# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 17:17:08 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy({(S)-hydroxy[(1R)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N
#
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
 G1M  G1M  2'-deoxy-5'-O-[(R)-hydroxy({(S)-hydroxy[(1R)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]guanosine  ligand  48  32  .  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_G1M
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
 G1M  N1    N  NR16   0  -0.727  -6.9581   2.4852   0.5909
 G1M  C2    C  CR6    0   0.687  -6.7201   1.6528   1.6469
 G1M  N2    N  NH2    0  -0.832  -7.5491   1.7494   2.6976
 G1M  N3    N  N      0  -0.515  -5.7604   0.7623   1.6513
 G1M  C4    C  CR56   0   0.505  -5.0404   0.7577   0.5202
 G1M  C5    C  CR56   0  -0.091  -5.1966   1.5516  -0.6012
 G1M  C6    C  CR6    0   0.503  -6.2410   2.5207  -0.6124
 G1M  O6    O  O      0  -0.474  -6.5457   3.3090  -1.4917
 G1M  N7    N  N      0  -0.444  -4.2521   1.2447  -1.5450
 G1M  C8    C  CR15   0   0.092  -3.5494   0.2928  -1.0099
 G1M  N9    N  NR5    0  -0.523  -3.9800  -0.0467   0.2483
 G1M  PA    P  P      0   1.334   2.1174  -1.7759  -0.3881
 G1M  PB    P  P      0   1.299   4.3637  -0.1253   0.6402
 G1M  PG    P  P      0   1.177   5.5367   2.7169   0.7870
 G1M  C1'   C  CR15   0   0.177  -3.4544  -1.0797   1.1317
 G1M  O1A   O  OP    -1  -0.812   2.0750  -1.3776  -1.8351
 G1M  O1B   O  OP    -1  -0.827   5.1202  -0.9134  -0.3979
 G1M  O1G   O  OP    -1  -0.916   5.3939   4.0136  -0.0297
 G1M  C2'   C  CH2    0  -0.541  -3.9685  -2.4774   0.8015
 G1M  O2A   O  O      0  -0.814   2.6199  -3.1398  -0.0156
 G1M  O2B   O  O      0  -0.811   4.7174  -0.2896   2.0941
 G1M  O2G   O  OP    -1  -0.914   5.2675   2.9317   2.2810
 G1M  C3'   C  CR15   0   0.014  -2.8621  -3.0444  -0.0833
 G1M  O3'   O  OH1    0  -0.662  -2.7291  -4.4381  -0.0586
 G1M  O3A   O  O2     0  -0.759   2.7434  -0.6276   0.5576
 G1M  C3B   C  CH1    0  -0.763   4.1526   1.6153   0.1607
 G1M  C3B2  C  CH3    0  -0.667   3.9774   1.7297  -1.3521
 G1M  O3G   O  O      0  -0.912   6.8329   1.9545   0.4831
 G1M  C4'   C  CR15   0   0.001  -1.6263  -2.3966   0.5352
 G1M  O4'   O  O      0  -0.493  -2.0627  -1.1185   0.9894
 G1M  C5'   C  CH2    0  -0.143  -0.4687  -2.2376  -0.4206
 G1M  O5'   O  O2     0  -0.624   0.5894  -1.5951   0.2422
 G1M  HN1   H  HNR6   0   0.425  -7.7297   3.1368   0.6588
 G1M  HN2   H  HNH2   0   0.414  -8.1227   2.5655   2.8268
 G1M  HN2A  H  HNH2   0   0.412  -7.2923   1.2521   3.5337
 G1M  H8    H  HCR5   0   0.286  -2.7004  -0.1844  -1.4743
 G1M  H1'   H  HCR5   0   0.270  -3.7336  -0.7753   2.1426
 G1M  H2'   H  HCH2   0   0.266  -4.0275  -3.0655   1.7199
 G1M  H2'A  H  HCH2   0   0.279  -4.9543  -2.4642   0.3383
 G1M  H3'   H  HCR5   0   0.217  -2.9909  -2.6850  -1.1150
 G1M  HO3'  H  HOH1   0   0.461  -3.4475  -4.8220  -0.5703
 G1M  H3B   H  HCH1   0   0.195   3.2311   1.9613   0.6453
 G1M  HC3B  H  HCH3   0   0.210   3.1914   1.0765  -1.7363
 G1M  HC3A  H  HCH3   0   0.199   3.7376   2.7561  -1.6278
 G1M  HC3C  H  HCH3   0   0.196   4.9025   1.4610  -1.8633
 G1M  H4'   H  HCR5   0   0.234  -1.3056  -2.9995   1.3964
 G1M  H5'   H  HCH2   0   0.210  -0.1938  -3.2410  -0.7707
 G1M  H5'A  H  HCH2   0   0.202  -0.7900  -1.6681  -1.3030

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
 G1M  N1    C2    single    1.366  0.020  1.366
 G1M  N1    C6    single    1.401  0.020  1.401
 G1M  N1    HN1   single    0.860  0.020  1.020
 G1M  C2    N2    single    1.342  0.020  1.342
 G1M  C2    N3    double    1.309  0.020  1.309
 G1M  N2    HN2   single    0.890  0.020  1.040
 G1M  N2    HN2A  single    0.890  0.020  1.040
 G1M  N3    C4    single    1.341  0.020  1.341
 G1M  C4    C5    aromatic  1.383  0.020  1.383
 G1M  C4    N9    aromatic  1.359  0.020  1.359
 G1M  C5    C6    single    1.425  0.020  1.425
 G1M  C5    N7    aromatic  1.370  0.020  1.370
 G1M  C6    O6    double    1.220  0.020  1.220
 G1M  N7    C8    aromatic  1.298  0.020  1.298
 G1M  C8    N9    aromatic  1.372  0.020  1.372
 G1M  C8    H8    single    0.930  0.020  1.080
 G1M  N9    C1'   single    1.457  0.020  1.457
 G1M  PA    O1A   deloc     1.502  0.020  1.502
 G1M  PA    O2A   deloc     1.501  0.020  1.501
 G1M  PA    O3A   single    1.614  0.020  1.614
 G1M  PA    O5'   single    1.663  0.020  1.663
 G1M  PB    O1B   deloc     1.507  0.020  1.507
 G1M  PB    O2B   deloc     1.505  0.020  1.505
 G1M  PB    O3A   single    1.698  0.020  1.698
 G1M  PB    C3B   single    1.818  0.020  1.818
 G1M  PG    O1G   deloc     1.539  0.020  1.539
 G1M  PG    O2G   deloc     1.533  0.020  1.533
 G1M  PG    C3B   single    1.877  0.020  1.877
 G1M  PG    O3G   deloc     1.534  0.020  1.534
 G1M  C1'   C2'   single    1.525  0.020  1.525
 G1M  C1'   O4'   single    1.400  0.020  1.400
 G1M  C1'   H1'   single    0.970  0.020  1.090
 G1M  C2'   C3'   single    1.526  0.020  1.526
 G1M  C2'   H2'   single    0.970  0.020  1.090
 G1M  C2'   H2'A  single    0.970  0.020  1.090
 G1M  C3'   O3'   single    1.400  0.020  1.400
 G1M  C3'   C4'   single    1.526  0.020  1.526
 G1M  C3'   H3'   single    0.970  0.020  1.090
 G1M  O3'   HO3'  single    0.850  0.020  0.980
 G1M  C3B   C3B2  single    1.527  0.020  1.527
 G1M  C3B   H3B   single    0.970  0.020  1.090
 G1M  C3B2  HC3B  single    0.970  0.020  1.090
 G1M  C3B2  HC3A  single    0.970  0.020  1.090
 G1M  C3B2  HC3C  single    0.970  0.020  1.090
 G1M  C4'   O4'   single    1.425  0.020  1.425
 G1M  C4'   C5'   single    1.510  0.020  1.510
 G1M  C4'   H4'   single    0.970  0.020  1.090
 G1M  C5'   O5'   single    1.404  0.020  1.404
 G1M  C5'   H5'   single    0.970  0.020  1.090
 G1M  C5'   H5'A  single    0.970  0.020  1.090

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
 G1M  HN1   N1    C6    115.56  3.000
 G1M  HN1   N1    C2    118.26  3.000
 G1M  C6    N1    C2    126.18  3.000
 G1M  N3    C2    N2    119.95  3.000
 G1M  N3    C2    N1    123.02  3.000
 G1M  N2    C2    N1    117.00  3.000
 G1M  HN2A  N2    HN2   116.09  3.000
 G1M  HN2A  N2    C2    117.22  3.000
 G1M  HN2   N2    C2    120.75  3.000
 G1M  C4    N3    C2    113.15  3.000
 G1M  N9    C4    C5    105.41  3.000
 G1M  N9    C4    N3    126.16  3.000
 G1M  C5    C4    N3    128.43  3.000
 G1M  N7    C5    C6    130.72  3.000
 G1M  N7    C5    C4    110.62  3.000
 G1M  C6    C5    C4    118.66  3.000
 G1M  O6    C6    C5    128.93  3.000
 G1M  O6    C6    N1    120.51  3.000
 G1M  C5    C6    N1    110.56  3.000
 G1M  C8    N7    C5    104.68  3.000
 G1M  H8    C8    N9    122.14  3.000
 G1M  H8    C8    N7    124.94  3.000
 G1M  N9    C8    N7    112.91  3.000
 G1M  C1'   N9    C8    128.17  3.000
 G1M  C1'   N9    C4    125.44  3.000
 G1M  C8    N9    C4    106.37  3.000
 G1M  O5'   PA    O3A    93.26  3.000
 G1M  O5'   PA    O2A   108.21  3.000
 G1M  O3A   PA    O2A   111.80  3.000
 G1M  O5'   PA    O1A   108.09  3.000
 G1M  O3A   PA    O1A   112.76  3.000
 G1M  O2A   PA    O1A   119.33  3.000
 G1M  C3B   PB    O3A    99.18  3.000
 G1M  C3B   PB    O2B   112.74  3.000
 G1M  O3A   PB    O2B   103.82  3.000
 G1M  C3B   PB    O1B   112.17  3.000
 G1M  O3A   PB    O1B   106.91  3.000
 G1M  O2B   PB    O1B   119.36  3.000
 G1M  O3G   PG    C3B   105.39  3.000
 G1M  O3G   PG    O2G   114.27  3.000
 G1M  C3B   PG    O2G   106.14  3.000
 G1M  O3G   PG    O1G   113.08  3.000
 G1M  C3B   PG    O1G   104.42  3.000
 G1M  O2G   PG    O1G   112.50  3.000
 G1M  H1'   C1'   O4'   110.86  3.000
 G1M  H1'   C1'   C2'   111.69  3.000
 G1M  O4'   C1'   C2'   106.72  3.000
 G1M  H1'   C1'   N9    105.75  3.000
 G1M  O4'   C1'   N9    108.46  3.000
 G1M  C2'   C1'   N9    113.37  3.000
 G1M  H2'A  C2'   H2'   108.37  3.000
 G1M  H2'A  C2'   C3'   114.46  3.000
 G1M  H2'   C2'   C3'   109.06  3.000
 G1M  H2'A  C2'   C1'   112.71  3.000
 G1M  H2'   C2'   C1'   109.24  3.000
 G1M  C3'   C2'   C1'   102.80  3.000
 G1M  H3'   C3'   C4'   109.65  3.000
 G1M  H3'   C3'   O3'   110.65  3.000
 G1M  C4'   C3'   O3'   109.78  3.000
 G1M  H3'   C3'   C2'   109.72  3.000
 G1M  C4'   C3'   C2'   101.21  3.000
 G1M  O3'   C3'   C2'   115.37  3.000
 G1M  HO3'  O3'   C3'   108.48  3.000
 G1M  PB    O3A   PA    127.51  3.000
 G1M  H3B   C3B   C3B2  108.51  3.000
 G1M  H3B   C3B   PG    106.68  3.000
 G1M  C3B2  C3B   PG    111.79  3.000
 G1M  H3B   C3B   PB    106.45  3.000
 G1M  C3B2  C3B   PB    110.27  3.000
 G1M  PG    C3B   PB    112.86  3.000
 G1M  HC3C  C3B2  HC3A  107.48  3.000
 G1M  HC3C  C3B2  HC3B  107.35  3.000
 G1M  HC3A  C3B2  HC3B  108.43  3.000
 G1M  HC3C  C3B2  C3B   110.40  3.000
 G1M  HC3A  C3B2  C3B   110.27  3.000
 G1M  HC3B  C3B2  C3B   112.72  3.000
 G1M  H4'   C4'   C5'   109.27  3.000
 G1M  H4'   C4'   O4'   109.37  3.000
 G1M  C5'   C4'   O4'   110.01  3.000
 G1M  H4'   C4'   C3'   108.72  3.000
 G1M  C5'   C4'   C3'   114.15  3.000
 G1M  O4'   C4'   C3'   105.19  3.000
 G1M  C4'   O4'   C1'   111.21  3.000
 G1M  H5'A  C5'   H5'   106.92  3.000
 G1M  H5'A  C5'   O5'   111.25  3.000
 G1M  H5'   C5'   O5'   112.35  3.000
 G1M  H5'A  C5'   C4'   109.81  3.000
 G1M  H5'   C5'   C4'   107.32  3.000
 G1M  O5'   C5'   C4'   109.10  3.000
 G1M  C5'   O5'   PA    117.63  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
 G1M  CONST_01  C8    N7   C5   C4    0.00   0.0  0
 G1M  CONST_02  N7    C8   N9   C4    0.00   0.0  0
 G1M  CONST_03  C8    N9   C4   C5    0.00   0.0  0
 G1M  CONST_04  N9    C8   N7   C5    0.00   0.0  0
 G1M  CONST_05  N9    C4   C5   N7    0.00   0.0  0
 G1M  CONST_06  C1'   N9   C4   N3    0.00   0.0  0
 G1M  CONST_07  C1'   N9   C4   C5  180.00   0.0  0
 G1M  CONST_08  C1'   N9   C8   N7  180.00   0.0  0
 G1M  CONST_09  C4    N3   C2   N1    0.00   0.0  0
 G1M  CONST_10  C5    C6   N1   C2    0.00   0.0  0
 G1M  CONST_11  C6    N1   C2   N3    0.00   0.0  0
 G1M  CONST_12  O6    C6   N1   C2  180.00   0.0  0
 G1M  CONST_13  C6    N1   C2   N2  180.00   0.0  0
 G1M  CONST_14  C4    N3   C2   N2  180.00   0.0  0
 G1M  CONST_15  H8    C8   N9   C4  180.00   0.0  0
 G1M  CONST_16  HN1   N1   C2   N3  180.00   0.0  0
 G1M  CONST_18  HN2A  N2   C2   N1  180.00   0.0  0
 G1M  Var_01    C4'   C5'  O5'  PA  158.98  30.0  1
 G1M  Var_02    O1B   PB   O3A  PA    2.76  30.0  1
 G1M  Var_03    O1A   PA   O3A  PB  -70.82  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
 G1M  chir_03  C1'  N9   C2'  O4'   negativ
 G1M  chir_04  C3'  O3'  C4'  C2'   positiv
 G1M  chir_05  C3B  PB   PG   C3B2  negativ
 G1M  chir_06  C4'  O4'  C5'  C3'   positiv

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
 G1M  plan-1  N1    0.020
 G1M  plan-1  C2    0.020
 G1M  plan-1  N2    0.020
 G1M  plan-1  N3    0.020
 G1M  plan-1  C4    0.020
 G1M  plan-1  C5    0.020
 G1M  plan-1  C6    0.020
 G1M  plan-1  O6    0.020
 G1M  plan-1  N7    0.020
 G1M  plan-1  C8    0.020
 G1M  plan-1  N9    0.020
 G1M  plan-1  C1'   0.020
 G1M  plan-1  HN1   0.020
 G1M  plan-1  HN2   0.020
 G1M  plan-1  HN2A  0.020
 G1M  plan-1  H8    0.020

