# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 23:38:44 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: N-(5-chloropyridin-2-yl)-2-oxo-2-(pyrrolidin-1-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(NC(=O)C(=O)N2CCCC2)nc1
#
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
 5HO  5HO  N-(5-chloropyridin-2-yl)-2-oxo-2-(pyrrolidin-1-yl)acetamide  ligand  29  17  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5HO
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
 5HO  C4   C   CR6   0  -0.127   4.1146   0.0833  -0.1646
 5HO  C5   C   CR16  0  -0.029   3.2058  -0.9329   0.0674
 5HO  C6   C   C     0   0.455  -2.2790   0.6359   0.3038
 5HO  N1   N   N     0  -0.421   1.8978  -0.7234   0.1276
 5HO  C7   C   CH2   0  -0.266  -4.6848   0.5828   0.2720
 5HO  C8   C   CH2   0  -0.488  -5.6893  -0.5602   0.2877
 5HO  N2   N   NT    0  -0.466  -3.3861  -0.0956   0.2377
 5HO  C9   C   CH2   0  -0.476  -4.9731  -1.6572  -0.4890
 5HO  C10  C   CH2   0  -0.262  -3.5313  -1.5354  -0.0118
 5HO  O1   O   O     0  -0.493  -2.2829   1.8622   0.3607
 5HO  C    C   C     0   0.453  -0.9264  -0.0978   0.3534
 5HO  O    O   O     0  -0.410  -0.8139  -1.2537   0.6894
 5HO  C1   C   CR6   0   0.539   1.4446   0.5058  -0.0365
 5HO  CL   CL  CL    0  -0.116   5.8039  -0.2602  -0.2324
 5HO  C3   C   CR16  0  -0.086   3.6452   1.3776  -0.3433
 5HO  C2   C   CR16  0  -0.400   2.2867   1.5967  -0.2778
 5HO  H1   H   HCR6  0   0.286   3.5438  -1.9533   0.2068
 5HO  H3   H   HCH2  0   0.257  -4.7581   1.2304   1.1455
 5HO  H4   H   HCH2  0   0.242  -5.8792  -0.8845   1.3130
 5HO  H5   H   HCH2  0   0.257  -6.6421  -0.2694  -0.1518
 5HO  H6   H   HCH2  0   0.255  -5.3746  -2.6526  -0.3032
 5HO  H7   H   HCH2  0   0.242  -5.0343  -1.4653  -1.5625
 5HO  H8   H   HCH2  0   0.259  -2.8189  -1.8874  -0.7538
 5HO  H9   H   HCH2  0   0.247  -3.3767  -2.1014   0.9076
 5HO  H11  H   HCR6  0   0.300   4.3246   2.1984  -0.5278
 5HO  H12  H   HCR6  0   0.295   1.8857   2.5929  -0.4108
 5HO  N    N   NH1   0  -0.722   0.0783   0.7469   0.0156
 5HO  H2   H   HCH2  0   0.247  -4.8019   1.2092  -0.6164
 5HO  H10  H   HNH1  0   0.428  -0.2133   1.6997  -0.1591

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
 5HO  CL   C4   single    1.725  0.020  1.725
 5HO  C4   C3   aromatic  1.388  0.020  1.388
 5HO  C4   C5   aromatic  1.383  0.020  1.383
 5HO  C3   C2   aromatic  1.378  0.020  1.378
 5HO  C5   N1   aromatic  1.326  0.020  1.326
 5HO  C2   C1   aromatic  1.399  0.020  1.399
 5HO  N1   C1   aromatic  1.320  0.020  1.320
 5HO  C1   N    single    1.388  0.020  1.388
 5HO  N    C    single    1.355  0.020  1.355
 5HO  O1   C6   double    1.228  0.020  1.228
 5HO  C    C6   single    1.540  0.020  1.540
 5HO  C    O    double    1.209  0.020  1.209
 5HO  C6   N2   single    1.329  0.020  1.329
 5HO  N2   C7   single    1.466  0.020  1.466
 5HO  N2   C10  single    1.468  0.020  1.468
 5HO  C7   C8   single    1.522  0.020  1.522
 5HO  C10  C9   single    1.524  0.020  1.524
 5HO  C9   C8   single    1.523  0.020  1.523
 5HO  C5   H1   single    0.930  0.020  1.080
 5HO  C7   H2   single    0.970  0.020  1.090
 5HO  C7   H3   single    0.970  0.020  1.090
 5HO  C8   H4   single    0.970  0.020  1.090
 5HO  C8   H5   single    0.970  0.020  1.090
 5HO  C9   H6   single    0.970  0.020  1.090
 5HO  C9   H7   single    0.970  0.020  1.090
 5HO  C10  H8   single    0.970  0.020  1.090
 5HO  C10  H9   single    0.970  0.020  1.090
 5HO  N    H10  single    0.860  0.020  1.020
 5HO  C3   H11  single    0.930  0.020  1.080
 5HO  C2   H12  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
 5HO  C3   C4   CL   120.78  3.000
 5HO  C3   C4   C5   118.98  3.000
 5HO  CL   C4   C5   120.25  3.000
 5HO  H1   C5   N1   116.78  3.000
 5HO  H1   C5   C4   120.56  3.000
 5HO  N1   C5   C4   122.67  3.000
 5HO  C    C6   O1   118.51  3.000
 5HO  C    C6   N2   118.12  3.000
 5HO  O1   C6   N2   123.34  3.000
 5HO  C1   N1   C5   118.68  3.000
 5HO  H3   C7   H2   107.68  3.000
 5HO  H3   C7   N2   110.70  3.000
 5HO  H2   C7   N2   109.94  3.000
 5HO  H3   C7   C8   113.18  3.000
 5HO  H2   C7   C8   111.59  3.000
 5HO  N2   C7   C8   103.74  3.000
 5HO  H5   C8   H4   107.83  3.000
 5HO  H5   C8   C9   113.46  3.000
 5HO  H4   C8   C9   110.28  3.000
 5HO  H5   C8   C7   111.89  3.000
 5HO  H4   C8   C7   110.34  3.000
 5HO  C9   C8   C7   103.02  3.000
 5HO  C10  N2   C7   111.73  3.000
 5HO  C10  N2   C6   129.10  3.000
 5HO  C7   N2   C6   118.84  3.000
 5HO  H7   C9   H6   107.92  3.000
 5HO  H7   C9   C10  110.29  3.000
 5HO  H6   C9   C10  111.62  3.000
 5HO  H7   C9   C8   110.38  3.000
 5HO  H6   C9   C8   113.44  3.000
 5HO  C10  C9   C8   103.16  3.000
 5HO  H9   C10  H8   108.33  3.000
 5HO  H9   C10  C9   110.89  3.000
 5HO  H8   C10  C9   112.36  3.000
 5HO  H9   C10  N2   110.58  3.000
 5HO  H8   C10  N2   111.63  3.000
 5HO  C9   C10  N2   103.01  3.000
 5HO  N    C    O    126.60  3.000
 5HO  O    C    C6   123.11  3.000
 5HO  N    C    C6   110.26  3.000
 5HO  C2   C1   N    117.61  3.000
 5HO  N    C1   N1   119.65  3.000
 5HO  C2   C1   N1   122.73  3.000
 5HO  H11  C3   C2   120.46  3.000
 5HO  H11  C3   C4   121.14  3.000
 5HO  C2   C3   C4   118.40  3.000
 5HO  H12  C2   C3   120.40  3.000
 5HO  H12  C2   C1   121.06  3.000
 5HO  C3   C2   C1   118.54  3.000
 5HO  H10  N    C1   116.15  3.000
 5HO  H10  N    C    114.61  3.000
 5HO  C1   N    C    129.10  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
 5HO  CONST_01  C1   C2   C3  C4     0.00   0.0  0
 5HO  CONST_02  C1   N1   C5  C4     0.00   0.0  0
 5HO  CONST_03  C2   C3   C4  C5     0.00   0.0  0
 5HO  CONST_04  C2   C1   N1  C5     0.00   0.0  0
 5HO  CONST_05  C3   C4   C5  N1     0.00   0.0  0
 5HO  CONST_06  C3   C2   C1  N1     0.00   0.0  0
 5HO  CONST_07  N    C1   N1  C5   180.00   0.0  0
 5HO  CONST_08  CL   C4   C5  N1   180.00   0.0  0
 5HO  CONST_09  C3   C2   C1  N    180.00   0.0  0
 5HO  CONST_10  C2   C3   C4  CL   180.00   0.0  0
 5HO  CONST_11  H12  C2   C3  C4   180.00   0.0  0
 5HO  CONST_12  H11  C3   C4  C5   180.00   0.0  0
 5HO  CONST_13  H1   C5   N1  C1   180.00   0.0  0
 5HO  CONST_14  O1   C6   N2  C7     0.00   0.0  0
 5HO  CONST_15  C    C6   N2  C7   180.00   0.0  0
 5HO  CONST_16  O1   C6   N2  C10  180.00   0.0  0
 5HO  CONST_17  C    C6   N2  C10    0.00   0.0  0
 5HO  CONST_18  C    N    C1  N1     0.00   0.0  0
 5HO  CONST_19  C2   C1   N   C    180.00   0.0  0
 5HO  CONST_20  H10  N    C1  N1   180.00   0.0  0
 5HO  CONST_21  C1   N    C   C6   180.00   0.0  0
 5HO  CONST_23  C1   N    C   O      0.00   0.0  0
 5HO  Var_01    C9   C10  N2  C7    14.17  30.0  1
 5HO  Var_02    C10  C9   C8  C7    39.43  30.0  1
 5HO  Var_03    C10  N2   C7  C8    10.28  30.0  1
 5HO  Var_04    N2   C10  C9  C8   -32.78  30.0  1
 5HO  Var_05    C9   C8   C7  N2   -30.49  30.0  1

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
 5HO  plan-1  C4   0.020
 5HO  plan-1  C5   0.020
 5HO  plan-1  N1   0.020
 5HO  plan-1  C1   0.020
 5HO  plan-1  CL   0.020
 5HO  plan-1  C3   0.020
 5HO  plan-1  C2   0.020
 5HO  plan-1  H1   0.020
 5HO  plan-1  H11  0.020
 5HO  plan-1  H12  0.020
 5HO  plan-1  N    0.020
 5HO  plan-2  C6   0.020
 5HO  plan-2  C7   0.020
 5HO  plan-2  N2   0.020
 5HO  plan-2  C10  0.020
 5HO  plan-2  O1   0.020
 5HO  plan-2  C    0.020
 5HO  plan-2  O    0.020
 5HO  plan-2  C1   0.020
 5HO  plan-2  N    0.020
 5HO  plan-2  H10  0.020

