# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 16:16:35 2021
#   Inital geometry file: a 162 line input string
#   Ligand name: N-acetyl-L-alpha-aspartyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-hydroxypropan-2-yl]-L-valinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](CC(O)=O)NC(C)=O)C(=O)N[C@H](CO)CC(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
 2Z9  2Z9  N-acetyl-L-alpha-aspartyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-hydroxypropan-2-yl]-L-valinamide  peptide  67  35  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2Z9
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
 2Z9  C     C  C     0   0.536   -7.5541  72.5862  27.3392
 2Z9  O     O  O     0  -0.496   -6.3320  72.6497  27.3352
 2Z9  CH3   C  CH3   0  -0.778   -8.3669  72.7551  28.5951
 2Z9  N     N  NH1   0  -0.624   -8.2552  72.3586  26.2134
 2Z9  CA    C  CH1   0  -0.198   -7.5978  72.2683  24.9386
 2Z9  C1    C  C     0   0.568   -6.9725  73.6165  24.5656
 2Z9  O1    O  O     0  -0.479   -7.4976  74.6704  24.8771
 2Z9  CB    C  CH2   0  -0.611   -8.5951  71.8753  23.8574
 2Z9  CG    C  C     0   0.559   -9.0962  70.4608  24.0060
 2Z9  OD1   O  O     0  -0.433   -8.5733  69.6116  24.6806
 2Z9  OD2   O  OH1   0  -0.589  -10.1770  70.2515  23.2674
 2Z9  N1    N  NH1   0  -0.626   -5.8474  73.5146  23.8420
 2Z9  CA1   C  CH1   0  -0.248   -5.1170  74.6426  23.3290
 2Z9  C2    C  C     0   0.579   -4.8383  74.4353  21.8415
 2Z9  O2    O  O     0  -0.478   -4.8079  73.3229  21.3423
 2Z9  CB1   C  CH2   0  -0.411   -3.7982  74.8610  24.0816
 2Z9  CG1   C  CH2   0  -0.597   -4.0404  75.1524  25.5529
 2Z9  CD    C  C     0   0.556   -2.7734  75.4353  26.3100
 2Z9  OE1   O  O     0  -0.444   -1.6606  75.3858  25.8480
 2Z9  OE2   O  OH1   0  -0.596   -3.0188  75.7506  27.5778
 2Z9  N2    N  NH1   0  -0.626   -4.6070  75.5751  21.1727
 2Z9  CA2   C  CH1   0  -0.229   -4.2174  75.6380  19.7896
 2Z9  C3    C  C     0   0.571   -2.9255  76.4460  19.6697
 2Z9  O3    O  O     0  -0.481   -2.5074  77.1333  20.5874
 2Z9  CB2   C  CH1   0  -0.229   -5.3321  76.2260  18.8952
 2Z9  CG11  C  CH3   0  -0.656   -6.6053  75.3976  19.0166
 2Z9  CG2   C  CH3   0  -0.673   -5.6031  77.6968  19.1908
 2Z9  N3    N  NH1   0  -0.641   -2.3231  76.3527  18.4738
 2Z9  CA3   C  CH1   0  -0.116   -1.1313  77.0908  18.1109
 2Z9  C4    C  CH2   0  -0.130   -1.5289  78.3843  17.4042
 2Z9  O4    O  OH1   0  -0.667   -0.3632  79.1260  17.1423
 2Z9  CB3   C  CH2   0  -0.599   -0.2388  76.2221  17.2398
 2Z9  CG3   C  C     0   0.558    0.2970  75.0155  17.9618
 2Z9  OD11  O  O     0  -0.436    0.3843  74.9078  19.1589
 2Z9  OD21  O  OH1   0  -0.594    0.7030  74.0771  17.1140
 2Z9  H1    H  HCH3  0   0.267   -7.9829  72.0931  29.3702
 2Z9  H2    H  HCH3  0   0.269   -8.2581  73.7779  28.9573
 2Z9  H3    H  HCH3  0   0.251   -9.4267  72.5514  28.4557
 2Z9  H     H  HNH1  0   0.406   -9.2604  72.4164  26.2420
 2Z9  HA    H  HCH1  0   0.286   -6.8128  71.5093  24.9935
 2Z9  HB2   H  HCH2  0   0.298   -9.4358  72.5730  23.8300
 2Z9  HB3   H  HCH2  0   0.318   -8.1182  71.9426  22.8745
 2Z9  HD2   H  HOH1  0   0.484  -10.4560  69.3262  23.3400
 2Z9  H4    H  HNH1  0   0.402   -5.4760  72.5982  23.6434
 2Z9  HA1   H  HCH1  0   0.286   -5.7457  75.5265  23.4533
 2Z9  HB21  H  HCH2  0   0.251   -3.1658  73.9772  23.9671
 2Z9  HB31  H  HCH2  0   0.251   -3.2625  75.6933  23.6197
 2Z9  HG2   H  HCH2  0   0.282   -4.7125  76.0077  25.6700
 2Z9  HG3   H  HCH2  0   0.292   -4.5444  74.3131  26.0419
 2Z9  HE2   H  HOH1  0   0.480   -2.1869  75.9287  28.0412
 2Z9  H5    H  HNH1  0   0.403   -4.6099  76.4393  21.6926
 2Z9  HA2   H  HCH1  0   0.296   -4.0251  74.6154  19.4559
 2Z9  HB    H  HCH1  0   0.236   -4.9831  76.1450  17.8612
 2Z9  HG11  H  HCH3  0   0.238   -7.3469  75.7356  18.2918
 2Z9  HG12  H  HCH3  0   0.232   -6.4163  74.3386  18.8346
 2Z9  HG13  H  HCH3  0   0.223   -7.0500  75.4951  20.0078
 2Z9  HG21  H  HCH3  0   0.243   -6.4103  78.0649  18.5571
 2Z9  HG22  H  HCH3  0   0.223   -5.9110  77.8503  20.2270
 2Z9  HG23  H  HCH3  0   0.235   -4.7328  78.3273  19.0025
 2Z9  H6    H  HNH1  0   0.405   -2.7469  75.7727  17.7655
 2Z9  HA3   H  HCH1  0   0.266   -0.6065  77.3447  19.0327
 2Z9  HB22  H  HCH2  0   0.277   -0.7659  75.9123  16.3330
 2Z9  HB32  H  HCH2  0   0.309    0.6218  76.8041  16.8979
 2Z9  HD21  H  HOH1  0   0.480    1.0893  73.3342  17.6016
 2Z9  H30   H  HOH1  0   0.461   -0.6040  79.8965  16.6206
 2Z9  HXT   H  HCH2  0   0.198   -2.0746  78.1374  16.4838
 2Z9  H32   H  HCH2  0   0.212   -2.2214  78.9336  18.0552

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
 2Z9  C     O     double  1.231  0.020  1.231
 2Z9  C     CH3   single  1.505  0.020  1.505
 2Z9  C     N     single  1.346  0.020  1.346
 2Z9  CH3   H1    single  0.970  0.020  1.090
 2Z9  CH3   H2    single  0.970  0.020  1.090
 2Z9  CH3   H3    single  0.970  0.020  1.090
 2Z9  N     CA    single  1.458  0.019  1.458
 2Z9  N     H     single  0.860  0.020  0.860
 2Z9  CA    C1    single  1.532  0.020  1.532
 2Z9  CA    CB    single  1.521  0.033  1.521
 2Z9  CA    HA    single  0.970  0.020  0.970
 2Z9  C1    O1    double  1.218  0.020  1.218
 2Z9  C1    N1    single  1.342  0.020  1.342
 2Z9  CB    CG    single  1.508  0.020  1.508
 2Z9  CB    HB2   single  0.970  0.020  1.090
 2Z9  CB    HB3   single  0.970  0.020  1.090
 2Z9  CG    OD1   double  1.204  0.020  1.204
 2Z9  CG    OD2   single  1.326  0.020  1.326
 2Z9  OD2   HD2   single  0.850  0.020  0.980
 2Z9  N1    CA1   single  1.438  0.020  1.438
 2Z9  N1    H4    single  0.860  0.020  1.020
 2Z9  CA1   C2    single  1.527  0.020  1.527
 2Z9  CA1   CB1   single  1.534  0.020  1.534
 2Z9  CA1   HA1   single  0.970  0.020  1.090
 2Z9  C2    O2    double  1.220  0.020  1.220
 2Z9  C2    N2    single  1.342  0.020  1.342
 2Z9  CB1   CG1   single  1.519  0.020  1.519
 2Z9  CB1   HB21  single  0.970  0.020  1.090
 2Z9  CB1   HB31  single  0.970  0.020  1.090
 2Z9  CG1   CD    single  1.503  0.020  1.503
 2Z9  CG1   HG2   single  0.970  0.020  1.090
 2Z9  CG1   HG3   single  0.970  0.020  1.090
 2Z9  CD    OE1   double  1.206  0.020  1.206
 2Z9  CD    OE2   single  1.329  0.020  1.329
 2Z9  OE2   HE2   single  0.850  0.020  0.980
 2Z9  N2    CA2   single  1.438  0.020  1.438
 2Z9  N2    H5    single  0.860  0.020  1.020
 2Z9  CA2   C3    single  1.529  0.020  1.529
 2Z9  CA2   CB2   single  1.545  0.020  1.545
 2Z9  CA2   HA2   single  0.970  0.020  1.090
 2Z9  C3    O3    double  1.220  0.020  1.220
 2Z9  C3    N3    single  1.342  0.020  1.342
 2Z9  CB2   CG11  single  1.524  0.020  1.524
 2Z9  CB2   CG2   single  1.525  0.020  1.525
 2Z9  CB2   HB    single  0.970  0.020  1.090
 2Z9  CG11  HG11  single  0.970  0.020  1.090
 2Z9  CG11  HG12  single  0.970  0.020  1.090
 2Z9  CG11  HG13  single  0.970  0.020  1.090
 2Z9  CG2   HG21  single  0.970  0.020  1.090
 2Z9  CG2   HG22  single  0.970  0.020  1.090
 2Z9  CG2   HG23  single  0.970  0.020  1.090
 2Z9  N3    CA3   single  1.448  0.020  1.448
 2Z9  N3    H6    single  0.860  0.020  1.020
 2Z9  CA3   C4    single  1.527  0.020  1.527
 2Z9  CA3   CB3   single  1.520  0.020  1.520
 2Z9  CA3   HA3   single  0.970  0.020  1.090
 2Z9  C4    O4    single  1.406  0.020  1.406
 2Z9  CB3   CG3   single  1.505  0.020  1.505
 2Z9  CB3   HB22  single  0.970  0.020  1.090
 2Z9  CB3   HB32  single  0.970  0.020  1.090
 2Z9  CG3   OD11  double  1.205  0.020  1.205
 2Z9  CG3   OD21  single  1.328  0.020  1.328
 2Z9  OD21  HD21  single  0.850  0.020  0.980
 2Z9  O4    H30   single  0.850  0.020  0.980
 2Z9  C4    HXT   single  0.970  0.020  1.090
 2Z9  C4    H32   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
 2Z9  N     C     CH3   115.83  3.000
 2Z9  N     C     O     121.76  3.000
 2Z9  CH3   C     O     122.42  3.000
 2Z9  H3    CH3   H2    108.37  3.000
 2Z9  H3    CH3   H1    108.70  3.000
 2Z9  H2    CH3   H1    107.37  3.000
 2Z9  H3    CH3   C     113.45  3.000
 2Z9  H2    CH3   C     109.18  3.000
 2Z9  H1    CH3   C     109.58  3.000
 2Z9  H     N     CA    114.00  3.000
 2Z9  H     N     C     119.11  3.000
 2Z9  CA    N     C     111.00  2.800
 2Z9  HA    CA    CB    109.00  3.000
 2Z9  HA    CA    C1    109.27  3.000
 2Z9  CB    CA    C1    108.76  3.000
 2Z9  HA    CA    N     110.00  3.000
 2Z9  CB    CA    N     110.40  1.500
 2Z9  C1    CA    N     110.32  3.000
 2Z9  N1    C1    O1    124.41  3.000
 2Z9  N1    C1    CA    114.00  3.000
 2Z9  O1    C1    CA    121.55  3.000
 2Z9  HB3   CB    HB2   105.86  3.000
 2Z9  HB3   CB    CG    106.92  3.000
 2Z9  HB2   CB    CG    110.23  3.000
 2Z9  HB3   CB    CA    109.66  3.000
 2Z9  HB2   CB    CA    110.91  3.000
 2Z9  CG    CB    CA    112.95  3.000
 2Z9  OD2   CG    OD1   123.70  3.000
 2Z9  OD2   CG    CB    111.36  3.000
 2Z9  OD1   CG    CB    124.92  3.000
 2Z9  HD2   OD2   CG    110.11  3.000
 2Z9  H4    N1    CA1   117.09  3.000
 2Z9  H4    N1    C1    118.95  3.000
 2Z9  CA1   N1    C1    123.97  3.000
 2Z9  HA1   CA1   CB1   108.90  3.000
 2Z9  HA1   CA1   C2    109.01  3.000
 2Z9  CB1   CA1   C2    109.89  3.000
 2Z9  HA1   CA1   N1    107.57  3.000
 2Z9  CB1   CA1   N1    111.91  3.000
 2Z9  C2    CA1   N1    109.49  3.000
 2Z9  N2    C2    O2    124.51  3.000
 2Z9  N2    C2    CA1   113.68  3.000
 2Z9  O2    C2    CA1   121.79  3.000
 2Z9  HB31  CB1   HB21  106.75  3.000
 2Z9  HB31  CB1   CG1   109.97  3.000
 2Z9  HB21  CB1   CG1   110.42  3.000
 2Z9  HB31  CB1   CA1   108.82  3.000
 2Z9  HB21  CB1   CA1   109.32  3.000
 2Z9  CG1   CB1   CA1   111.43  3.000
 2Z9  HG3   CG1   HG2   105.59  3.000
 2Z9  HG3   CG1   CD    107.92  3.000
 2Z9  HG2   CG1   CD    108.47  3.000
 2Z9  HG3   CG1   CB1   111.04  3.000
 2Z9  HG2   CG1   CB1   110.58  3.000
 2Z9  CD    CG1   CB1   112.93  3.000
 2Z9  OE2   CD    OE1   123.06  3.000
 2Z9  OE2   CD    CG1   111.69  3.000
 2Z9  OE1   CD    CG1   125.26  3.000
 2Z9  HE2   OE2   CD    109.96  3.000
 2Z9  H5    N2    CA2   117.33  3.000
 2Z9  H5    N2    C2    118.07  3.000
 2Z9  CA2   N2    C2    124.28  3.000
 2Z9  HA2   CA2   CB2   107.84  3.000
 2Z9  HA2   CA2   C3    108.78  3.000
 2Z9  CB2   CA2   C3    111.29  3.000
 2Z9  HA2   CA2   N2    107.48  3.000
 2Z9  CB2   CA2   N2    112.20  3.000
 2Z9  C3    CA2   N2    109.11  3.000
 2Z9  N3    C3    O3    123.74  3.000
 2Z9  N3    C3    CA2   114.36  3.000
 2Z9  O3    C3    CA2   121.89  3.000
 2Z9  HB    CB2   CG2   108.14  3.000
 2Z9  HB    CB2   CG11  107.55  3.000
 2Z9  CG2   CB2   CG11  111.13  3.000
 2Z9  HB    CB2   CA2   106.78  3.000
 2Z9  CG2   CB2   CA2   112.52  3.000
 2Z9  CG11  CB2   CA2   110.47  3.000
 2Z9  HG13  CG11  HG12  108.00  3.000
 2Z9  HG13  CG11  HG11  107.40  3.000
 2Z9  HG12  CG11  HG11  107.92  3.000
 2Z9  HG13  CG11  CB2   111.38  3.000
 2Z9  HG12  CG11  CB2   111.69  3.000
 2Z9  HG11  CG11  CB2   110.29  3.000
 2Z9  HG23  CG2   HG22  107.91  3.000
 2Z9  HG23  CG2   HG21  107.17  3.000
 2Z9  HG22  CG2   HG21  107.18  3.000
 2Z9  HG23  CG2   CB2   112.47  3.000
 2Z9  HG22  CG2   CB2   111.71  3.000
 2Z9  HG21  CG2   CB2   110.16  3.000
 2Z9  H6    N3    CA3   117.57  3.000
 2Z9  H6    N3    C3    118.49  3.000
 2Z9  CA3   N3    C3    123.86  3.000
 2Z9  HA3   CA3   CB3   109.56  3.000
 2Z9  HA3   CA3   C4    108.62  3.000
 2Z9  CB3   CA3   C4    111.83  3.000
 2Z9  HA3   CA3   N3    107.63  3.000
 2Z9  CB3   CA3   N3    109.61  3.000
 2Z9  C4    CA3   N3    109.48  3.000
 2Z9  H32   C4    HXT   107.22  3.000
 2Z9  H32   C4    O4    111.68  3.000
 2Z9  HXT   C4    O4    111.99  3.000
 2Z9  H32   C4    CA3   108.29  3.000
 2Z9  HXT   C4    CA3   109.08  3.000
 2Z9  O4    C4    CA3   108.49  3.000
 2Z9  H30   O4    C4    108.43  3.000
 2Z9  HB32  CB3   HB22  105.71  3.000
 2Z9  HB32  CB3   CG3   107.25  3.000
 2Z9  HB22  CB3   CG3   110.02  3.000
 2Z9  HB32  CB3   CA3   109.69  3.000
 2Z9  HB22  CB3   CA3   110.74  3.000
 2Z9  CG3   CB3   CA3   113.10  3.000
 2Z9  OD21  CG3   OD11  123.29  3.000
 2Z9  OD21  CG3   CB3   111.65  3.000
 2Z9  OD11  CG3   CB3   125.04  3.000
 2Z9  HD21  OD21  CG3   110.02  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
 2Z9  CONST_01  CA    N     C    O       0.00   0.0  0
 2Z9  CONST_02  CA    N     C    CH3   180.00   0.0  0
 2Z9  CONST_03  CA1   N1    C1   CA    180.00   0.0  0
 2Z9  CONST_04  CA1   N1    C1   O1      0.00   0.0  0
 2Z9  CONST_05  CA2   N2    C2   CA1   180.00   0.0  0
 2Z9  CONST_06  CA2   N2    C2   O2      0.00   0.0  0
 2Z9  CONST_07  CA3   N3    C3   CA2   180.00   0.0  0
 2Z9  CONST_08  CA3   N3    C3   O3      0.00   0.0  0
 2Z9  CONST_09  H     N     C    O     180.00   0.0  0
 2Z9  CONST_10  H4    N1    C1   CA      0.00   0.0  0
 2Z9  CONST_11  H5    N2    C2   CA1     0.00   0.0  0
 2Z9  CONST_12  H6    N3    C3   CA2     0.00   0.0  0
 2Z9  CONST_13  HD2   OD2   CG   CB    180.00   0.0  0
 2Z9  CONST_14  HE2   OE2   CD   CG1   180.00   0.0  0
 2Z9  CONST_15  HD21  OD21  CG3  CB3   180.00   0.0  0
 2Z9  Var_01    OD1   CG    CB   CA    -16.63  30.0  3
 2Z9  Var_02    CD    CG1   CB1  CA1  -177.32  30.0  3
 2Z9  Var_03    OE1   CD    CG1  CB1    -3.24  30.0  3
 2Z9  Var_04    OD11  CG3   CB3  CA3   -21.44  30.0  3
 2Z9  Var_05    H1    CH3   C    O     -51.26  30.0  3
 2Z9  Var_06    HG11  CG11  CB2  CA2  -172.75  30.0  3
 2Z9  Var_07    HG21  CG2   CB2  CA2  -178.62  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
 2Z9  chir_01  CA   N   C1  CB   positiv
 2Z9  chir_02  CA1  N1  C2  CB1  positiv
 2Z9  chir_03  CA2  N2  C3  CB2  positiv
 2Z9  chir_04  CA3  N3  C4  CB3  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
 2Z9  plan-1  C     0.020
 2Z9  plan-1  O     0.020
 2Z9  plan-1  CH3   0.020
 2Z9  plan-1  N     0.020
 2Z9  plan-1  CA    0.020
 2Z9  plan-1  H     0.020
 2Z9  plan-2  CG1   0.020
 2Z9  plan-2  CD    0.020
 2Z9  plan-2  OE1   0.020
 2Z9  plan-2  OE2   0.020
 2Z9  plan-2  HE2   0.020
 2Z9  plan-3  CB3   0.020
 2Z9  plan-3  CG3   0.020
 2Z9  plan-3  OD11  0.020
 2Z9  plan-3  OD21  0.020
 2Z9  plan-3  HD21  0.020
 2Z9  plan-4  CA    0.020
 2Z9  plan-4  C1    0.020
 2Z9  plan-4  O1    0.020
 2Z9  plan-4  N1    0.020
 2Z9  plan-4  CA1   0.020
 2Z9  plan-4  H4    0.020
 2Z9  plan-5  CA1   0.020
 2Z9  plan-5  C2    0.020
 2Z9  plan-5  O2    0.020
 2Z9  plan-5  N2    0.020
 2Z9  plan-5  CA2   0.020
 2Z9  plan-5  H5    0.020
 2Z9  plan-6  CA2   0.020
 2Z9  plan-6  C3    0.020
 2Z9  plan-6  O3    0.020
 2Z9  plan-6  N3    0.020
 2Z9  plan-6  CA3   0.020
 2Z9  plan-6  H6    0.020
 2Z9  plan-7  CB    0.020
 2Z9  plan-7  CG    0.020
 2Z9  plan-7  OD1   0.020
 2Z9  plan-7  OD2   0.020
 2Z9  plan-7  HD2   0.020

