# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 12:12:59 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 5'-O-[(S)-[(8-bromooctanoyl)oxy](hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC(=O)CCCCCCCBr)[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
 SH5  SH5  5'-O-[(S)-[(8-bromooctanoyl)oxy](hydroxy)phosphoryl]adenosine  ligand  60  33  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SH5
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
 SH5  BRA  BR  BR    0  -0.159  -10.6885  -2.8207   1.0609
 SH5  CAB  C   CH2   0  -0.503   -8.7336  -2.7679   1.3363
 SH5  CAC  C   CH2   0  -0.414   -8.1045  -1.5833   0.6373
 SH5  CAD  C   CH2   0  -0.421   -6.5946  -1.5646   0.8699
 SH5  CAE  C   CH2   0  -0.414   -5.9171  -0.3934   0.1691
 SH5  CAF  C   CH2   0  -0.418   -4.4116  -0.3551   0.3983
 SH5  CAG  C   CH2   0  -0.423   -3.7372   0.7985  -0.3332
 SH5  CAH  C   CH2   0  -0.585   -2.2406   0.8328  -0.0694
 SH5  CAI  C   C     0   0.618   -1.5275   1.9182  -0.8116
 SH5  OAJ  O   O     0  -0.404   -1.9964   2.6760  -1.6089
 SH5  OAK  O   O2    0  -0.581   -0.2073   1.9602  -0.4763
 SH5  PAL  P   P     0   1.471    0.8263   2.9967  -1.2006
 SH5  OAN  O   OH1   0  -0.726    0.3738   4.4631  -0.7994
 SH5  OAM  O   O     0  -0.680    0.9888   2.8546  -2.6535
 SH5  O5'  O   O2    0  -0.576    2.0714   2.6119  -0.2886
 SH5  C5'  C   CH2   0  -0.179    3.3823   3.0598  -0.6505
 SH5  C4'  C   CH1   0  -0.044    4.2929   2.8023   0.5312
 SH5  O4'  O   O2    0  -0.487    4.2438   1.4268   0.9086
 SH5  C3'  C   CH1   0  -0.034    5.7497   3.1011   0.1963
 SH5  O3'  O   OH1   0  -0.665    6.4088   3.4757   1.3755
 SH5  C2'  C   CH1   0  -0.048    6.2260   1.7289  -0.2896
 SH5  O2'  O   OH1   0  -0.651    7.5982   1.5072  -0.1803
 SH5  C1'  C   CH1   0   0.212    5.4732   0.8008   0.6625
 SH5  N9   N   NR5   0  -0.539    5.2369  -0.5161   0.1332
 SH5  C8   C   CR15  0   0.115    4.4501  -0.8524  -0.9364
 SH5  N7   N   N     0  -0.448    4.4259  -2.1282  -1.1775
 SH5  C5   C   CR56  0  -0.012    5.2408  -2.6727  -0.2182
 SH5  C4   C   CR56  0   0.493    5.7529  -1.6874   0.6106
 SH5  N3   N   N     0  -0.457    6.5697  -1.8690   1.6448
 SH5  C2   C   CR16  0   0.047    6.8637  -3.1463   1.8163
 SH5  N1   N   N     0  -0.474    6.4550  -4.1924   1.1034
 SH5  C6   C   CR6   0   0.461    5.6327  -3.9937   0.0669
 SH5  N6   N   NH2   0  -0.816    5.2106  -5.0402  -0.6437
 SH5  H1   H   HCH2  0   0.284   -8.5829  -2.7328   2.4146
 SH5  H2   H   HCH2  0   0.285   -8.3503  -3.7143   0.9568
 SH5  H3   H   HCH2  0   0.236   -8.3083  -1.6320  -0.4352
 SH5  H4   H   HCH2  0   0.237   -8.5434  -0.6533   1.0071
 SH5  H5   H   HCH2  0   0.221   -6.3892  -1.5154   1.9441
 SH5  H6   H   HCH2  0   0.221   -6.1571  -2.5033   0.5148
 SH5  H7   H   HCH2  0   0.215   -6.1203  -0.4484  -0.9055
 SH5  H8   H   HCH2  0   0.216   -6.3621   0.5447   0.5171
 SH5  H9   H   HCH2  0   0.217   -4.2083  -0.2788   1.4717
 SH5  H10  H   HCH2  0   0.217   -3.9690  -1.3015   0.0700
 SH5  H11  H   HCH2  0   0.232   -3.9227   0.7041  -1.4061
 SH5  H12  H   HCH2  0   0.232   -4.1888   1.7436  -0.0199
 SH5  H13  H   HCH2  0   0.287   -2.0331   0.9548   0.9980
 SH5  H14  H   HCH2  0   0.289   -1.7747  -0.1181  -0.3504
 SH5  H15  H   HOH1  0   0.505    0.3210   4.6601   0.1465
 SH5  H16  H   HCH2  0   0.248    3.7173   2.5303  -1.5464
 SH5  H17  H   HCH2  0   0.265    3.3880   4.1306  -0.8697
 SH5  H18  H   HCH1  0   0.277    3.9557   3.4087   1.3772
 SH5  H19  H   HCH1  0   0.260    5.8434   3.8671  -0.5850
 SH5  H20  H   HOH1  0   0.452    7.3545   3.3381   1.2453
 SH5  H21  H   HCH1  0   0.252    5.8715   1.5702  -1.3166
 SH5  H22  H   HOH1  0   0.471    8.0367   1.8686  -0.9574
 SH5  H23  H   HCH1  0   0.266    6.0459   0.6611   1.5859
 SH5  H24  H   HCR5  0   0.292    3.9049  -0.1103  -1.5003
 SH5  H25  H   HCR6  0   0.253    7.5244  -3.3771   2.6453
 SH5  H26  H   HNH2  0   0.411    4.6436  -4.9135  -1.4635
 SH5  H27  H   HNH2  0   0.404    5.5608  -5.9615  -0.4454

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
 SH5  O3'  C3'  single    1.402  0.020  1.402
 SH5  O2'  C2'  single    1.394  0.020  1.394
 SH5  C2'  C3'  single    1.532  0.020  1.532
 SH5  C2'  C1'  single    1.528  0.020  1.528
 SH5  C3'  C4'  single    1.524  0.020  1.524
 SH5  C4'  C5'  single    1.514  0.020  1.514
 SH5  C4'  O4'  single    1.427  0.020  1.427
 SH5  OAM  PAL  double    1.469  0.020  1.469
 SH5  C5'  O5'  single    1.432  0.020  1.432
 SH5  C1'  O4'  single    1.401  0.020  1.401
 SH5  C1'  N9   single    1.439  0.020  1.439
 SH5  O5'  PAL  single    1.591  0.020  1.591
 SH5  PAL  OAN  single    1.586  0.020  1.586
 SH5  PAL  OAK  single    1.633  0.020  1.633
 SH5  N9   C8   aromatic  1.370  0.020  1.370
 SH5  N9   C4   aromatic  1.366  0.020  1.366
 SH5  C8   N7   aromatic  1.299  0.020  1.299
 SH5  OAK  CAI  single    1.363  0.020  1.363
 SH5  C4   N3   aromatic  1.330  0.020  1.330
 SH5  C4   C5   aromatic  1.386  0.020  1.386
 SH5  N3   C2   aromatic  1.322  0.020  1.322
 SH5  N7   C5   aromatic  1.371  0.020  1.371
 SH5  CAI  OAJ  double    1.196  0.020  1.196
 SH5  CAI  CAH  single    1.496  0.020  1.496
 SH5  C5   C6   aromatic  1.407  0.020  1.407
 SH5  C2   N1   aromatic  1.330  0.020  1.330
 SH5  CAH  CAG  single    1.520  0.020  1.520
 SH5  C6   N1   aromatic  1.338  0.020  1.338
 SH5  C6   N6   single    1.334  0.020  1.334
 SH5  CAG  CAF  single    1.523  0.020  1.523
 SH5  CAF  CAE  single    1.523  0.020  1.523
 SH5  CAE  CAD  single    1.524  0.020  1.524
 SH5  CAD  CAC  single    1.528  0.020  1.528
 SH5  CAC  CAB  single    1.512  0.020  1.512
 SH5  BRA  CAB  single    1.975  0.020  1.975
 SH5  CAB  H1   single    0.970  0.020  1.090
 SH5  CAB  H2   single    0.970  0.020  1.090
 SH5  CAC  H3   single    0.970  0.020  1.090
 SH5  CAC  H4   single    0.970  0.020  1.090
 SH5  CAD  H5   single    0.970  0.020  1.090
 SH5  CAD  H6   single    0.970  0.020  1.090
 SH5  CAE  H7   single    0.970  0.020  1.090
 SH5  CAE  H8   single    0.970  0.020  1.090
 SH5  CAF  H9   single    0.970  0.020  1.090
 SH5  CAF  H10  single    0.970  0.020  1.090
 SH5  CAG  H11  single    0.970  0.020  1.090
 SH5  CAG  H12  single    0.970  0.020  1.090
 SH5  CAH  H13  single    0.970  0.020  1.090
 SH5  CAH  H14  single    0.970  0.020  1.090
 SH5  OAN  H15  single    0.850  0.020  0.980
 SH5  C5'  H16  single    0.970  0.020  1.090
 SH5  C5'  H17  single    0.970  0.020  1.090
 SH5  C4'  H18  single    0.970  0.020  1.090
 SH5  C3'  H19  single    0.970  0.020  1.090
 SH5  O3'  H20  single    0.850  0.020  0.980
 SH5  C2'  H21  single    0.970  0.020  1.090
 SH5  O2'  H22  single    0.850  0.020  0.980
 SH5  C1'  H23  single    0.970  0.020  1.090
 SH5  C8   H24  single    0.930  0.020  1.080
 SH5  C2   H25  single    0.930  0.020  1.080
 SH5  N6   H26  single    0.860  0.020  1.020
 SH5  N6   H27  single    0.860  0.020  1.020

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
 SH5  H2   CAB  H1   108.92  3.000
 SH5  H2   CAB  CAC  111.91  3.000
 SH5  H1   CAB  CAC  112.00  3.000
 SH5  H2   CAB  BRA  106.06  3.000
 SH5  H1   CAB  BRA  106.01  3.000
 SH5  CAC  CAB  BRA  111.61  3.000
 SH5  H4   CAC  H3   107.17  3.000
 SH5  H4   CAC  CAD  109.57  3.000
 SH5  H3   CAC  CAD  109.52  3.000
 SH5  H4   CAC  CAB  110.07  3.000
 SH5  H3   CAC  CAB  109.94  3.000
 SH5  CAD  CAC  CAB  110.50  3.000
 SH5  H6   CAD  H5   106.37  3.000
 SH5  H6   CAD  CAE  109.40  3.000
 SH5  H5   CAD  CAE  109.47  3.000
 SH5  H6   CAD  CAC  109.57  3.000
 SH5  H5   CAD  CAC  109.59  3.000
 SH5  CAE  CAD  CAC  112.26  3.000
 SH5  H8   CAE  H7   106.23  3.000
 SH5  H8   CAE  CAF  109.41  3.000
 SH5  H7   CAE  CAF  109.41  3.000
 SH5  H8   CAE  CAD  109.37  3.000
 SH5  H7   CAE  CAD  109.28  3.000
 SH5  CAF  CAE  CAD  112.93  3.000
 SH5  H10  CAF  H9   106.20  3.000
 SH5  H10  CAF  CAG  109.36  3.000
 SH5  H9   CAF  CAG  109.62  3.000
 SH5  H10  CAF  CAE  109.43  3.000
 SH5  H9   CAF  CAE  109.43  3.000
 SH5  CAG  CAF  CAE  112.60  3.000
 SH5  H12  CAG  H11  106.62  3.000
 SH5  H12  CAG  CAH  109.72  3.000
 SH5  H11  CAG  CAH  109.84  3.000
 SH5  H12  CAG  CAF  109.52  3.000
 SH5  H11  CAG  CAF  109.32  3.000
 SH5  CAH  CAG  CAF  111.69  3.000
 SH5  H14  CAH  H13  105.45  3.000
 SH5  H14  CAH  CAI  107.44  3.000
 SH5  H13  CAH  CAI  108.22  3.000
 SH5  H14  CAH  CAG  110.77  3.000
 SH5  H13  CAH  CAG  111.01  3.000
 SH5  CAI  CAH  CAG  113.56  3.000
 SH5  OAK  CAI  OAJ  121.63  3.000
 SH5  OAJ  CAI  CAH  127.14  3.000
 SH5  OAK  CAI  CAH  111.23  3.000
 SH5  PAL  OAK  CAI  121.57  3.000
 SH5  O5'  PAL  OAM  117.20  3.000
 SH5  O5'  PAL  OAN  107.57  3.000
 SH5  OAM  PAL  OAN  111.79  3.000
 SH5  OAN  PAL  OAK  107.10  3.000
 SH5  O5'  PAL  OAK   95.02  3.000
 SH5  OAM  PAL  OAK  116.57  3.000
 SH5  H15  OAN  PAL  116.81  3.000
 SH5  C5'  O5'  PAL  119.74  3.000
 SH5  H17  C5'  H16  107.97  3.000
 SH5  H17  C5'  C4'  108.67  3.000
 SH5  H16  C5'  C4'  111.90  3.000
 SH5  H17  C5'  O5'  111.22  3.000
 SH5  H16  C5'  O5'  109.64  3.000
 SH5  C4'  C5'  O5'  107.47  3.000
 SH5  H18  C4'  C3'  110.84  3.000
 SH5  H18  C4'  O4'  108.61  3.000
 SH5  C3'  C4'  O4'  106.25  3.000
 SH5  H18  C4'  C5'  108.90  3.000
 SH5  O4'  C4'  C5'  110.47  3.000
 SH5  C3'  C4'  C5'  111.72  3.000
 SH5  C1'  O4'  C4'  110.73  3.000
 SH5  H19  C3'  C2'  111.88  3.000
 SH5  H19  C3'  O3'  111.84  3.000
 SH5  C2'  C3'  O3'  111.11  3.000
 SH5  H19  C3'  C4'  111.99  3.000
 SH5  C2'  C3'  C4'  101.02  3.000
 SH5  O3'  C3'  C4'  108.48  3.000
 SH5  H20  O3'  C3'  108.02  3.000
 SH5  H21  C2'  C1'  109.63  3.000
 SH5  H21  C2'  O2'  111.60  3.000
 SH5  C1'  C2'  O2'  109.84  3.000
 SH5  H21  C2'  C3'  109.02  3.000
 SH5  C1'  C2'  C3'  101.14  3.000
 SH5  O2'  C2'  C3'  115.06  3.000
 SH5  H22  O2'  C2'  108.98  3.000
 SH5  H23  C1'  N9   106.21  3.000
 SH5  H23  C1'  C2'  110.19  3.000
 SH5  N9   C1'  C2'  114.05  3.000
 SH5  H23  C1'  O4'  111.57  3.000
 SH5  N9   C1'  O4'  109.23  3.000
 SH5  C2'  C1'  O4'  105.68  3.000
 SH5  C4   N9   C8   106.22  3.000
 SH5  C4   N9   C1'  126.45  3.000
 SH5  C8   N9   C1'  127.32  3.000
 SH5  H24  C8   N7   124.67  3.000
 SH5  H24  C8   N9   121.95  3.000
 SH5  N7   C8   N9   113.38  3.000
 SH5  C5   N7   C8   104.42  3.000
 SH5  C6   C5   C4   116.32  3.000
 SH5  C6   C5   N7   132.84  3.000
 SH5  C4   C5   N7   110.84  3.000
 SH5  N3   C4   C5   126.50  3.000
 SH5  C5   C4   N9   105.13  3.000
 SH5  N3   C4   N9   128.36  3.000
 SH5  C2   N3   C4   111.67  3.000
 SH5  H25  C2   N1   115.43  3.000
 SH5  H25  C2   N3   116.11  3.000
 SH5  N1   C2   N3   128.46  3.000
 SH5  C6   N1   C2   119.16  3.000
 SH5  N6   C6   N1   119.40  3.000
 SH5  N6   C6   C5   122.73  3.000
 SH5  N1   C6   C5   117.88  3.000
 SH5  H27  N6   H26  118.23  3.000
 SH5  H27  N6   C6   120.25  3.000
 SH5  H26  N6   C6   120.96  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
 SH5  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 SH5  CONST_02  C2   N3   C4   N9   180.00   0.0  0
 SH5  CONST_03  N7   C5   C4   N9     0.00   0.0  0
 SH5  CONST_04  C6   C5   C4   N9   180.00   0.0  0
 SH5  CONST_05  N3   C4   N9   C8   180.00   0.0  0
 SH5  CONST_06  C5   C4   N9   C8     0.00   0.0  0
 SH5  CONST_07  C4   C5   N7   C8     0.00   0.0  0
 SH5  CONST_08  C6   C5   N7   C8   180.00   0.0  0
 SH5  CONST_09  C4   N9   C8   N7     0.00   0.0  0
 SH5  CONST_10  N3   C4   C5   N7   180.00   0.0  0
 SH5  CONST_11  N1   C6   C5   N7   180.00   0.0  0
 SH5  CONST_12  C2   N3   C4   C5     0.00   0.0  0
 SH5  CONST_13  C2   N1   C6   C5     0.00   0.0  0
 SH5  CONST_14  N1   C2   N3   C4     0.00   0.0  0
 SH5  CONST_15  N1   C6   C5   C4     0.00   0.0  0
 SH5  CONST_16  C6   C5   C4   N3     0.00   0.0  0
 SH5  CONST_17  C6   N1   C2   N3     0.00   0.0  0
 SH5  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 SH5  CONST_19  N3   C4   N9   C1'    0.00   0.0  0
 SH5  CONST_20  C5   C4   N9   C1'  180.00   0.0  0
 SH5  CONST_21  N6   C6   C5   N7     0.00   0.0  0
 SH5  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 SH5  CONST_23  N6   C6   N1   C2   180.00   0.0  0
 SH5  CONST_24  H24  C8   N9   C1'    0.00   0.0  0
 SH5  CONST_25  H25  C2   N3   C4   180.00   0.0  0
 SH5  CONST_26  H26  N6   C6   C5     0.00   0.0  0
 SH5  CONST_27  H27  N6   C6   C5   180.00   0.0  0
 SH5  Var_01    C4'  C5'  O5'  PAL  168.16  30.0  2
 SH5  Var_02    CAD  CAC  CAB  BRA  179.83  30.0  1
 SH5  Var_03    CAE  CAD  CAC  CAB  179.37  30.0  1
 SH5  Var_04    CAF  CAE  CAD  CAC  179.64  30.0  1
 SH5  Var_05    CAG  CAF  CAE  CAD  178.59  30.0  1
 SH5  Var_06    CAH  CAG  CAF  CAE  178.92  30.0  1
 SH5  Var_07    CAI  CAH  CAG  CAF  177.71  30.0  1
 SH5  Var_08    OAK  CAI  CAH  CAG  176.11  30.0  2
 SH5  Var_09    OAM  PAL  OAK  CAI  -60.66  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
 SH5  chir_02  C4'  C3'  C5'  O4'  negativ
 SH5  chir_03  C3'  O3'  C2'  C4'  negativ
 SH5  chir_04  C2'  O2'  C1'  C3'  negativ
 SH5  chir_05  C1'  O4'  N9   C2'  negativ
 SH5  chir_06  PAL  O5'  OAN  OAK  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
 SH5  plan-1  C1'  0.020
 SH5  plan-1  N9   0.020
 SH5  plan-1  C8   0.020
 SH5  plan-1  N7   0.020
 SH5  plan-1  C5   0.020
 SH5  plan-1  C4   0.020
 SH5  plan-1  N3   0.020
 SH5  plan-1  C2   0.020
 SH5  plan-1  N1   0.020
 SH5  plan-1  C6   0.020
 SH5  plan-1  N6   0.020
 SH5  plan-1  H24  0.020
 SH5  plan-1  H25  0.020
 SH5  plan-2  C6   0.020
 SH5  plan-2  N6   0.020
 SH5  plan-2  H26  0.020
 SH5  plan-2  H27  0.020
 SH5  plan-3  CAH  0.020
 SH5  plan-3  CAI  0.020
 SH5  plan-3  OAJ  0.020
 SH5  plan-3  OAK  0.020

