# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:37:30 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[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
 GMP  GMP  'guanosine                '  ligand  33  20  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GMP
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
 GMP  O5'   O  OH1   0  -0.667   3.9257   2.1364   0.8685
 GMP  C5'   C  CH2   0  -0.157   3.9358   1.1400  -0.1217
 GMP  C4'   C  CH1   0  -0.049   3.3635  -0.1336   0.4690
 GMP  O4'   O  O2    0  -0.491   2.0442   0.0819   0.9794
 GMP  C3'   C  CH1   0  -0.039   3.2298  -1.2527  -0.5651
 GMP  O3'   O  OH1   0  -0.667   3.2340  -2.5282   0.0190
 GMP  C2'   C  CH1   0  -0.014   1.8210  -0.9824  -1.0915
 GMP  O2'   O  OH1   0  -0.653   1.1580  -2.0489  -1.6887
 GMP  C1'   C  CH1   0   0.204   1.0950  -0.5775   0.1917
 GMP  N9    N  NR5   0  -0.534  -0.0268   0.3006  -0.0334
 GMP  C8    C  CR15  0   0.092   0.0192   1.5975  -0.4842
 GMP  N7    N  N     0  -0.443  -1.1555   2.1329  -0.6015
 GMP  C5    C  CR56  0  -0.098  -2.0272   1.1479  -0.2129
 GMP  C6    C  CR6   0   0.505  -3.4493   1.1493  -0.1324
 GMP  O6    O  O     0  -0.474  -4.2302   2.0456  -0.4045
 GMP  N1    N  NR16  0  -0.728  -3.9167  -0.0876   0.3303
 GMP  C2    C  CR6   0   0.692  -3.1469  -1.1639   0.6691
 GMP  N2    N  NH2   0  -0.832  -3.7861  -2.2458   1.1338
 GMP  N3    N  N     0  -0.511  -1.8394  -1.1609   0.5865
 GMP  C4    C  CR56  0   0.509  -1.3416   0.0024   0.1481
 GMP  HO5'  H  HOH1  0   0.459   4.3223   2.9303   0.4989
 GMP  H5'1  H  HCH2  0   0.198   3.3613   1.4417  -1.0089
 GMP  H5'2  H  HCH2  0   0.216   4.9528   0.9153  -0.4685
 GMP  H4'   H  HCH1  0   0.258   3.9989  -0.4472   1.3046
 GMP  H3'   H  HCH1  0   0.252   3.9882  -1.1646  -1.3537
 GMP  HO3'  H  HOH1  0   0.457   4.0896  -2.6674   0.4372
 GMP  H2'   H  HCH1  0   0.244   1.8752  -0.1133  -1.7615
 GMP  HO2'  H  HOH1  0   0.464   1.5236  -2.1874  -2.5680
 GMP  H1'   H  HCH1  0   0.262   0.6954  -1.4646   0.6953
 GMP  H8    H  HCR5  0   0.292   0.9547   2.0946  -0.6921
 GMP  HN1   H  HNR6  0   0.425  -4.9213  -0.1679   0.4244
 GMP  HN21  H  HNH2  0   0.415  -4.7783  -2.3555   1.0110
 GMP  HN22  H  HNH2  0   0.413  -3.2521  -3.0904   1.2511

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
 GMP  O5'  C5'   single    1.405  0.020  1.405
 GMP  O5'  HO5'  single    0.850  0.020  0.980
 GMP  C5'  C4'   single    1.516  0.020  1.516
 GMP  C5'  H5'1  single    0.970  0.020  1.090
 GMP  C5'  H5'2  single    0.970  0.020  1.090
 GMP  C4'  O4'   single    1.431  0.020  1.431
 GMP  C4'  C3'   single    1.530  0.020  1.530
 GMP  C4'  H4'   single    0.970  0.020  1.090
 GMP  O4'  C1'   single    1.399  0.020  1.399
 GMP  C3'  O3'   single    1.403  0.020  1.403
 GMP  C3'  C2'   single    1.528  0.020  1.528
 GMP  C3'  H3'   single    0.970  0.020  1.090
 GMP  O3'  HO3'  single    0.850  0.020  0.980
 GMP  C2'  O2'   single    1.390  0.020  1.390
 GMP  C2'  C1'   single    1.529  0.020  1.529
 GMP  C2'  H2'   single    0.970  0.020  1.090
 GMP  O2'  HO2'  single    0.850  0.020  0.980
 GMP  C1'  N9    single    1.442  0.020  1.442
 GMP  C1'  H1'   single    0.970  0.020  1.090
 GMP  N9   C8    aromatic  1.374  0.020  1.374
 GMP  N9   C4    aromatic  1.360  0.020  1.360
 GMP  C8   N7    aromatic  1.296  0.020  1.296
 GMP  C8   H8    single    0.930  0.020  1.080
 GMP  N7   C5    aromatic  1.371  0.020  1.371
 GMP  C5   C6    single    1.424  0.020  1.424
 GMP  C5   C4    aromatic  1.383  0.020  1.383
 GMP  C6   O6    double    1.219  0.020  1.219
 GMP  C6   N1    single    1.401  0.020  1.401
 GMP  N1   C2    single    1.366  0.020  1.366
 GMP  N1   HN1   single    0.860  0.020  1.020
 GMP  C2   N2    single    1.340  0.020  1.340
 GMP  C2   N3    double    1.310  0.020  1.310
 GMP  N2   HN21  single    0.890  0.020  1.040
 GMP  N2   HN22  single    0.890  0.020  1.040
 GMP  N3   C4    single    1.339  0.020  1.339

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
 GMP  HO5'  O5'  C5'   108.16  3.000
 GMP  H5'2  C5'  H5'1  106.58  3.000
 GMP  H5'2  C5'  C4'   107.51  3.000
 GMP  H5'1  C5'  C4'   110.35  3.000
 GMP  H5'2  C5'  O5'   112.00  3.000
 GMP  H5'1  C5'  O5'   111.75  3.000
 GMP  C4'   C5'  O5'   108.57  3.000
 GMP  H4'   C4'  C3'   110.91  3.000
 GMP  H4'   C4'  O4'   107.81  3.000
 GMP  C3'   C4'  O4'   105.71  3.000
 GMP  H4'   C4'  C5'   108.58  3.000
 GMP  C3'   C4'  C5'   112.60  3.000
 GMP  O4'   C4'  C5'   111.13  3.000
 GMP  C1'   O4'  C4'   110.72  3.000
 GMP  H3'   C3'  C2'   112.05  3.000
 GMP  H3'   C3'  O3'   111.72  3.000
 GMP  C2'   C3'  O3'   107.88  3.000
 GMP  H3'   C3'  C4'   111.50  3.000
 GMP  C2'   C3'  C4'   100.60  3.000
 GMP  O3'   C3'  C4'   112.55  3.000
 GMP  HO3'  O3'  C3'   108.36  3.000
 GMP  H2'   C2'  C1'   109.01  3.000
 GMP  H2'   C2'  O2'   111.61  3.000
 GMP  C1'   C2'  O2'   109.71  3.000
 GMP  H2'   C2'  C3'   107.73  3.000
 GMP  C1'   C2'  C3'   101.27  3.000
 GMP  O2'   C2'  C3'   116.86  3.000
 GMP  HO2'  O2'  C2'   108.77  3.000
 GMP  H1'   C1'  N9    106.32  3.000
 GMP  H1'   C1'  C2'   110.15  3.000
 GMP  N9    C1'  C2'   113.55  3.000
 GMP  H1'   C1'  O4'   111.75  3.000
 GMP  N9    C1'  O4'   109.19  3.000
 GMP  C2'   C1'  O4'   105.98  3.000
 GMP  C4    N9   C8    106.44  3.000
 GMP  C4    N9   C1'   126.69  3.000
 GMP  C8    N9   C1'   126.87  3.000
 GMP  H8    C8   N7    125.29  3.000
 GMP  H8    C8   N9    121.79  3.000
 GMP  N7    C8   N9    112.91  3.000
 GMP  C5    N7   C8    104.70  3.000
 GMP  C4    C5   C6    118.75  3.000
 GMP  C4    C5   N7    110.72  3.000
 GMP  C6    C5   N7    130.53  3.000
 GMP  N1    C6   O6    120.60  3.000
 GMP  N1    C6   C5    110.54  3.000
 GMP  O6    C6   C5    128.86  3.000
 GMP  HN1   N1   C2    118.28  3.000
 GMP  HN1   N1   C6    115.59  3.000
 GMP  C2    N1   C6    126.13  3.000
 GMP  N3    C2   N2    119.99  3.000
 GMP  N3    C2   N1    123.02  3.000
 GMP  N2    C2   N1    116.97  3.000
 GMP  HN22  N2   HN21  116.51  3.000
 GMP  HN22  N2   C2    117.71  3.000
 GMP  HN21  N2   C2    121.09  3.000
 GMP  C4    N3   C2    113.18  3.000
 GMP  N3    C4   C5    128.37  3.000
 GMP  N3    C4   N9    126.40  3.000
 GMP  C5    C4   N9    105.23  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
 GMP  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 GMP  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 GMP  CONST_03  C5    C4  N9  C8     0.00  0.0  0
 GMP  CONST_04  C4    C5  N7  C8     0.00  0.0  0
 GMP  CONST_05  C4    N9  C8  N7     0.00  0.0  0
 GMP  CONST_06  N7    C8  N9  C1'  180.00  0.0  0
 GMP  CONST_07  C5    C4  N9  C1'  180.00  0.0  0
 GMP  CONST_08  N3    C4  N9  C1'    0.00  0.0  0
 GMP  CONST_09  C2    N1  C6  C5     0.00  0.0  0
 GMP  CONST_10  N3    C2  N1  C6     0.00  0.0  0
 GMP  CONST_11  C4    N3  C2  N1     0.00  0.0  0
 GMP  CONST_12  N2    C2  N1  C6   180.00  0.0  0
 GMP  CONST_13  C2    N1  C6  O6   180.00  0.0  0
 GMP  CONST_14  C4    N3  C2  N2   180.00  0.0  0
 GMP  CONST_15  H8    C8  N9  C1'    0.00  0.0  0
 GMP  CONST_16  HN1   N1  C6  C5   180.00  0.0  0
 GMP  CONST_18  HN22  N2  C2  N1   180.00  0.0  0

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
 GMP  chir_01  C4'  C5'  O4'  C3'  negativ
 GMP  chir_02  C3'  O3'  C4'  C2'  positiv
 GMP  chir_03  C2'  O2'  C3'  C1'  positiv
 GMP  chir_04  C1'  O4'  N9   C2'  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
 GMP  plan-1  C1'   0.020
 GMP  plan-1  N9    0.020
 GMP  plan-1  C8    0.020
 GMP  plan-1  N7    0.020
 GMP  plan-1  C5    0.020
 GMP  plan-1  C6    0.020
 GMP  plan-1  O6    0.020
 GMP  plan-1  N1    0.020
 GMP  plan-1  C2    0.020
 GMP  plan-1  N2    0.020
 GMP  plan-1  N3    0.020
 GMP  plan-1  C4    0.020
 GMP  plan-1  H8    0.020
 GMP  plan-1  HN1   0.020
 GMP  plan-1  HN21  0.020
 GMP  plan-1  HN22  0.020

