# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:52:26 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 1-{(4S)-4-amino-5-[(2-aminoethyl)amino]pentyl}-3-nitroguanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCNC[C@@H](N)CCCNC(=N)N[N+]([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
 DP3  DP3  1-{(4S)-4-amino-5-[(2-aminoethyl)amino]pentyl}-3-nitroguanidine  ligand  38  17  .  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_DP3
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
 DP3  N2'   N  NH2    0  -0.802  -8.5281   0.4398   0.0152
 DP3  C2'   C  CH2    0  -0.296  -7.3142  -0.3329   0.2328
 DP3  C1'   C  CH2    0  -0.259  -6.0841   0.5324   0.0113
 DP3  N1'   N  NH1    0  -0.604  -4.8692  -0.2254   0.2369
 DP3  C     C  CH2    0  -0.242  -3.6584   0.5301  -0.0193
 DP3  CA    C  CH1    0  -0.120  -2.4195  -0.3542   0.1363
 DP3  N     N  NH2    0  -0.788  -2.4475  -1.5383  -0.7127
 DP3  CB    C  CH2    0  -0.421  -1.1530   0.4545  -0.1204
 DP3  CG    C  CH2    0  -0.456   0.1331  -0.3137   0.1527
 DP3  CD    C  CH2    0  -0.226   1.3622   0.5223  -0.1647
 DP3  NE    N  NH1    0  -0.661   2.5671  -0.2133   0.1558
 DP3  CZ    C  C      0   0.646   3.7833   0.3668   0.0010
 DP3  NH2   N  N      0  -0.646   3.9348   1.5526  -0.4163
 DP3  NH1   N  NC1    0  -0.546   4.7882  -0.5192   0.4701
 DP3  NO    N  N      1   0.613   6.0487  -0.5931   0.0238
 DP3  O2    O  O      0  -0.420   6.7413  -1.4413   0.5389
 DP3  O3    O  O     -1  -0.413   6.4076   0.1684  -0.8425
 DP3  H2'1  H  HNH2   0   0.339  -8.5998   0.6792  -0.9663
 DP3  H2'2  H  HNH2   0   0.349  -9.3334  -0.1412   0.2091
 DP3  H11   H  HCH2   0   0.214  -7.3179  -0.6887   1.2675
 DP3  H12   H  HCH2   0   0.192  -7.2326  -1.2250  -0.4034
 DP3  H1'1  H  HCH2   0   0.214  -6.0766   0.8882  -1.0246
 DP3  H1'2  H  HCH2   0   0.187  -6.1560   1.4289   0.6468
 DP3  H1'   H  HNH1   0   0.337  -4.8566  -0.5372   1.2020
 DP3  H1    H  HCH2   0   0.208  -3.6989   0.9057  -1.0483
 DP3  H2    H  HCH2   0   0.188  -3.5661   1.4146   0.6321
 DP3  HA    H  HCH1   0   0.211  -2.3921  -0.7012   1.1783
 DP3  HN1   H  HNH2   0   0.340  -3.3618  -1.9663  -0.6192
 DP3  HN2   H  HNH2   0   0.329  -2.3940  -1.2418  -1.6822
 DP3  HB1   H  HCH2   0   0.214  -1.1608   0.8067  -1.1591
 DP3  HB2   H  HCH2   0   0.225  -1.1762   1.3514   0.5058
 DP3  HG1   H  HCH2   0   0.225   0.1612  -0.6194   1.2029
 DP3  HG2   H  HCH2   0   0.231   0.1470  -1.2292  -0.4439
 DP3  HD1   H  HCH2   0   0.221   1.3501   0.8189  -1.2197
 DP3  HD2   H  HCH2   0   0.231   1.3551   1.4444   0.4205
 DP3  HNE   H  HNH1   0   0.397   2.5186  -1.2146   0.0434
 DP3  HH2   H  H      0   0.348   4.8896   1.8758  -0.3588
 DP3  HH1   H  HNC1   0   0.442   4.5642  -1.2329   1.1511

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
 DP3  N2'  C2'   single  1.455  0.020  1.455
 DP3  N2'  H2'1  single  0.890  0.020  1.040
 DP3  N2'  H2'2  single  0.890  0.020  1.040
 DP3  C2'  C1'   single  1.520  0.020  1.520
 DP3  C2'  H11   single  0.970  0.020  1.090
 DP3  C2'  H12   single  0.970  0.020  1.090
 DP3  C1'  N1'   single  1.450  0.020  1.450
 DP3  C1'  H1'1  single  0.970  0.020  1.090
 DP3  C1'  H1'2  single  0.970  0.020  1.090
 DP3  N1'  C     single  1.450  0.020  1.450
 DP3  N1'  H1'   single  0.890  0.020  1.040
 DP3  C    CA    single  1.530  0.020  1.530
 DP3  C    H1    single  0.970  0.020  1.090
 DP3  C    H2    single  0.970  0.020  1.090
 DP3  CA   N     single  1.457  0.020  1.457
 DP3  CA   CB    single  1.524  0.020  1.524
 DP3  CA   HA    single  0.970  0.020  1.090
 DP3  N    HN1   single  0.890  0.020  1.040
 DP3  N    HN2   single  0.890  0.020  1.040
 DP3  CB   CG    single  1.523  0.020  1.523
 DP3  CB   HB1   single  0.970  0.020  1.090
 DP3  CB   HB2   single  0.970  0.020  1.090
 DP3  CG   CD    single  1.520  0.020  1.520
 DP3  CG   HG1   single  0.970  0.020  1.090
 DP3  CG   HG2   single  0.970  0.020  1.090
 DP3  CD   NE    single  1.448  0.020  1.448
 DP3  CD   HD1   single  0.970  0.020  1.090
 DP3  CD   HD2   single  0.970  0.020  1.090
 DP3  NE   CZ    single  1.356  0.020  1.356
 DP3  NE   HNE   single  0.890  0.020  1.040
 DP3  CZ   NH2   double  1.266  0.020  1.266
 DP3  CZ   NH1   single  1.419  0.020  1.419
 DP3  NH2  HH2   single  0.890  0.020  1.040
 DP3  NH1  NO    single  1.339  0.020  1.339
 DP3  NH1  HH1   single  0.860  0.020  1.020
 DP3  NO   O2    double  1.210  0.020  1.210
 DP3  NO   O3    single  1.208  0.020  1.208

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
 DP3  H2'2  N2'  H2'1  105.37  3.000
 DP3  H2'2  N2'  C2'   109.29  3.000
 DP3  H2'1  N2'  C2'   109.24  3.000
 DP3  H12   C2'  H11   106.48  3.000
 DP3  H12   C2'  C1'   108.53  3.000
 DP3  H11   C2'  C1'   109.01  3.000
 DP3  H12   C2'  N2'   113.98  3.000
 DP3  H11   C2'  N2'   108.13  3.000
 DP3  C1'   C2'  N2'   110.54  3.000
 DP3  H1'2  C1'  H1'1  106.36  3.000
 DP3  H1'2  C1'  N1'   112.99  3.000
 DP3  H1'1  C1'  N1'   108.14  3.000
 DP3  H1'2  C1'  C2'   109.06  3.000
 DP3  H1'1  C1'  C2'   109.16  3.000
 DP3  N1'   C1'  C2'   110.97  3.000
 DP3  H1'   N1'  C     108.53  3.000
 DP3  H1'   N1'  C1'   108.62  3.000
 DP3  C     N1'  C1'   113.58  3.000
 DP3  H2    C    H1    106.43  3.000
 DP3  H2    C    CA    109.63  3.000
 DP3  H1    C    CA    108.87  3.000
 DP3  H2    C    N1'   112.56  3.000
 DP3  H1    C    N1'   108.27  3.000
 DP3  CA    C    N1'   110.92  3.000
 DP3  HA    CA   CB    107.85  3.000
 DP3  HA    CA   N     107.24  3.000
 DP3  CB    CA   N     110.42  3.000
 DP3  HA    CA   C     107.41  3.000
 DP3  CB    CA   C     110.42  3.000
 DP3  N     CA   C     113.25  3.000
 DP3  HN2   N    HN1   105.00  3.000
 DP3  HN2   N    CA    108.55  3.000
 DP3  HN1   N    CA    107.86  3.000
 DP3  HB2   CB   HB1   106.18  3.000
 DP3  HB2   CB   CG    109.20  3.000
 DP3  HB1   CB   CG    109.75  3.000
 DP3  HB2   CB   CA    108.72  3.000
 DP3  HB1   CB   CA    108.90  3.000
 DP3  CG    CB   CA    113.82  3.000
 DP3  HG2   CG   HG1   106.83  3.000
 DP3  HG2   CG   CD    109.66  3.000
 DP3  HG1   CG   CD    109.47  3.000
 DP3  HG2   CG   CB    109.60  3.000
 DP3  HG1   CG   CB    109.56  3.000
 DP3  CD    CG   CB    111.60  3.000
 DP3  HD2   CD   HD1   106.69  3.000
 DP3  HD2   CD   NE    108.41  3.000
 DP3  HD1   CD   NE    111.09  3.000
 DP3  HD2   CD   CG    110.31  3.000
 DP3  HD1   CD   CG    109.94  3.000
 DP3  NE    CD   CG    110.33  3.000
 DP3  HNE   NE   CZ    117.06  3.000
 DP3  HNE   NE   CD    116.08  3.000
 DP3  CZ    NE   CD    120.25  3.000
 DP3  NH1   CZ   NH2   127.50  3.000
 DP3  NH1   CZ   NE    109.27  3.000
 DP3  NH2   CZ   NE    123.05  3.000
 DP3  HH2   NH2  CZ    113.21  3.000
 DP3  HH1   NH1  NO    113.19  3.000
 DP3  HH1   NH1  CZ    120.41  3.000
 DP3  NO    NH1  CZ    126.20  3.000
 DP3  O3    NO   O2    125.24  3.000
 DP3  O3    NO   NH1   118.93  3.000
 DP3  O2    NO   NH1   115.82  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
 DP3  CONST_01  NH2   CZ   NE   CD      0.00   0.0  0
 DP3  CONST_02  NH1   CZ   NE   CD    180.00   0.0  0
 DP3  CONST_05  HH2   NH2  CZ   NE    180.00   0.0  0
 DP3  Var_01    N1'   C1'  C2'  N2'   179.51  30.0  3
 DP3  Var_02    C     N1'  C1'  C2'   177.31  30.0  3
 DP3  Var_03    CA    C    N1'  C1'  -175.80  30.0  3
 DP3  Var_04    CD    CG   CB   CA    178.04  30.0  3
 DP3  Var_05    NE    CD   CG   CB    177.67  30.0  3
 DP3  Var_06    CZ    NE   CD   CG   -177.34  30.0  3
 DP3  Var_07    O2    NO   NH1  CZ   -178.39  30.0  2
 DP3  Var_08    H2'1  N2'  C2'  C1'    67.80  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
 DP3  chir_01  CA  C  N  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
 DP3  plan-1  CD   0.020
 DP3  plan-1  NE   0.020
 DP3  plan-1  CZ   0.020
 DP3  plan-1  NH2  0.020
 DP3  plan-1  NH1  0.020
 DP3  plan-1  NO   0.020
 DP3  plan-1  HNE  0.020
 DP3  plan-1  HH2  0.020
 DP3  plan-1  HH1  0.020
 DP3  plan-2  NH1  0.020
 DP3  plan-2  NO   0.020
 DP3  plan-2  O2   0.020
 DP3  plan-2  O3   0.020

