# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Oct 23 16:37:40 2020
#
#   Inital geometry file: a 118 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine
#   CSD Mogul values: True
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
APC        APC '5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine' ligand 45 31 .
2020-10-23 2020-10-23
;
CIF prepared directly in eLBOW
;
#
data_comp_APC
#
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
APC         PG     P   P      0    .       1.2390   -0.2390   -7.0920
APC         O1G    O   O      0    .       1.7660    1.1350   -6.9440
APC         O2G    O   OP    -1    .       2.1730   -1.0660   -8.1090
APC         O3G    O   OP    -1    .      -0.2620   -0.1790   -7.6710
APC         PB     P   P      0    .       0.2820   -0.0930   -4.6940
APC         O1B    O   O      0    .       0.8240    1.2790   -4.5830
APC         O2B    O   OP    -1    .      -1.2020   -0.0350   -5.3140
APC         O3B    O   O2     0    .       1.2310   -0.9680   -5.6560
APC         PA     P   P      0    .      -0.8510    0.1320   -1.9520
APC         O1A    O   O      0    .      -0.3090    1.5050   -1.8410
APC         O2A    O   OP    -1    .      -2.3360    0.1900   -2.5710
APC         C3A    C   CH2    0    .       0.2220   -0.8580   -3.0410
APC        O5'     O   O2     0    .      -0.9050   -0.5420   -0.4910
APC        C5'     C   CH2    0    .      -1.7570    0.2760    0.3110
APC        C4'     C   CH1    0    .      -1.8520   -0.3130    1.7200
APC        O4'     O   O2     0    .      -0.5490   -0.3390    2.3420
APC        C3'     C   CH1    0    .      -2.7060    0.5960    2.6300
APC        O3'     O   OH1    0    .      -4.0430    0.0990    2.7210
APC        C2'     C   CH1    0    .      -2.0040    0.5180    4.0060
APC        O2'     O   OH1    0    .      -2.8870   -0.0260    4.9890
APC        C1'     C   CH1    0    .      -0.8070   -0.4260    3.7610
APC         N9     N   NR5    0    .       0.3610    0.0230    4.5200
APC         C8     C   CR15   0    .       1.3040    0.9130    4.0980
APC         N7     N   N      0    .       2.2010    1.0840    5.0250
APC         C5     C   CR56   0    .       1.8900    0.3210    6.1000
APC         C6     C   CR6    0    .       2.4790    0.0950    7.3550
APC         N6     N   NH2    0    .       3.6460    0.7450    7.7170
APC         N1     N   N      0    .       1.8870   -0.7530    8.1890
APC         C2     C   CR16   0    .       0.7730   -1.3780    7.8520
APC         N3     N   N      0    .       0.1890   -1.2020    6.6860
APC         C4     C   CR56   0    .       0.7090   -0.3730    5.7870
APC        H3A1    H   HCH2   0    .       1.2270   -0.8970   -2.6220
APC        H3A2    H   HCH2   0    .      -0.1760   -1.8690   -3.1230
APC        H5'1    H   HCH2   0    .      -2.7510    0.3120   -0.1340
APC        H5'2    H   HCH2   0    .      -1.3470    1.2840    0.3660
APC        H4'     H   HCH1   0    .      -2.2740   -1.3170    1.6820
APC        H3'     H   HCH1   0    .      -2.7050    1.6200    2.2560
APC        HO3'    H   HOH1   0    .      -4.5270    0.7050    3.2990
APC        H2'     H   HCH1   0    .      -1.6540    1.5040    4.3120
APC        HO2'    H   HOH1   0    .      -3.6400    0.5760    5.0520
APC        H1'     H   HCH1   0    .      -1.0670   -1.4480    4.0370
APC         H8     H   HCR5   0    .       1.3060    1.4040    3.1360
APC        HN61    H   HNH2   0    .       4.0410    0.5840    8.5880
APC        HN62    H   HNH2   0    .       4.0710    1.3590    7.0980
APC         H2     H   HCR6   0    .       0.3250   -2.0600    8.5600
#
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
APC   PG      O1G   deloc         1.491 0.020     1.491
APC   PG      O2G   deloc         1.533 0.032     1.533
APC   PG      O3G   deloc         1.533 0.028     1.533
APC   PG      O3B   single        1.600 0.028     1.600
APC   PB      O1B   deloc         1.509 0.022     1.509
APC   PB      O2B   deloc         1.558 0.025     1.558
APC   PB      O3B   single        1.610 0.022     1.610
APC   PB      C3A   single        1.822 0.022     1.822
APC   PA      O1A   deloc         1.509 0.022     1.509
APC   PA      O2A   deloc         1.558 0.025     1.558
APC   PA      C3A   single        1.821 0.022     1.821
APC   PA     O5'    single        1.577 0.022     1.577
APC   C3A    H3A1   single        0.970 0.012     1.090
APC   C3A    H3A2   single        0.970 0.012     1.090
APC  O5'     C5'    single        1.443 0.012     1.443
APC  C5'     C4'    single        1.508 0.015     1.508
APC  C5'     H5'1   single        0.970 0.011     1.090
APC  C5'     H5'2   single        0.970 0.011     1.090
APC  C4'     O4'    single        1.444 0.011     1.444
APC  C4'     C3'    single        1.526 0.011     1.526
APC  C4'     H4'    single        0.970 0.013     1.090
APC  O4'     C1'    single        1.416 0.013     1.416
APC  C3'     O3'    single        1.423 0.011     1.423
APC  C3'     C2'    single        1.531 0.012     1.531
APC  C3'     H3'    single        0.970 0.013     1.090
APC  O3'     HO3'   single        0.850 0.013     0.980
APC  C2'     O2'    single        1.423 0.013     1.423
APC  C2'     C1'    single        1.531 0.012     1.531
APC  C2'     H2'    single        0.970 0.014     1.090
APC  O2'     HO2'   single        0.850 0.014     0.980
APC  C1'      N9    single        1.459 0.014     1.459
APC  C1'     H1'    single        0.970 0.012     1.090
APC   N9      C8    aromatic      1.370 0.012     1.370
APC   N9      C4    aromatic      1.374 0.010     1.374
APC   C8      N7    aromatic      1.310 0.010     1.310
APC   C8      H8    single        0.930 0.010     1.080
APC   N7      C5    aromatic      1.387 0.010     1.387
APC   C5      C6    aromatic      1.409 0.010     1.409
APC   C5      C4    aromatic      1.388 0.010     1.388
APC   C6      N6    single        1.337 0.011     1.337
APC   C6      N1    aromatic      1.350 0.014     1.350
APC   N6     HN61   single        0.860 0.010     1.020
APC   N6     HN62   single        0.860 0.010     1.020
APC   N1      C2    aromatic      1.334 0.010     1.334
APC   C2      N3    aromatic      1.334 0.011     1.334
APC   C2      H2    single        0.930 0.011     1.080
APC   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
APC   O3B     PG      O3G         104.48 1.135
APC   O3B     PG      O2G         104.48 1.135
APC   O3G     PG      O2G         108.70 2.785
APC   O3B     PG      O1G         110.47 1.644
APC   O3G     PG      O1G         113.32 2.534
APC   O2G     PG      O1G         113.32 2.534
APC   C3A     PB      O3B         109.47 3.000
APC   C3A     PB      O2B         109.52 3.000
APC   O3B     PB      O2B         109.45 3.000
APC   C3A     PB      O1B         109.47 3.000
APC   O3B     PB      O1B         109.45 3.000
APC   O2B     PB      O1B         111.98 4.307
APC   PB      O3B     PG          106.84 3.000
APC  O5'      PA      C3A         109.56 3.000
APC  O5'      PA      O2A         104.02 4.312
APC   C3A     PA      O2A         109.46 3.000
APC  O5'      PA      O1A         110.24 4.525
APC   C3A     PA      O1A         109.47 3.000
APC   O2A     PA      O1A         111.98 4.307
APC  H3A2     C3A    H3A1         109.43 3.000
APC  H3A2     C3A     PA          109.52 3.000
APC  H3A1     C3A     PA          109.45 3.000
APC  H3A2     C3A     PB          109.47 3.000
APC  H3A1     C3A     PB          109.48 3.000
APC   PA      C3A     PB          109.48 3.000
APC  C5'     O5'      PA          106.85 3.000
APC  H5'2    C5'     H5'1         109.47 3.000
APC  H5'2    C5'     C4'          109.45 3.000
APC  H5'1    C5'     C4'          109.40 3.000
APC  H5'2    C5'     O5'          109.50 3.000
APC  H5'1    C5'     O5'          109.51 3.000
APC  C4'     C5'     O5'          108.83 2.328
APC  H4'     C4'     C3'          127.39 3.000
APC  H4'     C4'     O4'          127.39 3.000
APC  C3'     C4'     O4'          105.22 1.298
APC  H4'     C4'     C5'          127.39 3.000
APC  C3'     C4'     C5'          115.19 1.760
APC  O4'     C4'     C5'          109.53 1.437
APC  C1'     O4'     C4'          109.40 1.607
APC  H3'     C3'     C2'          124.08 3.000
APC  H3'     C3'     O3'          124.08 3.000
APC  C2'     C3'     O3'          111.83 2.669
APC  H3'     C3'     C4'          124.08 3.000
APC  C2'     C3'     C4'          102.49 1.000
APC  O3'     C3'     C4'          111.06 2.498
APC  HO3'    O3'     C3'          106.75 3.000
APC  H2'     C2'     C1'          124.71 3.000
APC  H2'     C2'     O2'          124.71 3.000
APC  C1'     C2'     O2'          110.58 2.794
APC  H2'     C2'     C3'          124.71 3.000
APC  C1'     C2'     C3'          101.56 1.191
APC  O2'     C2'     C3'          111.83 2.669
APC  HO2'    O2'     C2'          106.81 3.000
APC  H1'     C1'      N9          122.96 3.000
APC  H1'     C1'     C2'          122.96 3.000
APC   N9     C1'     C2'          114.08 1.531
APC  H1'     C1'     O4'          122.96 3.000
APC   N9     C1'     O4'          108.36 1.260
APC  C2'     C1'     O4'          106.53 1.175
APC   C4      N9      C8          105.72 1.000
APC   C4      N9     C1'          126.88 1.798
APC   C8      N9     C1'          126.78 1.942
APC   H8      C8      N7          122.96 3.000
APC   H8      C8      N9          122.96 3.000
APC   N7      C8      N9          114.08 1.000
APC   C5      N7      C8          103.68 1.000
APC   C4      C5      C6          116.99 1.000
APC   C4      C5      N7          110.69 1.000
APC   C6      C5      N7          132.07 1.184
APC   N1      C6      N6          118.11 1.227
APC   N1      C6      C5          117.60 1.000
APC   N6      C6      C5          123.59 1.076
APC  HN62     N6     HN61         119.98 3.000
APC  HN62     N6      C6          119.99 3.000
APC  HN61     N6      C6          120.02 3.000
APC   C2      N1      C6          118.58 1.047
APC   H2      C2      N3          115.66 3.000
APC   H2      C2      N1          115.66 3.000
APC   N3      C2      N1          128.69 1.000
APC   C4      N3      C2          112.03 2.344
APC   N3      C4      C5          126.80 1.000
APC   N3      C4      N9          127.04 1.148
APC   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
APC CONST_01       C5      N7      C8      N9           -0.22   0.0 0
APC CONST_02       N7      C5      C4      N9           -0.38   0.0 0
APC CONST_03       C6      C5      C4      N9         -179.64   0.0 0
APC CONST_04       C2      N3      C4      N9          180.00   0.0 0
APC CONST_05       C5      C4      N9      C8            0.25   0.0 0
APC CONST_06       N3      C4      N9      C8          179.95   0.0 0
APC CONST_07       C6      C5      N7      C8          179.46   0.0 0
APC CONST_08       C4      C5      N7      C8            0.37   0.0 0
APC CONST_09       C4      N9      C8      N7           -0.03   0.0 0
APC CONST_10       N1      C6      C5      N7         -179.59   0.0 0
APC CONST_11       N3      C4      C5      N7          179.86   0.0 0
APC CONST_12       C2      N1      C6      C5            0.28   0.0 0
APC CONST_13       C2      N3      C4      C5           -0.33   0.0 0
APC CONST_14       N3      C4      C5      C6            0.60   0.0 0
APC CONST_15       N3      C2      N1      C6            0.00   0.0 0
APC CONST_16       C4      C5      C6      N1           -0.58   0.0 0
APC CONST_17       C4      N3      C2      N1            0.02   0.0 0
APC CONST_18       N7      C8      N9     C1'          179.94   0.0 0
APC CONST_19       C5      C4      N9     C1'         -179.72   0.0 0
APC CONST_20       N3      C4      N9     C1'           -0.02   0.0 0
APC CONST_21       N6      C6      C5      N7            0.69   0.0 0
APC CONST_22       C4      C5      C6      N6          179.70   0.0 0
APC CONST_23       C2      N1      C6      N6         -179.99   0.0 0
APC CONST_24       H8      C8      N9     C1'           -0.04   0.0 0
APC CONST_25       H2      C2      N1      C6          179.95   0.0 0
APC CONST_26      HN61     N6      C6      C5          179.71   0.0 0
APC CONST_27      HN62     N6      C6      C5           -0.55   0.0 0
APC Var_01        C4'     C5'     O5'      PA          179.98  30.0 3
APC Var_02         O1B     PB      O3B     PG          -60.00  30.0 1
APC Var_03         O1A     PA      C3A     PB          -59.99  30.0 1
APC Var_04         PA      C3A     PB      O1B          60.01  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
APC chir_03  C4'     C5'     O4'     C3'    negativ
APC chir_04  C3'     O3'     C4'     C2'    positiv
APC chir_05  C2'     O2'     C3'     C1'    positiv
APC chir_06  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
APC plan-1    C1' 0.020
APC plan-1     N9 0.020
APC plan-1     C8 0.020
APC plan-1     N7 0.020
APC plan-1     C5 0.020
APC plan-1     C6 0.020
APC plan-1     N6 0.020
APC plan-1     N1 0.020
APC plan-1     C2 0.020
APC plan-1     N3 0.020
APC plan-1     C4 0.020
APC plan-1     H8 0.020
APC plan-1     H2 0.020
APC plan-2     C6 0.020
APC plan-2     N6 0.020
APC plan-2   HN61 0.020
APC plan-2   HN62 0.020
