# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Oct 21 13:28:50 2020
#
#   Inital geometry file: a 91 line input string
#   Ligand name: 3-carboxy-1-[5-O-(hydroxyphosphinato)-beta-D-ribofuranosyl]pyridinium
#   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)[n+]2cccc(c2)C(O)=O
#
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
NCN        NCN '3-carboxy-1-[5-O-(hydroxyphosphinato)-beta-D-ribofuranosyl]pyridinium' ligand 34 22 .
2020-10-21 2020-10-21
;
CIF prepared directly in eLBOW
;
#
data_comp_NCN
#
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
NCN         P      P   P      0    .      17.6050   80.6750   18.3320
NCN         O1P    O   OP    -1    .      16.8470   81.8110   17.6060
NCN         O2P    O   O      0    .      16.7050   79.4290   18.7590
NCN         O3P    O   OP    -1    .      18.8550   80.2510   17.5190
NCN        O5'     O   O2     0    .      18.1240   81.3550   19.7970
NCN        C5'     C   CH2    0    .      19.3970   82.0500   19.9130
NCN        C4'     C   CH1    0    .      19.4430   83.5730   19.5240
NCN        O4'     O   O2     0    .      18.5160   84.3830   20.2730
NCN        C3'     C   CH1    0    .      20.8310   84.3020   19.8190
NCN        O3'     O   OH1    0    .      22.0790   83.8600   19.0940
NCN        C2'     C   CH1    0    .      20.4640   85.7250   19.4110
NCN        O2'     O   OH1    0    .      20.7120   86.0220   17.9670
NCN        C1'     C   CH1    0    .      19.0060   85.8200   20.1170
NCN         N1     N   NR6    1    .      18.9010   86.3630   21.5720
NCN         C6     C   CR16   0    .      19.4650   85.5620   22.6200
NCN         C5     C   CR16   0    .      19.3750   85.9960   23.9710
NCN         C4     C   CR16   0    .      18.7350   87.1860   24.2660
NCN         C3     C   CR6    0    .      18.1660   88.0040   23.2830
NCN         C2     C   CR16   0    .      18.2490   87.5890   21.9380
NCN         C7     C   C      0    .      17.4980   89.2750   23.8200
NCN         O7     O   OC    -1    .      16.8200   89.2030   24.9470
NCN         O8     O   O      0    .      17.6290   90.3510   23.0780
NCN        H5'1    H   HCH2   0    .      19.7880   81.9250   20.9490
NCN        H5'2    H   HCH2   0    .      20.1690   81.4990   19.3260
NCN        H4'     H   HCH1   0    .      19.2160   83.5150   18.4330
NCN        H3'     H   HCH1   0    .      21.1500   84.0960   20.8670
NCN        HO'3    H   HOH1   0    .      22.9050   84.2940   19.2690
NCN        H2'     H   HCH1   0    .      21.0890   86.5840   19.7460
NCN        HO'2    H   HOH1   0    .      20.4830   86.9080   17.7120
NCN        H1'     H   HCH1   0    .      18.4500   86.5290   19.4610
NCN         H6     H   HCR6   0    .      19.9690   84.6090   22.3860
NCN         H5     H   HCR6   0    .      19.8050   85.4040   24.7960
NCN         H4     H   HCR6   0    .      18.6760   87.4930   25.3230
NCN         H2     H   HCR6   0    .      17.7980   88.2310   21.1620
#
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
NCN   P       O1P   deloc         1.491 0.020     1.491
NCN   P       O2P   deloc         1.533 0.032     1.533
NCN   P       O3P   deloc         1.533 0.028     1.533
NCN   P      O5'    single        1.601 0.028     1.601
NCN  O5'     C5'    single        1.443 0.032     1.443
NCN  C5'     C4'    single        1.508 0.015     1.508
NCN  C5'     H5'1   single        0.970 0.011     1.090
NCN  C5'     H5'2   single        0.970 0.011     1.090
NCN  C4'     O4'    single        1.444 0.011     1.444
NCN  C4'     C3'    single        1.526 0.011     1.526
NCN  C4'     H4'    single        0.970 0.013     1.090
NCN  O4'     C1'    single        1.404 0.013     1.404
NCN  C3'     O3'    single        1.423 0.011     1.423
NCN  C3'     C2'    single        1.531 0.012     1.531
NCN  C3'     H3'    single        0.970 0.013     1.090
NCN  O3'     HO'3   single        0.850 0.013     0.980
NCN  C2'     O2'    single        1.423 0.013     1.423
NCN  C2'     C1'    single        1.538 0.012     1.538
NCN  C2'     H2'    single        0.970 0.010     1.090
NCN  O2'     HO'2   single        0.850 0.010     0.980
NCN  C1'      N1    single        1.499 0.010     1.499
NCN  C1'     H1'    single        0.970 0.017     1.090
NCN   N1      C6    aromatic      1.346 0.017     1.346
NCN   N1      C2    aromatic      1.342 0.010     1.342
NCN   C6      C5    aromatic      1.374 0.010     1.374
NCN   C6      H6    single        0.930 0.012     1.080
NCN   C5      C4    aromatic      1.386 0.012     1.386
NCN   C5      H5    single        0.930 0.010     1.080
NCN   C4      C3    aromatic      1.392 0.010     1.392
NCN   C4      H4    single        0.930 0.010     1.080
NCN   C3      C2    aromatic      1.382 0.010     1.382
NCN   C3      C7    single        1.488 0.010     1.488
NCN   C2      H2    single        0.930 0.013     1.080
NCN   C7      O7    deloc         1.305 0.013     1.305
NCN   C7      O8    deloc         1.224 0.021     1.224
#
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
NCN  O5'      P       O3P         106.53 2.580
NCN  O5'      P       O2P         106.53 2.580
NCN   O3P     P       O2P         108.70 2.785
NCN  O5'      P       O1P         106.57 2.496
NCN   O3P     P       O1P         113.32 2.534
NCN   O2P     P       O1P         113.32 2.534
NCN  C5'     O5'      P           117.05 1.000
NCN  H5'2    C5'     H5'1         101.01 3.000
NCN  H5'2    C5'     C4'          109.15 3.000
NCN  H5'1    C5'     C4'          109.17 3.000
NCN  H5'2    C5'     O5'          109.12 3.000
NCN  H5'1    C5'     O5'          109.12 3.000
NCN  C4'     C5'     O5'          108.83 2.328
NCN  H4'     C4'     C3'          127.39 3.000
NCN  H4'     C4'     O4'          127.39 3.000
NCN  C3'     C4'     O4'          105.22 1.298
NCN  H4'     C4'     C5'          127.39 3.000
NCN  C3'     C4'     C5'          115.19 1.760
NCN  O4'     C4'     C5'          109.53 1.437
NCN  C1'     O4'     C4'          110.33 1.000
NCN  H3'     C3'     C2'          124.08 3.000
NCN  H3'     C3'     O3'          124.08 3.000
NCN  C2'     C3'     O3'          111.83 2.669
NCN  H3'     C3'     C4'          124.08 3.000
NCN  C2'     C3'     C4'          102.49 1.000
NCN  O3'     C3'     C4'          111.06 2.498
NCN  HO'3    O3'     C3'          119.80 3.000
NCN  H2'     C2'     C1'          126.02 3.000
NCN  H2'     C2'     O2'          126.02 3.000
NCN  C1'     C2'     O2'          107.97 3.395
NCN  H2'     C2'     C3'          126.02 3.000
NCN  C1'     C2'     C3'          101.99 1.000
NCN  O2'     C2'     C3'          111.83 2.669
NCN  HO'2    O2'     C2'          113.86 3.000
NCN  H1'     C1'      N1          123.74 3.000
NCN  H1'     C1'     C2'          123.74 3.000
NCN   N1     C1'     C2'          112.51 1.097
NCN  H1'     C1'     O4'          123.74 3.000
NCN   N1     C1'     O4'          108.25 1.000
NCN  C2'     C1'     O4'          107.57 1.000
NCN   C2      N1      C6          122.02 1.000
NCN   C2      N1     C1'          118.56 2.043
NCN   C6      N1     C1'          119.60 1.961
NCN   H6      C6      C5          119.94 3.000
NCN   H6      C6      N1          119.94 3.000
NCN   C5      C6      N1          120.12 1.000
NCN   H5      C5      C4          120.05 3.000
NCN   H5      C5      C6          120.05 3.000
NCN   C4      C5      C6          119.91 1.000
NCN   H4      C4      C3          119.82 3.000
NCN   H4      C4      C5          119.82 3.000
NCN   C3      C4      C5          120.37 1.000
NCN   C7      C3      C2          119.91 1.525
NCN   C7      C3      C4          120.36 1.451
NCN   C2      C3      C4          118.88 1.000
NCN   H2      C2      C3          119.71 3.000
NCN   H2      C2      N1          119.71 3.000
NCN   C3      C2      N1          120.59 1.000
NCN   O8      C7      O7          123.39 1.504
NCN   O8      C7      C3          121.69 1.910
NCN   O7      C7      C3          114.67 1.890
#
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
NCN CONST_01       C4      C5      C6      N1            0.42   0.0 0
NCN CONST_02       C4      C3      C2      N1           -0.18   0.0 0
NCN CONST_03       C3      C2      N1      C6            0.28   0.0 0
NCN CONST_04       C3      C4      C5      C6           -0.32   0.0 0
NCN CONST_05       C2      N1      C6      C5           -0.40   0.0 0
NCN CONST_06       C2      C3      C4      C5            0.20   0.0 0
NCN CONST_07       C5      C6      N1     C1'         -178.77   0.0 0
NCN CONST_08       C3      C2      N1     C1'          178.53   0.0 0
NCN CONST_09       C7      C3      C2      N1         -179.60   0.0 0
NCN CONST_10       C7      C3      C4      C5          179.69   0.0 0
NCN CONST_11       H6      C6      N1     C1'            1.19   0.0 0
NCN CONST_12       H2      C2      N1     C1'           -1.45   0.0 0
NCN CONST_13       H5      C5      C6      N1         -179.60   0.0 0
NCN CONST_14       H4      C4      C5      C6          179.64   0.0 0
NCN Var_01         O7      C7      C3      C4          -38.77  30.0 2
NCN Var_02        C4'     C5'     O5'      P            85.12  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
NCN chir_01  C4'     C5'     O4'     C3'    negativ
NCN chir_02  C3'     O3'     C4'     C2'    positiv
NCN chir_03  C2'     O2'     C3'     C1'    positiv
NCN chir_04  C1'     O4'      N1     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
NCN plan-1    C1' 0.020
NCN plan-1     N1 0.020
NCN plan-1     C6 0.020
NCN plan-1     C5 0.020
NCN plan-1     C4 0.020
NCN plan-1     C3 0.020
NCN plan-1     C2 0.020
NCN plan-1     C7 0.020
NCN plan-1     H6 0.020
NCN plan-1     H5 0.020
NCN plan-1     H4 0.020
NCN plan-1     H2 0.020
NCN plan-2     C3 0.020
NCN plan-2     C7 0.020
NCN plan-2     O7 0.020
NCN plan-2     O8 0.020
