# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 19 13:47:39 2020
#   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  59  35  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.114   2.2673  -1.2337  -0.6395
 A4Y  C13   C  CH1    0  -0.049  -0.9640   0.6857  -1.7435
 A4Y  C17   C  CR6    0  -0.087  -3.6097   2.4725  -0.9435
 A4Y  C20   C  CR6    0   0.342  -3.9962   4.6634   0.5562
 A4Y  C21   C  CH3    0  -0.731  -4.2096   5.8729   1.4132
 A4Y  C26   C  CT     0   0.272  -3.4196  -0.6240   0.8859
 A4Y  C28   C  CT     0   0.092  -3.7511  -1.9501   0.1141
 A4Y  O01   O  OP    -1  -0.834   4.6477  -3.2852  -0.9215
 A4Y  O03   O  O2     0  -0.777   6.0052  -1.0990  -0.5886
 A4Y  P04   P  P      0   1.225   7.6321  -1.6825  -0.6842
 A4Y  O05   O  OP    -1  -0.896   8.4091  -0.4142  -0.3594
 A4Y  O06   O  O      0  -0.896   7.7052  -2.7730   0.3728
 A4Y  O07   O  OP    -1  -0.896   7.7714  -2.1601  -2.1211
 A4Y  O08   O  O      0  -0.832   4.5305  -2.0041   1.3227
 A4Y  O09   O  O2     0  -0.631   3.6285  -0.9342  -0.8242
 A4Y  C11   C  CH2    0  -0.465   1.4368  -0.1007  -1.2176
 A4Y  C12   C  CH1    0  -0.383  -0.0546  -0.3563  -1.1009
 A4Y  N15   N  NT     0  -0.420  -2.2891   0.4004  -1.1861
 A4Y  C16   C  CH2    0  -0.374  -3.3613   1.2197  -1.7326
 A4Y  C18   C  CR16   0  -0.091  -4.3204   3.5542  -1.3861
 A4Y  N19   N  N      0  -0.452  -4.5320   4.6579  -0.6540
 A4Y  N22   N  N      0  -0.476  -3.2817   3.6784   1.0935
 A4Y  C23   C  CR6    0   0.524  -3.0915   2.5847   0.3601
 A4Y  N24   N  NH1    0  -0.630  -2.3385   1.5963   0.8716
 A4Y  C25   C  CT     0   0.105  -2.2711   0.2767   0.2512
 A4Y  C29   C  CH3    0  -0.679  -2.5700  -2.8707  -0.1625
 A4Y  C30   C  C      0   0.432  -4.8271  -2.7857   0.8984
 A4Y  O31   O  O      0  -0.569  -4.4993  -3.3851   1.9279
 A4Y  O32   O  OC    -1  -0.610  -5.9512  -2.8146   0.3381
 A4Y  O33   O  OH1    0  -0.699  -4.3778  -1.5983  -1.1021
 A4Y  O34   O  OH1    0  -0.676  -4.6062   0.1449   0.8920
 A4Y  S35   S  S2     0   0.025  -0.6019  -0.4004   0.6383
 A4Y  H101  H  HCH2   0   0.191   1.9932  -2.1758  -1.1341
 A4Y  H102  H  HCH2   0   0.189   2.0362  -1.3595   0.4272
 A4Y  H1    H  HCH1   0   0.258  -1.0235   0.4622  -2.8138
 A4Y  H213  H  HCH3   0   0.250  -4.7582   5.6072   2.3182
 A4Y  H211  H  HCH3   0   0.249  -3.2551   6.2946   1.7303
 A4Y  H212  H  HCH3   0   0.242  -4.7705   6.6368   0.8804
 A4Y  H112  H  HCH2   0   0.240   1.7011   0.8356  -0.7216
 A4Y  H111  H  HCH2   0   0.243   1.6798   0.0130  -2.2795
 A4Y  H5    H  HCH1   0   0.279  -0.2857  -1.3285  -1.5446
 A4Y  H142  H  HCH3   0   0.233  -0.2349   2.3780  -0.5616
 A4Y  H143  H  HCH3   0   0.243   0.4568   2.2536  -2.1812
 A4Y  H141  H  HCH3   0   0.243  -1.1831   2.8312  -1.9804
 A4Y  H161  H  HCH2   0   0.270  -4.2729   0.6282  -1.8104
 A4Y  H162  H  HCH2   0   0.264  -3.0931   1.4761  -2.7598
 A4Y  H181  H  HCR6   0   0.255  -4.7479   3.5514  -2.3854
 A4Y  H241  H  HNH1   0   0.382  -2.0091   1.7209   1.8159
 A4Y  H273  H  HCH3   0   0.253  -3.9255  -1.2306   2.8996
 A4Y  H272  H  HCH3   0   0.238  -2.2649  -1.5932   2.4722
 A4Y  H271  H  HCH3   0   0.217  -2.7487   0.0600   2.8422
 A4Y  H293  H  HCH3   0   0.236  -1.8661  -2.4218  -0.8578
 A4Y  H291  H  HCH3   0   0.225  -2.0329  -3.1335   0.7458
 A4Y  H292  H  HCH3   0   0.224  -2.9297  -3.7975  -0.6157
 A4Y  H331  H  HOH1   0   0.432  -5.2679  -2.0038  -0.9809
 A4Y  H341  H  HOH1   0   0.441  -5.0448  -0.0231   0.0480
 A4Y  C14   C  CH3    0  -0.694  -0.4535   2.1186  -1.5964
 A4Y  P02   P  P      0   1.331   4.7420  -1.9896  -0.1665
 A4Y  C27   C  CH3    0  -0.684  -3.0623  -0.8633   2.3538

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    1.523  0.020  1.523
 A4Y  O06  P04   deloc     1.520  0.020  1.520
 A4Y  O05  P04   deloc     1.522  0.020  1.522
 A4Y  C27  C26   single    1.530  0.020  1.530
 A4Y  O31  C30   deloc     1.236  0.020  1.236
 A4Y  P04  O07   deloc     1.521  0.020  1.521
 A4Y  P04  O03   single    1.731  0.020  1.731
 A4Y  C28  O33   single    1.413  0.020  1.413
 A4Y  C28  C30   single    1.572  0.020  1.572
 A4Y  C28  C26   single    1.570  0.020  1.570
 A4Y  C30  O32   deloc     1.256  0.020  1.256
 A4Y  C26  O34   single    1.414  0.020  1.414
 A4Y  C26  C25   single    1.592  0.020  1.592
 A4Y  O03  P02   single    1.602  0.020  1.602
 A4Y  S35  C25   single    1.842  0.020  1.842
 A4Y  S35  C12   single    1.824  0.020  1.824
 A4Y  C10  C11   single    1.519  0.020  1.519
 A4Y  C10  O09   single    1.406  0.020  1.406
 A4Y  C25  N24   single    1.460  0.020  1.460
 A4Y  C25  N15   single    1.443  0.020  1.443
 A4Y  C12  C11   single    1.518  0.020  1.518
 A4Y  C12  C13   single    1.525  0.020  1.525
 A4Y  P02  O09   single    1.669  0.020  1.669
 A4Y  P02  O08   deloc     1.504  0.020  1.504
 A4Y  P02  O01   deloc     1.502  0.020  1.502
 A4Y  N24  C23   single    1.344  0.020  1.344
 A4Y  C13  N15   single    1.466  0.020  1.466
 A4Y  C13  C14   single    1.528  0.020  1.528
 A4Y  N15  C16   single    1.456  0.020  1.456
 A4Y  C16  C17   single    1.501  0.020  1.501
 A4Y  C23  C17   aromatic  1.407  0.020  1.407
 A4Y  C23  N22   aromatic  1.331  0.020  1.331
 A4Y  C17  C18   aromatic  1.368  0.020  1.368
 A4Y  N22  C20   aromatic  1.330  0.020  1.330
 A4Y  C18  N19   aromatic  1.341  0.020  1.341
 A4Y  C20  N19   aromatic  1.324  0.020  1.324
 A4Y  C20  C21   single    1.498  0.020  1.498
 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  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  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  106.64  3.000
 A4Y  H102  C10  C11   109.87  3.000
 A4Y  H101  C10  C11   109.38  3.000
 A4Y  H102  C10  O09   110.83  3.000
 A4Y  H101  C10  O09   111.41  3.000
 A4Y  C11   C10  O09   108.69  3.000
 A4Y  H1    C13  N15   106.43  3.000
 A4Y  H1    C13  C14   107.67  3.000
 A4Y  N15   C13  C14   116.62  3.000
 A4Y  H1    C13  C12   107.74  3.000
 A4Y  C14   C13  C12   113.63  3.000
 A4Y  N15   C13  C12   104.24  3.000
 A4Y  C23   C17  C18   115.34  3.000
 A4Y  C18   C17  C16   125.16  3.000
 A4Y  C23   C17  C16   119.50  3.000
 A4Y  N22   C20  N19   125.71  3.000
 A4Y  N19   C20  C21   117.97  3.000
 A4Y  N22   C20  C21   116.32  3.000
 A4Y  H212  C21  H211  108.81  3.000
 A4Y  H212  C21  H213  108.55  3.000
 A4Y  H211  C21  H213  107.04  3.000
 A4Y  H212  C21  C20   111.13  3.000
 A4Y  H211  C21  C20   110.73  3.000
 A4Y  H213  C21  C20   110.46  3.000
 A4Y  O34   C26  C27   106.08  3.000
 A4Y  O34   C26  C25   107.44  3.000
 A4Y  C27   C26  C25   107.62  3.000
 A4Y  C25   C26  C28   115.75  3.000
 A4Y  O34   C26  C28   106.52  3.000
 A4Y  C27   C26  C28   112.89  3.000
 A4Y  O33   C28  C30   104.96  3.000
 A4Y  C30   C28  C29   107.47  3.000
 A4Y  O33   C28  C29   109.77  3.000
 A4Y  C30   C28  C26   110.39  3.000
 A4Y  O33   C28  C26   107.85  3.000
 A4Y  C29   C28  C26   115.86  3.000
 A4Y  P04   O03  P02   124.62  3.000
 A4Y  O07   P04  O06   115.30  3.000
 A4Y  O07   P04  O05   114.61  3.000
 A4Y  O06   P04  O05   115.13  3.000
 A4Y  O07   P04  O03   104.13  3.000
 A4Y  O05   P04  O03   100.78  3.000
 A4Y  O06   P04  O03   104.39  3.000
 A4Y  P02   O09  C10   117.35  3.000
 A4Y  H111  C11  H112  107.32  3.000
 A4Y  H111  C11  C12   108.06  3.000
 A4Y  H112  C11  C12   110.33  3.000
 A4Y  H111  C11  C10   108.97  3.000
 A4Y  H112  C11  C10   109.53  3.000
 A4Y  C12   C11  C10   112.48  3.000
 A4Y  H5    C12  S35   107.58  3.000
 A4Y  H5    C12  C11   109.04  3.000
 A4Y  S35   C12  C11   111.86  3.000
 A4Y  H5    C12  C13   108.09  3.000
 A4Y  C11   C12  C13   116.01  3.000
 A4Y  S35   C12  C13   103.85  3.000
 A4Y  C25   N15  C16   115.55  3.000
 A4Y  C16   N15  C13   114.43  3.000
 A4Y  C25   N15  C13   112.60  3.000
 A4Y  H162  C16  H161  105.41  3.000
 A4Y  H162  C16  N15   107.71  3.000
 A4Y  H161  C16  N15   109.72  3.000
 A4Y  H162  C16  C17   109.82  3.000
 A4Y  H161  C16  C17   110.62  3.000
 A4Y  N15   C16  C17   113.22  3.000
 A4Y  H181  C18  N19   116.22  3.000
 A4Y  H181  C18  C17   119.99  3.000
 A4Y  N19   C18  C17   123.78  3.000
 A4Y  C18   N19  C20   116.02  3.000
 A4Y  C23   N22  C20   117.57  3.000
 A4Y  N24   C23  N22   118.36  3.000
 A4Y  N22   C23  C17   121.57  3.000
 A4Y  N24   C23  C17   120.02  3.000
 A4Y  H241  N24  C25   119.66  3.000
 A4Y  H241  N24  C23   116.67  3.000
 A4Y  C25   N24  C23   121.95  3.000
 A4Y  S35   C25  N24   106.55  3.000
 A4Y  N24   C25  N15   110.20  3.000
 A4Y  S35   C25  N15   104.60  3.000
 A4Y  N15   C25  C26   115.89  3.000
 A4Y  N24   C25  C26   107.99  3.000
 A4Y  S35   C25  C26   111.23  3.000
 A4Y  H292  C29  H291  107.70  3.000
 A4Y  H292  C29  H293  107.35  3.000
 A4Y  H291  C29  H293  108.32  3.000
 A4Y  H292  C29  C28   109.44  3.000
 A4Y  H291  C29  C28   112.18  3.000
 A4Y  H293  C29  C28   111.65  3.000
 A4Y  O32   C30  O31   126.71  3.000
 A4Y  O32   C30  C28   113.72  3.000
 A4Y  O31   C30  C28   119.47  3.000
 A4Y  H331  O33  C28   101.09  3.000
 A4Y  H341  O34  C26   106.42  3.000
 A4Y  C25   S35  C12    93.59  3.000
 A4Y  H141  C14  H143  106.79  3.000
 A4Y  H141  C14  H142  108.27  3.000
 A4Y  H143  C14  H142  108.22  3.000
 A4Y  H141  C14  C13   110.82  3.000
 A4Y  H143  C14  C13   110.09  3.000
 A4Y  H142  C14  C13   112.45  3.000
 A4Y  O09   P02  O08   107.60  3.000
 A4Y  O08   P02  O03   112.15  3.000
 A4Y  O09   P02  O03    94.05  3.000
 A4Y  O08   P02  O01   118.71  3.000
 A4Y  O09   P02  O01   107.78  3.000
 A4Y  O03   P02  O01   113.36  3.000
 A4Y  H271  C27  H272  107.98  3.000
 A4Y  H271  C27  H273  106.85  3.000
 A4Y  H272  C27  H273  107.54  3.000
 A4Y  H271  C27  C26   111.38  3.000
 A4Y  H272  C27  C26   112.39  3.000
 A4Y  H273  C27  C26   110.47  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  Var_01    C17   C16  N15  C13   -91.64  30.0  1
 A4Y  Var_02    C25   N24  C23  C17   -13.83  30.0  1
 A4Y  Var_03    C23   C17  C16  N15   -16.19  30.0  1
 A4Y  Var_04    H213  C21  C20  N19   118.11  30.0  2
 A4Y  Var_05    C12   C11  C10  O09   178.28  30.0  3
 A4Y  Var_06    O03   P02  O09  C10  -176.03  30.0  2
 A4Y  Var_07    O06   P04  O03  P02   -30.73  30.0  3
 A4Y  Var_08    C11   C10  O09  P02   175.68  30.0  1
 A4Y  Var_09    O09   P02  O03  P04  -161.44  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

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-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

