# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:47:55 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  27  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  -0.579  -1.3079   1.4917   0.2992
 NMK  CA   C  CH1    0  -0.195  -1.2308   0.1972  -0.3523
 NMK  CB   C  CH2    0  -0.423   0.0515  -0.5236   0.0773
 NMK  CG   C  CH2    0  -0.416   1.3203   0.1976  -0.3566
 NMK  CD   C  CH2    0  -0.450   2.5817  -0.4436   0.2085
 NMK  CE   C  CH2    0  -0.302   3.8220   0.2561  -0.3070
 NMK  NZ   N  NT3    1  -0.777   5.0578  -0.3377   0.2690
 NMK  C    C  C      0   0.392  -2.4391  -0.7355  -0.0844
 NMK  O    O  O      0  -0.610  -3.0778  -0.5454   0.9706
 NMK  CN   C  CH3    0  -0.519  -2.3123   2.3609  -0.2786
 NMK  OXT  O  OC    -1  -0.619  -2.6453  -1.6330  -0.9269
 NMK  H    H  HNH1   0   0.325  -1.5552   1.3262   1.2682
 NMK  HA   H  HCH1   0   0.201  -1.1687   0.3728  -1.4334
 NMK  HB2  H  HCH2   0   0.209   0.0456  -0.6390   1.1677
 NMK  HB3  H  HCH2   0   0.221   0.0494  -1.5351  -0.3372
 NMK  HG2  H  HCH2   0   0.217   1.3728   0.2037  -1.4503
 NMK  HG3  H  HCH2   0   0.227   1.2648   1.2425  -0.0434
 NMK  HD2  H  HCH2   0   0.243   2.5606  -0.3970   1.3015
 NMK  HD3  H  HCH2   0   0.242   2.6197  -1.5028  -0.0637
 NMK  HE2  H  HCH2   0   0.289   3.9114   0.1728  -1.3882
 NMK  HE3  H  HCH2   0   0.289   3.8295   1.3112  -0.0416
 NMK  HZ1  H  HNT3   0   0.468   5.0773  -0.2624   1.2855
 NMK  HZ3  H  HNT3   0   0.468   5.1479  -1.3268   0.0392
 NMK  HM1  H  HCH3   0   0.213  -2.0219   2.6422  -1.2933
 NMK  HM2  H  HCH3   0   0.188  -3.3196   1.9270  -0.3319
 NMK  HM3  H  HCH3   0   0.222  -2.3822   3.2807   0.3042
 NMK  HZ2  H  HNT3   0   0.477   5.8957   0.1261  -0.0797

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  1.514  0.020  1.514
 NMK  CD  CG   single  1.524  0.020  1.524
 NMK  CG  CB   single  1.523  0.020  1.523
 NMK  CA  N    single  1.451  0.020  1.451
 NMK  CA  CB   single  1.532  0.020  1.532
 NMK  CA  C    single  1.550  0.020  1.550
 NMK  N   CN   single  1.449  0.020  1.449
 NMK  C   O    deloc   1.248  0.020  1.248
 NMK  C   OXT  deloc   1.248  0.020  1.248
 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  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   108.06  3.000
 NMK  H    N   CA   107.24  3.000
 NMK  CN   N   CA   113.14  3.000
 NMK  HA   CA  C    108.10  3.000
 NMK  HA   CA  CB   107.71  3.000
 NMK  C    CA  CB   108.72  3.000
 NMK  HA   CA  N    107.62  3.000
 NMK  C    CA  N    114.70  3.000
 NMK  CB   CA  N    109.77  3.000
 NMK  HB3  CB  HB2  106.24  3.000
 NMK  HB3  CB  CG   109.38  3.000
 NMK  HB2  CB  CG   109.74  3.000
 NMK  HB3  CB  CA   109.11  3.000
 NMK  HB2  CB  CA   108.89  3.000
 NMK  CG   CB  CA   113.24  3.000
 NMK  HG3  CG  HG2  106.47  3.000
 NMK  HG3  CG  CD   109.77  3.000
 NMK  HG2  CG  CD   109.46  3.000
 NMK  HG3  CG  CB   109.22  3.000
 NMK  HG2  CG  CB   109.10  3.000
 NMK  CD   CG  CB   112.64  3.000
 NMK  HD3  CD  HD2  106.88  3.000
 NMK  HD3  CD  CE   109.52  3.000
 NMK  HD2  CD  CE   109.65  3.000
 NMK  HD3  CD  CG   110.10  3.000
 NMK  HD2  CD  CG   109.67  3.000
 NMK  CE   CD  CG   110.94  3.000
 NMK  HE3  CE  HE2  108.43  3.000
 NMK  HE3  CE  NZ   106.68  3.000
 NMK  HE2  CE  NZ   106.62  3.000
 NMK  HE3  CE  CD   111.75  3.000
 NMK  HE2  CE  CD   111.73  3.000
 NMK  NZ   CE  CD   111.36  3.000
 NMK  HZ2  NZ  HZ3  106.97  3.000
 NMK  HZ2  NZ  HZ1  106.97  3.000
 NMK  HZ3  NZ  HZ1  107.15  3.000
 NMK  HZ2  NZ  CE   111.64  3.000
 NMK  HZ3  NZ  CE   111.93  3.000
 NMK  HZ1  NZ  CE   111.88  3.000
 NMK  OXT  C   O    126.56  3.000
 NMK  OXT  C   CA   116.42  3.000
 NMK  O    C   CA   116.97  3.000
 NMK  HM3  CN  HM2  107.47  3.000
 NMK  HM3  CN  HM1  107.23  3.000
 NMK  HM2  CN  HM1  107.49  3.000
 NMK  HM3  CN  N    109.70  3.000
 NMK  HM2  CN  N    114.73  3.000
 NMK  HM1  CN  N    109.92  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  Var_01  CD   CG  CB  CA  173.58  30.0  1
 NMK  Var_02  CE   CD  CG  CB  176.89  30.0  1
 NMK  Var_03  NZ   CE  CD  CG  178.39  30.0  1
 NMK  Var_04  HM1  CN  N   CA  -67.18  30.0  3
 NMK  Var_05  HZ1  NZ  CE  CD  -60.52  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

