# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 22 13:59:06 2020
#
#   Inital geometry file: a 101 line input string
#   Ligand name: adenosine 3',5'-bis(dihydrogen phosphate)
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O[P](O)(O)=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
A3P        A3P 'adenosine 3',5'-bis(dihydrogen phosphate)' RNA 38 27 .
2020-10-22 2020-10-22
;
CIF prepared directly in eLBOW
;
#
data_comp_A3P
#
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
A3P         P1     P   P      0    .       3.0470   -0.3190   -2.4190
A3P         O1P    O   O      0    .       2.0800   -0.6810   -3.4790
A3P         O2P    O   OP    -1    .       4.3140    0.4220   -3.0800
A3P         O3P    O   OP    -1    .       3.5400   -1.6530   -1.6640
A3P         P2     P   P      0    .      -2.7280    0.0730   -3.8070
A3P         O4P    O   O      0    .      -2.9320   -1.3690   -3.5490
A3P         O5P    O   OP    -1    .      -4.1490    0.7730   -4.0960
A3P         O6P    O   OP    -1    .      -1.7680    0.2590   -5.0860
A3P        O5'     O   O2     0    .      -2.0450    0.7580   -2.5200
A3P        C5'     C   CH2    0    .      -0.7940    0.0970   -2.3160
A3P        C4'     C   CH1    0    .      -0.0900    0.7030   -1.1000
A3P        O4'     O   O2     0    .      -0.8880    0.5160    0.0880
A3P        C3'     C   CH1    0    .       1.2290   -0.0450   -0.8120
A3P        O3'     O   O2     0    .       2.3400    0.6660   -1.3610
A3P        C2'     C   CH1    0    .       1.3140   -0.0770    0.7320
A3P        O2'     O   OH1    0    .       2.4810    0.6120    1.1830
A3P        C1'     C   CH1    0    .       0.0330    0.6540    1.1910
A3P         N9     N   NR5    0    .      -0.5120    0.0210    2.3940
A3P         C8     C   CR15   0    .      -1.3960   -1.0150    2.4290
A3P         N7     N   N      0    .      -1.6670   -1.3260    3.6630
A3P         C5     C   CR56   0    .      -0.9720   -0.5150    4.4960
A3P         C6     C   CR6    0    .      -0.8730   -0.3820    5.8910
A3P         N6     N   NH2    0    .      -1.5880   -1.2150    6.7340
A3P         N1     N   N      0    .      -0.0720    0.5580    6.3830
A3P         C2     C   CR16   0    .       0.6120    1.3570    5.5860
A3P         N3     N   N      0    .       0.5470    1.2730    4.2740
A3P         C4     C   CR56   0    .      -0.2260    0.3620    3.6910
A3P        H5'1    H   HCH2   0    .      -0.1680    0.2230   -3.1990
A3P        H5'2    H   HCH2   0    .      -0.9680   -0.9640   -2.1430
A3P        H4'     H   HCH1   0    .       0.1030    1.7630   -1.2650
A3P        H3'     H   HCH1   0    .       1.1890   -1.0580   -1.2140
A3P        H2'     H   HCH1   0    .       1.3150   -1.1050    1.0930
A3P        HO2'    H   HOH1   0    .       2.4810    0.5600    2.1490
A3P        H1'     H   HCH1   0    .       0.2440    1.7070    1.3790
A3P         H8     H   HCR5   0    .      -1.8110   -1.5050    1.5610
A3P        HN61    H   HNH2   0    .      -1.5080   -1.1160    7.6960
A3P        HN62    H   HNH2   0    .      -2.1710   -1.8950    6.3640
A3P         H2     H   HCR6   0    .       1.2510    2.1080    6.0270
#
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
A3P   P1      O1P   deloc         1.480 0.020     1.480
A3P   P1      O2P   deloc         1.610 0.020     1.610
A3P   P1      O3P   deloc         1.610 0.020     1.610
A3P   P1     O3'    single        1.609 0.020     1.609
A3P   P2      O4P   deloc         1.479 0.020     1.479
A3P   P2      O5P   deloc         1.610 0.020     1.610
A3P   P2      O6P   deloc         1.610 0.020     1.610
A3P   P2     O5'    single        1.610 0.020     1.610
A3P  O5'     C5'    single        1.430 0.020     1.430
A3P  C5'     C4'    single        1.508 0.020     1.508
A3P  C5'     H5'1   single        0.970 0.011     1.090
A3P  C5'     H5'2   single        0.970 0.011     1.090
A3P  C4'     O4'    single        1.444 0.011     1.444
A3P  C4'     C3'    single        1.527 0.011     1.527
A3P  C4'     H4'    single        0.970 0.015     1.090
A3P  O4'     C1'    single        1.416 0.015     1.416
A3P  C3'     O3'    single        1.453 0.011     1.453
A3P  C3'     C2'    single        1.527 0.010     1.527
A3P  C3'     H3'    single        0.970 0.012     1.090
A3P  C2'     O2'    single        1.423 0.012     1.423
A3P  C2'     C1'    single        1.531 0.012     1.531
A3P  C2'     H2'    single        0.970 0.014     1.090
A3P  O2'     HO2'   single        0.850 0.014     0.980
A3P  C1'      N9    single        1.459 0.014     1.459
A3P  C1'     H1'    single        0.970 0.012     1.090
A3P   N9      C8    aromatic      1.370 0.012     1.370
A3P   N9      C4    aromatic      1.374 0.010     1.374
A3P   C8      N7    aromatic      1.310 0.010     1.310
A3P   C8      H8    single        0.930 0.010     1.080
A3P   N7      C5    aromatic      1.387 0.010     1.387
A3P   C5      C6    aromatic      1.409 0.010     1.409
A3P   C5      C4    aromatic      1.388 0.010     1.388
A3P   C6      N6    single        1.337 0.011     1.337
A3P   C6      N1    aromatic      1.350 0.014     1.350
A3P   N6     HN61   single        0.860 0.010     1.020
A3P   N6     HN62   single        0.860 0.010     1.020
A3P   N1      C2    aromatic      1.334 0.010     1.334
A3P   C2      N3    aromatic      1.334 0.011     1.334
A3P   C2      H2    single        0.930 0.011     1.080
A3P   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
A3P  O3'      P1      O3P         109.47 3.000
A3P  O3'      P1      O2P         109.51 3.000
A3P   O3P     P1      O2P         109.45 3.000
A3P  O3'      P1      O1P         109.49 3.000
A3P   O3P     P1      O1P         109.47 3.000
A3P   O2P     P1      O1P         109.44 3.000
A3P  O5'      P2      O6P         109.45 3.000
A3P  O5'      P2      O5P         109.44 3.000
A3P   O6P     P2      O5P         109.48 3.000
A3P  O5'      P2      O4P         109.50 3.000
A3P   O6P     P2      O4P         109.48 3.000
A3P   O5P     P2      O4P         109.48 3.000
A3P  C5'     O5'      P2          106.77 3.000
A3P  H5'2    C5'     H5'1         109.46 3.000
A3P  H5'2    C5'     C4'          109.46 3.000
A3P  H5'1    C5'     C4'          109.50 3.000
A3P  H5'2    C5'     O5'          109.47 3.000
A3P  H5'1    C5'     O5'          109.49 3.000
A3P  C4'     C5'     O5'          109.44 3.000
A3P  H4'     C4'     C3'          127.70 3.000
A3P  H4'     C4'     O4'          127.70 3.000
A3P  C3'     C4'     O4'          104.61 1.570
A3P  H4'     C4'     C5'          127.70 3.000
A3P  C3'     C4'     C5'          114.98 2.006
A3P  O4'     C4'     C5'          109.53 1.437
A3P  C1'     O4'     C4'          109.40 1.607
A3P  H3'     C3'     C2'          128.48 3.000
A3P  H3'     C3'     O3'          128.48 3.000
A3P  C2'     C3'     O3'          110.56 3.000
A3P  H3'     C3'     C4'          128.48 3.000
A3P  C2'     C3'     C4'          103.03 1.280
A3P  O3'     C3'     C4'          110.59 3.000
A3P  C3'     O3'      P1          106.84 3.000
A3P  H2'     C2'     C1'          124.71 3.000
A3P  H2'     C2'     O2'          124.71 3.000
A3P  C1'     C2'     O2'          110.58 2.794
A3P  H2'     C2'     C3'          124.71 3.000
A3P  C1'     C2'     C3'          100.55 1.117
A3P  O2'     C2'     C3'          110.96 2.888
A3P  HO2'    O2'     C2'          106.82 3.000
A3P  H1'     C1'      N9          122.96 3.000
A3P  H1'     C1'     C2'          122.96 3.000
A3P   N9     C1'     C2'          114.08 1.531
A3P  H1'     C1'     O4'          122.96 3.000
A3P   N9     C1'     O4'          108.36 1.260
A3P  C2'     C1'     O4'          106.53 1.175
A3P   C4      N9      C8          105.72 1.000
A3P   C4      N9     C1'          126.88 1.798
A3P   C8      N9     C1'          126.78 1.942
A3P   H8      C8      N7          122.96 3.000
A3P   H8      C8      N9          122.96 3.000
A3P   N7      C8      N9          114.08 1.000
A3P   C5      N7      C8          103.68 1.000
A3P   C4      C5      C6          116.99 1.000
A3P   C4      C5      N7          110.69 1.000
A3P   C6      C5      N7          132.07 1.184
A3P   N1      C6      N6          118.11 1.227
A3P   N1      C6      C5          117.60 1.000
A3P   N6      C6      C5          123.59 1.076
A3P  HN62     N6     HN61         119.98 3.000
A3P  HN62     N6      C6          120.03 3.000
A3P  HN61     N6      C6          119.99 3.000
A3P   C2      N1      C6          118.58 1.047
A3P   H2      C2      N3          115.66 3.000
A3P   H2      C2      N1          115.66 3.000
A3P   N3      C2      N1          128.69 1.000
A3P   C4      N3      C2          112.03 2.344
A3P   N3      C4      C5          126.80 1.000
A3P   N3      C4      N9          127.04 1.148
A3P   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
A3P CONST_01       C5      N7      C8      N9           -0.24   0.0 0
A3P CONST_02       N7      C5      C4      N9           -0.31   0.0 0
A3P CONST_03       C6      C5      C4      N9         -179.64   0.0 0
A3P CONST_04       C2      N3      C4      N9          179.91   0.0 0
A3P CONST_05       C5      C4      N9      C8            0.17   0.0 0
A3P CONST_06       N3      C4      N9      C8         -179.91   0.0 0
A3P CONST_07       C6      C5      N7      C8          179.51   0.0 0
A3P CONST_08       C4      C5      N7      C8            0.34   0.0 0
A3P CONST_09       C4      N9      C8      N7            0.04   0.0 0
A3P CONST_10       N1      C6      C5      N7         -179.62   0.0 0
A3P CONST_11       N3      C4      C5      N7          179.75   0.0 0
A3P CONST_12       C2      N1      C6      C5            0.38   0.0 0
A3P CONST_13       C2      N3      C4      C5           -0.18   0.0 0
A3P CONST_14       N3      C4      C5      C6            0.43   0.0 0
A3P CONST_15       N3      C2      N1      C6           -0.13   0.0 0
A3P CONST_16       C4      C5      C6      N1           -0.53   0.0 0
A3P CONST_17       C4      N3      C2      N1            0.02   0.0 0
A3P CONST_18       N7      C8      N9     C1'         -179.98   0.0 0
A3P CONST_19       C5      C4      N9     C1'         -179.82   0.0 0
A3P CONST_20       N3      C4      N9     C1'            0.11   0.0 0
A3P CONST_21       N6      C6      C5      N7            0.69   0.0 0
A3P CONST_22       C4      C5      C6      N6          179.79   0.0 0
A3P CONST_23       C2      N1      C6      N6         -179.93   0.0 0
A3P CONST_24       H8      C8      N9     C1'           -0.03   0.0 0
A3P CONST_25       H2      C2      N1      C6          179.96   0.0 0
A3P CONST_26      HN61     N6      C6      C5          179.71   0.0 0
A3P CONST_27      HN62     N6      C6      C5           -0.51   0.0 0
A3P Var_01        C4'     C5'     O5'      P2         -179.96  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
A3P chir_01  C4'     C5'     O4'     C3'    negativ
A3P chir_02  C3'     O3'     C2'     C4'    negativ
A3P chir_03  C2'     O2'     C1'     C3'    negativ
A3P chir_04  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
A3P plan-1    C1' 0.020
A3P plan-1     N9 0.020
A3P plan-1     C8 0.020
A3P plan-1     N7 0.020
A3P plan-1     C5 0.020
A3P plan-1     C6 0.020
A3P plan-1     N6 0.020
A3P plan-1     N1 0.020
A3P plan-1     C2 0.020
A3P plan-1     N3 0.020
A3P plan-1     C4 0.020
A3P plan-1     H8 0.020
A3P plan-1     H2 0.020
A3P plan-2     C6 0.020
A3P plan-2     N6 0.020
A3P plan-2   HN61 0.020
A3P plan-2   HN62 0.020
