# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 23:46:09 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (2~{S})-2-(3-azanylpropanoylamino)-3-(3-methylimidazol-4-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cncc1C[C@H](NC(=O)CCN)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
 8V3  8V3  '(2~{S})-2-(3-azanylpropanoylamino)-3-(3-methylimidazol-4-yl)propanoic acid'  ligand  33  17  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8V3
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
 8V3  C11  C  CH2   0  -0.589  -1.6614  -0.8293  -0.8334
 8V3  C12  C  CR5   0   0.313  -2.0720   0.5833  -0.6242
 8V3  C13  C  CR15  0  -0.265  -1.9588   1.6771  -1.4396
 8V3  C15  C  CR15  0   0.082  -2.8572   2.3787   0.3495
 8V3  C02  C  C     0   0.543  -0.0071  -2.6437  -0.4061
 8V3  C04  C  CH1   0  -0.161  -0.3657  -1.2005  -0.0841
 8V3  C08  C  CH2   0  -0.582   2.9241   0.6221  -0.3617
 8V3  C09  C  CH2   0  -0.270   3.6547   1.3316   0.7710
 8V3  N05  N  NH1   0  -0.642   0.6959  -0.3152  -0.4623
 8V3  N10  N  NH2   0  -0.800   4.6702   2.2186   0.2271
 8V3  N14  N  N     0  -0.446  -2.4502   2.7901  -0.8233
 8V3  N16  N  NR5   0  -0.442  -2.6535   1.0557   0.5243
 8V3  O01  O  OH1   0  -0.590  -0.7130  -3.4845   0.3351
 8V3  O03  O  O     0  -0.429   0.7767  -2.9794  -1.2534
 8V3  O07  O  O     0  -0.498   2.1189  -1.1332   1.0659
 8V3  H1   H  HCH2  0   0.293  -2.4525  -1.5161  -0.5256
 8V3  H2   H  HCH2  0   0.294  -1.5124  -0.9868  -1.9039
 8V3  H3   H  HCR5  0   0.258  -1.5540   1.7042  -2.4411
 8V3  H4   H  HCR5  0   0.279  -3.3125   2.9895   1.1153
 8V3  H5   H  HCH1  0   0.291  -0.5397  -1.1292   0.9931
 8V3  H6   H  HCH2  0   0.271   3.6468   0.0632  -0.9633
 8V3  H7   H  HCH2  0   0.249   2.4630   1.3566  -1.0271
 8V3  H8   H  HCH2  0   0.204   2.9182   1.8402   1.4075
 8V3  H9   H  HCH2  0   0.227   4.1487   0.5889   1.3986
 8V3  H10  H  HCH3  0   0.264  -3.6423  -0.5591   1.4164
 8V3  H11  H  HCH3  0   0.261  -2.1346  -0.0798   2.2152
 8V3  H12  H  HCH3  0   0.276  -3.5784   0.9217   2.3734
 8V3  H13  H  HNH1  0   0.403   0.5451   0.3360  -1.2163
 8V3  H14  H  HNH2  0   0.341   4.2242   2.9910  -0.2526
 8V3  H15  H  HNH2  0   0.350   5.1918   2.6351   0.9875
 8V3  H18  H  HOH1  0   0.486  -0.5231  -4.4003   0.0805
 8V3  C06  C  C     0   0.566   1.8923  -0.3525   0.1520
 8V3  C17  C  CH3   0  -0.537  -3.0168   0.2875   1.6933

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
 8V3  C15  N14  aromatic  1.308  0.020  1.308
 8V3  C15  N16  aromatic  1.350  0.020  1.350
 8V3  N14  C13  aromatic  1.364  0.020  1.364
 8V3  O03  C02  double    1.202  0.020  1.202
 8V3  O01  C02  single    1.325  0.020  1.325
 8V3  N16  C17  single    1.445  0.020  1.445
 8V3  N16  C12  aromatic  1.371  0.020  1.371
 8V3  C13  C12  aromatic  1.369  0.020  1.369
 8V3  C02  C04  single    1.522  0.020  1.522
 8V3  C12  C11  single    1.486  0.020  1.486
 8V3  C04  C11  single    1.542  0.020  1.542
 8V3  C04  N05  single    1.433  0.020  1.433
 8V3  N05  C06  single    1.345  0.020  1.345
 8V3  O07  C06  double    1.223  0.020  1.223
 8V3  C06  C08  single    1.510  0.020  1.510
 8V3  C08  C09  single    1.523  0.020  1.523
 8V3  C09  N10  single    1.454  0.020  1.454
 8V3  C11  H1   single    0.970  0.020  1.090
 8V3  C11  H2   single    0.970  0.020  1.090
 8V3  C13  H3   single    0.930  0.020  1.080
 8V3  C15  H4   single    0.930  0.020  1.080
 8V3  C04  H5   single    0.970  0.020  1.090
 8V3  C08  H6   single    0.970  0.020  1.090
 8V3  C08  H7   single    0.970  0.020  1.090
 8V3  C09  H8   single    0.970  0.020  1.090
 8V3  C09  H9   single    0.970  0.020  1.090
 8V3  C17  H10  single    0.970  0.020  1.090
 8V3  C17  H11  single    0.970  0.020  1.090
 8V3  C17  H12  single    0.970  0.020  1.090
 8V3  N05  H13  single    0.860  0.020  1.020
 8V3  N10  H14  single    0.890  0.020  1.040
 8V3  N10  H15  single    0.890  0.020  1.040
 8V3  O01  H18  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
 8V3  H2   C11  H1   106.52  3.000
 8V3  H2   C11  C04  109.08  3.000
 8V3  H1   C11  C04  108.69  3.000
 8V3  H2   C11  C12  108.22  3.000
 8V3  H1   C11  C12  110.98  3.000
 8V3  C04  C11  C12  113.12  3.000
 8V3  N16  C12  C13  104.99  3.000
 8V3  C13  C12  C11  130.76  3.000
 8V3  N16  C12  C11  124.23  3.000
 8V3  H3   C13  N14  122.22  3.000
 8V3  H3   C13  C12  127.09  3.000
 8V3  N14  C13  C12  110.68  3.000
 8V3  H4   C15  N16  121.73  3.000
 8V3  H4   C15  N14  126.09  3.000
 8V3  N16  C15  N14  112.18  3.000
 8V3  O03  C02  O01  124.38  3.000
 8V3  O01  C02  C04  110.98  3.000
 8V3  O03  C02  C04  124.58  3.000
 8V3  H5   C04  N05  109.73  3.000
 8V3  H5   C04  C02  107.93  3.000
 8V3  N05  C04  C02  110.83  3.000
 8V3  H5   C04  C11  109.22  3.000
 8V3  N05  C04  C11  110.21  3.000
 8V3  C02  C04  C11  108.88  3.000
 8V3  H7   C08  H6   106.70  3.000
 8V3  H7   C08  C09  110.00  3.000
 8V3  H6   C08  C09  109.27  3.000
 8V3  H7   C08  C06  110.65  3.000
 8V3  H6   C08  C06  107.99  3.000
 8V3  C09  C08  C06  112.06  3.000
 8V3  H9   C09  H8   106.59  3.000
 8V3  H9   C09  N10  108.32  3.000
 8V3  H8   C09  N10  113.75  3.000
 8V3  H9   C09  C08  109.15  3.000
 8V3  H8   C09  C08  108.96  3.000
 8V3  N10  C09  C08  109.93  3.000
 8V3  H13  N05  C06  119.51  3.000
 8V3  H13  N05  C04  119.07  3.000
 8V3  C06  N05  C04  121.40  3.000
 8V3  H15  N10  H14  105.61  3.000
 8V3  H15  N10  C09  109.27  3.000
 8V3  H14  N10  C09  109.57  3.000
 8V3  C15  N14  C13  105.11  3.000
 8V3  C17  N16  C15  126.00  3.000
 8V3  C17  N16  C12  126.94  3.000
 8V3  C15  N16  C12  107.04  3.000
 8V3  H18  O01  C02  110.39  3.000
 8V3  O07  C06  N05  121.58  3.000
 8V3  O07  C06  C08  122.67  3.000
 8V3  N05  C06  C08  115.76  3.000
 8V3  H12  C17  H11  108.41  3.000
 8V3  H12  C17  H10  108.44  3.000
 8V3  H11  C17  H10  108.98  3.000
 8V3  H12  C17  N16  109.02  3.000
 8V3  H11  C17  N16  111.31  3.000
 8V3  H10  C17  N16  110.62  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
 8V3  CONST_01  N14  C15  N16  C12    0.00   0.0  0
 8V3  CONST_02  C15  N14  C13  C12    0.00   0.0  0
 8V3  CONST_03  N16  C15  N14  C13    0.00   0.0  0
 8V3  CONST_04  C15  N16  C12  C13    0.00   0.0  0
 8V3  CONST_05  N16  C12  C13  N14    0.00   0.0  0
 8V3  CONST_06  C15  N16  C12  C11  180.00   0.0  0
 8V3  CONST_07  N14  C13  C12  C11  180.00   0.0  0
 8V3  CONST_08  C17  N16  C12  C13  180.00   0.0  0
 8V3  CONST_09  N14  C15  N16  C17  180.00   0.0  0
 8V3  CONST_10  H4   C15  N16  C12  180.00   0.0  0
 8V3  CONST_11  H3   C13  N14  C15  180.00   0.0  0
 8V3  CONST_12  O07  C06  N05  C04    0.00   0.0  0
 8V3  CONST_13  C08  C06  N05  C04  180.00   0.0  0
 8V3  CONST_14  H13  N05  C06  C08    0.00   0.0  0
 8V3  CONST_15  H18  O01  C02  C04  180.00   0.0  0
 8V3  Var_01    C04  C11  C12  C13  102.93  30.0  2
 8V3  Var_02    H10  C17  N16  C12  -53.13  30.0  2
 8V3  Var_03    N10  C09  C08  C06  177.82  30.0  3
 8V3  Var_04    N05  C06  C08  C09  134.98  30.0  1
 8V3  Var_05    H14  N10  C09  C08   68.66  30.0  3

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
 8V3  chir_01  C04  C02  C11  N05  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
 8V3  plan-1  C11  0.020
 8V3  plan-1  C12  0.020
 8V3  plan-1  C13  0.020
 8V3  plan-1  C15  0.020
 8V3  plan-1  N14  0.020
 8V3  plan-1  N16  0.020
 8V3  plan-1  H3   0.020
 8V3  plan-1  H4   0.020
 8V3  plan-1  C17  0.020
 8V3  plan-2  C04  0.020
 8V3  plan-2  C08  0.020
 8V3  plan-2  N05  0.020
 8V3  plan-2  O07  0.020
 8V3  plan-2  H13  0.020
 8V3  plan-2  C06  0.020
 8V3  plan-3  C02  0.020
 8V3  plan-3  C04  0.020
 8V3  plan-3  O01  0.020
 8V3  plan-3  O03  0.020
 8V3  plan-3  H18  0.020

