# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 09:33:36 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: (2E)-N-hydroxy-3-{1-[2-(1H-indol-3-yl)ethyl]piperidin-4-yl}prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)\C=C\C1CCN(CC1)CCc2c[nH]c3ccccc23
#
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
 LTO  LTO  "(2E)-N-hydroxy-3-{1-[2-(1H-indol-3-yl)ethyl]piperidin-4-yl}prop-2-enamide"
  ligand  46  23  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LTO
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
 LTO  C13  C  CH1   0  -0.323  -24.3960  -41.1688  35.0021
 LTO  C15  C  C1    0  -0.402  -21.9809  -41.5742  34.4736
 LTO  C20  C  CH2   0  -0.419  -24.8094  -40.4544  36.2925
 LTO  C21  C  CH2   0  -0.279  -26.2552  -40.7599  36.6511
 LTO  C22  C  CR56  0   0.026  -31.7843  -40.7814  35.1475
 LTO  C01  C  CR16  0  -0.266  -32.7483  -42.7846  34.2524
 LTO  C02  C  CR16  0  -0.282  -33.9804  -42.4670  34.8490
 LTO  C03  C  CR16  0  -0.305  -34.1402  -41.3168  35.5976
 LTO  C04  C  CR56  0   0.355  -33.0321  -40.4822  35.7392
 LTO  C06  C  CR15  0  -0.089  -31.6123  -38.8430  36.2469
 LTO  C07  C  CR5   0   0.015  -30.8879  -39.7139  35.4830
 LTO  C08  C  CH2   0  -0.547  -29.4503  -39.5977  35.0980
 LTO  C09  C  CH2   0  -0.253  -28.5469  -40.4984  35.9429
 LTO  C11  C  CH2   0  -0.289  -26.8318  -41.1329  34.3688
 LTO  C12  C  CH2   0  -0.416  -25.4128  -40.8480  33.9035
 LTO  C14  C  C1    0  -0.128  -23.0244  -40.7543  34.5885
 LTO  C16  C  C     0   0.494  -20.6384  -41.1717  33.9889
 LTO  C23  C  CR16  0  -0.372  -31.6534  -41.9549  34.3954
 LTO  N05  N  NR15  0  -0.687  -32.8926  -39.2999  36.4030
 LTO  N10  N  NT    0  -0.422  -27.1490  -40.3850  35.5715
 LTO  N18  N  NH1   0  -0.380  -20.2225  -39.9594  34.4141
 LTO  O17  O  O     0  -0.475  -19.9580  -41.9050  33.2907
 LTO  O19  O  OH1   0  -0.540  -19.1448  -39.3703  33.8223
 LTO  H1   H  HCH1  0   0.240  -24.4080  -42.2497  35.1844
 LTO  H2   H  H     0   0.270  -22.0994  -42.6368  34.6596
 LTO  H4   H  HCH2  0   0.238  -24.1571  -40.7542  37.1154
 LTO  H5   H  HCH2  0   0.221  -24.6932  -39.3736  36.1643
 LTO  H6   H  HCH2  0   0.236  -26.5311  -40.1981  37.5465
 LTO  H7   H  HCH2  0   0.185  -26.3497  -41.8306  36.9072
 LTO  H9   H  HCR6  0   0.245  -34.8207  -43.1370  34.7198
 LTO  H10  H  HCR6  0   0.255  -35.0905  -41.0732  36.0560
 LTO  H11  H  HCR5  0   0.277  -31.3049  -37.9108  36.6958
 LTO  H12  H  HCH2  0   0.234  -29.3394  -39.8400  34.0371
 LTO  H13  H  HCH2  0   0.237  -29.1141  -38.5649  35.2156
 LTO  H14  H  HCH2  0   0.229  -28.6508  -40.1907  36.9865
 LTO  H15  H  HCH2  0   0.196  -28.9024  -41.5413  35.8937
 LTO  H16  H  HCH2  0   0.240  -27.5277  -40.8596  33.5739
 LTO  H17  H  HCH2  0   0.188  -26.9533  -42.2192  34.5336
 LTO  H18  H  HCH2  0   0.238  -25.1960  -41.4342  33.0078
 LTO  H19  H  HCH2  0   0.221  -25.3301  -39.7925  33.6254
 LTO  H20  H  H     0   0.260  -22.9169  -39.6967  34.3529
 LTO  H22  H  HCR6  0   0.237  -30.7075  -42.2095  33.9316
 LTO  H23  H  HNR5  0   0.405  -33.6180  -38.8243  36.9128
 LTO  H25  H  HNH1  0   0.415  -20.8177  -39.3283  34.9309
 LTO  H26  H  HOH1  0   0.475  -18.3939  -39.5360  34.4072
 LTO  H8   H  HCR6  0   0.241  -32.6610  -43.6949  33.6730

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
 LTO  O17  C16  double    1.220  0.020  1.220
 LTO  C01  C23  aromatic  1.381  0.020  1.381
 LTO  C01  C02  aromatic  1.405  0.020  1.405
 LTO  C23  C22  aromatic  1.400  0.020  1.400
 LTO  C16  C15  single    1.483  0.020  1.483
 LTO  C16  N18  single    1.350  0.020  1.350
 LTO  C12  C11  single    1.520  0.020  1.520
 LTO  C12  C13  single    1.531  0.020  1.531
 LTO  C15  C14  double    1.332  0.020  1.332
 LTO  C11  N10  single    1.451  0.020  1.451
 LTO  O19  N18  single    1.363  0.020  1.363
 LTO  C08  C07  single    1.493  0.020  1.493
 LTO  C08  C09  single    1.530  0.020  1.530
 LTO  C02  C03  aromatic  1.382  0.020  1.382
 LTO  C14  C13  single    1.491  0.020  1.491
 LTO  C22  C07  aromatic  1.434  0.020  1.434
 LTO  C22  C04  aromatic  1.413  0.020  1.413
 LTO  N10  C09  single    1.451  0.020  1.451
 LTO  N10  C21  single    1.451  0.020  1.451
 LTO  C13  C20  single    1.532  0.020  1.532
 LTO  C07  C06  aromatic  1.366  0.020  1.366
 LTO  C03  C04  aromatic  1.394  0.020  1.394
 LTO  C04  N05  aromatic  1.363  0.020  1.363
 LTO  C20  C21  single    1.521  0.020  1.521
 LTO  C06  N05  aromatic  1.368  0.020  1.368
 LTO  C13  H1   single    0.970  0.020  1.090
 LTO  C15  H2   single    0.930  0.020  1.080
 LTO  C20  H4   single    0.970  0.020  1.090
 LTO  C20  H5   single    0.970  0.020  1.090
 LTO  C21  H6   single    0.970  0.020  1.090
 LTO  C21  H7   single    0.970  0.020  1.090
 LTO  C01  H8   single    0.930  0.020  1.080
 LTO  C02  H9   single    0.930  0.020  1.080
 LTO  C03  H10  single    0.930  0.020  1.080
 LTO  C06  H11  single    0.930  0.020  1.080
 LTO  C08  H12  single    0.970  0.020  1.090
 LTO  C08  H13  single    0.970  0.020  1.090
 LTO  C09  H14  single    0.970  0.020  1.090
 LTO  C09  H15  single    0.970  0.020  1.090
 LTO  C11  H16  single    0.970  0.020  1.090
 LTO  C11  H17  single    0.970  0.020  1.090
 LTO  C12  H18  single    0.970  0.020  1.090
 LTO  C12  H19  single    0.970  0.020  1.090
 LTO  C14  H20  single    0.930  0.020  1.080
 LTO  C23  H22  single    0.930  0.020  1.080
 LTO  N05  H23  single    0.860  0.020  1.020
 LTO  N18  H25  single    0.860  0.020  1.020
 LTO  O19  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
 LTO  H1   C13  C14  109.28  3.000
 LTO  H1   C13  C12  108.58  3.000
 LTO  C14  C13  C12  110.70  3.000
 LTO  H1   C13  C20  108.48  3.000
 LTO  C14  C13  C20  110.62  3.000
 LTO  C12  C13  C20  109.12  3.000
 LTO  H2   C15  C16  114.87  3.000
 LTO  H2   C15  C14  120.16  3.000
 LTO  C16  C15  C14  124.77  3.000
 LTO  H5   C20  H4   107.21  3.000
 LTO  H5   C20  C21  109.09  3.000
 LTO  H4   C20  C21  109.58  3.000
 LTO  H5   C20  C13  109.46  3.000
 LTO  H4   C20  C13  110.21  3.000
 LTO  C21  C20  C13  111.19  3.000
 LTO  H7   C21  H6   106.67  3.000
 LTO  H7   C21  N10  111.72  3.000
 LTO  H6   C21  N10  108.75  3.000
 LTO  H7   C21  C20  109.31  3.000
 LTO  H6   C21  C20  109.27  3.000
 LTO  N10  C21  C20  111.00  3.000
 LTO  C23  C22  C07  133.74  3.000
 LTO  C07  C22  C04  107.25  3.000
 LTO  C23  C22  C04  119.01  3.000
 LTO  H8   C01  C23  119.78  3.000
 LTO  H8   C01  C02  119.21  3.000
 LTO  C23  C01  C02  121.01  3.000
 LTO  H9   C02  C03  119.35  3.000
 LTO  H9   C02  C01  119.34  3.000
 LTO  C03  C02  C01  121.31  3.000
 LTO  H10  C03  C04  121.31  3.000
 LTO  H10  C03  C02  121.21  3.000
 LTO  C04  C03  C02  117.47  3.000
 LTO  N05  C04  C03  130.54  3.000
 LTO  N05  C04  C22  107.29  3.000
 LTO  C03  C04  C22  122.17  3.000
 LTO  H11  C06  N05  120.49  3.000
 LTO  H11  C06  C07  129.20  3.000
 LTO  N05  C06  C07  110.31  3.000
 LTO  C08  C07  C06  127.24  3.000
 LTO  C06  C07  C22  105.90  3.000
 LTO  C08  C07  C22  126.85  3.000
 LTO  H13  C08  H12  106.42  3.000
 LTO  H13  C08  C09  108.38  3.000
 LTO  H12  C08  C09  110.20  3.000
 LTO  H13  C08  C07  110.01  3.000
 LTO  H12  C08  C07  109.30  3.000
 LTO  C09  C08  C07  112.35  3.000
 LTO  H15  C09  H14  106.15  3.000
 LTO  H15  C09  N10  111.90  3.000
 LTO  H14  C09  N10  108.30  3.000
 LTO  H15  C09  C08  109.98  3.000
 LTO  H14  C09  C08  107.79  3.000
 LTO  N10  C09  C08  112.43  3.000
 LTO  H17  C11  H16  106.54  3.000
 LTO  H17  C11  N10  111.03  3.000
 LTO  H16  C11  N10  109.58  3.000
 LTO  H17  C11  C12  109.41  3.000
 LTO  H16  C11  C12  108.99  3.000
 LTO  N10  C11  C12  111.17  3.000
 LTO  H19  C12  H18  107.11  3.000
 LTO  H19  C12  C11  109.20  3.000
 LTO  H18  C12  C11  109.61  3.000
 LTO  H19  C12  C13  109.52  3.000
 LTO  H18  C12  C13  110.14  3.000
 LTO  C11  C12  C13  111.16  3.000
 LTO  H20  C14  C15  120.12  3.000
 LTO  H20  C14  C13  114.89  3.000
 LTO  C15  C14  C13  124.98  3.000
 LTO  O17  C16  N18  123.24  3.000
 LTO  N18  C16  C15  114.81  3.000
 LTO  O17  C16  C15  121.93  3.000
 LTO  H22  C23  C01  120.43  3.000
 LTO  H22  C23  C22  120.56  3.000
 LTO  C01  C23  C22  119.02  3.000
 LTO  H23  N05  C06  125.07  3.000
 LTO  H23  N05  C04  125.66  3.000
 LTO  C06  N05  C04  109.26  3.000
 LTO  C11  N10  C09  112.49  3.000
 LTO  C09  N10  C21  112.52  3.000
 LTO  C11  N10  C21  110.42  3.000
 LTO  H25  N18  O19  114.72  3.000
 LTO  H25  N18  C16  122.73  3.000
 LTO  O19  N18  C16  119.65  3.000
 LTO  H26  O19  N18  106.11  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
 LTO  CONST_01  C02  C01  C23  C22     0.00   0.0  0
 LTO  CONST_02  N05  C06  C07  C22     0.00   0.0  0
 LTO  CONST_03  C02  C03  C04  C22     0.00   0.0  0
 LTO  CONST_04  C06  N05  C04  C22     0.00   0.0  0
 LTO  CONST_05  C07  C22  C23  C01   180.00   0.0  0
 LTO  CONST_06  C04  C22  C23  C01     0.00   0.0  0
 LTO  CONST_07  C04  C03  C02  C01     0.00   0.0  0
 LTO  CONST_08  N05  C04  C03  C02   180.00   0.0  0
 LTO  CONST_09  C23  C01  C02  C03     0.00   0.0  0
 LTO  CONST_10  C23  C22  C04  C03     0.00   0.0  0
 LTO  CONST_11  C07  C22  C04  C03   180.00   0.0  0
 LTO  CONST_12  C06  N05  C04  C03   180.00   0.0  0
 LTO  CONST_13  C06  C07  C22  C04     0.00   0.0  0
 LTO  CONST_14  C07  C06  N05  C04     0.00   0.0  0
 LTO  CONST_15  C23  C22  C07  C06   180.00   0.0  0
 LTO  CONST_16  N05  C04  C22  C07     0.00   0.0  0
 LTO  CONST_17  N05  C04  C22  C23   180.00   0.0  0
 LTO  CONST_18  C08  C07  C22  C04   180.00   0.0  0
 LTO  CONST_19  C23  C22  C07  C08     0.00   0.0  0
 LTO  CONST_20  N05  C06  C07  C08   180.00   0.0  0
 LTO  CONST_21  H8   C01  C23  C22   180.00   0.0  0
 LTO  CONST_22  H11  C06  C07  C22   180.00   0.0  0
 LTO  CONST_23  H10  C03  C04  C22   180.00   0.0  0
 LTO  CONST_24  H23  N05  C04  C22   180.00   0.0  0
 LTO  CONST_25  H10  C03  C02  C01   180.00   0.0  0
 LTO  CONST_26  H22  C23  C01  C02   180.00   0.0  0
 LTO  CONST_27  H8   C01  C02  C03   180.00   0.0  0
 LTO  CONST_28  H23  N05  C04  C03     0.00   0.0  0
 LTO  CONST_29  H22  C23  C22  C04   180.00   0.0  0
 LTO  CONST_30  H9   C02  C03  C04   180.00   0.0  0
 LTO  CONST_31  H11  C06  N05  C04   180.00   0.0  0
 LTO  CONST_32  H22  C23  C22  C07     0.00   0.0  0
 LTO  CONST_33  H23  N05  C06  C07   180.00   0.0  0
 LTO  CONST_34  H9   C02  C01  C23   180.00   0.0  0
 LTO  CONST_35  H10  C03  C04  N05     0.00   0.0  0
 LTO  CONST_36  O19  N18  C16  C15   180.00   0.0  0
 LTO  CONST_38  H25  N18  C16  C15     0.00   0.0  0
 LTO  CONST_39  H25  N18  C16  O17   180.00   0.0  0
 LTO  Var_01    N10  C11  C12  C13    57.13  30.0  1
 LTO  Var_02    N10  C21  C20  C13   -57.35  30.0  1
 LTO  Var_03    C11  N10  C21  C20    60.96  30.0  1
 LTO  Var_04    C12  C11  N10  C21   -60.91  30.0  1
 LTO  Var_05    C09  N10  C21  C20  -172.45  30.0  1
 LTO  Var_06    C12  C11  N10  C09   172.48  30.0  1
 LTO  Var_07    H16  C11  C12  C13   178.02  30.0  1
 LTO  Var_08    H17  C11  C12  C13   -65.85  30.0  1
 LTO  Var_09    H6   C21  C20  C13  -177.28  30.0  1
 LTO  Var_10    H7   C21  C20  C13    66.34  30.0  1
 LTO  Var_11    H16  C11  N10  C21   178.55  30.0  1
 LTO  Var_12    H17  C11  N10  C21    61.13  30.0  1
 LTO  Var_13    H6   C21  N10  C11  -178.80  30.0  1
 LTO  Var_14    H7   C21  N10  C11   -61.33  30.0  1
 LTO  Var_15    H18  C12  C11  N10   179.13  30.0  1
 LTO  Var_16    H19  C12  C11  N10   -63.82  30.0  1
 LTO  Var_17    H4   C20  C21  N10  -179.44  30.0  1
 LTO  Var_18    H5   C20  C21  N10    63.47  30.0  1
 LTO  Var_19    C08  C09  N10  C21   156.09  30.0  3
 LTO  Var_20    C09  C08  C07  C22   -76.88  30.0  1
 LTO  Var_21    C09  C08  C07  C06   101.70  30.0  1
 LTO  Var_22    N10  C09  C08  C07  -179.91  30.0  3
 LTO  Var_23    C11  N10  C09  C08   -78.44  30.0  1
 LTO  Var_24    H14  C09  N10  C21    37.10  30.0  3
 LTO  Var_25    H15  C09  N10  C21   -79.55  30.0  3
 LTO  Var_26    H12  C08  C07  C22    45.78  30.0  1
 LTO  Var_27    H13  C08  C07  C22   162.29  30.0  1
 LTO  Var_28    H12  C08  C07  C06  -135.65  30.0  1
 LTO  Var_29    H13  C08  C07  C06   -19.13  30.0  1
 LTO  Var_30    H16  C11  N10  C09    51.94  30.0  1
 LTO  Var_31    H17  C11  N10  C09   -65.47  30.0  1
 LTO  Var_32    H6   C21  N10  C09   -52.21  30.0  1
 LTO  Var_33    H7   C21  N10  C09    65.26  30.0  1
 LTO  Var_34    H14  C09  N10  C11   162.58  30.0  3
 LTO  Var_35    H15  C09  N10  C11    45.92  30.0  3
 LTO  Var_36    C16  C15  C14  C13   176.38   0.0  2
 LTO  Var_37    H2   C15  C14  C13     1.78   0.0  2
 LTO  Var_38    H14  C09  C08  C07   -60.62  30.0  3
 LTO  Var_39    H15  C09  C08  C07    54.68  30.0  3
 LTO  Var_40    H12  C08  C09  N10    57.95  30.0  1
 LTO  Var_41    H13  C08  C09  N10   -58.14  30.0  1
 LTO  Var_42    O17  C16  C15  C14  -142.72  30.0  2
 LTO  Var_43    N18  C16  C15  C14    39.21  30.0  2
 LTO  Var_44    H20  C14  C15  C16    -2.30   0.0  2
 LTO  Var_45    H2   C15  C16  N18  -145.94  30.0  2
 LTO  Var_46    H2   C15  C16  O17    32.13  30.0  2
 LTO  Var_47    H20  C14  C15  H2   -176.89   0.0  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
 LTO  chir_01  C13  C12  C14  C20  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
 LTO  plan-1  C22  0.020
 LTO  plan-1  C01  0.020
 LTO  plan-1  C02  0.020
 LTO  plan-1  C03  0.020
 LTO  plan-1  C04  0.020
 LTO  plan-1  C06  0.020
 LTO  plan-1  C07  0.020
 LTO  plan-1  C08  0.020
 LTO  plan-1  C23  0.020
 LTO  plan-1  N05  0.020
 LTO  plan-1  H9   0.020
 LTO  plan-1  H10  0.020
 LTO  plan-1  H11  0.020
 LTO  plan-1  H22  0.020
 LTO  plan-1  H23  0.020
 LTO  plan-1  H8   0.020
 LTO  plan-2  C15  0.020
 LTO  plan-2  C16  0.020
 LTO  plan-2  N18  0.020
 LTO  plan-2  O17  0.020
 LTO  plan-2  O19  0.020
 LTO  plan-2  H25  0.020
 LTO  plan-3  C13  0.020
 LTO  plan-3  C15  0.020
 LTO  plan-3  C14  0.020
 LTO  plan-3  C16  0.020
 LTO  plan-3  H2   0.020
 LTO  plan-3  H20  0.020

