# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:51:05 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 1-acetyl-N-(5-methylpyridin-2-yl)piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC(CC1)C(=O)Nc2ccc(C)cn2
#
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
 HAU  HAU  1-acetyl-N-(5-methylpyridin-2-yl)piperidine-4-carboxamide  ligand  38  19  .  2021-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HAU
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
 HAU  C     C  C     0   0.515   4.9828   0.1594  -0.4247
 HAU  O     O  O     0  -0.509   5.6857  -0.8444  -0.4396
 HAU  C1    C  CH3   0  -0.807   5.3138   1.3435  -1.3038
 HAU  N1    N  NT    0  -0.434   3.8959   0.2640   0.3723
 HAU  O1    O  O     0  -0.437  -0.4089  -1.7044  -0.5357
 HAU  N2    N  N     0  -0.416  -3.1362  -0.9434  -0.4833
 HAU  C3    C  CH2   0  -0.319   3.4485  -0.8526   1.1860
 HAU  N3    N  NH1   0  -0.731  -1.2908   0.1346   0.4929
 HAU  C4    C  CH2   0  -0.413   2.1025  -1.3716   0.6943
 HAU  C5    C  CH1   0  -0.437   1.0728  -0.2481   0.6794
 HAU  C6    C  CH2   0  -0.417   1.5975   0.9378  -0.1435
 HAU  C7    C  CH2   0  -0.318   2.9643   1.3757   0.3683
 HAU  C8    C  C     0   0.571  -0.2735  -0.7094   0.1433
 HAU  C9    C  CR6   0   0.513  -2.6429   0.0951   0.1610
 HAU  C10   C  CR16  0  -0.396  -3.4357   1.1817   0.5504
 HAU  C11   C  CR16  0  -0.169  -4.7777   1.1577   0.2426
 HAU  C12   C  CR6   0   0.002  -5.3205   0.0707  -0.4455
 HAU  C13   C  CR16  0  -0.111  -4.4352  -0.9431  -0.7739
 HAU  C14   C  CH3   0  -0.725  -6.7711   0.0072  -0.8121
 HAU  H1    H  HCH3  0   0.264   4.5218   1.5382  -2.0283
 HAU  H1A   H  HCH3  0   0.265   5.4593   2.2565  -0.7262
 HAU  H1B   H  HCH3  0   0.268   6.2306   1.1338  -1.8483
 HAU  H3    H  HCH2  0   0.267   4.1962  -1.6396   1.1635
 HAU  H3A   H  HCH2  0   0.240   3.3615  -0.5126   2.2236
 HAU  HN3   H  HNH1  0   0.420  -1.0229   0.9311   1.0516
 HAU  H4    H  HCH2  0   0.235   2.2221  -1.7872  -0.3089
 HAU  H4A   H  HCH2  0   0.249   1.7736  -2.1847   1.3448
 HAU  H5    H  HCH1  0   0.267   0.9260   0.0998   1.7102
 HAU  H6    H  HCH2  0   0.243   1.6779   0.6506  -1.1958
 HAU  H6A   H  HCH2  0   0.253   0.9129   1.7871  -0.0898
 HAU  H7    H  HCH2  0   0.248   2.8678   1.7535   1.3918
 HAU  H7A   H  HCH2  0   0.280   3.3422   2.1968  -0.2345
 HAU  H10   H  HCR6  0   0.278  -3.0041   2.0223   1.0787
 HAU  H11   H  HCR6  0   0.267  -5.4083   1.9878   0.5379
 HAU  H13   H  HCR6  0   0.252  -4.7963  -1.8199  -1.3036
 HAU  H14   H  HCH3  0   0.249  -7.0243   0.7614  -1.5592
 HAU  H14A  H  HCH3  0   0.246  -7.0337  -0.9664  -1.2241
 HAU  H14B  H  HCH3  0   0.248  -7.4081   0.1860   0.0547

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
 HAU  C    O     double    1.225  0.020  1.225
 HAU  C    C1    single    1.511  0.020  1.511
 HAU  C    N1    single    1.352  0.020  1.352
 HAU  N1   C3    single    1.452  0.020  1.452
 HAU  N1   C7    single    1.450  0.020  1.450
 HAU  O1   C8    double    1.212  0.020  1.212
 HAU  N2   C9    aromatic  1.318  0.020  1.318
 HAU  N2   C13   aromatic  1.331  0.020  1.331
 HAU  C3   C4    single    1.524  0.020  1.524
 HAU  N3   C8    single    1.367  0.020  1.367
 HAU  N3   C9    single    1.393  0.020  1.393
 HAU  C4   C5    single    1.524  0.020  1.524
 HAU  C5   C6    single    1.536  0.020  1.536
 HAU  C5   C8    single    1.521  0.020  1.521
 HAU  C6   C7    single    1.524  0.020  1.524
 HAU  C9   C10   aromatic  1.400  0.020  1.400
 HAU  C10  C11   aromatic  1.377  0.020  1.377
 HAU  C11  C12   aromatic  1.396  0.020  1.396
 HAU  C12  C13   aromatic  1.385  0.020  1.385
 HAU  C12  C14   single    1.498  0.020  1.498
 HAU  C1   H1    single    0.970  0.020  1.090
 HAU  C1   H1A   single    0.970  0.020  1.090
 HAU  C1   H1B   single    0.970  0.020  1.090
 HAU  C3   H3    single    0.970  0.020  1.090
 HAU  C3   H3A   single    0.970  0.020  1.090
 HAU  N3   HN3   single    0.860  0.020  1.020
 HAU  C4   H4    single    0.970  0.020  1.090
 HAU  C4   H4A   single    0.970  0.020  1.090
 HAU  C5   H5    single    0.970  0.020  1.090
 HAU  C6   H6    single    0.970  0.020  1.090
 HAU  C6   H6A   single    0.970  0.020  1.090
 HAU  C7   H7    single    0.970  0.020  1.090
 HAU  C7   H7A   single    0.970  0.020  1.090
 HAU  C10  H10   single    0.930  0.020  1.080
 HAU  C11  H11   single    0.930  0.020  1.080
 HAU  C13  H13   single    0.930  0.020  1.080
 HAU  C14  H14   single    0.970  0.020  1.090
 HAU  C14  H14A  single    0.970  0.020  1.090
 HAU  C14  H14B  single    0.970  0.020  1.090

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
 HAU  N1    C    C1    117.28  3.000
 HAU  N1    C    O     122.12  3.000
 HAU  C1    C    O     120.60  3.000
 HAU  H1B   C1   H1A   108.33  3.000
 HAU  H1B   C1   H1    108.31  3.000
 HAU  H1A   C1   H1    107.42  3.000
 HAU  H1B   C1   C     108.96  3.000
 HAU  H1A   C1   C     112.16  3.000
 HAU  H1    C1   C     111.53  3.000
 HAU  C7    N1   C3    113.14  3.000
 HAU  C7    N1   C     125.04  3.000
 HAU  C3    N1   C     121.23  3.000
 HAU  C13   N2   C9    118.15  3.000
 HAU  H3A   C3   H3    107.41  3.000
 HAU  H3A   C3   C4    109.95  3.000
 HAU  H3    C3   C4    110.77  3.000
 HAU  H3A   C3   N1    108.46  3.000
 HAU  H3    C3   N1    109.48  3.000
 HAU  C4    C3   N1    110.68  3.000
 HAU  HN3   N3   C9    114.33  3.000
 HAU  HN3   N3   C8    115.55  3.000
 HAU  C9    N3   C8    130.08  3.000
 HAU  H4A   C4   H4    107.26  3.000
 HAU  H4A   C4   C5    110.56  3.000
 HAU  H4    C4   C5    110.21  3.000
 HAU  H4A   C4   C3    109.11  3.000
 HAU  H4    C4   C3    109.22  3.000
 HAU  C5    C4   C3    110.41  3.000
 HAU  H5    C5   C8    107.98  3.000
 HAU  H5    C5   C6    107.70  3.000
 HAU  C8    C5   C6    110.35  3.000
 HAU  H5    C5   C4    108.35  3.000
 HAU  C8    C5   C4    112.21  3.000
 HAU  C6    C5   C4    110.10  3.000
 HAU  H6A   C6   H6    107.31  3.000
 HAU  H6A   C6   C7    108.80  3.000
 HAU  H6    C6   C7    109.43  3.000
 HAU  H6A   C6   C5    111.10  3.000
 HAU  H6    C6   C5    109.75  3.000
 HAU  C7    C6   C5    110.38  3.000
 HAU  H7A   C7   H7    106.76  3.000
 HAU  H7A   C7   C6    110.05  3.000
 HAU  H7    C7   C6    109.50  3.000
 HAU  H7A   C7   N1    110.94  3.000
 HAU  H7    C7   N1    108.57  3.000
 HAU  C6    C7   N1    110.91  3.000
 HAU  C5    C8   N3    112.41  3.000
 HAU  C5    C8   O1    123.05  3.000
 HAU  N3    C8   O1    124.53  3.000
 HAU  C10   C9   N3    117.47  3.000
 HAU  C10   C9   N2    122.38  3.000
 HAU  N3    C9   N2    120.14  3.000
 HAU  H10   C10  C11   120.74  3.000
 HAU  H10   C10  C9    120.83  3.000
 HAU  C11   C10  C9    118.43  3.000
 HAU  H11   C11  C12   120.30  3.000
 HAU  H11   C11  C10   119.53  3.000
 HAU  C12   C11  C10   120.17  3.000
 HAU  C14   C12  C13   122.00  3.000
 HAU  C14   C12  C11   122.02  3.000
 HAU  C13   C12  C11   115.99  3.000
 HAU  H13   C13  C12   119.59  3.000
 HAU  H13   C13  N2    115.52  3.000
 HAU  C12   C13  N2    124.89  3.000
 HAU  H14B  C14  H14A  107.84  3.000
 HAU  H14B  C14  H14   107.17  3.000
 HAU  H14A  C14  H14   107.63  3.000
 HAU  H14B  C14  C12   111.37  3.000
 HAU  H14A  C14  C12   111.35  3.000
 HAU  H14   C14  C12   111.28  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
 HAU  CONST_01  C11  C10  C9   N2     0.00   0.0  0
 HAU  CONST_02  C11  C12  C13  N2     0.00   0.0  0
 HAU  CONST_03  C12  C13  N2   C9     0.00   0.0  0
 HAU  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 HAU  CONST_05  C13  N2   C9   C10    0.00   0.0  0
 HAU  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 HAU  CONST_07  C14  C12  C13  N2   180.00   0.0  0
 HAU  CONST_08  C13  N2   C9   N3   180.00   0.0  0
 HAU  CONST_09  C11  C10  C9   N3   180.00   0.0  0
 HAU  CONST_10  C14  C12  C11  C10  180.00   0.0  0
 HAU  CONST_11  H10  C10  C9   N2   180.00   0.0  0
 HAU  CONST_12  H13  C13  N2   C9   180.00   0.0  0
 HAU  CONST_13  H11  C11  C10  C9   180.00   0.0  0
 HAU  CONST_14  C3   N1   C    O      0.00   0.0  0
 HAU  CONST_15  C7   N1   C    O    180.00   0.0  0
 HAU  CONST_16  C3   N1   C    C1   180.00   0.0  0
 HAU  CONST_17  C7   N1   C    C1     0.00   0.0  0
 HAU  CONST_18  C9   N3   C8   C5   180.00   0.0  0
 HAU  CONST_19  C8   N3   C9   N2     0.00   0.0  0
 HAU  CONST_20  C10  C9   N3   C8   180.00   0.0  0
 HAU  CONST_21  HN3  N3   C9   N2   180.00   0.0  0
 HAU  CONST_22  C9   N3   C8   O1     0.00   0.0  0
 HAU  Var_01    C5   C4   C3   N1   -56.24  30.0  1
 HAU  Var_02    C5   C6   C7   N1    55.32  30.0  1
 HAU  Var_03    C6   C7   N1   C3   -58.46  30.0  1
 HAU  Var_04    C7   N1   C3   C4    58.78  30.0  1
 HAU  Var_05    H14  C14  C12  C11   67.45  30.0  2
 HAU  Var_06    H1   C1   C    N1   -63.08  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
 HAU  chir_01  C5  C4  C6  C8  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
 HAU  plan-1  N2   0.020
 HAU  plan-1  N3   0.020
 HAU  plan-1  C9   0.020
 HAU  plan-1  C10  0.020
 HAU  plan-1  C11  0.020
 HAU  plan-1  C12  0.020
 HAU  plan-1  C13  0.020
 HAU  plan-1  C14  0.020
 HAU  plan-1  H10  0.020
 HAU  plan-1  H11  0.020
 HAU  plan-1  H13  0.020
 HAU  plan-2  O1   0.020
 HAU  plan-2  N3   0.020
 HAU  plan-2  C5   0.020
 HAU  plan-2  C8   0.020
 HAU  plan-2  C9   0.020
 HAU  plan-2  HN3  0.020
 HAU  plan-3  C    0.020
 HAU  plan-3  O    0.020
 HAU  plan-3  C1   0.020
 HAU  plan-3  N1   0.020
 HAU  plan-3  C3   0.020
 HAU  plan-3  C7   0.020

