# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:45:10 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: D-phenylalanyl-N~5~-[(E)-(2,2-dihydroxyhydrazino)(imino)methyl]-D-ornithinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccccc1)C(=O)N[C@H](CCCNC(=N)NN(O)O)C(N)=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
 D7P  D7P  D-phenylalanyl-N~5~-[(E)-(2,2-dihydroxyhydrazino)(imino)methyl]-D-ornithinamide  ligand  51  26  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D7P
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
 D7P  N1'   N  NH2   0  -0.799  -0.7822  -4.4718  -0.2840
 D7P  N'    N  NH2   0  -0.785  -3.5492   0.7362   2.2294
 D7P  CA'   C  CH1   0  -0.227  -3.0685   0.3044   0.9359
 D7P  O'    O  O     0  -0.491  -2.4749  -1.8194   1.8810
 D7P  CB'   C  CH2   0  -0.530  -4.1657  -0.0839  -0.0860
 D7P  CG'   C  CR6   0   0.129  -5.0534   1.0808  -0.4105
 D7P  CD1   C  CR16  0  -0.302  -4.6609   2.0257  -1.3579
 D7P  CE1   C  CR16  0  -0.241  -5.4531   3.1314  -1.6320
 D7P  CZ'   C  CR16  0  -0.270  -6.6554   3.3120  -0.9583
 D7P  CE2   C  CR16  0  -0.241  -7.0564   2.3796  -0.0118
 D7P  CD2   C  CR16  0  -0.318  -6.2592   1.2742   0.2599
 D7P  N     N  NH1   0  -0.632  -1.0783  -0.9456   0.3458
 D7P  CA    C  CH1   0  -0.194  -0.3074  -2.1503   0.1850
 D7P  C     C  C     0   0.517  -1.1297  -3.2087  -0.5586
 D7P  O     O  O     0  -0.478  -1.9929  -2.8992  -1.3630
 D7P  CB    C  CH2   0  -0.460   0.9767  -1.8572  -0.5930
 D7P  CG    C  CH2   0  -0.460   1.9331  -0.9454   0.1640
 D7P  CD    C  CH2   0  -0.228   3.2074  -0.7000  -0.6290
 D7P  NE    N  NH1   0  -0.670   4.1139   0.1319   0.1279
 D7P  CZ    C  C     0   0.612   5.2615   0.5991  -0.4395
 D7P  NH1   N  NH1   0  -0.511   6.0449   1.3115   0.4711
 D7P  NH2   N  N     0  -0.704   5.5022   0.4524  -1.6833
 D7P  NO    N  NT    0   0.138   7.3542   1.4970   0.1121
 D7P  O2    O  OH1   0  -0.551   7.7609   2.6921   0.6876
 D7P  O3    O  OH1   0  -0.561   8.1119   0.4929   0.7209
 D7P  H1'1  H  HNH2  0   0.408  -0.0921  -4.6945   0.4128
 D7P  H1'2  H  HNH2  0   0.404  -1.2077  -5.2414  -0.7749
 D7P  HN'2  H  HNH2  0   0.344  -4.0871  -0.0058   2.6614
 D7P  HA'   H  HCH1  0   0.261  -2.4824   1.1216   0.5037
 D7P  HB'1  H  HCH2  0   0.258  -3.6904  -0.4618  -0.9950
 D7P  HB'2  H  HCH2  0   0.255  -4.7546  -0.9040   0.3328
 D7P  HD1   H  HCR6  0   0.247  -3.7254   1.8929  -1.8896
 D7P  HE1   H  HCR6  0   0.254  -5.1334   3.8520  -2.3740
 D7P  HZ'   H  HCR6  0   0.254  -7.2770   4.1714  -1.1738
 D7P  HE2   H  HCR6  0   0.254  -7.9933   2.5091   0.5149
 D7P  HD2   H  HCR6  0   0.251  -6.5853   0.5455   0.9930
 D7P  HN    H  HNH1  0   0.402  -0.9579  -0.2204  -0.3443
 D7P  HA    H  HCH1  0   0.275  -0.0355  -2.5346   1.1727
 D7P  HB1   H  HCH2  0   0.257   1.4750  -2.8059  -0.8062
 D7P  HB2   H  HCH2  0   0.246   0.7206  -1.4187  -1.5628
 D7P  HG1   H  HCH2  0   0.240   1.4578   0.0127   0.3878
 D7P  HG2   H  HCH2  0   0.233   2.1781  -1.4086   1.1254
 D7P  HD1A  H  HCH2  0   0.215   3.6692  -1.6580  -0.8994
 D7P  HD2A  H  HCH2  0   0.233   2.9686  -0.1954  -1.5663
 D7P  HNE   H  HNH1  0   0.383   4.1357  -0.0476   1.1197
 D7P  HH1   H  HNH1  0   0.382   5.8932   1.1164   1.4576
 D7P  HH2   H  H     0   0.327   6.3622   0.9232  -1.9370
 D7P  HO2   H  HOH1  0   0.473   8.2083   3.1580  -0.0285
 D7P  HO3   H  HOH1  0   0.472   8.7269   0.2097   0.0338
 D7P  C'    C  C     0   0.572  -2.1786  -0.9137   1.1166
 D7P  HN'1  H  HNH2  0   0.356  -4.1806   1.5194   2.1157

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
 D7P  N1'  C     single    1.338  0.020  1.338
 D7P  N1'  H1'1  single    0.860  0.020  1.020
 D7P  N1'  H1'2  single    0.860  0.020  1.020
 D7P  N'   CA'   single    1.446  0.020  1.446
 D7P  N'   HN'1  single    0.890  0.020  1.040
 D7P  N'   HN'2  single    0.890  0.020  1.040
 D7P  CA'  C'    single    1.519  0.020  1.519
 D7P  CA'  CB'   single    1.549  0.020  1.549
 D7P  CA'  HA'   single    0.970  0.020  1.090
 D7P  C'   O'    double    1.222  0.020  1.222
 D7P  C'   N     single    1.344  0.020  1.344
 D7P  CB'  CG'   single    1.500  0.020  1.500
 D7P  CB'  HB'1  single    0.970  0.020  1.090
 D7P  CB'  HB'2  single    0.970  0.020  1.090
 D7P  CG'  CD1   aromatic  1.394  0.020  1.394
 D7P  CG'  CD2   aromatic  1.393  0.020  1.393
 D7P  CD1  CE1   aromatic  1.387  0.020  1.387
 D7P  CD1  HD1   single    0.930  0.020  1.080
 D7P  CE1  CZ'   aromatic  1.390  0.020  1.390
 D7P  CE1  HE1   single    0.930  0.020  1.080
 D7P  CZ'  CE2   aromatic  1.388  0.020  1.388
 D7P  CZ'  HZ'   single    0.930  0.020  1.080
 D7P  CE2  CD2   aromatic  1.390  0.020  1.390
 D7P  CE2  HE2   single    0.930  0.020  1.080
 D7P  CD2  HD2   single    0.930  0.020  1.080
 D7P  N    CA    single    1.439  0.020  1.439
 D7P  N    HN    single    0.860  0.020  1.020
 D7P  CA   C     single    1.533  0.020  1.533
 D7P  CA   CB    single    1.530  0.020  1.530
 D7P  CA   HA    single    0.970  0.020  1.090
 D7P  C    O     double    1.220  0.020  1.220
 D7P  CB   CG    single    1.523  0.020  1.523
 D7P  CB   HB1   single    0.970  0.020  1.090
 D7P  CB   HB2   single    0.970  0.020  1.090
 D7P  CG   CD    single    1.521  0.020  1.521
 D7P  CG   HG1   single    0.970  0.020  1.090
 D7P  CG   HG2   single    0.970  0.020  1.090
 D7P  CD   NE    single    1.445  0.020  1.445
 D7P  CD   HD1A  single    0.970  0.020  1.090
 D7P  CD   HD2A  single    0.970  0.020  1.090
 D7P  NE   CZ    single    1.363  0.020  1.363
 D7P  NE   HNE   single    0.890  0.020  1.040
 D7P  CZ   NH1   single    1.397  0.020  1.397
 D7P  CZ   NH2   double    1.275  0.020  1.275
 D7P  NH1  NO    single    1.370  0.020  1.370
 D7P  NH1  HH1   single    0.890  0.020  1.040
 D7P  NH2  HH2   single    0.890  0.020  1.040
 D7P  NO   O2    single    1.387  0.020  1.387
 D7P  NO   O3    single    1.397  0.020  1.397
 D7P  O2   HO2   single    0.850  0.020  0.980
 D7P  O3   HO3   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
 D7P  H1'2  N1'  H1'1  117.28  3.000
 D7P  H1'2  N1'  C     120.76  3.000
 D7P  H1'1  N1'  C     121.96  3.000
 D7P  HN'2  N'   HN'1  106.46  3.000
 D7P  HN'2  N'   CA'   109.83  3.000
 D7P  HN'1  N'   CA'   109.75  3.000
 D7P  HA'   CA'  CB'   107.82  3.000
 D7P  HA'   CA'  C'    109.38  3.000
 D7P  CB'   CA'  C'    107.00  3.000
 D7P  HA'   CA'  N'    107.95  3.000
 D7P  CB'   CA'  N'    115.45  3.000
 D7P  C'    CA'  N'    109.13  3.000
 D7P  HB'2  CB'  HB'1  107.07  3.000
 D7P  HB'2  CB'  CG'   110.28  3.000
 D7P  HB'1  CB'  CG'   110.24  3.000
 D7P  HB'2  CB'  CA'   108.48  3.000
 D7P  HB'1  CB'  CA'   109.10  3.000
 D7P  CG'   CB'  CA'   111.55  3.000
 D7P  CD2   CG'  CD1   118.45  3.000
 D7P  CD2   CG'  CB'   121.06  3.000
 D7P  CD1   CG'  CB'   120.44  3.000
 D7P  HD1   CD1  CE1   119.57  3.000
 D7P  HD1   CD1  CG'   119.53  3.000
 D7P  CE1   CD1  CG'   120.90  3.000
 D7P  HE1   CE1  CZ'   120.07  3.000
 D7P  HE1   CE1  CD1   119.82  3.000
 D7P  CZ'   CE1  CD1   120.11  3.000
 D7P  HZ'   CZ'  CE2   120.21  3.000
 D7P  HZ'   CZ'  CE1   120.23  3.000
 D7P  CE2   CZ'  CE1   119.55  3.000
 D7P  HE2   CE2  CD2   119.77  3.000
 D7P  HE2   CE2  CZ'   120.10  3.000
 D7P  CD2   CE2  CZ'   120.13  3.000
 D7P  HD2   CD2  CE2   119.63  3.000
 D7P  HD2   CD2  CG'   119.51  3.000
 D7P  CE2   CD2  CG'   120.86  3.000
 D7P  HN    N    CA    117.50  3.000
 D7P  HN    N    C'    118.24  3.000
 D7P  CA    N    C'    121.50  3.000
 D7P  HA    CA   CB    108.53  3.000
 D7P  HA    CA   C     109.19  3.000
 D7P  CB    CA   C     109.63  3.000
 D7P  HA    CA   N     109.04  3.000
 D7P  CB    CA   N     110.24  3.000
 D7P  C     CA   N     110.17  3.000
 D7P  O     C    CA    121.62  3.000
 D7P  O     C    N1'   123.95  3.000
 D7P  CA    C    N1'   114.38  3.000
 D7P  HB2   CB   HB1   106.36  3.000
 D7P  HB2   CB   CG    110.33  3.000
 D7P  HB1   CB   CG    109.30  3.000
 D7P  HB2   CB   CA    109.32  3.000
 D7P  HB1   CB   CA    108.40  3.000
 D7P  CG    CB   CA    112.90  3.000
 D7P  HG2   CG   HG1   106.77  3.000
 D7P  HG2   CG   CD    109.79  3.000
 D7P  HG1   CG   CD    109.25  3.000
 D7P  HG2   CG   CB    108.89  3.000
 D7P  HG1   CG   CB    110.71  3.000
 D7P  CD    CG   CB    111.32  3.000
 D7P  HD2A  CD   HD1A  106.51  3.000
 D7P  HD2A  CD   NE    108.74  3.000
 D7P  HD1A  CD   NE    111.58  3.000
 D7P  HD2A  CD   CG    109.83  3.000
 D7P  HD1A  CD   CG    109.89  3.000
 D7P  NE    CD   CG    110.21  3.000
 D7P  HNE   NE   CZ    116.90  3.000
 D7P  HNE   NE   CD    115.25  3.000
 D7P  CZ    NE   CD    120.51  3.000
 D7P  NH2   CZ   NH1   126.07  3.000
 D7P  NH2   CZ   NE    121.70  3.000
 D7P  NH1   CZ   NE    112.07  3.000
 D7P  HH1   NH1  NO    115.00  3.000
 D7P  HH1   NH1  CZ    116.81  3.000
 D7P  NO    NH1  CZ    115.73  3.000
 D7P  HH2   NH2  CZ    110.56  3.000
 D7P  O3    NO   O2    106.21  3.000
 D7P  O3    NO   NH1   107.86  3.000
 D7P  O2    NO   NH1   106.74  3.000
 D7P  HO2   O2   NO    104.13  3.000
 D7P  HO3   O3   NO    104.25  3.000
 D7P  N     C'   O'    122.67  3.000
 D7P  N     C'   CA'   115.49  3.000
 D7P  O'    C'   CA'   121.79  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
 D7P  CONST_01  CZ'   CE1  CD1  CG'     0.00   0.0  0
 D7P  CONST_02  CZ'   CE2  CD2  CG'     0.00   0.0  0
 D7P  CONST_03  CE2   CD2  CG'  CD1     0.00   0.0  0
 D7P  CONST_04  CE2   CZ'  CE1  CD1     0.00   0.0  0
 D7P  CONST_05  CD2   CG'  CD1  CE1     0.00   0.0  0
 D7P  CONST_06  CD2   CE2  CZ'  CE1     0.00   0.0  0
 D7P  CONST_07  CE1   CD1  CG'  CB'   180.00   0.0  0
 D7P  CONST_08  CE2   CD2  CG'  CB'   180.00   0.0  0
 D7P  CONST_09  HE1   CE1  CD1  CG'   180.00   0.0  0
 D7P  CONST_10  HE2   CE2  CD2  CG'   180.00   0.0  0
 D7P  CONST_11  HD2   CD2  CG'  CD1   180.00   0.0  0
 D7P  CONST_12  HZ'   CZ'  CE1  CD1   180.00   0.0  0
 D7P  CONST_13  HD1   CD1  CE1  CZ'   180.00   0.0  0
 D7P  CONST_14  CA    N    C'   CA'   180.00   0.0  0
 D7P  CONST_15  CA    N    C'   O'      0.00   0.0  0
 D7P  CONST_16  NH1   CZ   NE   CD    180.00   0.0  0
 D7P  CONST_17  NH2   CZ   NE   CD      0.00   0.0  0
 D7P  CONST_20  HN    N    C'   CA'     0.00   0.0  0
 D7P  CONST_21  H1'1  N1'  C    CA      0.00   0.0  0
 D7P  CONST_22  H1'2  N1'  C    CA    180.00   0.0  0
 D7P  CONST_24  HH2   NH2  CZ   NE    180.00   0.0  0
 D7P  Var_01    CD1   CG'  CB'  CA'    82.32  30.0  2
 D7P  Var_02    CD    CG   CB   CA    178.88  30.0  3
 D7P  Var_03    NE    CD   CG   CB   -178.19  30.0  3
 D7P  Var_04    CZ    NE   CD   CG   -173.08  30.0  3
 D7P  Var_05    O2    NO   NH1  CZ    150.29  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
 D7P  chir_01  CA'  N'  C'  CB'  negativ
 D7P  chir_02  CA   N   C   CB   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
 D7P  plan-1  CB'   0.020
 D7P  plan-1  CG'   0.020
 D7P  plan-1  CD1   0.020
 D7P  plan-1  CE1   0.020
 D7P  plan-1  CZ'   0.020
 D7P  plan-1  CE2   0.020
 D7P  plan-1  CD2   0.020
 D7P  plan-1  HD1   0.020
 D7P  plan-1  HE1   0.020
 D7P  plan-1  HZ'   0.020
 D7P  plan-1  HE2   0.020
 D7P  plan-1  HD2   0.020
 D7P  plan-2  N1'   0.020
 D7P  plan-2  CA    0.020
 D7P  plan-2  C     0.020
 D7P  plan-2  O     0.020
 D7P  plan-2  H1'1  0.020
 D7P  plan-2  H1'2  0.020
 D7P  plan-3  CA'   0.020
 D7P  plan-3  O'    0.020
 D7P  plan-3  N     0.020
 D7P  plan-3  CA    0.020
 D7P  plan-3  HN    0.020
 D7P  plan-3  C'    0.020
 D7P  plan-4  CD    0.020
 D7P  plan-4  NE    0.020
 D7P  plan-4  CZ    0.020
 D7P  plan-4  NH1   0.020
 D7P  plan-4  NH2   0.020
 D7P  plan-4  NO    0.020
 D7P  plan-4  HNE   0.020
 D7P  plan-4  HH1   0.020
 D7P  plan-4  HH2   0.020

