# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 12:59:10 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (2R)-3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-2-(pyrimidin-5-yl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)[C@@H](Cn1cnc(n1)c2cc(cc(c2)C(F)(F)F)C(F)(F)F)c3cncnc3
#
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
 6L8  6L8  (2R)-3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-2-(pyrimidin-5-yl)propanamide  ligand  42  30  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6L8
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
 6L8  C9   C  CR16  0  -0.340  -4.0931   0.6373  -0.0746
 6L8  C10  C  CR6   0  -0.148  -3.9018  -0.7359  -0.0827
 6L8  C11  C  CR16  0  -0.319  -2.6418  -1.2780   0.1251
 6L8  C6   C  CR6   0   0.064  -1.5519  -0.4445   0.3445
 6L8  C7   C  CR16  0  -0.313  -1.7401   0.9339   0.3579
 6L8  C8   C  CR6   0  -0.146  -3.0028   1.4660   0.1515
 6L8  C12  C  CT    0   1.064  -3.1555   2.9569   0.1536
 6L8  C13  C  CT    0   1.064  -5.0455  -1.6718  -0.3330
 6L8  F2   F  F     0  -0.299  -6.2183  -1.0406  -0.4115
 6L8  F1   F  F     0  -0.311  -4.8818  -2.3463  -1.4790
 6L8  F3   F  F     0  -0.310  -5.1521  -2.5876   0.6379
 6L8  F6   F  F     0  -0.299  -4.4326   3.3433   0.1335
 6L8  F5   F  F     0  -0.309  -2.5920   3.5075   1.2357
 6L8  F4   F  F     0  -0.312  -2.5588   3.5095  -0.9111
 6L8  C5   C  CR5   0   0.349  -0.2242  -1.0173   0.5597
 6L8  N3   N  N     0  -0.474   0.0143  -2.3469   0.5950
 6L8  C4   C  CR15  0   0.123   1.3068  -2.4117   0.8071
 6L8  N2   N  NR5   0  -0.266   1.8154  -1.1792   0.9008
 6L8  N4   N  N     0  -0.281   0.8482  -0.2780   0.7399
 6L8  C3   C  CH2   0  -0.262   3.1880  -0.7733   1.0936
 6L8  C2   C  CH1   0  -0.510   3.7711  -0.1499  -0.1738
 6L8  C1'  C  CR6   0   0.032   5.1889   0.2970   0.0635
 6L8  C4'  C  CR16  0  -0.052   5.5470   1.6359  -0.0102
 6L8  N2'  N  N     0  -0.385   6.7865   2.0585   0.1966
 6L8  C3'  C  CR16  0   0.055   7.6862   1.1312   0.4834
 6L8  N1'  N  N     0  -0.387   7.4638  -0.1705   0.5846
 6L8  C2'  C  CR16  0  -0.030   6.2208  -0.5812   0.3747
 6L8  C1   C  C     0   0.557   3.7361  -1.1461  -1.3326
 6L8  O1   O  O     0  -0.477   3.9498  -2.3345  -1.1479
 6L8  N1   N  NH2   0  -0.790   3.4885  -0.6069  -2.5279
 6L8  H1   H  HCR6  0   0.288  -5.0753   1.0557  -0.2404
 6L8  H2   H  HCR6  0   0.283  -2.4917  -2.3502   0.1193
 6L8  H3   H  HCR6  0   0.283  -0.8899   1.5813   0.5323
 6L8  H4   H  HCR5  0   0.309   1.9029  -3.3057   0.9017
 6L8  H5   H  HCH2  0   0.302   3.2247  -0.0535   1.9102
 6L8  H6   H  HCH2  0   0.285   3.7492  -1.6546   1.3977
 6L8  H7   H  HCH1  0   0.309   3.1779   0.7332  -0.4271
 6L8  H8   H  HCR6  0   0.282   4.8020   2.3907  -0.2433
 6L8  H9   H  HCR6  0   0.269   8.7023   1.4691   0.6521
 6L8  H10  H  HCR6  0   0.279   6.0450  -1.6488   0.4519
 6L8  H11  H  HNH2  0   0.415   3.3129   0.3764  -2.6453
 6L8  H12  H  HNH2  0   0.409   3.5015  -1.1768  -3.3590

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
 6L8  C3'  N2'  aromatic  1.324  0.020  1.324
 6L8  C3'  N1'  aromatic  1.324  0.020  1.324
 6L8  F1   C13  single    1.340  0.020  1.340
 6L8  N2'  C4'  aromatic  1.326  0.020  1.326
 6L8  N1'  C2'  aromatic  1.326  0.020  1.326
 6L8  C13  F2   single    1.334  0.020  1.334
 6L8  C13  C10  single    1.499  0.020  1.499
 6L8  C13  F3   single    1.339  0.020  1.339
 6L8  F4   C12  single    1.340  0.020  1.340
 6L8  C4'  C1'  aromatic  1.388  0.020  1.388
 6L8  F5   C12  single    1.339  0.020  1.339
 6L8  C9   C10  aromatic  1.387  0.020  1.387
 6L8  C9   C8   aromatic  1.388  0.020  1.388
 6L8  C2'  C1'  aromatic  1.390  0.020  1.390
 6L8  C10  C11  aromatic  1.387  0.020  1.387
 6L8  C12  C8   single    1.499  0.020  1.499
 6L8  C12  F6   single    1.334  0.020  1.334
 6L8  C8   C7   aromatic  1.386  0.020  1.386
 6L8  C11  C6   aromatic  1.390  0.020  1.390
 6L8  C1'  C2   single    1.505  0.020  1.505
 6L8  C7   C6   aromatic  1.391  0.020  1.391
 6L8  C6   C5   single    1.462  0.020  1.462
 6L8  C5   N3   aromatic  1.351  0.020  1.351
 6L8  C5   N4   aromatic  1.315  0.020  1.315
 6L8  N3   C4   aromatic  1.311  0.020  1.311
 6L8  N4   N2   aromatic  1.332  0.020  1.332
 6L8  C2   C1   single    1.528  0.020  1.528
 6L8  C2   C3   single    1.528  0.020  1.528
 6L8  C4   N2   aromatic  1.337  0.020  1.337
 6L8  C1   O1   double    1.221  0.020  1.221
 6L8  C1   N1   single    1.334  0.020  1.334
 6L8  N2   C3   single    1.444  0.020  1.444
 6L8  C9   H1   single    0.930  0.020  1.080
 6L8  C11  H2   single    0.930  0.020  1.080
 6L8  C7   H3   single    0.930  0.020  1.080
 6L8  C4   H4   single    0.930  0.020  1.080
 6L8  C3   H5   single    0.970  0.020  1.090
 6L8  C3   H6   single    0.970  0.020  1.090
 6L8  C2   H7   single    0.970  0.020  1.090
 6L8  C4'  H8   single    0.930  0.020  1.080
 6L8  C3'  H9   single    0.930  0.020  1.080
 6L8  C2'  H10  single    0.930  0.020  1.080
 6L8  N1   H11  single    0.860  0.020  1.020
 6L8  N1   H12  single    0.860  0.020  1.020

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
 6L8  H1   C9   C8   120.53  3.000
 6L8  H1   C9   C10  120.54  3.000
 6L8  C8   C9   C10  118.94  3.000
 6L8  C13  C10  C11  118.29  3.000
 6L8  C11  C10  C9   120.76  3.000
 6L8  C13  C10  C9   120.94  3.000
 6L8  H2   C11  C6   119.09  3.000
 6L8  H2   C11  C10  120.81  3.000
 6L8  C6   C11  C10  120.11  3.000
 6L8  C5   C6   C7   120.64  3.000
 6L8  C5   C6   C11  120.04  3.000
 6L8  C7   C6   C11  119.32  3.000
 6L8  H3   C7   C8   120.66  3.000
 6L8  H3   C7   C6   119.19  3.000
 6L8  C8   C7   C6   120.15  3.000
 6L8  C12  C8   C7   118.33  3.000
 6L8  C7   C8   C9   120.72  3.000
 6L8  C12  C8   C9   120.94  3.000
 6L8  F4   C12  F5   106.57  3.000
 6L8  F5   C12  F6   107.22  3.000
 6L8  F4   C12  F6   107.15  3.000
 6L8  F6   C12  C8   112.68  3.000
 6L8  F5   C12  C8   111.56  3.000
 6L8  F4   C12  C8   111.33  3.000
 6L8  F3   C13  F1   106.60  3.000
 6L8  F3   C13  F2   107.23  3.000
 6L8  F1   C13  F2   107.18  3.000
 6L8  F3   C13  C10  111.51  3.000
 6L8  F2   C13  C10  112.65  3.000
 6L8  F1   C13  C10  111.34  3.000
 6L8  N4   C5   N3   113.93  3.000
 6L8  N4   C5   C6   122.72  3.000
 6L8  N3   C5   C6   123.34  3.000
 6L8  C4   N3   C5   103.11  3.000
 6L8  H4   C4   N2   123.22  3.000
 6L8  H4   C4   N3   126.86  3.000
 6L8  N2   C4   N3   109.93  3.000
 6L8  C3   N2   N4   121.07  3.000
 6L8  C3   N2   C4   129.06  3.000
 6L8  N4   N2   C4   109.83  3.000
 6L8  N2   N4   C5   103.20  3.000
 6L8  H6   C3   H5   107.96  3.000
 6L8  H6   C3   C2   111.44  3.000
 6L8  H5   C3   C2   109.85  3.000
 6L8  H6   C3   N2   107.44  3.000
 6L8  H5   C3   N2   108.53  3.000
 6L8  C2   C3   N2   111.50  3.000
 6L8  H7   C2   C1   109.77  3.000
 6L8  H7   C2   C1'  107.92  3.000
 6L8  C1   C2   C1'  109.55  3.000
 6L8  H7   C2   C3   108.33  3.000
 6L8  C1   C2   C3   110.75  3.000
 6L8  C1'  C2   C3   110.47  3.000
 6L8  C2'  C1'  C4'  115.46  3.000
 6L8  C2'  C1'  C2   123.14  3.000
 6L8  C4'  C1'  C2   121.40  3.000
 6L8  H8   C4'  N2'  116.96  3.000
 6L8  H8   C4'  C1'  120.33  3.000
 6L8  N2'  C4'  C1'  122.71  3.000
 6L8  C3'  N2'  C4'  116.49  3.000
 6L8  H9   C3'  N1'  116.87  3.000
 6L8  H9   C3'  N2'  116.90  3.000
 6L8  N1'  C3'  N2'  126.23  3.000
 6L8  C2'  N1'  C3'  116.73  3.000
 6L8  H10  C2'  N1'  116.46  3.000
 6L8  H10  C2'  C1'  121.16  3.000
 6L8  N1'  C2'  C1'  122.38  3.000
 6L8  N1   C1   O1   124.12  3.000
 6L8  N1   C1   C2   114.83  3.000
 6L8  O1   C1   C2   121.03  3.000
 6L8  H12  N1   H11  117.31  3.000
 6L8  H12  N1   C1   120.52  3.000
 6L8  H11  N1   C1   122.14  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
 6L8  CONST_01  C6   C11  C10  C9      0.00   0.0  0
 6L8  CONST_02  C6   C7   C8   C9      0.00   0.0  0
 6L8  CONST_03  C7   C8   C9   C10     0.00   0.0  0
 6L8  CONST_04  C7   C6   C11  C10     0.00   0.0  0
 6L8  CONST_05  C5   C6   C11  C10   180.00   0.0  0
 6L8  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 6L8  CONST_07  C8   C7   C6   C11     0.00   0.0  0
 6L8  CONST_08  N3   C5   C6   C11     0.00   0.0  0
 6L8  CONST_09  N4   C5   C6   C11   180.00   0.0  0
 6L8  CONST_10  C4   N3   C5   C6    180.00   0.0  0
 6L8  CONST_11  N2   N4   C5   C6    180.00   0.0  0
 6L8  CONST_12  N3   C5   C6   C7    180.00   0.0  0
 6L8  CONST_13  N4   C5   C6   C7      0.00   0.0  0
 6L8  CONST_14  C5   C6   C7   C8    180.00   0.0  0
 6L8  CONST_15  N2   C4   N3   C5      0.00   0.0  0
 6L8  CONST_16  C4   N2   N4   C5      0.00   0.0  0
 6L8  CONST_17  N2   N4   C5   N3      0.00   0.0  0
 6L8  CONST_18  N4   N2   C4   N3      0.00   0.0  0
 6L8  CONST_19  N4   C5   N3   C4      0.00   0.0  0
 6L8  CONST_20  C3'  N2'  C4'  C1'     0.00   0.0  0
 6L8  CONST_21  C3'  N1'  C2'  C1'     0.00   0.0  0
 6L8  CONST_22  N1'  C3'  N2'  C4'     0.00   0.0  0
 6L8  CONST_23  N1'  C2'  C1'  C4'     0.00   0.0  0
 6L8  CONST_24  C2'  N1'  C3'  N2'     0.00   0.0  0
 6L8  CONST_25  C2'  C1'  C4'  N2'     0.00   0.0  0
 6L8  CONST_26  C12  C8   C9   C10   180.00   0.0  0
 6L8  CONST_27  C13  C10  C11  C6    180.00   0.0  0
 6L8  CONST_28  C12  C8   C7   C6    180.00   0.0  0
 6L8  CONST_29  C13  C10  C9   C8    180.00   0.0  0
 6L8  CONST_30  C3   N2   N4   C5    180.00   0.0  0
 6L8  CONST_31  C3   N2   C4   N3    180.00   0.0  0
 6L8  CONST_32  N2'  C4'  C1'  C2    180.00   0.0  0
 6L8  CONST_33  N1'  C2'  C1'  C2    180.00   0.0  0
 6L8  CONST_34  H2   C11  C10  C9    180.00   0.0  0
 6L8  CONST_35  H3   C7   C8   C9    180.00   0.0  0
 6L8  CONST_36  H1   C9   C10  C11   180.00   0.0  0
 6L8  CONST_37  H4   C4   N3   C5    180.00   0.0  0
 6L8  CONST_38  H9   C3'  N2'  C4'   180.00   0.0  0
 6L8  CONST_39  H10  C2'  C1'  C4'   180.00   0.0  0
 6L8  CONST_40  H8   C4'  N2'  C3'   180.00   0.0  0
 6L8  CONST_41  H11  N1   C1   C2      0.00   0.0  0
 6L8  CONST_42  H12  N1   C1   C2    180.00   0.0  0
 6L8  Var_01    F1   C13  C10  C9    114.66  30.0  3
 6L8  Var_02    F4   C12  C8   C9   -110.49  30.0  3
 6L8  Var_03    C2   C3   N2   C4    108.75  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
 6L8  chir_01  C2  C1'  C1  C3  negativ

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
 6L8  plan-1  C6   0.020
 6L8  plan-1  C5   0.020
 6L8  plan-1  N3   0.020
 6L8  plan-1  C4   0.020
 6L8  plan-1  N2   0.020
 6L8  plan-1  N4   0.020
 6L8  plan-1  C3   0.020
 6L8  plan-1  H4   0.020
 6L8  plan-2  C9   0.020
 6L8  plan-2  C10  0.020
 6L8  plan-2  C11  0.020
 6L8  plan-2  C6   0.020
 6L8  plan-2  C7   0.020
 6L8  plan-2  C8   0.020
 6L8  plan-2  C12  0.020
 6L8  plan-2  C13  0.020
 6L8  plan-2  C5   0.020
 6L8  plan-2  H1   0.020
 6L8  plan-2  H2   0.020
 6L8  plan-2  H3   0.020
 6L8  plan-3  C2   0.020
 6L8  plan-3  C1'  0.020
 6L8  plan-3  C4'  0.020
 6L8  plan-3  N2'  0.020
 6L8  plan-3  C3'  0.020
 6L8  plan-3  N1'  0.020
 6L8  plan-3  C2'  0.020
 6L8  plan-3  H8   0.020
 6L8  plan-3  H9   0.020
 6L8  plan-3  H10  0.020
 6L8  plan-4  C2   0.020
 6L8  plan-4  C1   0.020
 6L8  plan-4  O1   0.020
 6L8  plan-4  N1   0.020
 6L8  plan-4  H11  0.020
 6L8  plan-4  H12  0.020

