# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 04:43:13 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 1-(3-methylbenzene-1-carbonyl)piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)C(=O)N2CCC(CC2)C(N)=O
#
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
 NZJ  NZJ  1-(3-methylbenzene-1-carbonyl)piperidine-4-carboxamide  ligand  36  18  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NZJ
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
 NZJ  N1   N  NT    0  -0.443  -0.3694   1.0446  -0.6541
 NZJ  C4   C  CR16  0  -0.230   3.6390  -0.4439  -1.6809
 NZJ  C5   C  CR16  0  -0.281   2.4592   0.2664  -1.5072
 NZJ  C6   C  CR6   0  -0.052   1.9626   0.4681  -0.2241
 NZJ  C7   C  CR16  0  -0.330   2.6550  -0.0388   0.8720
 NZJ  C8   C  C     0   0.516   0.7651   1.3329   0.0197
 NZJ  C10  C  CH2   0  -0.412  -1.7237  -0.9742  -0.3328
 NZJ  C13  C  CH2   0  -0.323  -1.5330   1.9051  -0.5145
 NZJ  C11  C  CH1   0  -0.395  -2.9718  -0.1165  -0.1416
 NZJ  C12  C  CH2   0  -0.421  -2.5814   1.2697   0.3877
 NZJ  C14  C  C     0   0.539  -3.9546  -0.7616   0.8177
 NZJ  C2   C  CR6   0   0.111   3.8231  -0.7756   0.7084
 NZJ  C3   C  CR16  0  -0.295   4.3098  -0.9648  -0.5850
 NZJ  C9   C  CH2   0  -0.325  -0.6923  -0.2641  -1.2030
 NZJ  N2   N  NH2   0  -0.802  -5.2447  -0.6627   0.4662
 NZJ  O1   O  O     0  -0.489   0.8669   2.2885   0.7789
 NZJ  O2   O  O     0  -0.494  -3.5882  -1.3017   1.8527
 NZJ  H1   H  HCR6  0   0.259   4.0369  -0.5901  -2.6766
 NZJ  H2   H  HCR6  0   0.265   1.9395   0.6709  -2.3670
 NZJ  H3   H  HCR6  0   0.253   2.2719   0.1338   1.8711
 NZJ  H4   H  HCH2  0   0.234  -1.2780  -1.2052   0.6377
 NZJ  H5   H  HCH2  0   0.252  -1.9828  -1.9247  -0.8046
 NZJ  H6   H  HCH2  0   0.268  -1.2273   2.8740  -0.1299
 NZJ  H7   H  HCH2  0   0.248  -1.9520   2.0670  -1.5125
 NZJ  H8   H  HCH3  0   0.250   4.4138  -2.4450   1.9244
 NZJ  H9   H  HCH3  0   0.247   5.6122  -1.1657   1.8414
 NZJ  H10  H  HCH3  0   0.245   4.1652  -0.9562   2.8277
 NZJ  H11  H  HCH1  0   0.255  -3.4525   0.0193  -1.1177
 NZJ  H12  H  HCH2  0   0.240  -2.1849   1.1828   1.4033
 NZJ  H13  H  HCH2  0   0.251  -3.4563   1.9217   0.4329
 NZJ  H14  H  HCR6  0   0.252   5.2261  -1.5236  -0.7352
 NZJ  H15  H  HCH2  0   0.246  -1.0805  -0.1305  -2.2170
 NZJ  H16  H  HCH2  0   0.277   0.2027  -0.8742  -1.2797
 NZJ  H17  H  HNH2  0   0.407  -5.5315  -0.1972  -0.3770
 NZJ  H18  H  HNH2  0   0.399  -5.9706  -0.9849   1.0860
 NZJ  C1   C  CH3   0  -0.724   4.5408  -1.3614   1.8892

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
 NZJ  C4   C3   aromatic  1.387  0.020  1.387
 NZJ  C4   C5   aromatic  1.388  0.020  1.388
 NZJ  C3   C2   aromatic  1.395  0.020  1.395
 NZJ  C5   C6   aromatic  1.391  0.020  1.391
 NZJ  C2   C1   single    1.501  0.020  1.501
 NZJ  C2   C7   aromatic  1.391  0.020  1.391
 NZJ  C6   C7   aromatic  1.392  0.020  1.392
 NZJ  C6   C8   single    1.497  0.020  1.497
 NZJ  O2   C14  double    1.224  0.020  1.224
 NZJ  C8   O1   double    1.225  0.020  1.225
 NZJ  C8   N1   single    1.351  0.020  1.351
 NZJ  C10  C9   single    1.525  0.020  1.525
 NZJ  C10  C11  single    1.526  0.020  1.526
 NZJ  C9   N1   single    1.455  0.020  1.455
 NZJ  N1   C13  single    1.454  0.020  1.454
 NZJ  C14  N2   single    1.341  0.020  1.341
 NZJ  C14  C11  single    1.517  0.020  1.517
 NZJ  C13  C12  single    1.522  0.020  1.522
 NZJ  C11  C12  single    1.534  0.020  1.534
 NZJ  C4   H1   single    0.930  0.020  1.080
 NZJ  C5   H2   single    0.930  0.020  1.080
 NZJ  C7   H3   single    0.930  0.020  1.080
 NZJ  C10  H4   single    0.970  0.020  1.090
 NZJ  C10  H5   single    0.970  0.020  1.090
 NZJ  C13  H6   single    0.970  0.020  1.090
 NZJ  C13  H7   single    0.970  0.020  1.090
 NZJ  C1   H8   single    0.970  0.020  1.090
 NZJ  C1   H9   single    0.970  0.020  1.090
 NZJ  C1   H10  single    0.970  0.020  1.090
 NZJ  C11  H11  single    0.970  0.020  1.090
 NZJ  C12  H12  single    0.970  0.020  1.090
 NZJ  C12  H13  single    0.970  0.020  1.090
 NZJ  C3   H14  single    0.930  0.020  1.080
 NZJ  C9   H15  single    0.970  0.020  1.090
 NZJ  C9   H16  single    0.970  0.020  1.090
 NZJ  N2   H17  single    0.860  0.020  1.020
 NZJ  N2   H18  single    0.860  0.020  1.020

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
 NZJ  C9   N1   C13  113.00  3.000
 NZJ  C13  N1   C8   119.87  3.000
 NZJ  C9   N1   C8   124.50  3.000
 NZJ  H1   C4   C3   119.91  3.000
 NZJ  H1   C4   C5   119.79  3.000
 NZJ  C3   C4   C5   120.30  3.000
 NZJ  H2   C5   C6   120.46  3.000
 NZJ  H2   C5   C4   119.98  3.000
 NZJ  C6   C5   C4   119.55  3.000
 NZJ  C8   C6   C7   118.69  3.000
 NZJ  C8   C6   C5   121.31  3.000
 NZJ  C7   C6   C5   119.74  3.000
 NZJ  H3   C7   C2   119.32  3.000
 NZJ  H3   C7   C6   119.47  3.000
 NZJ  C2   C7   C6   121.20  3.000
 NZJ  O1   C8   C6   119.02  3.000
 NZJ  O1   C8   N1   123.07  3.000
 NZJ  C6   C8   N1   117.86  3.000
 NZJ  H5   C10  H4   107.24  3.000
 NZJ  H5   C10  C9   108.61  3.000
 NZJ  H4   C10  C9   109.23  3.000
 NZJ  H5   C10  C11  110.43  3.000
 NZJ  H4   C10  C11  109.95  3.000
 NZJ  C9   C10  C11  111.28  3.000
 NZJ  H7   C13  H6   107.38  3.000
 NZJ  H7   C13  C12  109.79  3.000
 NZJ  H6   C13  C12  110.87  3.000
 NZJ  H7   C13  N1   107.84  3.000
 NZJ  H6   C13  N1   109.67  3.000
 NZJ  C12  C13  N1   111.16  3.000
 NZJ  H11  C11  C14  109.36  3.000
 NZJ  H11  C11  C12  107.87  3.000
 NZJ  C14  C11  C12  109.32  3.000
 NZJ  H11  C11  C10  108.45  3.000
 NZJ  C12  C11  C10  110.05  3.000
 NZJ  C14  C11  C10  111.71  3.000
 NZJ  H13  C12  H12  107.42  3.000
 NZJ  H13  C12  C11  110.47  3.000
 NZJ  H12  C12  C11  109.93  3.000
 NZJ  H13  C12  C13  109.09  3.000
 NZJ  H12  C12  C13  109.50  3.000
 NZJ  C11  C12  C13  110.36  3.000
 NZJ  O2   C14  N2   122.85  3.000
 NZJ  N2   C14  C11  115.22  3.000
 NZJ  O2   C14  C11  121.90  3.000
 NZJ  C3   C2   C1   120.64  3.000
 NZJ  C1   C2   C7   121.05  3.000
 NZJ  C3   C2   C7   118.30  3.000
 NZJ  H14  C3   C2   119.58  3.000
 NZJ  H14  C3   C4   119.55  3.000
 NZJ  C2   C3   C4   120.87  3.000
 NZJ  H16  C9   H15  107.19  3.000
 NZJ  H16  C9   C10  109.65  3.000
 NZJ  H15  C9   C10  110.23  3.000
 NZJ  H16  C9   N1   110.42  3.000
 NZJ  H15  C9   N1   108.57  3.000
 NZJ  C10  C9   N1   110.71  3.000
 NZJ  H18  N2   H17  117.31  3.000
 NZJ  H18  N2   C14  120.56  3.000
 NZJ  H17  N2   C14  121.92  3.000
 NZJ  H10  C1   H9   108.05  3.000
 NZJ  H10  C1   H8   107.54  3.000
 NZJ  H9   C1   H8   107.09  3.000
 NZJ  H10  C1   C2   111.59  3.000
 NZJ  H9   C1   C2   111.44  3.000
 NZJ  H8   C1   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
 NZJ  CONST_01  C7   C2   C3   C4     0.00   0.0  0
 NZJ  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 NZJ  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 NZJ  CONST_04  C2   C7   C6   C5     0.00   0.0  0
 NZJ  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 NZJ  CONST_06  C3   C2   C7   C6     0.00   0.0  0
 NZJ  CONST_07  C1   C2   C3   C4   180.00   0.0  0
 NZJ  CONST_08  C8   C6   C5   C4   180.00   0.0  0
 NZJ  CONST_09  C1   C2   C7   C6   180.00   0.0  0
 NZJ  CONST_10  C2   C7   C6   C8   180.00   0.0  0
 NZJ  CONST_12  C13  N1   C8   C6   180.00   0.0  0
 NZJ  CONST_13  H14  C3   C4   C5   180.00   0.0  0
 NZJ  CONST_14  H3   C7   C6   C5   180.00   0.0  0
 NZJ  CONST_15  H1   C4   C5   C6   180.00   0.0  0
 NZJ  CONST_16  H2   C5   C6   C7   180.00   0.0  0
 NZJ  CONST_17  O1   C8   N1   C13    0.00   0.0  0
 NZJ  CONST_19  H17  N2   C14  C11    0.00   0.0  0
 NZJ  CONST_20  H18  N2   C14  C11  180.00   0.0  0
 NZJ  Var_01    C11  C10  C9   N1    55.05  30.0  1
 NZJ  Var_02    C11  C12  C13  N1   -55.93  30.0  1
 NZJ  Var_03    C13  N1   C9   C10  -57.81  30.0  1
 NZJ  Var_04    C9   N1   C13  C12   58.71  30.0  1
 NZJ  Var_05    C5   C6   C8   N1    54.90  30.0  2
 NZJ  Var_06    H8   C1   C2   C7   107.47  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
 NZJ  chir_01  C11  C10  C14  C12  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
 NZJ  plan-1  C4   0.020
 NZJ  plan-1  C5   0.020
 NZJ  plan-1  C6   0.020
 NZJ  plan-1  C7   0.020
 NZJ  plan-1  C8   0.020
 NZJ  plan-1  C2   0.020
 NZJ  plan-1  C3   0.020
 NZJ  plan-1  H1   0.020
 NZJ  plan-1  H2   0.020
 NZJ  plan-1  H3   0.020
 NZJ  plan-1  H14  0.020
 NZJ  plan-1  C1   0.020
 NZJ  plan-2  N1   0.020
 NZJ  plan-2  C6   0.020
 NZJ  plan-2  C8   0.020
 NZJ  plan-2  C13  0.020
 NZJ  plan-2  C9   0.020
 NZJ  plan-2  O1   0.020
 NZJ  plan-3  C11  0.020
 NZJ  plan-3  C14  0.020
 NZJ  plan-3  N2   0.020
 NZJ  plan-3  O2   0.020
 NZJ  plan-3  H17  0.020
 NZJ  plan-3  H18  0.020

