# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 21:22:42 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: O-methyl-N-[(2S)-4-methyl-2-(sulfanylmethyl)pentanoyl]-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C[C@H](NC(=O)[C@@H](CS)CC(C)C)C(O)=O)cc1
#
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
 0QI  0QI  O-methyl-N-[(2S)-4-methyl-2-(sulfanylmethyl)pentanoyl]-L-tyrosine  peptide  47  23  .  2016-04-22  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_0QI
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
 0QI  C1   C  C      0   0.557  -3.0262  23.6803  47.5371
 0QI  O1   O  O      0  -0.502  -2.2898  24.3558  48.2485
 0QI  C2   C  CH1    0  -0.381  -3.1388  22.1733  47.7276
 0QI  CH   C  CH2    0  -0.535  -1.7719  21.5144  47.5819
 0QI  S    S  S2     0  -0.255  -1.1499  21.7514  45.8807
 0QI  C3   C  CH2    0  -0.382  -3.7061  21.8623  49.1183
 0QI  C4   C  CH1    0  -0.249  -5.0512  22.5088  49.4596
 0QI  CM   C  CH3    0  -0.647  -5.4338  22.1467  50.8914
 0QI  C5   C  CH3    0  -0.655  -6.1635  22.1029  48.4976
 0QI  N    N  NH1    0  -0.624  -3.7985  24.1892  46.5747
 0QI  CA   C  CH1    0  -0.222  -3.9842  25.5957  46.3131
 0QI  C    C  C      0   0.419  -5.2903  25.7974  45.4926
 0QI  O    O  O      0  -0.580  -5.5609  26.9730  45.2017
 0QI  CB   C  CH2    0  -0.493  -2.7594  26.2642  45.6781
 0QI  CG   C  C      0   0.108  -2.1263  25.5602  44.5062
 0QI  CD1  C  C1     0  -0.301  -2.8422  24.8433  43.5544
 0QI  CD2  C  C1     0  -0.298  -0.7437  25.6426  44.3278
 0QI  CE1  C  C1     0  -0.366  -2.2211  24.2463  42.4615
 0QI  CE2  C  C1     0  -0.327  -0.1063  25.0600  43.2475
 0QI  CZ   C  C      0   0.360  -0.8444  24.3573  42.2949
 0QI  OH   O  O2     0  -0.471  -0.1520  23.8254  41.2661
 0QI  OXT  O  OC    -1  -0.595  -5.9525  24.7742  45.2214
 0QI  C6   C  CH3    0  -0.433  -0.8649  23.1315  40.2649
 0QI  H2   H  HCH1   0   0.260  -3.8039  21.7492  46.9688
 0QI  HH1  H  HCH2   0   0.267  -1.0668  21.9487  48.2899
 0QI  HH2  H  HCH2   0   0.276  -1.8556  20.4477  47.7879
 0QI  HS   H  HSH1   0   0.224   0.0331  21.1491  46.0441
 0QI  H31  H  HCH2   0   0.227  -3.8078  20.7755  49.2079
 0QI  H32  H  HCH2   0   0.226  -2.9692  22.1632  49.8691
 0QI  H4   H  HCH1   0   0.222  -4.9390  23.5980  49.4131
 0QI  HM1  H  HCH3   0   0.225  -6.3682  22.6282  51.1837
 0QI  HM2  H  HCH3   0   0.213  -5.5699  21.0676  50.9967
 0QI  HM3  H  HCH3   0   0.224  -4.6644  22.4548  51.6015
 0QI  H51  H  HCH3   0   0.227  -7.1205  22.5162  48.8204
 0QI  H52  H  HCH3   0   0.222  -5.9925  22.4570  47.4807
 0QI  H53  H  HCH3   0   0.214  -6.2695  21.0158  48.4602
 0QI  H    H  HNH1   0   0.391  -4.4362  23.5895  46.0705
 0QI  HA   H  HCH1   0   0.253  -4.1500  26.1093  47.2680
 0QI  HB2  H  HCH2   0   0.246  -3.0610  27.2736  45.3871
 0QI  HB3  H  HCH2   0   0.239  -1.9963  26.3965  46.4471
 0QI  HD1  H  H      0   0.248  -3.9118  24.7157  43.6514
 0QI  HD2  H  H      0   0.243  -0.1458  26.1776  45.0572
 0QI  HE1  H  H      0   0.271  -2.8315  23.6994  41.7553
 0QI  HE2  H  H      0   0.253   0.9681  25.1439  43.1366
 0QI  HC1  H  HCH3   0   0.255  -0.1323  22.8098  39.5284
 0QI  HC2  H  HCH3   0   0.224  -1.3753  22.2485  40.6596
 0QI  HC3  H  HCH3   0   0.224  -1.6027  23.7694  39.7704

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
 0QI  C1   O1   double    1.227  0.020  1.227
 0QI  C1   C2   single    1.523  0.020  1.523
 0QI  C2   CH   single    1.524  0.020  1.524
 0QI  C2   C3   single    1.534  0.020  1.534
 0QI  C2   H2   single    0.970  0.020  1.090
 0QI  CH   S    single    1.827  0.020  1.827
 0QI  CH   HH1  single    0.970  0.020  1.090
 0QI  CH   HH2  single    0.970  0.020  1.090
 0QI  S    HS   single    1.200  0.020  1.300
 0QI  C3   C4   single    1.531  0.020  1.531
 0QI  C3   H31  single    0.970  0.020  1.090
 0QI  C3   H32  single    0.970  0.020  1.090
 0QI  C4   CM   single    1.526  0.020  1.526
 0QI  C4   C5   single    1.526  0.020  1.526
 0QI  C4   H4   single    0.970  0.020  1.090
 0QI  CM   HM1  single    0.970  0.020  1.090
 0QI  CM   HM2  single    0.970  0.020  1.090
 0QI  CM   HM3  single    0.970  0.020  1.090
 0QI  C5   H51  single    0.970  0.020  1.090
 0QI  C5   H52  single    0.970  0.020  1.090
 0QI  C5   H53  single    0.970  0.020  1.090
 0QI  N    CA   single    1.458  0.019  1.458
 0QI  N    H    single    0.860  0.020  0.860
 0QI  CA   C    single    1.525  0.021  1.525
 0QI  CA   CB   single    1.521  0.033  1.521
 0QI  CA   HA   single    0.970  0.020  0.970
 0QI  C    O    deloc     1.231  0.020  1.231
 0QI  C    OXT  deloc     1.249  0.020  1.249
 0QI  CB   CG   single    1.507  0.020  1.507
 0QI  CB   HB2  single    0.970  0.020  1.090
 0QI  CB   HB3  single    0.970  0.020  1.090
 0QI  CG   CD1  aromatic  1.390  0.020  1.390
 0QI  CG   CD2  aromatic  1.397  0.020  1.397
 0QI  CD1  CE1  aromatic  1.392  0.020  1.392
 0QI  CD1  HD1  single    0.930  0.020  1.080
 0QI  CD2  CE2  aromatic  1.383  0.020  1.383
 0QI  CD2  HD2  single    0.930  0.020  1.080
 0QI  CE1  CZ   aromatic  1.391  0.020  1.391
 0QI  CE1  HE1  single    0.930  0.020  1.080
 0QI  CE2  CZ   aromatic  1.395  0.020  1.395
 0QI  CE2  HE2  single    0.930  0.020  1.080
 0QI  CZ   OH   single    1.349  0.020  1.349
 0QI  C6   HC1  single    0.970  0.020  1.090
 0QI  C6   HC2  single    0.970  0.020  1.090
 0QI  C6   HC3  single    0.970  0.020  1.090
 0QI  C1   N    single    1.335  0.020  1.335
 0QI  OH   C6   single    1.411  0.020  1.411

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
 0QI  N    C1   C2   115.13  3.000
 0QI  N    C1   O1   123.75  3.000
 0QI  C2   C1   O1   121.11  3.000
 0QI  H2   C2   C3   108.99  3.000
 0QI  H2   C2   CH   108.13  3.000
 0QI  C3   C2   CH   109.31  3.000
 0QI  H2   C2   C1   109.97  3.000
 0QI  C3   C2   C1   109.96  3.000
 0QI  CH   C2   C1   110.45  3.000
 0QI  HH2  CH   HH1  108.48  3.000
 0QI  HH2  CH   S    109.22  3.000
 0QI  HH1  CH   S    109.46  3.000
 0QI  HH2  CH   C2   109.65  3.000
 0QI  HH1  CH   C2   110.24  3.000
 0QI  S    CH   C2   109.77  3.000
 0QI  HS   S    CH    97.41  3.000
 0QI  H32  C3   H31  106.21  3.000
 0QI  H32  C3   C4   108.82  3.000
 0QI  H31  C3   C4   108.61  3.000
 0QI  H32  C3   C2   108.51  3.000
 0QI  H31  C3   C2   108.04  3.000
 0QI  C4   C3   C2   116.20  3.000
 0QI  H4   C4   C5   108.20  3.000
 0QI  H4   C4   CM   107.53  3.000
 0QI  C5   C4   CM   110.23  3.000
 0QI  H4   C4   C3   108.68  3.000
 0QI  C5   C4   C3   112.81  3.000
 0QI  CM   C4   C3   109.23  3.000
 0QI  HM3  CM   HM2  107.69  3.000
 0QI  HM3  CM   HM1  107.75  3.000
 0QI  HM2  CM   HM1  107.66  3.000
 0QI  HM3  CM   C4   111.52  3.000
 0QI  HM2  CM   C4   110.85  3.000
 0QI  HM1  CM   C4   111.19  3.000
 0QI  H53  C5   H52  107.84  3.000
 0QI  H53  C5   H51  107.57  3.000
 0QI  H52  C5   H51  106.88  3.000
 0QI  H53  C5   C4   110.91  3.000
 0QI  H52  C5   C4   112.79  3.000
 0QI  H51  C5   C4   110.62  3.000
 0QI  H    N    CA   114.00  3.000
 0QI  H    N    C1   119.92  3.000
 0QI  CA   N    C1   125.24  3.000
 0QI  HA   CA   CB   109.00  3.000
 0QI  HA   CA   C    110.00  3.000
 0QI  CB   CA   C    110.50  1.500
 0QI  HA   CA   N    110.00  3.000
 0QI  CB   CA   N    110.40  1.500
 0QI  C    CA   N    111.00  2.800
 0QI  OXT  C    O    127.57  3.000
 0QI  OXT  C    CA   120.80  1.700
 0QI  O    C    CA   120.80  1.700
 0QI  HB3  CB   HB2  105.58  3.000
 0QI  HB3  CB   CG   108.11  3.000
 0QI  HB2  CB   CG   109.90  3.000
 0QI  HB3  CB   CA   108.64  3.000
 0QI  HB2  CB   CA   107.01  3.000
 0QI  CG   CB   CA   117.01  3.000
 0QI  CD2  CG   CD1  116.93  3.000
 0QI  CD2  CG   CB   119.20  3.000
 0QI  CD1  CG   CB   123.86  3.000
 0QI  HD1  CD1  CE1  117.46  3.000
 0QI  HD1  CD1  CG   120.59  3.000
 0QI  CE1  CD1  CG   121.94  3.000
 0QI  HD2  CD2  CE2  118.63  3.000
 0QI  HD2  CD2  CG   119.28  3.000
 0QI  CE2  CD2  CG   122.08  3.000
 0QI  HE1  CE1  CZ   121.37  3.000
 0QI  HE1  CE1  CD1  118.53  3.000
 0QI  CZ   CE1  CD1  120.10  3.000
 0QI  HE2  CE2  CZ   119.59  3.000
 0QI  HE2  CE2  CD2  120.29  3.000
 0QI  CZ   CE2  CD2  120.11  3.000
 0QI  OH   CZ   CE2  116.60  3.000
 0QI  OH   CZ   CE1  124.58  3.000
 0QI  CE2  CZ   CE1  118.82  3.000
 0QI  C6   OH   CZ   118.39  3.000
 0QI  HC3  C6   HC2  108.62  3.000
 0QI  HC3  C6   HC1  108.71  3.000
 0QI  HC2  C6   HC1  108.67  3.000
 0QI  HC3  C6   OH   112.01  3.000
 0QI  HC2  C6   OH   112.12  3.000
 0QI  HC1  C6   OH   106.59  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
 0QI  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 0QI  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 0QI  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 0QI  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 0QI  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 0QI  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 0QI  CONST_07  CE1  CD1  CG   CB    180.00   0.0  0
 0QI  CONST_08  CE2  CD2  CG   CB    180.00   0.0  0
 0QI  CONST_09  OH   CZ   CE1  CD1   180.00   0.0  0
 0QI  CONST_10  OH   CZ   CE2  CD2   180.00   0.0  0
 0QI  CONST_11  HE1  CE1  CD1  CG    180.00   0.0  0
 0QI  CONST_12  HE2  CE2  CD2  CG    180.00   0.0  0
 0QI  CONST_13  HD2  CD2  CG   CD1   180.00   0.0  0
 0QI  CONST_14  HD1  CD1  CG   CD2   180.00   0.0  0
 0QI  CONST_15  CA   N    C1   O1      0.00   0.0  0
 0QI  CONST_16  CA   N    C1   C2    180.00   0.0  0
 0QI  CONST_17  H    N    C1   O1    180.00   0.0  0
 0QI  Var_01    CD1  CG   CB   CA     35.03  30.0  2
 0QI  Var_02    HC1  C6   OH   CZ    178.64  30.0  3
 0QI  Var_03    CM   C4   C3   C2   -177.50  30.0  3
 0QI  Var_04    HM1  CM   C4   C3    177.47  30.0  3
 0QI  Var_05    H51  C5   C4   C3    175.33  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
 0QI  chir_01  C2  C1  CH  C3  negativ
 0QI  chir_02  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
 0QI  plan-1  CB   0.020
 0QI  plan-1  CG   0.020
 0QI  plan-1  CD1  0.020
 0QI  plan-1  CD2  0.020
 0QI  plan-1  CE1  0.020
 0QI  plan-1  CE2  0.020
 0QI  plan-1  CZ   0.020
 0QI  plan-1  OH   0.020
 0QI  plan-1  HD1  0.020
 0QI  plan-1  HD2  0.020
 0QI  plan-1  HE1  0.020
 0QI  plan-1  HE2  0.020
 0QI  plan-2  C1   0.020
 0QI  plan-2  O1   0.020
 0QI  plan-2  C2   0.020
 0QI  plan-2  N    0.020
 0QI  plan-2  CA   0.020
 0QI  plan-2  H    0.020
 0QI  plan-3  CA   0.020
 0QI  plan-3  C    0.020
 0QI  plan-3  O    0.020
 0QI  plan-3  OXT  0.020

