# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul  5 01:54:22 2017
#
#   Inital geometry file: a 108 line input string
#   Ligand name: 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine
#   Quantum optimisation: True
#   Method: AM1
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCC[C@H]([NH3+])C(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
SAO        SAO '5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine' ligand 46 26 .
2017-07-05 2017-07-05
;
CIF prepared directly in eLBOW
;
#
data_comp_SAO
#
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
SAO         N      N   NT3    1    .       4.1910    1.6764    0.3379
SAO         CA     C   CH1    0    .       4.5055    0.5874    1.3052
SAO         CB     C   CH2    0    .       4.5927   -0.7868    0.6644
SAO         CG     C   CH2    0    .       3.2743   -1.3226    0.1724
SAO         SD     S   S2     0    .       2.9559   -0.6378   -1.4417
SAO         C      C   C      0    .       5.9225    0.8894    2.0092
SAO         O      O   O      0    .       6.5846    1.8190    1.4838
SAO         OXT    O   OC    -1    .       6.1790    0.1628    2.9835
SAO        C5'     C   CH2    0    .       1.1929   -0.5701   -1.5436
SAO        C4'     C   CR15   0    .       0.7018    0.8647   -1.5251
SAO        O4'     O   O      0    .      -0.6436    0.9104   -2.0255
SAO        C3'     C   CR15   0    .       0.7153    1.5002   -0.1179
SAO        O3'     O   OH1    0    .       1.5540    2.6324   -0.0803
SAO        C2'     C   CR15   0    .      -0.7606    1.7942    0.2222
SAO        O2'     O   OH1    0    .      -0.9347    3.1929    0.2797
SAO        C1'     C   CR15   0    .      -1.5759    1.2298   -0.9888
SAO         N9     N   NR5    0    .      -2.3748    0.0743   -0.6560
SAO         C8     C   CR15   0    .      -2.4492   -1.1706   -1.3319
SAO         N7     N   N      0    .      -3.3972   -1.9833   -0.8474
SAO         C5     C   CR56   0    .      -4.0087   -1.2607    0.1891
SAO         C6     C   CR6    0    .      -5.0871   -1.5631    1.0892
SAO         N6     N   NH2    0    .      -5.7115   -2.7772    1.0354
SAO         N1     N   N      0    .      -5.4678   -0.6088    2.0079
SAO         C2     C   CR16   0    .      -4.7923    0.5684    2.0125
SAO         N3     N   N      0    .      -3.7633    0.9894    1.2366
SAO         C4     C   CR56   0    .      -3.3840    0.0486    0.3202
SAO         HN2    H   HNT3   0    .       5.0965    2.1184    0.0849
SAO         H3     H   HNT3   0    .       3.7131    1.3110   -0.4990
SAO         HN1    H   HNT3   0    .       3.5996    2.3794    0.7815
SAO         HA     H   HCH1   0    .       3.7194    0.5935    2.1081
SAO         HB1    H   HCH2   0    .       5.3473   -0.7871   -0.1681
SAO         HB2    H   HCH2   0    .       4.9962   -1.4704    1.4682
SAO         HG2    H   HCH2   0    .       3.3254   -2.4358    0.0795
SAO         HG1    H   HCH2   0    .       2.4468   -1.0767    0.8798
SAO        H5'2    H   HCH2   0    .       0.9056   -1.0330   -2.5234
SAO        H5'1    H   HCH2   0    .       0.7120   -1.1687   -0.7336
SAO        H4'     H   HCR5   0    .       1.2990    1.4893   -2.2491
SAO        H3'     H   HCR5   0    .       1.1576    0.7967    0.6417
SAO        HO3'    H   HOH1   0    .       1.0734    3.3915   -0.4402
SAO        H2'     H   HCR5   0    .      -1.0451    1.3156    1.1961
SAO        HO2'    H   HOH1   0    .      -1.7568    3.3555    0.7632
SAO        H1'     H   HCR5   0    .      -2.2485    2.0312   -1.4246
SAO         H8     H   HCR5   0    .      -1.7698   -1.3909   -2.1659
SAO        HN61    H   HNH2   0    .      -5.4364   -3.4286    0.3430
SAO        HN62    H   HNH2   0    .      -6.4700   -2.9852    1.6362
SAO         H2     H   HCR6   0    .      -5.1431    1.2994    2.7741
#
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
SAO   N6      C6    single        1.366 0.020     1.366
SAO   C6      C5    aromatic      1.437 0.020     1.437
SAO   C6      N1    aromatic      1.378 0.020     1.378
SAO   N7      C5    aromatic      1.404 0.020     1.404
SAO   N7      C8    aromatic      1.339 0.020     1.339
SAO   C5      C4    aromatic      1.457 0.020     1.457
SAO   N1      C2    aromatic      1.357 0.020     1.357
SAO   C8      N9    aromatic      1.419 0.020     1.419
SAO   C4      N9    aromatic      1.404 0.020     1.404
SAO   C4      N3    aromatic      1.367 0.020     1.367
SAO   C2      N3    aromatic      1.356 0.020     1.356
SAO   N9     C1'    single        1.444 0.020     1.444
SAO  C1'     C2'    single        1.565 0.020     1.565
SAO  C1'     O4'    single        1.430 0.020     1.430
SAO  C2'     O2'    single        1.411 0.020     1.411
SAO  C2'     C3'    single        1.543 0.020     1.543
SAO  O4'     C4'    single        1.436 0.020     1.436
SAO  C5'     C4'    single        1.517 0.020     1.517
SAO  C5'      SD    single        1.767 0.020     1.767
SAO  C3'     C4'    single        1.544 0.020     1.544
SAO  C3'     O3'    single        1.409 0.020     1.409
SAO   SD      CG    single        1.782 0.020     1.782
SAO   CG      CB    single        1.506 0.020     1.506
SAO   CB      CA    single        1.519 0.020     1.519
SAO   N       CA    single        1.490 0.020     1.490
SAO   CA      C     single        1.611 0.020     1.611
SAO   O       C     deloc         1.256 0.020     1.256
SAO   C       OXT   deloc         1.242 0.020     1.242
SAO   N       HN2   single        0.890 0.020     1.040
SAO   N       H3    single        0.890 0.020     1.040
SAO   N       HN1   single        0.890 0.020     1.040
SAO   CA      HA    single        0.970 0.020     1.090
SAO   CB      HB1   single        0.970 0.020     1.090
SAO   CB      HB2   single        0.970 0.020     1.090
SAO   CG      HG2   single        0.970 0.020     1.090
SAO   CG      HG1   single        0.970 0.020     1.090
SAO  C5'     H5'2   single        0.970 0.020     1.090
SAO  C5'     H5'1   single        0.970 0.020     1.090
SAO  C4'     H4'    single        0.970 0.020     1.090
SAO  C3'     H3'    single        0.970 0.020     1.090
SAO  O3'     HO3'   single        0.850 0.020     0.980
SAO  C2'     H2'    single        0.970 0.020     1.090
SAO  O2'     HO2'   single        0.850 0.020     0.980
SAO  C1'     H1'    single        0.970 0.020     1.090
SAO   C8      H8    single        0.930 0.020     1.080
SAO   N6     HN61   single        0.860 0.020     1.020
SAO   N6     HN62   single        0.860 0.020     1.020
SAO   C2      H2    single        0.930 0.020     1.080
#
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
SAO   HN1     N       H3          109.18 3.000
SAO   HN1     N       HN2         108.54 3.000
SAO   H3      N       HN2         110.93 3.000
SAO   HN1     N       CA          110.10 3.000
SAO   H3      N       CA          111.46 3.000
SAO   HN2     N       CA          106.56 3.000
SAO   HA      CA      C           107.58 3.000
SAO   HA      CA      CB          110.28 3.000
SAO   C       CA      CB          107.67 3.000
SAO   HA      CA      N           108.19 3.000
SAO   C       CA      N           109.41 3.000
SAO   CB      CA      N           113.55 3.000
SAO   HB2     CB      HB1         106.69 3.000
SAO   HB2     CB      CG          109.26 3.000
SAO   HB1     CB      CG          110.23 3.000
SAO   HB2     CB      CA          105.54 3.000
SAO   HB1     CB      CA          110.57 3.000
SAO   CG      CB      CA          114.17 3.000
SAO   HG1     CG      HG2         107.81 3.000
SAO   HG1     CG      SD          110.92 3.000
SAO   HG2     CG      SD          108.39 3.000
SAO   HG1     CG      CB          111.32 3.000
SAO   HG2     CG      CB          109.96 3.000
SAO   SD      CG      CB          108.40 3.000
SAO  C5'      SD      CG          104.20 3.000
SAO   OXT     C       O           130.69 3.000
SAO   OXT     C       CA          114.51 3.000
SAO   O       C       CA          114.80 3.000
SAO  H5'1    C5'     H5'2         107.60 3.000
SAO  H5'1    C5'     C4'          111.04 3.000
SAO  H5'2    C5'     C4'          108.56 3.000
SAO  H5'1    C5'      SD          111.56 3.000
SAO  H5'2    C5'      SD          106.88 3.000
SAO  C4'     C5'      SD          111.02 3.000
SAO  H4'     C4'     C3'          110.64 3.000
SAO  H4'     C4'     O4'          104.76 3.000
SAO  C3'     C4'     O4'          108.22 3.000
SAO  H4'     C4'     C5'          110.16 3.000
SAO  C3'     C4'     C5'          113.43 3.000
SAO  O4'     C4'     C5'          109.22 3.000
SAO  C1'     O4'     C4'          111.42 3.000
SAO  H3'     C3'     C2'          110.25 3.000
SAO  H3'     C3'     O3'          104.48 3.000
SAO  C2'     C3'     O3'          114.23 3.000
SAO  H3'     C3'     C4'          111.17 3.000
SAO  O3'     C3'     C4'          111.11 3.000
SAO  C2'     C3'     C4'          105.72 3.000
SAO  HO3'    O3'     C3'          108.94 3.000
SAO  H2'     C2'     C1'          112.69 3.000
SAO  H2'     C2'     O2'          110.88 3.000
SAO  C1'     C2'     O2'          108.95 3.000
SAO  H2'     C2'     C3'          110.65 3.000
SAO  O2'     C2'     C3'          108.42 3.000
SAO  C1'     C2'     C3'          105.01 3.000
SAO  HO2'    O2'     C2'          106.97 3.000
SAO  H1'     C1'      N9          109.03 3.000
SAO  H1'     C1'     C2'          110.59 3.000
SAO   N9     C1'     C2'          113.49 3.000
SAO  H1'     C1'     O4'          105.42 3.000
SAO  C2'     C1'     O4'          107.56 3.000
SAO   N9     C1'     O4'          110.43 3.000
SAO   C4      N9      C8          106.11 3.000
SAO   C4      N9     C1'          124.93 3.000
SAO   C8      N9     C1'          128.44 3.000
SAO   H8      C8      N7          126.23 3.000
SAO   H8      C8      N9          120.36 3.000
SAO   N7      C8      N9          113.41 3.000
SAO   C5      N7      C8          105.26 3.000
SAO   C4      C5      C6          117.04 3.000
SAO   C4      C5      N7          110.02 3.000
SAO   C6      C5      N7          132.94 3.000
SAO   N1      C6      N6          121.01 3.000
SAO   N1      C6      C5          118.63 3.000
SAO   N6      C6      C5          120.35 3.000
SAO  HN62     N6     HN61         119.95 3.000
SAO  HN62     N6      C6          120.87 3.000
SAO  HN61     N6      C6          119.04 3.000
SAO   C2      N1      C6          117.73 3.000
SAO   H2      C2      N3          115.29 3.000
SAO   H2      C2      N1          114.53 3.000
SAO   N3      C2      N1          130.18 3.000
SAO   C4      N3      C2          112.37 3.000
SAO   N3      C4      C5          124.05 3.000
SAO   N3      C4      N9          130.75 3.000
SAO   C5      C4      N9          105.19 3.000
#
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
SAO CONST_01       C5      N7      C8      N9            0.80   0.0 0
SAO CONST_02       C6      C5      C4      N9          179.61   0.0 0
SAO CONST_03       N7      C5      C4      N9           -0.73   0.0 0
SAO CONST_04       C2      N3      C4      N9         -179.73   0.0 0
SAO CONST_05       C6      C5      N7      C8          179.56   0.0 0
SAO CONST_06       C4      C5      N7      C8           -0.02   0.0 0
SAO CONST_07       C5      C4      N9      C8            1.14   0.0 0
SAO CONST_08       N3      C4      N9      C8         -179.19   0.0 0
SAO CONST_09       N1      C6      C5      N7         -179.27   0.0 0
SAO CONST_10       N3      C4      C5      N7          179.58   0.0 0
SAO CONST_11       C4      N9      C8      N7           -1.28   0.0 0
SAO CONST_12       C2      N1      C6      C5           -0.28   0.0 0
SAO CONST_13       C2      N3      C4      C5           -0.13   0.0 0
SAO CONST_14       N3      C4      C5      C6           -0.08   0.0 0
SAO CONST_15       N3      C2      N1      C6            0.05   0.0 0
SAO CONST_16       C4      C5      C6      N1            0.29   0.0 0
SAO CONST_17       C4      N3      C2      N1            0.16   0.0 0
SAO CONST_18       N7      C8      N9     C1'         -173.19   0.0 0
SAO CONST_19       C5      C4      N9     C1'          173.42   0.0 0
SAO CONST_20       N3      C4      N9     C1'           -6.92   0.0 0
SAO CONST_21       N6      C6      C5      N7            1.16   0.0 0
SAO CONST_22       C4      C5      C6      N6         -179.28   0.0 0
SAO CONST_23       C2      N1      C6      N6          179.28   0.0 0
SAO CONST_24       H8      C8      N9     C1'            6.75   0.0 0
SAO CONST_25       H2      C2      N1      C6          179.98   0.0 0
SAO CONST_26      HN61     N6      C6      C5           -2.61   0.0 0
SAO CONST_27      HN62     N6      C6      C5         -178.44   0.0 0
SAO Var_01        C4'     C5'      SD      CG          110.87  30.0 1
SAO Var_02         SD      CG      CB      CA           83.02  30.0 1
#
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
SAO chir_01   CA      CB      N       C     positiv
SAO chir_02  C4'     O4'     C5'     C3'    positiv
SAO chir_03  C3'     O3'     C4'     C2'    positiv
SAO chir_04  C2'     O2'     C3'     C1'    positiv
SAO 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
SAO plan-1    C1' 0.020
SAO plan-1     N9 0.020
SAO plan-1     C8 0.020
SAO plan-1     N7 0.020
SAO plan-1     C5 0.020
SAO plan-1     C6 0.020
SAO plan-1     N6 0.020
SAO plan-1     N1 0.020
SAO plan-1     C2 0.020
SAO plan-1     N3 0.020
SAO plan-1     C4 0.020
SAO plan-1     H8 0.020
SAO plan-1     H2 0.020
SAO plan-2     C6 0.020
SAO plan-2     N6 0.020
SAO plan-2   HN61 0.020
SAO plan-2   HN62 0.020
SAO plan-3     CA 0.020
SAO plan-3      C 0.020
SAO plan-3      O 0.020
SAO plan-3    OXT 0.020
