# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 20:17:30 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)C[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
 A12  A12  5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]adenosine  ligand  44  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_A12
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
 A12  PB    P  P     0   1.375  -3.7515   2.3823  -0.4546
 A12  O1B   O  O     0  -0.699  -3.7985   2.9743   0.8994
 A12  O2B   O  OH1   0  -0.740  -2.5008   2.9742  -1.2641
 A12  O3B   O  OH1   0  -0.738  -5.0443   2.5756  -1.3815
 A12  PA    P  P     0   1.379  -2.4294  -0.0507   0.7265
 A12  O1A   O  O     0  -0.689  -2.8981  -0.0599   2.1274
 A12  O2A   O  OH1   0  -0.742  -1.0898   0.8224   0.6007
 A12  C3A   C  CH2   0  -1.038  -3.6018   0.5809  -0.4948
 A12  O5'   O  O2    0  -0.589  -2.1090  -1.4832   0.0785
 A12  C5'   C  CH2   0  -0.190  -1.1866  -2.3935   0.6803
 A12  C4'   C  CH1   0  -0.016  -0.0523  -2.6500  -0.2911
 A12  O4'   O  O2    0  -0.501   0.6381  -1.4304  -0.5778
 A12  C3'   C  CH1   0  -0.040   0.9897  -3.6110   0.2717
 A12  O3'   O  OH1   0  -0.665   1.5585  -4.3238  -0.7936
 A12  C2'   C  CH1   0  -0.051   2.0001  -2.6361   0.8828
 A12  O2'   O  OH1   0  -0.651   3.2964  -3.1320   1.0110
 A12  C1'   C  CH1   0   0.218   1.9756  -1.5124  -0.1497
 A12  N9    N  NR5   0  -0.551   2.4095  -0.2372   0.3433
 A12  C8    C  CR15  0   0.112   2.0191   0.4088   1.4892
 A12  N7    N  N     0  -0.446   2.5562   1.5818   1.6271
 A12  C5    C  CR56  0  -0.009   3.3428   1.7334   0.5128
 A12  C6    C  CR6   0   0.462   4.1777   2.7734   0.0632
 A12  N6    N  NH2   0  -0.815   4.3505   3.9061   0.7436
 A12  N1    N  N     0  -0.474   4.8171   2.6034  -1.0999
 A12  C2    C  CR16  0   0.047   4.6414   1.4729  -1.7777
 A12  N3    N  N     0  -0.458   3.8896   0.4329  -1.4594
 A12  C4    C  CR56  0   0.494   3.2621   0.6172  -0.3016
 A12  HOB2  H  HOH1  0   0.494  -2.4335   2.7152  -2.1925
 A12  HXT   H  HOH1  0   0.499  -5.3525   3.4905  -1.4493
 A12  HOA2  H  HOH1  0   0.488  -0.5732   0.6873  -0.2052
 A12  H3A1  H  HCH2  0   0.339  -3.3216   0.2501  -1.4972
 A12  H3A2  H  HCH2  0   0.343  -4.5770   0.1428  -0.2689
 A12  H5'1  H  HCH2  0   0.271  -1.7167  -3.3271   0.8736
 A12  H5'2  H  HCH2  0   0.238  -0.8198  -2.0224   1.6429
 A12  H4'   H  HCH1  0   0.275  -0.4712  -3.0444  -1.2220
 A12  H3'   H  HCH1  0   0.260   0.5588  -4.2810   1.0271
 A12  HO3'  H  HOH1  0   0.452   2.4080  -4.6734  -0.4994
 A12  H2'   H  HCH1  0   0.253   1.6064  -2.2771   1.8423
 A12  HO2'  H  HOH1  0   0.472   3.3659  -3.6175   1.8393
 A12  H1'   H  HCH1  0   0.265   2.6408  -1.7574  -0.9842
 A12  H8    H  HCR5  0   0.296   1.3317  -0.0377   2.1914
 A12  HN61  H  HNH2  0   0.405   4.9541   4.6264   0.3868
 A12  HN62  H  HNH2  0   0.412   3.8844   4.0649   1.6193
 A12  H2    H  HCR6  0   0.254   5.1876   1.4003  -2.7121

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
 A12  PB   O1B   double    1.479  0.020  1.479
 A12  PB   O2B   single    1.603  0.020  1.603
 A12  PB   O3B   single    1.602  0.020  1.602
 A12  PB   C3A   single    1.808  0.020  1.808
 A12  O2B  HOB2  single    0.850  0.020  0.980
 A12  O3B  HXT   single    0.850  0.020  0.980
 A12  PA   O1A   double    1.477  0.020  1.477
 A12  PA   O2A   single    1.604  0.020  1.604
 A12  PA   C3A   single    1.807  0.020  1.807
 A12  PA   O5'   single    1.604  0.020  1.604
 A12  O2A  HOA2  single    0.850  0.020  0.980
 A12  C3A  H3A1  single    0.970  0.020  1.090
 A12  C3A  H3A2  single    0.970  0.020  1.090
 A12  O5'  C5'   single    1.429  0.020  1.429
 A12  C5'  C4'   single    1.515  0.020  1.515
 A12  C5'  H5'1  single    0.970  0.020  1.090
 A12  C5'  H5'2  single    0.970  0.020  1.090
 A12  C4'  O4'   single    1.430  0.020  1.430
 A12  C4'  C3'   single    1.525  0.020  1.525
 A12  C4'  H4'   single    0.970  0.020  1.090
 A12  O4'  C1'   single    1.407  0.020  1.407
 A12  C3'  O3'   single    1.402  0.020  1.402
 A12  C3'  C2'   single    1.531  0.020  1.531
 A12  C3'  H3'   single    0.970  0.020  1.090
 A12  O3'  HO3'  single    0.850  0.020  0.980
 A12  C2'  O2'   single    1.394  0.020  1.394
 A12  C2'  C1'   single    1.526  0.020  1.526
 A12  C2'  H2'   single    0.970  0.020  1.090
 A12  O2'  HO2'  single    0.850  0.020  0.980
 A12  C1'  N9    single    1.434  0.020  1.434
 A12  C1'  H1'   single    0.970  0.020  1.090
 A12  N9   C8    aromatic  1.372  0.020  1.372
 A12  N9   C4    aromatic  1.369  0.020  1.369
 A12  C8   N7    aromatic  1.297  0.020  1.297
 A12  C8   H8    single    0.930  0.020  1.080
 A12  N7   C5    aromatic  1.372  0.020  1.372
 A12  C5   C6    aromatic  1.407  0.020  1.407
 A12  C5   C4    aromatic  1.384  0.020  1.384
 A12  C6   N6    single    1.333  0.020  1.333
 A12  C6   N1    aromatic  1.338  0.020  1.338
 A12  N6   HN61  single    0.860  0.020  1.020
 A12  N6   HN62  single    0.860  0.020  1.020
 A12  N1   C2    aromatic  1.330  0.020  1.330
 A12  C2   N3    aromatic  1.322  0.020  1.322
 A12  C2   H2    single    0.930  0.020  1.080
 A12  N3   C4    aromatic  1.330  0.020  1.330

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
 A12  C3A   PB   O3B   100.03  3.000
 A12  C3A   PB   O2B   106.98  3.000
 A12  O3B   PB   O2B   107.03  3.000
 A12  C3A   PB   O1B   114.96  3.000
 A12  O3B   PB   O1B   117.11  3.000
 A12  O2B   PB   O1B   109.84  3.000
 A12  HOB2  O2B  PB    116.14  3.000
 A12  HXT   O3B  PB    114.30  3.000
 A12  O5'   PA   C3A    99.71  3.000
 A12  O5'   PA   O2A   106.71  3.000
 A12  C3A   PA   O2A   107.37  3.000
 A12  O5'   PA   O1A   116.15  3.000
 A12  C3A   PA   O1A   115.93  3.000
 A12  O2A   PA   O1A   110.05  3.000
 A12  HOA2  O2A  PA    115.83  3.000
 A12  H3A2  C3A  H3A1  107.30  3.000
 A12  H3A2  C3A  PA    107.41  3.000
 A12  H3A1  C3A  PA    110.36  3.000
 A12  H3A2  C3A  PB    108.72  3.000
 A12  H3A1  C3A  PB    110.09  3.000
 A12  PA    C3A  PB    112.77  3.000
 A12  C5'   O5'  PA    121.84  3.000
 A12  H5'2  C5'  H5'1  107.28  3.000
 A12  H5'2  C5'  C4'   111.73  3.000
 A12  H5'1  C5'  C4'   109.42  3.000
 A12  H5'2  C5'  O5'   111.75  3.000
 A12  H5'1  C5'  O5'   107.83  3.000
 A12  C4'   C5'  O5'   108.73  3.000
 A12  H4'   C4'  C3'   110.38  3.000
 A12  H4'   C4'  O4'   108.76  3.000
 A12  C3'   C4'  O4'   106.35  3.000
 A12  H4'   C4'  C5'   108.65  3.000
 A12  C3'   C4'  C5'   112.43  3.000
 A12  O4'   C4'  C5'   110.21  3.000
 A12  C1'   O4'  C4'   110.38  3.000
 A12  H3'   C3'  C2'   111.90  3.000
 A12  H3'   C3'  O3'   111.82  3.000
 A12  C2'   C3'  O3'   111.05  3.000
 A12  H3'   C3'  C4'   111.73  3.000
 A12  C2'   C3'  C4'   101.36  3.000
 A12  O3'   C3'  C4'   108.49  3.000
 A12  HO3'  O3'  C3'   108.05  3.000
 A12  H2'   C2'  C1'   110.17  3.000
 A12  H2'   C2'  O2'   111.69  3.000
 A12  C1'   C2'  O2'   109.82  3.000
 A12  H2'   C2'  C3'   108.69  3.000
 A12  C1'   C2'  C3'   100.85  3.000
 A12  O2'   C2'  C3'   115.08  3.000
 A12  HO2'  O2'  C2'   109.01  3.000
 A12  H1'   C1'  N9    106.09  3.000
 A12  H1'   C1'  C2'   109.95  3.000
 A12  N9    C1'  C2'   114.66  3.000
 A12  H1'   C1'  O4'   111.02  3.000
 A12  N9    C1'  O4'   109.90  3.000
 A12  C2'   C1'  O4'   105.31  3.000
 A12  C4    N9   C8    106.07  3.000
 A12  C4    N9   C1'   125.56  3.000
 A12  C8    N9   C1'   128.28  3.000
 A12  H8    C8   N7    124.65  3.000
 A12  H8    C8   N9    121.99  3.000
 A12  N7    C8   N9    113.36  3.000
 A12  C5    N7   C8    104.53  3.000
 A12  C4    C5   C6    116.26  3.000
 A12  C4    C5   N7    110.81  3.000
 A12  C6    C5   N7    132.93  3.000
 A12  N1    C6   N6    119.33  3.000
 A12  N1    C6   C5    117.86  3.000
 A12  N6    C6   C5    122.81  3.000
 A12  HN62  N6   HN61  118.35  3.000
 A12  HN62  N6   C6    121.28  3.000
 A12  HN61  N6   C6    120.38  3.000
 A12  C2    N1   C6    119.20  3.000
 A12  H2    C2   N3    116.17  3.000
 A12  H2    C2   N1    115.43  3.000
 A12  N3    C2   N1    128.39  3.000
 A12  C4    N3   C2    111.65  3.000
 A12  N3    C4   C5    126.63  3.000
 A12  N3    C4   N9    128.15  3.000
 A12  C5    C4   N9    105.22  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
 A12  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 A12  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 A12  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 A12  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 A12  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 A12  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 A12  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 A12  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 A12  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 A12  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 A12  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 A12  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 A12  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 A12  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 A12  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 A12  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 A12  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 A12  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 A12  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 A12  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 A12  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 A12  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 A12  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 A12  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 A12  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 A12  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 A12  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 A12  Var_01    C4'   C5'  O5'  PA   -119.00  30.0  3
 A12  Var_02    O1A   PA   C3A  PB     75.31  30.0  1
 A12  Var_03    PA    C3A  PB   O1B   -41.96  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
 A12  chir_02  C4'  C5'  O4'  C3'  negativ
 A12  chir_03  C3'  O3'  C4'  C2'  positiv
 A12  chir_04  C2'  O2'  C3'  C1'  positiv
 A12  chir_05  C1'  O4'  N9   C2'  negativ
 A12  chir_06  PA   O2A  C3A  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
 A12  plan-1  C1'   0.020
 A12  plan-1  N9    0.020
 A12  plan-1  C8    0.020
 A12  plan-1  N7    0.020
 A12  plan-1  C5    0.020
 A12  plan-1  C6    0.020
 A12  plan-1  N6    0.020
 A12  plan-1  N1    0.020
 A12  plan-1  C2    0.020
 A12  plan-1  N3    0.020
 A12  plan-1  C4    0.020
 A12  plan-1  H8    0.020
 A12  plan-1  H2    0.020
 A12  plan-2  C6    0.020
 A12  plan-2  N6    0.020
 A12  plan-2  HN61  0.020
 A12  plan-2  HN62  0.020

