# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 23:48:51 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3S)-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCN1CCN(CC1)c2cc(c(C#N)c(n2)N3CCC[C@H](CO)C3)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
 A3Y  A3Y  6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3S)-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile  ligand  55  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A3Y
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
 A3Y  N3   N  NT    0  -0.417  -4.9321   0.5243  -0.4893
 A3Y  C4   C  CR6   0   0.570   0.8352  -0.7072   0.5107
 A3Y  N2   N  NT    0  -0.495  -2.4443   0.5172   0.8985
 A3Y  C7   C  CH2   0  -0.272  -4.1378   1.7295  -0.3587
 A3Y  C6   C  CH2   0  -0.329  -3.2901   1.6952   0.9040
 A3Y  C9   C  CH2   0  -0.328  -3.2183  -0.7016   0.7501
 A3Y  C13  C  CH2   0  -0.434   1.2536  -3.7472  -1.2895
 A3Y  C8   C  CH2   0  -0.289  -4.0729  -0.6443  -0.5045
 A3Y  N5   N  NS    0  -0.270   4.0606   0.4847  -0.3289
 A3Y  C16  C  CH2   0  -0.319   2.6649  -2.3651   0.7885
 A3Y  C1   C  CR16  0  -0.531  -0.3574   1.7327   1.0309
 A3Y  C2   C  CR6   0  -0.037   0.9918   1.6753   0.8496
 A3Y  C3   C  CR6   0  -0.184   1.6422   0.4654   0.5321
 A3Y  N1   N  N     0  -0.532  -0.4832  -0.6226   0.6309
 A3Y  C5   C  CR6   0   0.610  -1.1003   0.5336   0.8354
 A3Y  C10  C  CH2   0  -0.293  -5.7973   0.6003  -1.6519
 A3Y  C11  C  CH2   0  -0.179  -6.8475  -0.4876  -1.7247
 A3Y  O1   O  OH1   0  -0.669  -7.6801  -0.4175  -0.5901
 A3Y  N4   N  NT    0  -0.492   1.3515  -1.9448   0.3358
 A3Y  C12  C  CH2   0  -0.312   0.5389  -3.0568  -0.1334
 A3Y  C14  C  CH2   0  -0.425   2.6681  -4.1747  -0.9111
 A3Y  C15  C  CH1   0  -0.278   3.4660  -3.0015  -0.3434
 A3Y  C17  C  CH2   0  -0.132   4.8337  -3.4092   0.1737
 A3Y  O2   O  OH1   0  -0.671   5.5826  -3.9683  -0.8811
 A3Y  F1   F  F     0  -0.312   2.2995   3.2932  -0.2306
 A3Y  F2   F  F     0  -0.293   1.1013   3.9656   1.4217
 A3Y  F3   F  F     0  -0.309   2.8482   2.7705   1.7851
 A3Y  H4   H  HCH2  0   0.198  -3.4701   1.8812  -1.2253
 A3Y  H5   H  HCH2  0   0.249  -4.8022   2.5947  -0.3069
 A3Y  H2   H  HCH2  0   0.251  -3.9369   1.6630   1.7855
 A3Y  H3   H  HCH2  0   0.273  -2.7066   2.6087   0.9627
 A3Y  H8   H  HCH2  0   0.284  -2.5554  -1.5597   0.7152
 A3Y  H9   H  HCH2  0   0.247  -3.8670  -0.8028   1.6260
 A3Y  H18  H  HCH2  0   0.239   0.6668  -4.6144  -1.6008
 A3Y  H17  H  HCH2  0   0.224   1.2878  -3.0630  -2.1426
 A3Y  H7   H  HCH2  0   0.249  -4.6780  -1.5514  -0.5363
 A3Y  H6   H  HCH2  0   0.199  -3.4181  -0.6573  -1.3935
 A3Y  H23  H  HCH2  0   0.271   3.2034  -1.5405   1.2480
 A3Y  H22  H  HCH2  0   0.250   2.5182  -3.1106   1.5818
 A3Y  H1   H  HCR6  0   0.291  -0.8370   2.6551   1.3118
 A3Y  H10  H  HCH2  0   0.236  -6.3032   1.5700  -1.6318
 A3Y  H11  H  HCH2  0   0.199  -5.2225   0.5715  -2.5937
 A3Y  H13  H  HCH2  0   0.208  -7.4100  -0.3312  -2.6543
 A3Y  H12  H  HCH2  0   0.198  -6.3766  -1.4744  -1.8180
 A3Y  H14  H  HOH1  0   0.453  -8.3574  -1.0936  -0.6790
 A3Y  H16  H  HCH2  0   0.272  -0.4365  -2.6913  -0.4410
 A3Y  H15  H  HCH2  0   0.227   0.3813  -3.7684   0.6864
 A3Y  H19  H  HCH2  0   0.211   2.6165  -4.9661  -0.1531
 A3Y  H20  H  HCH2  0   0.242   3.1747  -4.6014  -1.7777
 A3Y  H21  H  HCH1  0   0.235   3.5996  -2.2450  -1.1254
 A3Y  H24  H  HCH2  0   0.201   5.3341  -2.5253   0.5930
 A3Y  H25  H  HCH2  0   0.187   4.7058  -4.1247   0.9983
 A3Y  H26  H  HOH1  0   0.454   6.4261  -4.2638  -0.5276
 A3Y  C18  C  CSP   0  -0.004   2.9777   0.4691   0.0763
 A3Y  C19  C  CT    0   1.074   1.8081   2.9343   0.9616

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
 A3Y  C10  C11  single    1.514  0.020  1.514
 A3Y  C10  N3   single    1.451  0.020  1.451
 A3Y  C11  O1   single    1.409  0.020  1.409
 A3Y  C7   N3   single    1.449  0.020  1.449
 A3Y  C7   C6   single    1.521  0.020  1.521
 A3Y  N3   C8   single    1.451  0.020  1.451
 A3Y  C6   N2   single    1.450  0.020  1.450
 A3Y  C8   C9   single    1.519  0.020  1.519
 A3Y  F1   C19  single    1.339  0.020  1.339
 A3Y  F3   C19  single    1.337  0.020  1.337
 A3Y  C1   C5   aromatic  1.424  0.020  1.424
 A3Y  C1   C2   aromatic  1.363  0.020  1.363
 A3Y  N2   C5   single    1.346  0.020  1.346
 A3Y  N2   C9   single    1.451  0.020  1.451
 A3Y  C19  C2   single    1.505  0.020  1.505
 A3Y  C19  F2   single    1.332  0.020  1.332
 A3Y  C5   N1   aromatic  1.326  0.020  1.326
 A3Y  C2   C3   aromatic  1.410  0.020  1.410
 A3Y  N1   C4   aromatic  1.327  0.020  1.327
 A3Y  C3   C18  single    1.411  0.020  1.411
 A3Y  C3   C4   aromatic  1.424  0.020  1.424
 A3Y  C18  N5   triple    1.156  0.020  1.156
 A3Y  C4   N4   single    1.352  0.020  1.352
 A3Y  N4   C16  single    1.451  0.020  1.451
 A3Y  N4   C12  single    1.455  0.020  1.455
 A3Y  C16  C15  single    1.526  0.020  1.526
 A3Y  O2   C17  single    1.409  0.020  1.409
 A3Y  C12  C13  single    1.524  0.020  1.524
 A3Y  C15  C17  single    1.518  0.020  1.518
 A3Y  C15  C14  single    1.528  0.020  1.528
 A3Y  C13  C14  single    1.525  0.020  1.525
 A3Y  C7   H4   single    0.970  0.020  1.090
 A3Y  C7   H5   single    0.970  0.020  1.090
 A3Y  C6   H2   single    0.970  0.020  1.090
 A3Y  C6   H3   single    0.970  0.020  1.090
 A3Y  C9   H8   single    0.970  0.020  1.090
 A3Y  C9   H9   single    0.970  0.020  1.090
 A3Y  C13  H18  single    0.970  0.020  1.090
 A3Y  C13  H17  single    0.970  0.020  1.090
 A3Y  C8   H7   single    0.970  0.020  1.090
 A3Y  C8   H6   single    0.970  0.020  1.090
 A3Y  C16  H23  single    0.970  0.020  1.090
 A3Y  C16  H22  single    0.970  0.020  1.090
 A3Y  C1   H1   single    0.930  0.020  1.080
 A3Y  C10  H10  single    0.970  0.020  1.090
 A3Y  C10  H11  single    0.970  0.020  1.090
 A3Y  C11  H13  single    0.970  0.020  1.090
 A3Y  C11  H12  single    0.970  0.020  1.090
 A3Y  O1   H14  single    0.850  0.020  0.980
 A3Y  C12  H16  single    0.970  0.020  1.090
 A3Y  C12  H15  single    0.970  0.020  1.090
 A3Y  C14  H19  single    0.970  0.020  1.090
 A3Y  C14  H20  single    0.970  0.020  1.090
 A3Y  C15  H21  single    0.970  0.020  1.090
 A3Y  C17  H24  single    0.970  0.020  1.090
 A3Y  C17  H25  single    0.970  0.020  1.090
 A3Y  O2   H26  single    0.850  0.020  0.980

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
 A3Y  C10  N3   C8   112.77  3.000
 A3Y  C8   N3   C7   110.25  3.000
 A3Y  C10  N3   C7   110.82  3.000
 A3Y  N4   C4   N1   116.71  3.000
 A3Y  N4   C4   C3   122.64  3.000
 A3Y  N1   C4   C3   120.63  3.000
 A3Y  C5   N2   C9   122.56  3.000
 A3Y  C9   N2   C6   111.81  3.000
 A3Y  C5   N2   C6   124.95  3.000
 A3Y  H5   C7   H4   107.23  3.000
 A3Y  H5   C7   C6   108.51  3.000
 A3Y  H4   C7   C6   108.51  3.000
 A3Y  H5   C7   N3   109.25  3.000
 A3Y  H4   C7   N3   112.02  3.000
 A3Y  C6   C7   N3   111.19  3.000
 A3Y  H3   C6   H2   107.40  3.000
 A3Y  H3   C6   C7   108.99  3.000
 A3Y  H2   C6   C7   109.88  3.000
 A3Y  H3   C6   N2   111.73  3.000
 A3Y  H2   C6   N2   108.91  3.000
 A3Y  C7   C6   N2   109.88  3.000
 A3Y  H9   C9   H8   108.34  3.000
 A3Y  H9   C9   C8   109.33  3.000
 A3Y  H8   C9   C8   110.31  3.000
 A3Y  H9   C9   N2   108.17  3.000
 A3Y  H8   C9   N2   109.98  3.000
 A3Y  C8   C9   N2   110.65  3.000
 A3Y  H17  C13  H18  106.92  3.000
 A3Y  H17  C13  C14  109.85  3.000
 A3Y  H18  C13  C14  110.26  3.000
 A3Y  H17  C13  C12  108.83  3.000
 A3Y  H18  C13  C12  108.90  3.000
 A3Y  C14  C13  C12  111.93  3.000
 A3Y  H6   C8   H7   107.20  3.000
 A3Y  H6   C8   C9   109.32  3.000
 A3Y  H7   C8   C9   107.74  3.000
 A3Y  H6   C8   N3   111.67  3.000
 A3Y  H7   C8   N3   109.97  3.000
 A3Y  C9   C8   N3   110.79  3.000
 A3Y  H22  C16  H23  106.01  3.000
 A3Y  H22  C16  C15  108.83  3.000
 A3Y  H23  C16  C15  111.72  3.000
 A3Y  H22  C16  N4   107.51  3.000
 A3Y  H23  C16  N4   111.13  3.000
 A3Y  C15  C16  N4   111.38  3.000
 A3Y  H1   C1   C5   121.65  3.000
 A3Y  H1   C1   C2   120.78  3.000
 A3Y  C5   C1   C2   117.57  3.000
 A3Y  C3   C2   C1   121.53  3.000
 A3Y  C3   C2   C19  118.98  3.000
 A3Y  C1   C2   C19  119.47  3.000
 A3Y  C2   C3   C18  120.47  3.000
 A3Y  C18  C3   C4   122.26  3.000
 A3Y  C2   C3   C4   116.66  3.000
 A3Y  C5   N1   C4   122.14  3.000
 A3Y  N1   C5   C1   120.83  3.000
 A3Y  N1   C5   N2   117.47  3.000
 A3Y  C1   C5   N2   121.66  3.000
 A3Y  H11  C10  H10  106.24  3.000
 A3Y  H11  C10  C11  107.55  3.000
 A3Y  H10  C10  C11  108.48  3.000
 A3Y  H11  C10  N3   111.83  3.000
 A3Y  H10  C10  N3   107.90  3.000
 A3Y  C11  C10  N3   114.48  3.000
 A3Y  H12  C11  H13  106.02  3.000
 A3Y  H12  C11  O1   111.52  3.000
 A3Y  H13  C11  O1   111.84  3.000
 A3Y  H12  C11  C10  110.65  3.000
 A3Y  H13  C11  C10  107.08  3.000
 A3Y  O1   C11  C10  109.60  3.000
 A3Y  H14  O1   C11  107.87  3.000
 A3Y  C12  N4   C16  112.62  3.000
 A3Y  C12  N4   C4   121.87  3.000
 A3Y  C16  N4   C4   124.76  3.000
 A3Y  H15  C12  H16  107.51  3.000
 A3Y  H15  C12  N4   109.57  3.000
 A3Y  H16  C12  N4   109.61  3.000
 A3Y  H15  C12  C13  109.90  3.000
 A3Y  H16  C12  C13  111.02  3.000
 A3Y  N4   C12  C13  109.20  3.000
 A3Y  H20  C14  H19  106.77  3.000
 A3Y  H20  C14  C15  110.67  3.000
 A3Y  H19  C14  C15  108.76  3.000
 A3Y  H20  C14  C13  110.08  3.000
 A3Y  H19  C14  C13  109.26  3.000
 A3Y  C15  C14  C13  111.17  3.000
 A3Y  H21  C15  C17  108.58  3.000
 A3Y  H21  C15  C14  109.17  3.000
 A3Y  C17  C15  C14  113.00  3.000
 A3Y  H21  C15  C16  107.78  3.000
 A3Y  C14  C15  C16  108.77  3.000
 A3Y  C17  C15  C16  109.41  3.000
 A3Y  H25  C17  H24  106.88  3.000
 A3Y  H25  C17  O2   111.41  3.000
 A3Y  H24  C17  O2   111.26  3.000
 A3Y  H25  C17  C15  109.00  3.000
 A3Y  H24  C17  C15  108.92  3.000
 A3Y  O2   C17  C15  109.29  3.000
 A3Y  H26  O2   C17  108.24  3.000
 A3Y  C3   C18  N5   180.00  3.000
 A3Y  F3   C19  F2   107.15  3.000
 A3Y  F2   C19  F1   107.15  3.000
 A3Y  F3   C19  F1   107.21  3.000
 A3Y  F2   C19  C2   112.68  3.000
 A3Y  F3   C19  C2   111.44  3.000
 A3Y  F1   C19  C2   110.93  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
 A3Y  CONST_01  C1   C5   N1   C4      0.00   0.0  0
 A3Y  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 A3Y  CONST_03  N1   C5   C1   C2      0.00   0.0  0
 A3Y  CONST_04  N1   C4   C3   C2      0.00   0.0  0
 A3Y  CONST_05  C5   C1   C2   C3      0.00   0.0  0
 A3Y  CONST_06  C5   N1   C4   C3      0.00   0.0  0
 A3Y  CONST_07  N2   C5   N1   C4    180.00   0.0  0
 A3Y  CONST_08  C2   C1   C5   N2    180.00   0.0  0
 A3Y  CONST_09  N4   C4   C3   C2    180.00   0.0  0
 A3Y  CONST_10  N4   C4   N1   C5    180.00   0.0  0
 A3Y  CONST_11  C19  C2   C3   C4    180.00   0.0  0
 A3Y  CONST_12  C1   C2   C3   C18   180.00   0.0  0
 A3Y  CONST_14  N4   C4   C3   C18     0.00   0.0  0
 A3Y  CONST_15  C5   C1   C2   C19   180.00   0.0  0
 A3Y  CONST_16  H1   C1   C5   N2      0.00   0.0  0
 A3Y  Var_01    N2   C6   C7   N3     56.88  30.0  1
 A3Y  Var_02    N2   C9   C8   N3    -56.18  30.0  1
 A3Y  Var_03    C15  C16  N4   C4   -127.93  30.0  1
 A3Y  Var_04    C13  C12  N4   C4    130.22  30.0  1
 A3Y  Var_05    C9   C8   N3   C7     57.27  30.0  1
 A3Y  Var_06    C5   N2   C6   C7    114.74  30.0  1
 A3Y  Var_07    C8   N3   C7   C6    -57.91  30.0  1
 A3Y  Var_08    C1   C5   N2   C6     12.58  30.0  2
 A3Y  Var_09    C8   C9   N2   C6     55.93  30.0  1
 A3Y  Var_10    N1   C4   N4   C16  -149.65  30.0  2
 A3Y  Var_11    C14  C13  C12  N4     54.68  30.0  1
 A3Y  Var_12    C15  C14  C13  C12   -53.08  30.0  1
 A3Y  Var_13    C11  C10  N3   C7   -168.93  30.0  1
 A3Y  Var_14    F1   C19  C2   C1   -111.27  30.0  2
 A3Y  Var_15    O1   C11  C10  N3     59.96  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
 A3Y  chir_01  C15  C16  C17  C14  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
 A3Y  plan-1  C4   0.020
 A3Y  plan-1  N2   0.020
 A3Y  plan-1  N5   0.020
 A3Y  plan-1  C1   0.020
 A3Y  plan-1  C2   0.020
 A3Y  plan-1  C3   0.020
 A3Y  plan-1  N1   0.020
 A3Y  plan-1  C5   0.020
 A3Y  plan-1  N4   0.020
 A3Y  plan-1  H1   0.020
 A3Y  plan-1  C18  0.020
 A3Y  plan-1  C19  0.020

