# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:20:47 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 1-{(4S)-4-amino-5-[(2-aminoethyl)(hydroxy)amino]pentyl}-3-nitroguanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN(O)C[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
 3HX  3HX  1-{(4S)-4-amino-5-[(2-aminoethyl)(hydroxy)amino]pentyl}-3-nitroguanidine  ligand  39  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3HX
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
 3HX  NO    N  N      1   0.612   0.5136   1.5776   8.2449
 3HX  O2    O  O     -1  -0.420   0.5413   2.4863   9.0436
 3HX  O3    O  O      0  -0.413   0.5250   0.4028   8.5252
 3HX  N     N  NH2    0  -0.796  -3.2054   2.8309   0.5114
 3HX  CA    C  CH1    0  -0.124  -1.9322   2.2133   0.1582
 3HX  C     C  CH2    0  -0.242  -2.1343   1.4903  -1.1723
 3HX  CB    C  CH2    0  -0.420  -1.3616   1.2742   1.2246
 3HX  CG    C  CH2    0  -0.465  -1.1130   1.9549   2.5637
 3HX  CD    C  CH2    0  -0.228  -0.5059   0.9969   3.5760
 3HX  NE    N  NH1    0  -0.658  -0.3189   1.6610   4.8482
 3HX  CZ    C  C      0   0.646   0.3670   1.0526   5.8476
 3HX  NH1   N  NC1    0  -0.546   0.4651   1.9354   6.9549
 3HX  NH2   N  N      0  -0.646   0.8949  -0.0922   5.7288
 3HX  NA    N  NT     0  -0.212  -0.9258   0.8756  -1.6868
 3HX  O1'   O  OH1    0  -0.584  -0.0445   1.9196  -2.0566
 3HX  C1'   C  CH2    0  -0.270  -1.1796   0.0745  -2.8703
 3HX  C2'   C  CH2    0  -0.308   0.0632  -0.6629  -3.3603
 3HX  HN2   H  HNH2   0   0.336  -3.8389   2.1248   0.8705
 3HX  HA    H  HCH1   0   0.222  -1.2198   3.0294   0.0020
 3HX  H1    H  HCH2   0   0.222  -2.8619   0.6853  -1.0264
 3HX  H2    H  HCH2   0   0.211  -2.5766   2.1907  -1.8966
 3HX  HB1   H  HCH2   0   0.223  -0.4261   0.8419   0.8594
 3HX  HB2   H  HCH2   0   0.209  -2.0536   0.4339   1.3606
 3HX  HG1   H  HCH2   0   0.220  -2.0530   2.3490   2.9628
 3HX  HG2   H  HCH2   0   0.229  -0.4427   2.8093   2.4290
 3HX  HD1   H  HCH2   0   0.222  -1.1445   0.1120   3.6820
 3HX  HD2   H  HCH2   0   0.236   0.4648   0.6423   3.2254
 3HX  HNE   H  HNH1   0   0.396  -1.0466   2.3052   5.1193
 3HX  HNH1  H  HNC1   0   0.442   0.3978   2.9360   6.8212
 3HX  HNH2  H  H      0   0.347   1.4794  -0.3428   6.5132
 3HX  HO1'  H  HOH1   0   0.462   0.7298   1.7817  -1.5020
 3HX  HNB1  H  HNH2   0   0.340  -0.5688  -1.0095  -5.2594
 3HX  HNB2  H  HNH2   0   0.339  -0.8720  -2.2328  -4.2513
 3HX  H1'1  H  HCH2   0   0.194  -1.6034   0.6761  -3.6912
 3HX  H1'2  H  HCH2   0   0.225  -1.9387  -0.6640  -2.5968
 3HX  H2'1  H  HCH2   0   0.217   0.4746  -1.2539  -2.5376
 3HX  H2'2  H  HCH2   0   0.221   0.8347   0.0567  -3.6411
 3HX  HN1   H  HNH2   0   0.351  -3.0763   3.4938   1.2647
 3HX  NB    N  NH2    0  -0.790  -0.1727  -1.5416  -4.4940

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
 3HX  NO   NH1   single  1.340  0.020  1.340
 3HX  NO   O3    double  1.208  0.020  1.208
 3HX  NO   O2    single  1.210  0.020  1.210
 3HX  N    CA    single  1.459  0.020  1.459
 3HX  N    HN1   single  0.890  0.020  1.040
 3HX  N    HN2   single  0.890  0.020  1.040
 3HX  CA   CB    single  1.531  0.020  1.531
 3HX  CA   C     single  1.528  0.020  1.528
 3HX  CA   HA    single  0.970  0.020  1.090
 3HX  C    NA    single  1.450  0.020  1.450
 3HX  C    H1    single  0.970  0.020  1.090
 3HX  C    H2    single  0.970  0.020  1.090
 3HX  CB   CG    single  1.523  0.020  1.523
 3HX  CB   HB1   single  0.970  0.020  1.090
 3HX  CB   HB2   single  0.970  0.020  1.090
 3HX  CG   CD    single  1.520  0.020  1.520
 3HX  CG   HG1   single  0.970  0.020  1.090
 3HX  CG   HG2   single  0.970  0.020  1.090
 3HX  CD   NE    single  1.447  0.020  1.447
 3HX  CD   HD1   single  0.970  0.020  1.090
 3HX  CD   HD2   single  0.970  0.020  1.090
 3HX  NE   CZ    single  1.356  0.020  1.356
 3HX  NE   HNE   single  0.890  0.020  1.040
 3HX  CZ   NH2   double  1.266  0.020  1.266
 3HX  CZ   NH1   single  1.420  0.020  1.420
 3HX  NH1  HNH1  single  0.860  0.020  1.020
 3HX  NH2  HNH2  single  0.890  0.020  1.040
 3HX  NA   O1'   single  1.415  0.020  1.415
 3HX  NA   C1'   single  1.451  0.020  1.451
 3HX  O1'  HO1'  single  0.850  0.020  0.980
 3HX  NB   C2'   single  1.454  0.020  1.454
 3HX  NB   HNB1  single  0.890  0.020  1.040
 3HX  NB   HNB2  single  0.890  0.020  1.040
 3HX  C1'  C2'   single  1.526  0.020  1.526
 3HX  C1'  H1'1  single  0.970  0.020  1.090
 3HX  C1'  H1'2  single  0.970  0.020  1.090
 3HX  C2'  H2'1  single  0.970  0.020  1.090
 3HX  C2'  H2'2  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
 3HX  NH1   NO   O3    118.92  3.000
 3HX  O3    NO   O2    125.24  3.000
 3HX  NH1   NO   O2    115.84  3.000
 3HX  HN2   N    HN1   105.80  3.000
 3HX  HN2   N    CA    109.64  3.000
 3HX  HN1   N    CA    110.26  3.000
 3HX  HA    CA   CB    108.31  3.000
 3HX  HA    CA   C     108.34  3.000
 3HX  CB    CA   C     111.44  3.000
 3HX  HA    CA   N     106.68  3.000
 3HX  C     CA   N     107.21  3.000
 3HX  CB    CA   N     114.60  3.000
 3HX  H2    C    H1    106.77  3.000
 3HX  H2    C    NA    111.79  3.000
 3HX  H1    C    NA    106.83  3.000
 3HX  H2    C    CA    108.97  3.000
 3HX  H1    C    CA    108.65  3.000
 3HX  NA    C    CA    113.54  3.000
 3HX  HB2   CB   HB1   106.16  3.000
 3HX  HB2   CB   CG    109.66  3.000
 3HX  HB1   CB   CG    109.32  3.000
 3HX  HB2   CB   CA    108.73  3.000
 3HX  HB1   CB   CA    109.19  3.000
 3HX  CG    CB   CA    113.52  3.000
 3HX  HG2   CG   HG1   106.85  3.000
 3HX  HG2   CG   CD    109.23  3.000
 3HX  HG1   CG   CD    109.09  3.000
 3HX  HG2   CG   CB    109.93  3.000
 3HX  HG1   CG   CB    109.96  3.000
 3HX  CD    CG   CB    111.66  3.000
 3HX  HD2   CD   HD1   106.67  3.000
 3HX  HD2   CD   NE    108.46  3.000
 3HX  HD1   CD   NE    111.14  3.000
 3HX  HD2   CD   CG    110.25  3.000
 3HX  HD1   CD   CG    109.90  3.000
 3HX  NE    CD   CG    110.35  3.000
 3HX  HNE   NE   CZ    116.95  3.000
 3HX  HNE   NE   CD    115.85  3.000
 3HX  CZ    NE   CD    120.48  3.000
 3HX  NH2   CZ   NH1   127.35  3.000
 3HX  NH1   CZ   NE    109.31  3.000
 3HX  NH2   CZ   NE    123.18  3.000
 3HX  HNH1  NH1  CZ    120.49  3.000
 3HX  HNH1  NH1  NO    113.19  3.000
 3HX  CZ    NH1  NO    125.98  3.000
 3HX  HNH2  NH2  CZ    113.13  3.000
 3HX  C1'   NA   O1'   107.63  3.000
 3HX  C1'   NA   C     112.18  3.000
 3HX  O1'   NA   C     107.39  3.000
 3HX  HO1'  O1'  NA    104.16  3.000
 3HX  H1'2  C1'  H1'1  106.73  3.000
 3HX  H1'2  C1'  C2'   108.62  3.000
 3HX  H1'1  C1'  C2'   109.74  3.000
 3HX  H1'2  C1'  NA    106.86  3.000
 3HX  H1'1  C1'  NA    111.92  3.000
 3HX  C2'   C1'  NA    112.71  3.000
 3HX  H2'2  C2'  H2'1  106.49  3.000
 3HX  H2'2  C2'  C1'   109.85  3.000
 3HX  H2'1  C2'  C1'   109.03  3.000
 3HX  H2'2  C2'  NB    108.21  3.000
 3HX  H2'1  C2'  NB    108.74  3.000
 3HX  C1'   C2'  NB    114.23  3.000
 3HX  HNB2  NB   HNB1  105.64  3.000
 3HX  HNB2  NB   C2'   109.74  3.000
 3HX  HNB1  NB   C2'   109.59  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
 3HX  CONST_03  NH2   CZ   NE   CD      0.00   0.0  0
 3HX  CONST_04  NH1   CZ   NE   CD    180.00   0.0  0
 3HX  CONST_05  HNH2  NH2  CZ   NE    180.00   0.0  0
 3HX  Var_01    CZ    NH1  NO   O2   -177.06  30.0  2
 3HX  Var_02    CD    CG   CB   CA   -178.16  30.0  3
 3HX  Var_03    O1'   NA   C    CA    -68.31  30.0  3
 3HX  Var_04    C2'   C1'  NA   C    -175.64  30.0  3
 3HX  Var_05    NE    CD   CG   CB   -178.28  30.0  3
 3HX  Var_06    CZ    NE   CD   CG   -171.41  30.0  3
 3HX  Var_07    NB    C2'  C1'  NA    176.31  30.0  3
 3HX  Var_08    HNB1  NB   C2'  C1'    57.04  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
 3HX  chir_01  CA  N  CB  C  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
 3HX  plan-1  NO    0.020
 3HX  plan-1  CD    0.020
 3HX  plan-1  NE    0.020
 3HX  plan-1  CZ    0.020
 3HX  plan-1  NH1   0.020
 3HX  plan-1  NH2   0.020
 3HX  plan-1  HNE   0.020
 3HX  plan-1  HNH1  0.020
 3HX  plan-1  HNH2  0.020
 3HX  plan-2  NO    0.020
 3HX  plan-2  O2    0.020
 3HX  plan-2  O3    0.020
 3HX  plan-2  NH1   0.020

