# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 11:41:52 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: N-[(2S)-2-amino-3-phenylpropyl]-D-methionyl-L-alanyl-L-isoleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)[C@H](NC(=O)[C@H](C)NC(=O)[C@@H](CCSC)NC[C@@H](N)Cc1ccccc1)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
 3AI  3AI  N-[(2S)-2-amino-3-phenylpropyl]-D-methionyl-L-alanyl-L-isoleucine  peptide  69  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3AI
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
 3AI  O     O  O      0  -0.493   -0.2296  -0.3015   1.6599
 3AI  C1    C  C      0   0.549   -0.0368  -0.4046   0.4570
 3AI  N1    N  NH1    0  -0.598   -2.4061  -0.1427   0.0531
 3AI  CE    C  CH3    0  -0.763   -1.5911  -5.7491   0.8558
 3AI  CA1   C  CH1    0  -0.208   -1.1777  -0.6106  -0.5367
 3AI  CB1   C  CH2    0  -0.450   -1.1722  -2.0738  -1.0295
 3AI  CG1   C  CH2    0  -0.559   -1.2840  -3.1011   0.0863
 3AI  C     C  CH2    0  -0.258   -3.5588  -0.1190  -0.8234
 3AI  N     N  NH2    0  -0.780   -4.2886   2.0696   0.1287
 3AI  CA    C  CH1    0  -0.105   -4.6792   0.7039  -0.1796
 3AI  CB    C  CH2    0  -0.529   -5.9215   0.6978  -1.0713
 3AI  CG    C  CR6    0   0.169   -7.1059   1.3610  -0.4281
 3AI  CZ    C  CR16   0  -0.276   -9.2893   2.5915   0.8283
 3AI  CD1   C  CR16   0  -0.317   -7.4481   2.6784  -0.7210
 3AI  CD2   C  CR16   0  -0.312   -7.8774   0.6697   0.5043
 3AI  CE1   C  CR16   0  -0.243   -8.5305   3.2902  -0.1018
 3AI  CE2   C  CR16   0  -0.240   -8.9583   1.2764   1.1298
 3AI  N2    N  NH1    0  -0.641    1.1842  -0.3858  -0.0956
 3AI  CA2   C  CH1    0  -0.202    2.4063  -0.3195   0.6700
 3AI  C2    C  C      0   0.560    3.5181   0.1602  -0.2544
 3AI  O1    O  O      0  -0.506    3.5174  -0.1283  -1.4452
 3AI  CB2   C  CH3    0  -0.645    2.7994  -1.6792   1.2518
 3AI  N3    N  NH1    0  -0.635    4.4745   0.8780   0.3357
 3AI  CA3   C  CH1    0  -0.143    5.7531   1.1139  -0.3031
 3AI  C3    C  C      0   0.408    6.5177  -0.2125  -0.5478
 3AI  O2    O  O      0  -0.593    6.2179  -1.1825   0.1689
 3AI  CB3   C  CH1    0  -0.269    6.5646   2.1095   0.5476
 3AI  CG2   C  CH2    0  -0.406    7.7280   2.7167  -0.2416
 3AI  CG3   C  CH3    0  -0.668    7.0442   1.5049   1.8667
 3AI  CD3   C  CH3    0  -0.671    8.3157   3.9615   0.4109
 3AI  OXT   O  OC    -1  -0.607    7.3916  -0.1738  -1.4371
 3AI  HN1   H  HNH1   0   0.346   -2.6197  -0.6494   0.9035
 3AI  HE    H  HCH3   0   0.261   -2.4948  -5.4786   1.4002
 3AI  HEA   H  HCH3   0   0.273   -1.6664  -6.7919   0.5528
 3AI  HEB   H  HCH3   0   0.261   -0.7273  -5.6387   1.5096
 3AI  HA1   H  HCH1   0   0.273   -0.9795   0.0114  -1.4169
 3AI  HB1   H  HCH2   0   0.256   -1.9979  -2.2030  -1.7333
 3AI  HB1A  H  HCH2   0   0.246   -0.2593  -2.2551  -1.6030
 3AI  HG1   H  HCH2   0   0.259   -2.1675  -2.9228   0.7035
 3AI  HG1A  H  HCH2   0   0.264   -0.4098  -3.0698   0.7408
 3AI  H     H  HCH2   0   0.216   -3.2684   0.3566  -1.7670
 3AI  HA    H  HCH2   0   0.199   -3.9413  -1.1180  -1.0820
 3AI  HAA   H  HCH1   0   0.223   -4.9431   0.2126   0.7667
 3AI  HB    H  HCH2   0   0.240   -5.6793   1.1933  -2.0172
 3AI  HBA   H  HCH2   0   0.248   -6.1694  -0.3375  -1.3187
 3AI  HZ    H  HCR6   0   0.251  -10.1333   3.0669   1.3112
 3AI  HD1   H  HCR6   0   0.240   -6.8628   3.2336  -1.4444
 3AI  HD2   H  HCR6   0   0.243   -7.6293  -0.3585   0.7432
 3AI  HE1   H  HCR6   0   0.251   -8.7802   4.3151  -0.3455
 3AI  HE2   H  HCR6   0   0.251   -9.5447   0.7196   1.8496
 3AI  HN2   H  HNH1   0   0.397    1.2823  -0.4924  -1.0949
 3AI  HA2   H  HCH1   0   0.270    2.2726   0.3963   1.4842
 3AI  HB2   H  HCH3   0   0.231    2.9188  -2.4158   0.4569
 3AI  HB2A  H  HCH3   0   0.241    3.7415  -1.6122   1.7948
 3AI  HB2B  H  HCH3   0   0.242    2.0306  -2.0316   1.9378
 3AI  HN3   H  HNH1   0   0.392    4.4124   1.0025   1.3339
 3AI  HA3   H  HCH1   0   0.233    5.5612   1.5891  -1.2697
 3AI  HB3   H  HCH1   0   0.222    5.8750   2.9312   0.7820
 3AI  HG2   H  HCH2   0   0.218    8.5084   1.9656  -0.3782
 3AI  HG2A  H  HCH2   0   0.214    7.3779   2.9765  -1.2445
 3AI  HG3   H  HCH3   0   0.232    7.4840   2.2700   2.5065
 3AI  HG3A  H  HCH3   0   0.223    6.2397   1.0403   2.4392
 3AI  HG3B  H  HCH3   0   0.223    7.8041   0.7412   1.6955
 3AI  HD3   H  HCH3   0   0.215    7.5604   4.7413   0.5280
 3AI  HD3A  H  HCH3   0   0.220    8.7314   3.7541   1.3977
 3AI  HD3B  H  HCH3   0   0.228    9.1215   4.3746  -0.1972
 3AI  HN    H  HNH2   0   0.341   -3.3697   2.0392   0.5570
 3AI  SD    S  S2     0  -0.039   -1.4094  -4.7579  -0.6423
 3AI  HNA   H  HNH2   0   0.329   -4.1631   2.5801  -0.7392

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
 3AI  O    C1    double    1.223  0.020  1.223
 3AI  C1   N2    single    1.340  0.020  1.340
 3AI  C1   CA1   single    1.527  0.020  1.527
 3AI  N1   CA1   single    1.441  0.020  1.441
 3AI  N1   C     single    1.448  0.020  1.448
 3AI  N1   HN1   single    0.890  0.020  1.040
 3AI  O1   C2    double    1.225  0.020  1.225
 3AI  C2   N3    single    1.333  0.020  1.333
 3AI  C2   CA2   single    1.523  0.020  1.523
 3AI  N2   CA2   single    1.444  0.020  1.444
 3AI  N2   HN2   single    0.860  0.020  1.020
 3AI  O2   C3    deloc     1.243  0.020  1.243
 3AI  C3   CA3   single    1.550  0.020  1.550
 3AI  C3   OXT   deloc     1.247  0.020  1.247
 3AI  N3   CA3   single    1.449  0.020  1.449
 3AI  N3   HN3   single    0.860  0.020  1.020
 3AI  SD   CE    single    1.805  0.020  1.805
 3AI  SD   CG1   single    1.814  0.020  1.814
 3AI  CE   HE    single    0.970  0.020  1.090
 3AI  CE   HEA   single    0.970  0.020  1.090
 3AI  CE   HEB   single    0.970  0.020  1.090
 3AI  CA1  CB1   single    1.544  0.020  1.544
 3AI  CA1  HA1   single    0.970  0.020  1.090
 3AI  CA2  CB2   single    1.530  0.020  1.530
 3AI  CA2  HA2   single    0.970  0.020  1.090
 3AI  CA3  CB3   single    1.541  0.020  1.541
 3AI  CA3  HA3   single    0.970  0.020  1.090
 3AI  CB1  CG1   single    1.521  0.020  1.521
 3AI  CB1  HB1   single    0.970  0.020  1.090
 3AI  CB1  HB1A  single    0.970  0.020  1.090
 3AI  CB2  HB2   single    0.970  0.020  1.090
 3AI  CB2  HB2A  single    0.970  0.020  1.090
 3AI  CB2  HB2B  single    0.970  0.020  1.090
 3AI  CB3  CG2   single    1.531  0.020  1.531
 3AI  CB3  CG3   single    1.528  0.020  1.528
 3AI  CB3  HB3   single    0.970  0.020  1.090
 3AI  CD3  CG2   single    1.523  0.020  1.523
 3AI  CD3  HD3   single    0.970  0.020  1.090
 3AI  CD3  HD3A  single    0.970  0.020  1.090
 3AI  CD3  HD3B  single    0.970  0.020  1.090
 3AI  CG1  HG1   single    0.970  0.020  1.090
 3AI  CG1  HG1A  single    0.970  0.020  1.090
 3AI  CG2  HG2   single    0.970  0.020  1.090
 3AI  CG2  HG2A  single    0.970  0.020  1.090
 3AI  CG3  HG3   single    0.970  0.020  1.090
 3AI  CG3  HG3A  single    0.970  0.020  1.090
 3AI  CG3  HG3B  single    0.970  0.020  1.090
 3AI  C    CA    single    1.525  0.021  1.525
 3AI  C    H     single    0.970  0.020  1.090
 3AI  C    HA    single    0.970  0.020  1.090
 3AI  N    CA    single    1.458  0.019  1.458
 3AI  N    HN    single    0.890  0.020  1.040
 3AI  N    HNA   single    0.890  0.020  1.040
 3AI  CA   CB    single    1.521  0.033  1.521
 3AI  CA   HAA   single    0.970  0.020  1.090
 3AI  CB   CG    single    1.502  0.020  1.502
 3AI  CB   HB    single    0.970  0.020  1.090
 3AI  CB   HBA   single    0.970  0.020  1.090
 3AI  CG   CD1   aromatic  1.392  0.020  1.392
 3AI  CG   CD2   aromatic  1.394  0.020  1.394
 3AI  CZ   CE1   aromatic  1.389  0.020  1.389
 3AI  CZ   CE2   aromatic  1.389  0.020  1.389
 3AI  CZ   HZ    single    0.930  0.020  1.080
 3AI  CD1  CE1   aromatic  1.389  0.020  1.389
 3AI  CD1  HD1   single    0.930  0.020  1.080
 3AI  CD2  CE2   aromatic  1.388  0.020  1.388
 3AI  CD2  HD2   single    0.930  0.020  1.080
 3AI  CE1  HE1   single    0.930  0.020  1.080
 3AI  CE2  HE2   single    0.930  0.020  1.080

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
 3AI  N2    C1   CA1   114.48  3.000
 3AI  CA1   C1   O     122.26  3.000
 3AI  N2    C1   O     123.23  3.000
 3AI  HN1   N1   C     110.40  3.000
 3AI  HN1   N1   CA1   111.17  3.000
 3AI  C     N1   CA1   115.86  3.000
 3AI  HEB   CE   HEA   108.61  3.000
 3AI  HEB   CE   HE    109.44  3.000
 3AI  HEA   CE   HE    108.64  3.000
 3AI  HEB   CE   SD    111.27  3.000
 3AI  HEA   CE   SD    107.57  3.000
 3AI  HE    CE   SD    111.22  3.000
 3AI  HA1   CA1  CB1   106.31  3.000
 3AI  HA1   CA1  N1    107.38  3.000
 3AI  CB1   CA1  N1    116.20  3.000
 3AI  HA1   CA1  C1    108.12  3.000
 3AI  CB1   CA1  C1    109.44  3.000
 3AI  N1    CA1  C1    109.08  3.000
 3AI  HB1A  CB1  HB1   105.88  3.000
 3AI  HB1A  CB1  CG1   109.53  3.000
 3AI  HB1   CB1  CG1   109.70  3.000
 3AI  HB1A  CB1  CA1   109.13  3.000
 3AI  HB1   CB1  CA1   108.35  3.000
 3AI  CG1   CB1  CA1   113.93  3.000
 3AI  HG1A  CG1  HG1   107.69  3.000
 3AI  HG1A  CG1  CB1   111.18  3.000
 3AI  HG1   CG1  CB1   111.34  3.000
 3AI  HG1A  CG1  SD    108.79  3.000
 3AI  HG1   CG1  SD    108.67  3.000
 3AI  CB1   CG1  SD    109.11  3.000
 3AI  HA    C    H     106.48  3.000
 3AI  HA    C    CA    110.00  3.000
 3AI  H     C    CA    108.82  3.000
 3AI  HA    C    N1    113.83  3.000
 3AI  H     C    N1    108.50  3.000
 3AI  CA    C    N1    109.67  3.000
 3AI  HNA   N    HN    105.32  3.000
 3AI  HNA   N    CA    108.93  3.000
 3AI  HN    N    CA    107.75  3.000
 3AI  HAA   CA   CB    107.79  3.000
 3AI  HAA   CA   N     107.58  3.000
 3AI  CB    CA   N     110.40  1.500
 3AI  HAA   CA   C     107.31  3.000
 3AI  CB    CA   C     110.50  1.500
 3AI  N     CA   C     111.00  2.800
 3AI  HBA   CB   HB    106.46  3.000
 3AI  HBA   CB   CG    109.65  3.000
 3AI  HB    CB   CG    110.15  3.000
 3AI  HBA   CB   CA    108.67  3.000
 3AI  HB    CB   CA    108.80  3.000
 3AI  CG    CB   CA    112.90  3.000
 3AI  CD2   CG   CD1   118.29  3.000
 3AI  CD2   CG   CB    120.26  3.000
 3AI  CD1   CG   CB    121.43  3.000
 3AI  HZ    CZ   CE2   120.31  3.000
 3AI  HZ    CZ   CE1   120.26  3.000
 3AI  CE2   CZ   CE1   119.43  3.000
 3AI  HD1   CD1  CE1   119.53  3.000
 3AI  HD1   CD1  CG    119.50  3.000
 3AI  CE1   CD1  CG    120.97  3.000
 3AI  HD2   CD2  CE2   119.55  3.000
 3AI  HD2   CD2  CG    119.41  3.000
 3AI  CE2   CD2  CG    121.03  3.000
 3AI  HE1   CE1  CD1   119.76  3.000
 3AI  HE1   CE1  CZ    120.06  3.000
 3AI  CD1   CE1  CZ    120.18  3.000
 3AI  HE2   CE2  CD2   119.76  3.000
 3AI  HE2   CE2  CZ    120.14  3.000
 3AI  CD2   CE2  CZ    120.10  3.000
 3AI  HN2   N2   CA2   116.58  3.000
 3AI  HN2   N2   C1    119.67  3.000
 3AI  CA2   N2   C1    123.59  3.000
 3AI  HA2   CA2  CB2   109.29  3.000
 3AI  HA2   CA2  C2    109.59  3.000
 3AI  CB2   CA2  C2    108.84  3.000
 3AI  HA2   CA2  N2    108.77  3.000
 3AI  CB2   CA2  N2    112.23  3.000
 3AI  C2    CA2  N2    108.09  3.000
 3AI  N3    C2   O1    123.87  3.000
 3AI  N3    C2   CA2   115.11  3.000
 3AI  O1    C2   CA2   121.01  3.000
 3AI  HB2B  CB2  HB2A  108.44  3.000
 3AI  HB2B  CB2  HB2   108.54  3.000
 3AI  HB2A  CB2  HB2   108.07  3.000
 3AI  HB2B  CB2  CA2   110.23  3.000
 3AI  HB2A  CB2  CA2   110.92  3.000
 3AI  HB2   CB2  CA2   110.56  3.000
 3AI  HN3   N3   CA3   118.09  3.000
 3AI  HN3   N3   C2    117.43  3.000
 3AI  CA3   N3   C2    121.70  3.000
 3AI  HA3   CA3  CB3   107.43  3.000
 3AI  HA3   CA3  C3    108.58  3.000
 3AI  CB3   CA3  C3    112.35  3.000
 3AI  HA3   CA3  N3    107.78  3.000
 3AI  CB3   CA3  N3    109.07  3.000
 3AI  C3    CA3  N3    111.44  3.000
 3AI  OXT   C3   O2    127.18  3.000
 3AI  OXT   C3   CA3   115.56  3.000
 3AI  O2    C3   CA3   117.24  3.000
 3AI  HB3   CB3  CG3   108.00  3.000
 3AI  HB3   CB3  CG2   106.88  3.000
 3AI  CG3   CB3  CG2   111.30  3.000
 3AI  HB3   CB3  CA3   105.70  3.000
 3AI  CG3   CB3  CA3   112.72  3.000
 3AI  CG2   CB3  CA3   111.83  3.000
 3AI  HG2A  CG2  HG2   106.12  3.000
 3AI  HG2A  CG2  CD3   108.79  3.000
 3AI  HG2   CG2  CD3   109.87  3.000
 3AI  HG2A  CG2  CB3   108.89  3.000
 3AI  HG2   CG2  CB3   109.56  3.000
 3AI  CD3   CG2  CB3   113.35  3.000
 3AI  HG3B  CG3  HG3A  107.33  3.000
 3AI  HG3B  CG3  HG3   107.61  3.000
 3AI  HG3A  CG3  HG3   106.76  3.000
 3AI  HG3B  CG3  CB3   111.11  3.000
 3AI  HG3A  CG3  CB3   112.94  3.000
 3AI  HG3   CG3  CB3   110.83  3.000
 3AI  HD3B  CD3  HD3A  107.15  3.000
 3AI  HD3B  CD3  HD3   107.48  3.000
 3AI  HD3A  CD3  HD3   107.61  3.000
 3AI  HD3B  CD3  CG2   110.83  3.000
 3AI  HD3A  CD3  CG2   112.28  3.000
 3AI  HD3   CD3  CG2   111.26  3.000
 3AI  CG1   SD   CE    100.08  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
 3AI  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 3AI  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 3AI  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 3AI  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 3AI  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 3AI  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 3AI  CONST_07  CE1  CD1  CG   CB    180.00   0.0  0
 3AI  CONST_08  CE2  CD2  CG   CB    180.00   0.0  0
 3AI  CONST_09  HE1  CE1  CD1  CG    180.00   0.0  0
 3AI  CONST_10  HE2  CE2  CD2  CG    180.00   0.0  0
 3AI  CONST_11  HD1  CD1  CE1  CZ    180.00   0.0  0
 3AI  CONST_12  HD2  CD2  CE2  CZ    180.00   0.0  0
 3AI  CONST_13  HZ   CZ   CE1  CD1   180.00   0.0  0
 3AI  CONST_14  CA2  N2   C1   O       0.00   0.0  0
 3AI  CONST_15  CA2  N2   C1   CA1   180.00   0.0  0
 3AI  CONST_17  CA3  N3   C2   O1      0.00   0.0  0
 3AI  CONST_18  HN2  N2   C1   O     180.00   0.0  0
 3AI  CONST_19  HN3  N3   C2   CA2     0.00   0.0  0
 3AI  Var_01    CD1  CG   CB   CA     98.46  30.0  2
 3AI  Var_02    CA1  CB1  CG1  SD    175.16  30.0  1
 3AI  Var_03    CB1  CG1  SD   CE   -177.92  30.0  3
 3AI  Var_04    CA   C    N1   CA1  -166.30  30.0  3
 3AI  Var_05    HE   CE   SD   CG1    61.81  30.0  3
 3AI  Var_06    HD3  CD3  CG2  CB3   -58.95  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
 3AI  chir_01  CA1  C1   N1   CB1  positiv
 3AI  chir_02  CA   N    C    CB   positiv
 3AI  chir_03  CA2  N2   CB2  C2   negativ
 3AI  chir_04  CA3  N3   C3   CB3  positiv
 3AI  chir_05  CB3  CA3  CG2  CG3  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
 3AI  plan-1  CB   0.020
 3AI  plan-1  CG   0.020
 3AI  plan-1  CZ   0.020
 3AI  plan-1  CD1  0.020
 3AI  plan-1  CD2  0.020
 3AI  plan-1  CE1  0.020
 3AI  plan-1  CE2  0.020
 3AI  plan-1  HZ   0.020
 3AI  plan-1  HD1  0.020
 3AI  plan-1  HD2  0.020
 3AI  plan-1  HE1  0.020
 3AI  plan-1  HE2  0.020
 3AI  plan-2  O    0.020
 3AI  plan-2  C1   0.020
 3AI  plan-2  CA1  0.020
 3AI  plan-2  N2   0.020
 3AI  plan-2  CA2  0.020
 3AI  plan-2  HN2  0.020
 3AI  plan-3  CA2  0.020
 3AI  plan-3  C2   0.020
 3AI  plan-3  O1   0.020
 3AI  plan-3  N3   0.020
 3AI  plan-3  CA3  0.020
 3AI  plan-3  HN3  0.020
 3AI  plan-4  CA3  0.020
 3AI  plan-4  C3   0.020
 3AI  plan-4  O2   0.020
 3AI  plan-4  OXT  0.020

