# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 06:15:39 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 4-iodo-N-methyl-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@H](Cc1ccc(I)cc1)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
 HJY  HJY  4-iodo-N-methyl-D-phenylalanine  D-peptide  25  14  .  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
;

data_comp_HJY
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
 HJY  CN    C  CH3    0  -0.519   5.0620  85.5781  74.5174
 HJY  N     N  NH1    0  -0.583   5.7835  86.5147  75.3554
 HJY  CA    C  CH1    0  -0.176   7.2258  86.4238  75.2020
 HJY  CB    C  CH2    0  -0.515   7.8729  87.2970  76.2904
 HJY  CG    C  CR6    0   0.143   9.3723  87.2564  76.2811
 HJY  CD1   C  CR16   0  -0.306  10.0558  86.1759  76.8336
 HJY  CE1   C  CR16   0  -0.209  11.4415  86.1095  76.8170
 HJY  CZ    C  CR6    0  -0.239  12.1579  87.1468  76.2370
 HJY  I     I  I      0   0.035  14.2622  87.0640  76.2063
 HJY  CE2   C  CR16   0  -0.210  11.5077  88.2389  75.6837
 HJY  CD2   C  CR16   0  -0.297  10.1198  88.2827  75.7122
 HJY  C     C  C      0   0.395   7.7538  86.8582  73.8110
 HJY  O     O  O      0  -0.609   7.2064  87.8657  73.3144
 HJY  HN12  H  HCH3   0   0.224   3.9884  85.7177  74.6509
 HJY  HN13  H  HCH3   0   0.190   5.2739  85.6616  73.4429
 HJY  HN11  H  HCH3   0   0.215   5.2957  84.5550  74.8185
 HJY  H2    H  HNH1   0   0.327   5.5128  87.4538  75.0849
 HJY  HA    H  HCH1   0   0.205   7.5173  85.3831  75.3836
 HJY  HB1   H  HCH2   0   0.234   7.5325  88.3285  76.1612
 HJY  HB2   H  HCH2   0   0.241   7.5005  86.9609  77.2614
 HJY  HD1   H  HCR6   0   0.254   9.4981  85.3654  77.2884
 HJY  HE1   H  HCR6   0   0.273  11.9444  85.2577  77.2549
 HJY  HE2   H  HCR6   0   0.273  12.0612  89.0524  75.2340
 HJY  HD2   H  HCR6   0   0.254   9.6128  89.1350  75.2759
 HJY  OXT   O  OC    -1  -0.601   8.6917  86.1974  73.3267

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
 HJY  O    C     deloc     1.231  0.020  1.231
 HJY  C    CA    single    1.525  0.021  1.525
 HJY  CN   N     single    1.449  0.020  1.449
 HJY  N    CA    single    1.458  0.019  1.458
 HJY  CA   CB    single    1.521  0.033  1.521
 HJY  CE2  CD2   aromatic  1.389  0.020  1.389
 HJY  CE2  CZ    aromatic  1.386  0.020  1.386
 HJY  CD2  CG    aromatic  1.391  0.020  1.391
 HJY  I    CZ    single    2.106  0.020  2.106
 HJY  CZ   CE1   aromatic  1.388  0.020  1.388
 HJY  CG   CB    single    1.500  0.020  1.500
 HJY  CG   CD1   aromatic  1.393  0.020  1.393
 HJY  CE1  CD1   aromatic  1.387  0.020  1.387
 HJY  CN   HN12  single    0.970  0.020  1.090
 HJY  CN   HN13  single    0.970  0.020  1.090
 HJY  CN   HN11  single    0.970  0.020  1.090
 HJY  N    H2    single    0.890  0.020  1.040
 HJY  CA   HA    single    0.970  0.020  0.970
 HJY  CB   HB1   single    0.970  0.020  1.090
 HJY  CB   HB2   single    0.970  0.020  1.090
 HJY  CD1  HD1   single    0.930  0.020  1.080
 HJY  CE1  HE1   single    0.930  0.020  1.080
 HJY  CE2  HE2   single    0.930  0.020  1.080
 HJY  CD2  HD2   single    0.930  0.020  1.080
 HJY  C    OXT   deloc     1.245  0.020  1.245

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
 HJY  HN11  CN   HN13  107.44  3.000
 HJY  HN11  CN   HN12  107.27  3.000
 HJY  HN13  CN   HN12  107.45  3.000
 HJY  HN11  CN   N     109.85  3.000
 HJY  HN13  CN   N     114.87  3.000
 HJY  HN12  CN   N     109.66  3.000
 HJY  H2    N    CA    107.14  3.000
 HJY  H2    N    CN    108.14  3.000
 HJY  CA    N    CN    113.12  3.000
 HJY  HA    CA   C     110.00  3.000
 HJY  HA    CA   CB    109.00  3.000
 HJY  C     CA   CB    110.50  1.500
 HJY  HA    CA   N     110.00  3.000
 HJY  CB    CA   N     110.40  1.500
 HJY  C     CA   N     111.00  2.800
 HJY  HB2   CB   HB1   106.79  3.000
 HJY  HB2   CB   CG    109.75  3.000
 HJY  HB1   CB   CG    109.62  3.000
 HJY  HB2   CB   CA    108.11  3.000
 HJY  HB1   CB   CA    108.71  3.000
 HJY  CG    CB   CA    113.63  3.000
 HJY  CD2   CG   CD1   118.08  3.000
 HJY  CD1   CG   CB    120.60  3.000
 HJY  CD2   CG   CB    121.31  3.000
 HJY  HD1   CD1  CE1   118.89  3.000
 HJY  HD1   CD1  CG    119.61  3.000
 HJY  CE1   CD1  CG    121.50  3.000
 HJY  HE1   CE1  CZ    121.18  3.000
 HJY  HE1   CE1  CD1   119.81  3.000
 HJY  CZ    CE1  CD1   119.01  3.000
 HJY  CE2   CZ   I     119.59  3.000
 HJY  I     CZ   CE1   119.51  3.000
 HJY  CE2   CZ   CE1   120.90  3.000
 HJY  HE2   CE2  CD2   119.74  3.000
 HJY  HE2   CE2  CZ    121.23  3.000
 HJY  CD2   CE2  CZ    119.03  3.000
 HJY  HD2   CD2  CE2   118.95  3.000
 HJY  HD2   CD2  CG    119.57  3.000
 HJY  CE2   CD2  CG    121.47  3.000
 HJY  OXT   C    O     127.10  3.000
 HJY  OXT   C    CA    120.80  1.700
 HJY  O     C    CA    120.80  1.700

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
 HJY  CONST_01  CZ    CE2  CD2  CG      0.00   0.0  0
 HJY  CONST_02  CZ    CE1  CD1  CG      0.00   0.0  0
 HJY  CONST_03  CE2   CD2  CG   CD1     0.00   0.0  0
 HJY  CONST_04  CE2   CZ   CE1  CD1     0.00   0.0  0
 HJY  CONST_05  CD2   CE2  CZ   CE1     0.00   0.0  0
 HJY  CONST_06  CD2   CG   CD1  CE1     0.00   0.0  0
 HJY  CONST_07  CE2   CD2  CG   CB    180.00   0.0  0
 HJY  CONST_08  CE1   CD1  CG   CB    180.00   0.0  0
 HJY  CONST_09  I     CZ   CE1  CD1   180.00   0.0  0
 HJY  CONST_10  CD2   CE2  CZ   I     180.00   0.0  0
 HJY  CONST_11  HE2   CE2  CD2  CG    180.00   0.0  0
 HJY  CONST_12  HE1   CE1  CD1  CG    180.00   0.0  0
 HJY  CONST_13  HD2   CD2  CG   CD1   180.00   0.0  0
 HJY  CONST_14  HD1   CD1  CE1  CZ    180.00   0.0  0
 HJY  Var_01    CD2   CG   CB   CA    100.84  30.0  2
 HJY  Var_02    HN12  CN   N    CA   -178.05  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
 HJY  chir_01  CA  C  N  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
 HJY  plan-1  CB   0.020
 HJY  plan-1  CG   0.020
 HJY  plan-1  CD1  0.020
 HJY  plan-1  CE1  0.020
 HJY  plan-1  CZ   0.020
 HJY  plan-1  I    0.020
 HJY  plan-1  CE2  0.020
 HJY  plan-1  CD2  0.020
 HJY  plan-1  HD1  0.020
 HJY  plan-1  HE1  0.020
 HJY  plan-1  HE2  0.020
 HJY  plan-1  HD2  0.020
 HJY  plan-2  CA   0.020
 HJY  plan-2  C    0.020
 HJY  plan-2  O    0.020
 HJY  plan-2  OXT  0.020

