# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 13:13:13 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (4R)-4-{[N~5~-(N-nitrocarbamimidoyl)-L-ornithyl]amino}-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)N[N+]([O-])=O)C(=O)N[C@H]1CN[C@@H](C1)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
 DP9  DP9  (4R)-4-{[N~5~-(N-nitrocarbamimidoyl)-L-ornithyl]amino}-L-prolinamide  ligand  45  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DP9
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
 DP9  NH2   N  N      0  -0.649  -5.3943  -0.6333  -1.6498
 DP9  CZ    C  C      0   0.649  -5.3755  -0.3083  -0.4264
 DP9  NH1   N  NC1    0  -0.546  -6.4783  -0.2366   0.4640
 DP9  NO    N  N      1   0.614  -7.5553  -1.0348   0.4522
 DP9  O2    O  O     -1  -0.412  -7.6705  -1.8490  -0.4324
 DP9  O3    O  O      0  -0.419  -8.3454  -0.8657   1.3527
 DP9  NE    N  NH1    0  -0.661  -4.2584   0.1303   0.2079
 DP9  CD    C  CH2    0  -0.235  -3.0015   0.2195  -0.5028
 DP9  CG    C  CH2    0  -0.454  -1.9849   1.0062   0.3075
 DP9  CB    C  CH2    0  -0.416  -0.6392   1.0669  -0.4003
 DP9  CA    C  CH1    0  -0.229   0.3921   1.9076   0.3580
 DP9  N     N  NH2    0  -0.777  -0.0239   3.2944   0.4088
 DP9  C     C  C      0   0.537   1.7523   1.7160  -0.3151
 DP9  O     O  O      0  -0.501   2.0494   2.3302  -1.3315
 DP9  N2'   N  NH1    0  -0.644   2.5527   0.8055   0.2606
 DP9  CG'   C  CH1    0  -0.060   3.8604   0.4479  -0.2315
 DP9  CD'   C  CH2    0  -0.283   5.0025   1.2651   0.3761
 DP9  N'    N  NH1    0  -0.610   6.1372   0.3910   0.1619
 DP9  CA'   C  CH1    0  -0.172   5.7040  -0.9171   0.6021
 DP9  C'    C  C      0   0.485   6.5588  -2.0347   0.0249
 DP9  O'    O  O      0  -0.480   7.2264  -1.9024  -0.9878
 DP9  N1'   N  NH2    0  -0.801   6.4758  -3.1855   0.7098
 DP9  CB'   C  CH2    0  -0.488   4.2422  -1.0064   0.1045
 DP9  HH2   H  H      0   0.349  -6.3243  -0.8125  -1.9990
 DP9  HH1   H  HNC1   0   0.441  -6.4373   0.3590   1.2808
 DP9  HNE   H  HNH1   0   0.396  -4.1916  -0.0545   1.1975
 DP9  HD1   H  HCH2   0   0.238  -3.1836   0.7159  -1.4570
 DP9  HD2   H  HCH2   0   0.223  -2.6093  -0.7769  -0.7394
 DP9  HG1   H  HCH2   0   0.225  -1.8515   0.5402   1.2898
 DP9  HG2   H  HCH2   0   0.239  -2.3575   2.0165   0.4849
 DP9  HB1   H  HCH2   0   0.229  -0.7633   1.4804  -1.4069
 DP9  HB2   H  HCH2   0   0.236  -0.2498   0.0525  -0.5304
 DP9  HA    H  HCH1   0   0.247   0.4445   1.5364   1.3869
 DP9  HN1   H  HNH2   0   0.352   0.5938   3.8187   1.0160
 DP9  HN2   H  HNH2   0   0.340   0.0743   3.7040  -0.5128
 DP9  H2'   H  HNH1   0   0.398   2.2661   0.4092   1.1422
 DP9  HG'   H  HCH1   0   0.265   3.8603   0.5860  -1.3122
 DP9  HD'1  H  HCH2   0   0.241   5.1394   2.2285  -0.1174
 DP9  HD'2  H  HCH2   0   0.202   4.7855   1.4565   1.4385
 DP9  HN'   H  HNH1   0   0.356   6.9615   0.7031   0.6580
 DP9  HA'   H  HCH1   0   0.247   5.7015  -1.0074   1.6993
 DP9  H1'1  H  HNH2   0   0.406   5.9439  -3.2571   1.5598
 DP9  H1'2  H  HNH2   0   0.401   6.9643  -4.0091   0.3984
 DP9  HB'1  H  HCH2   0   0.257   3.6011  -1.4253   0.8803
 DP9  HB'2  H  HCH2   0   0.265   4.1422  -1.6458  -0.7723

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
 DP9  NH2  CZ    double  1.266  0.020  1.266
 DP9  NH2  HH2   single  0.890  0.020  1.040
 DP9  CZ   NH1   single  1.419  0.020  1.419
 DP9  CZ   NE    single  1.357  0.020  1.357
 DP9  NH1  NO    single  1.341  0.020  1.341
 DP9  NH1  HH1   single  0.860  0.020  1.020
 DP9  NO   O2    single  1.208  0.020  1.208
 DP9  NO   O3    double  1.210  0.020  1.210
 DP9  NE   CD    single  1.447  0.020  1.447
 DP9  NE   HNE   single  0.890  0.020  1.040
 DP9  CD   CG    single  1.520  0.020  1.520
 DP9  CD   HD1   single  0.970  0.020  1.090
 DP9  CD   HD2   single  0.970  0.020  1.090
 DP9  CG   CB    single  1.522  0.020  1.522
 DP9  CG   HG1   single  0.970  0.020  1.090
 DP9  CG   HG2   single  0.970  0.020  1.090
 DP9  CB   CA    single  1.531  0.020  1.531
 DP9  CB   HB1   single  0.970  0.020  1.090
 DP9  CB   HB2   single  0.970  0.020  1.090
 DP9  CA   N     single  1.449  0.020  1.449
 DP9  CA   C     single  1.530  0.020  1.530
 DP9  CA   HA    single  0.970  0.020  1.090
 DP9  N    HN1   single  0.890  0.020  1.040
 DP9  N    HN2   single  0.890  0.020  1.040
 DP9  C    O     double  1.224  0.020  1.224
 DP9  C    N2'   single  1.342  0.020  1.342
 DP9  N2'  CG'   single  1.442  0.020  1.442
 DP9  N2'  H2'   single  0.860  0.020  1.020
 DP9  CG'  CD'   single  1.530  0.020  1.530
 DP9  CG'  CB'   single  1.541  0.020  1.541
 DP9  CG'  HG'   single  0.970  0.020  1.090
 DP9  CD'  N'    single  1.448  0.020  1.448
 DP9  CD'  HD'1  single  0.970  0.020  1.090
 DP9  CD'  HD'2  single  0.970  0.020  1.090
 DP9  N'   CA'   single  1.447  0.020  1.447
 DP9  N'   HN'   single  0.890  0.020  1.040
 DP9  CA'  C'    single  1.521  0.020  1.521
 DP9  CA'  CB'   single  1.547  0.020  1.547
 DP9  CA'  HA'   single  0.970  0.020  1.090
 DP9  C'   O'    double  1.220  0.020  1.220
 DP9  C'   N1'   single  1.342  0.020  1.342
 DP9  N1'  H1'1  single  0.860  0.020  1.020
 DP9  N1'  H1'2  single  0.860  0.020  1.020
 DP9  CB'  HB'1  single  0.970  0.020  1.090
 DP9  CB'  HB'2  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
 DP9  HH2   NH2  CZ    113.17  3.000
 DP9  NE    CZ   NH1   109.27  3.000
 DP9  NE    CZ   NH2   123.14  3.000
 DP9  NH1   CZ   NH2   127.43  3.000
 DP9  HH1   NH1  NO    112.97  3.000
 DP9  HH1   NH1  CZ    120.32  3.000
 DP9  NO    NH1  CZ    126.06  3.000
 DP9  O3    NO   O2    125.25  3.000
 DP9  O3    NO   NH1   115.77  3.000
 DP9  O2    NO   NH1   118.98  3.000
 DP9  HNE   NE   CD    115.83  3.000
 DP9  HNE   NE   CZ    116.97  3.000
 DP9  CD    NE   CZ    120.36  3.000
 DP9  HD2   CD   HD1   106.53  3.000
 DP9  HD2   CD   CG    110.25  3.000
 DP9  HD1   CD   CG    110.02  3.000
 DP9  HD2   CD   NE    111.15  3.000
 DP9  HD1   CD   NE    108.22  3.000
 DP9  CG    CD   NE    110.56  3.000
 DP9  HG2   CG   HG1   106.83  3.000
 DP9  HG2   CG   CB    109.92  3.000
 DP9  HG1   CG   CB    109.05  3.000
 DP9  HG2   CG   CD    109.73  3.000
 DP9  HG1   CG   CD    109.84  3.000
 DP9  CB    CG   CD    111.36  3.000
 DP9  HB2   CB   HB1   106.32  3.000
 DP9  HB2   CB   CA    109.16  3.000
 DP9  HB1   CB   CA    108.91  3.000
 DP9  HB2   CB   CG    109.45  3.000
 DP9  HB1   CB   CG    110.02  3.000
 DP9  CA    CB   CG    112.77  3.000
 DP9  HA    CA   C     109.17  3.000
 DP9  HA    CA   N     107.78  3.000
 DP9  C     CA   N     113.00  3.000
 DP9  HA    CA   CB    108.14  3.000
 DP9  C     CA   CB    108.19  3.000
 DP9  N     CA   CB    110.46  3.000
 DP9  HN2   N    HN1   106.08  3.000
 DP9  HN2   N    CA    109.10  3.000
 DP9  HN1   N    CA    109.97  3.000
 DP9  N2'   C    O     123.49  3.000
 DP9  N2'   C    CA    115.25  3.000
 DP9  O     C    CA    121.22  3.000
 DP9  H2'   N2'  CG'   117.30  3.000
 DP9  H2'   N2'  C     118.18  3.000
 DP9  CG'   N2'  C     124.23  3.000
 DP9  HG'   CG'  CB'   109.63  3.000
 DP9  HG'   CG'  CD'   109.04  3.000
 DP9  CB'   CG'  CD'   103.45  3.000
 DP9  HG'   CG'  N2'   107.88  3.000
 DP9  CB'   CG'  N2'   112.60  3.000
 DP9  CD'   CG'  N2'   114.13  3.000
 DP9  HD'2  CD'  HD'1  107.92  3.000
 DP9  HD'2  CD'  N'    113.71  3.000
 DP9  HD'1  CD'  N'    111.58  3.000
 DP9  HD'2  CD'  CG'   109.20  3.000
 DP9  HD'1  CD'  CG'   112.68  3.000
 DP9  N'    CD'  CG'   101.76  3.000
 DP9  HN'   N'   CA'   111.95  3.000
 DP9  HN'   N'   CD'   112.32  3.000
 DP9  CA'   N'   CD'   105.44  3.000
 DP9  HA'   CA'  CB'   108.28  3.000
 DP9  HA'   CA'  C'    108.62  3.000
 DP9  CB'   CA'  C'    111.51  3.000
 DP9  HA'   CA'  N'    112.22  3.000
 DP9  CB'   CA'  N'    103.73  3.000
 DP9  C'    CA'  N'    112.38  3.000
 DP9  N1'   C'   O'    123.40  3.000
 DP9  N1'   C'   CA'   113.69  3.000
 DP9  O'    C'   CA'   122.88  3.000
 DP9  H1'2  N1'  H1'1  117.38  3.000
 DP9  H1'2  N1'  C'    120.91  3.000
 DP9  H1'1  N1'  C'    121.69  3.000
 DP9  HB'2  CB'  HB'1  107.04  3.000
 DP9  HB'2  CB'  CA'   112.30  3.000
 DP9  HB'1  CB'  CA'   110.43  3.000
 DP9  HB'2  CB'  CG'   110.83  3.000
 DP9  HB'1  CB'  CG'   111.85  3.000
 DP9  CA'   CB'  CG'   104.47  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
 DP9  CONST_01  CG'   N2'  C    CA   180.00   0.0  0
 DP9  CONST_02  CG'   N2'  C    O      0.00   0.0  0
 DP9  CONST_03  H1'1  N1'  C'   CA'    0.00   0.0  0
 DP9  CONST_04  H1'2  N1'  C'   CA'  180.00   0.0  0
 DP9  CONST_06  CD    NE   CZ   NH2    0.00   0.0  0
 DP9  CONST_07  CD    NE   CZ   NH1  180.00   0.0  0
 DP9  CONST_09  H2'   N2'  C    CA     0.00   0.0  0
 DP9  CONST_12  HH2   NH2  CZ   NH1    0.00   0.0  0
 DP9  Var_01    CA'   N'   CD'  CG'  -47.31  30.0  1
 DP9  Var_02    O2    NO   NH1  CZ    -4.85  30.0  2
 DP9  Var_03    CG    CD   NE   CZ   167.75  30.0  3
 DP9  Var_04    CB    CG   CD   NE   177.87  30.0  3
 DP9  Var_05    CA    CB   CG   CD   177.35  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
 DP9  chir_01  CA   CB   N    C    positiv
 DP9  chir_02  CG'  N2'  CD'  CB'  negativ
 DP9  chir_03  CA'  N'   C'   CB'  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
 DP9  plan-1  CA    0.020
 DP9  plan-1  C     0.020
 DP9  plan-1  O     0.020
 DP9  plan-1  N2'   0.020
 DP9  plan-1  CG'   0.020
 DP9  plan-1  H2'   0.020
 DP9  plan-2  CA'   0.020
 DP9  plan-2  C'    0.020
 DP9  plan-2  O'    0.020
 DP9  plan-2  N1'   0.020
 DP9  plan-2  H1'1  0.020
 DP9  plan-2  H1'2  0.020
 DP9  plan-3  NH2   0.020
 DP9  plan-3  CZ    0.020
 DP9  plan-3  NH1   0.020
 DP9  plan-3  NO    0.020
 DP9  plan-3  NE    0.020
 DP9  plan-3  CD    0.020
 DP9  plan-3  HH2   0.020
 DP9  plan-3  HH1   0.020
 DP9  plan-3  HNE   0.020
 DP9  plan-4  NH1   0.020
 DP9  plan-4  NO    0.020
 DP9  plan-4  O2    0.020
 DP9  plan-4  O3    0.020

