# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 18:27:10 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1
#
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
 NYW  NYW  '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  46  28  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NYW
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
 NYW  C6    C  CR6   0   0.453  -4.1328  -2.6545  -0.0240
 NYW  C4    C  CR56  0   0.507  -3.2216  -0.4848  -0.2583
 NYW  C2    C  CR6   0   0.525  -5.1773  -0.9442  -1.1668
 NYW  PB    P  P     0   1.372   4.3335  -1.9334  -0.7208
 NYW  O1B   O  OH1   0  -0.739   3.9517  -2.6897   0.6401
 NYW  O2B   O  O     0  -0.699   5.7397  -1.4778  -0.6647
 NYW  O3B   O  OH1   0  -0.735   3.9411  -2.8987  -1.9368
 NYW  PA    P  P     0   1.395   2.8240   0.3557   0.5531
 NYW  O1A   O  OH1   0  -0.733   4.2634   0.7033   1.1631
 NYW  O2A   O  O     0  -0.687   1.9852  -0.2868   1.5908
 NYW  C3A   C  CH2   0  -1.046   3.1119  -0.6165  -0.9417
 NYW  C5'   C  CH2   0  -0.178   1.3547   2.5603   0.6533
 NYW  C4'   C  CH1   0  -0.021   0.1462   2.8514  -0.2129
 NYW  O4'   O  O2    0  -0.491  -0.4610   1.6303  -0.6385
 NYW  C3'   C  CH1   0  -0.046  -0.9207   3.6219   0.5602
 NYW  O3'   O  OH1   0  -0.666  -1.6087   4.4592  -0.3307
 NYW  C2'   C  CH1   0  -0.041  -1.8189   2.4793   1.0458
 NYW  O2'   O  OH1   0  -0.652  -3.1348   2.8464   1.3278
 NYW  C1'   C  CH1   0   0.224  -1.7770   1.5491  -0.1628
 NYW  N9    N  NR5   0  -0.551  -2.0898   0.1772   0.1243
 NYW  C8    C  CR15  0   0.079  -1.3280  -0.7260   0.8291
 NYW  N7    N  N     0  -0.452  -1.8848  -1.8943   0.9220
 NYW  C5    C  CR56  0  -0.049  -3.0767  -1.7652   0.2493
 NYW  N6    N  NH2   0  -0.820  -4.1381  -3.9159   0.4221
 NYW  N1    N  N     0  -0.521  -5.1688  -2.2147  -0.7336
 NYW  N3    N  N     0  -0.513  -4.2413  -0.0167  -0.9664
 NYW  N2    N  NH2   0  -0.824  -6.2458  -0.5852  -1.9231
 NYW  H1    H  HOH1  0   0.493   3.0531  -3.0412   0.6961
 NYW  H2    H  HOH1  0   0.499   4.5971  -3.5855  -2.1223
 NYW  H3    H  HOH1  0   0.493   4.9162   1.0557   0.5434
 NYW  H3A2  H  HCH2  0   0.344   3.4670   0.0297  -1.7483
 NYW  H3A1  H  HCH2  0   0.339   2.1511  -1.0288  -1.2595
 NYW  H5'2  H  HCH2  0   0.239   1.0627   2.1018   1.6012
 NYW  H5'1  H  HCH2  0   0.263   1.8720   3.4945   0.8783
 NYW  H4'   H  HCH1  0   0.269   0.4638   3.4143  -1.0963
 NYW  H3'   H  HCH1  0   0.256  -0.4898   4.1871   1.3976
 NYW  HO3'  H  HOH1  0   0.450  -2.4625   4.6745   0.0628
 NYW  H2'   H  HCH1  0   0.248  -1.3424   1.9840   1.9022
 NYW  HO2'  H  HOH1  0   0.470  -3.1804   3.1707   2.2326
 NYW  H1'   H  HCH1  0   0.256  -2.5043   1.8789  -0.9137
 NYW  H8    H  HCR5  0   0.297  -0.3579  -0.4676   1.2288
 NYW  HN61  H  HNH2  0   0.406  -3.3152  -4.3059   0.8471
 NYW  HN62  H  HNH2  0   0.398  -4.8432  -4.5555   0.0985
 NYW  H22   H  HNH2  0   0.387  -7.0677  -1.1616  -1.8622
 NYW  H21   H  HNH2  0   0.387  -6.4154   0.3991  -2.0420
 NYW  O5'   O  O2    0  -0.586   2.2417   1.7094  -0.0735

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
 NYW  N2   C2    single    1.357  0.020  1.357
 NYW  C2   N1    aromatic  1.342  0.020  1.342
 NYW  C2   N3    aromatic  1.333  0.020  1.333
 NYW  N1   C6    aromatic  1.330  0.020  1.330
 NYW  N3   C4    aromatic  1.327  0.020  1.327
 NYW  O2'  C2'   single    1.395  0.020  1.395
 NYW  C6   N6    single    1.338  0.020  1.338
 NYW  C6   C5    aromatic  1.407  0.020  1.407
 NYW  C4   C5    aromatic  1.385  0.020  1.385
 NYW  C4   N9    aromatic  1.366  0.020  1.366
 NYW  C2'  C1'   single    1.526  0.020  1.526
 NYW  C2'  C3'   single    1.532  0.020  1.532
 NYW  C5   N7    aromatic  1.375  0.020  1.375
 NYW  C1'  N9    single    1.436  0.020  1.436
 NYW  C1'  O4'   single    1.402  0.020  1.402
 NYW  N9   C8    aromatic  1.376  0.020  1.376
 NYW  O3'  C3'   single    1.403  0.020  1.403
 NYW  C3'  C4'   single    1.526  0.020  1.526
 NYW  N7   C8    aromatic  1.297  0.020  1.297
 NYW  O4'  C4'   single    1.429  0.020  1.429
 NYW  C4'  C5'   single    1.515  0.020  1.515
 NYW  C5'  O5'   single    1.428  0.020  1.428
 NYW  O5'  PA    single    1.601  0.020  1.601
 NYW  O2A  PA    double    1.481  0.020  1.481
 NYW  PA   O1A   single    1.602  0.020  1.602
 NYW  PA   C3A   single    1.806  0.020  1.806
 NYW  O2B  PB    double    1.479  0.020  1.479
 NYW  C3A  PB    single    1.810  0.020  1.810
 NYW  PB   O3B   single    1.601  0.020  1.601
 NYW  PB   O1B   single    1.603  0.020  1.603
 NYW  O1B  H1    single    0.850  0.020  0.980
 NYW  O3B  H2    single    0.850  0.020  0.980
 NYW  O1A  H3    single    0.850  0.020  0.980
 NYW  C3A  H3A2  single    0.970  0.020  1.090
 NYW  C3A  H3A1  single    0.970  0.020  1.090
 NYW  C5'  H5'2  single    0.970  0.020  1.090
 NYW  C5'  H5'1  single    0.970  0.020  1.090
 NYW  C4'  H4'   single    0.970  0.020  1.090
 NYW  C3'  H3'   single    0.970  0.020  1.090
 NYW  O3'  HO3'  single    0.850  0.020  0.980
 NYW  C2'  H2'   single    0.970  0.020  1.090
 NYW  O2'  HO2'  single    0.850  0.020  0.980
 NYW  C1'  H1'   single    0.970  0.020  1.090
 NYW  C8   H8    single    0.930  0.020  1.080
 NYW  N6   HN61  single    0.860  0.020  1.020
 NYW  N6   HN62  single    0.860  0.020  1.020
 NYW  N2   H22   single    0.890  0.020  1.040
 NYW  N2   H21   single    0.890  0.020  1.040

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
 NYW  N1    C6   N6    119.10  3.000
 NYW  N6    C6   C5    122.27  3.000
 NYW  N1    C6   C5    118.62  3.000
 NYW  N3    C4   C5    127.03  3.000
 NYW  C5    C4   N9    104.99  3.000
 NYW  N3    C4   N9    127.97  3.000
 NYW  N2    C2   N3    116.90  3.000
 NYW  N3    C2   N1    127.27  3.000
 NYW  N2    C2   N1    115.79  3.000
 NYW  C3A   PB   O3B   100.40  3.000
 NYW  O3B   PB   O2B   116.58  3.000
 NYW  C3A   PB   O2B   114.98  3.000
 NYW  O3B   PB   O1B   107.57  3.000
 NYW  C3A   PB   O1B   106.63  3.000
 NYW  O2B   PB   O1B   109.85  3.000
 NYW  H1    O1B  PB    116.24  3.000
 NYW  H2    O3B  PB    114.04  3.000
 NYW  O5'   PA   C3A   100.90  3.000
 NYW  C3A   PA   O2A   115.89  3.000
 NYW  O5'   PA   O2A   115.78  3.000
 NYW  C3A   PA   O1A   106.79  3.000
 NYW  O2A   PA   O1A   109.65  3.000
 NYW  O5'   PA   O1A   107.00  3.000
 NYW  H3    O1A  PA    116.23  3.000
 NYW  H3A1  C3A  H3A2  107.11  3.000
 NYW  H3A1  C3A  PA    107.68  3.000
 NYW  H3A2  C3A  PA    110.14  3.000
 NYW  H3A1  C3A  PB    110.76  3.000
 NYW  H3A2  C3A  PB    107.52  3.000
 NYW  PA    C3A  PB    113.47  3.000
 NYW  H5'1  C5'  H5'2  107.88  3.000
 NYW  H5'1  C5'  C4'   109.36  3.000
 NYW  H5'2  C5'  C4'   111.31  3.000
 NYW  H5'1  C5'  O5'   108.70  3.000
 NYW  H5'2  C5'  O5'   110.95  3.000
 NYW  C4'   C5'  O5'   108.60  3.000
 NYW  H4'   C4'  C3'   110.61  3.000
 NYW  H4'   C4'  O4'   108.81  3.000
 NYW  C3'   C4'  O4'   106.58  3.000
 NYW  H4'   C4'  C5'   109.19  3.000
 NYW  O4'   C4'  C5'   110.18  3.000
 NYW  C3'   C4'  C5'   111.40  3.000
 NYW  C1'   O4'  C4'   110.33  3.000
 NYW  H3'   C3'  C2'   111.84  3.000
 NYW  H3'   C3'  O3'   111.68  3.000
 NYW  C2'   C3'  O3'   111.03  3.000
 NYW  H3'   C3'  C4'   111.83  3.000
 NYW  O3'   C3'  C4'   108.81  3.000
 NYW  C2'   C3'  C4'   101.18  3.000
 NYW  HO3'  O3'  C3'   107.95  3.000
 NYW  H2'   C2'  C1'   109.32  3.000
 NYW  H2'   C2'  O2'   111.75  3.000
 NYW  C1'   C2'  O2'   110.27  3.000
 NYW  H2'   C2'  C3'   109.22  3.000
 NYW  C1'   C2'  C3'   100.80  3.000
 NYW  O2'   C2'  C3'   114.88  3.000
 NYW  HO2'  O2'  C2'   108.87  3.000
 NYW  H1'   C1'  N9    106.25  3.000
 NYW  H1'   C1'  C2'   109.94  3.000
 NYW  N9    C1'  C2'   114.72  3.000
 NYW  H1'   C1'  O4'   111.90  3.000
 NYW  N9    C1'  O4'   109.13  3.000
 NYW  C2'   C1'  O4'   105.03  3.000
 NYW  C8    N9   C1'   127.51  3.000
 NYW  C8    N9   C4    106.51  3.000
 NYW  C1'   N9   C4    125.98  3.000
 NYW  H8    C8   N7    125.05  3.000
 NYW  H8    C8   N9    121.97  3.000
 NYW  N7    C8   N9    112.96  3.000
 NYW  C5    N7   C8    104.63  3.000
 NYW  N7    C5   C4    110.91  3.000
 NYW  N7    C5   C6    133.34  3.000
 NYW  C4    C5   C6    115.75  3.000
 NYW  HN62  N6   HN61  117.61  3.000
 NYW  HN62  N6   C6    119.68  3.000
 NYW  HN61  N6   C6    120.25  3.000
 NYW  C2    N1   C6    119.33  3.000
 NYW  C2    N3   C4    111.99  3.000
 NYW  H21   N2   H22   115.48  3.000
 NYW  H21   N2   C2    117.22  3.000
 NYW  H22   N2   C2    117.26  3.000
 NYW  C5'   O5'  PA    122.03  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
 NYW  CONST_01  N3    C2   N1   C6      0.00   0.0  0
 NYW  CONST_02  N3    C4   C5   C6      0.00   0.0  0
 NYW  CONST_03  N9    C4   C5   C6    180.00   0.0  0
 NYW  CONST_04  C8    N7   C5   C6    180.00   0.0  0
 NYW  CONST_05  N1    C2   N3   C4      0.00   0.0  0
 NYW  CONST_06  N1    C6   C5   C4      0.00   0.0  0
 NYW  CONST_07  C8    N7   C5   C4      0.00   0.0  0
 NYW  CONST_08  N7    C8   N9   C4      0.00   0.0  0
 NYW  CONST_09  C5    C6   N1   C2      0.00   0.0  0
 NYW  CONST_10  C5    C4   N3   C2      0.00   0.0  0
 NYW  CONST_11  N9    C4   N3   C2    180.00   0.0  0
 NYW  CONST_12  N7    C5   C4   N9      0.00   0.0  0
 NYW  CONST_13  C5    N7   C8   N9      0.00   0.0  0
 NYW  CONST_14  N3    C4   N9   C8    180.00   0.0  0
 NYW  CONST_15  C5    C4   N9   C8      0.00   0.0  0
 NYW  CONST_16  N1    C6   C5   N7    180.00   0.0  0
 NYW  CONST_17  N3    C4   C5   N7    180.00   0.0  0
 NYW  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 NYW  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 NYW  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 NYW  CONST_21  N2    C2   N1   C6    180.00   0.0  0
 NYW  CONST_22  N2    C2   N3   C4    180.00   0.0  0
 NYW  CONST_23  N6    C6   C5   C4    180.00   0.0  0
 NYW  CONST_24  N6    C6   N1   C2    180.00   0.0  0
 NYW  CONST_25  N6    C6   C5   N7      0.00   0.0  0
 NYW  CONST_26  H8    C8   N9   C4    180.00   0.0  0
 NYW  CONST_27  HN61  N6   C6   C5      0.00   0.0  0
 NYW  CONST_28  HN62  N6   C6   C5    180.00   0.0  0
 NYW  Var_01    C4'   C5'  O5'  PA   -129.13  30.0  1
 NYW  Var_02    O5'   PA   C3A  PB    157.64  30.0  1
 NYW  Var_03    PA    C3A  PB   O1B    46.90  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
 NYW  chir_02  C4'  C3'  O4'  C5'  positiv
 NYW  chir_03  C3'  O3'  C2'  C4'  negativ
 NYW  chir_04  C2'  O2'  C1'  C3'  negativ
 NYW  chir_05  C1'  O4'  N9   C2'  negativ
 NYW  chir_06  PA   O2A  O1A  C3A  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
 NYW  plan-1  C6    0.020
 NYW  plan-1  C4    0.020
 NYW  plan-1  C2    0.020
 NYW  plan-1  C1'   0.020
 NYW  plan-1  N9    0.020
 NYW  plan-1  C8    0.020
 NYW  plan-1  N7    0.020
 NYW  plan-1  C5    0.020
 NYW  plan-1  N6    0.020
 NYW  plan-1  N1    0.020
 NYW  plan-1  N3    0.020
 NYW  plan-1  N2    0.020
 NYW  plan-1  H8    0.020
 NYW  plan-2  C6    0.020
 NYW  plan-2  N6    0.020
 NYW  plan-2  HN61  0.020
 NYW  plan-2  HN62  0.020
 NYW  plan-3  C2    0.020
 NYW  plan-3  N2    0.020
 NYW  plan-3  H22   0.020
 NYW  plan-3  H21   0.020

