# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 10:54:44 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: (2E)-N-hydroxy-3-[1-(2-phenylethyl)piperidin-4-yl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)/C=C/C1CCN(CC1)CCc2ccccc2
#
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
 LS6  LS6  "(2E)-N-hydroxy-3-[1-(2-phenylethyl)piperidin-4-yl]prop-2-enamide"
  ligand  42  20  .  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_LS6
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
 LS6  C10  C  CH2   0  -0.287  -47.7463   2.9980  -5.7120
 LS6  C13  C  C1    0  -0.103  -46.2022  -0.3526  -6.7515
 LS6  C15  C  C     0   0.518  -44.7366  -2.3195  -6.5985
 LS6  C20  C  CH2   0  -0.281  -49.4399   1.7015  -6.7865
 LS6  C01  C  CH2   0  -0.528  -49.3758   5.4510  -6.6383
 LS6  C02  C  CR6   0   0.128  -50.4815   6.4271  -6.3490
 LS6  C03  C  CR16  0  -0.306  -51.4038   6.7771  -7.3330
 LS6  C04  C  CR16  0  -0.238  -52.4530   7.6423  -7.0527
 LS6  C05  C  CR16  0  -0.272  -52.5973   8.1732  -5.7772
 LS6  C06  C  CR16  0  -0.238  -51.6853   7.8310  -4.7871
 LS6  C07  C  CR16  0  -0.306  -50.6384   6.9650  -5.0731
 LS6  C08  C  CH2   0  -0.250  -49.8321   4.0207  -6.3448
 LS6  C11  C  CH2   0  -0.419  -46.6653   2.0078  -6.1153
 LS6  C12  C  CH1   0  -0.328  -47.2443   0.5996  -6.2744
 LS6  C14  C  C1    0  -0.424  -45.7848  -1.4177  -6.0706
 LS6  C19  C  CH2   0  -0.420  -48.4293   0.6610  -7.2405
 LS6  N09  N  NT    0  -0.419  -48.8366   3.0177  -6.6706
 LS6  N17  N  NH1   0  -0.394  -44.4227  -3.3106  -5.7278
 LS6  O16  O  O     0  -0.467  -44.1799  -2.1737  -7.6729
 LS6  O18  O  OH1   0  -0.540  -43.6452  -4.3465  -6.1547
 LS6  H1   H  HCH2  0   0.241  -47.3044   3.9932  -5.6402
 LS6  H2   H  HCH2  0   0.187  -48.1133   2.7421  -4.7012
 LS6  H3   H  H     0   0.258  -45.7636  -0.1379  -7.7234
 LS6  H5   H  HCH2  0   0.238  -50.2568   1.7559  -7.5101
 LS6  H6   H  HCH2  0   0.186  -49.8880   1.3748  -5.8305
 LS6  H7   H  HCH2  0   0.240  -49.0752   5.5149  -7.6866
 LS6  H8   H  HCH2  0   0.246  -48.5005   5.7087  -6.0380
 LS6  H9   H  HCR6  0   0.244  -51.2980   6.3681  -8.3316
 LS6  H10  H  HCR6  0   0.250  -53.1579   7.9039  -7.8318
 LS6  H11  H  HCR6  0   0.251  -53.4124   8.8506  -5.5573
 LS6  H12  H  HCR6  0   0.250  -51.7872   8.2415  -3.7904
 LS6  H13  H  HCR6  0   0.244  -49.9290   6.7057  -4.2951
 LS6  H14  H  HCH2  0   0.234  -50.7214   3.8211  -6.9489
 LS6  H15  H  HCH2  0   0.195  -50.1538   3.9489  -5.2911
 LS6  H16  H  HCH2  0   0.239  -45.8763   2.0081  -5.3603
 LS6  H17  H  HCH2  0   0.223  -46.2097   2.3267  -7.0581
 LS6  H18  H  HCH1  0   0.239  -47.6134   0.2654  -5.2976
 LS6  H19  H  H     0   0.262  -46.2145  -1.6441  -5.0994
 LS6  H21  H  HCH2  0   0.239  -48.9190  -0.3133  -7.3008
 LS6  H22  H  HCH2  0   0.222  -48.0728   0.9093  -8.2451
 LS6  H24  H  HNH1  0   0.411  -45.0474  -3.5557  -4.9718
 LS6  H25  H  HOH1  0   0.475  -42.7635  -4.1817  -5.7966

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
 LS6  O16  C15  double    1.219  0.020  1.219
 LS6  C04  C03  aromatic  1.389  0.020  1.389
 LS6  C04  C05  aromatic  1.389  0.020  1.389
 LS6  C19  C20  single    1.520  0.020  1.520
 LS6  C19  C12  single    1.530  0.020  1.530
 LS6  C03  C02  aromatic  1.393  0.020  1.393
 LS6  O18  N17  single    1.364  0.020  1.364
 LS6  C15  N17  single    1.356  0.020  1.356
 LS6  C15  C14  single    1.480  0.020  1.480
 LS6  C05  C06  aromatic  1.389  0.020  1.389
 LS6  C20  N09  single    1.453  0.020  1.453
 LS6  C13  C12  single    1.490  0.020  1.490
 LS6  C13  C14  double    1.331  0.020  1.331
 LS6  C12  C11  single    1.531  0.020  1.531
 LS6  N09  C08  single    1.450  0.020  1.450
 LS6  N09  C10  single    1.452  0.020  1.452
 LS6  C02  C01  single    1.503  0.020  1.503
 LS6  C02  C07  aromatic  1.394  0.020  1.394
 LS6  C06  C07  aromatic  1.388  0.020  1.388
 LS6  C01  C08  single    1.530  0.020  1.530
 LS6  C11  C10  single    1.520  0.020  1.520
 LS6  C10  H1   single    0.970  0.020  1.090
 LS6  C10  H2   single    0.970  0.020  1.090
 LS6  C13  H3   single    0.930  0.020  1.080
 LS6  C20  H5   single    0.970  0.020  1.090
 LS6  C20  H6   single    0.970  0.020  1.090
 LS6  C01  H7   single    0.970  0.020  1.090
 LS6  C01  H8   single    0.970  0.020  1.090
 LS6  C03  H9   single    0.930  0.020  1.080
 LS6  C04  H10  single    0.930  0.020  1.080
 LS6  C05  H11  single    0.930  0.020  1.080
 LS6  C06  H12  single    0.930  0.020  1.080
 LS6  C07  H13  single    0.930  0.020  1.080
 LS6  C08  H14  single    0.970  0.020  1.090
 LS6  C08  H15  single    0.970  0.020  1.090
 LS6  C11  H16  single    0.970  0.020  1.090
 LS6  C11  H17  single    0.970  0.020  1.090
 LS6  C12  H18  single    0.970  0.020  1.090
 LS6  C14  H19  single    0.930  0.020  1.080
 LS6  C19  H21  single    0.970  0.020  1.090
 LS6  C19  H22  single    0.970  0.020  1.090
 LS6  N17  H24  single    0.890  0.020  1.040
 LS6  O18  H25  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
 LS6  H2   C10  H1   106.58  3.000
 LS6  H2   C10  N09  110.95  3.000
 LS6  H1   C10  N09  109.58  3.000
 LS6  H2   C10  C11  109.14  3.000
 LS6  H1   C10  C11  108.88  3.000
 LS6  N09  C10  C11  111.57  3.000
 LS6  H3   C13  C14  119.24  3.000
 LS6  H3   C13  C12  116.23  3.000
 LS6  C14  C13  C12  124.53  3.000
 LS6  O16  C15  N17  123.21  3.000
 LS6  N17  C15  C14  112.35  3.000
 LS6  O16  C15  C14  124.41  3.000
 LS6  H6   C20  H5   106.52  3.000
 LS6  H6   C20  N09  111.54  3.000
 LS6  H5   C20  N09  108.55  3.000
 LS6  H6   C20  C19  109.01  3.000
 LS6  H5   C20  C19  109.48  3.000
 LS6  N09  C20  C19  111.60  3.000
 LS6  H8   C01  H7   107.05  3.000
 LS6  H8   C01  C08  110.75  3.000
 LS6  H7   C01  C08  108.72  3.000
 LS6  H8   C01  C02  109.30  3.000
 LS6  H7   C01  C02  110.43  3.000
 LS6  C08  C01  C02  110.54  3.000
 LS6  C07  C02  C03  118.37  3.000
 LS6  C07  C02  C01  120.65  3.000
 LS6  C03  C02  C01  120.94  3.000
 LS6  H9   C03  C04  119.66  3.000
 LS6  H9   C03  C02  119.41  3.000
 LS6  C04  C03  C02  120.93  3.000
 LS6  H10  C04  C05  120.05  3.000
 LS6  H10  C04  C03  119.81  3.000
 LS6  C05  C04  C03  120.13  3.000
 LS6  H11  C05  C06  120.26  3.000
 LS6  H11  C05  C04  120.25  3.000
 LS6  C06  C05  C04  119.49  3.000
 LS6  H12  C06  C07  119.80  3.000
 LS6  H12  C06  C05  120.07  3.000
 LS6  C07  C06  C05  120.13  3.000
 LS6  H13  C07  C06  119.65  3.000
 LS6  H13  C07  C02  119.40  3.000
 LS6  C06  C07  C02  120.95  3.000
 LS6  H15  C08  H14  106.17  3.000
 LS6  H15  C08  N09  111.68  3.000
 LS6  H14  C08  N09  107.93  3.000
 LS6  H15  C08  C01  109.32  3.000
 LS6  H14  C08  C01  107.89  3.000
 LS6  N09  C08  C01  113.50  3.000
 LS6  H17  C11  H16  107.14  3.000
 LS6  H17  C11  C12  109.63  3.000
 LS6  H16  C11  C12  110.20  3.000
 LS6  H17  C11  C10  109.55  3.000
 LS6  H16  C11  C10  109.27  3.000
 LS6  C12  C11  C10  110.96  3.000
 LS6  H18  C12  C19  108.30  3.000
 LS6  H18  C12  C11  108.36  3.000
 LS6  C19  C12  C11  108.76  3.000
 LS6  H18  C12  C13  109.03  3.000
 LS6  C11  C12  C13  110.89  3.000
 LS6  C19  C12  C13  111.42  3.000
 LS6  H19  C14  C15  118.18  3.000
 LS6  H19  C14  C13  120.01  3.000
 LS6  C15  C14  C13  121.81  3.000
 LS6  H22  C19  H21  107.33  3.000
 LS6  H22  C19  C12  109.65  3.000
 LS6  H21  C19  C12  110.26  3.000
 LS6  H22  C19  C20  109.60  3.000
 LS6  H21  C19  C20  109.21  3.000
 LS6  C12  C19  C20  110.72  3.000
 LS6  C08  N09  C20  111.07  3.000
 LS6  C08  N09  C10  112.12  3.000
 LS6  C20  N09  C10  110.63  3.000
 LS6  H24  N17  O18  113.72  3.000
 LS6  H24  N17  C15  120.95  3.000
 LS6  O18  N17  C15  119.09  3.000
 LS6  H25  O18  N17  105.96  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
 LS6  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 LS6  CONST_02  C05  C06  C07  C02     0.00   0.0  0
 LS6  CONST_03  C06  C05  C04  C03     0.00   0.0  0
 LS6  CONST_04  C06  C07  C02  C03     0.00   0.0  0
 LS6  CONST_05  C07  C02  C03  C04     0.00   0.0  0
 LS6  CONST_06  C07  C06  C05  C04     0.00   0.0  0
 LS6  CONST_07  C04  C03  C02  C01   180.00   0.0  0
 LS6  CONST_08  C06  C07  C02  C01   180.00   0.0  0
 LS6  CONST_09  H10  C04  C03  C02   180.00   0.0  0
 LS6  CONST_10  H12  C06  C07  C02   180.00   0.0  0
 LS6  CONST_11  H11  C05  C04  C03   180.00   0.0  0
 LS6  CONST_12  H13  C07  C02  C03   180.00   0.0  0
 LS6  CONST_13  H12  C06  C05  C04   180.00   0.0  0
 LS6  CONST_14  H9   C03  C04  C05   180.00   0.0  0
 LS6  CONST_15  H13  C07  C06  C05   180.00   0.0  0
 LS6  CONST_16  H10  C04  C05  C06   180.00   0.0  0
 LS6  CONST_17  H9   C03  C02  C07   180.00   0.0  0
 LS6  CONST_18  H11  C05  C06  C07   180.00   0.0  0
 LS6  CONST_19  O18  N17  C15  C14   180.00   0.0  0
 LS6  CONST_20  O18  N17  C15  O16     0.00   0.0  0
 LS6  Var_01    C19  C20  N09  C10   -59.55  30.0  1
 LS6  Var_02    C11  C10  N09  C20    59.21  30.0  1
 LS6  Var_03    N09  C20  C19  C12    57.61  30.0  1
 LS6  Var_04    N09  C10  C11  C12   -57.11  30.0  1
 LS6  Var_05    C19  C20  N09  C08   175.27  30.0  1
 LS6  Var_06    C11  C10  N09  C08  -176.20  30.0  1
 LS6  Var_07    H5   C20  N09  C10   179.71  30.0  1
 LS6  Var_08    H6   C20  N09  C10    62.65  30.0  1
 LS6  Var_09    H1   C10  N09  C20   179.86  30.0  1
 LS6  Var_10    H2   C10  N09  C20   -62.72  30.0  1
 LS6  Var_11    H5   C20  C19  C12   177.81  30.0  1
 LS6  Var_12    H6   C20  C19  C12   -66.03  30.0  1
 LS6  Var_13    H1   C10  C11  C12  -178.17  30.0  1
 LS6  Var_14    H2   C10  C11  C12    65.86  30.0  1
 LS6  Var_15    H21  C19  C20  N09   179.20  30.0  1
 LS6  Var_16    H22  C19  C20  N09   -63.48  30.0  1
 LS6  Var_17    H16  C11  C10  N09  -178.82  30.0  1
 LS6  Var_18    H17  C11  C10  N09    64.08  30.0  1
 LS6  Var_19    C01  C08  N09  C10    73.95  30.0  3
 LS6  Var_20    C01  C08  N09  C20  -161.70  30.0  3
 LS6  Var_21    N09  C08  C01  C02   176.87  30.0  3
 LS6  Var_22    C08  C01  C02  C03   -89.46  30.0  2
 LS6  Var_23    C08  C01  C02  C07    88.06  30.0  2
 LS6  Var_24    H14  C08  N09  C10  -166.51  30.0  3
 LS6  Var_25    H15  C08  N09  C10   -50.18  30.0  3
 LS6  Var_26    H14  C08  N09  C20   -42.17  30.0  3
 LS6  Var_27    H15  C08  N09  C20    74.17  30.0  3
 LS6  Var_28    H7   C01  C02  C03    30.89  30.0  2
 LS6  Var_29    H8   C01  C02  C03   148.40  30.0  2
 LS6  Var_30    H7   C01  C02  C07  -151.59  30.0  2
 LS6  Var_31    H8   C01  C02  C07   -34.08  30.0  2
 LS6  Var_32    H5   C20  N09  C08    54.52  30.0  1
 LS6  Var_33    H6   C20  N09  C08   -62.54  30.0  1
 LS6  Var_34    H1   C10  N09  C08   -55.55  30.0  1
 LS6  Var_35    H2   C10  N09  C08    61.87  30.0  1
 LS6  Var_36    C12  C13  C14  C15  -179.54   0.0  2
 LS6  Var_37    H19  C14  C13  C12     0.40   0.0  2
 LS6  Var_38    H14  C08  C01  C02    57.32  30.0  3
 LS6  Var_39    H15  C08  C01  C02   -57.73  30.0  3
 LS6  Var_40    H7   C01  C08  N09    55.50  30.0  2
 LS6  Var_41    H8   C01  C08  N09   -61.84  30.0  2
 LS6  Var_42    O16  C15  C14  C13    -0.14  30.0  2
 LS6  Var_43    N17  C15  C14  C13   177.61  30.0  2
 LS6  Var_44    H3   C13  C14  C15     0.10   0.0  2
 LS6  Var_45    H19  C14  C15  N17    -2.33  30.0  2
 LS6  Var_46    H19  C14  C15  O16   179.92  30.0  2
 LS6  Var_47    H19  C14  C13  H3   -179.96   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
 LS6  chir_01  C12  C19  C13  C11  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
 LS6  plan-1  C01  0.020
 LS6  plan-1  C02  0.020
 LS6  plan-1  C03  0.020
 LS6  plan-1  C04  0.020
 LS6  plan-1  C05  0.020
 LS6  plan-1  C06  0.020
 LS6  plan-1  C07  0.020
 LS6  plan-1  H9   0.020
 LS6  plan-1  H10  0.020
 LS6  plan-1  H11  0.020
 LS6  plan-1  H12  0.020
 LS6  plan-1  H13  0.020
 LS6  plan-2  C15  0.020
 LS6  plan-2  C14  0.020
 LS6  plan-2  N17  0.020
 LS6  plan-2  O16  0.020
 LS6  plan-2  O18  0.020
 LS6  plan-2  H24  0.020
 LS6  plan-3  C13  0.020
 LS6  plan-3  C15  0.020
 LS6  plan-3  C12  0.020
 LS6  plan-3  C14  0.020
 LS6  plan-3  H3   0.020
 LS6  plan-3  H19  0.020

