# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Oct 22 13:59:57 2020
#
#   Inital geometry file: a 115 line input string
#   Ligand name: 2'-deoxycytidine 5'-(tetrahydrogen triphosphate)
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2
#
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
DCP        DCP '2'-deoxycytidine 5'-(tetrahydrogen triphosphate)' ligand 40 28 .
2020-10-22 2020-10-22
;
CIF prepared directly in eLBOW
;
#
data_comp_DCP
#
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
DCP         N1     N   NR6    0    .       0.3030    0.6270   -5.1690
DCP         C2     C   CR6    0    .       0.7940   -0.6180   -5.0380
DCP         N3     N   N      0    .       1.8570   -1.0150   -5.7350
DCP         C4     C   CR6    0    .       2.4600   -0.1890   -6.5790
DCP         C5     C   CR16   0    .       1.9740    1.1240   -6.7360
DCP         C6     C   CR16   0    .       0.8890    1.5110   -6.0250
DCP         O2     O   O      0    .       0.2570   -1.3970   -4.2670
DCP         N4     N   NH2    0    .       3.5580   -0.6100   -7.2930
DCP        C1'     C   CH1    0    .      -0.8670    1.0340   -4.3890
DCP        C2'     C   CH2    0    .      -2.0640    0.1240   -4.7250
DCP        C3'     C   CH1    0    .      -2.4580   -0.5010   -3.3650
DCP        C4'     C   CH1    0    .      -1.8370    0.4970   -2.3560
DCP        O4'     O   O2     0    .      -0.5950    0.8870   -2.9850
DCP        O3'     O   OH1    0    .      -3.8790   -0.5540   -3.2210
DCP        C5'     C   CH2    0    .      -1.5730   -0.1870   -1.0130
DCP        O5'     O   O2     0    .      -1.0000    0.7530   -0.1030
DCP         PA     P   P      0    .      -0.7500   -0.0300    1.2800
DCP         O1A    O   O      0    .      -2.0390   -0.5430    1.7960
DCP         O2A    O   OP    -1    .       0.2540   -1.2620    1.0250
DCP         O3A    O   O2     0    .      -0.1030    0.9750    2.3580
DCP         PB     P   P      0    .       0.1180    0.1290    3.7090
DCP         O1B    O   O      0    .      -1.1830   -0.3860    4.1880
DCP         O2B    O   OP    -1    .       1.1090   -1.1040    3.4130
DCP         O3B    O   O2     0    .       0.7660    1.0790    4.8360
DCP         PG     P   P      0    .       0.9600    0.1730    6.1530
DCP         O1G    O   O      0    .       1.8570   -0.9610    5.8430
DCP         O2G    O   OP    -1    .       1.6080    1.0640    7.3270
DCP         O3G    O   OP    -1    .      -0.4700   -0.3880    6.6330
DCP         H5     H   HCR6   0    .       2.4540    1.8090   -7.4200
DCP         H6     H   HCR6   0    .       0.4940    2.5110   -6.1310
DCP        HN41    H   HNH2   0    .       3.8930   -1.5130   -7.1800
DCP        HN42    H   HNH2   0    .       3.9950   -0.0050   -7.9130
DCP        H1'     H   HCH1   0    .      -1.1180    2.0720   -4.6110
DCP        H2'1    H   HCH2   0    .      -2.8890    0.7110   -5.1280
DCP        H2'2    H   HCH2   0    .      -1.7670   -0.6520   -5.4300
DCP        H3'     H   HCH1   0    .      -2.0200   -1.4930   -3.2510
DCP        H4'     H   HCH1   0    .      -2.4860    1.3620   -2.2230
DCP        HO3'    H   HOH1   0    .      -4.2110   -1.1180   -3.9330
DCP        H5'1    H   HCH2   0    .      -2.5110   -0.5620   -0.6060
DCP        H5'2    H   HCH2   0    .      -0.8820   -1.0180   -1.1590
#
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
DCP   N1      C2    single        1.398 0.020     1.398
DCP   N1      C6    single        1.375 0.012     1.375
DCP   N1     C1'    single        1.475 0.016     1.475
DCP   C2      N3    single        1.358 0.017     1.358
DCP   C2      O2    double        1.232 0.013     1.232
DCP   N3      C4    double        1.341 0.014     1.341
DCP   C4      C5    single        1.426 0.012     1.426
DCP   C4      N4    single        1.334 0.012     1.334
DCP   C5      C6    double        1.345 0.018     1.345
DCP   C5      H5    single        0.930 0.012     1.080
DCP   C6      H6    single        0.930 0.012     1.080
DCP   N4     HN41   single        0.860 0.012     1.020
DCP   N4     HN42   single        0.860 0.012     1.020
DCP  C1'     C2'    single        1.521 0.012     1.521
DCP  C1'     O4'    single        1.418 0.012     1.418
DCP  C1'     H1'    single        0.970 0.013     1.090
DCP  C2'     C3'    single        1.523 0.013     1.523
DCP  C2'     H2'1   single        0.970 0.011     1.090
DCP  C2'     H2'2   single        0.970 0.011     1.090
DCP  C3'     C4'    single        1.527 0.011     1.527
DCP  C3'     O3'    single        1.428 0.012     1.428
DCP  C3'     H3'    single        0.970 0.010     1.090
DCP  C4'     O4'    single        1.444 0.010     1.444
DCP  C4'     C5'    single        1.508 0.011     1.508
DCP  C4'     H4'    single        0.970 0.011     1.090
DCP  O3'     HO3'   single        0.850 0.011     0.980
DCP  C5'     O5'    single        1.443 0.011     1.443
DCP  C5'     H5'1   single        0.970 0.015     1.090
DCP  C5'     H5'2   single        0.970 0.015     1.090
DCP  O5'      PA    single        1.579 0.015     1.579
DCP   PA      O1A   deloc         1.477 0.010     1.477
DCP   PA      O2A   deloc         1.529 0.022     1.529
DCP   PA      O3A   single        1.592 0.030     1.592
DCP   O3A     PB    single        1.592 0.011     1.592
DCP   PB      O1B   deloc         1.477 0.011     1.477
DCP   PB      O2B   deloc         1.529 0.022     1.529
DCP   PB      O3B   single        1.592 0.030     1.592
DCP   O3B     PG    single        1.600 0.011     1.600
DCP   PG      O1G   deloc         1.491 0.022     1.491
DCP   PG      O2G   deloc         1.533 0.032     1.533
DCP   PG      O3G   deloc         1.533 0.028     1.533
#
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
DCP  C1'      N1      C6          121.66 1.386
DCP  C1'      N1      C2          117.84 1.410
DCP   C6      N1      C2          120.46 1.000
DCP   O2      C2      N3          122.46 1.171
DCP   O2      C2      N1          118.97 1.035
DCP   N3      C2      N1          118.79 1.000
DCP   C4      N3      C2          120.24 1.075
DCP   N4      C4      C5          120.44 1.000
DCP   N4      C4      N3          118.10 1.000
DCP   C5      C4      N3          121.42 1.000
DCP   H5      C5      C6          121.21 3.000
DCP   H5      C5      C4          121.21 3.000
DCP   C6      C5      C4          117.58 1.000
DCP   H6      C6      C5          119.10 3.000
DCP   H6      C6      N1          119.10 3.000
DCP   C5      C6      N1          121.80 1.181
DCP  HN42     N4     HN41         119.97 3.000
DCP  HN42     N4      C4          120.02 3.000
DCP  HN41     N4      C4          120.01 3.000
DCP  H1'     C1'     O4'          126.89 3.000
DCP  H1'     C1'     C2'          126.89 3.000
DCP  O4'     C1'     C2'          106.23 1.052
DCP  H1'     C1'      N1          126.89 3.000
DCP  O4'     C1'      N1          108.01 1.000
DCP  C2'     C1'      N1          113.92 1.278
DCP  H2'2    C2'     H2'1         110.53 3.000
DCP  H2'2    C2'     C3'          110.51 3.000
DCP  H2'1    C2'     C3'          110.47 3.000
DCP  H2'2    C2'     C1'          110.48 3.000
DCP  H2'1    C2'     C1'          110.53 3.000
DCP  C3'     C2'     C1'          102.57 1.360
DCP  H3'     C3'     O3'          124.87 3.000
DCP  H3'     C3'     C4'          124.87 3.000
DCP  O3'     C3'     C4'          110.26 2.320
DCP  H3'     C3'     C2'          124.87 3.000
DCP  O3'     C3'     C2'          110.97 2.419
DCP  C4'     C3'     C2'          102.59 1.017
DCP  H4'     C4'     C5'          125.23 3.000
DCP  H4'     C4'     O4'          125.23 3.000
DCP  C5'     C4'     O4'          109.53 1.437
DCP  H4'     C4'     C3'          125.23 3.000
DCP  C5'     C4'     C3'          114.72 1.915
DCP  O4'     C4'     C3'          105.64 1.084
DCP  C4'     O4'     C1'          109.55 1.311
DCP  HO3'    O3'     C3'          106.78 3.000
DCP  H5'2    C5'     H5'1         109.47 3.000
DCP  H5'2    C5'     O5'          109.43 3.000
DCP  H5'1    C5'     O5'          109.51 3.000
DCP  H5'2    C5'     C4'          109.42 3.000
DCP  H5'1    C5'     C4'          109.47 3.000
DCP  O5'     C5'     C4'          108.83 2.328
DCP   PA     O5'     C5'          121.27 1.000
DCP   O3A     PA      O2A         106.94 1.880
DCP   O3A     PA      O1A         111.24 2.719
DCP   O2A     PA      O1A         114.42 3.527
DCP   O3A     PA     O5'          102.67 2.380
DCP   O2A     PA     O5'          108.07 2.651
DCP   O1A     PA     O5'          110.65 3.490
DCP   PB      O3A     PA          136.83 1.000
DCP   O3B     PB      O2B         106.94 1.880
DCP   O3B     PB      O1B         111.24 2.719
DCP   O2B     PB      O1B         114.42 3.527
DCP   O3B     PB      O3A         101.57 1.536
DCP   O2B     PB      O3A         106.94 1.880
DCP   O1B     PB      O3A         111.24 2.719
DCP   PG      O3B     PB          139.87 1.000
DCP   O3G     PG      O2G         108.70 2.785
DCP   O3G     PG      O1G         113.32 2.534
DCP   O2G     PG      O1G         113.32 2.534
DCP   O3G     PG      O3B         104.48 1.135
DCP   O2G     PG      O3B         104.48 1.135
DCP   O1G     PG      O3B         110.47 1.644
#
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
DCP CONST_01       C4      N3      C2      N1           -0.00   0.0 0
DCP CONST_02       C5      C4      N3      C2            0.25   0.0 0
DCP CONST_03       C6      N1      C2      N3            0.04   0.0 0
DCP CONST_04       C1'     N1      C2      N3         -180.00   0.0 0
DCP CONST_05       N4      C4      N3      C2          179.95   0.0 0
DCP CONST_06       O2      C2      N3      C4         -179.97   0.0 0
DCP CONST_07       O2      C2      N1      C6         -179.99   0.0 0
DCP CONST_08       C1'     N1      C2      O2           -0.04   0.0 0
DCP CONST_09      HN41     N4      C4      N3            0.01   0.0 0
DCP CONST_10      HN42     N4      C4      N3          179.72   0.0 0
DCP Var_01         O1A     PA     O5'     C5'          -59.96  30.0 3
DCP Var_02         O1B     PB      O3A     PA          -60.03  30.0 3
DCP Var_03         O1G     PG      O3B     PB           60.00  30.0 3
DCP Var_04        H5'1    C5'     O5'      PA           59.95  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
DCP chir_01   C1'     N1     C2'     O4'    negativ
DCP chir_02  C3'     O3'     C4'     C2'    positiv
DCP chir_03  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
DCP plan-1     N1 0.020
DCP plan-1     C2 0.020
DCP plan-1     N3 0.020
DCP plan-1     C4 0.020
DCP plan-1     C5 0.020
DCP plan-1     C6 0.020
DCP plan-1     O2 0.020
DCP plan-1     N4 0.020
DCP plan-1    C1' 0.020
DCP plan-1     H5 0.020
DCP plan-1     H6 0.020
DCP plan-1   HN41 0.020
DCP plan-1   HN42 0.020
