# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 02:11:44 2021
#   Inital geometry file: a 51 line input string
#   Ligand name: pentanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CCCC(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
 P6W  P6W  'pentanediamide           '  ligand  19  9  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_P6W
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
 P6W  C01  C  CH2   0  -0.437  -23.1286  29.2636  -24.8282
 P6W  C02  C  CH2   0  -0.572  -22.2152  28.0413  -24.8960
 P6W  C03  C  C     0   0.507  -20.7662  28.4323  -25.0961
 P6W  C06  C  CH2   0  -0.574  -23.1274  30.0963  -26.1089
 P6W  C07  C  C     0   0.509  -23.6351  29.2997  -27.2927
 P6W  N05  N  NH2   0  -0.795  -20.1873  27.9586  -26.2093
 P6W  N09  N  NH2   0  -0.796  -22.7925  29.2038  -28.3316
 P6W  O04  O  O     0  -0.498  -20.1776  29.1429  -24.2920
 P6W  O08  O  O     0  -0.497  -24.7392  28.7716  -27.2818
 P6W  H1   H  HCH2  0   0.247  -22.8277  29.8987  -23.9941
 P6W  H2   H  HCH2  0   0.247  -24.1449  28.9311  -24.6134
 P6W  H3   H  HCH2  0   0.279  -22.2810  27.4935  -23.9527
 P6W  H4   H  HCH2  0   0.247  -22.5545  27.3528  -25.6733
 P6W  H5   H  HCH2  0   0.248  -22.1334  30.5076  -26.3006
 P6W  H6   H  HCH2  0   0.280  -23.7933  30.9528  -25.9780
 P6W  H7   H  HNH2  0   0.399  -19.2270  28.1763  -26.4220
 P6W  H8   H  HNH2  0   0.403  -20.6928  27.3988  -26.8733
 P6W  H9   H  HNH2  0   0.399  -23.0566  28.6991  -29.1626
 P6W  H10  H  HNH2  0   0.404  -21.8934  29.6519  -28.3293

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
 P6W  N09  C07  single  1.341  0.020  1.341
 P6W  C07  O08  double  1.224  0.020  1.224
 P6W  C07  C06  single  1.514  0.020  1.514
 P6W  C06  C01  single  1.528  0.020  1.528
 P6W  C02  C01  single  1.527  0.020  1.527
 P6W  C02  C03  single  1.514  0.020  1.514
 P6W  C03  O04  double  1.224  0.020  1.224
 P6W  C03  N05  single  1.341  0.020  1.341
 P6W  C01  H1   single  0.970  0.020  1.090
 P6W  C01  H2   single  0.970  0.020  1.090
 P6W  C02  H3   single  0.970  0.020  1.090
 P6W  C02  H4   single  0.970  0.020  1.090
 P6W  C06  H5   single  0.970  0.020  1.090
 P6W  C06  H6   single  0.970  0.020  1.090
 P6W  N05  H7   single  0.860  0.020  1.020
 P6W  N05  H8   single  0.860  0.020  1.020
 P6W  N09  H9   single  0.860  0.020  1.020
 P6W  N09  H10  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
 P6W  H2   C01  H1   106.49  3.000
 P6W  H2   C01  C06  109.40  3.000
 P6W  H1   C01  C06  108.88  3.000
 P6W  H2   C01  C02  108.78  3.000
 P6W  H1   C01  C02  109.57  3.000
 P6W  C06  C01  C02  113.49  3.000
 P6W  H4   C02  H3   106.23  3.000
 P6W  H4   C02  C03  111.46  3.000
 P6W  H3   C02  C03  107.53  3.000
 P6W  H4   C02  C01  110.50  3.000
 P6W  H3   C02  C01  109.08  3.000
 P6W  C03  C02  C01  111.81  3.000
 P6W  O04  C03  N05  122.88  3.000
 P6W  N05  C03  C02  115.57  3.000
 P6W  O04  C03  C02  121.55  3.000
 P6W  H6   C06  H5   106.28  3.000
 P6W  H6   C06  C07  107.56  3.000
 P6W  H5   C06  C07  111.46  3.000
 P6W  H6   C06  C01  109.04  3.000
 P6W  H5   C06  C01  110.67  3.000
 P6W  C07  C06  C01  111.61  3.000
 P6W  O08  C07  N09  122.87  3.000
 P6W  O08  C07  C06  121.50  3.000
 P6W  N09  C07  C06  115.63  3.000
 P6W  H8   N05  H7   117.42  3.000
 P6W  H8   N05  C03  121.88  3.000
 P6W  H7   N05  C03  120.68  3.000
 P6W  H10  N09  H9   117.38  3.000
 P6W  H10  N09  C07  121.91  3.000
 P6W  H9   N09  C07  120.67  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
 P6W  CONST_01  H7   N05  C03  C02   180.00   0.0  0
 P6W  CONST_02  H8   N05  C03  C02     0.00   0.0  0
 P6W  CONST_03  H9   N09  C07  C06   180.00   0.0  0
 P6W  CONST_04  H10  N09  C07  C06     0.00   0.0  0
 P6W  Var_01    N09  C07  C06  C01  -122.60  30.0  1
 P6W  Var_02    O04  C03  C02  C01    59.58  30.0  3
 P6W  Var_03    C07  C06  C01  C02    61.88  30.0  1
 P6W  Var_04    C06  C01  C02  C03    61.95  30.0  3

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
 P6W  plan-1  C02  0.020
 P6W  plan-1  C03  0.020
 P6W  plan-1  N05  0.020
 P6W  plan-1  O04  0.020
 P6W  plan-1  H7   0.020
 P6W  plan-1  H8   0.020
 P6W  plan-2  C06  0.020
 P6W  plan-2  C07  0.020
 P6W  plan-2  N09  0.020
 P6W  plan-2  O08  0.020
 P6W  plan-2  H9   0.020
 P6W  plan-2  H10  0.020

