# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:34:15 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  40  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.681  -2.7757  -1.7648  -1.1113
 SNW  CAF  C  CH1    0   0.035  -2.8549  -0.4191  -0.7090
 SNW  CAG  C  CH1    0   0.001  -4.1195  -0.1529   0.1022
 SNW  OAC  O  OH1    0  -0.677  -5.2223  -0.4603  -0.7211
 SNW  CAH  C  CH1    0  -0.014  -4.1349   1.2863   0.6070
 SNW  OAI  O  OH1    0  -0.671  -4.3035   2.1428  -0.4992
 SNW  CAO  C  CH2    0  -0.229  -2.8301   1.5418   1.3485
 SNW  OAN  O  O2     0  -0.515  -1.7068   1.2640   0.5440
 SNW  CAM  C  CT     0   0.481  -1.6025  -0.0869   0.1217
 SNW  OAQ  O  OH1    0  -0.732  -1.5216  -0.9409   1.1992
 SNW  CAL  C  CH2    0  -0.342  -0.3383  -0.1478  -0.7398
 SNW  N    N  NH1    0  -0.618   0.8385   0.1749   0.0402
 SNW  CA   C  CH1    0  -0.189   1.9725  -0.7124  -0.0960
 SNW  C    C  C      0   0.458   1.7959  -2.0166   0.7171
 SNW  O    O  O      0  -0.601   0.7586  -2.1589   1.4123
 SNW  CB   C  CH2    0  -0.449   3.2595  -0.0052   0.3360
 SNW  CG   C  CH2    0  -0.592   3.6765   1.1062  -0.6166
 SNW  CD   C  C      0   0.531   5.0166   1.7279  -0.2748
 SNW  OE1  O  O      0  -0.495   5.8279   1.1890   0.4644
 SNW  NE2  N  NH2    0  -0.806   5.2475   2.9137  -0.8624
 SNW  OXT  O  OC    -1  -0.591   2.7090  -2.8512   0.6202
 SNW  H1   H  HOH1   0   0.446  -3.5545  -1.9543  -1.6438
 SNW  H2   H  HCH1   0   0.202  -2.8573   0.2476  -1.5846
 SNW  H3   H  HCH1   0   0.219  -4.1027  -0.8052   0.9858
 SNW  H4   H  HOH1   0   0.453  -6.0018  -0.5612  -0.1667
 SNW  H5   H  HCH1   0   0.215  -4.9592   1.4053   1.3275
 SNW  H6   H  HOH1   0   0.450  -4.2980   3.0505  -0.1803
 SNW  H7   H  HCH2   0   0.238  -2.7588   2.5938   1.6378
 SNW  H8   H  HCH2   0   0.208  -2.8218   0.9557   2.2754
 SNW  H9   H  HOH1   0   0.462  -0.5880  -1.2861   1.2937
 SNW  H10  H  HCH2   0   0.238  -0.2519  -1.1562  -1.1503
 SNW  H11  H  HCH2   0   0.221  -0.4562   0.5209  -1.6008
 SNW  H12  H  HNH1   0   0.350   1.1011   1.1348  -0.1172
 SNW  H14  H  HCH1   0   0.200   2.1215  -1.0309  -1.1435
 SNW  H15  H  HCH2   0   0.227   3.1310   0.3917   1.3481
 SNW  H16  H  HCH2   0   0.272   3.7517   0.7045  -1.6339
 SNW  H17  H  HNH2   0   0.404   4.5900   3.3225  -1.5036
 SNW  H18  H  HNH2   0   0.396   6.1433   3.3640  -0.7695
 SNW  H13  H  HCH2   0   0.241   4.0549  -0.7466   0.3855
 SNW  H20  H  HCH2   0   0.252   2.9291   1.9022  -0.6720

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  1.409  0.020  1.409
 SNW  CAH  CAG  single  1.525  0.020  1.525
 SNW  CAH  OAI  single  1.409  0.020  1.409
 SNW  CAG  OAC  single  1.410  0.020  1.410
 SNW  CAG  CAF  single  1.526  0.020  1.526
 SNW  OAQ  CAM  single  1.377  0.020  1.377
 SNW  OAN  CAM  single  1.419  0.020  1.419
 SNW  NE2  CD   single  1.343  0.020  1.343
 SNW  CAM  CAF  single  1.539  0.020  1.539
 SNW  CAM  CAL  single  1.531  0.020  1.531
 SNW  CAF  OAB  single  1.407  0.020  1.407
 SNW  CD   CG   single  1.516  0.020  1.516
 SNW  CD   OE1  double  1.223  0.020  1.223
 SNW  CG   CB   single  1.522  0.020  1.522
 SNW  O    C    deloc   1.257  0.020  1.257
 SNW  N    CAL  single  1.448  0.020  1.448
 SNW  N    CA   single  1.446  0.020  1.446
 SNW  C    CA   single  1.547  0.020  1.547
 SNW  C    OXT  deloc   1.241  0.020  1.241
 SNW  CA   CB   single  1.531  0.020  1.531
 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  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  107.52  3.000
 SNW  H2   CAF  CAM  107.48  3.000
 SNW  H2   CAF  CAG  108.39  3.000
 SNW  CAM  CAF  CAG  110.48  3.000
 SNW  H2   CAF  OAB  110.61  3.000
 SNW  CAM  CAF  OAB  108.36  3.000
 SNW  CAG  CAF  OAB  111.44  3.000
 SNW  H3   CAG  CAH  107.12  3.000
 SNW  H3   CAG  OAC  110.62  3.000
 SNW  CAH  CAG  OAC  113.02  3.000
 SNW  H3   CAG  CAF  108.14  3.000
 SNW  OAC  CAG  CAF  107.44  3.000
 SNW  CAH  CAG  CAF  110.42  3.000
 SNW  H4   OAC  CAG  108.67  3.000
 SNW  H5   CAH  CAO  107.74  3.000
 SNW  H5   CAH  OAI  111.01  3.000
 SNW  CAO  CAH  OAI  112.51  3.000
 SNW  H5   CAH  CAG  109.03  3.000
 SNW  OAI  CAH  CAG  108.36  3.000
 SNW  CAO  CAH  CAG  108.11  3.000
 SNW  H6   OAI  CAH  108.21  3.000
 SNW  H8   CAO  H7   106.86  3.000
 SNW  H8   CAO  OAN  111.78  3.000
 SNW  H7   CAO  OAN  106.78  3.000
 SNW  H8   CAO  CAH  109.18  3.000
 SNW  H7   CAO  CAH  110.26  3.000
 SNW  OAN  CAO  CAH  111.84  3.000
 SNW  CAM  OAN  CAO  114.59  3.000
 SNW  CAL  CAM  OAQ  111.53  3.000
 SNW  CAL  CAM  OAN  105.43  3.000
 SNW  OAQ  CAM  OAN  111.20  3.000
 SNW  CAL  CAM  CAF  111.08  3.000
 SNW  OAN  CAM  CAF  107.83  3.000
 SNW  OAQ  CAM  CAF  109.64  3.000
 SNW  H9   OAQ  CAM  110.05  3.000
 SNW  H11  CAL  H10  106.05  3.000
 SNW  H11  CAL  N    111.99  3.000
 SNW  H10  CAL  N    110.12  3.000
 SNW  H11  CAL  CAM  109.19  3.000
 SNW  H10  CAL  CAM  108.27  3.000
 SNW  N    CAL  CAM  111.04  3.000
 SNW  H12  N    CA   111.43  3.000
 SNW  H12  N    CAL  109.87  3.000
 SNW  CA   N    CAL  116.73  3.000
 SNW  H14  CA   CB   106.70  3.000
 SNW  H14  CA   C    105.70  3.000
 SNW  CB   CA   C    109.70  3.000
 SNW  H14  CA   N    111.83  3.000
 SNW  CB   CA   N    110.44  3.000
 SNW  C    CA   N    112.22  3.000
 SNW  OXT  C    O    125.06  3.000
 SNW  OXT  C    CA   116.23  3.000
 SNW  O    C    CA   118.71  3.000
 SNW  H13  CB   H15  106.90  3.000
 SNW  H13  CB   CG   109.00  3.000
 SNW  H15  CB   CG   110.25  3.000
 SNW  H13  CB   CA   108.22  3.000
 SNW  H15  CB   CA   109.25  3.000
 SNW  CG   CB   CA   113.02  3.000
 SNW  H20  CG   H16  105.47  3.000
 SNW  H20  CG   CD   108.48  3.000
 SNW  H16  CG   CD   107.38  3.000
 SNW  H20  CG   CB   112.10  3.000
 SNW  H16  CG   CB   109.39  3.000
 SNW  CD   CG   CB   113.60  3.000
 SNW  NE2  CD   OE1  122.65  3.000
 SNW  OE1  CD   CG   122.82  3.000
 SNW  NE2  CD   CG   114.53  3.000
 SNW  H18  NE2  H17  117.31  3.000
 SNW  H18  NE2  CD   120.49  3.000
 SNW  H17  NE2  CD   121.71  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  Var_01    H7   CAO  OAN  CAM   177.33  30.0  1
 SNW  Var_02    CA   N    CAL  CAM   132.52  30.0  1
 SNW  Var_03    CD   CG   CB   CA   -174.53  30.0  2
 SNW  Var_04    NE2  CD   CG   CB   -163.47  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

