0.020
 417  plan-2  N24  0.020
 417  plan-2  C25  0.020
 417  plan-2  C26  0.020
 417  plan-2  C33  0.020
 417  plan-2  N34  0.020
 417  plan-2  N35  0.020
 417  plan-2  C39  0.020

