# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:37:46 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)C[P](O)(O)=O)O3
#
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
 GGH  GGH  2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]guanosine  ligand  45  31  .  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_GGH
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
 GGH  C2    C  C      0   0.678   2.6525   4.1484   1.7979
 GGH  C4    C  CR5    0   0.492   1.5115   2.7673   0.4979
 GGH  C5    C  CR5    0  -0.094   0.8907   3.7618  -0.2326
 GGH  C6    C  C      0   0.493   1.1709   5.1202   0.0833
 GGH  P1    P  P      0   1.352   1.9290  -0.6533  -4.7356
 GGH  P2    P  P      0   1.274  -0.0372   1.4758  -5.2986
 GGH  O6    O  O      0  -0.481   0.7280   6.1359  -0.4301
 GGH  O1A   O  OP    -1  -0.815   1.2480  -1.8451  -5.3328
 GGH  O2A   O  O      0  -0.819   3.1175  -0.0452  -5.4208
 GGH  O3A   O  O2     0  -0.736   0.8711   0.5011  -4.3090
 GGH  O5'   O  O2     0  -0.627   2.4537  -1.0371  -3.2214
 GGH  O1B   O  O      0  -0.830  -0.3548   0.7374  -6.5732
 GGH  O2B   O  OP    -1  -0.842   0.7155   2.7825  -5.4333
 GGH  C3B   C  CH2    0  -1.019  -1.5023   1.7469  -4.2652
 GGH  P3    P  P      0   1.194  -2.4556   0.3432  -3.4841
 GGH  O1G   O  OP    -1  -0.894  -2.6948  -0.7003  -4.5739
 GGH  O2G   O  OP    -1  -0.836  -1.6012  -0.1727  -2.3043
 GGH  O3G   O  O      0  -0.923  -3.7460   1.0250  -2.9981
 GGH  C5'   C  CH2    0  -0.190   1.5198  -1.6057  -2.3258
 GGH  C4'   C  CH1    0  -0.041   2.0929  -1.5484  -0.9231
 GGH  O4'   O  O2     0  -0.495   2.4134  -0.2161  -0.5357
 GGH  C1'   C  CH1    0   0.226   1.4669   0.2776   0.3828
 GGH  N9    N  NR5    0  -0.547   1.0385   1.5972  -0.0131
 GGH  N3    N  N      0  -0.513   2.3867   2.9013   1.5066
 GGH  N2    N  NH2    0  -0.833   3.5475   4.4392   2.7592
 GGH  N1    N  NH1    0  -0.724   2.0890   5.2025   1.1393
 GGH  N7    N  N      0  -0.465   0.0618   3.2166  -1.1817
 GGH  C8    C  CR15   0   0.048   0.1743   1.9297  -1.0349
 GGH  C2'   C  CH2    0  -0.585   0.3439  -0.7535   0.4395
 GGH  C3'   C  CH1    0   0.003   1.0812  -2.0396   0.1164
 GGH  O3'   O  OH1    0  -0.677   1.7023  -2.5038   1.2945
 GGH  H3B1  H  HCH2   0   0.228  -1.2222   2.4503  -3.4755
 GGH  H3B2  H  HCH2   0   0.203  -2.2010   2.2943  -4.9100
 GGH  H5'1  H  HCH2   0   0.265   0.5507  -1.0938  -2.3739
 GGH  H5'2  H  HCH2   0   0.188   1.3452  -2.6625  -2.5677
 GGH  H4'   H  HCH1   0   0.235   3.0164  -2.1395  -0.8879
 GGH  H1'   H  HCH1   0   0.245   1.9357   0.4006   1.3629
 GGH  HN21  H  HNH2   0   0.411   3.5737   5.3590   3.1661
 GGH  HN22  H  HNH2   0   0.409   3.8187   3.6862   3.3690
 GGH  HN1   H  HNH1   0   0.422   2.3470   6.1391   1.4229
 GGH  H8    H  HCR5   0   0.363  -0.3663   1.1737  -1.6128
 GGH  H2'1  H  HCH2   0   0.299  -0.4150  -0.5683  -0.3224
 GGH  H2'2  H  HCH2   0   0.268  -0.1449  -0.7758   1.4133
 GGH  H3'   H  HCH1   0   0.239   0.4140  -2.7998  -0.3084
 GGH  HO3'  H  HOH1   0   0.451   2.2273  -3.2803   1.0764

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
 GGH  C2   N2    single    1.345  0.020  1.345
 GGH  C2   N1    single    1.365  0.020  1.365
 GGH  C2   N3    double    1.308  0.020  1.308
 GGH  C4   N3    single    1.342  0.020  1.342
 GGH  C4   C5    aromatic  1.381  0.020  1.381
 GGH  C4   N9    aromatic  1.362  0.020  1.362
 GGH  C5   C6    single    1.423  0.020  1.423
 GGH  C5   N7    aromatic  1.373  0.020  1.373
 GGH  C6   N1    single    1.402  0.020  1.402
 GGH  C6   O6    double    1.221  0.020  1.221
 GGH  P1   O5'   single    1.648  0.020  1.648
 GGH  P1   O3A   single    1.623  0.020  1.623
 GGH  P1   O2A   deloc     1.501  0.020  1.501
 GGH  P1   O1A   deloc     1.497  0.020  1.497
 GGH  P2   O1B   deloc     1.507  0.020  1.507
 GGH  P2   O3A   single    1.660  0.020  1.660
 GGH  P2   O2B   deloc     1.514  0.020  1.514
 GGH  P2   C3B   single    1.813  0.020  1.813
 GGH  O5'  C5'   single    1.413  0.020  1.413
 GGH  C3B  P3    single    1.868  0.020  1.868
 GGH  C3B  H3B1  single    0.970  0.020  1.090
 GGH  C3B  H3B2  single    0.970  0.020  1.090
 GGH  P3   O3G   deloc     1.538  0.020  1.538
 GGH  P3   O1G   deloc     1.528  0.020  1.528
 GGH  P3   O2G   deloc     1.545  0.020  1.545
 GGH  C5'  C4'   single    1.516  0.020  1.516
 GGH  C5'  H5'1  single    0.970  0.020  1.090
 GGH  C5'  H5'2  single    0.970  0.020  1.090
 GGH  C4'  C3'   single    1.531  0.020  1.531
 GGH  C4'  O4'   single    1.424  0.020  1.424
 GGH  C4'  H4'   single    0.970  0.020  1.090
 GGH  O4'  C1'   single    1.408  0.020  1.408
 GGH  C1'  C2'   single    1.526  0.020  1.526
 GGH  C1'  N9    single    1.443  0.020  1.443
 GGH  C1'  H1'   single    0.970  0.020  1.090
 GGH  N9   C8    aromatic  1.379  0.020  1.379
 GGH  N2   HN21  single    0.890  0.020  1.040
 GGH  N2   HN22  single    0.890  0.020  1.040
 GGH  N1   HN1   single    0.860  0.020  1.020
 GGH  N7   C8    aromatic  1.300  0.020  1.300
 GGH  C8   H8    single    0.930  0.020  1.080
 GGH  C2'  C3'   single    1.517  0.020  1.517
 GGH  C2'  H2'1  single    0.970  0.020  1.090
 GGH  C2'  H2'2  single    0.970  0.020  1.090
 GGH  C3'  O3'   single    1.410  0.020  1.410
 GGH  C3'  H3'   single    0.970  0.020  1.090
 GGH  O3'  HO3'  single    0.850  0.020  0.980

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
 GGH  N1    C2   N2    116.91  3.000
 GGH  N1    C2   N3    123.03  3.000
 GGH  N2    C2   N3    120.03  3.000
 GGH  N3    C4   N9    126.47  3.000
 GGH  N9    C4   C5    105.32  3.000
 GGH  N3    C4   C5    128.21  3.000
 GGH  N7    C5   C6    130.66  3.000
 GGH  N7    C5   C4    110.55  3.000
 GGH  C6    C5   C4    118.79  3.000
 GGH  N1    C6   O6    120.36  3.000
 GGH  O6    C6   C5    129.01  3.000
 GGH  N1    C6   C5    110.63  3.000
 GGH  O5'   P1   O3A    97.56  3.000
 GGH  O3A   P1   O2A   110.37  3.000
 GGH  O5'   P1   O2A   105.17  3.000
 GGH  O2A   P1   O1A   120.05  3.000
 GGH  O3A   P1   O1A   112.00  3.000
 GGH  O5'   P1   O1A   109.03  3.000
 GGH  C3B   P2   O2B   108.87  3.000
 GGH  C3B   P2   O1B   112.64  3.000
 GGH  O2B   P2   O1B   116.90  3.000
 GGH  C3B   P2   O3A   100.96  3.000
 GGH  O2B   P2   O3A   106.73  3.000
 GGH  O1B   P2   O3A   109.39  3.000
 GGH  P2    O3A  P1    128.16  3.000
 GGH  C5'   O5'  P1    117.75  3.000
 GGH  H3B2  C3B  H3B1  105.46  3.000
 GGH  H3B2  C3B  P3    107.20  3.000
 GGH  H3B1  C3B  P3    108.18  3.000
 GGH  H3B2  C3B  P2    104.73  3.000
 GGH  H3B1  C3B  P2    107.50  3.000
 GGH  P3    C3B  P2    122.57  3.000
 GGH  O3G   P3   O2G   111.75  3.000
 GGH  O2G   P3   O1G   113.78  3.000
 GGH  O3G   P3   O1G   113.38  3.000
 GGH  O2G   P3   C3B   106.74  3.000
 GGH  O1G   P3   C3B   107.15  3.000
 GGH  O3G   P3   C3B   103.13  3.000
 GGH  H5'2  C5'  H5'1  107.39  3.000
 GGH  H5'2  C5'  C4'   107.47  3.000
 GGH  H5'1  C5'  C4'   110.90  3.000
 GGH  H5'2  C5'  O5'   110.65  3.000
 GGH  H5'1  C5'  O5'   111.61  3.000
 GGH  C4'   C5'  O5'   108.74  3.000
 GGH  H4'   C4'  C3'   111.19  3.000
 GGH  H4'   C4'  O4'   107.81  3.000
 GGH  C3'   C4'  O4'   105.32  3.000
 GGH  H4'   C4'  C5'   109.11  3.000
 GGH  O4'   C4'  C5'   111.84  3.000
 GGH  C3'   C4'  C5'   111.47  3.000
 GGH  C1'   O4'  C4'   110.74  3.000
 GGH  H1'   C1'  C2'   111.00  3.000
 GGH  H1'   C1'  N9    105.69  3.000
 GGH  C2'   C1'  N9    114.19  3.000
 GGH  H1'   C1'  O4'   109.63  3.000
 GGH  N9    C1'  O4'   109.95  3.000
 GGH  C2'   C1'  O4'   106.38  3.000
 GGH  C8    N9   C1'   127.59  3.000
 GGH  C8    N9   C4    106.77  3.000
 GGH  C1'   N9   C4    125.44  3.000
 GGH  C4    N3   C2    113.27  3.000
 GGH  HN22  N2   HN21  115.60  3.000
 GGH  HN22  N2   C2    116.78  3.000
 GGH  HN21  N2   C2    120.26  3.000
 GGH  HN1   N1   C6    115.62  3.000
 GGH  HN1   N1   C2    118.32  3.000
 GGH  C6    N1   C2    126.06  3.000
 GGH  C8    N7   C5    105.23  3.000
 GGH  H8    C8   N7    125.54  3.000
 GGH  H8    C8   N9    122.30  3.000
 GGH  N7    C8   N9    112.12  3.000
 GGH  H2'2  C2'  H2'1  108.39  3.000
 GGH  H2'2  C2'  C3'   113.01  3.000
 GGH  H2'1  C2'  C3'   109.46  3.000
 GGH  H2'2  C2'  C1'   112.16  3.000
 GGH  H2'1  C2'  C1'   111.80  3.000
 GGH  C3'   C2'  C1'   101.96  3.000
 GGH  H3'   C3'  O3'   111.30  3.000
 GGH  H3'   C3'  C2'   111.98  3.000
 GGH  O3'   C3'  C2'   108.36  3.000
 GGH  H3'   C3'  C4'   111.18  3.000
 GGH  O3'   C3'  C4'   112.43  3.000
 GGH  C2'   C3'  C4'   101.17  3.000
 GGH  HO3'  O3'  C3'   108.45  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
 GGH  CONST_01  C8    N7   C5   C4      0.00   0.0  0
 GGH  CONST_02  N7    C8   N9   C4      0.00   0.0  0
 GGH  CONST_03  C8    N9   C4   C5      0.00   0.0  0
 GGH  CONST_04  N9    C8   N7   C5      0.00   0.0  0
 GGH  CONST_05  N7    C5   C4   N9      0.00   0.0  0
 GGH  CONST_06  C1'   N9   C4   C5    180.00   0.0  0
 GGH  CONST_07  N3    C4   N9   C1'     0.00   0.0  0
 GGH  CONST_08  N7    C8   N9   C1'   180.00   0.0  0
 GGH  CONST_09  C5    C6   N1   C2      0.00   0.0  0
 GGH  CONST_10  N1    C2   N3   C4      0.00   0.0  0
 GGH  CONST_11  N3    C2   N1   C6      0.00   0.0  0
 GGH  CONST_12  O6    C6   N1   C2    180.00   0.0  0
 GGH  CONST_13  N2    C2   N3   C4    180.00   0.0  0
 GGH  CONST_14  N2    C2   N1   C6    180.00   0.0  0
 GGH  CONST_15  H8    C8   N9   C4    180.00   0.0  0
 GGH  CONST_16  HN1   N1   C6   C5    180.00   0.0  0
 GGH  CONST_18  HN22  N2   C2   N3      0.00   0.0  0
 GGH  Var_01    C4'   C5'  O5'  P1   -165.67  30.0  3
 GGH  Var_02    O1B   P2   O3A  P1     30.59  30.0  1
 GGH  Var_03    O5'   P1   O3A  P2    176.01  30.0  1
 GGH  Var_04    O3G   P3   C3B  P2   -167.69  30.0  3
 GGH  Var_05    P3    C3B  P2   O3A   -51.61  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
 GGH  chir_03  C4'  C5'  C3'  O4'  positiv
 GGH  chir_04  C1'  O4'  N9   C2'  negativ
 GGH  chir_05  C3'  O3'  C4'  C2'  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
 GGH  plan-1  C2    0.020
 GGH  plan-1  C4    0.020
 GGH  plan-1  C5    0.020
 GGH  plan-1  C6    0.020
 GGH  plan-1  O6    0.020
 GGH  plan-1  C1'   0.020
 GGH  plan-1  N9    0.020
 GGH  plan-1  N3    0.020
 GGH  plan-1  N2    0.020
 GGH  plan-1  N1    0.020
 GGH  plan-1  N7    0.020
 GGH  plan-1  C8    0.020
 GGH  plan-1  HN21  0.020
 GGH  plan-1  HN22  0.020
 GGH  plan-1  HN1   0.020
 GGH  plan-1  H8    0.020

