# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 12:00:09 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 4-[(S)-amino(carboxy)methyl]benzene-1,2-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](C(O)=O)c1ccc(C(O)=O)c(c1)C(O)=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
 HVG  HVG  '4-[(S)-amino(carboxy)methyl]benzene-1,2-dicarboxylic acid'  ligand  23  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HVG
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
 HVG  C7   C  C      0   0.357   2.8441   1.1189   0.5025
 HVG  C6   C  CR6    0   0.109  -1.2719   0.2562  -0.5474
 HVG  C1   C  CR16   0  -0.279   0.4995   1.8135  -0.0445
 HVG  C5   C  CR6    0  -0.047   0.9983  -0.5311  -0.1334
 HVG  C4   C  CR6    0  -0.090   1.4278   0.7848   0.0744
 HVG  C3   C  CR16   0  -0.342  -0.3402  -0.7735  -0.4231
 HVG  C2   C  CR16   0  -0.338  -0.8327   1.5596  -0.3456
 HVG  C9   C  C      0   0.412  -3.3936  -0.4652   0.4835
 HVG  C10  C  CH1    0  -0.257  -2.7241  -0.0585  -0.8583
 HVG  N11  N  NH2    0  -0.800  -3.4752   1.0081  -1.4913
 HVG  O12  O  O      0  -0.606   3.3180   0.4316   1.4268
 HVG  O13  O  OC    -1  -0.614   1.6576  -2.7029   0.5156
 HVG  O15  O  OC    -1  -0.614   3.3898   2.0853  -0.0685
 HVG  O16  O  O      0  -0.609   2.9662  -1.5660  -0.8886
 HVG  H1   H  HCR6   0   0.231   0.8198   2.8368   0.1114
 HVG  H2   H  HCR6   0   0.223  -0.6687  -1.7947  -0.5825
 HVG  H3   H  HCR6   0   0.222  -1.5248   2.3890  -0.4304
 HVG  H4   H  HCH1   0   0.221  -2.7378  -0.9328  -1.5166
 HVG  H5   H  HNH2   0   0.335  -3.6923   1.7073  -0.7924
 HVG  H6   H  HNH2   0   0.335  -2.9143   1.4613  -2.2022
 HVG  C8   C  C      0   0.358   1.9694  -1.6977  -0.1537
 HVG  O14  O  O      0  -0.603  -3.9716   0.4437   1.1103
 HVG  O17  O  OC    -1  -0.603  -3.2568  -1.6509   0.8337

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
 HVG  N11  C10  single    1.450  0.020  1.450
 HVG  O14  C9   deloc     1.246  0.020  1.246
 HVG  C10  C9   single    1.554  0.020  1.554
 HVG  C10  C6   single    1.518  0.020  1.518
 HVG  C9   O17  deloc     1.244  0.020  1.244
 HVG  C3   C6   aromatic  1.394  0.020  1.394
 HVG  C3   C5   aromatic  1.391  0.020  1.391
 HVG  C6   C2   aromatic  1.390  0.020  1.390
 HVG  O16  C8   deloc     1.245  0.020  1.245
 HVG  C8   C5   single    1.518  0.020  1.518
 HVG  C8   O13  deloc     1.247  0.020  1.247
 HVG  C5   C4   aromatic  1.400  0.020  1.400
 HVG  C2   C1   aromatic  1.389  0.020  1.389
 HVG  C4   C1   aromatic  1.391  0.020  1.391
 HVG  C4   C7   single    1.517  0.020  1.517
 HVG  C7   O12  deloc     1.246  0.020  1.246
 HVG  C7   O15  deloc     1.248  0.020  1.248
 HVG  C1   H1   single    0.930  0.020  1.080
 HVG  C3   H2   single    0.930  0.020  1.080
 HVG  C2   H3   single    0.930  0.020  1.080
 HVG  C10  H4   single    0.970  0.020  1.090
 HVG  N11  H5   single    0.890  0.020  1.040
 HVG  N11  H6   single    0.890  0.020  1.040

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
 HVG  O15  C7   O12  126.90  3.000
 HVG  O15  C7   C4   116.72  3.000
 HVG  O12  C7   C4   116.31  3.000
 HVG  C10  C6   C2   121.75  3.000
 HVG  C2   C6   C3   117.93  3.000
 HVG  C10  C6   C3   120.29  3.000
 HVG  H1   C1   C2   119.16  3.000
 HVG  H1   C1   C4   119.27  3.000
 HVG  C2   C1   C4   121.57  3.000
 HVG  C8   C5   C3   118.61  3.000
 HVG  C8   C5   C4   121.88  3.000
 HVG  C3   C5   C4   119.35  3.000
 HVG  C5   C4   C1   118.55  3.000
 HVG  C1   C4   C7   118.98  3.000
 HVG  C5   C4   C7   122.37  3.000
 HVG  H2   C3   C5   119.10  3.000
 HVG  H2   C3   C6   118.68  3.000
 HVG  C5   C3   C6   122.21  3.000
 HVG  H3   C2   C1   119.32  3.000
 HVG  H3   C2   C6   120.30  3.000
 HVG  C1   C2   C6   120.38  3.000
 HVG  O17  C9   O14  127.21  3.000
 HVG  O17  C9   C10  116.44  3.000
 HVG  O14  C9   C10  116.31  3.000
 HVG  H4   C10  N11  108.58  3.000
 HVG  H4   C10  C9   107.75  3.000
 HVG  N11  C10  C9   110.27  3.000
 HVG  H4   C10  C6   107.50  3.000
 HVG  C9   C10  C6   106.83  3.000
 HVG  N11  C10  C6   115.63  3.000
 HVG  H6   N11  H5   107.12  3.000
 HVG  H6   N11  C10  110.41  3.000
 HVG  H5   N11  C10  108.53  3.000
 HVG  O16  C8   O13  127.01  3.000
 HVG  O13  C8   C5   116.89  3.000
 HVG  O16  C8   C5   116.01  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
 HVG  CONST_01  C4   C5  C3  C6    0.00   0.0  0
 HVG  CONST_02  C4   C1  C2  C6    0.00   0.0  0
 HVG  CONST_03  C3   C6  C2  C1    0.00   0.0  0
 HVG  CONST_04  C3   C5  C4  C1    0.00   0.0  0
 HVG  CONST_05  C2   C6  C3  C5    0.00   0.0  0
 HVG  CONST_06  C2   C1  C4  C5    0.00   0.0  0
 HVG  CONST_07  C3   C5  C4  C7  180.00   0.0  0
 HVG  CONST_08  C2   C1  C4  C7  180.00   0.0  0
 HVG  CONST_09  C8   C5  C3  C6  180.00   0.0  0
 HVG  CONST_10  C10  C6  C2  C1  180.00   0.0  0
 HVG  CONST_11  C8   C5  C4  C1  180.00   0.0  0
 HVG  CONST_12  C10  C6  C3  C5  180.00   0.0  0
 HVG  CONST_13  H1   C1  C2  C6  180.00   0.0  0
 HVG  CONST_14  H2   C3  C5  C4  180.00   0.0  0
 HVG  CONST_15  H3   C2  C1  C4  180.00   0.0  0
 HVG  Var_01    O12  C7  C4  C1  130.65  30.0  2
 HVG  Var_02    O16  C8  C5  C4  -50.14  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
 HVG  chir_01  C10  N11  C9  C6  positiv

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
 HVG  plan-1  C7   0.020
 HVG  plan-1  C6   0.020
 HVG  plan-1  C1   0.020
 HVG  plan-1  C5   0.020
 HVG  plan-1  C4   0.020
 HVG  plan-1  C3   0.020
 HVG  plan-1  C2   0.020
 HVG  plan-1  C10  0.020
 HVG  plan-1  H1   0.020
 HVG  plan-1  H2   0.020
 HVG  plan-1  H3   0.020
 HVG  plan-1  C8   0.020
 HVG  plan-2  C7   0.020
 HVG  plan-2  C4   0.020
 HVG  plan-2  O12  0.020
 HVG  plan-2  O15  0.020
 HVG  plan-3  C9   0.020
 HVG  plan-3  C10  0.020
 HVG  plan-3  O14  0.020
 HVG  plan-3  O17  0.020
 HVG  plan-4  C5   0.020
 HVG  plan-4  O13  0.020
 HVG  plan-4  O16  0.020
 HVG  plan-4  C8   0.020

