# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 13:38:52 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 4-(6-methyl-1,2,4,5-tetrazin-3-yl)-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nnc(nn1)c2ccc(C[C@H](N)C(O)=O)cc2
#
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
 DJD  DJD  4-(6-methyl-1,2,4,5-tetrazin-3-yl)-L-phenylalanine  L-peptide  31  19  .  2022-09-22  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_DJD
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
 DJD  N     N  NH2    0  -0.796  -3.4584  -1.2046   1.2545
 DJD  CA    C  CH1    0  -0.194  -3.7704   0.0140   0.5371
 DJD  C     C  C      0   0.405  -5.2887   0.1216   0.2649
 DJD  O     O  O      0  -0.603  -5.9282  -0.9459   0.1991
 DJD  CB    C  CH2    0  -0.529  -3.0484   0.1719  -0.8256
 DJD  CG    C  CR6    0   0.133  -1.5587   0.1399  -0.6847
 DJD  CD1   C  CR16   0  -0.305  -0.8362  -1.0386  -0.8659
 DJD  CD2   C  CR16   0  -0.283  -0.8579   1.2856  -0.3059
 DJD  CE1   C  CR16   0  -0.255   0.5356  -1.0764  -0.6771
 DJD  CE2   C  CR16   0  -0.254   0.5113   1.2601  -0.1167
 DJD  CZ    C  CR6    0   0.006   1.2266   0.0740  -0.2977
 DJD  C02   C  CR6    0   0.341   5.2233  -0.0168   0.2594
 DJD  C07   C  CR6    0   0.367   2.6787   0.0401  -0.0944
 DJD  N03   N  N      0  -0.212   4.5838   1.1408   0.4193
 DJD  N04   N  N      0  -0.246   3.3032   1.1699   0.2396
 DJD  N05   N  N      0  -0.212   4.6000  -1.1481  -0.0643
 DJD  N06   N  N      0  -0.246   3.3189  -1.1197  -0.2428
 DJD  H     H  HNH2   0   0.329  -3.9041  -1.9828   0.7856
 DJD  H2    H  HNH2   0   0.336  -2.4617  -1.3842   1.2504
 DJD  HA    H  HCH1   0   0.214  -3.4746   0.8667   1.1578
 DJD  HB3   H  HCH2   0   0.240  -3.3777  -0.6280  -1.4951
 DJD  HB2   H  HCH2   0   0.244  -3.3556   1.1201  -1.2720
 DJD  HD1   H  HCR6   0   0.259  -1.3517  -1.9408  -1.1721
 DJD  HD2   H  HCR6   0   0.254  -1.3953   2.2151  -0.1587
 DJD  HE1   H  HCR6   0   0.261   1.0684  -2.0053  -0.8282
 DJD  HE2   H  HCR6   0   0.260   1.0260   2.1653   0.1745
 DJD  H011  H  HCH3   0   0.277   7.1927   0.1666  -0.5152
 DJD  H013  H  HCH3   0   0.268   7.0166   0.7145   1.1483
 DJD  H012  H  HCH3   0   0.268   7.0307  -1.0215   0.7740
 DJD  OXT   O  OC    -1  -0.617  -5.7331   1.2720   0.0843
 DJD  C01   C  CH3    0  -0.710   6.6988  -0.0430   0.4357

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
 DJD  O    C     deloc     1.231  0.020  1.231
 DJD  C    CA    single    1.525  0.021  1.525
 DJD  CA   N     single    1.458  0.019  1.458
 DJD  CA   CB    single    1.530  0.020  1.530
 DJD  CB   CG    single    1.497  0.020  1.497
 DJD  CD2  CG    aromatic  1.396  0.020  1.396
 DJD  CD2  CE2   aromatic  1.382  0.020  1.382
 DJD  CG   CD1   aromatic  1.394  0.020  1.394
 DJD  CE2  CZ    aromatic  1.397  0.020  1.397
 DJD  CD1  CE1   aromatic  1.385  0.020  1.385
 DJD  CZ   CE1   aromatic  1.395  0.020  1.395
 DJD  CZ   C07   single    1.467  0.020  1.467
 DJD  N04  N03   aromatic  1.293  0.020  1.293
 DJD  N04  C07   aromatic  1.333  0.020  1.333
 DJD  N03  C02   aromatic  1.332  0.020  1.332
 DJD  C07  N06   aromatic  1.333  0.020  1.333
 DJD  C02  N05   aromatic  1.332  0.020  1.332
 DJD  C02  C01   single    1.486  0.020  1.486
 DJD  N06  N05   aromatic  1.294  0.020  1.294
 DJD  N    H     single    0.860  0.020  0.860
 DJD  N    H2    single    0.890  0.020  1.040
 DJD  CA   HA    single    0.970  0.020  0.970
 DJD  CB   HB3   single    0.970  0.020  1.090
 DJD  CB   HB2   single    0.970  0.020  1.090
 DJD  CD1  HD1   single    0.930  0.020  1.080
 DJD  CD2  HD2   single    0.930  0.020  1.080
 DJD  CE1  HE1   single    0.930  0.020  1.080
 DJD  CE2  HE2   single    0.930  0.020  1.080
 DJD  C01  H011  single    0.970  0.020  1.090
 DJD  C01  H013  single    0.970  0.020  1.090
 DJD  C01  H012  single    0.970  0.020  1.090
 DJD  C    OXT   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
 DJD  H2    N    H     107.17  3.000
 DJD  H2    N    CA    111.05  3.000
 DJD  H     N    CA    114.00  3.000
 DJD  HA    CA   CB    109.00  3.000
 DJD  HA    CA   C     109.00  3.000
 DJD  CB    CA   C     110.10  1.900
 DJD  HA    CA   N     110.00  3.000
 DJD  CB    CA   N     110.50  1.700
 DJD  C     CA   N     111.00  2.800
 DJD  OXT   C    O     126.87  3.000
 DJD  OXT   C    CA    116.10  3.000
 DJD  O     C    CA    120.80  1.700
 DJD  HB2   CB   HB3   107.46  3.000
 DJD  HB2   CB   CG    109.70  3.000
 DJD  HB3   CB   CG    109.97  3.000
 DJD  HB2   CB   CA    108.47  3.000
 DJD  HB3   CB   CA    108.87  3.000
 DJD  CG    CB   CA    112.25  3.000
 DJD  CD2   CG   CD1   117.97  3.000
 DJD  CD1   CG   CB    121.44  3.000
 DJD  CD2   CG   CB    120.52  3.000
 DJD  HD1   CD1  CE1   119.15  3.000
 DJD  HD1   CD1  CG    119.61  3.000
 DJD  CE1   CD1  CG    121.23  3.000
 DJD  HD2   CD2  CE2   119.24  3.000
 DJD  HD2   CD2  CG    119.47  3.000
 DJD  CE2   CD2  CG    121.29  3.000
 DJD  HE1   CE1  CZ    120.16  3.000
 DJD  HE1   CE1  CD1   119.48  3.000
 DJD  CZ    CE1  CD1   120.35  3.000
 DJD  HE2   CE2  CZ    120.14  3.000
 DJD  HE2   CE2  CD2   119.53  3.000
 DJD  CZ    CE2  CD2   120.34  3.000
 DJD  C07   CZ   CE2   120.57  3.000
 DJD  C07   CZ   CE1   120.62  3.000
 DJD  CE2   CZ   CE1   118.81  3.000
 DJD  N05   C02  N03   122.87  3.000
 DJD  N05   C02  C01   118.59  3.000
 DJD  N03   C02  C01   118.54  3.000
 DJD  N06   C07  N04   122.70  3.000
 DJD  N06   C07  CZ    118.69  3.000
 DJD  N04   C07  CZ    118.61  3.000
 DJD  N04   N03  C02   118.57  3.000
 DJD  N03   N04  C07   118.64  3.000
 DJD  N06   N05  C02   118.58  3.000
 DJD  N05   N06  C07   118.63  3.000
 DJD  H012  C01  H013  109.49  3.000
 DJD  H012  C01  H011  107.80  3.000
 DJD  H013  C01  H011  107.74  3.000
 DJD  H012  C01  C02   110.85  3.000
 DJD  H013  C01  C02   110.83  3.000
 DJD  H011  C01  C02   110.03  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
 DJD  CONST_01  CZ    CE2  CD2  CG     0.00   0.0  0
 DJD  CONST_02  CZ    CE1  CD1  CG     0.00   0.0  0
 DJD  CONST_03  CE2   CD2  CG   CD1    0.00   0.0  0
 DJD  CONST_04  CE2   CZ   CE1  CD1    0.00   0.0  0
 DJD  CONST_05  C07   CZ   CE1  CD1  180.00   0.0  0
 DJD  CONST_06  CE1   CD1  CG   CD2    0.00   0.0  0
 DJD  CONST_07  CE1   CZ   CE2  CD2    0.00   0.0  0
 DJD  CONST_08  C07   CZ   CE2  CD2  180.00   0.0  0
 DJD  CONST_09  N04   C07  CZ   CE1  180.00   0.0  0
 DJD  CONST_10  N06   C07  CZ   CE1    0.00   0.0  0
 DJD  CONST_11  N04   C07  CZ   CE2    0.00   0.0  0
 DJD  CONST_12  N06   C07  CZ   CE2  180.00   0.0  0
 DJD  CONST_13  N03   N04  C07  CZ   180.00   0.0  0
 DJD  CONST_14  N05   N06  C07  CZ   180.00   0.0  0
 DJD  CONST_15  C07   N04  N03  C02    0.00   0.0  0
 DJD  CONST_16  C07   N06  N05  C02    0.00   0.0  0
 DJD  CONST_17  N06   C07  N04  N03    0.00   0.0  0
 DJD  CONST_18  N06   N05  C02  N03    0.00   0.0  0
 DJD  CONST_19  N05   C02  N03  N04    0.00   0.0  0
 DJD  CONST_20  N05   N06  C07  N04    0.00   0.0  0
 DJD  CONST_21  CE2   CD2  CG   CB   180.00   0.0  0
 DJD  CONST_22  CE1   CD1  CG   CB   180.00   0.0  0
 DJD  CONST_23  N04   N03  C02  C01  180.00   0.0  0
 DJD  CONST_24  N06   N05  C02  C01  180.00   0.0  0
 DJD  CONST_25  HE2   CE2  CD2  CG   180.00   0.0  0
 DJD  CONST_26  HE1   CE1  CD1  CG   180.00   0.0  0
 DJD  CONST_27  HD2   CD2  CG   CD1  180.00   0.0  0
 DJD  CONST_28  HD1   CD1  CG   CD2  180.00   0.0  0
 DJD  Var_01    CD2   CG   CB   CA   -81.83  30.0  2
 DJD  Var_02    H011  C01  C02  N03  -89.40  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
 DJD  chir_01  CA  C  N  CB  negativ

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
 DJD  plan-1  CB   0.020
 DJD  plan-1  CG   0.020
 DJD  plan-1  CD1  0.020
 DJD  plan-1  CD2  0.020
 DJD  plan-1  CE1  0.020
 DJD  plan-1  CE2  0.020
 DJD  plan-1  CZ   0.020
 DJD  plan-1  C07  0.020
 DJD  plan-1  HD1  0.020
 DJD  plan-1  HD2  0.020
 DJD  plan-1  HE1  0.020
 DJD  plan-1  HE2  0.020
 DJD  plan-2  CZ   0.020
 DJD  plan-2  C02  0.020
 DJD  plan-2  C07  0.020
 DJD  plan-2  N03  0.020
 DJD  plan-2  N04  0.020
 DJD  plan-2  N05  0.020
 DJD  plan-2  N06  0.020
 DJD  plan-2  C01  0.020
 DJD  plan-3  CA   0.020
 DJD  plan-3  C    0.020
 DJD  plan-3  O    0.020
 DJD  plan-3  OXT  0.020

