# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 18:52:03 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 3-[2-(4-bromophenyl)-2-oxoethyl]-L-histidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cncn1CC(=O)c2ccc(Br)cc2)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
 OLD  OLD  3-[2-(4-bromophenyl)-2-oxoethyl]-L-histidine  L-peptide  34  21  .  2016-04-26  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OLD
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
 OLD  N    N   NH2    0  -0.796  16.5069  13.7475  34.0630
 OLD  CA   C   CH1    0  -0.163  15.9864  13.2529  32.7979
 OLD  CB   C   CH2    0  -0.557  17.1113  12.8643  31.8120
 OLD  CG   C   CR5    0   0.309  16.6373  12.4060  30.4777
 OLD  CD2  C   CR15   0  -0.269  16.2666  13.1183  29.3699
 OLD  ND1  N   NR5    0  -0.441  16.4397  11.0932  30.1249
 OLD  CE1  C   CR15   0   0.079  15.9916  11.0802  28.8478
 OLD  NE2  N   N      0  -0.446  15.8647  12.2849  28.3631
 OLD  CH   C   CH2    0  -0.481  16.7812   9.9303  30.8917
 OLD  CG1  C   CR6    0  -0.010  18.7360   8.3882  31.5205
 OLD  CD1  C   CR16   0  -0.250  20.0628   7.9862  31.3645
 OLD  CE3  C   CR16   0  -0.212  20.5679   6.9115  32.0734
 OLD  CD3  C   CR16   0  -0.284  17.9185   7.6851  32.4041
 OLD  CE2  C   CR16   0  -0.204  18.4100   6.6067  33.1227
 OLD  CZ   C   CR6    0  -0.111  19.7341   6.2309  32.9519
 OLD  BR   BR  BR     0  -0.021  20.4161   4.7730  33.9300
 OLD  C9   C   C      0   0.370  18.2451   9.5558  30.7425
 OLD  O2   O   O      0  -0.366  18.9786  10.1883  30.0200
 OLD  C    C   C      0   0.415  15.0694  12.0385  33.0629
 OLD  O    O   O      0  -0.589  13.9492  12.0299  32.5245
 OLD  OXT  O   OC    -1  -0.610  15.5625  11.1434  33.7881
 OLD  HN   H   HNH2   0   0.328  16.9501  12.9747  34.5457
 OLD  HNA  H   HNH2   0   0.334  17.2322  14.4356  33.8965
 OLD  HA   H   HCH1   0   0.203  15.3955  14.0467  32.3315
 OLD  HB   H   HCH2   0   0.253  17.7515  13.7380  31.6626
 OLD  HBA  H   HCH2   0   0.239  17.7431  12.1077  32.2862
 OLD  HD2  H   HCR5   0   0.244  16.2716  14.1924  29.2550
 OLD  HE1  H   HCR5   0   0.273  15.7713  10.1567  28.3319
 OLD  HH   H   HCH2   0   0.316  16.5408  10.0951  31.9446
 OLD  HHA  H   HCH2   0   0.317  16.1606   9.0921  30.5644
 OLD  HD1  H   HCR6   0   0.276  20.7126   8.5167  30.6815
 OLD  HE3  H   HCR6   0   0.287  21.5992   6.6143  31.9406
 OLD  HD3  H   HCR6   0   0.280  16.8841   7.9633  32.5560
 OLD  HE2  H   HCR6   0   0.290  17.7607   6.0758  33.8055

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
 OLD  CA   N    single    1.458  0.019  1.458
 OLD  N    HN   single    0.890  0.020  1.040
 OLD  N    HNA  single    0.890  0.020  1.040
 OLD  CB   CA   single    1.530  0.020  1.530
 OLD  CA   C    single    1.525  0.021  1.525
 OLD  CA   HA   single    0.970  0.020  0.970
 OLD  CG   CB   single    1.488  0.020  1.488
 OLD  CB   HB   single    0.970  0.020  1.090
 OLD  CB   HBA  single    0.970  0.020  1.090
 OLD  CD2  CG   aromatic  1.368  0.020  1.368
 OLD  CG   ND1  aromatic  1.374  0.020  1.374
 OLD  NE2  CD2  aromatic  1.367  0.020  1.367
 OLD  CD2  HD2  single    0.930  0.020  1.080
 OLD  CE1  ND1  aromatic  1.353  0.020  1.353
 OLD  ND1  CH   single    1.434  0.020  1.434
 OLD  NE2  CE1  aromatic  1.305  0.020  1.305
 OLD  CE1  HE1  single    0.930  0.020  1.080
 OLD  C9   CH   single    1.518  0.020  1.518
 OLD  CH   HH   single    0.970  0.020  1.090
 OLD  CH   HHA  single    0.970  0.020  1.090
 OLD  CD1  CG1  aromatic  1.395  0.020  1.395
 OLD  CG1  CD3  aromatic  1.394  0.020  1.394
 OLD  CG1  C9   single    1.486  0.020  1.486
 OLD  CE3  CD1  aromatic  1.383  0.020  1.383
 OLD  CD1  HD1  single    0.930  0.020  1.080
 OLD  CE3  CZ   aromatic  1.389  0.020  1.389
 OLD  CE3  HE3  single    0.930  0.020  1.080
 OLD  CE2  CD3  aromatic  1.386  0.020  1.386
 OLD  CD3  HD3  single    0.930  0.020  1.080
 OLD  CZ   CE2  aromatic  1.387  0.020  1.387
 OLD  CE2  HE2  single    0.930  0.020  1.080
 OLD  CZ   BR   single    1.883  0.020  1.883
 OLD  O2   C9   double    1.208  0.020  1.208
 OLD  O    C    deloc     1.231  0.020  1.231
 OLD  C    OXT  deloc     1.253  0.020  1.253

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
 OLD  HNA  N    HN   106.44  3.000
 OLD  HNA  N    CA   110.12  3.000
 OLD  HN   N    CA   108.15  3.000
 OLD  HA   CA   C    109.00  3.000
 OLD  HA   CA   CB   109.00  3.000
 OLD  C    CA   CB   110.10  1.900
 OLD  HA   CA   N    110.00  3.000
 OLD  C    CA   N    111.00  2.800
 OLD  CB   CA   N    110.50  1.700
 OLD  HBA  CB   HB   105.88  3.000
 OLD  HBA  CB   CG   111.07  3.000
 OLD  HB   CB   CG   108.07  3.000
 OLD  HBA  CB   CA   108.53  3.000
 OLD  HB   CB   CA   108.21  3.000
 OLD  CG   CB   CA   114.68  3.000
 OLD  ND1  CG   CD2  104.51  3.000
 OLD  ND1  CG   CB   124.78  3.000
 OLD  CD2  CG   CB   130.68  3.000
 OLD  HD2  CD2  NE2  121.94  3.000
 OLD  HD2  CD2  CG   127.05  3.000
 OLD  NE2  CD2  CG   111.00  3.000
 OLD  CH   ND1  CE1  125.13  3.000
 OLD  CH   ND1  CG   127.11  3.000
 OLD  CE1  ND1  CG   107.41  3.000
 OLD  HE1  CE1  NE2  126.30  3.000
 OLD  HE1  CE1  ND1  121.75  3.000
 OLD  NE2  CE1  ND1  111.95  3.000
 OLD  CE1  NE2  CD2  105.11  3.000
 OLD  HHA  CH   HH   106.22  3.000
 OLD  HHA  CH   C9   109.20  3.000
 OLD  HH   CH   C9   110.13  3.000
 OLD  HHA  CH   ND1  109.05  3.000
 OLD  HH   CH   ND1  109.91  3.000
 OLD  C9   CH   ND1  112.15  3.000
 OLD  C9   CG1  CD3  122.29  3.000
 OLD  C9   CG1  CD1  118.81  3.000
 OLD  CD3  CG1  CD1  118.90  3.000
 OLD  HD1  CD1  CE3  119.04  3.000
 OLD  HD1  CD1  CG1  120.04  3.000
 OLD  CE3  CD1  CG1  120.92  3.000
 OLD  HE3  CE3  CZ   121.02  3.000
 OLD  HE3  CE3  CD1  119.92  3.000
 OLD  CZ   CE3  CD1  119.06  3.000
 OLD  HD3  CD3  CE2  117.79  3.000
 OLD  HD3  CD3  CG1  121.33  3.000
 OLD  CE2  CD3  CG1  120.87  3.000
 OLD  HE2  CE2  CZ   121.19  3.000
 OLD  HE2  CE2  CD3  119.76  3.000
 OLD  CZ   CE2  CD3  119.04  3.000
 OLD  BR   CZ   CE2  119.44  3.000
 OLD  BR   CZ   CE3  119.36  3.000
 OLD  CE2  CZ   CE3  121.21  3.000
 OLD  O2   C9   CG1  121.58  3.000
 OLD  O2   C9   CH   120.99  3.000
 OLD  CG1  C9   CH   117.43  3.000
 OLD  OXT  C    O    126.90  3.000
 OLD  OXT  C    CA   115.29  3.000
 OLD  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
 OLD  CONST_01  CE1  NE2  CD2  CG     0.00   0.0  0
 OLD  CONST_02  NE2  CE1  ND1  CG     0.00   0.0  0
 OLD  CONST_03  CE1  ND1  CG   CD2    0.00   0.0  0
 OLD  CONST_04  ND1  CE1  NE2  CD2    0.00   0.0  0
 OLD  CONST_05  NE2  CD2  CG   ND1    0.00   0.0  0
 OLD  CONST_06  CZ   CE3  CD1  CG1    0.00   0.0  0
 OLD  CONST_07  CZ   CE2  CD3  CG1    0.00   0.0  0
 OLD  CONST_08  CE2  CD3  CG1  CD1    0.00   0.0  0
 OLD  CONST_09  CE2  CZ   CE3  CD1    0.00   0.0  0
 OLD  CONST_10  CD3  CG1  CD1  CE3    0.00   0.0  0
 OLD  CONST_11  CD3  CE2  CZ   CE3    0.00   0.0  0
 OLD  CONST_12  NE2  CD2  CG   CB   180.00   0.0  0
 OLD  CONST_13  CE1  ND1  CG   CB   180.00   0.0  0
 OLD  CONST_14  CH   ND1  CG   CD2  180.00   0.0  0
 OLD  CONST_15  CH   ND1  CE1  NE2  180.00   0.0  0
 OLD  CONST_16  BR   CZ   CE3  CD1  180.00   0.0  0
 OLD  CONST_17  C9   CG1  CD1  CE3  180.00   0.0  0
 OLD  CONST_18  BR   CZ   CE2  CD3  180.00   0.0  0
 OLD  CONST_19  C9   CG1  CD3  CE2  180.00   0.0  0
 OLD  CONST_20  HE1  CE1  ND1  CG   180.00   0.0  0
 OLD  CONST_21  HD2  CD2  CG   ND1  180.00   0.0  0
 OLD  CONST_22  HE3  CE3  CD1  CG1  180.00   0.0  0
 OLD  CONST_23  HE2  CE2  CD3  CG1  180.00   0.0  0
 OLD  CONST_24  HD3  CD3  CG1  CD1  180.00   0.0  0
 OLD  CONST_25  HD1  CD1  CG1  CD3  180.00   0.0  0
 OLD  Var_01    CD2  CG   CB   CA    83.02  30.0  2
 OLD  Var_02    C9   CH   ND1  CG   -81.81  30.0  2
 OLD  Var_03    CG1  C9   CH   ND1  178.26  30.0  1
 OLD  Var_04    CD1  CG1  C9   CH   177.48  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
 OLD  chir_01  CA  N  CB  C  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
 OLD  plan-1  CB   0.020
 OLD  plan-1  CG   0.020
 OLD  plan-1  CD2  0.020
 OLD  plan-1  ND1  0.020
 OLD  plan-1  CE1  0.020
 OLD  plan-1  NE2  0.020
 OLD  plan-1  CH   0.020
 OLD  plan-1  HD2  0.020
 OLD  plan-1  HE1  0.020
 OLD  plan-2  CG1  0.020
 OLD  plan-2  CD1  0.020
 OLD  plan-2  CE3  0.020
 OLD  plan-2  CD3  0.020
 OLD  plan-2  CE2  0.020
 OLD  plan-2  CZ   0.020
 OLD  plan-2  BR   0.020
 OLD  plan-2  C9   0.020
 OLD  plan-2  HD1  0.020
 OLD  plan-2  HE3  0.020
 OLD  plan-2  HD3  0.020
 OLD  plan-2  HE2  0.020
 OLD  plan-3  CH   0.020
 OLD  plan-3  CG1  0.020
 OLD  plan-3  C9   0.020
 OLD  plan-3  O2   0.020
 OLD  plan-4  CA   0.020
 OLD  plan-4  C    0.020
 OLD  plan-4  O    0.020
 OLD  plan-4  OXT  0.020

