# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 03:38:08 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (2S)-2-amino-4-(7-hydroxy-2-oxo-2H-1-benzopyran-4-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC1=CC(=O)Oc2cc(O)ccc12)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
 DV7  DV7  '(2S)-2-amino-4-(7-hydroxy-2-oxo-2H-1-benzopyran-4-yl)butanoic acid'  L-peptide  31  19  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_DV7
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
 DV7  C    C  C      0   0.413  14.9606  51.2177  38.9539
 DV7  O    O  O      0  -0.597  15.9060  52.0286  39.0256
 DV7  CA   C  CH1    0  -0.213  15.1598  49.8305  39.6244
 DV7  N    N  NH2    0  -0.823  16.3836  49.7864  40.4132
 DV7  CB   C  CH2    0  -0.414  13.9518  49.4702  40.4892
 DV7  CG   C  CH2    0  -0.546  14.0463  48.0783  41.1298
 DV7  CD   C  CR6    0   0.303  14.0203  46.9706  40.1236
 DV7  CE2  C  CR66   0  -0.056  12.7901  46.6091  39.4591
 DV7  CZ3  C  CR16   0  -0.320  11.5403  47.1796  39.7300
 DV7  CH2  C  CR16   0  -0.373  10.4061  46.7872  39.0567
 DV7  CT   C  CR6    0   0.369  10.4880  45.7933  38.0723
 DV7  OI   O  OH1    0  -0.615   9.4222  45.3773  37.3779
 DV7  CH1  C  CR16   0  -0.418  11.7099  45.1973  37.7885
 DV7  CZ2  C  CR66   0   0.391  12.8350  45.6082  38.4833
 DV7  OH1  O  O      0  -0.469  13.9946  44.9861  38.1742
 DV7  CZ1  C  CR6    0   0.547  15.1738  45.2643  38.7955
 DV7  CE1  C  CR16   0  -0.572  15.1497  46.3026  39.7944
 DV7  OH2  O  O      0  -0.434  16.1379  44.6235  38.4546
 DV7  H2   H  HCH1   0   0.205  15.1959  49.1130  38.7890
 DV7  H3   H  HNH2   0   0.333  16.8723  48.9146  40.2635
 DV7  H4   H  HNH2   0   0.335  16.9862  50.5256  40.0731
 DV7  H6   H  HCH2   0   0.222  13.8650  50.2002  41.2991
 DV7  H7   H  HCH2   0   0.223  13.0434  49.5476  39.8916
 DV7  H8   H  HCH2   0   0.259  13.2217  47.9474  41.8350
 DV7  H9   H  HCH2   0   0.260  14.9668  48.0149  41.7124
 DV7  H10  H  HCR6   0   0.274  11.4498  47.9455  40.4882
 DV7  H11  H  HCR6   0   0.281   9.4527  47.2465  39.2896
 DV7  H12  H  HOH1   0   0.480   8.6261  45.8476  37.6531
 DV7  H13  H  HCR6   0   0.286  11.7836  44.4205  37.0378
 DV7  H14  H  HCR6   0   0.275  16.0929  46.5296  40.2732
 DV7  O1   O  OC    -1  -0.605  13.8726  51.3933  38.3727

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
 DV7  OI   CT   single    1.338  0.020  1.338
 DV7  CH1  CT   aromatic  1.389  0.020  1.389
 DV7  CH1  CZ2  aromatic  1.385  0.020  1.385
 DV7  OH1  CZ2  single    1.352  0.020  1.352
 DV7  OH1  CZ1  single    1.362  0.020  1.362
 DV7  OH2  CZ1  double    1.207  0.020  1.207
 DV7  CT   CH2  aromatic  1.401  0.020  1.401
 DV7  CZ2  CE2  aromatic  1.399  0.020  1.399
 DV7  CZ1  CE1  single    1.441  0.020  1.441
 DV7  C    CA   single    1.525  0.021  1.525
 DV7  C    O    deloc     1.231  0.020  1.231
 DV7  CH2  CZ3  aromatic  1.376  0.020  1.376
 DV7  CE2  CZ3  aromatic  1.400  0.020  1.400
 DV7  CE2  CD   single    1.444  0.020  1.444
 DV7  CE1  CD   double    1.353  0.020  1.353
 DV7  CA   CB   single    1.521  0.033  1.521
 DV7  CA   N    single    1.458  0.019  1.458
 DV7  CD   CG   single    1.497  0.020  1.497
 DV7  CB   CG   single    1.535  0.020  1.535
 DV7  CA   H2   single    0.970  0.020  1.090
 DV7  N    H3   single    0.890  0.020  1.040
 DV7  N    H4   single    0.890  0.020  1.040
 DV7  CB   H6   single    0.970  0.020  1.090
 DV7  CB   H7   single    0.970  0.020  1.090
 DV7  CG   H8   single    0.970  0.020  1.090
 DV7  CG   H9   single    0.970  0.020  1.090
 DV7  CZ3  H10  single    0.930  0.020  1.080
 DV7  CH2  H11  single    0.930  0.020  1.080
 DV7  OI   H12  single    0.850  0.020  0.980
 DV7  CH1  H13  single    0.930  0.020  1.080
 DV7  CE1  H14  single    0.930  0.020  1.080
 DV7  C    O1   deloc     1.246  0.020  1.246

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
 DV7  O1   C    CA   116.05  3.000
 DV7  O1   C    O    126.65  3.000
 DV7  CA   C    O    120.80  1.700
 DV7  H2   CA   CB   107.54  3.000
 DV7  H2   CA   N    111.30  3.000
 DV7  CB   CA   N    110.40  1.500
 DV7  H2   CA   C    104.98  3.000
 DV7  N    CA   C    111.00  2.800
 DV7  CB   CA   C    110.50  1.500
 DV7  H4   N    H3   106.99  3.000
 DV7  H4   N    CA   107.21  3.000
 DV7  H3   N    CA   110.62  3.000
 DV7  H7   CB   H6   107.00  3.000
 DV7  H7   CB   CG   110.15  3.000
 DV7  H6   CB   CG   107.52  3.000
 DV7  H7   CB   CA   109.37  3.000
 DV7  H6   CB   CA   108.92  3.000
 DV7  CG   CB   CA   113.65  3.000
 DV7  H9   CG   H8   106.56  3.000
 DV7  H9   CG   CD   109.30  3.000
 DV7  H8   CG   CD   109.39  3.000
 DV7  H9   CG   CB   109.11  3.000
 DV7  H8   CG   CB   109.36  3.000
 DV7  CD   CG   CB   112.92  3.000
 DV7  CE1  CD   CE2  118.40  3.000
 DV7  CE1  CD   CG   120.97  3.000
 DV7  CE2  CD   CG   120.62  3.000
 DV7  CZ2  CE2  CZ3  117.08  3.000
 DV7  CZ3  CE2  CD   124.70  3.000
 DV7  CZ2  CE2  CD   118.22  3.000
 DV7  H10  CZ3  CH2  118.42  3.000
 DV7  H10  CZ3  CE2  119.93  3.000
 DV7  CH2  CZ3  CE2  121.65  3.000
 DV7  H11  CH2  CT   120.21  3.000
 DV7  H11  CH2  CZ3  119.94  3.000
 DV7  CT   CH2  CZ3  119.85  3.000
 DV7  CH1  CT   OI   117.47  3.000
 DV7  CH1  CT   CH2  119.96  3.000
 DV7  OI   CT   CH2  122.57  3.000
 DV7  H12  OI   CT   110.96  3.000
 DV7  H13  CH1  CZ2  120.36  3.000
 DV7  H13  CH1  CT   120.63  3.000
 DV7  CZ2  CH1  CT   119.01  3.000
 DV7  OH1  CZ2  CH1  116.47  3.000
 DV7  OH1  CZ2  CE2  121.09  3.000
 DV7  CH1  CZ2  CE2  122.44  3.000
 DV7  CZ1  OH1  CZ2  123.00  3.000
 DV7  OH2  CZ1  CE1  126.28  3.000
 DV7  CE1  CZ1  OH1  116.68  3.000
 DV7  OH2  CZ1  OH1  117.04  3.000
 DV7  H14  CE1  CZ1  116.32  3.000
 DV7  H14  CE1  CD   121.10  3.000
 DV7  CZ1  CE1  CD   122.58  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
 DV7  CONST_01  CT   CH1  CZ2  CE2    0.00   0.0  0
 DV7  CONST_02  CT   CH2  CZ3  CE2    0.00   0.0  0
 DV7  CONST_03  CH1  CT   CH2  CZ3    0.00   0.0  0
 DV7  CONST_04  CH1  CZ2  CE2  CZ3    0.00   0.0  0
 DV7  CONST_05  CZ2  CH1  CT   CH2    0.00   0.0  0
 DV7  CONST_06  CZ2  CE2  CZ3  CH2    0.00   0.0  0
 DV7  CONST_07  OI   CT   CH2  CZ3  180.00   0.0  0
 DV7  CONST_08  CZ2  CH1  CT   OI   180.00   0.0  0
 DV7  CONST_09  H10  CZ3  CE2  CD     0.00   0.0  0
 DV7  CONST_10  H13  CH1  CZ2  CE2  180.00   0.0  0
 DV7  CONST_11  H11  CH2  CZ3  CE2  180.00   0.0  0
 DV7  Var_01    OH1  CZ1  CE1  CD     0.67  30.0  1
 DV7  Var_02    CZ1  CE1  CD   CE2    1.00  30.0  1
 DV7  Var_03    CE1  CD   CE2  CZ3  177.68  30.0  1
 DV7  Var_04    CE1  CZ1  OH1  CZ2   -1.86  30.0  1
 DV7  Var_05    CE2  CD   CG   CB   -74.20  30.0  2
 DV7  Var_06    CD   CG   CB   CA   -65.61  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
 DV7  chir_01  CA  C  CB  N  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
 DV7  plan-1  C    0.020
 DV7  plan-1  O    0.020
 DV7  plan-1  CA   0.020
 DV7  plan-1  O1   0.020
 DV7  plan-2  CD   0.020
 DV7  plan-2  CE2  0.020
 DV7  plan-2  CZ3  0.020
 DV7  plan-2  CH2  0.020
 DV7  plan-2  CT   0.020
 DV7  plan-2  OI   0.020
 DV7  plan-2  CH1  0.020
 DV7  plan-2  CZ2  0.020
 DV7  plan-2  OH1  0.020
 DV7  plan-2  H10  0.020
 DV7  plan-2  H11  0.020
 DV7  plan-2  H13  0.020
 DV7  plan-3  OH1  0.020
 DV7  plan-3  CZ1  0.020
 DV7  plan-3  CE1  0.020
 DV7  plan-3  OH2  0.020

