# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 21 11:14:59 2017
#
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]guanosine
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](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
GNP        GNP '5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]guanosine' ligand 49 32 .
#
data_comp_GNP
#
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
GNP         PG     P   P      0    .       2.5711   -5.8033    4.2202
GNP         O1G    O   O      0    .       3.6504   -6.1383    3.2949
GNP         O2G    O   OH1    0    .       3.0461   -4.5587    5.1908
GNP         O3G    O   OH1    0    .       2.2148   -7.1185    5.1479
GNP         N3B    N   NH1    0    .       1.1897   -5.3398    3.3376
GNP         PB     P   P      0    .       1.1582   -5.5271    1.6447
GNP         O1B    O   O      0    .       2.5621   -5.4167    1.0999
GNP         O2B    O   OH1    0    .       0.5369   -7.0067    1.2671
GNP         O3A    O   O2     0    .       0.2160   -4.3491    0.9789
GNP         PA     P   P      0    .       0.5091   -3.6687   -0.4942
GNP         O1A    O   O      0    .       1.9994   -3.5896   -0.7246
GNP         O2A    O   OH1    0    .      -0.1809   -4.5918   -1.6729
GNP        O5'     O   O2     0    .      -0.1350   -2.1514   -0.5369
GNP        C5'     C   CH2    0    .       0.3229   -1.2596   -1.5135
GNP        C4'     C   CH1    0    .      -0.7060   -0.1110   -1.6886
GNP        O4'     O   O2     0    .      -0.5058    0.8125   -0.7885
GNP        C3'     C   CH1    0    .      -0.4966    0.5876   -3.0511
GNP        O3'     O   OH1    0    .      -1.5296    0.3075   -3.8842
GNP        C2'     C   CH1    0    .      -0.4576    2.0984   -2.7407
GNP        O2'     O   OH1    0    .      -1.3748    2.8349   -3.6622
GNP        C1'     C   CH1    0    .      -0.8749    2.2119   -1.5078
GNP         N9     N   NR5    0    .      -0.2034    3.3068   -0.8496
GNP         C8     C   CR15   0    .       1.0732    3.3239   -0.4578
GNP         N7     N   N      0    .       1.2597    4.4098    0.2978
GNP         C5     C   CR56   0    .       0.0945    5.0669    0.3739
GNP         C6     C   CR6    0    .      -0.2705    6.2308    1.0154
GNP         O6     O   OC     0    .       0.5217    6.8195    1.6707
GNP         N1     N   NR16   0    .      -1.5146    6.6711    0.9282
GNP         C2     C   CR6    0    .      -2.4294    5.9794    0.2094
GNP         N2     N   NH2    0    .      -3.7998    6.4482    0.1122
GNP         N3     N   N      0    .      -2.0738    4.8371   -0.4210
GNP         C4     C   CR56   0    .      -0.8096    4.3858   -0.3348
GNP        HOG2    H   HOH1   0    .       3.9646   -4.6451    5.3859
GNP        HOG3    H   HOH1   0    .       2.9934   -7.4092    5.5935
GNP        HNB3    H   HNH1   0    .       0.3999   -4.9496    3.8127
GNP        HOB2    H   HOH1   0    .      -0.2785   -7.1312    1.7242
GNP        HOA2    H   HOH1   0    .      -1.1134   -4.4520   -1.6761
GNP        H5'2    H   HCH2   0    .       1.2775   -0.8461   -1.2065
GNP        H5'1    H   HCH2   0    .       0.4424   -1.7847   -2.4552
GNP        H4'     H   HCH1   0    .      -1.7194   -0.4917   -1.6151
GNP        H3'     H   HCH1   0    .       0.4423    0.2732   -3.4906
GNP        HO3'    H   HOH1   0    .      -1.2122    0.2534   -4.7721
GNP        H2'     H   HCH1   0    .       0.5564    2.4735   -2.8295
GNP        HO2'    H   HOH1   0    .      -0.8659    3.3244   -4.2873
GNP        H1'     H   HCH1   0    .      -1.9490    2.3638   -1.4930
GNP         H8     H   HCR5   0    .       1.8267    2.5881   -0.7116
GNP         HN1    H   HNR6   0    .      -1.7811    7.5134    1.3984
GNP        HN21    H   HNH2   0    .      -4.0667    7.3105    0.5482
GNP        HN22    H   HNH2   0    .      -4.4803    5.9073   -0.3871
#
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
GNP   PG      O1G   double        1.461 0.020     1.461
GNP   PG      O2G   single        1.648 0.020     1.648
GNP   PG      O3G   single        1.648 0.020     1.648
GNP   PG      N3B   single        1.704 0.020     1.704
GNP   O2G    HOG2   single        0.850 0.020     0.980
GNP   O3G    HOG3   single        0.850 0.020     0.980
GNP   N3B     PB    single        1.703 0.020     1.703
GNP   N3B    HNB3   single        0.860 0.020     1.020
GNP   PB      O1B   double        1.510 0.020     1.510
GNP   PB      O2B   single        1.649 0.020     1.649
GNP   PB      O3A   single        1.649 0.020     1.649
GNP   O2B    HOB2   single        0.850 0.020     0.980
GNP   O3A     PA    single        1.592 0.020     1.592
GNP   PA      O1A   double        1.478 0.011     1.478
GNP   PA      O2A   single        1.527 0.023     1.527
GNP   PA     O5'    single        1.575 0.032     1.575
GNP   O2A    HOA2   single        0.850 0.010     0.980
GNP  O5'     C5'    single        1.443 0.010     1.443
GNP  C5'     C4'    single        1.508 0.015     1.508
GNP  C5'     H5'2   single        0.970 0.012     1.090
GNP  C5'     H5'1   single        0.970 0.012     1.090
GNP  C4'     O4'    single        1.444 0.012     1.444
GNP  C4'     C3'    single        1.526 0.011     1.526
GNP  C4'     H4'    single        0.970 0.013     1.090
GNP  O4'     C1'    single        1.416 0.013     1.416
GNP  C3'     O3'    single        1.423 0.011     1.423
GNP  C3'     C2'    single        1.531 0.012     1.531
GNP  C3'     H3'    single        0.970 0.013     1.090
GNP  O3'     HO3'   single        0.850 0.013     0.980
GNP  C2'     O2'    single        1.423 0.013     1.423
GNP  C2'     C1'    single        1.531 0.012     1.531
GNP  C2'     H2'    single        0.970 0.014     1.090
GNP  O2'     HO2'   single        0.850 0.014     0.980
GNP  C1'      N9    single        1.472 0.014     1.472
GNP  C1'     H1'    single        0.970 0.017     1.090
GNP   N9      C8    aromatic      1.371 0.017     1.371
GNP   N9      C4    aromatic      1.373 0.014     1.373
GNP   C8      N7    aromatic      1.315 0.013     1.315
GNP   C8      H8    single        0.930 0.016     1.080
GNP   N7      C5    aromatic      1.386 0.016     1.386
GNP   C5      C6    aromatic      1.447 0.010     1.447
GNP   C5      C4    aromatic      1.381 0.031     1.381
GNP   C6      O6    double        1.230 0.026     1.230
GNP   C6      N1    aromatic      1.382 0.015     1.382
GNP   N1      C2    aromatic      1.368 0.012     1.368
GNP   N1      HN1   single        0.860 0.013     1.020
GNP   C2      N2    single        1.334 0.013     1.334
GNP   C2      N3    aromatic      1.329 0.013     1.329
GNP   N2     HN21   single        0.860 0.010     1.020
GNP   N2     HN22   single        0.860 0.010     1.020
GNP   N3      C4    aromatic      1.345 0.010     1.345
#
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
GNP   N3B     PG      O3G         109.47 3.000
GNP   N3B     PG      O2G         109.47 3.000
GNP   O3G     PG      O2G         109.47 3.000
GNP   N3B     PG      O1G         109.47 3.000
GNP   O3G     PG      O1G         109.47 3.000
GNP   O2G     PG      O1G         109.47 3.000
GNP  HOG2     O2G     PG          109.47 3.000
GNP  HOG3     O3G     PG          109.47 3.000
GNP  HNB3     N3B     PB          120.00 3.000
GNP  HNB3     N3B     PG          120.00 3.000
GNP   PB      N3B     PG          120.00 3.000
GNP   O3A     PB      O2B         109.47 3.000
GNP   O3A     PB      O1B         109.47 3.000
GNP   O2B     PB      O1B         109.47 3.000
GNP   O3A     PB      N3B         109.47 3.000
GNP   O2B     PB      N3B         109.47 3.000
GNP   O1B     PB      N3B         109.47 3.000
GNP  HOB2     O2B     PB          109.47 3.000
GNP   PA      O3A     PB          123.64 3.000
GNP  O5'      PA      O2A         108.19 3.739
GNP  O5'      PA      O1A         109.31 3.698
GNP   O2A     PA      O1A         114.24 4.103
GNP  O5'      PA      O3A         102.67 2.380
GNP   O2A     PA      O3A         106.94 1.880
GNP   O1A     PA      O3A         111.24 2.719
GNP  HOA2     O2A     PA          109.47 3.000
GNP  C5'     O5'      PA          121.27 1.000
GNP  H5'1    C5'     H5'2         109.47 3.000
GNP  H5'1    C5'     C4'          109.47 3.000
GNP  H5'2    C5'     C4'          109.47 3.000
GNP  H5'1    C5'     O5'          109.47 3.000
GNP  H5'2    C5'     O5'          109.47 3.000
GNP  C4'     C5'     O5'          108.73 2.347
GNP  H4'     C4'     C3'          127.37 3.000
GNP  H4'     C4'     O4'          127.37 3.000
GNP  C3'     C4'     O4'          105.26 1.264
GNP  H4'     C4'     C5'          127.37 3.000
GNP  C3'     C4'     C5'          115.29 1.748
GNP  O4'     C4'     C5'          109.56 1.473
GNP  C1'     O4'     C4'          109.40 1.565
GNP  H3'     C3'     C2'          124.05 3.000
GNP  H3'     C3'     O3'          124.05 3.000
GNP  C2'     C3'     O3'          111.90 2.651
GNP  H3'     C3'     C4'          124.05 3.000
GNP  C2'     C3'     C4'          102.48 1.000
GNP  O3'     C3'     C4'          111.06 2.548
GNP  HO3'    O3'     C3'          109.47 3.000
GNP  H2'     C2'     C1'          124.73 3.000
GNP  H2'     C2'     O2'          124.73 3.000
GNP  C1'     C2'     O2'          110.53 2.746
GNP  H2'     C2'     C3'          124.73 3.000
GNP  C1'     C2'     C3'          101.54 1.182
GNP  O2'     C2'     C3'          111.90 2.651
GNP  HO2'    O2'     C2'          109.47 3.000
GNP  H1'     C1'      N9          123.29 3.000
GNP  H1'     C1'     C2'          123.29 3.000
GNP   N9     C1'     C2'          113.42 1.697
GNP  H1'     C1'     O4'          123.29 3.000
GNP   N9     C1'     O4'          108.34 1.149
GNP  C2'     C1'     O4'          106.54 1.160
GNP   C4      N9      C8          105.81 1.294
GNP   C4      N9     C1'          126.82 2.082
GNP   C8      N9     C1'          126.96 2.297
GNP   H8      C8      N7          123.24 3.000
GNP   H8      C8      N9          123.24 3.000
GNP   N7      C8      N9          113.52 1.351
GNP   C5      N7      C8          104.57 1.191
GNP   C4      C5      C6          118.83 1.367
GNP   C4      C5      N7          110.44 1.000
GNP   C6      C5      N7          130.60 2.185
GNP   N1      C6      O6          120.30 1.406
GNP   N1      C6      C5          112.64 1.804
GNP   O6      C6      C5          126.45 2.354
GNP   HN1     N1      C2          117.43 3.000
GNP   HN1     N1      C6          117.43 3.000
GNP   C2      N1      C6          125.13 1.054
GNP   N3      C2      N2          119.70 1.000
GNP   N3      C2      N1          123.15 1.000
GNP   N2      C2      N1          117.03 1.000
GNP  HN22     N2     HN21         120.00 3.000
GNP  HN22     N2      C2          120.00 3.000
GNP  HN21     N2      C2          120.00 3.000
GNP   C4      N3      C2          112.35 1.000
GNP   N3      C4      C5          128.13 1.000
GNP   N3      C4      N9          126.01 1.000
GNP   C5      C4      N9          105.87 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
GNP CONST_01       C5      N7      C8      N9           -0.00   0.0 0
GNP CONST_02       N7      C5      C4      N9            0.00   0.0 0
GNP CONST_03       C6      C5      C4      N9          180.00   0.0 0
GNP CONST_04       C2      N3      C4      N9         -180.00   0.0 0
GNP CONST_05       C5      C4      N9      C8           -0.00   0.0 0
GNP CONST_06       N3      C4      N9      C8          180.00   0.0 0
GNP CONST_07       C6      C5      N7      C8         -180.00   0.0 0
GNP CONST_08       C4      C5      N7      C8           -0.00   0.0 0
GNP CONST_09       C4      N9      C8      N7            0.00   0.0 0
GNP CONST_10       N1      C6      C5      N7          180.00   0.0 0
GNP CONST_11       N3      C4      C5      N7         -180.00   0.0 0
GNP CONST_12       C2      N1      C6      C5            0.00   0.0 0
GNP CONST_13       C2      N3      C4      C5            0.00   0.0 0
GNP CONST_14       N3      C4      C5      C6           -0.00   0.0 0
GNP CONST_15       N3      C2      N1      C6           -0.00   0.0 0
GNP CONST_16       C4      C5      C6      N1            0.00   0.0 0
GNP CONST_17       C4      N3      C2      N1            0.00   0.0 0
GNP CONST_18       N7      C8      N9     C1'         -170.03   0.0 0
GNP CONST_19       C5      C4      N9     C1'          170.14   0.0 0
GNP CONST_20       N3      C4      N9     C1'           -9.86   0.0 0
GNP CONST_21       O6      C6      C5      N7           -1.80   0.0 0
GNP CONST_22       N2      C2      N1      C6          179.65   0.0 0
GNP CONST_23       C4      C5      C6      O6          178.20   0.0 0
GNP CONST_24       C2      N1      C6      O6         -178.20   0.0 0
GNP CONST_25       C4      N3      C2      N2         -179.66   0.0 0
GNP CONST_26       H8      C8      N9     C1'           10.19   0.0 0
GNP CONST_27       HN1     N1      C6      C5          179.64   0.0 0
GNP CONST_28      HN21     N2      C2      N1            2.52   0.0 0
GNP CONST_29      HN22     N2      C2      N1         -177.18   0.0 0
GNP Var_01        C4'     C5'     O5'      PA          161.07  30.0 3
GNP Var_02         O1B     PB      N3B     PG          -29.06  30.0 3
GNP Var_03         PB      N3B     PG      O1G           8.38  30.0 3
GNP Var_04         O1A     PA      O3A     PB          -34.15  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
GNP chir_03  C4'     C5'     O4'     C3'    negativ
GNP chir_04  C3'     O3'     C4'     C2'    positiv
GNP chir_05  C2'     O2'     C3'     C1'    positiv
GNP chir_06  C1'     O4'      N9     C2'    negativ
GNP chir_07   PB      O1B     O2B     O3A   both
GNP chir_08   PA      O1A     O2A    O5'    both
#
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
GNP plan-1    C1' 0.020
GNP plan-1     N9 0.020
GNP plan-1     C8 0.020
GNP plan-1     N7 0.020
GNP plan-1     C5 0.020
GNP plan-1     C6 0.020
GNP plan-1     O6 0.020
GNP plan-1     N1 0.020
GNP plan-1     C2 0.020
GNP plan-1     N2 0.020
GNP plan-1     N3 0.020
GNP plan-1     C4 0.020
GNP plan-1     H8 0.020
GNP plan-1    HN1 0.020
GNP plan-2     C2 0.020
GNP plan-2     N2 0.020
GNP plan-2   HN21 0.020
GNP plan-2   HN22 0.020
