# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:32:33 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[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
 GP2  GP2  5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]guanosine  ligand  42  28  .  2021-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GP2
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
 GP2  O6    O  O      0  -0.477  -3.7939   0.1642  -4.5267
 GP2  C6    C  CR6    0   0.498  -2.6114  -0.1197  -4.4249
 GP2  C5    C  CR56   0  -0.098  -1.7457   0.0401  -3.3061
 GP2  N7    N  N      0  -0.455  -1.9901   0.5334  -2.0500
 GP2  C4    C  CR56   0   0.503  -0.4265  -0.3566  -3.4254
 GP2  N3    N  N      0  -0.510   0.1869  -0.8956  -4.4890
 GP2  C2    C  CR6    0   0.683  -0.6067  -1.0526  -5.5174
 GP2  N1    N  NR16   0  -0.725  -1.9226  -0.6899  -5.5038
 GP2  N2    N  NH2    0  -0.832  -0.1462  -1.6289  -6.6406
 GP2  N9    N  NR5    0  -0.540   0.1372  -0.0897  -2.2173
 GP2  C8    C  CR15   0   0.040  -0.8536   0.4457  -1.4257
 GP2  C1'   C  CH1    0   0.227   1.5194  -0.3039  -1.8633
 GP2  C2'   C  CH1    0  -0.054   2.3513   0.9777  -1.8043
 GP2  O2'   O  OH1    0  -0.654   2.8150   1.3050  -3.0810
 GP2  C3'   C  CH1    0  -0.030   3.4384   0.5724  -0.8050
 GP2  O3'   O  OH1    0  -0.671   4.3956  -0.2551  -1.4156
 GP2  O4'   O  O2     0  -0.489   1.5902  -0.8683  -0.5889
 GP2  C4'   C  CH1    0  -0.044   2.6246  -0.2490   0.1845
 GP2  C5'   C  CH2    0  -0.133   2.0383   0.6127   1.2892
 GP2  O5'   O  O2     0  -0.635   1.1775  -0.1595   2.0771
 GP2  PA    P  P      0   1.278  -0.1416   0.6215   2.7745
 GP2  O1A   O  O      0  -0.821   0.4029   1.5233   3.8536
 GP2  O2A   O  OP    -1  -0.804  -0.9178   1.2678   1.6461
 GP2  C3A   C  CH2    0  -0.999  -0.9739  -0.8408   3.4302
 GP2  PB    P  P      0   1.167  -2.2865  -0.4977   4.7257
 GP2  O1B   O  O      0  -0.908  -3.0649   0.7122   4.1978
 GP2  O3B   O  OP    -1  -0.921  -3.1166  -1.7905   4.7617
 GP2  O2B   O  OP    -1  -0.911  -1.5251  -0.2353   6.0281
 GP2  HN1   H  HNR6   0   0.423  -2.4737  -0.8553  -6.3364
 GP2  HN21  H  HNH2   0   0.410   0.8507  -1.7385  -6.7212
 GP2  HN22  H  HNH2   0   0.412  -0.6467  -1.5260  -7.5075
 GP2  H8    H  HCR5   0   0.337  -0.6904   0.7227  -0.3874
 GP2  H1'   H  HCH1   0   0.253   1.9310  -0.9742  -2.6265
 GP2  H1    H  HCH1   0   0.249   1.7521   1.7892  -1.3726
 GP2  H2'   H  HOH1   0   0.468   3.0726   2.2320  -3.0878
 GP2  H3'   H  HCH1   0   0.247   3.9036   1.4452  -0.3278
 GP2  H2    H  HOH1   0   0.448   4.6392   0.1467  -2.2578
 GP2  H4'   H  HCH1   0   0.252   3.2330  -1.0428   0.6297
 GP2  H5'1  H  HCH2   0   0.206   2.8757   1.0115   1.8779
 GP2  H5'2  H  HCH2   0   0.190   1.5201   1.4768   0.8539
 GP2  H3A1  H  HCH2   0   0.211  -0.2287  -1.5197   3.8565
 GP2  H3A2  H  HCH2   0   0.211  -1.4241  -1.3695   2.5847

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
 GP2  O6   C6    double    1.220  0.020  1.220
 GP2  C6   C5    single    1.424  0.020  1.424
 GP2  C6   N1    single    1.401  0.020  1.401
 GP2  C5   N7    aromatic  1.371  0.020  1.371
 GP2  C5   C4    aromatic  1.383  0.020  1.383
 GP2  N7   C8    aromatic  1.300  0.020  1.300
 GP2  C4   N3    single    1.341  0.020  1.341
 GP2  C4   N9    aromatic  1.360  0.020  1.360
 GP2  N3   C2    double    1.308  0.020  1.308
 GP2  C2   N1    single    1.365  0.020  1.365
 GP2  C2   N2    single    1.344  0.020  1.344
 GP2  N1   HN1   single    0.860  0.020  1.020
 GP2  N2   HN21  single    0.890  0.020  1.040
 GP2  N2   HN22  single    0.890  0.020  1.040
 GP2  N9   C8    aromatic  1.377  0.020  1.377
 GP2  N9   C1'   single    1.443  0.020  1.443
 GP2  C8   H8    single    0.930  0.020  1.080
 GP2  C1'  C2'   single    1.529  0.020  1.529
 GP2  C1'  O4'   single    1.396  0.020  1.396
 GP2  C1'  H1'   single    0.970  0.020  1.090
 GP2  C2'  O2'   single    1.397  0.020  1.397
 GP2  C2'  C3'   single    1.531  0.020  1.531
 GP2  C2'  H1    single    0.970  0.020  1.090
 GP2  O2'  H2'   single    0.850  0.020  0.980
 GP2  C3'  O3'   single    1.405  0.020  1.405
 GP2  C3'  C4'   single    1.522  0.020  1.522
 GP2  C3'  H3'   single    0.970  0.020  1.090
 GP2  O3'  H2    single    0.850  0.020  0.980
 GP2  O4'  C4'   single    1.432  0.020  1.432
 GP2  C4'  C5'   single    1.519  0.020  1.519
 GP2  C4'  H4'   single    0.970  0.020  1.090
 GP2  C5'  O5'   single    1.399  0.020  1.399
 GP2  C5'  H5'1  single    0.970  0.020  1.090
 GP2  C5'  H5'2  single    0.970  0.020  1.090
 GP2  O5'  PA    single    1.684  0.020  1.684
 GP2  PA   O1A   deloc     1.508  0.020  1.508
 GP2  PA   O2A   deloc     1.514  0.020  1.514
 GP2  PA   C3A   single    1.806  0.020  1.806
 GP2  C3A  PB    single    1.876  0.020  1.876
 GP2  C3A  H3A1  single    0.970  0.020  1.090
 GP2  C3A  H3A2  single    0.970  0.020  1.090
 GP2  PB   O1B   deloc     1.532  0.020  1.532
 GP2  PB   O3B   deloc     1.537  0.020  1.537
 GP2  PB   O2B   deloc     1.531  0.020  1.531

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
 GP2  N1    C6   C5    110.60  3.000
 GP2  N1    C6   O6    120.45  3.000
 GP2  C5    C6   O6    128.95  3.000
 GP2  C4    C5   N7    110.63  3.000
 GP2  C4    C5   C6    118.70  3.000
 GP2  N7    C5   C6    130.67  3.000
 GP2  C8    N7   C5    105.06  3.000
 GP2  N9    C4   N3    126.44  3.000
 GP2  N9    C4   C5    105.22  3.000
 GP2  N3    C4   C5    128.33  3.000
 GP2  C2    N3   C4    113.22  3.000
 GP2  N2    C2   N1    116.91  3.000
 GP2  N2    C2   N3    120.04  3.000
 GP2  N1    C2   N3    123.03  3.000
 GP2  HN1   N1   C2    118.25  3.000
 GP2  HN1   N1   C6    115.61  3.000
 GP2  C2    N1   C6    126.13  3.000
 GP2  HN22  N2   HN21  115.78  3.000
 GP2  HN22  N2   C2    120.38  3.000
 GP2  HN21  N2   C2    116.95  3.000
 GP2  C1'   N9   C8    127.31  3.000
 GP2  C1'   N9   C4    125.88  3.000
 GP2  C8    N9   C4    106.79  3.000
 GP2  H8    C8   N9    122.71  3.000
 GP2  H8    C8   N7    124.96  3.000
 GP2  N9    C8   N7    112.30  3.000
 GP2  H1'   C1'  O4'   111.69  3.000
 GP2  H1'   C1'  C2'   109.59  3.000
 GP2  O4'   C1'  C2'   106.03  3.000
 GP2  H1'   C1'  N9    106.24  3.000
 GP2  O4'   C1'  N9    109.43  3.000
 GP2  C2'   C1'  N9    113.97  3.000
 GP2  H1    C2'  C3'   109.07  3.000
 GP2  H1    C2'  O2'   111.56  3.000
 GP2  C3'   C2'  O2'   115.01  3.000
 GP2  H1    C2'  C1'   109.76  3.000
 GP2  C3'   C2'  C1'   100.93  3.000
 GP2  O2'   C2'  C1'   109.97  3.000
 GP2  H2'   O2'  C2'   108.72  3.000
 GP2  H3'   C3'  C4'   111.90  3.000
 GP2  H3'   C3'  O3'   111.62  3.000
 GP2  C4'   C3'  O3'   109.21  3.000
 GP2  H3'   C3'  C2'   111.96  3.000
 GP2  C4'   C3'  C2'   100.81  3.000
 GP2  O3'   C3'  C2'   110.86  3.000
 GP2  H2    O3'  C3'   107.83  3.000
 GP2  C4'   O4'  C1'   110.79  3.000
 GP2  H4'   C4'  C5'   109.28  3.000
 GP2  H4'   C4'  O4'   107.90  3.000
 GP2  C5'   C4'  O4'   111.06  3.000
 GP2  H4'   C4'  C3'   111.02  3.000
 GP2  C5'   C4'  C3'   111.91  3.000
 GP2  O4'   C4'  C3'   105.57  3.000
 GP2  H5'2  C5'  H5'1  106.66  3.000
 GP2  H5'2  C5'  O5'   111.55  3.000
 GP2  H5'1  C5'  O5'   111.56  3.000
 GP2  H5'2  C5'  C4'   109.90  3.000
 GP2  H5'1  C5'  C4'   107.55  3.000
 GP2  O5'   C5'  C4'   109.51  3.000
 GP2  PA    O5'  C5'   117.33  3.000
 GP2  C3A   PA   O2A   112.33  3.000
 GP2  C3A   PA   O1A   113.01  3.000
 GP2  O2A   PA   O1A   117.58  3.000
 GP2  C3A   PA   O5'    97.81  3.000
 GP2  O2A   PA   O5'   106.91  3.000
 GP2  O1A   PA   O5'   106.91  3.000
 GP2  H3A2  C3A  H3A1  106.35  3.000
 GP2  H3A2  C3A  PB    109.52  3.000
 GP2  H3A1  C3A  PB    108.72  3.000
 GP2  H3A2  C3A  PA    107.48  3.000
 GP2  H3A1  C3A  PA    109.26  3.000
 GP2  PB    C3A  PA    115.16  3.000
 GP2  O2B   PB   O3B   113.13  3.000
 GP2  O2B   PB   O1B   114.22  3.000
 GP2  O3B   PB   O1B   113.45  3.000
 GP2  O2B   PB   C3A   105.71  3.000
 GP2  O3B   PB   C3A   103.90  3.000
 GP2  O1B   PB   C3A   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
 GP2  CONST_01  N9    C8   N7   C5     0.00   0.0  0
 GP2  CONST_02  C8    N9   C4   C5     0.00   0.0  0
 GP2  CONST_03  N9    C4   C5   N7     0.00   0.0  0
 GP2  CONST_04  C4    N9   C8   N7     0.00   0.0  0
 GP2  CONST_05  C8    N7   C5   C4     0.00   0.0  0
 GP2  CONST_06  C1'   N9   C4   C5   180.00   0.0  0
 GP2  CONST_07  C1'   N9   C8   N7   180.00   0.0  0
 GP2  CONST_08  C1'   N9   C4   N3     0.00   0.0  0
 GP2  CONST_09  N3    C2   N1   C6     0.00   0.0  0
 GP2  CONST_10  C2    N1   C6   C5     0.00   0.0  0
 GP2  CONST_11  N1    C2   N3   C4     0.00   0.0  0
 GP2  CONST_12  C2    N1   C6   O6   180.00   0.0  0
 GP2  CONST_13  N2    C2   N1   C6   180.00   0.0  0
 GP2  CONST_14  N2    C2   N3   C4   180.00   0.0  0
 GP2  CONST_15  H8    C8   N7   C5   180.00   0.0  0
 GP2  CONST_16  HN1   N1   C6   C5   180.00   0.0  0
 GP2  CONST_17  HN21  N2   C2   N3     0.00   0.0  0
 GP2  Var_01    O1A   PA   O5'  C5'  -70.57  30.0  3
 GP2  Var_02    PB    C3A  PA   O5'  163.79  30.0  3
 GP2  Var_03    O1B   PB   C3A  PA    42.73  30.0  3
 GP2  Var_04    H5'1  C5'  O5'  PA    92.64  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
 GP2  chir_01  C1'  N9   C2'  O4'  negativ
 GP2  chir_02  C2'  O2'  C3'  C1'  positiv
 GP2  chir_03  C3'  O3'  C4'  C2'  positiv
 GP2  chir_04  C4'  O4'  C3'  C5'  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
 GP2  plan-1  O6    0.020
 GP2  plan-1  C6    0.020
 GP2  plan-1  C5    0.020
 GP2  plan-1  N7    0.020
 GP2  plan-1  C4    0.020
 GP2  plan-1  N3    0.020
 GP2  plan-1  C2    0.020
 GP2  plan-1  N1    0.020
 GP2  plan-1  N2    0.020
 GP2  plan-1  N9    0.020
 GP2  plan-1  C8    0.020
 GP2  plan-1  C1'   0.020
 GP2  plan-1  HN1   0.020
 GP2  plan-1  HN21  0.020
 GP2  plan-1  HN22  0.020
 GP2  plan-1  H8    0.020

