# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Oct 21 17:37:46 2020
#
#   Inital geometry file: a 99 line input string
#   Ligand name: 6-(phosphonooxy)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c(O[P](O)(O)=O)ncnc23
#
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
IMO        IMO '6-(phosphonooxy)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine' ligand 37 27 .
2020-10-21 2020-10-21
;
CIF prepared directly in eLBOW
;
#
data_comp_IMO
#
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
IMO         P      P   P      0    .      -1.1040   -0.6310    5.4250
IMO         O1     O   OP    -1    .      -2.3050   -0.9030    6.4620
IMO         C2     C   CR16   0    .       1.9450    1.6920    3.5330
IMO        C1'     C   CH1    0    .       1.1770    0.4550   -0.7110
IMO        C2'     C   CH1    0    .       1.9490   -0.8750   -0.8550
IMO        C3'     C   CH1    0    .       1.9330   -1.1560   -2.3740
IMO        C4'     C   CH1    0    .       1.1530    0.0350   -2.9720
IMO        C5'     C   CH2    0    .       0.2720   -0.4240   -4.1350
IMO         O2     O   OP    -1    .      -1.1640   -1.7170    4.2380
IMO         O3     O   O      0    .       0.1910   -0.7420    6.1310
IMO         PA     P   P      0    .      -1.3890    0.1280   -5.8370
IMO         O1A    O   OP    -1    .      -2.2800    1.3280   -6.4350
IMO         O2A    O   OP    -1    .      -0.4290   -0.4540   -6.9910
IMO         O3A    O   O      0    .      -2.2770   -0.9480   -5.3440
IMO        O5'     O   O2     0    .      -0.4900    0.6810   -4.6210
IMO        O4'     O   O2     0    .       0.3350    0.5210   -1.8820
IMO         N9     N   NR5    0    .       0.3630    0.4430    0.5050
IMO         C4     C   CR56   0    .       0.7590    0.8610    1.7510
IMO         N3     N   N      0    .       1.8730    1.3770    2.2570
IMO         N1     N   N      0    .       0.9330    1.5220    4.3640
IMO         C6     C   CR6    0    .      -0.2210    1.0180    3.9470
IMO         O6     O   O2     0    .      -1.2540    0.8470    4.8070
IMO         C5     C   CR56   0    .      -0.3480    0.6660    2.5950
IMO         N7     N   N      0    .      -1.3410    0.1420    1.8360
IMO         C8     C   CR15   0    .      -0.9250    0.0110    0.6090
IMO        O2'     O   OH1    0    .       3.2910   -0.7310   -0.3860
IMO        O3'     O   OH1    0    .       3.2650   -1.1910   -2.8900
IMO         H2     H   HCR6   0    .       2.8670    2.1060    3.9150
IMO        H1'     H   HCH1   0    .       1.8710    1.2960   -0.6950
IMO        H2'     H   HCH1   0    .       1.4390   -1.6720   -0.3140
IMO        H3'     H   HCH1   0    .       1.4180   -2.0930   -2.5840
IMO        H4'     H   HCH1   0    .       1.8430    0.8110   -3.3030
IMO        H5'1    H   HCH2   0    .       0.9020   -0.8110   -4.9360
IMO        H5'2    H   HCH2   0    .      -0.4010   -1.2090   -3.7920
IMO         H81    H   HCR5   0    .      -1.5140   -0.3820   -0.2050
IMO        HO'2    H   HOH1   0    .       3.7380   -1.5720   -0.5570
IMO        HO'3    H   HOH1   0    .       3.7120   -1.9340   -2.4610
#
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
IMO   P       O1    deloc         1.533 0.020     1.533
IMO   P       O2    deloc         1.533 0.028     1.533
IMO   P       O3    deloc         1.491 0.028     1.491
IMO   P       O6    single        1.578 0.032     1.578
IMO   C2      N3    aromatic      1.334 0.011     1.334
IMO   C2      N1    aromatic      1.334 0.011     1.334
IMO   C2      H2    single        0.930 0.011     1.080
IMO  C1'     C2'    single        1.531 0.011     1.531
IMO  C1'     O4'    single        1.416 0.014     1.416
IMO  C1'      N9    single        1.459 0.011     1.459
IMO  C1'     H1'    single        0.970 0.012     1.090
IMO  C2'     C3'    single        1.531 0.012     1.531
IMO  C2'     O2'    single        1.423 0.013     1.423
IMO  C2'     H2'    single        0.970 0.012     1.090
IMO  C3'     C4'    single        1.526 0.012     1.526
IMO  C3'     O3'    single        1.423 0.013     1.423
IMO  C3'     H3'    single        0.970 0.012     1.090
IMO  C4'     C5'    single        1.508 0.012     1.508
IMO  C4'     O4'    single        1.444 0.011     1.444
IMO  C4'     H4'    single        0.970 0.011     1.090
IMO  C5'     O5'    single        1.443 0.011     1.443
IMO  C5'     H5'1   single        0.970 0.015     1.090
IMO  C5'     H5'2   single        0.970 0.015     1.090
IMO   PA      O1A   deloc         1.533 0.015     1.533
IMO   PA      O2A   deloc         1.533 0.028     1.533
IMO   PA      O3A   deloc         1.491 0.028     1.491
IMO   PA     O5'    single        1.601 0.032     1.601
IMO   N9      C4    aromatic      1.374 0.032     1.374
IMO   N9      C8    aromatic      1.370 0.010     1.370
IMO   C4      N3    aromatic      1.338 0.010     1.338
IMO   C4      C5    aromatic      1.388 0.012     1.388
IMO   N1      C6    aromatic      1.319 0.011     1.319
IMO   C6      O6    single        1.376 0.012     1.376
IMO   C6      C5    aromatic      1.416 0.010     1.416
IMO   C5      N7    aromatic      1.387 0.021     1.387
IMO   N7      C8    aromatic      1.310 0.010     1.310
IMO   C8      H81   single        0.930 0.010     1.080
IMO  O2'     HO'2   single        0.850 0.010     0.980
IMO  O3'     HO'3   single        0.850 0.010     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
IMO   O6      P       O3          110.68 2.023
IMO   O6      P       O2          104.86 2.444
IMO   O3      P       O2          113.32 2.534
IMO   O6      P       O1          104.86 2.444
IMO   O3      P       O1          113.32 2.534
IMO   O2      P       O1          108.70 2.785
IMO   H2      C2      N1          115.66 3.000
IMO   H2      C2      N3          115.66 3.000
IMO   N1      C2      N3          128.69 1.000
IMO  H1'     C1'      N9          125.82 3.000
IMO  H1'     C1'     O4'          125.82 3.000
IMO   N9     C1'     O4'          108.36 1.260
IMO  H1'     C1'     C2'          125.82 3.000
IMO   N9     C1'     C2'          114.08 1.531
IMO  O4'     C1'     C2'          106.53 1.175
IMO  H2'     C2'     O2'          124.08 3.000
IMO  H2'     C2'     C3'          124.08 3.000
IMO  O2'     C2'     C3'          111.83 2.669
IMO  H2'     C2'     C1'          124.08 3.000
IMO  O2'     C2'     C1'          110.58 2.794
IMO  C3'     C2'     C1'          101.56 1.191
IMO  H3'     C3'     O3'          124.47 3.000
IMO  H3'     C3'     C4'          124.47 3.000
IMO  O3'     C3'     C4'          111.06 2.498
IMO  H3'     C3'     C2'          124.47 3.000
IMO  O3'     C3'     C2'          111.83 2.669
IMO  C4'     C3'     C2'          102.49 1.000
IMO  H4'     C4'     O4'          125.23 3.000
IMO  H4'     C4'     C5'          125.23 3.000
IMO  O4'     C4'     C5'          109.53 1.437
IMO  H4'     C4'     C3'          125.23 3.000
IMO  O4'     C4'     C3'          105.22 1.298
IMO  C5'     C4'     C3'          115.19 1.760
IMO  H5'2    C5'     H5'1         109.42 3.000
IMO  H5'2    C5'     O5'          109.58 3.000
IMO  H5'1    C5'     O5'          109.46 3.000
IMO  H5'2    C5'     C4'          109.43 3.000
IMO  H5'1    C5'     C4'          109.41 3.000
IMO  O5'     C5'     C4'          108.83 2.328
IMO  O5'      PA      O3A         106.57 2.496
IMO  O5'      PA      O2A         106.53 2.580
IMO   O3A     PA      O2A         113.32 2.534
IMO  O5'      PA      O1A         106.53 2.580
IMO   O3A     PA      O1A         113.32 2.534
IMO   O2A     PA      O1A         108.70 2.785
IMO   PA     O5'     C5'          117.05 1.000
IMO  C4'     O4'     C1'          109.40 1.607
IMO   C8      N9      C4          105.72 1.000
IMO   C8      N9     C1'          126.78 1.942
IMO   C4      N9     C1'          126.88 1.798
IMO   C5      C4      N3          126.80 1.000
IMO   C5      C4      N9          105.76 1.000
IMO   N3      C4      N9          127.04 1.148
IMO   C4      N3      C2          112.03 2.344
IMO   C6      N1      C2          115.86 1.457
IMO   C5      C6      O6          120.73 3.000
IMO   C5      C6      N1          120.24 1.000
IMO   O6      C6      N1          120.77 3.000
IMO   C6      O6      P           106.78 3.000
IMO   N7      C5      C6          133.49 1.505
IMO   N7      C5      C4          110.69 1.000
IMO   C6      C5      C4          115.47 1.000
IMO   C8      N7      C5          103.68 1.000
IMO   H81     C8      N7          122.96 3.000
IMO   H81     C8      N9          122.96 3.000
IMO   N7      C8      N9          114.08 1.000
IMO  HO'2    O2'     C2'          106.75 3.000
IMO  HO'3    O3'     C3'          106.82 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
IMO CONST_01       N9      C4      N3      C2          179.62   0.0 0
IMO CONST_02       C5      C4      N3      C2            0.54   0.0 0
IMO CONST_03       C5      C6      N1      C2           -0.01   0.0 0
IMO CONST_04       C6      C5      C4      N9         -179.84   0.0 0
IMO CONST_05       N7      C5      C4      N9            0.33   0.0 0
IMO CONST_06       C5      N7      C8      N9            0.03   0.0 0
IMO CONST_07       N7      C8      N9      C4            0.18   0.0 0
IMO CONST_08       N1      C2      N3      C4           -0.30   0.0 0
IMO CONST_09       N1      C6      C5      C4            0.26   0.0 0
IMO CONST_10       C8      N7      C5      C4           -0.22   0.0 0
IMO CONST_11       C6      N1      C2      N3            0.03   0.0 0
IMO CONST_12       C8      N9      C4      N3         -179.47   0.0 0
IMO CONST_13       C6      C5      C4      N3           -0.52   0.0 0
IMO CONST_14       N7      C5      C4      N3          179.65   0.0 0
IMO CONST_15       N7      C5      C6      N1         -179.97   0.0 0
IMO CONST_16       C8      N7      C5      C6          179.99   0.0 0
IMO CONST_17       C8      N9      C4      C5           -0.31   0.0 0
IMO CONST_18       N3      C4      N9     C1'            0.72   0.0 0
IMO CONST_19       C5      C4      N9     C1'          179.89   0.0 0
IMO CONST_20       N7      C8      N9     C1'          179.99   0.0 0
IMO CONST_21       O6      C6      N1      C2          179.99   0.0 0
IMO CONST_22       O6      C6      C5      C4         -179.75   0.0 0
IMO CONST_23       N7      C5      C6      O6            0.02   0.0 0
IMO CONST_24       H81     C8      N9     C1'           -0.00   0.0 0
IMO CONST_25       H2      C2      N3      C4          179.74   0.0 0
IMO Var_01         N1      C6      O6      P           -89.96  30.0 1
IMO Var_02         O1A     PA     O5'     C5'          179.95  30.0 3
IMO Var_03        H5'1    C5'     O5'      PA           60.05  30.0 1
#
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
IMO chir_01  C1'     C2'     O4'      N9    negativ
IMO chir_02  C2'     O2'     C3'     C1'    positiv
IMO chir_03  C3'     O3'     C4'     C2'    positiv
IMO chir_04  C4'     O4'     C3'     C5'    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
IMO plan-1     C2 0.020
IMO plan-1    C1' 0.020
IMO plan-1     N9 0.020
IMO plan-1     C4 0.020
IMO plan-1     N3 0.020
IMO plan-1     N1 0.020
IMO plan-1     C6 0.020
IMO plan-1     O6 0.020
IMO plan-1     C5 0.020
IMO plan-1     N7 0.020
IMO plan-1     C8 0.020
IMO plan-1     H2 0.020
IMO plan-1    H81 0.020
