# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 12:37:33 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{R},3~{S},4~{R},5~{R})-2,3,4,5-tetrakis(oxidanyl)oxan-2-yl]methylamino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CC[C@H](NC[C@@]1(O)OC[C@@H](O)[C@@H](O)[C@@H]1O)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
 SNW  SNW  '(2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{R},3~{S},4~{R},5~{R})-2,3,4,5-tetrakis(oxidanyl)oxan-2-yl]methylamino]pentanoic acid'  ligand  41  21  .  2021-08-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SNW
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
 SNW  OAB  O  OH1   0  -0.676  -2.8215  -1.8472  -0.9763
 SNW  CAF  C  CH1   0   0.033  -2.8428  -0.4727  -0.6865
 SNW  CAG  C  CH1   0   0.004  -4.0819  -0.0861   0.1195
 SNW  OAC  O  OH1   0  -0.674  -5.2043  -0.3956  -0.6724
 SNW  CAH  C  CH1   0  -0.018  -4.0232   1.3850   0.5221
 SNW  OAI  O  OH1   0  -0.670  -4.1690   2.1691  -0.6387
 SNW  CAO  C  CH2   0  -0.233  -2.6988   1.6349   1.2281
 SNW  OAN  O  O2    0  -0.510  -1.6023   1.2516   0.4238
 SNW  CAM  C  CT    0   0.451  -1.5677  -0.1210   0.0893
 SNW  OAQ  O  OH1   0  -0.685  -1.4863  -0.9179   1.2207
 SNW  CAL  C  CH2   0  -0.311  -0.3070  -0.3071  -0.7569
 SNW  N    N  NH1   0  -0.638   0.8529  -0.1181   0.0908
 SNW  CA   C  CH1   0  -0.172   2.0434  -0.8377  -0.2857
 SNW  C    C  C     0   0.551   2.0028  -2.2392   0.3075
 SNW  O    O  O     0  -0.432   1.2960  -2.5875   1.2183
 SNW  CB   C  CH2   0  -0.460   3.3051  -0.1198   0.2153
 SNW  CG   C  CH2   0  -0.591   3.5772   1.1520  -0.5739
 SNW  CD   C  C     0   0.531   4.8466   1.8633  -0.1450
 SNW  OE1  O  O     0  -0.491   5.5997   1.4157   0.7073
 SNW  NE2  N  NH2   0  -0.805   5.0745   3.0224  -0.7817
 SNW  OXT  O  OH1   0  -0.592   2.8693  -3.0438  -0.2948
 SNW  H1   H  HOH1  0   0.451  -3.5896  -2.0430  -1.5218
 SNW  H2   H  HCH1  0   0.216  -2.8298   0.1234  -1.6108
 SNW  H3   H  HCH1  0   0.223  -4.0862  -0.6760   1.0463
 SNW  H4   H  HOH1  0   0.455  -5.9883  -0.3877  -0.1150
 SNW  H5   H  HCH1  0   0.221  -4.8303   1.5888   1.2426
 SNW  H6   H  HOH1  0   0.452  -4.1531   3.0956  -0.3798
 SNW  H7   H  HCH2  0   0.246  -2.5738   2.6998   1.4384
 SNW  H8   H  HCH2  0   0.215  -2.6938   1.1149   2.1928
 SNW  H9   H  HOH1  0   0.448  -0.5392  -0.9680   1.4388
 SNW  H10  H  HCH2  0   0.254  -0.3025  -1.3266  -1.1456
 SNW  H11  H  HCH2  0   0.232  -0.3266   0.3655  -1.6228
 SNW  H12  H  HNH1  0   0.369   1.0400   0.8650   0.2207
 SNW  H14  H  HCH1  0   0.255   2.1378  -0.9522  -1.3759
 SNW  H15  H  HCH2  0   0.252   3.1857   0.1012   1.2786
 SNW  H16  H  HCH2  0   0.279   3.6601   0.9148  -1.6395
 SNW  H17  H  HNH2  0   0.406   4.4552   3.3704  -1.4932
 SNW  H18  H  HNH2  0   0.399   5.9044   3.5577  -0.5865
 SNW  H19  H  HOH1  0   0.483   2.8611  -3.9179   0.1233
 SNW  H13  H  HCH2  0   0.264   4.1619  -0.7870   0.1234
 SNW  H20  H  HCH2  0   0.268   2.7487   1.8617  -0.4953

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
 SNW  CAO  CAH  single  1.522  0.020  1.522
 SNW  CAO  OAN  single  1.413  0.020  1.413
 SNW  CAH  CAG  single  1.526  0.020  1.526
 SNW  CAH  OAI  single  1.408  0.020  1.408
 SNW  CAG  OAC  single  1.408  0.020  1.408
 SNW  CAG  CAF  single  1.528  0.020  1.528
 SNW  OAQ  CAM  single  1.386  0.020  1.386
 SNW  OAN  CAM  single  1.413  0.020  1.413
 SNW  NE2  CD   single  1.342  0.020  1.342
 SNW  CAM  CAF  single  1.533  0.020  1.533
 SNW  CAM  CAL  single  1.530  0.020  1.530
 SNW  CAF  OAB  single  1.405  0.020  1.405
 SNW  CD   CG   single  1.517  0.020  1.517
 SNW  CD   OE1  double  1.222  0.020  1.222
 SNW  CG   CB   single  1.521  0.020  1.521
 SNW  O    C    double  1.204  0.020  1.204
 SNW  N    CAL  single  1.449  0.020  1.449
 SNW  N    CA   single  1.441  0.020  1.441
 SNW  C    CA   single  1.522  0.020  1.522
 SNW  C    OXT  single  1.327  0.020  1.327
 SNW  CA   CB   single  1.536  0.020  1.536
 SNW  OAB  H1   single  0.850  0.020  0.980
 SNW  CAF  H2   single  0.970  0.020  1.090
 SNW  CAG  H3   single  0.970  0.020  1.090
 SNW  OAC  H4   single  0.850  0.020  0.980
 SNW  CAH  H5   single  0.970  0.020  1.090
 SNW  OAI  H6   single  0.850  0.020  0.980
 SNW  CAO  H7   single  0.970  0.020  1.090
 SNW  CAO  H8   single  0.970  0.020  1.090
 SNW  OAQ  H9   single  0.850  0.020  0.980
 SNW  CAL  H10  single  0.970  0.020  1.090
 SNW  CAL  H11  single  0.970  0.020  1.090
 SNW  N    H12  single  0.890  0.020  1.040
 SNW  CA   H14  single  0.970  0.020  1.090
 SNW  CB   H15  single  0.970  0.020  1.090
 SNW  CG   H16  single  0.970  0.020  1.090
 SNW  NE2  H17  single  0.860  0.020  1.020
 SNW  NE2  H18  single  0.860  0.020  1.020
 SNW  OXT  H19  single  0.850  0.020  0.980
 SNW  CB   H13  single  0.970  0.020  1.090
 SNW  CG   H20  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
 SNW  H1   OAB  CAF  107.69  3.000
 SNW  H2   CAF  CAM  106.91  3.000
 SNW  H2   CAF  CAG  108.41  3.000
 SNW  CAM  CAF  CAG  110.45  3.000
 SNW  H2   CAF  OAB  110.90  3.000
 SNW  CAM  CAF  OAB  108.43  3.000
 SNW  CAG  CAF  OAB  111.64  3.000
 SNW  H3   CAG  CAH  107.17  3.000
 SNW  H3   CAG  OAC  110.69  3.000
 SNW  CAH  CAG  OAC  113.01  3.000
 SNW  H3   CAG  CAF  108.20  3.000
 SNW  OAC  CAG  CAF  107.11  3.000
 SNW  CAH  CAG  CAF  110.60  3.000
 SNW  H4   OAC  CAG  108.78  3.000
 SNW  H5   CAH  CAO  107.70  3.000
 SNW  H5   CAH  OAI  111.13  3.000
 SNW  CAO  CAH  OAI  112.40  3.000
 SNW  H5   CAH  CAG  108.83  3.000
 SNW  OAI  CAH  CAG  108.37  3.000
 SNW  CAO  CAH  CAG  108.31  3.000
 SNW  H6   OAI  CAH  108.21  3.000
 SNW  H8   CAO  H7   107.01  3.000
 SNW  H8   CAO  OAN  111.64  3.000
 SNW  H7   CAO  OAN  106.58  3.000
 SNW  H8   CAO  CAH  109.54  3.000
 SNW  H7   CAO  CAH  110.42  3.000
 SNW  OAN  CAO  CAH  111.52  3.000
 SNW  CAM  OAN  CAO  114.66  3.000
 SNW  CAL  CAM  OAQ  109.46  3.000
 SNW  CAL  CAM  OAN  105.62  3.000
 SNW  OAQ  CAM  OAN  111.51  3.000
 SNW  CAL  CAM  CAF  112.18  3.000
 SNW  OAN  CAM  CAF  108.79  3.000
 SNW  OAQ  CAM  CAF  109.26  3.000
 SNW  H9   OAQ  CAM  105.64  3.000
 SNW  H11  CAL  H10  106.97  3.000
 SNW  H11  CAL  N    113.34  3.000
 SNW  H10  CAL  N    109.09  3.000
 SNW  H11  CAL  CAM  110.33  3.000
 SNW  H10  CAL  CAM  108.31  3.000
 SNW  N    CAL  CAM  108.68  3.000
 SNW  H12  N    CA   111.53  3.000
 SNW  H12  N    CAL  110.53  3.000
 SNW  CA   N    CAL  116.31  3.000
 SNW  H14  CA   CB   107.54  3.000
 SNW  H14  CA   C    107.01  3.000
 SNW  CB   CA   C    108.98  3.000
 SNW  H14  CA   N    112.44  3.000
 SNW  CB   CA   N    111.10  3.000
 SNW  C    CA   N    109.63  3.000
 SNW  OXT  C    O    123.44  3.000
 SNW  OXT  C    CA   111.34  3.000
 SNW  O    C    CA   125.21  3.000
 SNW  H13  CB   H15  106.97  3.000
 SNW  H13  CB   CG   109.11  3.000
 SNW  H15  CB   CG   110.81  3.000
 SNW  H13  CB   CA   109.40  3.000
 SNW  H15  CB   CA   108.80  3.000
 SNW  CG   CB   CA   111.63  3.000
 SNW  H20  CG   H16  105.53  3.000
 SNW  H20  CG   CD   108.02  3.000
 SNW  H16  CG   CD   108.27  3.000
 SNW  H20  CG   CB   111.69  3.000
 SNW  H16  CG   CB   109.71  3.000
 SNW  CD   CG   CB   113.27  3.000
 SNW  NE2  CD   OE1  122.85  3.000
 SNW  OE1  CD   CG   122.75  3.000
 SNW  NE2  CD   CG   114.40  3.000
 SNW  H18  NE2  H17  117.46  3.000
 SNW  H18  NE2  CD   120.48  3.000
 SNW  H17  NE2  CD   122.01  3.000
 SNW  H19  OXT  C    110.22  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
 SNW  CONST_01  H17  NE2  CD   CG      0.00   0.0  0
 SNW  CONST_02  H18  NE2  CD   CG    180.00   0.0  0
 SNW  CONST_03  H19  OXT  C    CA    180.00   0.0  0
 SNW  Var_01    H7   CAO  OAN  CAM   177.75  30.0  1
 SNW  Var_02    CA   N    CAL  CAM   151.20  30.0  1
 SNW  Var_03    CD   CG   CB   CA   -177.76  30.0  1
 SNW  Var_04    NE2  CD   CG   CB   -176.91  30.0  2

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
 SNW  chir_01  CAF  CAG  CAM  OAB  negativ
 SNW  chir_02  CAG  OAC  CAH  CAF  positiv
 SNW  chir_03  CAH  OAI  CAO  CAG  positiv
 SNW  chir_04  CAM  OAN  CAL  CAF  positiv
 SNW  chir_05  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
 SNW  plan-1  CG   0.020
 SNW  plan-1  CD   0.020
 SNW  plan-1  OE1  0.020
 SNW  plan-1  NE2  0.020
 SNW  plan-1  H17  0.020
 SNW  plan-1  H18  0.020
 SNW  plan-2  CA   0.020
 SNW  plan-2  C    0.020
 SNW  plan-2  O    0.020
 SNW  plan-2  OXT  0.020
 SNW  plan-2  H19  0.020

