# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 10:31:41 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-8,9,10-tris(oxidanyl)-2-phenyl-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@]2(N=C(NC2=O)c3ccccc3)[C@H](O)[C@@H](O)[C@@H]1O
#
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
 HTE  HTE  (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-8,9,10-tris(oxidanyl)-2-phenyl-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one  ligand  38  22  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HTE
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
 HTE  C2'  C  CH1   0   0.001  -1.1491   1.4262  -0.4022
 HTE  C3'  C  CH1   0  -0.004  -2.6212   1.4395  -0.0177
 HTE  C4'  C  CH1   0  -0.006  -3.3094   0.1952  -0.5599
 HTE  C5'  C  CH1   0  -0.029  -2.5873  -1.0536  -0.0474
 HTE  O5'  O  O2    0  -0.488  -1.2097  -1.0047  -0.4009
 HTE  C1'  C  CR5   0   0.217  -0.4732   0.1119  -0.0002
 HTE  N1   N  N     0  -0.442   0.8156   0.0201  -0.6384
 HTE  C2   C  CR5   0   0.507   1.7043  -0.0076   0.2764
 HTE  N3   N  NR15  0  -0.726   1.2024   0.0316   1.5677
 HTE  C4   C  CR5   0   0.541  -0.1568   0.0858   1.5166
 HTE  O4   O  O     0  -0.417  -0.9192   0.0906   2.4521
 HTE  C5   C  CR6   0   0.029   3.1443  -0.0873   0.0222
 HTE  C6   C  CR16  0  -0.286   4.0803   0.1317   1.0313
 HTE  C7   C  CR16  0  -0.238   5.4369   0.0571   0.7514
 HTE  C8   C  CR16  0  -0.246   5.8672  -0.2375  -0.5344
 HTE  C9   C  CR16  0  -0.238   4.9371  -0.4551  -1.5451
 HTE  C10  C  CR16  0  -0.271   3.5834  -0.3779  -1.2705
 HTE  O2'  O  OH1   0  -0.666  -0.4194   2.4532   0.2134
 HTE  C6'  C  CH2   0  -0.158  -3.1453  -2.3183  -0.6633
 HTE  O4'  O  OH1   0  -0.671  -4.6489   0.2275  -0.1225
 HTE  O3'  O  OH1   0  -0.673  -3.1650   2.6204  -0.5585
 HTE  O6'  O  OH1   0  -0.668  -2.5214  -3.4306  -0.0700
 HTE  H1   H  HCH1  0   0.244  -1.0855   1.4924  -1.4995
 HTE  H2   H  HCH1  0   0.229  -2.7134   1.4394   1.0779
 HTE  H3   H  HCH1  0   0.229  -3.2491   0.2135  -1.6579
 HTE  H4   H  HCH1  0   0.237  -2.7107  -1.1123   1.0417
 HTE  H5   H  HNR5  0   0.425   1.7317  -0.0759   2.4200
 HTE  H6   H  HCR6  0   0.255   3.7738   0.3786   2.0393
 HTE  H7   H  HCR6  0   0.270   6.1563   0.2324   1.5397
 HTE  H8   H  HCR6  0   0.269   6.9258  -0.2970  -0.7503
 HTE  H9   H  HCR6  0   0.268   5.2693  -0.6871  -2.5481
 HTE  H10  H  HCR6  0   0.265   2.8578  -0.5477  -2.0544
 HTE  H11  H  HOH1  0   0.462  -0.8249   3.2971  -0.0125
 HTE  H12  H  HCH2  0   0.204  -4.2288  -2.3303  -0.4964
 HTE  H13  H  HCH2  0   0.201  -2.9870  -2.2886  -1.7504
 HTE  H14  H  HOH1  0   0.462  -5.2092  -0.1803  -0.7881
 HTE  H15  H  HOH1  0   0.456  -4.0677   2.7125  -0.2369
 HTE  H16  H  HOH1  0   0.457  -2.9288  -4.2253  -0.4260

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
 HTE  O3'  C3'  single    1.408  0.020  1.408
 HTE  O4'  C4'  single    1.410  0.020  1.410
 HTE  C3'  C4'  single    1.522  0.020  1.522
 HTE  C3'  C2'  single    1.522  0.020  1.522
 HTE  C4'  C5'  single    1.531  0.020  1.531
 HTE  O2'  C2'  single    1.402  0.020  1.402
 HTE  C2'  C1'  single    1.532  0.020  1.532
 HTE  O6'  C6'  single    1.407  0.020  1.407
 HTE  C5'  C6'  single    1.513  0.020  1.513
 HTE  C5'  O5'  single    1.423  0.020  1.423
 HTE  C1'  O5'  single    1.396  0.020  1.396
 HTE  C1'  N1   single    1.441  0.020  1.441
 HTE  C1'  C4   single    1.550  0.020  1.550
 HTE  N1   C2   double    1.276  0.020  1.276
 HTE  O4   C4   double    1.207  0.020  1.207
 HTE  C4   N3   single    1.361  0.020  1.361
 HTE  C2   N3   single    1.386  0.020  1.386
 HTE  C2   C5   single    1.464  0.020  1.464
 HTE  C5   C6   aromatic  1.394  0.020  1.394
 HTE  C5   C10  aromatic  1.396  0.020  1.396
 HTE  C6   C7   aromatic  1.387  0.020  1.387
 HTE  C10  C9   aromatic  1.383  0.020  1.383
 HTE  C7   C8   aromatic  1.388  0.020  1.388
 HTE  C9   C8   aromatic  1.391  0.020  1.391
 HTE  C2'  H1   single    0.970  0.020  1.090
 HTE  C3'  H2   single    0.970  0.020  1.090
 HTE  C4'  H3   single    0.970  0.020  1.090
 HTE  C5'  H4   single    0.970  0.020  1.090
 HTE  N3   H5   single    0.860  0.020  1.020
 HTE  C6   H6   single    0.930  0.020  1.080
 HTE  C7   H7   single    0.930  0.020  1.080
 HTE  C8   H8   single    0.930  0.020  1.080
 HTE  C9   H9   single    0.930  0.020  1.080
 HTE  C10  H10  single    0.930  0.020  1.080
 HTE  O2'  H11  single    0.850  0.020  0.980
 HTE  C6'  H12  single    0.970  0.020  1.090
 HTE  C6'  H13  single    0.970  0.020  1.090
 HTE  O4'  H14  single    0.850  0.020  0.980
 HTE  O3'  H15  single    0.850  0.020  0.980
 HTE  O6'  H16  single    0.850  0.020  0.980

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
 HTE  H1   C2'  O2'  111.31  3.000
 HTE  H1   C2'  C1'  106.72  3.000
 HTE  O2'  C2'  C1'  106.48  3.000
 HTE  H1   C2'  C3'  107.89  3.000
 HTE  C1'  C2'  C3'  111.60  3.000
 HTE  O2'  C2'  C3'  112.72  3.000
 HTE  H2   C3'  O3'  110.51  3.000
 HTE  H2   C3'  C4'  108.49  3.000
 HTE  O3'  C3'  C4'  111.98  3.000
 HTE  H2   C3'  C2'  109.44  3.000
 HTE  C4'  C3'  C2'  109.90  3.000
 HTE  O3'  C3'  C2'  106.49  3.000
 HTE  H3   C4'  O4'  111.19  3.000
 HTE  H3   C4'  C5'  108.79  3.000
 HTE  O4'  C4'  C5'  111.29  3.000
 HTE  H3   C4'  C3'  108.50  3.000
 HTE  C5'  C4'  C3'  109.54  3.000
 HTE  O4'  C4'  C3'  107.48  3.000
 HTE  H4   C5'  C6'  108.53  3.000
 HTE  H4   C5'  O5'  110.92  3.000
 HTE  C6'  C5'  O5'  106.53  3.000
 HTE  H4   C5'  C4'  108.83  3.000
 HTE  O5'  C5'  C4'  110.20  3.000
 HTE  C6'  C5'  C4'  111.81  3.000
 HTE  C1'  O5'  C5'  117.83  3.000
 HTE  C4   C1'  N1   104.47  3.000
 HTE  C4   C1'  O5'  112.03  3.000
 HTE  N1   C1'  O5'  107.08  3.000
 HTE  C4   C1'  C2'  111.19  3.000
 HTE  N1   C1'  C2'  109.46  3.000
 HTE  O5'  C1'  C2'  112.22  3.000
 HTE  C2   N1   C1'  107.87  3.000
 HTE  C5   C2   N3   121.29  3.000
 HTE  C5   C2   N1   124.18  3.000
 HTE  N3   C2   N1   114.53  3.000
 HTE  H5   N3   C4   124.04  3.000
 HTE  H5   N3   C2   126.44  3.000
 HTE  C4   N3   C2   109.13  3.000
 HTE  O4   C4   N3   127.00  3.000
 HTE  N3   C4   C1'  103.96  3.000
 HTE  O4   C4   C1'  129.03  3.000
 HTE  C10  C5   C6   119.47  3.000
 HTE  C10  C5   C2   118.77  3.000
 HTE  C6   C5   C2   121.75  3.000
 HTE  H6   C6   C7   118.51  3.000
 HTE  H6   C6   C5   121.34  3.000
 HTE  C7   C6   C5   120.15  3.000
 HTE  H7   C7   C8   120.24  3.000
 HTE  H7   C7   C6   119.65  3.000
 HTE  C8   C7   C6   120.11  3.000
 HTE  H8   C8   C9   120.05  3.000
 HTE  H8   C8   C7   120.00  3.000
 HTE  C9   C8   C7   119.95  3.000
 HTE  H9   C9   C10  119.77  3.000
 HTE  H9   C9   C8   120.13  3.000
 HTE  C10  C9   C8   120.09  3.000
 HTE  H10  C10  C9   120.25  3.000
 HTE  H10  C10  C5   119.53  3.000
 HTE  C9   C10  C5   120.21  3.000
 HTE  H11  O2'  C2'  108.65  3.000
 HTE  H13  C6'  H12  107.05  3.000
 HTE  H13  C6'  O6'  112.00  3.000
 HTE  H12  C6'  O6'  111.44  3.000
 HTE  H13  C6'  C5'  109.08  3.000
 HTE  H12  C6'  C5'  108.16  3.000
 HTE  O6'  C6'  C5'  109.00  3.000
 HTE  H14  O4'  C4'  109.24  3.000
 HTE  H15  O3'  C3'  108.30  3.000
 HTE  H16  O6'  C6'  108.03  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
 HTE  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 HTE  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 HTE  CONST_03  C9   C10  C5   C6     0.00   0.0  0
 HTE  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 HTE  CONST_05  C10  C5   C6   C7     0.00   0.0  0
 HTE  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 HTE  CONST_07  C7   C6   C5   C2   180.00   0.0  0
 HTE  CONST_08  C9   C10  C5   C2   180.00   0.0  0
 HTE  CONST_09  N3   C2   N1   C1'    0.00   0.0  0
 HTE  CONST_10  C5   C2   N1   C1'  180.00   0.0  0
 HTE  CONST_11  C2   N3   C4   C1'    0.00   0.0  0
 HTE  CONST_12  C4   N3   C2   N1     0.00   0.0  0
 HTE  CONST_13  C5   C2   N3   C4   180.00   0.0  0
 HTE  CONST_14  O4   C4   N3   C2   180.00   0.0  0
 HTE  CONST_15  H6   C6   C5   C2     0.00   0.0  0
 HTE  CONST_16  H10  C10  C5   C2     0.00   0.0  0
 HTE  CONST_17  H7   C7   C6   C5   180.00   0.0  0
 HTE  CONST_18  H9   C9   C10  C5   180.00   0.0  0
 HTE  CONST_19  H8   C8   C7   C6   180.00   0.0  0
 HTE  CONST_20  H5   N3   C4   C1'  180.00   0.0  0
 HTE  Var_01    C6   C5   C2   N1   167.98  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
 HTE  chir_01  C2'  C3'  O2'  C1'  negativ
 HTE  chir_02  C3'  O3'  C2'  C4'  positiv
 HTE  chir_03  C4'  O4'  C5'  C3'  positiv
 HTE  chir_04  C5'  O5'  C4'  C6'  negativ
 HTE  chir_05  C1'  N1   C2'  C4   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
 HTE  plan-1  C1'  0.020
 HTE  plan-1  N1   0.020
 HTE  plan-1  C2   0.020
 HTE  plan-1  N3   0.020
 HTE  plan-1  C4   0.020
 HTE  plan-1  O4   0.020
 HTE  plan-1  C5   0.020
 HTE  plan-1  H5   0.020
 HTE  plan-2  C2   0.020
 HTE  plan-2  C5   0.020
 HTE  plan-2  C6   0.020
 HTE  plan-2  C7   0.020
 HTE  plan-2  C8   0.020
 HTE  plan-2  C9   0.020
 HTE  plan-2  C10  0.020
 HTE  plan-2  H6   0.020
 HTE  plan-2  H7   0.020
 HTE  plan-2  H8   0.020
 HTE  plan-2  H9   0.020
 HTE  plan-2  H10  0.020

