# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon May 25 09:22:25 2020
#   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  64  35  .  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_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   0.526   6.4501  -0.2572   1.1530
 2Z9  O     O  O      0  -0.503   6.0493  -1.0840   1.9590
 2Z9  CH3   C  CH3    0  -0.775   7.7740   0.4471   1.3551
 2Z9  N     N  NH1    0  -0.632   5.8024   0.0898   0.0274
 2Z9  CA    C  CH1    0  -0.202   4.5234  -0.3913  -0.4366
 2Z9  C1    C  C      0   0.564   3.3752   0.2760   0.3216
 2Z9  O1    O  O      0  -0.478   3.4801   0.6788   1.4674
 2Z9  CB    C  CH2    0  -0.580   4.3713  -1.9129  -0.4195
 2Z9  CG    C  C      0   0.418   5.4157  -2.6370  -1.2908
 2Z9  OD1   O  O      0  -0.609   5.7935  -2.0501  -2.3239
 2Z9  OD2   O  OC    -1  -0.615   5.7634  -3.7718  -0.9110
 2Z9  N1    N  NH1    0  -0.630   2.2386   0.3498  -0.3946
 2Z9  CA1   C  CH1    0  -0.227   0.9680   0.7826   0.1288
 2Z9  C2    C  C      0   0.575  -0.1069  -0.1947  -0.3372
 2Z9  O2    O  O      0  -0.489  -0.0078  -0.7930  -1.3980
 2Z9  CB1   C  CH2    0  -0.392   0.5845   2.1988  -0.3273
 2Z9  CG1   C  CH2    0  -0.589   1.5591   3.2580   0.1555
 2Z9  CD    C  C      0   0.417   1.1877   4.7063  -0.2111
 2Z9  OE1   O  O      0  -0.607   0.1278   4.8977  -0.8386
 2Z9  OE2   O  OC    -1  -0.632   1.9964   5.5827   0.1605
 2Z9  N2    N  NH1    0  -0.625  -1.1606  -0.2896   0.4871
 2Z9  CA2   C  CH1    0  -0.220  -2.3817  -0.9827   0.1681
 2Z9  C3    C  C      0   0.560  -3.5633  -0.0625   0.4864
 2Z9  O3    O  O      0  -0.493  -3.4117   0.9848   1.1015
 2Z9  CB2   C  CH1    0  -0.230  -2.5175  -2.3287   0.9150
 2Z9  CG11  C  CH3    0  -0.655  -1.3521  -3.2547   0.5911
 2Z9  CG2   C  CH3    0  -0.673  -2.6721  -2.1452   2.4205
 2Z9  N3    N  NH1    0  -0.624  -4.7493  -0.5120   0.0663
 2Z9  CA3   C  CH1    0  -0.094  -6.0219   0.0939   0.4264
 2Z9  C4    C  CH2    0  -0.155  -6.4084  -0.2639   1.8540
 2Z9  O4    O  OH1    0  -0.672  -6.5434  -1.6620   1.9669
 2Z9  CB3   C  CH2    0  -0.597  -7.0673  -0.3106  -0.6008
 2Z9  CG3   C  C      0   0.413  -6.7973   0.2533  -2.0101
 2Z9  OD11  O  O      0  -0.606  -6.3431   1.4125  -2.0726
 2Z9  OD21  O  OC    -1  -0.619  -7.0878  -0.4843  -2.9732
 2Z9  H1    H  HCH3   0   0.260   7.7946   0.8970   2.3472
 2Z9  H2    H  HCH3   0   0.263   8.5809  -0.2851   1.3141
 2Z9  H3    H  HCH3   0   0.244   7.9798   1.2238   0.6208
 2Z9  H     H  HNH1   0   0.399   6.2397   0.7820  -0.5563
 2Z9  HA    H  HCH1   0   0.269   4.4636  -0.0809  -1.4817
 2Z9  HB2   H  HCH2   0   0.239   4.3870  -2.2925   0.5992
 2Z9  HB3   H  HCH2   0   0.239   3.3818  -2.1540  -0.8243
 2Z9  H4    H  HNH1   0   0.394   2.2406   0.0168  -1.3467
 2Z9  HA1   H  HCH1   0   0.269   1.0336   0.7662   1.2194
 2Z9  HB21  H  HCH2   0   0.223   0.5167   2.2129  -1.4185
 2Z9  HB31  H  HCH2   0   0.224  -0.4184   2.4190   0.0460
 2Z9  HG2   H  HCH2   0   0.225   1.6633   3.1931   1.2439
 2Z9  HG3   H  HCH2   0   0.228   2.5597   3.0549  -0.2382
 2Z9  H5    H  HNH1   0   0.399  -1.1806   0.3083   1.2992
 2Z9  HA2   H  HCH1   0   0.290  -2.3786  -1.1910  -0.9051
 2Z9  HB    H  HCH1   0   0.233  -3.4280  -2.8051   0.5378
 2Z9  HG11  H  HCH3   0   0.222  -0.4141  -2.8778   1.0010
 2Z9  HG12  H  HCH3   0   0.234  -1.5265  -4.2403   1.0251
 2Z9  HG13  H  HCH3   0   0.230  -1.2235  -3.3816  -0.4841
 2Z9  HG21  H  HCH3   0   0.239  -3.5813  -1.6003   2.6805
 2Z9  HG22  H  HCH3   0   0.237  -2.7320  -3.1166   2.9129
 2Z9  HG23  H  HCH3   0   0.221  -1.8198  -1.6163   2.8509
 2Z9  H6    H  HNH1   0   0.398  -4.7832  -1.4113  -0.3881
 2Z9  HA3   H  HCH1   0   0.246  -5.9046   1.1772   0.3804
 2Z9  HB22  H  HCH2   0   0.219  -7.1711  -1.3981  -0.6383
 2Z9  HB32  H  HCH2   0   0.242  -8.0372   0.0742  -0.2661
 2Z9  H30   H  HOH1   0   0.455  -6.6232  -1.8818   2.8986
 2Z9  HXT   H  HCH2   0   0.209  -5.6415   0.1189   2.5374
 2Z9  H32   H  HCH2   0   0.199  -7.3434   0.2591   2.0987

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  1.513  0.020  1.513
 2Z9  C     N     single  1.344  0.020  1.344
 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  1.529  0.020  1.529
 2Z9  CA    CB    single  1.521  0.033  1.521
 2Z9  CA    HA    single  0.970  0.020  0.970
 2Z9  C1    O1    double  1.219  0.020  1.219
 2Z9  C1    N1    single  1.345  0.020  1.345
 2Z9  CB    CG    single  1.541  0.020  1.541
 2Z9  CB    HB2   single  0.970  0.020  1.090
 2Z9  CB    HB3   single  0.970  0.020  1.090
 2Z9  CG    OD1   deloc   1.247  0.020  1.247
 2Z9  CG    OD2   deloc   1.246  0.020  1.246
 2Z9  N1    CA1   single  1.441  0.020  1.441
 2Z9  N1    H4    single  0.860  0.020  1.020
 2Z9  CA1   C2    single  1.526  0.020  1.526
 2Z9  CA1   CB1   single  1.536  0.020  1.536
 2Z9  CA1   HA1   single  0.970  0.020  1.090
 2Z9  C2    O2    double  1.222  0.020  1.222
 2Z9  C2    N2    single  1.341  0.020  1.341
 2Z9  CB1   CG1   single  1.518  0.020  1.518
 2Z9  CB1   HB21  single  0.970  0.020  1.090
 2Z9  CB1   HB31  single  0.970  0.020  1.090
 2Z9  CG1   CD    single  1.540  0.020  1.540
 2Z9  CG1   HG2   single  0.970  0.020  1.090
 2Z9  CG1   HG3   single  0.970  0.020  1.090
 2Z9  CD    OE1   deloc   1.247  0.020  1.247
 2Z9  CD    OE2   deloc   1.249  0.020  1.249
 2Z9  N2    CA2   single  1.440  0.020  1.440
 2Z9  N2    H5    single  0.860  0.020  1.020
 2Z9  CA2   C3    single  1.531  0.020  1.531
 2Z9  CA2   CB2   single  1.545  0.020  1.545
 2Z9  CA2   HA2   single  0.970  0.020  1.090
 2Z9  C3    O3    double  1.224  0.020  1.224
 2Z9  C3    N3    single  1.336  0.020  1.336
 2Z9  CB2   CG11  single  1.523  0.020  1.523
 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  1.455  0.020  1.455
 2Z9  N3    H6    single  0.860  0.020  1.020
 2Z9  CA3   C4    single  1.522  0.020  1.522
 2Z9  CA3   CB3   single  1.520  0.020  1.520
 2Z9  CA3   HA3   single  0.970  0.020  1.090
 2Z9  C4    O4    single  1.409  0.020  1.409
 2Z9  CB3   CG3   single  1.542  0.020  1.542
 2Z9  CB3   HB22  single  0.970  0.020  1.090
 2Z9  CB3   HB32  single  0.970  0.020  1.090
 2Z9  CG3   OD11  deloc   1.247  0.020  1.247
 2Z9  CG3   OD21  deloc   1.247  0.020  1.247
 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   114.41  3.000
 2Z9  N     C     O     124.67  3.000
 2Z9  CH3   C     O     120.91  3.000
 2Z9  H3    CH3   H2    108.29  3.000
 2Z9  H3    CH3   H1    108.42  3.000
 2Z9  H2    CH3   H1    107.31  3.000
 2Z9  H3    CH3   C     114.04  3.000
 2Z9  H2    CH3   C     109.27  3.000
 2Z9  H1    CH3   C     109.29  3.000
 2Z9  H     N     CA    114.00  3.000
 2Z9  H     N     C     117.02  3.000
 2Z9  CA    N     C     111.00  2.800
 2Z9  HA    CA    CB    109.00  3.000
 2Z9  HA    CA    C1    108.02  3.000
 2Z9  CB    CA    C1    110.73  3.000
 2Z9  HA    CA    N     110.00  3.000
 2Z9  CB    CA    N     110.40  1.500
 2Z9  C1    CA    N     111.14  3.000
 2Z9  N1    C1    O1    123.71  3.000
 2Z9  N1    C1    CA    113.22  3.000
 2Z9  O1    C1    CA    123.06  3.000
 2Z9  HB3   CB    HB2   106.40  3.000
 2Z9  HB3   CB    CG    107.44  3.000
 2Z9  HB2   CB    CG    110.85  3.000
 2Z9  HB3   CB    CA    107.73  3.000
 2Z9  HB2   CB    CA    110.89  3.000
 2Z9  CG    CB    CA    113.19  3.000
 2Z9  OD2   CG    OD1   126.63  3.000
 2Z9  OD2   CG    CB    116.40  3.000
 2Z9  OD1   CG    CB    116.92  3.000
 2Z9  H4    N1    CA1   116.35  3.000
 2Z9  H4    N1    C1    118.87  3.000
 2Z9  CA1   N1    C1    124.62  3.000
 2Z9  HA1   CA1   CB1   108.98  3.000
 2Z9  HA1   CA1   C2    109.73  3.000
 2Z9  CB1   CA1   C2    108.90  3.000
 2Z9  HA1   CA1   N1    107.77  3.000
 2Z9  CB1   CA1   N1    112.90  3.000
 2Z9  C2    CA1   N1    108.54  3.000
 2Z9  N2    C2    O2    124.24  3.000
 2Z9  N2    C2    CA1   114.27  3.000
 2Z9  O2    C2    CA1   121.45  3.000
 2Z9  HB31  CB1   HB21  106.34  3.000
 2Z9  HB31  CB1   CG1   109.88  3.000
 2Z9  HB21  CB1   CG1   110.38  3.000
 2Z9  HB31  CB1   CA1   108.27  3.000
 2Z9  HB21  CB1   CA1   108.88  3.000
 2Z9  CG1   CB1   CA1   112.86  3.000
 2Z9  HG3   CG1   HG2   105.05  3.000
 2Z9  HG3   CG1   CD    108.02  3.000
 2Z9  HG2   CG1   CD    108.38  3.000
 2Z9  HG3   CG1   CB1   110.07  3.000
 2Z9  HG2   CG1   CB1   109.62  3.000
 2Z9  CD    CG1   CB1   115.20  3.000
 2Z9  OE2   CD    OE1   126.34  3.000
 2Z9  OE2   CD    CG1   115.66  3.000
 2Z9  OE1   CD    CG1   118.00  3.000
 2Z9  H5    N2    CA2   116.55  3.000
 2Z9  H5    N2    C2    117.93  3.000
 2Z9  CA2   N2    C2    124.34  3.000
 2Z9  HA2   CA2   CB2   107.98  3.000
 2Z9  HA2   CA2   C3    108.71  3.000
 2Z9  CB2   CA2   C3    110.80  3.000
 2Z9  HA2   CA2   N2    107.87  3.000
 2Z9  CB2   CA2   N2    112.75  3.000
 2Z9  C3    CA2   N2    108.61  3.000
 2Z9  N3    C3    O3    123.77  3.000
 2Z9  N3    C3    CA2   114.68  3.000
 2Z9  O3    C3    CA2   121.54  3.000
 2Z9  HB    CB2   CG2   107.96  3.000
 2Z9  HB    CB2   CG11  107.37  3.000
 2Z9  CG2   CB2   CG11  111.14  3.000
 2Z9  HB    CB2   CA2   106.60  3.000
 2Z9  CG2   CB2   CA2   112.42  3.000
 2Z9  CG11  CB2   CA2   111.07  3.000
 2Z9  HG13  CG11  HG12  107.81  3.000
 2Z9  HG13  CG11  HG11  108.02  3.000
 2Z9  HG12  CG11  HG11  107.47  3.000
 2Z9  HG13  CG11  CB2   111.75  3.000
 2Z9  HG12  CG11  CB2   110.02  3.000
 2Z9  HG11  CG11  CB2   111.59  3.000
 2Z9  HG23  CG2   HG22  107.24  3.000
 2Z9  HG23  CG2   HG21  108.34  3.000
 2Z9  HG22  CG2   HG21  106.94  3.000
 2Z9  HG23  CG2   CB2   111.62  3.000
 2Z9  HG22  CG2   CB2   110.13  3.000
 2Z9  HG21  CG2   CB2   112.32  3.000
 2Z9  H6    N3    CA3   116.98  3.000
 2Z9  H6    N3    C3    118.14  3.000
 2Z9  CA3   N3    C3    123.96  3.000
 2Z9  HA3   CA3   CB3   108.04  3.000
 2Z9  HA3   CA3   C4    107.49  3.000
 2Z9  CB3   CA3   C4    113.37  3.000
 2Z9  HA3   CA3   N3    108.01  3.000
 2Z9  CB3   CA3   N3    108.87  3.000
 2Z9  C4    CA3   N3    110.89  3.000
 2Z9  H32   C4    HXT   106.87  3.000
 2Z9  H32   C4    O4    111.89  3.000
 2Z9  HXT   C4    O4    111.32  3.000
 2Z9  H32   C4    CA3   108.25  3.000
 2Z9  HXT   C4    CA3   108.97  3.000
 2Z9  O4    C4    CA3   109.44  3.000
 2Z9  H30   O4    C4    108.22  3.000
 2Z9  HB32  CB3   HB22  106.01  3.000
 2Z9  HB32  CB3   CG3   107.80  3.000
 2Z9  HB22  CB3   CG3   110.44  3.000
 2Z9  HB32  CB3   CA3   107.98  3.000
 2Z9  HB22  CB3   CA3   110.68  3.000
 2Z9  CG3   CB3   CA3   113.57  3.000
 2Z9  OD21  CG3   OD11  126.59  3.000
 2Z9  OD21  CG3   CB3   116.66  3.000
 2Z9  OD11  CG3   CB3   116.73  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  Var_01    OD1   CG    CB   CA    -33.16  30.0  3
 2Z9  Var_02    CD    CG1   CB1  CA1  -177.05  30.0  3
 2Z9  Var_03    OE1   CD    CG1  CB1     1.34  30.0  3
 2Z9  Var_04    OD11  CG3   CB3  CA3   -38.14  30.0  3
 2Z9  Var_05    H1    CH3   C    O     -53.25  30.0  3
 2Z9  Var_06    HG11  CG11  CB2  CA2    67.84  30.0  3
 2Z9  Var_07    HG21  CG2   CB2  CA2    62.76  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-3  CB3   0.020
 2Z9  plan-3  CG3   0.020
 2Z9  plan-3  OD11  0.020
 2Z9  plan-3  OD21  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

