# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 04:14:08 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: [(5~{S})-5-(methylamino)-6-oxidanyl-6-oxidanylidene-hexyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H](CCCC[NH3+])C(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
 NMK  NMK  '[(5~{S})-5-(methylamino)-6-oxidanyl-6-oxidanylidene-hexyl]azanium'  ligand  28  11  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NMK
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
 NMK  N    N  NH1   0  -0.575  -1.3394   1.4937   0.3170
 NMK  CA   C  CH1   0  -0.200  -1.2264   0.2124  -0.3287
 NMK  CB   C  CH2   0  -0.431   0.0504  -0.5094   0.1286
 NMK  CG   C  CH2   0  -0.422   1.3108   0.1994  -0.3468
 NMK  CD   C  CH2   0  -0.453   2.5749  -0.4270   0.2282
 NMK  CE   C  CH2   0  -0.303   3.8102   0.2500  -0.3282
 NMK  NZ   N  NT3   1  -0.777   5.0510  -0.3328   0.2475
 NMK  C    C  C     0   0.527  -2.4178  -0.7023  -0.0693
 NMK  O    O  O     0  -0.442  -3.1210  -0.6393   0.9083
 NMK  CN   C  CH3   0  -0.522  -2.3656   2.3593  -0.2291
 NMK  OXT  O  OH1   0  -0.591  -2.5722  -1.6096  -1.0259
 NMK  H    H  HNH1  0   0.346  -1.4866   1.3652   1.3104
 NMK  HA   H  HCH1  0   0.262  -1.1582   0.3771  -1.4095
 NMK  HB2  H  HCH2  0   0.234   0.0442  -0.5759   1.2216
 NMK  HB3  H  HCH2  0   0.246   0.0515  -1.5372  -0.2425
 NMK  HG2  H  HCH2  0   0.229   1.3493   0.1648  -1.4400
 NMK  HG3  H  HCH2  0   0.237   1.2611   1.2540  -0.0685
 NMK  HD2  H  HCH2  0   0.248   2.5660  -0.3404   1.3186
 NMK  HD3  H  HCH2  0   0.247   2.6054  -1.4949  -0.0071
 NMK  HE2  H  HCH2  0   0.291   3.8817   0.1321  -1.4075
 NMK  HE3  H  HCH2  0   0.291   3.8280   1.3127  -0.0958
 NMK  HZ1  H  HNT3  0   0.469   5.0873  -0.2238   1.2605
 NMK  HZ3  H  HNT3  0   0.469   5.1318  -1.3296   0.0491
 NMK  HM1  H  HCH3  0   0.226  -2.1252   2.6076  -1.2643
 NMK  HM2  H  HCH3  0   0.199  -3.3812   1.9437  -0.2147
 NMK  HM3  H  HCH3  0   0.236  -2.3857   3.2922   0.3339
 NMK  HXT  H  HOH1  0   0.481  -3.3013  -2.2102  -0.8077
 NMK  HZ2  H  HNT3  0   0.478   5.8851   0.1146  -0.1300

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
 NMK  NZ   CE   single  1.487  0.020  1.487
 NMK  CE   CD   single  1.515  0.020  1.515
 NMK  CD   CG   single  1.523  0.020  1.523
 NMK  CG   CB   single  1.522  0.020  1.522
 NMK  CA   N    single  1.439  0.020  1.439
 NMK  CA   CB   single  1.536  0.020  1.536
 NMK  CA   C    single  1.524  0.020  1.524
 NMK  N    CN   single  1.449  0.020  1.449
 NMK  C    O    double  1.206  0.020  1.206
 NMK  C    OXT  single  1.327  0.020  1.327
 NMK  N    H    single  0.860  0.020  1.020
 NMK  CA   HA   single  0.970  0.020  1.090
 NMK  CB   HB2  single  0.970  0.020  1.090
 NMK  CB   HB3  single  0.970  0.020  1.090
 NMK  CG   HG2  single  0.970  0.020  1.090
 NMK  CG   HG3  single  0.970  0.020  1.090
 NMK  CD   HD2  single  0.970  0.020  1.090
 NMK  CD   HD3  single  0.970  0.020  1.090
 NMK  CE   HE2  single  0.970  0.020  1.090
 NMK  CE   HE3  single  0.970  0.020  1.090
 NMK  NZ   HZ1  single  0.890  0.020  1.040
 NMK  NZ   HZ3  single  0.890  0.020  1.040
 NMK  CN   HM1  single  0.970  0.020  1.090
 NMK  CN   HM2  single  0.970  0.020  1.090
 NMK  CN   HM3  single  0.970  0.020  1.090
 NMK  OXT  HXT  single  0.850  0.020  0.980
 NMK  NZ   HZ2  single  0.890  0.020  1.040

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
 NMK  H    N    CN   110.03  3.000
 NMK  H    N    CA   109.80  3.000
 NMK  CN   N    CA   114.72  3.000
 NMK  HA   CA   C    107.87  3.000
 NMK  HA   CA   CB   108.21  3.000
 NMK  C    CA   CB   108.48  3.000
 NMK  HA   CA   N    108.29  3.000
 NMK  C    CA   N    113.36  3.000
 NMK  CB   CA   N    110.49  3.000
 NMK  HB3  CB   HB2  106.37  3.000
 NMK  HB3  CB   CG   109.34  3.000
 NMK  HB2  CB   CG   110.16  3.000
 NMK  HB3  CB   CA   109.98  3.000
 NMK  HB2  CB   CA   108.72  3.000
 NMK  CG   CB   CA   112.11  3.000
 NMK  HG3  CG   HG2  106.67  3.000
 NMK  HG3  CG   CD   109.80  3.000
 NMK  HG2  CG   CD   109.56  3.000
 NMK  HG3  CG   CB   109.42  3.000
 NMK  HG2  CG   CB   109.05  3.000
 NMK  CD   CG   CB   112.19  3.000
 NMK  HD3  CD   HD2  106.97  3.000
 NMK  HD3  CD   CE   109.55  3.000
 NMK  HD2  CD   CE   109.73  3.000
 NMK  HD3  CD   CG   110.08  3.000
 NMK  HD2  CD   CG   109.69  3.000
 NMK  CE   CD   CG   110.75  3.000
 NMK  HE3  CE   HE2  108.46  3.000
 NMK  HE3  CE   NZ   106.65  3.000
 NMK  HE2  CE   NZ   106.67  3.000
 NMK  HE3  CE   CD   111.80  3.000
 NMK  HE2  CE   CD   111.68  3.000
 NMK  NZ   CE   CD   111.30  3.000
 NMK  HZ2  NZ   HZ3  106.99  3.000
 NMK  HZ2  NZ   HZ1  106.98  3.000
 NMK  HZ3  NZ   HZ1  107.16  3.000
 NMK  HZ2  NZ   CE   111.56  3.000
 NMK  HZ3  NZ   CE   111.97  3.000
 NMK  HZ1  NZ   CE   111.87  3.000
 NMK  OXT  C    O    123.51  3.000
 NMK  OXT  C    CA   112.24  3.000
 NMK  O    C    CA   124.22  3.000
 NMK  HM3  CN   HM2  107.48  3.000
 NMK  HM3  CN   HM1  107.42  3.000
 NMK  HM2  CN   HM1  107.60  3.000
 NMK  HM3  CN   N    109.25  3.000
 NMK  HM2  CN   N    115.09  3.000
 NMK  HM1  CN   N    109.71  3.000
 NMK  HXT  OXT  C    110.41  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
 NMK  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 NMK  Var_01    CD   CG   CB  CA  173.87  30.0  1
 NMK  Var_02    CE   CD   CG  CB  176.68  30.0  1
 NMK  Var_03    NZ   CE   CD  CG  178.78  30.0  1
 NMK  Var_04    HM1  CN   N   CA  -63.51  30.0  3
 NMK  Var_05    HZ1  NZ   CE  CD  -60.67  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
 NMK  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
 NMK  plan-1  CA   0.020
 NMK  plan-1  C    0.020
 NMK  plan-1  O    0.020
 NMK  plan-1  OXT  0.020
 NMK  plan-1  HXT  0.020

