# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 13:40:58 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(3R)-piperidin-3-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N[C@@H]1CCCNC1)c2ccccc2
#
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
 89W  89W  "N-[(3R)-piperidin-3-yl]benzamide"
  ligand  31  15  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_89W
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
 89W  C10  C  CR6   0  -0.038   0.4664  3.9607   -8.4044
 89W  C13  C  CR16  0  -0.250  -0.9144  4.0934   -5.9855
 89W  C15  C  CR16  0  -0.292  -0.2472  2.8577   -7.9388
 89W  O01  O  O     0  -0.483   2.2618  4.6107   -9.8079
 89W  C02  C  C     0   0.523   1.2516  3.9320   -9.6790
 89W  N03  N  NH1   0  -0.649   0.7735  3.1243  -10.6414
 89W  C04  C  CH1   0  -0.073   1.4013  2.9424  -11.9334
 89W  C05  C  CH2   0  -0.434   0.6957  3.7432  -13.0265
 89W  C06  C  CH2   0  -0.437   1.3098  3.4477  -14.3913
 89W  C07  C  CH2   0  -0.291   1.3391  1.9493  -14.6514
 89W  N08  N  NH1   0  -0.597   2.0614  1.2830  -13.5817
 89W  C09  C  CH2   0  -0.281   1.4186  1.4589  -12.2955
 89W  C11  C  CR16  0  -0.270   0.4950  5.1247   -7.6389
 89W  C12  C  CR16  0  -0.241  -0.2010  5.1947   -6.4423
 89W  C14  C  CR16  0  -0.239  -0.9311  2.9238   -6.7327
 89W  H1   H  HCR6  0   0.262  -1.4512  4.1451   -5.0471
 89W  H2   H  HCR6  0   0.260  -0.2554  1.9282   -8.4951
 89W  H3   H  HNH1  0   0.400  -0.1395  2.7141  -10.5175
 89W  H4   H  HCH1  0   0.245   2.4333  3.2857  -11.8482
 89W  H5   H  HCH2  0   0.240   0.7451  4.8105  -12.7992
 89W  H6   H  HCH2  0   0.215  -0.3649  3.4676  -13.0370
 89W  H7   H  HCH2  0   0.219   2.3304  3.8390  -14.4315
 89W  H8   H  HCH2  0   0.232   0.7423  3.9511  -15.1765
 89W  H9   H  HCH2  0   0.186   0.3029  1.5847  -14.7512
 89W  H10  H  HCH2  0   0.232   1.8422  1.7397  -15.5974
 89W  H11  H  HNH1  0   0.354   2.1441  0.2960  -13.7850
 89W  H13  H  HCH2  0   0.188   0.3810  1.0811  -12.2816
 89W  H14  H  HCH2  0   0.239   1.9749  0.9038  -11.5372
 89W  H15  H  HCR6  0   0.258   1.0562  5.9825   -7.9854
 89W  H16  H  HCR6  0   0.260  -0.1843  6.1084   -5.8626
 89W  H17  H  HCR6  0   0.262  -1.4716  2.0574   -6.3746

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
 89W  C07  C06  single    1.521  0.020  1.521
 89W  C07  N08  single    1.453  0.020  1.453
 89W  C06  C05  single    1.525  0.020  1.525
 89W  N08  C09  single    1.449  0.020  1.449
 89W  C05  C04  single    1.528  0.020  1.528
 89W  C09  C04  single    1.527  0.020  1.527
 89W  C04  N03  single    1.448  0.020  1.448
 89W  N03  C02  single    1.344  0.020  1.344
 89W  O01  C02  double    1.224  0.020  1.224
 89W  C02  C10  single    1.497  0.020  1.497
 89W  C10  C15  aromatic  1.394  0.020  1.394
 89W  C10  C11  aromatic  1.393  0.020  1.393
 89W  C15  C14  aromatic  1.388  0.020  1.388
 89W  C11  C12  aromatic  1.386  0.020  1.386
 89W  C14  C13  aromatic  1.388  0.020  1.388
 89W  C12  C13  aromatic  1.389  0.020  1.389
 89W  C13  H1   single    0.930  0.020  1.080
 89W  C15  H2   single    0.930  0.020  1.080
 89W  N03  H3   single    0.860  0.020  1.020
 89W  C04  H4   single    0.970  0.020  1.090
 89W  C05  H5   single    0.970  0.020  1.090
 89W  C05  H6   single    0.970  0.020  1.090
 89W  C06  H7   single    0.970  0.020  1.090
 89W  C06  H8   single    0.970  0.020  1.090
 89W  C07  H9   single    0.970  0.020  1.090
 89W  C07  H10  single    0.970  0.020  1.090
 89W  N08  H11  single    0.890  0.020  1.040
 89W  C09  H13  single    0.970  0.020  1.090
 89W  C09  H14  single    0.970  0.020  1.090
 89W  C11  H15  single    0.930  0.020  1.080
 89W  C12  H16  single    0.930  0.020  1.080
 89W  C14  H17  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
 89W  C11  C10  C02  118.22  3.000
 89W  C11  C10  C15  119.21  3.000
 89W  C02  C10  C15  122.52  3.000
 89W  H1   C13  C14  120.07  3.000
 89W  H1   C13  C12  120.12  3.000
 89W  C14  C13  C12  119.81  3.000
 89W  H2   C15  C14  118.91  3.000
 89W  H2   C15  C10  120.76  3.000
 89W  C14  C15  C10  120.32  3.000
 89W  N03  C02  O01  123.46  3.000
 89W  O01  C02  C10  120.79  3.000
 89W  N03  C02  C10  115.75  3.000
 89W  H3   N03  C04  116.81  3.000
 89W  H3   N03  C02  118.58  3.000
 89W  C04  N03  C02  124.06  3.000
 89W  H4   C04  C09  108.27  3.000
 89W  H4   C04  C05  109.14  3.000
 89W  C09  C04  C05  110.17  3.000
 89W  H4   C04  N03  107.52  3.000
 89W  C09  C04  N03  109.79  3.000
 89W  C05  C04  N03  111.86  3.000
 89W  H6   C05  H5   106.95  3.000
 89W  H6   C05  C06  109.41  3.000
 89W  H5   C05  C06  110.93  3.000
 89W  H6   C05  C04  108.79  3.000
 89W  H5   C05  C04  110.02  3.000
 89W  C06  C05  C04  110.65  3.000
 89W  H8   C06  H7   107.08  3.000
 89W  H8   C06  C07  109.95  3.000
 89W  H7   C06  C07  109.16  3.000
 89W  H8   C06  C05  110.17  3.000
 89W  H7   C06  C05  109.83  3.000
 89W  C07  C06  C05  110.58  3.000
 89W  H10  C07  H9   106.92  3.000
 89W  H10  C07  N08  108.72  3.000
 89W  H9   C07  N08  112.47  3.000
 89W  H10  C07  C06  110.25  3.000
 89W  H9   C07  C06  108.84  3.000
 89W  N08  C07  C06  109.60  3.000
 89W  H11  N08  C09  109.48  3.000
 89W  H11  N08  C07  109.90  3.000
 89W  C09  N08  C07  112.18  3.000
 89W  H14  C09  H13  107.22  3.000
 89W  H14  C09  N08  109.20  3.000
 89W  H13  C09  N08  112.74  3.000
 89W  H14  C09  C04  109.57  3.000
 89W  H13  C09  C04  108.58  3.000
 89W  N08  C09  C04  109.48  3.000
 89W  H15  C11  C12  119.79  3.000
 89W  H15  C11  C10  119.80  3.000
 89W  C12  C11  C10  120.41  3.000
 89W  H16  C12  C11  119.82  3.000
 89W  H16  C12  C13  120.07  3.000
 89W  C11  C12  C13  120.11  3.000
 89W  H17  C14  C15  119.70  3.000
 89W  H17  C14  C13  120.16  3.000
 89W  C15  C14  C13  120.13  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
 89W  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 89W  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 89W  CONST_03  C12  C11  C10  C15     0.00   0.0  0
 89W  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 89W  CONST_05  C14  C15  C10  C11     0.00   0.0  0
 89W  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 89W  CONST_07  C14  C15  C10  C02   180.00   0.0  0
 89W  CONST_08  C12  C11  C10  C02   180.00   0.0  0
 89W  CONST_09  H17  C14  C15  C10   180.00   0.0  0
 89W  CONST_10  H16  C12  C11  C10   180.00   0.0  0
 89W  CONST_11  H2   C15  C14  C13   180.00   0.0  0
 89W  CONST_12  H15  C11  C12  C13   180.00   0.0  0
 89W  CONST_13  H15  C11  C10  C15   180.00   0.0  0
 89W  CONST_14  H1   C13  C14  C15   180.00   0.0  0
 89W  CONST_15  H2   C15  C10  C11   180.00   0.0  0
 89W  CONST_16  H1   C13  C12  C11   180.00   0.0  0
 89W  CONST_17  H17  C14  C13  C12   180.00   0.0  0
 89W  CONST_18  H16  C12  C13  C14   180.00   0.0  0
 89W  CONST_19  C04  N03  C02  C10   180.00   0.0  0
 89W  CONST_20  C04  N03  C02  O01     0.00   0.0  0
 89W  CONST_21  H3   N03  C02  C10     0.00   0.0  0
 89W  CONST_22  H3   N03  C02  O01   180.00   0.0  0
 89W  Var_01    C07  C06  C05  C04    53.03  30.0  1
 89W  Var_02    C07  N08  C09  C04   -62.54  30.0  1
 89W  Var_03    N08  C07  C06  C05   -56.42  30.0  1
 89W  Var_04    C09  N08  C07  C06    62.21  30.0  1
 89W  Var_05    H7   C06  C05  C04   -67.50  30.0  1
 89W  Var_06    H8   C06  C05  C04   174.78  30.0  1
 89W  Var_07    H11  N08  C09  C04   175.18  30.0  1
 89W  Var_08    H9   C07  C06  C05    66.96  30.0  1
 89W  Var_09    H10  C07  C06  C05  -176.06  30.0  1
 89W  Var_10    H11  N08  C07  C06  -175.75  30.0  1
 89W  Var_11    H5   C05  C06  C07   175.43  30.0  1
 89W  Var_12    H6   C05  C06  C07   -66.81  30.0  1
 89W  Var_13    H13  C09  N08  C07    58.44  30.0  1
 89W  Var_14    H14  C09  N08  C07   177.50  30.0  1
 89W  Var_15    H7   C06  C07  N08    64.51  30.0  1
 89W  Var_16    H8   C06  C07  N08  -178.31  30.0  1
 89W  Var_17    H9   C07  N08  C09   -59.00  30.0  1
 89W  Var_18    H10  C07  N08  C09  -177.21  30.0  1
 89W  Var_19    N03  C02  C10  C15    30.84  30.0  2
 89W  Var_20    O01  C02  C10  C15  -149.09  30.0  2
 89W  Var_21    C11  C10  C02  O01    28.63  30.0  2
 89W  Var_22    C11  C10  C02  N03  -151.43  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
 89W  chir_01  C04  C05  C09  N03  positiv

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
 89W  plan-1  C10  0.020
 89W  plan-1  C13  0.020
 89W  plan-1  C15  0.020
 89W  plan-1  C02  0.020
 89W  plan-1  C11  0.020
 89W  plan-1  C12  0.020
 89W  plan-1  C14  0.020
 89W  plan-1  H1   0.020
 89W  plan-1  H2   0.020
 89W  plan-1  H15  0.020
 89W  plan-1  H16  0.020
 89W  plan-1  H17  0.020
 89W  plan-2  C10  0.020
 89W  plan-2  O01  0.020
 89W  plan-2  C02  0.020
 89W  plan-2  N03  0.020
 89W  plan-2  C04  0.020
 89W  plan-2  H3   0.020

