# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 10:54:13 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-2-naphthalen-2-yl-8,9,10-tris(oxidanyl)-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)c3ccc4ccccc4c3)[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
 HT8  HT8  (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-2-naphthalen-2-yl-8,9,10-tris(oxidanyl)-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one  ligand  44  26  .  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_HT8
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
 HT8  C2'  C  CH1   0   0.001  -2.2240   1.4226  -0.3472
 HT8  C3'  C  CH1   0  -0.005  -3.6832   1.4143   0.0829
 HT8  C4'  C  CH1   0  -0.005  -4.3829   0.1891  -0.4877
 HT8  C5'  C  CH1   0  -0.029  -3.6420  -1.0744  -0.0422
 HT8  O5'  O  O2    0  -0.488  -2.2755  -1.0075  -0.4339
 HT8  C1'  C  CR5   0   0.218  -1.5305   0.0974  -0.0177
 HT8  N1   N  N     0  -0.444  -0.2651   0.0354  -0.7044
 HT8  C2   C  CR5   0   0.518   0.6566  -0.0189   0.1762
 HT8  N3   N  NR15  0  -0.732   0.2011  -0.0306   1.4852
 HT8  C4   C  CR5   0   0.539  -1.1595   0.0172   1.4846
 HT8  O4   O  O     0  -0.417  -1.8876  -0.0165   2.4463
 HT8  C5   C  CR6   0   0.029   2.0832  -0.0759  -0.1416
 HT8  C6   C  CR16  0  -0.277   2.4655  -0.2409  -1.4970
 HT8  C7   C  CR16  0  -0.297   3.7829  -0.2921  -1.8412
 HT8  C8   C  CR66  0   0.113   4.7975  -0.1764  -0.8593
 HT8  C9   C  CR66  0   0.145   4.4198  -0.0065   0.4969
 HT8  C10  C  CR16  0  -0.358   3.0477   0.0404   0.8284
 HT8  C11  C  CR16  0  -0.306   6.1705  -0.2232  -1.1878
 HT8  C12  C  CR16  0  -0.250   7.1228  -0.1029  -0.2114
 HT8  C13  C  CR16  0  -0.256   6.7471   0.0680   1.1373
 HT8  C14  C  CR16  0  -0.305   5.4246   0.1149   1.4848
 HT8  O2'  O  OH1   0  -0.666  -1.4786   2.4300   0.2815
 HT8  O3'  O  OH1   0  -0.673  -4.2460   2.6141  -0.3929
 HT8  O4'  O  OH1   0  -0.672  -5.7095   0.1981  -0.0118
 HT8  C6'  C  CH2   0  -0.159  -4.2135  -2.3192  -0.6855
 HT8  O6'  O  OH1   0  -0.669  -3.5746  -3.4488  -0.1429
 HT8  H1   H  HCH1  0   0.244  -2.1959   1.5295  -1.4429
 HT8  H2   H  HCH1  0   0.230  -3.7432   1.3693   1.1798
 HT8  H3   H  HCH1  0   0.229  -4.3535   0.2497  -1.5853
 HT8  H4   H  HCH1  0   0.237  -3.7328  -1.1710   1.0476
 HT8  H5   H  HNR5  0   0.426   0.7603  -0.1597   2.3151
 HT8  H6   H  HCR6  0   0.264   1.6988  -0.3290  -2.2540
 HT8  H7   H  HCR6  0   0.263   4.0665  -0.4230  -2.8781
 HT8  H8   H  HCR6  0   0.253   2.7908   0.1844   1.8706
 HT8  H9   H  HCR6  0   0.261   6.4603  -0.3558  -2.2230
 HT8  H10  H  HCR6  0   0.265   8.1726  -0.1391  -0.4713
 HT8  H11  H  HCR6  0   0.265   7.5115   0.1616   1.8970
 HT8  H12  H  HCR6  0   0.261   5.1339   0.2457   2.5200
 HT8  H13  H  HOH1  0   0.462  -1.9144   3.2753   0.1281
 HT8  H14  H  HOH1  0   0.456  -5.1321   2.6986  -0.0264
 HT8  H15  H  HOH1  0   0.463  -6.2889  -0.1737  -0.6820
 HT8  H16  H  HCH2  0   0.206  -5.2929  -2.3387  -0.4944
 HT8  H17  H  HCH2  0   0.200  -4.0798  -2.2542  -1.7742
 HT8  H18  H  HOH1  0   0.457  -3.9796  -4.2323  -0.5255

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
 HT8  O3'  C3'  single    1.408  0.020  1.408
 HT8  O4'  C4'  single    1.409  0.020  1.409
 HT8  C3'  C4'  single    1.522  0.020  1.522
 HT8  C3'  C2'  single    1.521  0.020  1.521
 HT8  C4'  C5'  single    1.531  0.020  1.531
 HT8  O2'  C2'  single    1.402  0.020  1.402
 HT8  C2'  C1'  single    1.532  0.020  1.532
 HT8  O6'  C6'  single    1.407  0.020  1.407
 HT8  C5'  C6'  single    1.513  0.020  1.513
 HT8  C5'  O5'  single    1.423  0.020  1.423
 HT8  C1'  O5'  single    1.396  0.020  1.396
 HT8  C1'  N1   single    1.441  0.020  1.441
 HT8  C1'  C4   single    1.550  0.020  1.550
 HT8  O4   C4   double    1.207  0.020  1.207
 HT8  N1   C2   double    1.276  0.020  1.276
 HT8  C4   N3   single    1.361  0.020  1.361
 HT8  C2   N3   single    1.386  0.020  1.386
 HT8  C2   C5   single    1.463  0.020  1.463
 HT8  C6   C5   aromatic  1.418  0.020  1.418
 HT8  C6   C7   aromatic  1.363  0.020  1.363
 HT8  C5   C10  aromatic  1.373  0.020  1.373
 HT8  C7   C8   aromatic  1.417  0.020  1.417
 HT8  C10  C9   aromatic  1.412  0.020  1.412
 HT8  C8   C9   aromatic  1.418  0.020  1.418
 HT8  C8   C11  aromatic  1.412  0.020  1.412
 HT8  C9   C14  aromatic  1.414  0.020  1.414
 HT8  C11  C12  aromatic  1.369  0.020  1.369
 HT8  C14  C13  aromatic  1.368  0.020  1.368
 HT8  C12  C13  aromatic  1.410  0.020  1.410
 HT8  C2'  H1   single    0.970  0.020  1.090
 HT8  C3'  H2   single    0.970  0.020  1.090
 HT8  C4'  H3   single    0.970  0.020  1.090
 HT8  C5'  H4   single    0.970  0.020  1.090
 HT8  N3   H5   single    0.860  0.020  1.020
 HT8  C6   H6   single    0.930  0.020  1.080
 HT8  C7   H7   single    0.930  0.020  1.080
 HT8  C10  H8   single    0.930  0.020  1.080
 HT8  C11  H9   single    0.930  0.020  1.080
 HT8  C12  H10  single    0.930  0.020  1.080
 HT8  C13  H11  single    0.930  0.020  1.080
 HT8  C14  H12  single    0.930  0.020  1.080
 HT8  O2'  H13  single    0.850  0.020  0.980
 HT8  O3'  H14  single    0.850  0.020  0.980
 HT8  O4'  H15  single    0.850  0.020  0.980
 HT8  C6'  H16  single    0.970  0.020  1.090
 HT8  C6'  H17  single    0.970  0.020  1.090
 HT8  O6'  H18  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
 HT8  H1   C2'  O2'  111.28  3.000
 HT8  H1   C2'  C1'  106.64  3.000
 HT8  O2'  C2'  C1'  106.52  3.000
 HT8  H1   C2'  C3'  107.84  3.000
 HT8  C1'  C2'  C3'  111.64  3.000
 HT8  O2'  C2'  C3'  112.78  3.000
 HT8  H2   C3'  O3'  110.50  3.000
 HT8  H2   C3'  C4'  108.42  3.000
 HT8  O3'  C3'  C4'  112.05  3.000
 HT8  H2   C3'  C2'  109.55  3.000
 HT8  C4'  C3'  C2'  109.84  3.000
 HT8  O3'  C3'  C2'  106.45  3.000
 HT8  H3   C4'  O4'  111.21  3.000
 HT8  H3   C4'  C5'  108.84  3.000
 HT8  O4'  C4'  C5'  111.25  3.000
 HT8  H3   C4'  C3'  108.52  3.000
 HT8  C5'  C4'  C3'  109.44  3.000
 HT8  O4'  C4'  C3'  107.52  3.000
 HT8  H4   C5'  C6'  108.56  3.000
 HT8  H4   C5'  O5'  110.91  3.000
 HT8  C6'  C5'  O5'  106.52  3.000
 HT8  H4   C5'  C4'  108.75  3.000
 HT8  O5'  C5'  C4'  110.23  3.000
 HT8  C6'  C5'  C4'  111.86  3.000
 HT8  C1'  O5'  C5'  117.87  3.000
 HT8  C4   C1'  N1   104.45  3.000
 HT8  C4   C1'  O5'  112.08  3.000
 HT8  N1   C1'  O5'  107.01  3.000
 HT8  C4   C1'  C2'  111.21  3.000
 HT8  N1   C1'  C2'  109.41  3.000
 HT8  O5'  C1'  C2'  112.27  3.000
 HT8  C2   N1   C1'  107.89  3.000
 HT8  C5   C2   N3   121.70  3.000
 HT8  C5   C2   N1   123.79  3.000
 HT8  N3   C2   N1   114.51  3.000
 HT8  H5   N3   C4   123.97  3.000
 HT8  H5   N3   C2   126.56  3.000
 HT8  C4   N3   C2   109.13  3.000
 HT8  O4   C4   N3   126.99  3.000
 HT8  N3   C4   C1'  103.98  3.000
 HT8  O4   C4   C1'  129.02  3.000
 HT8  C10  C5   C6   119.72  3.000
 HT8  C10  C5   C2   121.89  3.000
 HT8  C6   C5   C2   118.38  3.000
 HT8  H6   C6   C7   120.38  3.000
 HT8  H6   C6   C5   119.18  3.000
 HT8  C7   C6   C5   120.44  3.000
 HT8  H7   C7   C8   119.07  3.000
 HT8  H7   C7   C6   119.98  3.000
 HT8  C8   C7   C6   120.95  3.000
 HT8  C11  C8   C9   119.04  3.000
 HT8  C11  C8   C7   122.16  3.000
 HT8  C9   C8   C7   118.81  3.000
 HT8  C14  C9   C10  121.57  3.000
 HT8  C14  C9   C8   119.27  3.000
 HT8  C10  C9   C8   119.16  3.000
 HT8  H8   C10  C9   117.43  3.000
 HT8  H8   C10  C5   121.64  3.000
 HT8  C9   C10  C5   120.93  3.000
 HT8  H9   C11  C12  120.41  3.000
 HT8  H9   C11  C8   119.11  3.000
 HT8  C12  C11  C8   120.48  3.000
 HT8  H10  C12  C13  119.48  3.000
 HT8  H10  C12  C11  120.03  3.000
 HT8  C13  C12  C11  120.49  3.000
 HT8  H11  C13  C14  120.12  3.000
 HT8  H11  C13  C12  119.59  3.000
 HT8  C14  C13  C12  120.30  3.000
 HT8  H12  C14  C13  120.42  3.000
 HT8  H12  C14  C9   119.15  3.000
 HT8  C13  C14  C9   120.43  3.000
 HT8  H13  O2'  C2'  108.57  3.000
 HT8  H14  O3'  C3'  108.30  3.000
 HT8  H15  O4'  C4'  109.24  3.000
 HT8  H17  C6'  H16  107.07  3.000
 HT8  H17  C6'  O6'  111.99  3.000
 HT8  H16  C6'  O6'  111.45  3.000
 HT8  H17  C6'  C5'  109.06  3.000
 HT8  H16  C6'  C5'  108.20  3.000
 HT8  O6'  C6'  C5'  108.97  3.000
 HT8  H18  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
 HT8  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 HT8  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 HT8  CONST_03  C14  C9   C10  C5   180.00   0.0  0
 HT8  CONST_04  C9   C10  C5   C6     0.00   0.0  0
 HT8  CONST_05  C9   C8   C7   C6     0.00   0.0  0
 HT8  CONST_06  C11  C8   C7   C6   180.00   0.0  0
 HT8  CONST_07  C10  C5   C6   C7     0.00   0.0  0
 HT8  CONST_08  C10  C9   C8   C7     0.00   0.0  0
 HT8  CONST_09  C14  C9   C8   C7   180.00   0.0  0
 HT8  CONST_10  C12  C11  C8   C7   180.00   0.0  0
 HT8  CONST_11  C13  C14  C9   C8     0.00   0.0  0
 HT8  CONST_12  C13  C12  C11  C8     0.00   0.0  0
 HT8  CONST_13  C12  C11  C8   C9     0.00   0.0  0
 HT8  CONST_14  C12  C13  C14  C9     0.00   0.0  0
 HT8  CONST_15  C11  C8   C9   C10  180.00   0.0  0
 HT8  CONST_16  C13  C14  C9   C10  180.00   0.0  0
 HT8  CONST_17  C14  C9   C8   C11    0.00   0.0  0
 HT8  CONST_18  C14  C13  C12  C11    0.00   0.0  0
 HT8  CONST_19  C7   C6   C5   C2   180.00   0.0  0
 HT8  CONST_20  C9   C10  C5   C2   180.00   0.0  0
 HT8  CONST_21  N3   C2   N1   C1'    0.00   0.0  0
 HT8  CONST_22  C5   C2   N1   C1'  180.00   0.0  0
 HT8  CONST_23  C2   N3   C4   C1'    0.00   0.0  0
 HT8  CONST_24  C4   N3   C2   N1     0.00   0.0  0
 HT8  CONST_25  C5   C2   N3   C4   180.00   0.0  0
 HT8  CONST_26  O4   C4   N3   C2   180.00   0.0  0
 HT8  CONST_27  H6   C6   C5   C2     0.00   0.0  0
 HT8  CONST_28  H8   C10  C5   C2     0.00   0.0  0
 HT8  CONST_29  H7   C7   C6   C5   180.00   0.0  0
 HT8  CONST_30  H9   C11  C8   C7     0.00   0.0  0
 HT8  CONST_31  H12  C14  C9   C8   180.00   0.0  0
 HT8  CONST_32  H10  C12  C11  C8   180.00   0.0  0
 HT8  CONST_33  H11  C13  C14  C9   180.00   0.0  0
 HT8  CONST_34  H5   N3   C4   C1'  180.00   0.0  0
 HT8  Var_01    C6   C5   C2   N1    -7.83  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
 HT8  chir_01  C2'  C3'  O2'  C1'  negativ
 HT8  chir_02  C3'  O3'  C2'  C4'  positiv
 HT8  chir_03  C4'  O4'  C5'  C3'  positiv
 HT8  chir_04  C5'  O5'  C4'  C6'  negativ
 HT8  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
 HT8  plan-1  C1'  0.020
 HT8  plan-1  N1   0.020
 HT8  plan-1  C2   0.020
 HT8  plan-1  N3   0.020
 HT8  plan-1  C4   0.020
 HT8  plan-1  O4   0.020
 HT8  plan-1  C5   0.020
 HT8  plan-1  H5   0.020
 HT8  plan-2  C2   0.020
 HT8  plan-2  C5   0.020
 HT8  plan-2  C6   0.020
 HT8  plan-2  C7   0.020
 HT8  plan-2  C8   0.020
 HT8  plan-2  C9   0.020
 HT8  plan-2  C10  0.020
 HT8  plan-2  C11  0.020
 HT8  plan-2  C12  0.020
 HT8  plan-2  C13  0.020
 HT8  plan-2  C14  0.020
 HT8  plan-2  H6   0.020
 HT8  plan-2  H7   0.020
 HT8  plan-2  H8   0.020
 HT8  plan-2  H9   0.020
 HT8  plan-2  H10  0.020
 HT8  plan-2  H11  0.020
 HT8  plan-2  H12  0.020

