# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 13:33:39 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: [2-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]amino]-1,3-thiazol-5-yl]-(4-methyl-2-pyrazin-2-yl-1,3-thiazol-5-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(sc1C(=O)c2sc(N[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)nc2)c4cnccn4
#
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
 XKA  XKA  '[2-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]amino]-1,3-thiazol-5-yl]-(4-methyl-2-pyrazin-2-yl-1,3-thiazol-5-yl)methanone'  ligand  50  31  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XKA
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
 XKA  N1   N  NH1   0  -0.693  -2.5057   0.1736  -0.5336
 XKA  C4   C  CH1   0   0.033  -5.7567   1.2795   0.5506
 XKA  C5   C  CH1   0  -0.013  -4.9639   0.0905   1.0983
 XKA  C6   C  CH2   0  -0.158  -5.7802  -0.7145   2.0880
 XKA  C10  C  CR16  0  -0.086   6.9776   3.3546  -1.3733
 XKA  C13  C  CR5   0   0.359  -1.5230  -0.7174  -0.3444
 XKA  C15  C  CR15  0   0.059  -0.5054  -2.6465  -0.2485
 XKA  C20  C  CR5   0  -0.431   3.0776  -1.5107   0.3485
 XKA  C1   C  CH1   0   0.120  -3.8241  -0.2262  -0.9708
 XKA  C2   C  CH1   0  -0.020  -4.5380   0.9658  -1.6235
 XKA  O2   O  OH1   0  -0.660  -5.6971   0.5311  -2.2794
 XKA  C3   C  CH1   0   0.002  -4.9475   1.9665  -0.5439
 XKA  O3   O  OH1   0  -0.668  -5.7220   3.0208  -1.0534
 XKA  O5   O  O2    0  -0.475  -4.5949  -0.7865   0.0502
 XKA  O6   O  OH1   0  -0.668  -4.9705  -1.7292   2.6314
 XKA  S14  S  S2    0   0.207   0.0797  -0.2048   0.0922
 XKA  C16  C  CR5   0  -0.391   0.5805  -1.8773   0.0698
 XKA  N17  N  N     0  -0.435  -1.6685  -2.0103  -0.4843
 XKA  C18  C  C     0   0.373   1.9064  -2.3998   0.3718
 XKA  O19  O  O     0  -0.404   2.0515  -3.5834   0.6333
 XKA  N02  N  N     0  -0.403   5.2194  -0.7818   0.7459
 XKA  S02  S  S2    0   0.306   3.1659  -0.0611  -0.5843
 XKA  N03  N  N     0  -0.379   4.9562   2.1286  -1.3403
 XKA  N04  N  N     0  -0.348   7.5851   2.5121  -0.5500
 XKA  C06  C  CR5   0   0.381   4.2822  -1.7327   0.9845
 XKA  C07  C  CR5   0   0.018   4.7824   0.1417  -0.0563
 XKA  C08  C  CR6   0   0.201   5.5637   1.2820  -0.5167
 XKA  C09  C  CR16  0  -0.109   5.6576   3.1621  -1.7688
 XKA  C11  C  CR16  0  -0.068   6.8849   1.4754  -0.1184
 XKA  C12  C  CH3   0  -0.733   4.6260  -2.8729   1.8817
 XKA  H1   H  HNH1  0   0.419  -2.2928   1.1513  -0.4138
 XKA  H2   H  HCH1  0   0.219  -6.6992   0.9090   0.1207
 XKA  H3   H  HCH1  0   0.223  -4.0664   0.4764   1.6066
 XKA  H4   H  HCH2  0   0.212  -6.1529  -0.0374   2.8636
 XKA  H5   H  HCH2  0   0.195  -6.6577  -1.1244   1.5682
 XKA  H7   H  HCR5  0   0.288  -0.4661  -3.7241  -0.3302
 XKA  H8   H  HCH1  0   0.276  -3.7019  -1.0226  -1.7087
 XKA  H9   H  HCH1  0   0.246  -3.8393   1.4486  -2.3214
 XKA  H10  H  HOH1  0   0.459  -5.4394   0.0345  -3.0624
 XKA  H11  H  HCH1  0   0.219  -4.0331   2.3573  -0.0714
 XKA  H12  H  HOH1  0   0.459  -5.1546   3.6120  -1.5580
 XKA  H14  H  HOH1  0   0.456  -5.4863  -2.1919   3.2976
 XKA  H15  H  HCR6  0   0.286   5.1708   3.8567  -2.4416
 XKA  H16  H  HCR6  0   0.285   7.3724   0.7807   0.5539
 XKA  H17  H  HCH3  0   0.261   4.7660  -3.7913   1.3123
 XKA  H18  H  HCH3  0   0.254   5.5515  -2.6547   2.4098
 XKA  H19  H  HCH3  0   0.256   3.8421  -3.0630   2.6127
 XKA  O4   O  OH1   0  -0.673  -6.0014   2.1570   1.6228
 XKA  H6   H  HCR6  0   0.289   7.5435   4.2046  -1.7336
 XKA  H13  H  HOH1  0   0.454  -6.5015   2.9080   1.2868

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
 XKA  C10  C09  aromatic  1.391  0.020  1.391
 XKA  C10  N04  aromatic  1.325  0.020  1.325
 XKA  C09  N03  aromatic  1.321  0.020  1.321
 XKA  N04  C11  aromatic  1.323  0.020  1.323
 XKA  N03  C08  aromatic  1.328  0.020  1.328
 XKA  C11  C08  aromatic  1.393  0.020  1.393
 XKA  C08  C07  single    1.457  0.020  1.457
 XKA  C07  S02  aromatic  1.713  0.020  1.713
 XKA  C07  N02  aromatic  1.299  0.020  1.299
 XKA  S02  C20  aromatic  1.726  0.020  1.726
 XKA  N02  C06  aromatic  1.356  0.020  1.356
 XKA  C20  C06  aromatic  1.380  0.020  1.380
 XKA  C20  C18  single    1.471  0.020  1.471
 XKA  C06  C12  single    1.491  0.020  1.491
 XKA  O19  C18  double    1.221  0.020  1.221
 XKA  C18  C16  single    1.457  0.020  1.457
 XKA  C16  C15  aromatic  1.368  0.020  1.368
 XKA  C16  S14  aromatic  1.746  0.020  1.746
 XKA  C15  N17  aromatic  1.347  0.020  1.347
 XKA  S14  C13  aromatic  1.738  0.020  1.738
 XKA  N17  C13  aromatic  1.309  0.020  1.309
 XKA  C13  N1   single    1.340  0.020  1.340
 XKA  N1   C1   single    1.445  0.020  1.445
 XKA  C6   C5   single    1.515  0.020  1.515
 XKA  C6   O6   single    1.407  0.020  1.407
 XKA  O5   C5   single    1.416  0.020  1.416
 XKA  O5   C1   single    1.397  0.020  1.397
 XKA  C5   C4   single    1.530  0.020  1.530
 XKA  C1   C2   single    1.535  0.020  1.535
 XKA  C4   O4   single    1.407  0.020  1.407
 XKA  C4   C3   single    1.525  0.020  1.525
 XKA  C2   C3   single    1.528  0.020  1.528
 XKA  C2   O2   single    1.401  0.020  1.401
 XKA  C3   O3   single    1.404  0.020  1.404
 XKA  N1   H1   single    0.860  0.020  1.020
 XKA  C4   H2   single    0.970  0.020  1.090
 XKA  C5   H3   single    0.970  0.020  1.090
 XKA  C6   H4   single    0.970  0.020  1.090
 XKA  C6   H5   single    0.970  0.020  1.090
 XKA  C10  H6   single    0.930  0.020  1.080
 XKA  C15  H7   single    0.930  0.020  1.080
 XKA  C1   H8   single    0.970  0.020  1.090
 XKA  C2   H9   single    0.970  0.020  1.090
 XKA  O2   H10  single    0.850  0.020  0.980
 XKA  C3   H11  single    0.970  0.020  1.090
 XKA  O3   H12  single    0.850  0.020  0.980
 XKA  O4   H13  single    0.850  0.020  0.980
 XKA  O6   H14  single    0.850  0.020  0.980
 XKA  C09  H15  single    0.930  0.020  1.080
 XKA  C11  H16  single    0.930  0.020  1.080
 XKA  C12  H17  single    0.970  0.020  1.090
 XKA  C12  H18  single    0.970  0.020  1.090
 XKA  C12  H19  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
 XKA  H1   N1   C1   119.80  3.000
 XKA  H1   N1   C13  118.26  3.000
 XKA  C1   N1   C13  121.85  3.000
 XKA  H2   C4   O4   111.02  3.000
 XKA  H2   C4   C3   109.02  3.000
 XKA  O4   C4   C3   111.00  3.000
 XKA  H2   C4   C5   108.79  3.000
 XKA  C3   C4   C5   109.40  3.000
 XKA  O4   C4   C5   107.57  3.000
 XKA  H3   C5   O5   110.26  3.000
 XKA  H3   C5   C6   108.90  3.000
 XKA  O5   C5   C6   107.16  3.000
 XKA  H3   C5   C4   108.37  3.000
 XKA  O5   C5   C4   110.57  3.000
 XKA  C6   C5   C4   111.57  3.000
 XKA  H5   C6   H4   107.09  3.000
 XKA  H5   C6   O6   111.91  3.000
 XKA  H4   C6   O6   111.60  3.000
 XKA  H5   C6   C5   108.63  3.000
 XKA  H4   C6   C5   108.52  3.000
 XKA  O6   C6   C5   108.99  3.000
 XKA  H6   C10  C09  120.66  3.000
 XKA  H6   C10  N04  117.78  3.000
 XKA  C09  C10  N04  121.57  3.000
 XKA  N17  C13  S14  114.88  3.000
 XKA  N17  C13  N1   124.08  3.000
 XKA  S14  C13  N1   121.03  3.000
 XKA  H7   C15  N17  119.27  3.000
 XKA  H7   C15  C16  123.29  3.000
 XKA  N17  C15  C16  117.43  3.000
 XKA  C06  C20  S02  109.84  3.000
 XKA  C06  C20  C18  126.19  3.000
 XKA  S02  C20  C18  123.86  3.000
 XKA  H8   C1   O5   105.25  3.000
 XKA  H8   C1   C2   109.32  3.000
 XKA  O5   C1   C2   111.45  3.000
 XKA  H8   C1   N1   107.69  3.000
 XKA  C2   C1   N1   109.75  3.000
 XKA  O5   C1   N1   113.16  3.000
 XKA  H9   C2   C3   109.34  3.000
 XKA  H9   C2   O2   111.40  3.000
 XKA  C3   C2   O2   108.20  3.000
 XKA  H9   C2   C1   108.38  3.000
 XKA  O2   C2   C1   110.05  3.000
 XKA  C3   C2   C1   109.44  3.000
 XKA  H10  O2   C2   108.63  3.000
 XKA  H11  C3   O3   110.33  3.000
 XKA  H11  C3   C2   108.25  3.000
 XKA  O3   C3   C2   112.54  3.000
 XKA  H11  C3   C4   107.02  3.000
 XKA  O3   C3   C4   107.82  3.000
 XKA  C2   C3   C4   110.75  3.000
 XKA  H12  O3   C3   109.05  3.000
 XKA  C1   O5   C5   115.89  3.000
 XKA  H14  O6   C6   107.81  3.000
 XKA  C16  S14  C13   88.78  3.000
 XKA  C18  C16  S14  127.01  3.000
 XKA  S14  C16  C15  108.29  3.000
 XKA  C18  C16  C15  124.67  3.000
 XKA  C15  N17  C13  110.61  3.000
 XKA  O19  C18  C16  120.02  3.000
 XKA  C16  C18  C20  120.31  3.000
 XKA  O19  C18  C20  119.67  3.000
 XKA  C07  N02  C06  112.00  3.000
 XKA  C07  S02  C20   88.92  3.000
 XKA  C09  N03  C08  117.20  3.000
 XKA  C11  N04  C10  117.26  3.000
 XKA  C12  C06  N02  118.86  3.000
 XKA  C12  C06  C20  126.98  3.000
 XKA  N02  C06  C20  114.16  3.000
 XKA  C08  C07  S02  120.10  3.000
 XKA  S02  C07  N02  115.07  3.000
 XKA  C08  C07  N02  124.83  3.000
 XKA  C11  C08  C07  121.79  3.000
 XKA  C07  C08  N03  116.71  3.000
 XKA  C11  C08  N03  121.50  3.000
 XKA  H15  C09  N03  117.71  3.000
 XKA  H15  C09  C10  120.96  3.000
 XKA  N03  C09  C10  121.33  3.000
 XKA  H16  C11  C08  121.03  3.000
 XKA  H16  C11  N04  117.83  3.000
 XKA  C08  C11  N04  121.14  3.000
 XKA  H19  C12  H18  108.77  3.000
 XKA  H19  C12  H17  107.23  3.000
 XKA  H18  C12  H17  108.27  3.000
 XKA  H19  C12  C06  111.81  3.000
 XKA  H18  C12  C06  109.57  3.000
 XKA  H17  C12  C06  111.08  3.000
 XKA  H13  O4   C4   108.11  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
 XKA  CONST_01  C08  N03  C09  C10    0.00   0.0  0
 XKA  CONST_02  C08  C11  N04  C10    0.00   0.0  0
 XKA  CONST_03  C15  C16  S14  C13    0.00   0.0  0
 XKA  CONST_04  C16  C15  N17  C13    0.00   0.0  0
 XKA  CONST_05  S14  C13  N17  C15    0.00   0.0  0
 XKA  CONST_06  C08  C07  S02  C20  180.00   0.0  0
 XKA  CONST_07  N02  C07  S02  C20    0.00   0.0  0
 XKA  CONST_08  C07  N02  C06  C20    0.00   0.0  0
 XKA  CONST_09  N17  C15  C16  S14    0.00   0.0  0
 XKA  CONST_10  N17  C13  S14  C16    0.00   0.0  0
 XKA  CONST_11  N03  C08  C07  N02  180.00   0.0  0
 XKA  CONST_12  C11  C08  C07  N02    0.00   0.0  0
 XKA  CONST_13  S02  C20  C06  N02    0.00   0.0  0
 XKA  CONST_14  N03  C08  C07  S02    0.00   0.0  0
 XKA  CONST_15  C11  C08  C07  S02  180.00   0.0  0
 XKA  CONST_16  C06  N02  C07  S02    0.00   0.0  0
 XKA  CONST_17  N04  C10  C09  N03    0.00   0.0  0
 XKA  CONST_18  N04  C11  C08  N03    0.00   0.0  0
 XKA  CONST_19  C07  C08  C11  N04  180.00   0.0  0
 XKA  CONST_20  C08  C07  N02  C06  180.00   0.0  0
 XKA  CONST_21  C07  S02  C20  C06    0.00   0.0  0
 XKA  CONST_22  C09  N03  C08  C07  180.00   0.0  0
 XKA  CONST_23  C11  N04  C10  C09    0.00   0.0  0
 XKA  CONST_24  C11  C08  N03  C09    0.00   0.0  0
 XKA  CONST_25  C16  S14  C13  N1   180.00   0.0  0
 XKA  CONST_26  C15  N17  C13  N1   180.00   0.0  0
 XKA  CONST_27  C18  C16  S14  C13  180.00   0.0  0
 XKA  CONST_28  C18  C16  C15  N17  180.00   0.0  0
 XKA  CONST_29  C07  S02  C20  C18  180.00   0.0  0
 XKA  CONST_30  N02  C06  C20  C18  180.00   0.0  0
 XKA  CONST_31  C12  C06  C20  S02  180.00   0.0  0
 XKA  CONST_32  C12  C06  N02  C07  180.00   0.0  0
 XKA  CONST_33  S14  C13  N1   C1   180.00   0.0  0
 XKA  CONST_34  N17  C13  N1   C1     0.00   0.0  0
 XKA  CONST_35  H16  C11  N04  C10  180.00   0.0  0
 XKA  CONST_36  H7   C15  N17  C13  180.00   0.0  0
 XKA  CONST_37  H6   C10  C09  N03  180.00   0.0  0
 XKA  CONST_38  H15  C09  C10  N04  180.00   0.0  0
 XKA  CONST_39  H1   N1   C13  S14    0.00   0.0  0
 XKA  Var_01    C20  C18  C16  C15  163.60  30.0  2
 XKA  Var_02    S02  C20  C18  C16  -25.36  30.0  1
 XKA  Var_03    H17  C12  C06  C20   73.68  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
 XKA  chir_01  C4  C5  O4  C3  negativ
 XKA  chir_02  C5  O5  C4  C6  negativ
 XKA  chir_03  C1  O5  N1  C2  positiv
 XKA  chir_04  C2  O2  C1  C3  positiv
 XKA  chir_05  C3  O3  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
 XKA  plan-1  N1   0.020
 XKA  plan-1  C13  0.020
 XKA  plan-1  C15  0.020
 XKA  plan-1  S14  0.020
 XKA  plan-1  C16  0.020
 XKA  plan-1  N17  0.020
 XKA  plan-1  C18  0.020
 XKA  plan-1  H7   0.020
 XKA  plan-2  C20  0.020
 XKA  plan-2  C18  0.020
 XKA  plan-2  N02  0.020
 XKA  plan-2  S02  0.020
 XKA  plan-2  C06  0.020
 XKA  plan-2  C07  0.020
 XKA  plan-2  C08  0.020
 XKA  plan-2  C12  0.020
 XKA  plan-3  C10  0.020
 XKA  plan-3  N03  0.020
 XKA  plan-3  N04  0.020
 XKA  plan-3  C07  0.020
 XKA  plan-3  C08  0.020
 XKA  plan-3  C09  0.020
 XKA  plan-3  C11  0.020
 XKA  plan-3  H15  0.020
 XKA  plan-3  H16  0.020
 XKA  plan-3  H6   0.020
 XKA  plan-4  N1   0.020
 XKA  plan-4  C13  0.020
 XKA  plan-4  C1   0.020
 XKA  plan-4  H1   0.020
 XKA  plan-5  C20  0.020
 XKA  plan-5  C16  0.020
 XKA  plan-5  C18  0.020
 XKA  plan-5  O19  0.020

