# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 10:02:50 2021
#   Inital geometry file: a 146 line input string
#   Ligand name: (2S,3S)-2,3-dihydroxy-3-[(7S,8R,9aS)-8-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2,7-dimethyl-5,7,8,10-tetrahydro-9aH-pyrimido[4,5-d][1,3]thiazolo[3,2-a]pyrimidin-9a-yl]-2-methylbutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@@H](CCO[P](O)(=O)O[P](O)(O)=O)S[C@]2(Nc3nc(C)ncc3CN12)[C@@](C)(O)[C@](C)(O)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
 A4Y  A4Y  '(2S,3S)-2,3-dihydroxy-3-[(7S,8R,9aS)-8-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2,7-dimethyl-5,7,8,10-tetrahydro-9aH-pyrimido[4,5-d][1,3]thiazolo[3,2-a]pyrimidin-9a-yl]-2-methylbutanoic acid'  ligand  63  35  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_A4Y
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
 A4Y  C10   C  CH2   0  -0.193   -7.4475  10.9166  -13.0550
 A4Y  C13   C  CH1   0  -0.054   -7.7541   7.9897  -11.7827
 A4Y  C17   C  CR6   0  -0.085   -7.8944   5.1954   -9.9892
 A4Y  C20   C  CR6   0   0.351   -6.2104   3.9479   -8.3170
 A4Y  C21   C  CH3   0  -0.732   -5.2750   3.2507   -7.3791
 A4Y  C26   C  CT    0   0.235   -7.3411   4.6606  -13.5706
 A4Y  C28   C  CT    0   0.084   -8.4171   5.0553  -14.6612
 A4Y  O01   O  OH1   0  -0.726   -6.1036  12.0701  -15.5859
 A4Y  O03   O  O2    0  -0.698   -8.1278  13.2106  -15.0326
 A4Y  P04   P  P     0   1.477   -9.2531  14.3209  -14.6822
 A4Y  O05   O  OH1   0  -0.725   -8.6155  15.5816  -15.3964
 A4Y  O06   O  O     0  -0.675  -10.5872  13.8689  -15.1013
 A4Y  O07   O  OH1   0  -0.737   -9.0506  14.6289  -13.1343
 A4Y  O08   O  O     0  -0.675   -5.8894  14.2870  -14.1926
 A4Y  O09   O  O2    0  -0.576   -6.8058  12.2001  -13.1128
 A4Y  C11   C  CH2   0  -0.468   -6.4228   9.7973  -13.1074
 A4Y  C12   C  CH1   0  -0.406   -7.1158   8.4437  -13.0899
 A4Y  N15   N  NT    0  -0.516   -8.0532   6.5710  -12.0330
 A4Y  C16   C  CH2   0  -0.372   -8.7885   5.8988  -10.9612
 A4Y  C18   C  CR16  0  -0.077   -8.2632   4.8000   -8.7280
 A4Y  N19   N  N     0  -0.446   -7.4445   4.1724   -7.8814
 A4Y  N22   N  N     0  -0.473   -5.7380   4.2916   -9.5082
 A4Y  C23   C  CR6   0   0.532   -6.5709   4.9067  -10.3463
 A4Y  N24   N  NH1   0  -0.644   -6.0875   5.2916  -11.5426
 A4Y  C25   C  CT    0   0.142   -6.9201   5.8384  -12.5908
 A4Y  C27   C  CH3   0  -0.702   -6.0768   4.0793  -14.1960
 A4Y  C29   C  CH3   0  -0.675   -7.9022   5.9064  -15.8235
 A4Y  C30   C  C     0   0.552   -8.9284   3.7358  -15.2696
 A4Y  O31   O  O     0  -0.439   -8.3506   3.1359  -16.1413
 A4Y  O32   O  OH1   0  -0.576  -10.0844   3.3380  -14.7662
 A4Y  O33   O  OH1   0  -0.686   -9.5273   5.6712  -14.0626
 A4Y  O34   O  OH1   0  -0.661   -7.8818   3.6182  -12.7815
 A4Y  S35   S  S2    0   0.071   -5.9242   7.1198  -13.4601
 A4Y  H101  H  HCH2  0   0.248   -8.1764  10.8033  -13.8614
 A4Y  H102  H  HCH2  0   0.264   -8.0017  10.9087  -12.1161
 A4Y  H1    H  HCH1  0   0.282   -8.7236   8.4839  -11.6705
 A4Y  H213  H  HCH3  0   0.246   -4.3083   3.0748   -7.8440
 A4Y  H211  H  HCH3  0   0.254   -5.1243   3.8453   -6.4770
 A4Y  H212  H  HCH3  0   0.253   -5.6932   2.2941   -7.0648
 A4Y  H2    H  HOH1  0   0.511   -5.1431  11.9524  -15.5933
 A4Y  H3    H  HOH1  0   0.510   -9.1971  16.3530  -15.4506
 A4Y  H4    H  HOH1  0   0.508   -9.6665  14.1703  -12.5462
 A4Y  H112  H  HCH2  0   0.267   -5.8524   9.8805  -14.0349
 A4Y  H111  H  HCH2  0   0.267   -5.7110   9.8875  -12.2855
 A4Y  H5    H  HCH1  0   0.293   -7.8827   8.4361  -13.8720
 A4Y  H142  H  HCH3  0   0.254   -7.3466   7.8168   -9.6620
 A4Y  H143  H  HCH3  0   0.240   -5.8877   7.9441  -10.6476
 A4Y  H141  H  HCH3  0   0.248   -6.8995   9.3593  -10.3525
 A4Y  H161  H  HCH2  0   0.290   -9.3879   6.6531  -10.4485
 A4Y  H162  H  HCH2  0   0.265   -9.5196   5.2083  -11.3888
 A4Y  H181  H  HCR6  0   0.264   -9.2698   4.9994   -8.3709
 A4Y  H241  H  HNH1  0   0.397   -5.1200   5.0826  -11.7337
 A4Y  H273  H  HCH3  0   0.250   -5.4334   3.6555  -13.4256
 A4Y  H272  H  HCH3  0   0.269   -6.3122   3.2746  -14.8868
 A4Y  H271  H  HCH3  0   0.246   -5.5042   4.8222  -14.7470
 A4Y  H293  H  HCH3  0   0.242   -7.0165   5.4891  -16.2963
 A4Y  H291  H  HCH3  0   0.248   -8.6804   5.9890  -16.5836
 A4Y  H292  H  HCH3  0   0.249   -7.6590   6.9116  -15.4921
 A4Y  H7    H  HOH1  0   0.483  -10.3486   2.5065  -15.1892
 A4Y  H331  H  HOH1  0   0.469   -9.1721   6.3116  -13.4116
 A4Y  H341  H  HOH1  0   0.456   -8.8102   3.7892  -12.5874
 A4Y  C14   C  CH3   0  -0.687   -6.9164   8.2863  -10.5455
 A4Y  P02   P  P     0   1.488   -6.6285  13.0439  -14.4448

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
 A4Y  C29  C28   single    1.530  0.020  1.530
 A4Y  O06  P04   double    1.470  0.020  1.470
 A4Y  O05  P04   single    1.583  0.020  1.583
 A4Y  C27  C26   single    1.526  0.020  1.526
 A4Y  O31  C30   double    1.206  0.020  1.206
 A4Y  P04  O07   single    1.591  0.020  1.591
 A4Y  P04  O03   single    1.619  0.020  1.619
 A4Y  C28  O33   single    1.404  0.020  1.404
 A4Y  C28  C30   single    1.540  0.020  1.540
 A4Y  C28  C26   single    1.582  0.020  1.582
 A4Y  C30  O32   single    1.322  0.020  1.322
 A4Y  C26  O34   single    1.415  0.020  1.415
 A4Y  C26  C25   single    1.589  0.020  1.589
 A4Y  O03  P02   single    1.619  0.020  1.619
 A4Y  S35  C25   single    1.841  0.020  1.841
 A4Y  S35  C12   single    1.819  0.020  1.819
 A4Y  C10  C11   single    1.518  0.020  1.518
 A4Y  C10  O09   single    1.436  0.020  1.436
 A4Y  C25  N24   single    1.446  0.020  1.446
 A4Y  C25  N15   single    1.460  0.020  1.460
 A4Y  C12  C11   single    1.521  0.020  1.521
 A4Y  C12  C13   single    1.524  0.020  1.524
 A4Y  P02  O09   single    1.587  0.020  1.587
 A4Y  P02  O08   double    1.468  0.020  1.468
 A4Y  P02  O01   single    1.589  0.020  1.589
 A4Y  N24  C23   single    1.347  0.020  1.347
 A4Y  C13  N15   single    1.471  0.020  1.471
 A4Y  C13  C14   single    1.523  0.020  1.523
 A4Y  N15  C16   single    1.463  0.020  1.463
 A4Y  C16  C17   single    1.496  0.020  1.496
 A4Y  C23  C17   aromatic  1.401  0.020  1.401
 A4Y  C23  N22   aromatic  1.332  0.020  1.332
 A4Y  C17  C18   aromatic  1.372  0.020  1.372
 A4Y  N22  C20   aromatic  1.327  0.020  1.327
 A4Y  C18  N19   aromatic  1.334  0.020  1.334
 A4Y  C20  N19   aromatic  1.328  0.020  1.328
 A4Y  C20  C21   single    1.497  0.020  1.497
 A4Y  C10  H101  single    0.970  0.020  1.090
 A4Y  C10  H102  single    0.970  0.020  1.090
 A4Y  C13  H1    single    0.970  0.020  1.090
 A4Y  C21  H213  single    0.970  0.020  1.090
 A4Y  C21  H211  single    0.970  0.020  1.090
 A4Y  C21  H212  single    0.970  0.020  1.090
 A4Y  O01  H2    single    0.850  0.020  0.980
 A4Y  O05  H3    single    0.850  0.020  0.980
 A4Y  O07  H4    single    0.850  0.020  0.980
 A4Y  C11  H112  single    0.970  0.020  1.090
 A4Y  C11  H111  single    0.970  0.020  1.090
 A4Y  C12  H5    single    0.970  0.020  1.090
 A4Y  C14  H142  single    0.970  0.020  1.090
 A4Y  C14  H143  single    0.970  0.020  1.090
 A4Y  C14  H141  single    0.970  0.020  1.090
 A4Y  C16  H161  single    0.970  0.020  1.090
 A4Y  C16  H162  single    0.970  0.020  1.090
 A4Y  C18  H181  single    0.930  0.020  1.080
 A4Y  N24  H241  single    0.860  0.020  1.020
 A4Y  C27  H273  single    0.970  0.020  1.090
 A4Y  C27  H272  single    0.970  0.020  1.090
 A4Y  C27  H271  single    0.970  0.020  1.090
 A4Y  C29  H293  single    0.970  0.020  1.090
 A4Y  C29  H291  single    0.970  0.020  1.090
 A4Y  C29  H292  single    0.970  0.020  1.090
 A4Y  O32  H7    single    0.850  0.020  0.980
 A4Y  O33  H331  single    0.850  0.020  0.980
 A4Y  O34  H341  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
 A4Y  H102  C10  H101  107.19  3.000
 A4Y  H102  C10  C11   111.56  3.000
 A4Y  H101  C10  C11   110.38  3.000
 A4Y  H102  C10  O09   105.56  3.000
 A4Y  H101  C10  O09   111.16  3.000
 A4Y  C11   C10  O09   110.85  3.000
 A4Y  H1    C13  N15   105.83  3.000
 A4Y  H1    C13  C14   108.43  3.000
 A4Y  N15   C13  C14   115.95  3.000
 A4Y  H1    C13  C12   108.95  3.000
 A4Y  C14   C13  C12   114.10  3.000
 A4Y  N15   C13  C12   103.09  3.000
 A4Y  C23   C17  C18   115.39  3.000
 A4Y  C18   C17  C16   124.88  3.000
 A4Y  C23   C17  C16   119.72  3.000
 A4Y  N22   C20  N19   125.56  3.000
 A4Y  N19   C20  C21   117.00  3.000
 A4Y  N22   C20  C21   117.44  3.000
 A4Y  H212  C21  H211  107.02  3.000
 A4Y  H212  C21  H213  108.81  3.000
 A4Y  H211  C21  H213  108.61  3.000
 A4Y  H212  C21  C20   110.46  3.000
 A4Y  H211  C21  C20   110.52  3.000
 A4Y  H213  C21  C20   111.29  3.000
 A4Y  O34   C26  C27   105.34  3.000
 A4Y  O34   C26  C25   107.67  3.000
 A4Y  C27   C26  C25   108.40  3.000
 A4Y  C25   C26  C28   114.86  3.000
 A4Y  O34   C26  C28   107.96  3.000
 A4Y  C27   C26  C28   112.09  3.000
 A4Y  O33   C28  C30   106.37  3.000
 A4Y  C30   C28  C29   106.75  3.000
 A4Y  O33   C28  C29   110.25  3.000
 A4Y  C30   C28  C26   106.52  3.000
 A4Y  O33   C28  C26   110.70  3.000
 A4Y  C29   C28  C26   115.69  3.000
 A4Y  H2    O01  P02   114.07  3.000
 A4Y  P04   O03  P02   129.46  3.000
 A4Y  O07   P04  O06   116.90  3.000
 A4Y  O07   P04  O05   103.50  3.000
 A4Y  O06   P04  O05   118.81  3.000
 A4Y  O07   P04  O03   104.77  3.000
 A4Y  O05   P04  O03    99.70  3.000
 A4Y  O06   P04  O03   111.00  3.000
 A4Y  H3    O05  P04   114.71  3.000
 A4Y  H4    O07  P04   114.75  3.000
 A4Y  P02   O09  C10   123.99  3.000
 A4Y  H111  C11  H112  107.03  3.000
 A4Y  H111  C11  C12   111.23  3.000
 A4Y  H112  C11  C12   108.40  3.000
 A4Y  H111  C11  C10   110.69  3.000
 A4Y  H112  C11  C10   109.01  3.000
 A4Y  C12   C11  C10   110.38  3.000
 A4Y  H5    C12  S35   107.95  3.000
 A4Y  H5    C12  C11   108.48  3.000
 A4Y  S35   C12  C11   110.30  3.000
 A4Y  H5    C12  C13   108.49  3.000
 A4Y  C11   C12  C13   117.77  3.000
 A4Y  S35   C12  C13   103.42  3.000
 A4Y  C25   N15  C16   116.06  3.000
 A4Y  C16   N15  C13   114.87  3.000
 A4Y  C25   N15  C13   113.02  3.000
 A4Y  H162  C16  H161  104.66  3.000
 A4Y  H162  C16  N15   109.87  3.000
 A4Y  H161  C16  N15   107.61  3.000
 A4Y  H162  C16  C17   110.91  3.000
 A4Y  H161  C16  C17   110.36  3.000
 A4Y  N15   C16  C17   113.05  3.000
 A4Y  H181  C18  N19   116.49  3.000
 A4Y  H181  C18  C17   119.88  3.000
 A4Y  N19   C18  C17   123.63  3.000
 A4Y  C18   N19  C20   116.20  3.000
 A4Y  C23   N22  C20   117.51  3.000
 A4Y  N24   C23  N22   117.81  3.000
 A4Y  N22   C23  C17   121.70  3.000
 A4Y  N24   C23  C17   120.45  3.000
 A4Y  H241  N24  C25   119.58  3.000
 A4Y  H241  N24  C23   116.98  3.000
 A4Y  C25   N24  C23   123.05  3.000
 A4Y  S35   C25  N24   107.10  3.000
 A4Y  N24   C25  N15   111.08  3.000
 A4Y  S35   C25  N15   104.53  3.000
 A4Y  N15   C25  C26   113.70  3.000
 A4Y  N24   C25  C26   108.62  3.000
 A4Y  S35   C25  C26   111.60  3.000
 A4Y  H271  C27  H272  107.33  3.000
 A4Y  H271  C27  H273  108.24  3.000
 A4Y  H272  C27  H273  106.82  3.000
 A4Y  H271  C27  C26   112.56  3.000
 A4Y  H272  C27  C26   111.31  3.000
 A4Y  H273  C27  C26   110.35  3.000
 A4Y  H292  C29  H291  107.59  3.000
 A4Y  H292  C29  H293  107.79  3.000
 A4Y  H291  C29  H293  107.89  3.000
 A4Y  H292  C29  C28   111.01  3.000
 A4Y  H291  C29  C28   109.35  3.000
 A4Y  H293  C29  C28   113.02  3.000
 A4Y  O32   C30  O31   123.00  3.000
 A4Y  O32   C30  C28   113.43  3.000
 A4Y  O31   C30  C28   123.56  3.000
 A4Y  H7    O32  C30   109.28  3.000
 A4Y  H331  O33  C28   106.46  3.000
 A4Y  H341  O34  C26   110.47  3.000
 A4Y  C25   S35  C12    93.22  3.000
 A4Y  H141  C14  H143  108.13  3.000
 A4Y  H141  C14  H142  106.66  3.000
 A4Y  H143  C14  H142  108.29  3.000
 A4Y  H141  C14  C13   110.11  3.000
 A4Y  H143  C14  C13   112.47  3.000
 A4Y  H142  C14  C13   110.96  3.000
 A4Y  O09   P02  O08   111.25  3.000
 A4Y  O08   P02  O03   116.20  3.000
 A4Y  O09   P02  O03   104.84  3.000
 A4Y  O08   P02  O01   118.41  3.000
 A4Y  O09   P02  O01   108.29  3.000
 A4Y  O03   P02  O01    96.21  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
 A4Y  CONST_01  C20   N22  C23  C17     0.00   0.0  0
 A4Y  CONST_02  C20   N19  C18  C17     0.00   0.0  0
 A4Y  CONST_03  N22   C23  C17  C18     0.00   0.0  0
 A4Y  CONST_04  N22   C20  N19  C18     0.00   0.0  0
 A4Y  CONST_05  C23   C17  C18  N19     0.00   0.0  0
 A4Y  CONST_06  C23   N22  C20  N19     0.00   0.0  0
 A4Y  CONST_07  C23   N22  C20  C21   180.00   0.0  0
 A4Y  CONST_08  C18   N19  C20  C21   180.00   0.0  0
 A4Y  CONST_09  H181  C18  N19  C20   180.00   0.0  0
 A4Y  CONST_10  H7    O32  C30  C28   180.00   0.0  0
 A4Y  Var_01    C17   C16  N15  C13   -93.90  30.0  1
 A4Y  Var_02    C25   N24  C23  C17    -9.08  30.0  1
 A4Y  Var_03    C23   C17  C16  N15   -17.80  30.0  1
 A4Y  Var_04    H213  C21  C20  N19   177.43  30.0  2
 A4Y  Var_05    C12   C11  C10  O09  -178.22  30.0  3
 A4Y  Var_06    O03   P02  O09  C10    55.82  30.0  2
 A4Y  Var_07    O06   P04  O03  P02  -161.83  30.0  2
 A4Y  Var_08    C11   C10  O09  P02    96.57  30.0  3
 A4Y  Var_09    O09   P02  O03  P04    85.58  30.0  3

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
 A4Y  chir_01  C13  C12  N15  C14  negativ
 A4Y  chir_02  C26  C27  C28  C25  positiv
 A4Y  chir_03  C28  C29  C30  C26  negativ
 A4Y  chir_05  C12  S35  C11  C13  positiv
 A4Y  chir_06  C25  N24  N15  S35  negativ
 A4Y  chir_07  P02  O09  O08  O01  both

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
 A4Y  plan-1  C28   0.020
 A4Y  plan-1  C30   0.020
 A4Y  plan-1  O31   0.020
 A4Y  plan-1  O32   0.020
 A4Y  plan-1  H7    0.020
 A4Y  plan-2  C17   0.020
 A4Y  plan-2  C20   0.020
 A4Y  plan-2  C21   0.020
 A4Y  plan-2  C16   0.020
 A4Y  plan-2  C18   0.020
 A4Y  plan-2  N19   0.020
 A4Y  plan-2  N22   0.020
 A4Y  plan-2  C23   0.020
 A4Y  plan-2  N24   0.020
 A4Y  plan-2  H181  0.020

