# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 06:01:26 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: L-beta-aspartyl-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)N[C@@H](Cc1[nH]cnc1)C(O)=O)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
 BDH  BDH  L-beta-aspartyl-L-histidine  ligand  31  19  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BDH
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
 BDH  O1    O  OC    -1  -0.622  -0.4739   0.1438   4.7607
 BDH  O2    O  O      0  -0.603   1.4773  -0.8801   4.4310
 BDH  O3    O  O      0  -0.505  -0.3481   1.5537   0.1881
 BDH  O4    O  O      0  -0.605  -3.1957  -0.4469  -3.3805
 BDH  O5    O  OC    -1  -0.594  -3.2006  -1.6806  -1.5204
 BDH  N1    N  NH2    0  -0.801   1.9432   0.4341   2.1291
 BDH  N2    N  NH1    0  -0.632  -1.0653  -0.4758  -0.5036
 BDH  C1    C  CH1    0  -0.204   0.5977   0.4833   2.6732
 BDH  C2    C  CH2    0  -0.592  -0.4638  -0.2143   1.8133
 BDH  C3    C  C      0   0.555  -0.6102   0.3810   0.4265
 BDH  C4    C  C      0   0.405   0.5404  -0.1342   4.0886
 BDH  C5    C  CH1    0  -0.206  -1.4266  -0.1091  -1.8496
 BDH  C7    C  C      0   0.420  -2.7392  -0.8100  -2.2817
 BDH  CB    C  CH2    0  -0.526  -0.3145  -0.4650  -2.8573
 BDH  CG    C  CR5    0   0.330   1.0198   0.0790  -2.4972
 BDH  ND1   N  NR15   0  -0.604   1.8409  -0.4843  -1.5610
 BDH  CD2   C  CR15   0  -0.270   1.7058   1.1809  -2.9305
 BDH  CE1   C  CR15   0   0.058   2.9502   0.2777  -1.4619
 BDH  NE2   N  N      0  -0.444   2.9028   1.2970  -2.2800
 BDH  HN11  H  HNH2   0   0.325   2.2772  -0.5210   2.1461
 BDH  HN12  H  HNH2   0   0.336   1.9376   0.7364   1.1635
 BDH  HN2   H  HNH1   0   0.381  -1.3884  -1.3843  -0.2060
 BDH  H1    H  HCH1   0   0.214   0.3126   1.5357   2.7619
 BDH  H21   H  HCH2   0   0.265  -1.4384  -0.1413   2.3059
 BDH  H22   H  HCH2   0   0.242  -0.2370  -1.2829   1.7377
 BDH  H5    H  HCH1   0   0.249  -1.5754   0.9718  -1.8826
 BDH  HB1   H  HCH2   0   0.256  -0.6001  -0.0756  -3.8344
 BDH  HB2   H  HCH2   0   0.246  -0.2560  -1.5537  -2.9564
 BDH  HD1   H  HNR5   0   0.407   1.6503  -1.3238  -1.0374
 BDH  HD2   H  HCR5   0   0.243   1.3890   1.8942  -3.6772
 BDH  HE1   H  HCR5   0   0.275   3.7619   0.0333  -0.7935

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
 BDH  O1   C4    deloc     1.248  0.020  1.248
 BDH  O2   C4    deloc     1.246  0.020  1.246
 BDH  O3   C3    double    1.225  0.020  1.225
 BDH  O4   C7    deloc     1.244  0.020  1.244
 BDH  O5   C7    deloc     1.245  0.020  1.245
 BDH  N1   C1    single    1.452  0.020  1.452
 BDH  N1   HN11  single    0.890  0.020  1.040
 BDH  N1   HN12  single    0.890  0.020  1.040
 BDH  N2   C3    single    1.344  0.020  1.344
 BDH  N2   C5    single    1.441  0.020  1.441
 BDH  N2   HN2   single    0.860  0.020  1.020
 BDH  C1   C2    single    1.534  0.020  1.534
 BDH  C1   C4    single    1.545  0.020  1.545
 BDH  C1   H1    single    0.970  0.020  1.090
 BDH  C2   C3    single    1.516  0.020  1.516
 BDH  C2   H21   single    0.970  0.020  1.090
 BDH  C2   H22   single    0.970  0.020  1.090
 BDH  C5   C7    single    1.549  0.020  1.549
 BDH  C5   CB    single    1.542  0.020  1.542
 BDH  C5   H5    single    0.970  0.020  1.090
 BDH  CB   CG    single    1.485  0.020  1.485
 BDH  CB   HB1   single    0.970  0.020  1.090
 BDH  CB   HB2   single    0.970  0.020  1.090
 BDH  CG   ND1   aromatic  1.367  0.020  1.367
 BDH  CG   CD2   aromatic  1.368  0.020  1.368
 BDH  ND1  CE1   aromatic  1.349  0.020  1.349
 BDH  ND1  HD1   single    0.860  0.020  1.020
 BDH  CD2  NE2   aromatic  1.367  0.020  1.367
 BDH  CD2  HD2   single    0.930  0.020  1.080
 BDH  CE1  NE2   aromatic  1.308  0.020  1.308
 BDH  CE1  HE1   single    0.930  0.020  1.080

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
 BDH  HN12  N1   HN11  107.45  3.000
 BDH  HN12  N1   C1    110.01  3.000
 BDH  HN11  N1   C1    109.36  3.000
 BDH  HN2   N2   C5    115.10  3.000
 BDH  HN2   N2   C3    118.58  3.000
 BDH  C5    N2   C3    124.68  3.000
 BDH  H1    C1   C4    107.49  3.000
 BDH  H1    C1   C2    107.61  3.000
 BDH  C4    C1   C2    107.82  3.000
 BDH  H1    C1   N1    107.73  3.000
 BDH  C4    C1   N1    111.34  3.000
 BDH  C2    C1   N1    114.57  3.000
 BDH  H22   C2   H21   106.29  3.000
 BDH  H22   C2   C3    109.88  3.000
 BDH  H21   C2   C3    107.43  3.000
 BDH  H22   C2   C1    109.82  3.000
 BDH  H21   C2   C1    109.49  3.000
 BDH  C3    C2   C1    113.64  3.000
 BDH  C2    C3   N2    114.54  3.000
 BDH  C2    C3   O3    122.22  3.000
 BDH  N2    C3   O3    123.24  3.000
 BDH  C1    C4   O2    117.59  3.000
 BDH  C1    C4   O1    115.74  3.000
 BDH  O2    C4   O1    126.63  3.000
 BDH  H5    C5   CB    107.88  3.000
 BDH  H5    C5   C7    108.90  3.000
 BDH  CB    C5   C7    108.92  3.000
 BDH  H5    C5   N2    108.32  3.000
 BDH  CB    C5   N2    111.76  3.000
 BDH  C7    C5   N2    110.96  3.000
 BDH  C5    C7   O5    117.37  3.000
 BDH  C5    C7   O4    115.16  3.000
 BDH  O5    C7   O4    127.45  3.000
 BDH  HB2   CB   HB1   106.75  3.000
 BDH  HB2   CB   CG    109.77  3.000
 BDH  HB1   CB   CG    108.78  3.000
 BDH  HB2   CB   C5    109.09  3.000
 BDH  HB1   CB   C5    108.32  3.000
 BDH  CG    CB   C5    113.88  3.000
 BDH  CD2   CG   ND1   104.34  3.000
 BDH  CD2   CG   CB    131.95  3.000
 BDH  ND1   CG   CB    123.70  3.000
 BDH  HD1   ND1  CE1   126.01  3.000
 BDH  HD1   ND1  CG    125.85  3.000
 BDH  CE1   ND1  CG    108.14  3.000
 BDH  HD2   CD2  NE2   121.98  3.000
 BDH  HD2   CD2  CG    127.13  3.000
 BDH  NE2   CD2  CG    110.89  3.000
 BDH  HE1   CE1  NE2   126.22  3.000
 BDH  HE1   CE1  ND1   122.39  3.000
 BDH  NE2   CE1  ND1   111.37  3.000
 BDH  CE1   NE2  CD2   105.26  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
 BDH  CONST_01  NE2  CE1  ND1  CG     0.00   0.0  0
 BDH  CONST_02  CE1  NE2  CD2  CG     0.00   0.0  0
 BDH  CONST_03  NE2  CD2  CG   ND1    0.00   0.0  0
 BDH  CONST_04  CD2  NE2  CE1  ND1    0.00   0.0  0
 BDH  CONST_05  CE1  ND1  CG   CD2    0.00   0.0  0
 BDH  CONST_06  CE1  ND1  CG   CB   180.00   0.0  0
 BDH  CONST_07  NE2  CD2  CG   CB   180.00   0.0  0
 BDH  CONST_08  HE1  CE1  ND1  CG   180.00   0.0  0
 BDH  CONST_09  HD2  CD2  CG   ND1  180.00   0.0  0
 BDH  CONST_10  HD1  ND1  CG   CD2  180.00   0.0  0
 BDH  CONST_11  C5   N2   C3   O3     0.00   0.0  0
 BDH  CONST_12  C5   N2   C3   C2   180.00   0.0  0
 BDH  CONST_13  HN2  N2   C3   O3   180.00   0.0  0
 BDH  Var_01    ND1  CG   CB   C5    79.10  30.0  2
 BDH  Var_02    C1   C2   C3   O3   -27.39  30.0  1

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
 BDH  chir_01  C1  N1  C2  C4  negativ
 BDH  chir_02  C5  N2  C7  CB  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
 BDH  plan-1  CB   0.020
 BDH  plan-1  CG   0.020
 BDH  plan-1  ND1  0.020
 BDH  plan-1  CD2  0.020
 BDH  plan-1  CE1  0.020
 BDH  plan-1  NE2  0.020
 BDH  plan-1  HD1  0.020
 BDH  plan-1  HD2  0.020
 BDH  plan-1  HE1  0.020
 BDH  plan-2  O3   0.020
 BDH  plan-2  N2   0.020
 BDH  plan-2  C2   0.020
 BDH  plan-2  C3   0.020
 BDH  plan-2  C5   0.020
 BDH  plan-2  HN2  0.020
 BDH  plan-3  O1   0.020
 BDH  plan-3  O2   0.020
 BDH  plan-3  C1   0.020
 BDH  plan-3  C4   0.020
 BDH  plan-4  O4   0.020
 BDH  plan-4  O5   0.020
 BDH  plan-4  C5   0.020
 BDH  plan-4  C7   0.020

