# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Oct 23 14:31:53 2020
#
#   Inital geometry file: a 112 line input string
#   Ligand name: 2'-deoxyadenosine 5'-(tetrahydrogen triphosphate)
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
#
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
DTP        DTP '2'-deoxyadenosine 5'-(tetrahydrogen triphosphate)' ligand 42 30 .
2020-10-23 2020-10-23
;
CIF prepared directly in eLBOW
;
#
data_comp_DTP
#
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
DTP         PG     P   P      0    .       1.1730   -0.2530   -6.6990
DTP         O1G    O   O      0    .       1.9470    0.9790   -6.4310
DTP         O2G    O   OP    -1    .       1.9490   -1.1480   -7.7890
DTP         O3G    O   OP    -1    .      -0.2810    0.1390   -7.2650
DTP         PB     P   P      0    .       0.2290   -0.1410   -4.2950
DTP         O1B    O   O      0    .      -1.0940    0.2170   -4.8530
DTP         O2B    O   OP    -1    .       1.0860    1.1970   -4.0430
DTP         O3B    O   O2     0    .       1.0090   -1.0920   -5.3340
DTP         PA     P   P      0    .      -0.7520    0.0820   -1.9140
DTP         O1A    O   O      0    .       0.0500    1.3090   -1.7200
DTP         O2A    O   OP    -1    .      -2.1750    0.4680   -2.5610
DTP         O3A    O   O2     0    .       0.0290   -0.9210   -2.9000
DTP        O5'     O   O2     0    .      -0.9870   -0.6360   -0.4930
DTP        C5'     C   CH2    0    .      -1.6820    0.2980    0.3330
DTP        C4'     C   CH1    0    .      -1.9370   -0.3250    1.7070
DTP        O4'     O   O2     0    .      -0.6920   -0.5550    2.4040
DTP        C3'     C   CH1    0    .      -2.6910    0.6690    2.6260
DTP        O3'     O   OH1    0    .      -4.1030    0.5770    2.4280
DTP        C2'     C   CH2    0    .      -2.2980    0.1680    4.0370
DTP        C1'     C   CH1    0    .      -1.0090   -0.6430    3.8040
DTP         N9     N   NR5    0    .       0.0840   -0.0780    4.5980
DTP         C8     C   CR15   0    .       0.9490    0.8980    4.2010
DTP         N7     N   N      0    .       1.7940    1.1570    5.1560
DTP         C5     C   CR56   0    .       1.5240    0.3700    6.2250
DTP         C6     C   CR6    0    .       2.0910    0.2060    7.5000
DTP         N6     N   NH2    0    .       3.1760    0.9680    7.8950
DTP         N1     N   N      0    .       1.5580   -0.6940    8.3190
DTP         C2     C   CR16   0    .       0.5230   -1.4260    7.9500
DTP         N3     N   N      0    .      -0.0360   -1.3100    6.7640
DTP         C4     C   CR56   0    .       0.4270   -0.4360    5.8780
DTP        H5'1    H   HCH2   0    .      -2.6340    0.5570   -0.1300
DTP        H5'2    H   HCH2   0    .      -1.0780    1.1990    0.4500
DTP        H4'     H   HCH1   0    .      -2.4970   -1.2550    1.6060
DTP        H3'     H   HCH1   0    .      -2.3430    1.6890    2.4640
DTP        HO3'    H   HOH1   0    .      -4.5160    1.1490    3.0900
DTP        H2'1    H   HCH2   0    .      -3.0810   -0.4690    4.4470
DTP        H2'2    H   HCH2   0    .      -2.1040    1.0100    4.7010
DTP        H1'     H   HCH1   0    .      -1.1700   -1.6840    4.0830
DTP         H8     H   HCR5   0    .       0.9340    1.3840    3.2370
DTP        HN61    H   HNH2   0    .       3.5570    0.8490    8.7800
DTP        HN62    H   HNH2   0    .       3.5590    1.6200    7.2870
DTP         H2     H   HCR6   0    .       0.1210   -2.1460    8.6470
#
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
DTP   PG      O1G   deloc         1.491 0.020     1.491
DTP   PG      O2G   deloc         1.533 0.032     1.533
DTP   PG      O3G   deloc         1.533 0.028     1.533
DTP   PG      O3B   single        1.600 0.028     1.600
DTP   PB      O1B   deloc         1.477 0.022     1.477
DTP   PB      O2B   deloc         1.529 0.022     1.529
DTP   PB      O3B   single        1.592 0.030     1.592
DTP   PB      O3A   single        1.592 0.011     1.592
DTP   PA      O1A   deloc         1.477 0.011     1.477
DTP   PA      O2A   deloc         1.529 0.022     1.529
DTP   PA      O3A   single        1.592 0.030     1.592
DTP   PA     O5'    single        1.579 0.011     1.579
DTP  O5'     C5'    single        1.443 0.010     1.443
DTP  C5'     C4'    single        1.508 0.015     1.508
DTP  C5'     H5'1   single        0.970 0.011     1.090
DTP  C5'     H5'2   single        0.970 0.011     1.090
DTP  C4'     O4'    single        1.444 0.011     1.444
DTP  C4'     C3'    single        1.527 0.011     1.527
DTP  C4'     H4'    single        0.970 0.012     1.090
DTP  O4'     C1'    single        1.418 0.012     1.418
DTP  C3'     O3'    single        1.428 0.013     1.428
DTP  C3'     C2'    single        1.523 0.010     1.523
DTP  C3'     H3'    single        0.970 0.011     1.090
DTP  O3'     HO3'   single        0.850 0.011     0.980
DTP  C2'     C1'    single        1.521 0.011     1.521
DTP  C2'     H2'1   single        0.970 0.012     1.090
DTP  C2'     H2'2   single        0.970 0.012     1.090
DTP  C1'      N9    single        1.457 0.012     1.457
DTP  C1'     H1'    single        0.970 0.011     1.090
DTP   N9      C8    aromatic      1.370 0.011     1.370
DTP   N9      C4    aromatic      1.374 0.010     1.374
DTP   C8      N7    aromatic      1.310 0.010     1.310
DTP   C8      H8    single        0.930 0.010     1.080
DTP   N7      C5    aromatic      1.387 0.010     1.387
DTP   C5      C6    aromatic      1.409 0.010     1.409
DTP   C5      C4    aromatic      1.388 0.010     1.388
DTP   C6      N6    single        1.337 0.011     1.337
DTP   C6      N1    aromatic      1.350 0.014     1.350
DTP   N6     HN61   single        0.860 0.010     1.020
DTP   N6     HN62   single        0.860 0.010     1.020
DTP   N1      C2    aromatic      1.334 0.010     1.334
DTP   C2      N3    aromatic      1.334 0.011     1.334
DTP   C2      H2    single        0.930 0.011     1.080
DTP   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
DTP   O3B     PG      O3G         104.48 1.135
DTP   O3B     PG      O2G         104.48 1.135
DTP   O3G     PG      O2G         108.70 2.785
DTP   O3B     PG      O1G         110.47 1.644
DTP   O3G     PG      O1G         113.32 2.534
DTP   O2G     PG      O1G         113.32 2.534
DTP   O3A     PB      O3B         101.57 1.536
DTP   O3A     PB      O2B         106.94 1.880
DTP   O3B     PB      O2B         106.94 1.880
DTP   O3A     PB      O1B         111.24 2.719
DTP   O3B     PB      O1B         111.24 2.719
DTP   O2B     PB      O1B         114.42 3.527
DTP   PB      O3B     PG          139.87 1.000
DTP  O5'      PA      O3A         102.67 2.380
DTP  O5'      PA      O2A         108.07 2.651
DTP   O3A     PA      O2A         106.94 1.880
DTP  O5'      PA      O1A         110.65 3.490
DTP   O3A     PA      O1A         111.24 2.719
DTP   O2A     PA      O1A         114.42 3.527
DTP   PA      O3A     PB          136.83 1.000
DTP  C5'     O5'      PA          121.27 1.000
DTP  H5'2    C5'     H5'1         109.44 3.000
DTP  H5'2    C5'     C4'          109.40 3.000
DTP  H5'1    C5'     C4'          109.43 3.000
DTP  H5'2    C5'     O5'          109.44 3.000
DTP  H5'1    C5'     O5'          109.57 3.000
DTP  C4'     C5'     O5'          108.83 2.328
DTP  H4'     C4'     C3'          127.18 3.000
DTP  H4'     C4'     O4'          127.18 3.000
DTP  C3'     C4'     O4'          105.64 1.084
DTP  H4'     C4'     C5'          127.18 3.000
DTP  C3'     C4'     C5'          114.72 1.915
DTP  O4'     C4'     C5'          109.53 1.437
DTP  C1'     O4'     C4'          109.55 1.311
DTP  H3'     C3'     C2'          124.52 3.000
DTP  H3'     C3'     O3'          124.52 3.000
DTP  C2'     C3'     O3'          110.97 2.419
DTP  H3'     C3'     C4'          124.52 3.000
DTP  C2'     C3'     C4'          102.59 1.017
DTP  O3'     C3'     C4'          110.26 2.320
DTP  HO3'    O3'     C3'          106.80 3.000
DTP  H2'2    C2'     H2'1         110.51 3.000
DTP  H2'2    C2'     C1'          110.48 3.000
DTP  H2'1    C2'     C1'          110.51 3.000
DTP  H2'2    C2'     C3'          110.52 3.000
DTP  H2'1    C2'     C3'          110.47 3.000
DTP  C1'     C2'     C3'          102.57 1.360
DTP  H1'     C1'      N9          122.64 3.000
DTP  H1'     C1'     C2'          122.64 3.000
DTP   N9     C1'     C2'          114.72 1.415
DTP  H1'     C1'     O4'          122.64 3.000
DTP   N9     C1'     O4'          108.17 1.038
DTP  C2'     C1'     O4'          106.23 1.052
DTP   C4      N9      C8          105.72 1.000
DTP   C4      N9     C1'          126.78 2.496
DTP   C8      N9     C1'          126.87 2.531
DTP   H8      C8      N7          122.96 3.000
DTP   H8      C8      N9          122.96 3.000
DTP   N7      C8      N9          114.08 1.000
DTP   C5      N7      C8          103.68 1.000
DTP   C4      C5      C6          116.99 1.000
DTP   C4      C5      N7          110.69 1.000
DTP   C6      C5      N7          132.07 1.184
DTP   N1      C6      N6          118.11 1.227
DTP   N1      C6      C5          117.60 1.000
DTP   N6      C6      C5          123.59 1.076
DTP  HN62     N6     HN61         119.91 3.000
DTP  HN62     N6      C6          120.05 3.000
DTP  HN61     N6      C6          120.04 3.000
DTP   C2      N1      C6          118.58 1.047
DTP   H2      C2      N3          115.66 3.000
DTP   H2      C2      N1          115.66 3.000
DTP   N3      C2      N1          128.69 1.000
DTP   C4      N3      C2          112.03 2.344
DTP   N3      C4      C5          126.80 1.000
DTP   N3      C4      N9          127.04 1.148
DTP   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
DTP CONST_01       C5      N7      C8      N9           -0.20   0.0 0
DTP CONST_02       N7      C5      C4      N9           -0.38   0.0 0
DTP CONST_03       C6      C5      C4      N9         -179.68   0.0 0
DTP CONST_04       C2      N3      C4      N9         -180.00   0.0 0
DTP CONST_05       C5      C4      N9      C8            0.27   0.0 0
DTP CONST_06       N3      C4      N9      C8         -179.89   0.0 0
DTP CONST_07       C6      C5      N7      C8          179.49   0.0 0
DTP CONST_08       C4      C5      N7      C8            0.36   0.0 0
DTP CONST_09       C4      N9      C8      N7           -0.05   0.0 0
DTP CONST_10       N1      C6      C5      N7         -179.56   0.0 0
DTP CONST_11       N3      C4      C5      N7          179.75   0.0 0
DTP CONST_12       C2      N1      C6      C5            0.29   0.0 0
DTP CONST_13       C2      N3      C4      C5           -0.17   0.0 0
DTP CONST_14       N3      C4      C5      C6            0.45   0.0 0
DTP CONST_15       N3      C2      N1      C6            0.00   0.0 0
DTP CONST_16       C4      C5      C6      N1           -0.51   0.0 0
DTP CONST_17       C4      N3      C2      N1           -0.06   0.0 0
DTP CONST_18       N7      C8      N9     C1'         -179.94   0.0 0
DTP CONST_19       C5      C4      N9     C1'         -179.84   0.0 0
DTP CONST_20       N3      C4      N9     C1'           -0.00   0.0 0
DTP CONST_21       N6      C6      C5      N7            0.69   0.0 0
DTP CONST_22       C4      C5      C6      N6          179.74   0.0 0
DTP CONST_23       C2      N1      C6      N6         -179.96   0.0 0
DTP CONST_24       H8      C8      N9     C1'            0.10   0.0 0
DTP CONST_25       H2      C2      N1      C6          180.00   0.0 0
DTP CONST_26      HN61     N6      C6      C5          179.71   0.0 0
DTP CONST_27      HN62     N6      C6      C5           -0.48   0.0 0
DTP Var_01        C4'     C5'     O5'      PA         -179.94  30.0 3
DTP Var_02         O1B     PB      O3B     PG           60.07  30.0 1
DTP Var_03         O1A     PA      O3A     PB          -59.91  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
DTP chir_03  C4'     C5'     O4'     C3'    negativ
DTP chir_04  C3'     O3'     C4'     C2'    positiv
DTP chir_05  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
DTP plan-1    C1' 0.020
DTP plan-1     N9 0.020
DTP plan-1     C8 0.020
DTP plan-1     N7 0.020
DTP plan-1     C5 0.020
DTP plan-1     C6 0.020
DTP plan-1     N6 0.020
DTP plan-1     N1 0.020
DTP plan-1     C2 0.020
DTP plan-1     N3 0.020
DTP plan-1     C4 0.020
DTP plan-1     H8 0.020
DTP plan-1     H2 0.020
DTP plan-2     C6 0.020
DTP plan-2     N6 0.020
DTP plan-2   HN61 0.020
DTP plan-2   HN62 0.020
