# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 18:48:07 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2~{S})-2-[[(3~{S},4~{R},5~{R})-3,4,5,6-tetrakis(oxidanyl)-2-oxidanylidene-hexyl]amino]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@H](O)C(=O)CN[C@@H](CCC(O)=O)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
 N7T  N7T  '(2~{S})-2-[[(3~{S},4~{R},5~{R})-3,4,5,6-tetrakis(oxidanyl)-2-oxidanylidene-hexyl]amino]pentanedioic acid'  ligand  38  21  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N7T
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
 N7T  OAN  O  OH1    0  -0.671   6.1180   1.4275   1.5717
 N7T  CAM  C  CH2    0  -0.159   4.7403   1.4761   1.2841
 N7T  CAL  C  CH1    0  -0.021   4.3891   0.3050   0.3794
 N7T  OAT  O  OH1    0  -0.660   4.6860  -0.9315   0.9851
 N7T  CAK  C  CH1    0  -0.031   2.9117   0.3722  -0.0441
 N7T  OAS  O  OH1    0  -0.658   2.6184   1.5649  -0.7312
 N7T  CAJ  C  CH1    0  -0.074   2.5032  -0.8500  -0.8867
 N7T  OAR  O  OH1    0  -0.673   3.2931  -0.9325  -2.0392
 N7T  CAI  C  C      0   0.332   1.0342  -0.7239  -1.2577
 N7T  OAQ  O  O      0  -0.396   0.7266  -0.4537  -2.3964
 N7T  CAH  C  CH2    0  -0.367   0.0343  -0.9864  -0.1697
 N7T  N    N  NH1    0  -0.602  -1.2858  -0.5207  -0.4920
 N7T  CA   C  CH1    0  -0.166  -2.2651  -0.8113   0.5411
 N7T  C    C  C      0   0.402  -2.6012  -2.3184   0.6386
 N7T  O    O  O      0  -0.600  -2.2594  -3.0666  -0.2960
 N7T  CB   C  CH2    0  -0.427  -3.5514  -0.0223   0.2772
 N7T  CG   C  CH2    0  -0.597  -3.3969   1.4851   0.4212
 N7T  CD   C  C      0   0.417  -4.6867   2.3115   0.2551
 N7T  OE1  O  OC    -1  -0.633  -4.5432   3.5524   0.2849
 N7T  OE2  O  O      0  -0.607  -5.7618   1.6972   0.1137
 N7T  OXT  O  OC    -1  -0.622  -3.2222  -2.6543   1.6689
 N7T  H1   H  HOH1   0   0.455   6.3299   2.1826   2.1272
 N7T  H2   H  HCH2   0   0.191   4.1320   1.4118   2.2004
 N7T  H3   H  HCH2   0   0.208   4.4643   2.4117   0.7866
 N7T  H4   H  HCH1   0   0.237   5.0158   0.3553  -0.5179
 N7T  H5   H  HOH1   0   0.446   4.2308  -0.9768   1.8333
 N7T  H6   H  HCH1   0   0.248   2.2976   0.3884   0.8630
 N7T  H7   H  HOH1   0   0.445   3.1287   1.5770  -1.5493
 N7T  H8   H  HCH1   0   0.256   2.6242  -1.7537  -0.2767
 N7T  H9   H  HOH1   0   0.449   2.7257  -0.7235  -2.7948
 N7T  H10  H  HCH2   0   0.276   0.0201  -2.0760  -0.0502
 N7T  H11  H  HCH2   0   0.229   0.4284  -0.6036   0.7861
 N7T  H12  H  HNH1   0   0.342  -1.2441   0.4815  -0.6278
 N7T  H14  H  HCH1   0   0.176  -1.8955  -0.5072   1.5383
 N7T  H15  H  HCH2   0   0.204  -3.9208  -0.2716  -0.7224
 N7T  H16  H  HCH2   0   0.216  -4.3083  -0.3679   0.9816
 N7T  H17  H  HCH2   0   0.222  -2.9788   1.7092   1.4104
 N7T  H18  H  HCH2   0   0.213  -2.6647   1.8824  -0.2905

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
 N7T  OAN  CAM  single  1.408  0.020  1.408
 N7T  OAT  CAL  single  1.409  0.020  1.409
 N7T  CAM  CAL  single  1.521  0.020  1.521
 N7T  CAL  CAK  single  1.538  0.020  1.538
 N7T  OAR  CAJ  single  1.400  0.020  1.400
 N7T  CAK  CAJ  single  1.540  0.020  1.540
 N7T  CAK  OAS  single  1.407  0.020  1.407
 N7T  CAJ  CAI  single  1.520  0.020  1.520
 N7T  CAI  CAH  single  1.501  0.020  1.501
 N7T  CAI  OAQ  double  1.210  0.020  1.210
 N7T  CAH  N    single  1.436  0.020  1.436
 N7T  N    CA   single  1.453  0.020  1.453
 N7T  O    C    deloc   1.245  0.020  1.245
 N7T  C    CA   single  1.547  0.020  1.547
 N7T  C    OXT  deloc   1.249  0.020  1.249
 N7T  CA   CB   single  1.532  0.020  1.532
 N7T  CB   CG   single  1.522  0.020  1.522
 N7T  CG   CD   single  1.541  0.020  1.541
 N7T  OE2  CD   deloc   1.246  0.020  1.246
 N7T  CD   OE1  deloc   1.249  0.020  1.249
 N7T  OAN  H1   single  0.850  0.020  0.980
 N7T  CAM  H2   single  0.970  0.020  1.090
 N7T  CAM  H3   single  0.970  0.020  1.090
 N7T  CAL  H4   single  0.970  0.020  1.090
 N7T  OAT  H5   single  0.850  0.020  0.980
 N7T  CAK  H6   single  0.970  0.020  1.090
 N7T  OAS  H7   single  0.850  0.020  0.980
 N7T  CAJ  H8   single  0.970  0.020  1.090
 N7T  OAR  H9   single  0.850  0.020  0.980
 N7T  CAH  H10  single  0.970  0.020  1.090
 N7T  CAH  H11  single  0.970  0.020  1.090
 N7T  N    H12  single  0.890  0.020  1.040
 N7T  CA   H14  single  0.970  0.020  1.090
 N7T  CB   H15  single  0.970  0.020  1.090
 N7T  CB   H16  single  0.970  0.020  1.090
 N7T  CG   H17  single  0.970  0.020  1.090
 N7T  CG   H18  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
 N7T  H1   OAN  CAM  107.86  3.000
 N7T  H3   CAM  H2   106.77  3.000
 N7T  H3   CAM  CAL  109.23  3.000
 N7T  H2   CAM  CAL  108.80  3.000
 N7T  H3   CAM  OAN  111.65  3.000
 N7T  H2   CAM  OAN  111.61  3.000
 N7T  CAL  CAM  OAN  108.71  3.000
 N7T  H4   CAL  CAK  108.78  3.000
 N7T  H4   CAL  OAT  105.78  3.000
 N7T  CAK  CAL  OAT  111.04  3.000
 N7T  H4   CAL  CAM  108.65  3.000
 N7T  CAK  CAL  CAM  110.60  3.000
 N7T  OAT  CAL  CAM  111.81  3.000
 N7T  H5   OAT  CAL  108.68  3.000
 N7T  H6   CAK  CAJ  108.43  3.000
 N7T  H6   CAK  OAS  105.95  3.000
 N7T  CAJ  CAK  OAS  110.50  3.000
 N7T  H6   CAK  CAL  108.13  3.000
 N7T  OAS  CAK  CAL  111.81  3.000
 N7T  CAJ  CAK  CAL  111.76  3.000
 N7T  H7   OAS  CAK  108.33  3.000
 N7T  H8   CAJ  CAI  108.09  3.000
 N7T  H8   CAJ  OAR  110.31  3.000
 N7T  CAI  CAJ  OAR  110.44  3.000
 N7T  H8   CAJ  CAK  108.69  3.000
 N7T  CAI  CAJ  CAK  108.91  3.000
 N7T  OAR  CAJ  CAK  110.35  3.000
 N7T  H9   OAR  CAJ  107.42  3.000
 N7T  CAH  CAI  OAQ  123.50  3.000
 N7T  OAQ  CAI  CAJ  119.59  3.000
 N7T  CAH  CAI  CAJ  116.90  3.000
 N7T  H11  CAH  H10  104.79  3.000
 N7T  H11  CAH  N    114.23  3.000
 N7T  H10  CAH  N    109.56  3.000
 N7T  H11  CAH  CAI  109.24  3.000
 N7T  H10  CAH  CAI  105.16  3.000
 N7T  N    CAH  CAI  113.14  3.000
 N7T  H12  N    CA   108.74  3.000
 N7T  H12  N    CAH  108.25  3.000
 N7T  CA   N    CAH  113.27  3.000
 N7T  H14  CA   CB   107.12  3.000
 N7T  H14  CA   C    106.47  3.000
 N7T  CB   CA   C    109.28  3.000
 N7T  H14  CA   N    111.15  3.000
 N7T  CB   CA   N    109.91  3.000
 N7T  C    CA   N    112.71  3.000
 N7T  OXT  C    O    126.45  3.000
 N7T  OXT  C    CA   114.96  3.000
 N7T  O    C    CA   118.58  3.000
 N7T  H16  CB   H15  106.48  3.000
 N7T  H16  CB   CG   108.86  3.000
 N7T  H15  CB   CG   110.26  3.000
 N7T  H16  CB   CA   107.96  3.000
 N7T  H15  CB   CA   108.87  3.000
 N7T  CG   CB   CA   114.11  3.000
 N7T  H18  CG   H17  104.89  3.000
 N7T  H18  CG   CD   107.15  3.000
 N7T  H17  CG   CD   107.85  3.000
 N7T  H18  CG   CB   111.44  3.000
 N7T  H17  CG   CB   109.05  3.000
 N7T  CD   CG   CB   115.85  3.000
 N7T  OE2  CD   OE1  126.25  3.000
 N7T  OE1  CD   CG   115.72  3.000
 N7T  OE2  CD   CG   118.03  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
 N7T  Var_01  N    CAH  CAI  CAJ   164.91  30.0  3
 N7T  Var_02  CA   N    CAH  CAI   178.15  30.0  3
 N7T  Var_03  CD   CG   CB   CA   -176.15  30.0  3
 N7T  Var_04  OE2  CD   CG   CB      5.00  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
 N7T  chir_01  CAL  OAT  CAM  CAK  positiv
 N7T  chir_02  CAK  OAS  CAL  CAJ  positiv
 N7T  chir_03  CAJ  OAR  CAK  CAI  negativ
 N7T  chir_04  CA   N    C    CB   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
 N7T  plan-1  CAJ  0.020
 N7T  plan-1  CAI  0.020
 N7T  plan-1  OAQ  0.020
 N7T  plan-1  CAH  0.020
 N7T  plan-2  CA   0.020
 N7T  plan-2  C    0.020
 N7T  plan-2  O    0.020
 N7T  plan-2  OXT  0.020
 N7T  plan-3  CG   0.020
 N7T  plan-3  CD   0.020
 N7T  plan-3  OE1  0.020
 N7T  plan-3  OE2  0.020

