# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 14:01:30 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: N-(3-oxopropyl)glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNCCC=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
 CL5  CL5  'N-(3-oxopropyl)glycine   '  ligand  17  9  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CL5
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
 CL5  C7   C  C1     0   0.171   1.8693   0.4548   0.7658
 CL5  C6   C  CH2    0  -0.579   0.5223   0.9657   0.3790
 CL5  O8   O  O      0  -0.389   2.3483   0.5256   1.8716
 CL5  C5   C  CH2    0  -0.246  -0.2794   1.6051   1.4987
 CL5  N4   N  NH1    0  -0.598  -1.5399   2.1012   0.9930
 CL5  C3   C  CH2    0  -0.401  -2.3653   2.7028   2.0167
 CL5  C12  C  C      0   0.390  -3.8312   2.8762   1.5790
 CL5  O13  O  O      0  -0.609  -4.2269   2.1721   0.6291
 CL5  O14  O  OC    -1  -0.623  -4.5101   3.6797   2.2479
 CL5  H7   H  H      0   0.203   2.4342  -0.0120  -0.0613
 CL5  H61  H  HCH2   0   0.268  -0.0225   0.1250  -0.0686
 CL5  H62  H  HCH2   0   0.271   0.6684   1.6720  -0.4466
 CL5  H51  H  HCH2   0   0.218   0.2846   2.4453   1.9143
 CL5  H52  H  HCH2   0   0.192  -0.4055   0.8849   2.3228
 CL5  HN4  H  HNH1   0   0.329  -2.0693   1.3467   0.5734
 CL5  H31  H  HCH2   0   0.214  -1.9515   3.6759   2.2995
 CL5  H32  H  HCH2   0   0.191  -2.3797   2.1062   2.9482

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
 CL5  C7   C6   single  1.492  0.020  1.492
 CL5  C7   O8   double  1.207  0.020  1.207
 CL5  C7   H7   single  0.930  0.020  1.080
 CL5  C6   C5   single  1.518  0.020  1.518
 CL5  C6   H61  single  0.970  0.020  1.090
 CL5  C6   H62  single  0.970  0.020  1.090
 CL5  C5   N4   single  1.446  0.020  1.446
 CL5  C5   H51  single  0.970  0.020  1.090
 CL5  C5   H52  single  0.970  0.020  1.090
 CL5  N4   C3   single  1.446  0.020  1.446
 CL5  N4   HN4  single  0.890  0.020  1.040
 CL5  C3   C12  single  1.540  0.020  1.540
 CL5  C3   H31  single  0.970  0.020  1.090
 CL5  C3   H32  single  0.970  0.020  1.090
 CL5  C12  O13  deloc   1.247  0.020  1.247
 CL5  C12  O14  deloc   1.247  0.020  1.247

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
 CL5  H7   C7   O8   120.51  3.000
 CL5  H7   C7   C6   114.34  3.000
 CL5  O8   C7   C6   125.15  3.000
 CL5  H62  C6   H61  104.64  3.000
 CL5  H62  C6   C5   110.76  3.000
 CL5  H61  C6   C5   111.18  3.000
 CL5  H62  C6   C7   107.19  3.000
 CL5  H61  C6   C7   106.96  3.000
 CL5  C5   C6   C7   115.45  3.000
 CL5  H52  C5   H51  106.07  3.000
 CL5  H52  C5   N4   112.71  3.000
 CL5  H51  C5   N4   108.59  3.000
 CL5  H52  C5   C6   109.68  3.000
 CL5  H51  C5   C6   109.36  3.000
 CL5  N4   C5   C6   110.30  3.000
 CL5  HN4  N4   C3   107.75  3.000
 CL5  HN4  N4   C5   110.19  3.000
 CL5  C3   N4   C5   113.13  3.000
 CL5  H32  C3   H31  105.47  3.000
 CL5  H32  C3   C12  106.72  3.000
 CL5  H31  C3   C12  109.47  3.000
 CL5  H32  C3   N4   112.28  3.000
 CL5  H31  C3   N4   109.69  3.000
 CL5  C12  C3   N4   112.90  3.000
 CL5  O14  C12  O13  126.86  3.000
 CL5  O14  C12  C3   116.02  3.000
 CL5  O13  C12  C3   117.07  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
 CL5  Var_01  N4   C5   C6  C7   177.98  30.0  3
 CL5  Var_02  C3   N4   C5  C6   178.95  30.0  3
 CL5  Var_03  C5   C6   C7  O8    -0.61  30.0  3
 CL5  Var_04  C12  C3   N4  C5  -164.22  30.0  3
 CL5  Var_05  O13  C12  C3  N4    20.13  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
 CL5  plan-1  C3   0.020
 CL5  plan-1  C12  0.020
 CL5  plan-1  O13  0.020
 CL5  plan-1  O14  0.020
 CL5  plan-2  C7   0.020
 CL5  plan-2  C6   0.020
 CL5  plan-2  O8   0.020
 CL5  plan-2  H7   0.020

