# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 04:47:10 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: (2E,4R)-2-{[(5S)-5-amino-5-carboxypentyl]imino}-4-hydroxyheptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN=C(C[C@H](O)CCC(O)=O)C(O)=O)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
 VPV  VPV  "(2E,4R)-2-{[(5S)-5-amino-5-carboxypentyl]imino}-4-hydroxyheptanedioic acid"  L-peptide  41  22  .  2022-08-11  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_VPV
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
 VPV  C    C  C      0   0.384  25.8201  -17.7144  14.5548
 VPV  N    N  NH2    0  -0.794  26.9881  -15.5202  14.9932
 VPV  O12  O  O      0  -0.623  28.0512  -23.2386   7.9353
 VPV  O11  O  OC    -1  -0.605  26.1863  -22.5315   8.9308
 VPV  C1   C  C      0   0.075  27.2595  -18.1519   6.8880
 VPV  C2   C  C      0   0.381  28.3320  -18.1610   5.7775
 VPV  C9   C  C      0   0.410  27.0555  -22.4920   8.0370
 VPV  C7   C  CH2    0  -0.453  25.5445  -20.7551   6.8514
 VPV  C6   C  CH1    0   0.089  25.4606  -19.6206   5.8318
 VPV  O10  O  OH1    0  -0.676  24.1244  -19.5812   5.3563
 VPV  C5   C  CH2    0  -0.560  25.8310  -18.2523   6.4239
 VPV  O4   O  OC    -1  -0.586  29.4613  -18.5805   6.0784
 VPV  O3   O  O      0  -0.591  27.9521  -17.7316   4.6698
 VPV  NZ   N  N      0  -0.365  27.6649  -18.0460   8.0847
 VPV  CE   C  CH2    0  -0.306  26.7649  -18.0136   9.2141
 VPV  CD   C  CH2    0  -0.418  27.4107  -17.2887  10.3866
 VPV  CG   C  CH2    0  -0.426  26.5129  -17.2432  11.6153
 VPV  CB   C  CH2    0  -0.411  27.1665  -16.5216  12.7873
 VPV  CA   C  CH1    0  -0.190  26.2702  -16.3362  14.0134
 VPV  O    O  O      0  -0.612  26.6608  -18.3310  15.2450
 VPV  OXT  O  OC    -1  -0.613  24.6776  -18.1087  14.2444
 VPV  H1   H  HNH2   0   0.331  26.3572  -15.2981  15.7552
 VPV  H2   H  HNH2   0   0.320  27.6951  -16.1142  15.4137
 VPV  H5   H  HCH2   0   0.232  27.6878  -20.6422   7.1702
 VPV  H6   H  HCH2   0   0.208  27.2040  -21.8192   5.9903
 VPV  H7   H  HCH2   0   0.215  25.2164  -20.3935   7.8291
 VPV  H8   H  HCH2   0   0.216  24.8286  -21.5276   6.5560
 VPV  H9   H  HCH1   0   0.187  26.1435  -19.8387   4.9985
 VPV  H10  H  HOH1   0   0.440  24.0494  -18.8520   4.7327
 VPV  H11  H  HCH2   0   0.241  25.6825  -17.4954   5.6492
 VPV  H12  H  HCH2   0   0.237  25.1239  -18.0363   7.2268
 VPV  H14  H  HCH2   0   0.204  25.7963  -17.5479   8.9955
 VPV  H15  H  HCH2   0   0.222  26.5437  -19.0467   9.5115
 VPV  H16  H  HCH2   0   0.209  28.3553  -17.7816  10.6361
 VPV  H17  H  HCH2   0   0.208  27.6658  -16.2691  10.0798
 VPV  H18  H  HCH2   0   0.203  25.5716  -16.7442  11.3604
 VPV  H19  H  HCH2   0   0.212  26.2458  -18.2647  11.9000
 VPV  H20  H  HCH2   0   0.199  28.0705  -17.0638  13.0882
 VPV  H21  H  HCH2   0   0.207  27.4995  -15.5322  12.4571
 VPV  H22  H  HCH1   0   0.191  25.3840  -15.7732  13.7010
 VPV  C8   C  CH2    0  -0.597  26.9224  -21.3955   6.9598

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
 VPV  O3   C2   deloc   1.247  0.020  1.247
 VPV  O12  C9   deloc   1.249  0.020  1.249
 VPV  C6   O10  single  1.419  0.020  1.419
 VPV  C6   C7   single  1.528  0.020  1.528
 VPV  C6   C5   single  1.536  0.020  1.536
 VPV  C8   C9   single  1.543  0.020  1.543
 VPV  C8   C7   single  1.523  0.020  1.523
 VPV  C9   O11  deloc   1.247  0.020  1.247
 VPV  C2   O4   deloc   1.242  0.020  1.242
 VPV  C2   C1   single  1.544  0.020  1.544
 VPV  C5   C1   single  1.505  0.020  1.505
 VPV  C1   NZ   double  1.268  0.020  1.268
 VPV  NZ   CE   single  1.445  0.020  1.445
 VPV  CE   CD   single  1.522  0.020  1.522
 VPV  CD   CG   single  1.522  0.020  1.522
 VPV  CG   CB   single  1.524  0.020  1.524
 VPV  CB   CA   single  1.530  0.020  1.530
 VPV  CA   C    single  1.525  0.021  1.525
 VPV  CA   N    single  1.458  0.019  1.458
 VPV  C    O    deloc   1.231  0.020  1.231
 VPV  C    OXT  deloc   1.248  0.020  1.248
 VPV  N    H1   single  0.890  0.020  1.040
 VPV  N    H2   single  0.890  0.020  1.040
 VPV  C8   H5   single  0.970  0.020  1.090
 VPV  C8   H6   single  0.970  0.020  1.090
 VPV  C7   H7   single  0.970  0.020  1.090
 VPV  C7   H8   single  0.970  0.020  1.090
 VPV  C6   H9   single  0.970  0.020  1.090
 VPV  O10  H10  single  0.850  0.020  0.980
 VPV  C5   H11  single  0.970  0.020  1.090
 VPV  C5   H12  single  0.970  0.020  1.090
 VPV  CE   H14  single  0.970  0.020  1.090
 VPV  CE   H15  single  0.970  0.020  1.090
 VPV  CD   H16  single  0.970  0.020  1.090
 VPV  CD   H17  single  0.970  0.020  1.090
 VPV  CG   H18  single  0.970  0.020  1.090
 VPV  CG   H19  single  0.970  0.020  1.090
 VPV  CB   H20  single  0.970  0.020  1.090
 VPV  CB   H21  single  0.970  0.020  1.090
 VPV  CA   H22  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
 VPV  OXT  C    O    126.66  3.000
 VPV  OXT  C    CA   117.43  3.000
 VPV  O    C    CA   120.80  1.700
 VPV  H2   N    H1   104.50  3.000
 VPV  H2   N    CA   107.03  3.000
 VPV  H1   N    CA   108.67  3.000
 VPV  NZ   C1   C5   126.86  3.000
 VPV  NZ   C1   C2   117.21  3.000
 VPV  C5   C1   C2   115.92  3.000
 VPV  O3   C2   O4   127.49  3.000
 VPV  O4   C2   C1   117.35  3.000
 VPV  O3   C2   C1   115.16  3.000
 VPV  C8   C9   O11  117.56  3.000
 VPV  O11  C9   O12  126.52  3.000
 VPV  C8   C9   O12  115.91  3.000
 VPV  H8   C7   H7   106.19  3.000
 VPV  H8   C7   C6   107.95  3.000
 VPV  H7   C7   C6   109.57  3.000
 VPV  H8   C7   C8   108.32  3.000
 VPV  H7   C7   C8   110.31  3.000
 VPV  C6   C7   C8   114.17  3.000
 VPV  H9   C6   C5   108.61  3.000
 VPV  H9   C6   O10  109.67  3.000
 VPV  C5   C6   O10  109.36  3.000
 VPV  H9   C6   C7   108.93  3.000
 VPV  C5   C6   C7   113.01  3.000
 VPV  O10  C6   C7   107.22  3.000
 VPV  H10  O10  C6   108.15  3.000
 VPV  H12  C5   H11  107.23  3.000
 VPV  H12  C5   C6   107.67  3.000
 VPV  H11  C5   C6   108.11  3.000
 VPV  H12  C5   C1   112.01  3.000
 VPV  H11  C5   C1   107.52  3.000
 VPV  C6   C5   C1   114.02  3.000
 VPV  CE   NZ   C1   122.72  3.000
 VPV  H15  CE   H14  106.00  3.000
 VPV  H15  CE   CD   108.97  3.000
 VPV  H14  CE   CD   109.02  3.000
 VPV  H15  CE   NZ   108.44  3.000
 VPV  H14  CE   NZ   113.83  3.000
 VPV  CD   CE   NZ   110.40  3.000
 VPV  H17  CD   H16  106.40  3.000
 VPV  H17  CD   CG   109.62  3.000
 VPV  H16  CD   CG   109.78  3.000
 VPV  H17  CD   CE   109.06  3.000
 VPV  H16  CD   CE   109.10  3.000
 VPV  CG   CD   CE   112.68  3.000
 VPV  H19  CG   H18  106.04  3.000
 VPV  H19  CG   CB   110.30  3.000
 VPV  H18  CG   CB   109.38  3.000
 VPV  H19  CG   CD   109.04  3.000
 VPV  H18  CG   CD   109.43  3.000
 VPV  CB   CG   CD   112.45  3.000
 VPV  H21  CB   H20  106.20  3.000
 VPV  H21  CB   CA   108.08  3.000
 VPV  H20  CB   CA   108.84  3.000
 VPV  H21  CB   CG   109.05  3.000
 VPV  H20  CB   CG   109.31  3.000
 VPV  CA   CB   CG   115.00  3.000
 VPV  H22  CA   CB   107.91  3.000
 VPV  H22  CA   N    107.53  3.000
 VPV  CB   CA   N    110.50  1.700
 VPV  H22  CA   C    108.79  3.000
 VPV  N    CA   C    111.00  2.800
 VPV  CB   CA   C    110.10  1.900
 VPV  H6   C8   H5   104.88  3.000
 VPV  H6   C8   C7   109.41  3.000
 VPV  H5   C8   C7   110.91  3.000
 VPV  H6   C8   C9   108.72  3.000
 VPV  H5   C8   C9   107.13  3.000
 VPV  C7   C8   C9   115.25  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
 VPV  Var_01  CE   NZ  C1  C2    179.46   0.0  2
 VPV  Var_02  CE   NZ  C1  C5      0.35   0.0  2
 VPV  Var_03  C7   C8  C9  O12   163.61  30.0  2
 VPV  Var_04  C7   C8  C9  O11   -17.84  30.0  2
 VPV  Var_05  CD   CE  NZ  C1   -154.87  30.0  3
 VPV  Var_06  C6   C5  C1  C2     69.11  30.0  1
 VPV  Var_07  C6   C7  C8  C9    176.79  30.0  3
 VPV  Var_08  NZ   C1  C5  C6   -111.77  30.0  3
 VPV  Var_09  O3   C2  C1  C5     26.94  30.0  2
 VPV  Var_10  O4   C2  C1  C5   -153.41  30.0  2
 VPV  Var_11  NZ   C1  C2  O4     27.38  30.0  2
 VPV  Var_12  NZ   C1  C2  O3   -152.26  30.0  2
 VPV  Var_13  CG   CD  CE  NZ   -179.10  30.0  3
 VPV  Var_14  CB   CG  CD  CE    179.76  30.0  3
 VPV  Var_15  CA   CB  CG  CD    174.98  30.0  3
 VPV  Var_16  H5   C8  C9  O12   -72.45  30.0  2
 VPV  Var_17  H6   C8  C9  O12    40.39  30.0  2
 VPV  Var_18  H5   C8  C9  O11   106.11  30.0  2
 VPV  Var_19  H6   C8  C9  O11  -141.05  30.0  2
 VPV  Var_20  H14  CE  NZ  C1    -31.89  30.0  3
 VPV  Var_21  H15  CE  NZ  C1     85.81  30.0  3
 VPV  Var_22  H11  C5  C1  C2    -50.72  30.0  1
 VPV  Var_23  H12  C5  C1  C2   -168.29  30.0  1
 VPV  Var_24  H7   C7  C8  C9     52.91  30.0  3
 VPV  Var_25  H8   C7  C8  C9    -62.91  30.0  3
 VPV  Var_26  H5   C8  C7  C6     54.86  30.0  1
 VPV  Var_27  H6   C8  C7  C6    -60.36  30.0  1
 VPV  Var_28  H11  C5  C1  NZ    128.39  30.0  1
 VPV  Var_29  H12  C5  C1  NZ     10.83  30.0  1
 VPV  Var_30  H16  CD  CE  NZ    -56.89  30.0  3
 VPV  Var_31  H17  CD  CE  NZ     58.93  30.0  3
 VPV  Var_32  H18  CG  CD  CE    -58.48  30.0  3
 VPV  Var_33  H19  CG  CD  CE     57.10  30.0  3
 VPV  Var_34  H20  CB  CG  CD    -62.27  30.0  3
 VPV  Var_35  H21  CB  CG  CD     53.43  30.0  3
 VPV  Var_36  H14  CE  CD  CG     55.16  30.0  1
 VPV  Var_37  H15  CE  CD  CG    -60.11  30.0  1
 VPV  Var_38  H16  CD  CG  CB     57.94  30.0  1
 VPV  Var_39  H17  CD  CG  CB    -58.59  30.0  1
 VPV  Var_40  H18  CG  CB  CA     53.19  30.0  1
 VPV  Var_41  H19  CG  CB  CA    -63.06  30.0  1

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
 VPV  chir_01  C6  O10  C7  C5  positiv
 VPV  chir_02  CA  CB   C   N   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
 VPV  plan-1  C    0.020
 VPV  plan-1  CA   0.020
 VPV  plan-1  O    0.020
 VPV  plan-1  OXT  0.020
 VPV  plan-2  C1   0.020
 VPV  plan-2  C2   0.020
 VPV  plan-2  O4   0.020
 VPV  plan-2  O3   0.020
 VPV  plan-3  O12  0.020
 VPV  plan-3  O11  0.020
 VPV  plan-3  C9   0.020
 VPV  plan-3  C8   0.020
 VPV  plan-4  C1   0.020
 VPV  plan-4  C2   0.020
 VPV  plan-4  C5   0.020
 VPV  plan-4  NZ   0.020
 VPV  plan-4  CE   0.020

