# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 15:15:09 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (7R,8S)-8-amino-7-{[(phosphonooxy)carbonyl]amino}nonanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[C@@H](CCCCCC(O)=O)NC(=O)O[P](O)(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
 DPU  DPU  '(7R,8S)-8-amino-7-{[(phosphonooxy)carbonyl]amino}nonanoic acid'  ligand  41  20  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DPU
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
 DPU  CA    C  CH2   0  -0.580  -5.3185  -0.3895  -0.2498
 DPU  C     C  C     0   0.550  -6.0905  -1.6323   0.0934
 DPU  OI1   O  OH1   0  -0.598  -7.3790  -1.5155  -0.2182
 DPU  OI2   O  O     0  -0.446  -5.6260  -2.6273   0.5924
 DPU  CB    C  CH2   0  -0.419  -3.8405  -0.4615   0.0972
 DPU  CG    C  CH2   0  -0.415  -3.1179   0.8297  -0.2635
 DPU  CD    C  CH2   0  -0.413  -1.6320   0.7948   0.0727
 DPU  CE    C  CH2   0  -0.436  -0.9249   2.0826  -0.3305
 DPU  CZ    C  CH1   0  -0.078   0.5493   2.1397   0.0690
 DPU  CH    C  CH1   0  -0.066   1.2428   3.4307  -0.4001
 DPU  CS    C  CH3   0  -0.670   2.6919   3.4859   0.0601
 DPU  N1    N  NH1   0  -0.642   1.2480   0.9824  -0.4623
 DPU  N2    N  NH2   0  -0.806   0.5320   4.5781   0.1503
 DPU  CN1   C  C     0   0.755   1.9218   0.1121   0.2872
 DPU  O12   O  O     0  -0.489   2.0853   0.1354   1.4844
 DPU  O2B   O  O     0  -0.689   4.6112  -1.5757   0.8350
 DPU  PB    P  P     0   1.457   3.3956  -2.0353   0.1484
 DPU  O1B   O  O2    0  -0.605   2.4426  -0.8818  -0.4960
 DPU  O3B   O  OH1   0  -0.731   2.4758  -2.9017   1.1110
 DPU  O2A   O  OH1   0  -0.726   3.5685  -2.8367  -1.2148
 DPU  HA1   H  HCH2  0   0.275  -5.7909   0.4549   0.2624
 DPU  HA2   H  HCH2  0   0.276  -5.4516  -0.1893  -1.3180
 DPU  HO1   H  HOH1  0   0.478  -7.8519  -2.3245   0.0271
 DPU  HB1   H  HCH2  0   0.226  -3.3745  -1.2987  -0.4289
 DPU  HB2   H  HCH2  0   0.226  -3.7194  -0.6609   1.1655
 DPU  HG1   H  HCH2  0   0.216  -3.5893   1.6699   0.2576
 DPU  HG2   H  HCH2  0   0.215  -3.2409   1.0302  -1.3335
 DPU  HD1   H  HCH2  0   0.218  -1.1695  -0.0603  -0.4287
 DPU  HD2   H  HCH2  0   0.216  -1.5048   0.6259   1.1475
 DPU  HE1   H  HCH2  0   0.235  -1.4412   2.9246   0.1368
 DPU  HE2   H  HCH2  0   0.221  -1.0144   2.2266  -1.4144
 DPU  HZ    H  HCH1  0   0.247   0.6235   2.0931   1.1577
 DPU  HH    H  HCH1  0   0.199   1.2353   3.4241  -1.5027
 DPU  HS1   H  HCH3  0   0.222   2.7577   3.4579   1.1494
 DPU  HS2   H  HCH3  0   0.231   3.2768   2.6596  -0.3413
 DPU  HS3   H  HCH3  0   0.235   3.1637   4.4099  -0.2799
 DPU  HN1   H  HNH1  0   0.407   1.1976   0.8185  -1.4572
 DPU  HN21  H  HNH2  0   0.349   1.0697   5.4175  -0.0282
 DPU  HN22  H  HNH2  0   0.351  -0.3443   4.7168  -0.3364
 DPU  HO3   H  HOH1  0   0.501   1.7002  -3.3162   0.7086
 DPU  HO2   H  HOH1  0   0.508   4.2798  -3.4918  -1.1980

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
 DPU  CA   C     single  1.503  0.020  1.503
 DPU  CA   CB    single  1.520  0.020  1.520
 DPU  CA   HA1   single  0.970  0.020  1.090
 DPU  CA   HA2   single  0.970  0.020  1.090
 DPU  C    OI1   single  1.331  0.020  1.331
 DPU  C    OI2   double  1.206  0.020  1.206
 DPU  OI1  HO1   single  0.850  0.020  0.980
 DPU  CB   CG    single  1.523  0.020  1.523
 DPU  CB   HB1   single  0.970  0.020  1.090
 DPU  CB   HB2   single  0.970  0.020  1.090
 DPU  CG   CD    single  1.524  0.020  1.524
 DPU  CG   HG1   single  0.970  0.020  1.090
 DPU  CG   HG2   single  0.970  0.020  1.090
 DPU  CD   CE    single  1.523  0.020  1.523
 DPU  CD   HD1   single  0.970  0.020  1.090
 DPU  CD   HD2   single  0.970  0.020  1.090
 DPU  CE   CZ    single  1.528  0.020  1.528
 DPU  CE   HE1   single  0.970  0.020  1.090
 DPU  CE   HE2   single  0.970  0.020  1.090
 DPU  CZ   CH    single  1.539  0.020  1.539
 DPU  CZ   N1    single  1.453  0.020  1.453
 DPU  CZ   HZ    single  0.970  0.020  1.090
 DPU  CH   CS    single  1.521  0.020  1.521
 DPU  CH   N2    single  1.458  0.020  1.458
 DPU  CH   HH    single  0.970  0.020  1.090
 DPU  CS   HS1   single  0.970  0.020  1.090
 DPU  CS   HS2   single  0.970  0.020  1.090
 DPU  CS   HS3   single  0.970  0.020  1.090
 DPU  N1   CN1   single  1.332  0.020  1.332
 DPU  N1   HN1   single  0.860  0.020  1.020
 DPU  N2   HN21  single  0.890  0.020  1.040
 DPU  N2   HN22  single  0.890  0.020  1.040
 DPU  CN1  O12   double  1.209  0.020  1.209
 DPU  CN1  O1B   single  1.368  0.020  1.368
 DPU  O2B  PB    double  1.470  0.020  1.470
 DPU  PB   O1B   single  1.629  0.020  1.629
 DPU  PB   O3B   single  1.588  0.020  1.588
 DPU  PB   O2A   single  1.591  0.020  1.591
 DPU  O3B  HO3   single  0.850  0.020  0.980
 DPU  O2A  HO2   single  0.850  0.020  0.980

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
 DPU  HA2   CA   HA1   105.24  3.000
 DPU  HA2   CA   CB    110.47  3.000
 DPU  HA1   CA   CB    110.44  3.000
 DPU  HA2   CA   C     108.15  3.000
 DPU  HA1   CA   C     108.02  3.000
 DPU  CB    CA   C     114.09  3.000
 DPU  OI2   C    OI1   122.83  3.000
 DPU  OI2   C    CA    125.37  3.000
 DPU  OI1   C    CA    111.80  3.000
 DPU  HO1   OI1  C     109.89  3.000
 DPU  HB2   CB   HB1   106.46  3.000
 DPU  HB2   CB   CG    109.48  3.000
 DPU  HB1   CB   CG    109.45  3.000
 DPU  HB2   CB   CA    109.84  3.000
 DPU  HB1   CB   CA    109.94  3.000
 DPU  CG    CB   CA    111.54  3.000
 DPU  HG2   CG   HG1   106.01  3.000
 DPU  HG2   CG   CD    109.22  3.000
 DPU  HG1   CG   CD    109.41  3.000
 DPU  HG2   CG   CB    109.47  3.000
 DPU  HG1   CG   CB    109.48  3.000
 DPU  CD    CG   CB    113.02  3.000
 DPU  HD2   CD   HD1   106.27  3.000
 DPU  HD2   CD   CE    109.64  3.000
 DPU  HD1   CD   CE    110.08  3.000
 DPU  HD2   CD   CG    109.46  3.000
 DPU  HD1   CD   CG    109.21  3.000
 DPU  CE    CD   CG    112.01  3.000
 DPU  HE2   CE   HE1   106.43  3.000
 DPU  HE2   CE   CZ    109.39  3.000
 DPU  HE1   CE   CZ    108.37  3.000
 DPU  HE2   CE   CD    109.54  3.000
 DPU  HE1   CE   CD    108.60  3.000
 DPU  CZ    CE   CD    114.21  3.000
 DPU  HZ    CZ   N1    107.33  3.000
 DPU  HZ    CZ   CH    108.00  3.000
 DPU  N1    CZ   CH    109.89  3.000
 DPU  HZ    CZ   CE    108.94  3.000
 DPU  N1    CZ   CE    109.79  3.000
 DPU  CH    CZ   CE    112.73  3.000
 DPU  HH    CH   N2    112.27  3.000
 DPU  HH    CH   CS    108.01  3.000
 DPU  N2    CH   CS    108.76  3.000
 DPU  HH    CH   CZ    107.26  3.000
 DPU  N2    CH   CZ    109.00  3.000
 DPU  CS    CH   CZ    111.56  3.000
 DPU  HS3   CS   HS2   107.17  3.000
 DPU  HS3   CS   HS1   107.85  3.000
 DPU  HS2   CS   HS1   108.42  3.000
 DPU  HS3   CS   CH    110.37  3.000
 DPU  HS2   CS   CH    111.87  3.000
 DPU  HS1   CS   CH    111.00  3.000
 DPU  HN1   N1   CN1   118.29  3.000
 DPU  HN1   N1   CZ    117.76  3.000
 DPU  CN1   N1   CZ    123.93  3.000
 DPU  HN22  N2   HN21  105.15  3.000
 DPU  HN22  N2   CH    110.40  3.000
 DPU  HN21  N2   CH    109.09  3.000
 DPU  O1B   CN1  O12   121.97  3.000
 DPU  O1B   CN1  N1    110.19  3.000
 DPU  O12   CN1  N1    127.84  3.000
 DPU  O2A   PB   O3B   107.91  3.000
 DPU  O2A   PB   O1B    94.67  3.000
 DPU  O3B   PB   O1B   106.69  3.000
 DPU  O2A   PB   O2B   117.90  3.000
 DPU  O3B   PB   O2B   111.49  3.000
 DPU  O1B   PB   O2B   116.56  3.000
 DPU  PB    O1B  CN1   120.70  3.000
 DPU  HO3   O3B  PB    116.49  3.000
 DPU  HO2   O2A  PB    113.97  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
 DPU  CONST_01  HO1  OI1  C    CA    180.00   0.0  0
 DPU  Var_01    CD   CG   CB   CA    179.91  30.0  3
 DPU  Var_02    CG   CB   CA   C    -179.53  30.0  3
 DPU  Var_03    CB   CA   C    OI1   179.45  30.0  2
 DPU  Var_04    CE   CD   CG   CB    178.51  30.0  3
 DPU  Var_05    CZ   CE   CD   CG    176.09  30.0  3
 DPU  Var_06    O12  CN1  N1   CZ     -1.22  30.0  2
 DPU  Var_07    O2B  PB   O1B  CN1   -57.96  30.0  2

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
 DPU  chir_01  CZ  CE  CH  N1  positiv
 DPU  chir_02  CH  N2  CZ  CS  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
 DPU  plan-1  CA   0.020
 DPU  plan-1  C    0.020
 DPU  plan-1  OI1  0.020
 DPU  plan-1  OI2  0.020
 DPU  plan-1  HO1  0.020
 DPU  plan-2  N1   0.020
 DPU  plan-2  CN1  0.020
 DPU  plan-2  O12  0.020
 DPU  plan-2  O1B  0.020

