# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Oct 23 16:35:07 2020
#
#   Inital geometry file: a 114 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]adenosine
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
#
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
SAP        SAP '5'-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]adenosine' ligand 45 31 .
2020-10-23 2020-10-23
;
CIF prepared directly in eLBOW
;
#
data_comp_SAP
#
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
SAP         PG     P   P      0    .      -6.3910   -1.4620    0.8920
SAP         S1G    S   S1     0    .      -7.6320   -0.1450    0.4460
SAP         O2G    O   OH1    0    .      -6.5890   -1.8860    2.4320
SAP         O3G    O   OH1    0    .      -6.6120   -2.7480   -0.0510
SAP         PB     P   P      0    .      -4.0950   -0.3150   -0.5890
SAP         O1B    O   O      0    .      -4.9590    0.6250   -1.3380
SAP         O2B    O   OP    -1    .      -3.6660   -1.5330   -1.5500
SAP         O3B    O   O2     0    .      -4.9020   -0.8900    0.6800
SAP         PA     P   P      0    .      -1.8030    1.5590   -0.7380
SAP         O1A    O   O      0    .      -1.5850    1.2370   -2.1650
SAP         O2A    O   OP    -1    .      -2.4800    3.0150   -0.6130
SAP         O3A    O   O2     0    .      -2.7760    0.4580   -0.0810
SAP        O5'     O   O2     0    .      -0.3910    1.5560    0.0350
SAP        C5'     C   CH2    0    .       0.7240    2.3510   -0.3770
SAP        C4'     C   CH1    0    .       1.9000    2.1100    0.5720
SAP        O4'     O   O2     0    .       2.3690    0.7580    0.4360
SAP        C3'     C   CH1    0    .       3.0700    3.0410    0.2010
SAP        O3'     O   OH1    0    .       3.3970    3.8960    1.2990
SAP        C2'     C   CH1    0    .       4.2420    2.0760   -0.1000
SAP        O2'     O   OH1    0    .       5.4670    2.5760    0.4400
SAP        C1'     C   CH1    0    .       3.7990    0.7860    0.6370
SAP         N9     N   NR5    0    .       4.4270   -0.3930    0.0360
SAP         C8     C   CR15   0    .       3.9190   -1.1500   -0.9770
SAP         N7     N   N      0    .       4.7390   -2.1200   -1.2620
SAP         C5     C   CR56   0    .       5.8210   -2.0470   -0.4510
SAP         C6     C   CR6    0    .       6.9970   -2.8030   -0.3020
SAP         N6     N   NH2    0    .       7.2370   -3.9050   -1.1040
SAP         N1     N   N      0    .       7.8740   -2.4340    0.6250
SAP         C2     C   CR16   0    .       7.6540   -1.3830    1.3950
SAP         N3     N   N      0    .       6.5680   -0.6470    1.2920
SAP         C4     C   CR56   0    .       5.6370   -0.9350    0.3880
SAP        HOG2    H   HOH1   0    .      -7.4660   -2.2410    2.6340
SAP        HOG3    H   HOH1   0    .      -5.9990   -3.4750    0.1250
SAP        H5'1    H   HCH2   0    .       1.0120    2.0740   -1.3910
SAP        H5'2    H   HCH2   0    .       0.4470    3.4050   -0.3530
SAP        H4'     H   HCH1   0    .       1.5890    2.2930    1.6010
SAP        H3'     H   HCH1   0    .       2.8240    3.6320   -0.6810
SAP        HO3'    H   HOH1   0    .       4.1280    4.5030    1.1210
SAP        H2'     H   HCH1   0    .       4.3350    1.8990   -1.1720
SAP        HO2'    H   HOH1   0    .       5.7400    3.4280    0.0730
SAP        H1'     H   HCH1   0    .       4.0360    0.8500    1.6990
SAP         H8     H   HCR5   0    .       2.9750   -0.9710   -1.4710
SAP        HN61    H   HNH2   0    .       6.5890   -4.1650   -1.7780
SAP        HN62    H   HNH2   0    .       8.0520   -4.4190   -0.9920
SAP         H2     H   HCR6   0    .       8.3940   -1.1180    2.1360
#
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
SAP   PG      S1G   double        1.864 0.020     1.864
SAP   PG      O2G   single        1.610 0.020     1.610
SAP   PG      O3G   single        1.610 0.020     1.610
SAP   PG      O3B   single        1.609 0.020     1.609
SAP   O2G    HOG2   single        0.850 0.020     0.980
SAP   O3G    HOG3   single        0.850 0.020     0.980
SAP   PB      O1B   deloc         1.477 0.020     1.477
SAP   PB      O2B   deloc         1.529 0.022     1.529
SAP   PB      O3B   single        1.592 0.030     1.592
SAP   PB      O3A   single        1.592 0.011     1.592
SAP   PA      O1A   deloc         1.477 0.011     1.477
SAP   PA      O2A   deloc         1.529 0.022     1.529
SAP   PA      O3A   single        1.592 0.030     1.592
SAP   PA     O5'    single        1.579 0.011     1.579
SAP  O5'     C5'    single        1.443 0.010     1.443
SAP  C5'     C4'    single        1.508 0.015     1.508
SAP  C5'     H5'1   single        0.970 0.011     1.090
SAP  C5'     H5'2   single        0.970 0.011     1.090
SAP  C4'     O4'    single        1.444 0.011     1.444
SAP  C4'     C3'    single        1.526 0.011     1.526
SAP  C4'     H4'    single        0.970 0.013     1.090
SAP  O4'     C1'    single        1.416 0.013     1.416
SAP  C3'     O3'    single        1.423 0.011     1.423
SAP  C3'     C2'    single        1.531 0.012     1.531
SAP  C3'     H3'    single        0.970 0.013     1.090
SAP  O3'     HO3'   single        0.850 0.013     0.980
SAP  C2'     O2'    single        1.423 0.013     1.423
SAP  C2'     C1'    single        1.531 0.012     1.531
SAP  C2'     H2'    single        0.970 0.014     1.090
SAP  O2'     HO2'   single        0.850 0.014     0.980
SAP  C1'      N9    single        1.459 0.014     1.459
SAP  C1'     H1'    single        0.970 0.012     1.090
SAP   N9      C8    aromatic      1.370 0.012     1.370
SAP   N9      C4    aromatic      1.374 0.010     1.374
SAP   C8      N7    aromatic      1.310 0.010     1.310
SAP   C8      H8    single        0.930 0.010     1.080
SAP   N7      C5    aromatic      1.387 0.010     1.387
SAP   C5      C6    aromatic      1.409 0.010     1.409
SAP   C5      C4    aromatic      1.388 0.010     1.388
SAP   C6      N6    single        1.337 0.011     1.337
SAP   C6      N1    aromatic      1.350 0.014     1.350
SAP   N6     HN61   single        0.860 0.010     1.020
SAP   N6     HN62   single        0.860 0.010     1.020
SAP   N1      C2    aromatic      1.334 0.010     1.334
SAP   C2      N3    aromatic      1.334 0.011     1.334
SAP   C2      H2    single        0.930 0.011     1.080
SAP   N3      C4    aromatic      1.338 0.011     1.338
#
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
SAP   O3B     PG      O3G         109.50 3.000
SAP   O3B     PG      O2G         109.48 3.000
SAP   O3G     PG      O2G         109.46 3.000
SAP   O3B     PG      S1G         109.48 3.000
SAP   O3G     PG      S1G         109.44 3.000
SAP   O2G     PG      S1G         109.46 3.000
SAP  HOG2     O2G     PG          114.08 3.000
SAP  HOG3     O3G     PG          114.01 3.000
SAP   O3A     PB      O3B         101.57 1.536
SAP   O3A     PB      O2B         106.94 1.880
SAP   O3B     PB      O2B         106.94 1.880
SAP   O3A     PB      O1B         111.24 2.719
SAP   O3B     PB      O1B         111.24 2.719
SAP   O2B     PB      O1B         114.42 3.527
SAP   PB      O3B     PG          134.00 3.000
SAP  O5'      PA      O3A         102.67 2.380
SAP  O5'      PA      O2A         108.07 2.651
SAP   O3A     PA      O2A         106.94 1.880
SAP  O5'      PA      O1A         110.65 3.490
SAP   O3A     PA      O1A         111.24 2.719
SAP   O2A     PA      O1A         114.42 3.527
SAP   PA      O3A     PB          136.83 1.000
SAP  C5'     O5'      PA          121.27 1.000
SAP  H5'2    C5'     H5'1         109.47 3.000
SAP  H5'2    C5'     C4'          109.51 3.000
SAP  H5'1    C5'     C4'          109.50 3.000
SAP  H5'2    C5'     O5'          109.45 3.000
SAP  H5'1    C5'     O5'          109.44 3.000
SAP  C4'     C5'     O5'          108.83 2.328
SAP  H4'     C4'     C3'          127.39 3.000
SAP  H4'     C4'     O4'          127.39 3.000
SAP  C3'     C4'     O4'          105.22 1.298
SAP  H4'     C4'     C5'          127.39 3.000
SAP  C3'     C4'     C5'          115.19 1.760
SAP  O4'     C4'     C5'          109.53 1.437
SAP  C1'     O4'     C4'          109.40 1.607
SAP  H3'     C3'     C2'          124.08 3.000
SAP  H3'     C3'     O3'          124.08 3.000
SAP  C2'     C3'     O3'          111.83 2.669
SAP  H3'     C3'     C4'          124.08 3.000
SAP  C2'     C3'     C4'          102.49 1.000
SAP  O3'     C3'     C4'          111.06 2.498
SAP  HO3'    O3'     C3'          114.02 3.000
SAP  H2'     C2'     C1'          124.71 3.000
SAP  H2'     C2'     O2'          124.71 3.000
SAP  C1'     C2'     O2'          110.58 2.794
SAP  H2'     C2'     C3'          124.71 3.000
SAP  C1'     C2'     C3'          101.56 1.191
SAP  O2'     C2'     C3'          111.83 2.669
SAP  HO2'    O2'     C2'          114.01 3.000
SAP  H1'     C1'      N9          122.96 3.000
SAP  H1'     C1'     C2'          122.96 3.000
SAP   N9     C1'     C2'          114.08 1.531
SAP  H1'     C1'     O4'          122.96 3.000
SAP   N9     C1'     O4'          108.36 1.260
SAP  C2'     C1'     O4'          106.53 1.175
SAP   C4      N9      C8          105.72 1.000
SAP   C4      N9     C1'          126.88 1.798
SAP   C8      N9     C1'          126.78 1.942
SAP   H8      C8      N7          122.96 3.000
SAP   H8      C8      N9          122.96 3.000
SAP   N7      C8      N9          114.08 1.000
SAP   C5      N7      C8          103.68 1.000
SAP   C4      C5      C6          116.99 1.000
SAP   C4      C5      N7          110.69 1.000
SAP   C6      C5      N7          132.07 1.184
SAP   N1      C6      N6          118.11 1.227
SAP   N1      C6      C5          117.60 1.000
SAP   N6      C6      C5          123.59 1.076
SAP  HN62     N6     HN61         119.95 3.000
SAP  HN62     N6      C6          120.05 3.000
SAP  HN61     N6      C6          120.00 3.000
SAP   C2      N1      C6          118.58 1.047
SAP   H2      C2      N3          115.66 3.000
SAP   H2      C2      N1          115.66 3.000
SAP   N3      C2      N1          128.69 1.000
SAP   C4      N3      C2          112.03 2.344
SAP   N3      C4      C5          126.80 1.000
SAP   N3      C4      N9          127.04 1.148
SAP   C5      C4      N9          105.76 1.000
#
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
SAP CONST_01       C5      N7      C8      N9            0.06   0.0 0
SAP CONST_02       N7      C5      C4      N9            0.38   0.0 0
SAP CONST_03       C6      C5      C4      N9         -179.83   0.0 0
SAP CONST_04       C2      N3      C4      N9          179.63   0.0 0
SAP CONST_05       C5      C4      N9      C8           -0.35   0.0 0
SAP CONST_06       N3      C4      N9      C8         -179.45   0.0 0
SAP CONST_07       C6      C5      N7      C8          179.98   0.0 0
SAP CONST_08       C4      C5      N7      C8           -0.27   0.0 0
SAP CONST_09       C4      N9      C8      N7            0.19   0.0 0
SAP CONST_10       N1      C6      C5      N7          179.93   0.0 0
SAP CONST_11       N3      C4      C5      N7          179.65   0.0 0
SAP CONST_12       C2      N1      C6      C5            0.08   0.0 0
SAP CONST_13       C2      N3      C4      C5            0.62   0.0 0
SAP CONST_14       N3      C4      C5      C6           -0.55   0.0 0
SAP CONST_15       N3      C2      N1      C6           -0.03   0.0 0
SAP CONST_16       C4      C5      C6      N1            0.21   0.0 0
SAP CONST_17       C4      N3      C2      N1           -0.33   0.0 0
SAP CONST_18       N7      C8      N9     C1'         -179.98   0.0 0
SAP CONST_19       C5      C4      N9     C1'          179.82   0.0 0
SAP CONST_20       N3      C4      N9     C1'            0.72   0.0 0
SAP CONST_21       N6      C6      C5      N7            0.05   0.0 0
SAP CONST_22       C4      C5      C6      N6         -179.68   0.0 0
SAP CONST_23       C2      N1      C6      N6          179.97   0.0 0
SAP CONST_24       H8      C8      N9     C1'            0.05   0.0 0
SAP CONST_25       H2      C2      N1      C6         -179.98   0.0 0
SAP CONST_26      HN61     N6      C6      C5           -0.11   0.0 0
SAP CONST_27      HN62     N6      C6      C5         -180.00   0.0 0
SAP Var_01        C4'     C5'     O5'      PA         -179.99  30.0 3
SAP Var_02         O1B     PB      O3B     PG           45.07  30.0 1
SAP Var_03         O1A     PA      O3A     PB          -39.94  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
SAP chir_03  C4'     C5'     O4'     C3'    negativ
SAP chir_04  C3'     O3'     C4'     C2'    positiv
SAP chir_05  C2'     O2'     C3'     C1'    positiv
SAP chir_06  C1'     O4'      N9     C2'    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
SAP plan-1    C1' 0.020
SAP plan-1     N9 0.020
SAP plan-1     C8 0.020
SAP plan-1     N7 0.020
SAP plan-1     C5 0.020
SAP plan-1     C6 0.020
SAP plan-1     N6 0.020
SAP plan-1     N1 0.020
SAP plan-1     C2 0.020
SAP plan-1     N3 0.020
SAP plan-1     C4 0.020
SAP plan-1     H8 0.020
SAP plan-1     H2 0.020
SAP plan-2     C6 0.020
SAP plan-2     N6 0.020
SAP plan-2   HN61 0.020
SAP plan-2   HN62 0.020
