# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 19:08:14 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-1-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)c3cccc4ccccc34)[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
 HTW  HTW  (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-2-naphthalen-1-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_HTW
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
 HTW  C2'  C  CH1   0   0.001  -1.8961  -1.0170   1.1668
 HTW  C3'  C  CH1   0  -0.004  -3.4004  -1.0398   0.9456
 HTW  C4'  C  CH1   0  -0.006  -3.9030   0.3646   0.6458
 HTW  C5'  C  CH1   0  -0.029  -3.1519   0.9261  -0.5646
 HTW  O5'  O  O2    0  -0.487  -1.7483   0.8934  -0.3341
 HTW  C1'  C  CR5   0   0.212  -1.1687  -0.3296   0.0079
 HTW  N1   N  N     0  -0.438   0.1930  -0.0529   0.3958
 HTW  C2   C  CR5   0   0.453   0.9625  -0.7042  -0.3849
 HTW  N3   N  NR15  0  -0.702   0.3025  -1.4538  -1.3488
 HTW  C4   C  CR5   0   0.543  -1.0397  -1.2727  -1.2150
 HTW  C6'  C  CH2   0  -0.158  -3.5096   2.3729  -0.8270
 HTW  O6'  O  OH1   0  -0.669  -2.8808   2.7923  -2.0134
 HTW  O4'  O  OH1   0  -0.671  -5.2861   0.2730   0.3881
 HTW  O3'  O  OH1   0  -0.672  -3.9720  -1.5678   2.1186
 HTW  O2'  O  OH1   0  -0.665  -1.3448  -2.3018   1.2732
 HTW  O4   O  O     0  -0.419  -1.9080  -1.7311  -1.9169
 HTW  C5   C  CR6   0   0.018   2.4281  -0.7369  -0.3243
 HTW  C10  C  CR66  0   0.119   3.2006   0.4063   0.0489
 HTW  C9   C  CR66  0   0.103   4.6144   0.2652   0.1122
 HTW  C8   C  CR16  0  -0.302   5.2136  -0.9814  -0.1812
 HTW  C7   C  CR16  0  -0.248   4.4516  -2.0552  -0.5435
 HTW  C6   C  CR16  0  -0.303   3.0550  -1.9256  -0.6209
 HTW  C14  C  CR16  0  -0.332   2.6457   1.6805   0.3212
 HTW  C13  C  CR16  0  -0.244   3.4477   2.7401   0.6501
 HTW  C12  C  CR16  0  -0.256   4.8460   2.5924   0.7274
 HTW  C11  C  CR16  0  -0.306   5.4142   1.3786   0.4608
 HTW  H1   H  HCH1  0   0.243  -1.6926  -0.4184   2.0685
 HTW  H2   H  HCH1  0   0.229  -3.6312  -1.6791   0.0812
 HTW  H3   H  HCH1  0   0.229  -3.7059   1.0053   1.5174
 HTW  H4   H  HCH1  0   0.236  -3.4188   0.3332  -1.4491
 HTW  H5   H  HNR5  0   0.426   0.7406  -1.9320  -2.1226
 HTW  H6   H  HCH2  0   0.206  -4.6006   2.4481  -0.9036
 HTW  H7   H  HCH2  0   0.200  -3.2031   2.9781   0.0374
 HTW  H8   H  HOH1  0   0.457  -3.1452   3.7002  -2.1856
 HTW  H9   H  HOH1  0   0.463  -5.7189   1.0711   0.7026
 HTW  H10  H  HOH1  0   0.456  -4.9099  -1.7131   1.9576
 HTW  H11  H  HOH1  0   0.461  -1.7970  -2.7728   1.9815
 HTW  H12  H  HCR6  0   0.267   6.2912  -1.0709  -0.1179
 HTW  H13  H  HCR6  0   0.270   4.9108  -3.0075  -0.7699
 HTW  H14  H  HCR6  0   0.273   2.4738  -2.7972  -0.8940
 HTW  H15  H  HCR6  0   0.262   1.5761   1.8178   0.2771
 HTW  H16  H  HCR6  0   0.263   3.0011   3.7048   0.8525
 HTW  H17  H  HCR6  0   0.262   5.4645   3.4401   0.9911
 HTW  H18  H  HCR6  0   0.261   6.4890   1.2525   0.5068

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
 HTW  O3'  C3'  single    1.408  0.020  1.408
 HTW  O4'  C4'  single    1.410  0.020  1.410
 HTW  C3'  C4'  single    1.521  0.020  1.521
 HTW  C3'  C2'  single    1.521  0.020  1.521
 HTW  C4'  C5'  single    1.531  0.020  1.531
 HTW  O2'  C2'  single    1.402  0.020  1.402
 HTW  C2'  C1'  single    1.531  0.020  1.531
 HTW  O6'  C6'  single    1.407  0.020  1.407
 HTW  C5'  C6'  single    1.513  0.020  1.513
 HTW  C5'  O5'  single    1.423  0.020  1.423
 HTW  C1'  O5'  single    1.396  0.020  1.396
 HTW  C1'  N1   single    1.443  0.020  1.443
 HTW  C1'  C4   single    1.550  0.020  1.550
 HTW  N1   C2   double    1.275  0.020  1.275
 HTW  O4   C4   double    1.207  0.020  1.207
 HTW  C4   N3   single    1.361  0.020  1.361
 HTW  C2   N3   single    1.388  0.020  1.388
 HTW  C2   C5   single    1.467  0.020  1.467
 HTW  C6   C5   aromatic  1.376  0.020  1.376
 HTW  C6   C7   aromatic  1.405  0.020  1.405
 HTW  C5   C10  aromatic  1.429  0.020  1.429
 HTW  C7   C8   aromatic  1.366  0.020  1.366
 HTW  C8   C9   aromatic  1.414  0.020  1.414
 HTW  C10  C9   aromatic  1.422  0.020  1.422
 HTW  C10  C14  aromatic  1.416  0.020  1.416
 HTW  C9   C11  aromatic  1.415  0.020  1.415
 HTW  C14  C13  aromatic  1.369  0.020  1.369
 HTW  C11  C12  aromatic  1.367  0.020  1.367
 HTW  C13  C12  aromatic  1.408  0.020  1.408
 HTW  C2'  H1   single    0.970  0.020  1.090
 HTW  C3'  H2   single    0.970  0.020  1.090
 HTW  C4'  H3   single    0.970  0.020  1.090
 HTW  C5'  H4   single    0.970  0.020  1.090
 HTW  N3   H5   single    0.860  0.020  1.020
 HTW  C6'  H6   single    0.970  0.020  1.090
 HTW  C6'  H7   single    0.970  0.020  1.090
 HTW  O6'  H8   single    0.850  0.020  0.980
 HTW  O4'  H9   single    0.850  0.020  0.980
 HTW  O3'  H10  single    0.850  0.020  0.980
 HTW  O2'  H11  single    0.850  0.020  0.980
 HTW  C8   H12  single    0.930  0.020  1.080
 HTW  C7   H13  single    0.930  0.020  1.080
 HTW  C6   H14  single    0.930  0.020  1.080
 HTW  C14  H15  single    0.930  0.020  1.080
 HTW  C13  H16  single    0.930  0.020  1.080
 HTW  C12  H17  single    0.930  0.020  1.080
 HTW  C11  H18  single    0.930  0.020  1.080

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
 HTW  H1   C2'  O2'  111.31  3.000
 HTW  H1   C2'  C1'  106.73  3.000
 HTW  O2'  C2'  C1'  106.38  3.000
 HTW  H1   C2'  C3'  108.06  3.000
 HTW  C1'  C2'  C3'  111.50  3.000
 HTW  O2'  C2'  C3'  112.72  3.000
 HTW  H2   C3'  O3'  110.59  3.000
 HTW  H2   C3'  C4'  108.20  3.000
 HTW  O3'  C3'  C4'  112.11  3.000
 HTW  H2   C3'  C2'  109.31  3.000
 HTW  C4'  C3'  C2'  109.97  3.000
 HTW  O3'  C3'  C2'  106.63  3.000
 HTW  H3   C4'  O4'  111.01  3.000
 HTW  H3   C4'  C5'  108.97  3.000
 HTW  O4'  C4'  C5'  111.14  3.000
 HTW  H3   C4'  C3'  108.80  3.000
 HTW  C5'  C4'  C3'  109.40  3.000
 HTW  O4'  C4'  C3'  107.46  3.000
 HTW  H4   C5'  C6'  108.61  3.000
 HTW  H4   C5'  O5'  110.98  3.000
 HTW  C6'  C5'  O5'  106.45  3.000
 HTW  H4   C5'  C4'  108.64  3.000
 HTW  O5'  C5'  C4'  110.34  3.000
 HTW  C6'  C5'  C4'  111.82  3.000
 HTW  C1'  O5'  C5'  118.00  3.000
 HTW  C4   C1'  N1   104.50  3.000
 HTW  C4   C1'  O5'  111.99  3.000
 HTW  N1   C1'  O5'  106.85  3.000
 HTW  C4   C1'  C2'  111.32  3.000
 HTW  N1   C1'  C2'  109.32  3.000
 HTW  O5'  C1'  C2'  112.42  3.000
 HTW  C2   N1   C1'  107.88  3.000
 HTW  C5   C2   N3   119.45  3.000
 HTW  C5   C2   N1   126.08  3.000
 HTW  N3   C2   N1   114.46  3.000
 HTW  H5   N3   C4   124.49  3.000
 HTW  H5   N3   C2   125.57  3.000
 HTW  C4   N3   C2   109.20  3.000
 HTW  O4   C4   N3   127.00  3.000
 HTW  N3   C4   C1'  103.92  3.000
 HTW  O4   C4   C1'  129.06  3.000
 HTW  H7   C6'  H6   107.14  3.000
 HTW  H7   C6'  O6'  112.00  3.000
 HTW  H6   C6'  O6'  111.44  3.000
 HTW  H7   C6'  C5'  108.92  3.000
 HTW  H6   C6'  C5'  108.24  3.000
 HTW  O6'  C6'  C5'  109.00  3.000
 HTW  H8   O6'  C6'  108.05  3.000
 HTW  H9   O4'  C4'  109.16  3.000
 HTW  H10  O3'  C3'  108.23  3.000
 HTW  H11  O2'  C2'  108.61  3.000
 HTW  C6   C5   C10  120.06  3.000
 HTW  C10  C5   C2   122.20  3.000
 HTW  C6   C5   C2   117.73  3.000
 HTW  C14  C10  C9   118.05  3.000
 HTW  C14  C10  C5   123.92  3.000
 HTW  C9   C10  C5   118.00  3.000
 HTW  C11  C9   C8   120.37  3.000
 HTW  C11  C9   C10  119.67  3.000
 HTW  C8   C9   C10  119.97  3.000
 HTW  H12  C8   C7   120.38  3.000
 HTW  H12  C8   C9   118.84  3.000
 HTW  C7   C8   C9   120.79  3.000
 HTW  H13  C7   C6   119.47  3.000
 HTW  H13  C7   C8   120.74  3.000
 HTW  C6   C7   C8   119.79  3.000
 HTW  H14  C6   C7   118.26  3.000
 HTW  H14  C6   C5   120.34  3.000
 HTW  C7   C6   C5   121.38  3.000
 HTW  H15  C14  C13  119.47  3.000
 HTW  H15  C14  C10  119.67  3.000
 HTW  C13  C14  C10  120.86  3.000
 HTW  H16  C13  C12  119.54  3.000
 HTW  H16  C13  C14  119.54  3.000
 HTW  C12  C13  C14  120.92  3.000
 HTW  H17  C12  C11  120.38  3.000
 HTW  H17  C12  C13  119.92  3.000
 HTW  C11  C12  C13  119.69  3.000
 HTW  H18  C11  C12  120.51  3.000
 HTW  H18  C11  C9   118.68  3.000
 HTW  C12  C11  C9   120.81  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
 HTW  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 HTW  CONST_02  C8   C9   C10  C5     0.00   0.0  0
 HTW  CONST_03  C11  C9   C10  C5   180.00   0.0  0
 HTW  CONST_04  C13  C14  C10  C5   180.00   0.0  0
 HTW  CONST_05  C7   C6   C5   C10    0.00   0.0  0
 HTW  CONST_06  C7   C8   C9   C10    0.00   0.0  0
 HTW  CONST_07  C12  C11  C9   C10    0.00   0.0  0
 HTW  CONST_08  C12  C13  C14  C10    0.00   0.0  0
 HTW  CONST_09  C6   C7   C8   C9     0.00   0.0  0
 HTW  CONST_10  C6   C5   C10  C9     0.00   0.0  0
 HTW  CONST_11  C13  C14  C10  C9     0.00   0.0  0
 HTW  CONST_12  C13  C12  C11  C9     0.00   0.0  0
 HTW  CONST_13  C14  C10  C9   C8   180.00   0.0  0
 HTW  CONST_14  C12  C11  C9   C8   180.00   0.0  0
 HTW  CONST_15  C11  C9   C8   C7   180.00   0.0  0
 HTW  CONST_16  C14  C10  C5   C6   180.00   0.0  0
 HTW  CONST_17  C11  C9   C10  C14    0.00   0.0  0
 HTW  CONST_18  C11  C12  C13  C14    0.00   0.0  0
 HTW  CONST_19  C7   C6   C5   C2   180.00   0.0  0
 HTW  CONST_20  C9   C10  C5   C2   180.00   0.0  0
 HTW  CONST_21  C14  C10  C5   C2     0.00   0.0  0
 HTW  CONST_22  N3   C2   N1   C1'    0.00   0.0  0
 HTW  CONST_23  C5   C2   N1   C1'  180.00   0.0  0
 HTW  CONST_24  C2   N3   C4   C1'    0.00   0.0  0
 HTW  CONST_25  C4   N3   C2   N1     0.00   0.0  0
 HTW  CONST_26  C5   C2   N3   C4   180.00   0.0  0
 HTW  CONST_27  O4   C4   N3   C2   180.00   0.0  0
 HTW  CONST_28  H14  C6   C5   C2     0.00   0.0  0
 HTW  CONST_29  H13  C7   C6   C5   180.00   0.0  0
 HTW  CONST_30  H15  C14  C10  C5     0.00   0.0  0
 HTW  CONST_31  H12  C8   C9   C10  180.00   0.0  0
 HTW  CONST_32  H18  C11  C9   C10  180.00   0.0  0
 HTW  CONST_33  H16  C13  C14  C10  180.00   0.0  0
 HTW  CONST_34  H17  C12  C11  C9   180.00   0.0  0
 HTW  CONST_35  H5   N3   C4   C1'  180.00   0.0  0
 HTW  Var_01    C6   C5   C2   N1   143.36  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
 HTW  chir_01  C2'  C3'  O2'  C1'  negativ
 HTW  chir_02  C3'  O3'  C2'  C4'  positiv
 HTW  chir_03  C4'  O4'  C5'  C3'  positiv
 HTW  chir_04  C5'  O5'  C4'  C6'  negativ
 HTW  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
 HTW  plan-1  C1'  0.020
 HTW  plan-1  N1   0.020
 HTW  plan-1  C2   0.020
 HTW  plan-1  N3   0.020
 HTW  plan-1  C4   0.020
 HTW  plan-1  O4   0.020
 HTW  plan-1  C5   0.020
 HTW  plan-1  H5   0.020
 HTW  plan-2  C2   0.020
 HTW  plan-2  C5   0.020
 HTW  plan-2  C10  0.020
 HTW  plan-2  C9   0.020
 HTW  plan-2  C8   0.020
 HTW  plan-2  C7   0.020
 HTW  plan-2  C6   0.020
 HTW  plan-2  C14  0.020
 HTW  plan-2  C13  0.020
 HTW  plan-2  C12  0.020
 HTW  plan-2  C11  0.020
 HTW  plan-2  H12  0.020
 HTW  plan-2  H13  0.020
 HTW  plan-2  H14  0.020
 HTW  plan-2  H15  0.020
 HTW  plan-2  H16  0.020
 HTW  plan-2  H17  0.020
 HTW  plan-2  H18  0.020

