# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:30:08 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 2,6-dimethyl-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(O)cc(C)c1C[C@H](N)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
 DI7  DI7  '2,6-dimethyl-L-tyrosine  '  L-peptide  29  15  .  2016-04-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DI7
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
 DI7  C     C  C      0   0.406  -48.1289  -33.3338  6.1470
 DI7  N     N  NH2    0  -0.805  -46.6439  -32.9190  4.2028
 DI7  O     O  O      0  -0.605  -49.3000  -33.7178  6.3385
 DI7  CA    C  CH1    0  -0.168  -47.4040  -33.9379  4.9212
 DI7  CB    C  CH2    0  -0.540  -46.4131  -35.0323  5.3550
 DI7  CD    C  CR6    0   0.037  -47.0324  -36.2127  6.0587
 DI7  CZ    C  CR6    0   0.370  -48.2395  -38.3862  7.3725
 DI7  CD1   C  CR6    0   0.072  -47.7491  -37.1811  5.3370
 DI7  CD2   C  CR6    0   0.086  -46.8972  -36.3748  7.4453
 DI7  CE1   C  CR16   0  -0.404  -48.3458  -38.2520  5.9949
 DI7  CE2   C  CR16   0  -0.453  -47.5039  -37.4511  8.0876
 DI7  CE3   C  CH3    0  -0.745  -47.8934  -37.1058  3.8414
 DI7  CE4   C  CH3    0  -0.763  -46.0788  -35.4266  8.2796
 DI7  OXT   O  OC    -1  -0.608  -47.4825  -32.5286  6.8487
 DI7  HN    H  HNH2   0   0.331  -46.3007  -33.3203  3.3377
 DI7  HNA   H  HNH2   0   0.334  -47.2608  -32.1662  3.9228
 DI7  HA    H  HCH1   0   0.188  -48.1721  -34.4008  4.2888
 DI7  HB    H  HCH2   0   0.232  -45.8825  -35.3758  4.4595
 DI7  HBA   H  HCH2   0   0.240  -45.6556  -34.5636  5.9840
 DI7  HOH   H  HOH1   0   0.468  -48.6998  -39.4278  8.9103
 DI7  HE1   H  HCR6   0   0.243  -48.8971  -38.9939  5.4282
 DI7  HE2   H  HCR6   0   0.251  -47.3933  -37.5596  9.1622
 DI7  HE3   H  HCH3   0   0.240  -46.9523  -36.8540  3.3511
 DI7  HE3A  H  HCH3   0   0.248  -48.2341  -38.0568  3.4343
 DI7  HE3B  H  HCH3   0   0.246  -48.6174  -36.3465  3.5426
 DI7  HE4   H  HCH3   0   0.253  -46.4077  -34.3943  8.1691
 DI7  HE4A  H  HCH3   0   0.244  -46.1382  -35.6879  9.3354
 DI7  HE4B  H  HCH3   0   0.238  -45.0245  -35.4572  7.9960
 DI7  OH    O  OH1    0  -0.639  -48.8519  -39.4397  7.9586

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
 DI7  CA   C     single    1.525  0.021  1.525
 DI7  C    O     deloc     1.231  0.020  1.231
 DI7  C    OXT   deloc     1.248  0.020  1.248
 DI7  N    CA    single    1.458  0.019  1.458
 DI7  N    HN    single    0.890  0.020  1.040
 DI7  N    HNA   single    0.890  0.020  1.040
 DI7  CA   CB    single    1.530  0.020  1.530
 DI7  CA   HA    single    0.970  0.020  0.970
 DI7  CB   CD    single    1.507  0.020  1.507
 DI7  CB   HB    single    0.970  0.020  1.090
 DI7  CB   HBA   single    0.970  0.020  1.090
 DI7  CD1  CD    aromatic  1.404  0.020  1.404
 DI7  CD   CD2   aromatic  1.403  0.020  1.403
 DI7  CZ   OH    single    1.352  0.020  1.352
 DI7  OH   HOH   single    0.850  0.020  0.980
 DI7  CE1  CZ    aromatic  1.388  0.020  1.388
 DI7  CZ   CE2   aromatic  1.388  0.020  1.388
 DI7  CE3  CD1   single    1.504  0.020  1.504
 DI7  CD1  CE1   aromatic  1.391  0.020  1.391
 DI7  CD2  CE2   aromatic  1.393  0.020  1.393
 DI7  CD2  CE4   single    1.505  0.020  1.505
 DI7  CE1  HE1   single    0.930  0.020  1.080
 DI7  CE2  HE2   single    0.930  0.020  1.080
 DI7  CE3  HE3   single    0.970  0.020  1.090
 DI7  CE3  HE3A  single    0.970  0.020  1.090
 DI7  CE3  HE3B  single    0.970  0.020  1.090
 DI7  CE4  HE4   single    0.970  0.020  1.090
 DI7  CE4  HE4A  single    0.970  0.020  1.090
 DI7  CE4  HE4B  single    0.970  0.020  1.090

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
 DI7  OXT   C    CA    117.04  3.000
 DI7  OXT   C    O     126.76  3.000
 DI7  CA    C    O     120.80  1.700
 DI7  HNA   N    HN    105.34  3.000
 DI7  HNA   N    CA    109.74  3.000
 DI7  HN    N    CA    108.66  3.000
 DI7  HA    CA   CB    109.00  3.000
 DI7  HA    CA   N     110.00  3.000
 DI7  CB    CA   N     110.50  1.700
 DI7  HA    CA   C     109.00  3.000
 DI7  CB    CA   C     110.10  1.900
 DI7  N     CA   C     111.00  2.800
 DI7  HBA   CB   HB    105.65  3.000
 DI7  HBA   CB   CD    110.65  3.000
 DI7  HB    CB   CD    109.56  3.000
 DI7  HBA   CB   CA    107.71  3.000
 DI7  HB    CB   CA    107.72  3.000
 DI7  CD    CB   CA    115.09  3.000
 DI7  CD2   CD   CD1   118.53  3.000
 DI7  CD2   CD   CB    120.82  3.000
 DI7  CD1   CD   CB    120.65  3.000
 DI7  CE2   CZ   CE1   119.12  3.000
 DI7  CE2   CZ   OH    122.79  3.000
 DI7  CE1   CZ   OH    118.08  3.000
 DI7  CE3   CD1  CE1   117.87  3.000
 DI7  CE1   CD1  CD    120.44  3.000
 DI7  CE3   CD1  CD    121.69  3.000
 DI7  CE4   CD2  CE2   117.92  3.000
 DI7  CE4   CD2  CD    121.85  3.000
 DI7  CE2   CD2  CD    120.22  3.000
 DI7  HE1   CE1  CD1   119.84  3.000
 DI7  HE1   CE1  CZ    119.44  3.000
 DI7  CD1   CE1  CZ    120.72  3.000
 DI7  HE2   CE2  CD2   119.30  3.000
 DI7  HE2   CE2  CZ    119.77  3.000
 DI7  CD2   CE2  CZ    120.93  3.000
 DI7  HE3B  CE3  HE3A  107.32  3.000
 DI7  HE3B  CE3  HE3   106.78  3.000
 DI7  HE3A  CE3  HE3   107.67  3.000
 DI7  HE3B  CE3  CD1   111.76  3.000
 DI7  HE3A  CE3  CD1   110.98  3.000
 DI7  HE3   CE3  CD1   112.08  3.000
 DI7  HE4B  CE4  HE4A  107.32  3.000
 DI7  HE4B  CE4  HE4   106.97  3.000
 DI7  HE4A  CE4  HE4   108.02  3.000
 DI7  HE4B  CE4  CD2   111.30  3.000
 DI7  HE4A  CE4  CD2   110.89  3.000
 DI7  HE4   CE4  CD2   112.13  3.000
 DI7  HOH   OH   CZ    110.29  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
 DI7  CONST_01  CZ   CE1  CD1  CD     0.00   0.0  0
 DI7  CONST_02  CZ   CE2  CD2  CD     0.00   0.0  0
 DI7  CONST_03  CE2  CD2  CD   CD1    0.00   0.0  0
 DI7  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 DI7  CONST_05  CE1  CD1  CD   CD2    0.00   0.0  0
 DI7  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 DI7  CONST_07  CE1  CD1  CD   CB   180.00   0.0  0
 DI7  CONST_08  CE2  CD2  CD   CB   180.00   0.0  0
 DI7  CONST_09  CD1  CE1  CZ   OH   180.00   0.0  0
 DI7  CONST_10  CD2  CE2  CZ   OH   180.00   0.0  0
 DI7  CONST_11  CE3  CD1  CE1  CZ   180.00   0.0  0
 DI7  CONST_12  CE4  CD2  CE2  CZ   180.00   0.0  0
 DI7  CONST_13  CE4  CD2  CD   CD1  180.00   0.0  0
 DI7  CONST_14  CE3  CD1  CD   CD2  180.00   0.0  0
 DI7  CONST_15  HE1  CE1  CD1  CD   180.00   0.0  0
 DI7  CONST_16  HE2  CE2  CD2  CD   180.00   0.0  0
 DI7  Var_01    CD1  CD   CB   CA    75.19  30.0  2
 DI7  Var_02    HE3  CE3  CD1  CD    44.13  30.0  2
 DI7  Var_03    HE4  CE4  CD2  CD    56.19  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
 DI7  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
 DI7  plan-1  CB   0.020
 DI7  plan-1  CD   0.020
 DI7  plan-1  CZ   0.020
 DI7  plan-1  CD1  0.020
 DI7  plan-1  CD2  0.020
 DI7  plan-1  CE1  0.020
 DI7  plan-1  CE2  0.020
 DI7  plan-1  CE3  0.020
 DI7  plan-1  CE4  0.020
 DI7  plan-1  HE1  0.020
 DI7  plan-1  HE2  0.020
 DI7  plan-1  OH   0.020
 DI7  plan-2  C    0.020
 DI7  plan-2  O    0.020
 DI7  plan-2  CA   0.020
 DI7  plan-2  OXT  0.020

