# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:54:53 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: [azanyl-[[(4~{S})-4-azanyl-5-(carboxyamino)pentyl]amino]methylidene]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=[NH2+])CNC(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
 OUR  OUR  '[azanyl-[[(4~{S})-4-azanyl-5-(carboxyamino)pentyl]amino]methylidene]azanium'  ligand  31  14  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OUR
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
 OUR  N     N  NH2    0  -0.793   1.2877   1.5755  -0.8559
 OUR  CA    C  CH1    0  -0.135   1.1590   0.5070   0.1285
 OUR  C     C  C      0   0.495   4.8513  -0.2532   0.2509
 OUR  O     O  O      0  -0.651   4.8757  -1.4884   0.4405
 OUR  CB    C  CH2    0  -0.421  -0.1126  -0.3349  -0.0085
 OUR  CG    C  CH2    0  -0.477  -1.3960   0.4628   0.1764
 OUR  CD    C  CH2    0  -0.269  -2.6190  -0.4238   0.0205
 OUR  NE    N  NH1    0  -0.635  -3.8338   0.3472   0.2278
 OUR  CZ    C  C      0   0.825  -5.0598  -0.1138   0.0218
 OUR  NH1   N  NH2    0  -0.815  -5.2491  -1.3241  -0.4845
 OUR  NH2   N  NC2    1  -0.821  -6.1084   0.6501   0.3088
 OUR  CM    C  CH2    0  -0.209   2.3883  -0.3949   0.0587
 OUR  N2    N  NH1    0  -0.665   3.5931   0.3681   0.2483
 OUR  O1    O  OC    -1  -0.665   5.8378   0.5015   0.0916
 OUR  H     H  HNH2   0   0.338   1.1603   1.1978  -1.7888
 OUR  H2    H  HNH2   0   0.351   0.5587   2.2653  -0.7285
 OUR  HA    H  HCH1   0   0.220   1.1511   0.9846   1.1155
 OUR  HB3   H  HCH2   0   0.220  -0.1178  -0.8166  -0.9935
 OUR  HB2   H  HCH2   0   0.224  -0.0864  -1.1430   0.7299
 OUR  HG3   H  HCH2   0   0.242  -1.4015   0.9255   1.1685
 OUR  HG2   H  HCH2   0   0.236  -1.4529   1.2728  -0.5555
 OUR  HD3   H  HCH2   0   0.254  -2.6227  -0.8492  -0.9862
 OUR  HD2   H  HCH2   0   0.258  -2.5773  -1.2545   0.7314
 OUR  HE    H  HNH1   0   0.425  -3.7457   1.2507   0.6672
 OUR  HH12  H  HNH2   0   0.445  -4.4840  -1.9084  -0.7754
 OUR  HH11  H  HNH2   0   0.434  -6.1762  -1.6690  -0.6667
 OUR  HH22  H  HNC2   0   0.431  -5.9935   1.5150   0.8093
 OUR  HM2   H  HCH2   0   0.210   2.3049  -1.1567   0.8357
 OUR  HM3   H  HCH2   0   0.178   2.3702  -0.9346  -0.9032
 OUR  HN2   H  HNH1   0   0.341   3.5637   1.2667  -0.2096
 OUR  HH21  H  HNC2   0   0.430  -7.0449   0.2921   0.2300

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
 OUR  NH2  CZ    double  1.329  0.020  1.329
 OUR  NH1  CZ    single  1.325  0.020  1.325
 OUR  CZ   NE    single  1.326  0.020  1.326
 OUR  NE   CD    single  1.454  0.020  1.454
 OUR  CD   CG    single  1.519  0.020  1.519
 OUR  CG   CB    single  1.522  0.020  1.522
 OUR  CB   CA    single  1.531  0.020  1.531
 OUR  N    CA    single  1.459  0.020  1.459
 OUR  CA   CM    single  1.526  0.020  1.526
 OUR  CM   N2    single  1.439  0.020  1.439
 OUR  N2   C     single  1.403  0.020  1.403
 OUR  C    O     deloc   1.250  0.020  1.250
 OUR  C    O1    deloc   1.252  0.020  1.252
 OUR  N    H     single  0.860  0.020  1.020
 OUR  N    H2    single  0.890  0.020  1.040
 OUR  CA   HA    single  0.970  0.020  1.090
 OUR  CB   HB3   single  0.970  0.020  1.090
 OUR  CB   HB2   single  0.970  0.020  1.090
 OUR  CG   HG3   single  0.970  0.020  1.090
 OUR  CG   HG2   single  0.970  0.020  1.090
 OUR  CD   HD3   single  0.970  0.020  1.090
 OUR  CD   HD2   single  0.970  0.020  1.090
 OUR  NE   HE    single  0.860  0.020  1.020
 OUR  NH1  HH12  single  0.860  0.020  1.020
 OUR  NH1  HH11  single  0.860  0.020  1.020
 OUR  NH2  HH22  single  0.860  0.020  1.020
 OUR  CM   HM2   single  0.970  0.020  1.090
 OUR  CM   HM3   single  0.970  0.020  1.090
 OUR  N2   HN2   single  0.890  0.020  1.040
 OUR  NH2  HH21  single  0.860  0.020  1.020

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
 OUR  H2    N    H     106.21  3.000
 OUR  H2    N    CA    110.54  3.000
 OUR  H     N    CA    109.68  3.000
 OUR  HA    CA   CM    107.72  3.000
 OUR  HA    CA   CB    108.30  3.000
 OUR  CM    CA   CB    109.87  3.000
 OUR  HA    CA   N     106.80  3.000
 OUR  CM    CA   N     109.33  3.000
 OUR  CB    CA   N     114.56  3.000
 OUR  O1    C    N2    116.06  3.000
 OUR  O1    C    O     126.83  3.000
 OUR  N2    C    O     117.09  3.000
 OUR  HB2   CB   HB3   106.36  3.000
 OUR  HB2   CB   CG    108.97  3.000
 OUR  HB3   CB   CG    109.59  3.000
 OUR  HB2   CB   CA    109.00  3.000
 OUR  HB3   CB   CA    109.01  3.000
 OUR  CG    CB   CA    113.65  3.000
 OUR  HG2   CG   HG3   107.06  3.000
 OUR  HG2   CG   CD    108.78  3.000
 OUR  HG3   CG   CD    109.62  3.000
 OUR  HG2   CG   CB    110.54  3.000
 OUR  HG3   CG   CB    109.62  3.000
 OUR  CD    CG   CB    111.13  3.000
 OUR  HD2   CD   HD3   107.65  3.000
 OUR  HD2   CD   NE    109.99  3.000
 OUR  HD3   CD   NE    109.57  3.000
 OUR  HD2   CD   CG    110.23  3.000
 OUR  HD3   CD   CG    108.94  3.000
 OUR  NE    CD   CG    110.41  3.000
 OUR  HE    NE   CZ    117.38  3.000
 OUR  HE    NE   CD    117.67  3.000
 OUR  CZ    NE   CD    124.48  3.000
 OUR  NH2   CZ   NH1   119.65  3.000
 OUR  NH1   CZ   NE    120.59  3.000
 OUR  NH2   CZ   NE    119.75  3.000
 OUR  HH11  NH1  HH12  116.72  3.000
 OUR  HH11  NH1  CZ    120.92  3.000
 OUR  HH12  NH1  CZ    122.17  3.000
 OUR  HH21  NH2  HH22  116.84  3.000
 OUR  HH21  NH2  CZ    120.88  3.000
 OUR  HH22  NH2  CZ    120.77  3.000
 OUR  HM3   CM   HM2   106.14  3.000
 OUR  HM3   CM   N2    112.84  3.000
 OUR  HM2   CM   N2    109.90  3.000
 OUR  HM3   CM   CA    108.41  3.000
 OUR  HM2   CM   CA    108.57  3.000
 OUR  N2    CM   CA    110.80  3.000
 OUR  HN2   N2   CM    112.84  3.000
 OUR  HN2   N2   C     114.92  3.000
 OUR  CM    N2   C     121.09  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
 OUR  CONST_01  NH2   CZ   NE  CD   180.00   0.0  0
 OUR  CONST_02  NH1   CZ   NE  CD     0.00   0.0  0
 OUR  CONST_03  HH22  NH2  CZ  NE     0.00   0.0  0
 OUR  CONST_04  HH21  NH2  CZ  NE   180.00   0.0  0
 OUR  CONST_05  HH12  NH1  CZ  NE     0.00   0.0  0
 OUR  CONST_06  HH11  NH1  CZ  NE   180.00   0.0  0
 OUR  CONST_07  HE    NE   CZ  NH1  180.00   0.0  0
 OUR  Var_01    CD    CG   CB  CA   179.64  30.0  1
 OUR  Var_02    C     N2   CM  CA   178.74  30.0  3
 OUR  Var_03    CM    N2   C   O    -18.54  30.0  2
 OUR  Var_04    NE    CD   CG  CB   178.80  30.0  1
 OUR  Var_05    CZ    NE   CD  CG   172.63  30.0  1

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
 OUR  chir_01  CA  CB  N  CM  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
 OUR  plan-1  CD    0.020
 OUR  plan-1  NE    0.020
 OUR  plan-1  CZ    0.020
 OUR  plan-1  NH1   0.020
 OUR  plan-1  NH2   0.020
 OUR  plan-1  HE    0.020
 OUR  plan-1  HH12  0.020
 OUR  plan-1  HH11  0.020
 OUR  plan-1  HH22  0.020
 OUR  plan-1  HH21  0.020
 OUR  plan-2  C     0.020
 OUR  plan-2  O     0.020
 OUR  plan-2  N2    0.020
 OUR  plan-2  O1    0.020

