# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 20:43:13 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  18  9  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   1.8974  0.5172   0.6997
 CL5  C6    C  CH2   0  -0.581   0.5052  0.9185   0.3409
 CL5  O8    O  O     0  -0.387   2.4085  0.6804   1.7806
 CL5  C5    C  CH2   0  -0.254  -0.2874  1.5592   1.4643
 CL5  N4    N  NH1   0  -0.600  -1.6052  1.9401   0.9906
 CL5  C3    C  CH2   0  -0.382  -2.3913  2.5536   2.0299
 CL5  C12   C  C     0   0.518  -3.7513  2.9667   1.5291
 CL5  O13   O  O     0  -0.439  -4.1761  2.7555   0.4226
 CL5  O14   O  OH1   0  -0.595  -4.4426  3.5892   2.4771
 CL5  H7    H  H     0   0.207   2.4615  0.0437  -0.1235
 CL5  H61   H  HCH2  0   0.272   0.0013  0.0220  -0.0403
 CL5  H62   H  HCH2  0   0.276   0.5734  1.5900  -0.5227
 CL5  H51   H  HCH2  0   0.232   0.2269  2.4605   1.8085
 CL5  H52   H  HCH2  0   0.207  -0.3288  0.8774   2.3259
 CL5  HN4   H  HNH1  0   0.348  -2.0860  1.1163   0.6489
 CL5  H31   H  HCH2  0   0.275  -1.8760  3.4488   2.3923
 CL5  H32   H  HCH2  0   0.248  -2.5374  1.9179   2.9183
 CL5  HO14  H  HOH1  0   0.483  -5.3182  3.8367   2.1440

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  1.493  0.020  1.493
 CL5  C7   O8    double  1.207  0.020  1.207
 CL5  C7   H7    single  0.930  0.020  1.080
 CL5  C6   C5    single  1.517  0.020  1.517
 CL5  C6   H61   single  0.970  0.020  1.090
 CL5  C6   H62   single  0.970  0.020  1.090
 CL5  C5   N4    single  1.451  0.020  1.451
 CL5  C5   H51   single  0.970  0.020  1.090
 CL5  C5   H52   single  0.970  0.020  1.090
 CL5  N4   C3    single  1.440  0.020  1.440
 CL5  N4   HN4   single  0.890  0.020  1.040
 CL5  C3   C12   single  1.507  0.020  1.507
 CL5  C3   H31   single  0.970  0.020  1.090
 CL5  C3   H32   single  0.970  0.020  1.090
 CL5  C12  O13   double  1.204  0.020  1.204
 CL5  C12  O14   single  1.328  0.020  1.328
 CL5  O14  HO14  single  0.850  0.020  0.980

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   120.61  3.000
 CL5  H7    C7   C6   114.36  3.000
 CL5  O8    C7   C6   125.03  3.000
 CL5  H62   C6   H61  104.80  3.000
 CL5  H62   C6   C5   110.93  3.000
 CL5  H61   C6   C5   111.26  3.000
 CL5  H62   C6   C7   107.22  3.000
 CL5  H61   C6   C7   107.00  3.000
 CL5  C5    C6   C7   115.02  3.000
 CL5  H52   C5   H51  106.39  3.000
 CL5  H52   C5   N4   112.60  3.000
 CL5  H51   C5   N4   108.27  3.000
 CL5  H52   C5   C6   109.76  3.000
 CL5  H51   C5   C6   109.61  3.000
 CL5  N4    C5   C6   110.10  3.000
 CL5  HN4   N4   C3   109.31  3.000
 CL5  HN4   N4   C5   109.12  3.000
 CL5  C3    N4   C5   111.83  3.000
 CL5  H32   C3   H31  105.49  3.000
 CL5  H32   C3   C12  107.84  3.000
 CL5  H31   C3   C12  108.10  3.000
 CL5  H32   C3   N4   114.10  3.000
 CL5  H31   C3   N4   109.29  3.000
 CL5  C12   C3   N4   111.69  3.000
 CL5  O14   C12  O13  123.68  3.000
 CL5  O14   C12  C3   111.17  3.000
 CL5  O13   C12  C3   125.15  3.000
 CL5  HO14  O14  C12  110.16  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  CONST_01  HO14  O14  C12  C3  180.00   0.0  0
 CL5  Var_01    N4    C5   C6   C7  178.38  30.0  3
 CL5  Var_02    C3    N4   C5   C6  180.00  30.0  3
 CL5  Var_03    C5    C6   C7   O8   -0.82  30.0  3
 CL5  Var_04    C12   C3   N4   C5  179.13  30.0  3
 CL5  Var_05    O13   C12  C3   N4    3.77  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-1  HO14  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

