# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 08:38:22 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 9-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphorothioyl]pentofuranosyl}-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)C3CC(O)C(CO[P@@](O)(=S)O[P@@](O)(=O)O[P](O)(O)=O)O3
#
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
 STP  STP  9-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphorothioyl]pentofuranosyl}-9H-purin-6-amine  ligand  46  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_STP
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
 STP  PG    P  P     0   1.460   0.6220   5.2020  -2.6660
 STP  O1G   O  O     0  -0.682  -0.0382   3.9003  -2.8730
 STP  O2G   O  OH1   0  -0.751   0.5275   5.8485  -1.2382
 STP  O3G   O  OH1   0  -0.729   0.2549   6.3804  -3.6640
 STP  PB    P  P     0   1.493   3.0230   4.8647  -4.2605
 STP  O1B   O  O     0  -0.665   2.2234   4.3434  -5.3734
 STP  O2B   O  OH1   0  -0.701   3.7887   6.2327  -4.4486
 STP  O3B   O  O2    0  -0.690   2.2437   5.1546  -2.8904
 STP  PA    P  P     0   1.216   4.2210   2.4598  -3.0245
 STP  S1A   S  S1    0  -0.470   5.8819   1.5264  -3.1947
 STP  O2A   O  OH1   0  -0.736   3.7813   2.8839  -1.5575
 STP  O3A   O  O2    0  -0.661   4.2241   3.8938  -3.7682
 STP  O5'   O  O2    0  -0.568   2.9575   1.7744  -3.7272
 STP  C5'   C  CH2   0  -0.210   2.4516   0.4858  -3.3500
 STP  C4'   C  CH1   0  -0.048   1.5352   0.6067  -2.1607
 STP  O4'   O  O2    0  -0.535   2.2984   0.7629  -0.9652
 STP  C3'   C  CH1   0   0.043   0.6730  -0.6108  -1.8312
 STP  O3'   O  OH1   0  -0.647  -0.3760  -0.8410  -2.7177
 STP  C2'   C  CH2   0  -0.586   0.2694  -0.2878  -0.3832
 STP  C1'   C  CH1   0   0.184   1.4497   0.5255   0.1508
 STP  N9    N  NR5   0  -0.523   1.0967   1.8067   0.7258
 STP  C8    C  CR15  0   0.154   0.3197   2.7618   0.1397
 STP  N7    N  N     0  -0.562   0.4945   3.9467   0.6504
 STP  C5    C  CR56  0   0.067   1.4399   3.7766   1.6347
 STP  C6    C  CR6   0   0.481   2.0525   4.6545   2.5493
 STP  N6    N  NH2   0  -0.814   1.7641   5.9521   2.6190
 STP  N1    N  N     0  -0.468   2.9744   4.1425   3.3719
 STP  C2    C  CR16  0   0.054   3.2707   2.8494   3.2976
 STP  N3    N  N     0  -0.453   2.7555   1.9350   2.4919
 STP  C4    C  CR56  0   0.479   1.8382   2.4543   1.6857
 STP  HOG2  H  HOH1  0   0.510   0.4208   5.2006  -0.4764
 STP  HOG3  H  HOH1  0   0.510  -0.6473   6.3459  -4.0105
 STP  HOB2  H  HOH1  0   0.516   4.1555   6.3734  -5.3336
 STP  HOA2  H  HOH1  0   0.503   3.3603   2.1400  -1.0692
 STP  H5'1  H  HCH2  0   0.285   1.8813   0.1280  -4.2056
 STP  H5'2  H  HCH2  0   0.260   3.2685  -0.2172  -3.1626
 STP  H4'   H  HCH1  0   0.256   0.8872   1.4824  -2.3217
 STP  H3'   H  HCH1  0   0.274   1.2964  -1.5091  -1.8517
 STP  HO3'  H  HOH1  0   0.451  -0.9866  -0.0957  -2.6973
 STP  H2'1  H  HCH2  0   0.285  -0.6573   0.2912  -0.3729
 STP  H2'2  H  HCH2  0   0.306   0.1020  -1.1774   0.2197
 STP  H1'   H  HCH1  0   0.309   2.0267  -0.0074   0.9036
 STP  H8    H  HCR5  0   0.318  -0.3621   2.5523  -0.6689
 STP  HN61  H  HNH2  0   0.410   2.1972   6.5252   3.3233
 STP  HN62  H  HNH2  0   0.415   1.0225   6.3579   2.0759
 STP  H2    H  HCR6  0   0.261   4.0310   2.5031   3.9890

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
 STP  PG   O1G   double    1.474  0.020  1.474
 STP  PG   O2G   single    1.570  0.020  1.570
 STP  PG   O3G   single    1.587  0.020  1.587
 STP  PG   O3B   single    1.638  0.020  1.638
 STP  O2G  HOG2  single    0.850  0.020  0.980
 STP  O3G  HOG3  single    0.850  0.020  0.980
 STP  PB   O1B   double    1.466  0.020  1.466
 STP  PB   O2B   single    1.579  0.020  1.579
 STP  PB   O3B   single    1.603  0.020  1.603
 STP  PB   O3A   single    1.621  0.020  1.621
 STP  O2B  HOB2  single    0.850  0.020  0.980
 STP  PA   S1A   double    1.913  0.020  1.913
 STP  PA   O2A   single    1.589  0.020  1.589
 STP  PA   O3A   single    1.615  0.020  1.615
 STP  PA   O5'   single    1.600  0.020  1.600
 STP  O2A  HOA2  single    0.850  0.020  0.980
 STP  O5'  C5'   single    1.435  0.020  1.435
 STP  C5'  C4'   single    1.506  0.020  1.506
 STP  C5'  H5'1  single    0.970  0.020  1.090
 STP  C5'  H5'2  single    0.970  0.020  1.090
 STP  C4'  O4'   single    1.427  0.020  1.427
 STP  C4'  C3'   single    1.528  0.020  1.528
 STP  C4'  H4'   single    0.970  0.020  1.090
 STP  O4'  C1'   single    1.422  0.020  1.422
 STP  C3'  O3'   single    1.393  0.020  1.393
 STP  C3'  C2'   single    1.538  0.020  1.538
 STP  C3'  H3'   single    0.970  0.020  1.090
 STP  O3'  HO3'  single    0.850  0.020  0.980
 STP  C2'  C1'   single    1.530  0.020  1.530
 STP  C2'  H2'1  single    0.970  0.020  1.090
 STP  C2'  H2'2  single    0.970  0.020  1.090
 STP  C1'  N9    single    1.448  0.020  1.448
 STP  C1'  H1'   single    0.970  0.020  1.090
 STP  N9   C8    aromatic  1.364  0.020  1.364
 STP  N9   C4    aromatic  1.375  0.020  1.375
 STP  C8   N7    aromatic  1.302  0.020  1.302
 STP  C8   H8    single    0.930  0.020  1.080
 STP  N7   C5    aromatic  1.375  0.020  1.375
 STP  C5   C6    aromatic  1.408  0.020  1.408
 STP  C5   C4    aromatic  1.382  0.020  1.382
 STP  C6   N6    single    1.331  0.020  1.331
 STP  C6   N1    aromatic  1.337  0.020  1.337
 STP  N6   HN61  single    0.860  0.020  1.020
 STP  N6   HN62  single    0.860  0.020  1.020
 STP  N1   C2    aromatic  1.329  0.020  1.329
 STP  C2   N3    aromatic  1.323  0.020  1.323
 STP  C2   H2    single    0.930  0.020  1.080
 STP  N3   C4    aromatic  1.327  0.020  1.327

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
 STP  O3B   PG   O3G    99.46  3.000
 STP  O3B   PG   O2G   101.31  3.000
 STP  O3G   PG   O2G   104.60  3.000
 STP  O3B   PG   O1G   113.49  3.000
 STP  O3G   PG   O1G   117.62  3.000
 STP  O2G   PG   O1G   117.67  3.000
 STP  HOG2  O2G  PG    115.46  3.000
 STP  HOG3  O3G  PG    114.49  3.000
 STP  O3A   PB   O3B   102.06  3.000
 STP  O3A   PB   O2B   101.29  3.000
 STP  O3B   PB   O2B   100.43  3.000
 STP  O3A   PB   O1B   114.93  3.000
 STP  O3B   PB   O1B   116.62  3.000
 STP  O2B   PB   O1B   118.82  3.000
 STP  HOB2  O2B  PB    114.74  3.000
 STP  PB    O3B  PG    127.14  3.000
 STP  O5'   PA   O3A   100.34  3.000
 STP  O5'   PA   O2A   107.53  3.000
 STP  O3A   PA   O2A   100.88  3.000
 STP  O5'   PA   S1A   115.95  3.000
 STP  O3A   PA   S1A   112.99  3.000
 STP  O2A   PA   S1A   116.91  3.000
 STP  HOA2  O2A  PA    112.00  3.000
 STP  PA    O3A  PB    132.08  3.000
 STP  C5'   O5'  PA    123.21  3.000
 STP  H5'2  C5'  H5'1  108.33  3.000
 STP  H5'2  C5'  C4'   111.76  3.000
 STP  H5'1  C5'  C4'   109.16  3.000
 STP  H5'2  C5'  O5'   111.03  3.000
 STP  H5'1  C5'  O5'   105.86  3.000
 STP  C4'   C5'  O5'   110.49  3.000
 STP  H4'   C4'  C3'   109.46  3.000
 STP  H4'   C4'  O4'   110.50  3.000
 STP  C3'   C4'  O4'   102.02  3.000
 STP  H4'   C4'  C5'   107.84  3.000
 STP  C3'   C4'  C5'   116.72  3.000
 STP  O4'   C4'  C5'   110.18  3.000
 STP  C1'   O4'  C4'   108.67  3.000
 STP  H3'   C3'  C2'   109.87  3.000
 STP  H3'   C3'  O3'   106.36  3.000
 STP  C2'   C3'  O3'   115.88  3.000
 STP  H3'   C3'  C4'   109.20  3.000
 STP  C2'   C3'  C4'   100.59  3.000
 STP  O3'   C3'  C4'   114.80  3.000
 STP  HO3'  O3'  C3'   109.63  3.000
 STP  H2'2  C2'  H2'1  107.32  3.000
 STP  H2'2  C2'  C1'   111.11  3.000
 STP  H2'1  C2'  C1'   111.67  3.000
 STP  H2'2  C2'  C3'   112.99  3.000
 STP  H2'1  C2'  C3'   110.05  3.000
 STP  C1'   C2'  C3'   103.76  3.000
 STP  H1'   C1'  N9    106.73  3.000
 STP  H1'   C1'  C2'   112.98  3.000
 STP  N9    C1'  C2'   114.90  3.000
 STP  H1'   C1'  O4'   107.95  3.000
 STP  N9    C1'  O4'   108.02  3.000
 STP  C2'   C1'  O4'   105.98  3.000
 STP  C4    N9   C8    106.10  3.000
 STP  C4    N9   C1'   124.23  3.000
 STP  C8    N9   C1'   126.02  3.000
 STP  H8    C8   N7    123.77  3.000
 STP  H8    C8   N9    123.13  3.000
 STP  N7    C8   N9    113.10  3.000
 STP  C5    N7   C8    105.10  3.000
 STP  C4    C5   C6    116.56  3.000
 STP  C4    C5   N7    110.05  3.000
 STP  C6    C5   N7    133.38  3.000
 STP  N1    C6   N6    119.36  3.000
 STP  N1    C6   C5    117.44  3.000
 STP  N6    C6   C5    123.20  3.000
 STP  HN62  N6   HN61  117.78  3.000
 STP  HN62  N6   C6    121.69  3.000
 STP  HN61  N6   C6    119.92  3.000
 STP  C2    N1   C6    119.46  3.000
 STP  H2    C2   N3    116.14  3.000
 STP  H2    C2   N1    115.56  3.000
 STP  N3    C2   N1    128.30  3.000
 STP  C4    N3   C2    111.63  3.000
 STP  N3    C4   C5    126.59  3.000
 STP  N3    C4   N9    127.77  3.000
 STP  C5    C4   N9    105.63  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
 STP  CONST_01  C5    N7   C8   N9    0.00   0.0  0
 STP  CONST_02  N7    C5   C4   N9    0.00   0.0  0
 STP  CONST_03  C6    C5   C4   N9  180.00   0.0  0
 STP  CONST_04  C2    N3   C4   N9  180.00   0.0  0
 STP  CONST_05  C5    C4   N9   C8    0.00   0.0  0
 STP  CONST_06  N3    C4   N9   C8  180.00   0.0  0
 STP  CONST_07  C6    C5   N7   C8  180.00   0.0  0
 STP  CONST_08  C4    C5   N7   C8    0.00   0.0  0
 STP  CONST_09  C4    N9   C8   N7    0.00   0.0  0
 STP  CONST_10  N1    C6   C5   N7  180.00   0.0  0
 STP  CONST_11  N3    C4   C5   N7  180.00   0.0  0
 STP  CONST_12  C2    N1   C6   C5    0.00   0.0  0
 STP  CONST_13  C2    N3   C4   C5    0.00   0.0  0
 STP  CONST_14  N3    C4   C5   C6    0.00   0.0  0
 STP  CONST_15  N3    C2   N1   C6    0.00   0.0  0
 STP  CONST_16  C4    C5   C6   N1    0.00   0.0  0
 STP  CONST_17  C4    N3   C2   N1    0.00   0.0  0
 STP  CONST_21  N6    C6   C5   N7    0.00   0.0  0
 STP  CONST_22  C4    C5   C6   N6  180.00   0.0  0
 STP  CONST_23  C2    N1   C6   N6  180.00   0.0  0
 STP  CONST_25  H2    C2   N1   C6  180.00   0.0  0
 STP  CONST_26  HN61  N6   C6   C5  180.00   0.0  0
 STP  CONST_27  HN62  N6   C6   C5    0.00   0.0  0
 STP  Var_01    C4'   C5'  O5'  PA   83.23  30.0  3
 STP  Var_02    O1B   PB   O3B  PG  -12.32  30.0  1
 STP  Var_03    S1A   PA   O3A  PB  161.22  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
 STP  chir_03  C4'  C5'  O4'  C3'  positiv
 STP  chir_04  C3'  O3'  C4'  C2'  negativ
 STP  chir_05  C1'  O4'  N9   C2'  negativ
 STP  chir_06  PB   O2B  O3B  O3A  both
 STP  chir_07  PA   O5'  O3A  O2A  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
 STP  plan-1  C1'   0.020
 STP  plan-1  N9    0.020
 STP  plan-1  C8    0.020
 STP  plan-1  N7    0.020
 STP  plan-1  C5    0.020
 STP  plan-1  C6    0.020
 STP  plan-1  N6    0.020
 STP  plan-1  N1    0.020
 STP  plan-1  C2    0.020
 STP  plan-1  N3    0.020
 STP  plan-1  C4    0.020
 STP  plan-1  H8    0.020
 STP  plan-1  H2    0.020
 STP  plan-2  C6    0.020
 STP  plan-2  N6    0.020
 STP  plan-2  HN61  0.020
 STP  plan-2  HN62  0.020

