# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 06:18:54 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 2-{[2-(1H-pyrazolo[3,4-c]pyridin-3-yl)-6-(trifluoromethyl)pyridin-4-yl]amino}ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCNc1cc(nc(c1)C(F)(F)F)c2n[nH]c3cnccc23
#
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
 L5Y  L5Y  2-{[2-(1H-pyrazolo[3,4-c]pyridin-3-yl)-6-(trifluoromethyl)pyridin-4-yl]amino}ethanol  ligand  35  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L5Y
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
 L5Y  O1    O  OH1   0  -0.656   5.4271  -3.1066  -0.3875
 L5Y  C2    C  CH2   0  -0.163   5.5964  -2.0030   0.4736
 L5Y  C3    C  CH2   0  -0.286   4.5795  -0.9442   0.1116
 L5Y  N4    N  NH1   0  -0.685   3.2438  -1.4764   0.2153
 L5Y  C5    C  CR6   0   0.532   2.1199  -0.7331   0.1722
 L5Y  C6    C  CR16  0  -0.396   0.8613  -1.3507   0.1035
 L5Y  C7    C  CR6   0   0.212  -0.2830  -0.5767   0.0963
 L5Y  N8    N  N     0  -0.484  -0.2620   0.7574   0.1553
 L5Y  C9    C  CR6   0  -0.011   0.9221   1.3320   0.2126
 L5Y  C10   C  CR16  0  -0.397   2.1343   0.6706   0.2158
 L5Y  C11   C  CT    0   1.038   0.9233   2.8393   0.2757
 L5Y  F12   F  F     0  -0.294  -0.3011   3.3527   0.2916
 L5Y  F13   F  F     0  -0.319   1.5573   3.2790   1.3742
 L5Y  F14   F  F     0  -0.316   1.5676   3.3715  -0.7733
 L5Y  C15   C  CR5   0   0.182  -1.6132  -1.1796   0.0247
 L5Y  N16   N  N     0  -0.221  -1.7765  -2.4784  -0.0774
 L5Y  N17   N  NR15  0  -0.540  -3.0787  -2.7120  -0.1197
 L5Y  C18   C  CR56  0   0.310  -3.8095  -1.5705  -0.0434
 L5Y  C19   C  CR16  0  -0.074  -5.1833  -1.3109  -0.0446
 L5Y  N20   N  N     0  -0.360  -5.6212  -0.0801   0.0485
 L5Y  C21   C  CR16  0  -0.064  -4.7411   0.9325   0.1438
 L5Y  C22   C  CR16  0  -0.371  -3.3732   0.7811   0.1504
 L5Y  C23   C  CR56  0   0.034  -2.8831  -0.5246   0.0528
 L5Y  HO1   H  HOH1  0   0.443   5.9576  -3.8314  -0.0505
 L5Y  H2    H  HCH2  0   0.206   5.4579  -2.2881   1.5226
 L5Y  H2A   H  HCH2  0   0.210   6.5951  -1.5612   0.3840
 L5Y  H3    H  HCH2  0   0.235   4.7119  -0.1186   0.8134
 L5Y  H3A   H  HCH2  0   0.232   4.7822  -0.5518  -0.8924
 L5Y  HN4   H  HNH1  0   0.372   3.1485  -2.4569   0.0067
 L5Y  H6    H  HCR6  0   0.254   0.7820  -2.4293   0.0621
 L5Y  H10   H  HCR6  0   0.261   3.0625   1.2231   0.2529
 L5Y  HN17  H  HNR5  0   0.382  -3.4042  -3.6595  -0.1915
 L5Y  H19   H  HCR6  0   0.236  -5.9196  -2.1044  -0.1206
 L5Y  H21   H  HCR6  0   0.237  -5.1764   1.9212   0.2201
 L5Y  H22   H  HCR6  0   0.259  -2.7085   1.6278   0.2271

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
 L5Y  O1   C2    single    1.410  0.020  1.410
 L5Y  O1   HO1   single    0.850  0.020  0.980
 L5Y  C2   C3    single    1.512  0.020  1.512
 L5Y  C2   H2    single    0.970  0.020  1.090
 L5Y  C2   H2A   single    0.970  0.020  1.090
 L5Y  C3   N4    single    1.442  0.020  1.442
 L5Y  C3   H3    single    0.970  0.020  1.090
 L5Y  C3   H3A   single    0.970  0.020  1.090
 L5Y  N4   C5    single    1.348  0.020  1.348
 L5Y  N4   HN4   single    0.890  0.020  1.040
 L5Y  C5   C6    aromatic  1.404  0.020  1.404
 L5Y  C5   C10   aromatic  1.404  0.020  1.404
 L5Y  C6   C7    aromatic  1.382  0.020  1.382
 L5Y  C6   H6    single    0.930  0.020  1.080
 L5Y  C7   N8    aromatic  1.336  0.020  1.336
 L5Y  C7   C15   single    1.462  0.020  1.462
 L5Y  N8   C9    aromatic  1.317  0.020  1.317
 L5Y  C9   C10   aromatic  1.381  0.020  1.381
 L5Y  C9   C11   single    1.509  0.020  1.509
 L5Y  C10  H10   single    0.930  0.020  1.080
 L5Y  C11  F12   single    1.328  0.020  1.328
 L5Y  C11  F13   single    1.342  0.020  1.342
 L5Y  C11  F14   single    1.341  0.020  1.341
 L5Y  C15  N16   aromatic  1.313  0.020  1.313
 L5Y  C15  C23   aromatic  1.429  0.020  1.429
 L5Y  N16  N17   aromatic  1.324  0.020  1.324
 L5Y  N17  C18   aromatic  1.358  0.020  1.358
 L5Y  N17  HN17  single    0.860  0.020  1.020
 L5Y  C18  C19   aromatic  1.398  0.020  1.398
 L5Y  C18  C23   aromatic  1.400  0.020  1.400
 L5Y  C19  N20   aromatic  1.310  0.020  1.310
 L5Y  C19  H19   single    0.930  0.020  1.080
 L5Y  N20  C21   aromatic  1.345  0.020  1.345
 L5Y  C21  C22   aromatic  1.376  0.020  1.376
 L5Y  C21  H21   single    0.930  0.020  1.080
 L5Y  C22  C23   aromatic  1.398  0.020  1.398
 L5Y  C22  H22   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
 L5Y  HO1   O1   C2   108.08  3.000
 L5Y  H2A   C2   H2   107.36  3.000
 L5Y  H2A   C2   C3   108.12  3.000
 L5Y  H2    C2   C3   109.05  3.000
 L5Y  H2A   C2   O1   112.03  3.000
 L5Y  H2    C2   O1   111.46  3.000
 L5Y  C3    C2   O1   108.73  3.000
 L5Y  H3A   C3   H3   107.19  3.000
 L5Y  H3A   C3   N4   111.66  3.000
 L5Y  H3    C3   N4   110.20  3.000
 L5Y  H3A   C3   C2   110.21  3.000
 L5Y  H3    C3   C2   107.11  3.000
 L5Y  N4    C3   C2   110.33  3.000
 L5Y  HN4   N4   C5   116.83  3.000
 L5Y  HN4   N4   C3   115.61  3.000
 L5Y  C5    N4   C3   124.51  3.000
 L5Y  C10   C5   C6   116.78  3.000
 L5Y  C10   C5   N4   122.79  3.000
 L5Y  C6    C5   N4   120.43  3.000
 L5Y  H6    C6   C7   119.83  3.000
 L5Y  H6    C6   C5   120.40  3.000
 L5Y  C7    C6   C5   119.77  3.000
 L5Y  C15   C7   N8   115.36  3.000
 L5Y  C15   C7   C6   121.52  3.000
 L5Y  N8    C7   C6   123.12  3.000
 L5Y  C9    N8   C7   116.86  3.000
 L5Y  C11   C9   C10  118.54  3.000
 L5Y  C11   C9   N8   116.00  3.000
 L5Y  C10   C9   N8   125.46  3.000
 L5Y  H10   C10  C9   120.60  3.000
 L5Y  H10   C10  C5   121.39  3.000
 L5Y  C9    C10  C5   118.01  3.000
 L5Y  F14   C11  F13  106.45  3.000
 L5Y  F14   C11  F12  107.39  3.000
 L5Y  F13   C11  F12  107.40  3.000
 L5Y  F14   C11  C9   111.36  3.000
 L5Y  F13   C11  C9   111.22  3.000
 L5Y  F12   C11  C9   112.72  3.000
 L5Y  C23   C15  N16  110.15  3.000
 L5Y  C23   C15  C7   128.20  3.000
 L5Y  N16   C15  C7   121.65  3.000
 L5Y  N17   N16  C15  107.42  3.000
 L5Y  HN17  N17  C18  128.52  3.000
 L5Y  HN17  N17  N16  119.18  3.000
 L5Y  C18   N17  N16  112.30  3.000
 L5Y  C23   C18  C19  120.76  3.000
 L5Y  C23   C18  N17  106.00  3.000
 L5Y  C19   C18  N17  133.24  3.000
 L5Y  H19   C19  N20  117.73  3.000
 L5Y  H19   C19  C18  122.08  3.000
 L5Y  N20   C19  C18  120.20  3.000
 L5Y  C21   N20  C19  119.59  3.000
 L5Y  H21   C21  C22  119.97  3.000
 L5Y  H21   C21  N20  115.43  3.000
 L5Y  C22   C21  N20  124.60  3.000
 L5Y  H22   C22  C23  121.45  3.000
 L5Y  H22   C22  C21  121.75  3.000
 L5Y  C23   C22  C21  116.79  3.000
 L5Y  C22   C23  C18  118.06  3.000
 L5Y  C22   C23  C15  137.81  3.000
 L5Y  C18   C23  C15  104.13  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
 L5Y  CONST_01  N8    C7   C6   C5     0.00   0.0  0
 L5Y  CONST_02  C15   C7   C6   C5   180.00   0.0  0
 L5Y  CONST_03  N8    C9   C10  C5     0.00   0.0  0
 L5Y  CONST_04  C9    C10  C5   C6     0.00   0.0  0
 L5Y  CONST_05  C9    N8   C7   C6     0.00   0.0  0
 L5Y  CONST_06  N16   C15  C7   C6     0.00   0.0  0
 L5Y  CONST_07  C23   C15  C7   C6   180.00   0.0  0
 L5Y  CONST_08  C10   C5   C6   C7     0.00   0.0  0
 L5Y  CONST_09  C10   C9   N8   C7     0.00   0.0  0
 L5Y  CONST_10  N17   N16  C15  C7   180.00   0.0  0
 L5Y  CONST_11  C18   C23  C15  C7   180.00   0.0  0
 L5Y  CONST_12  C22   C23  C15  C7     0.00   0.0  0
 L5Y  CONST_13  N16   C15  C7   N8   180.00   0.0  0
 L5Y  CONST_14  C23   C15  C7   N8     0.00   0.0  0
 L5Y  CONST_15  C15   C7   N8   C9   180.00   0.0  0
 L5Y  CONST_16  C18   N17  N16  C15    0.00   0.0  0
 L5Y  CONST_17  N17   C18  C23  C15    0.00   0.0  0
 L5Y  CONST_18  C19   C18  C23  C15  180.00   0.0  0
 L5Y  CONST_19  C21   C22  C23  C15  180.00   0.0  0
 L5Y  CONST_20  C18   C23  C15  N16    0.00   0.0  0
 L5Y  CONST_21  C22   C23  C15  N16  180.00   0.0  0
 L5Y  CONST_22  C19   C18  N17  N16  180.00   0.0  0
 L5Y  CONST_23  C23   C18  N17  N16    0.00   0.0  0
 L5Y  CONST_24  C23   C15  N16  N17    0.00   0.0  0
 L5Y  CONST_25  N20   C19  C18  N17  180.00   0.0  0
 L5Y  CONST_26  C22   C23  C18  N17  180.00   0.0  0
 L5Y  CONST_27  C21   N20  C19  C18    0.00   0.0  0
 L5Y  CONST_28  C21   C22  C23  C18    0.00   0.0  0
 L5Y  CONST_29  C22   C23  C18  C19    0.00   0.0  0
 L5Y  CONST_30  C22   C21  N20  C19    0.00   0.0  0
 L5Y  CONST_31  C23   C18  C19  N20    0.00   0.0  0
 L5Y  CONST_32  C23   C22  C21  N20    0.00   0.0  0
 L5Y  CONST_33  C7    C6   C5   N4   180.00   0.0  0
 L5Y  CONST_34  C9    C10  C5   N4   180.00   0.0  0
 L5Y  CONST_35  C11   C9   C10  C5   180.00   0.0  0
 L5Y  CONST_36  C11   C9   N8   C7   180.00   0.0  0
 L5Y  CONST_37  H10   C10  C5   C6   180.00   0.0  0
 L5Y  CONST_38  H6    C6   C7   N8   180.00   0.0  0
 L5Y  CONST_39  HN17  N17  N16  C15  180.00   0.0  0
 L5Y  CONST_40  H22   C22  C23  C15    0.00   0.0  0
 L5Y  CONST_41  H19   C19  C18  N17    0.00   0.0  0
 L5Y  CONST_42  H21   C21  N20  C19  180.00   0.0  0
 L5Y  CONST_43  C6    C5   N4   C3   180.00   0.0  0
 L5Y  CONST_44  C10   C5   N4   C3     0.00   0.0  0
 L5Y  CONST_45  HN4   N4   C5   C6     0.00   0.0  0
 L5Y  Var_01    F12   C11  C9   N8     1.35  30.0  2
 L5Y  Var_02    C5    N4   C3   C2   168.65  30.0  3
 L5Y  Var_03    N4    C3   C2   O1    58.21  30.0  3

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
 L5Y  plan-1  N4    0.020
 L5Y  plan-1  C5    0.020
 L5Y  plan-1  C6    0.020
 L5Y  plan-1  C7    0.020
 L5Y  plan-1  N8    0.020
 L5Y  plan-1  C9    0.020
 L5Y  plan-1  C10   0.020
 L5Y  plan-1  C11   0.020
 L5Y  plan-1  C15   0.020
 L5Y  plan-1  H6    0.020
 L5Y  plan-1  H10   0.020
 L5Y  plan-2  C7    0.020
 L5Y  plan-2  C15   0.020
 L5Y  plan-2  N16   0.020
 L5Y  plan-2  N17   0.020
 L5Y  plan-2  C18   0.020
 L5Y  plan-2  C19   0.020
 L5Y  plan-2  N20   0.020
 L5Y  plan-2  C21   0.020
 L5Y  plan-2  C22   0.020
 L5Y  plan-2  C23   0.020
 L5Y  plan-2  HN17  0.020
 L5Y  plan-2  H19   0.020
 L5Y  plan-2  H21   0.020
 L5Y  plan-2  H22   0.020
 L5Y  plan-3  C3    0.020
 L5Y  plan-3  N4    0.020
 L5Y  plan-3  C5    0.020
 L5Y  plan-3  HN4   0.020

