# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:30:45 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (2R,3R,4S,5S)-2-(hydroxymethyl)-5-(4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)pyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1N[C@H]([C@H](O)[C@@H]1O)c2c[nH]c3c(O)ncnc23
#
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
 IMH  IMH  (2R,3R,4S,5S)-2-(hydroxymethyl)-5-(4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)pyrrolidine-3,4-diol  ligand  33  19  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IMH
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
 IMH  O5'   O  OH1   0  -0.675   2.1696   0.4867   4.3449
 IMH  C5'   C  CH2   0  -0.129   1.3728  -0.4795   3.6972
 IMH  C4'   C  CH1   0  -0.101   0.1756   0.2093   3.0794
 IMH  N4'   N  NH1   0  -0.610   0.5550   1.1200   2.0041
 IMH  C3'   C  CH1   0  -0.010  -0.7784  -0.7755   2.4061
 IMH  O3'   O  OH1   0  -0.665  -1.6128  -1.3859   3.3583
 IMH  C2'   C  CH1   0   0.009  -1.5202   0.1110   1.4034
 IMH  O2'   O  OH1   0  -0.677  -2.4651   0.9191   2.0624
 IMH  C1'   C  CH1   0  -0.215  -0.3822   0.9945   0.8854
 IMH  C9    C  CR5   0  -0.015   0.2841   0.3838  -0.3104
 IMH  C8    C  CR15  0  -0.043   1.5526  -0.1295  -0.3893
 IMH  N7    N  NR15  0  -0.680   1.8048  -0.5961  -1.6432
 IMH  C5    C  CR56  0   0.145   0.6995  -0.3888  -2.4151
 IMH  C6    C  CR6   0   0.490   0.3695  -0.6409  -3.7471
 IMH  O6    O  OH1   0  -0.588   1.1739  -1.2140  -4.6385
 IMH  N1    N  N     0  -0.445  -0.8200  -0.2981  -4.1896
 IMH  C2    C  CR16  0   0.009  -1.6789   0.2842  -3.3434
 IMH  N3    N  N     0  -0.437  -1.4861   0.5699  -2.0780
 IMH  C4    C  CR56  0   0.163  -0.2741   0.2265  -1.6086
 IMH  HO'5  H  HOH1  0   0.453   2.9178   0.0376   4.7479
 IMH  H5'1  H  HCH2  0   0.182   1.9293  -0.9958   2.9029
 IMH  H5'2  H  HCH2  0   0.192   1.0211  -1.2466   4.3999
 IMH  H4'   H  HCH1  0   0.223  -0.3739   0.7291   3.8768
 IMH  HN'4  H  HNH1  0   0.360   0.6163   2.0723   2.3286
 IMH  H3'   H  HCH1  0   0.223  -0.2001  -1.5264   1.8503
 IMH  HO'3  H  HOH1  0   0.461  -2.0130  -2.1651   2.9599
 IMH  H2'   H  HCH1  0   0.233  -1.9900  -0.4726   0.6014
 IMH  HO'2  H  HOH1  0   0.442  -2.9111   0.3670   2.7159
 IMH  H1'   H  HCH1  0   0.257  -0.7850   1.9710   0.5970
 IMH  H8    H  HCR5  0   0.291   2.3058  -0.1898   0.3788
 IMH  HN7   H  HNR5  0   0.419   2.6736  -1.0176  -1.9262
 IMH  HO6   H  HOH1  0   0.486   2.0294  -1.4511  -4.2628
 IMH  H2    H  HCR6  0   0.250  -2.6436   0.5450  -3.7649

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
 IMH  O5'  C5'   single    1.410  0.020  1.410
 IMH  O5'  HO'5  single    0.850  0.020  0.980
 IMH  C5'  C4'   single    1.513  0.020  1.513
 IMH  C5'  H5'1  single    0.970  0.020  1.090
 IMH  C5'  H5'2  single    0.970  0.020  1.090
 IMH  C4'  N4'   single    1.459  0.020  1.459
 IMH  C4'  C3'   single    1.528  0.020  1.528
 IMH  C4'  H4'   single    0.970  0.020  1.090
 IMH  N4'  C1'   single    1.465  0.020  1.465
 IMH  N4'  HN'4  single    0.890  0.020  1.040
 IMH  C3'  O3'   single    1.405  0.020  1.405
 IMH  C3'  C2'   single    1.530  0.020  1.530
 IMH  C3'  H3'   single    0.970  0.020  1.090
 IMH  O3'  HO'3  single    0.850  0.020  0.980
 IMH  C2'  O2'   single    1.407  0.020  1.407
 IMH  C2'  C1'   single    1.531  0.020  1.531
 IMH  C2'  H2'   single    0.970  0.020  1.090
 IMH  O2'  HO'2  single    0.850  0.020  0.980
 IMH  C1'  C9    single    1.499  0.020  1.499
 IMH  C1'  H1'   single    0.970  0.020  1.090
 IMH  C9   C8    aromatic  1.371  0.020  1.371
 IMH  C9   C4    aromatic  1.422  0.020  1.422
 IMH  C8   N7    aromatic  1.361  0.020  1.361
 IMH  C8   H8    single    0.930  0.020  1.080
 IMH  N7   C5    aromatic  1.364  0.020  1.364
 IMH  N7   HN7   single    0.860  0.020  1.020
 IMH  C5   C6    aromatic  1.395  0.020  1.395
 IMH  C5   C4    aromatic  1.406  0.020  1.406
 IMH  C6   O6    single    1.330  0.020  1.330
 IMH  C6   N1    aromatic  1.315  0.020  1.315
 IMH  O6   HO6   single    0.850  0.020  0.980
 IMH  N1   C2    aromatic  1.339  0.020  1.339
 IMH  C2   N3    aromatic  1.312  0.020  1.312
 IMH  C2   H2    single    0.930  0.020  1.080
 IMH  N3   C4    aromatic  1.344  0.020  1.344

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
 IMH  HO'5  O5'  C5'   108.20  3.000
 IMH  H5'2  C5'  H5'1  107.25  3.000
 IMH  H5'2  C5'  C4'   109.01  3.000
 IMH  H5'1  C5'  C4'   108.63  3.000
 IMH  H5'2  C5'  O5'   111.46  3.000
 IMH  H5'1  C5'  O5'   111.59  3.000
 IMH  C4'   C5'  O5'   108.83  3.000
 IMH  H4'   C4'  C3'   108.20  3.000
 IMH  H4'   C4'  N4'   111.68  3.000
 IMH  C3'   C4'  N4'   103.88  3.000
 IMH  H4'   C4'  C5'   108.34  3.000
 IMH  C3'   C4'  C5'   112.37  3.000
 IMH  N4'   C4'  C5'   112.29  3.000
 IMH  HN'4  N4'  C1'   111.45  3.000
 IMH  HN'4  N4'  C4'   111.60  3.000
 IMH  C1'   N4'  C4'   110.06  3.000
 IMH  H3'   C3'  C2'   108.64  3.000
 IMH  H3'   C3'  O3'   111.00  3.000
 IMH  C2'   C3'  O3'   114.06  3.000
 IMH  H3'   C3'  C4'   109.56  3.000
 IMH  C2'   C3'  C4'   102.60  3.000
 IMH  O3'   C3'  C4'   110.62  3.000
 IMH  HO'3  O3'  C3'   108.55  3.000
 IMH  H2'   C2'  C1'   112.20  3.000
 IMH  H2'   C2'  O2'   111.11  3.000
 IMH  C1'   C2'  O2'   109.04  3.000
 IMH  H2'   C2'  C3'   112.23  3.000
 IMH  C1'   C2'  C3'   101.29  3.000
 IMH  O2'   C2'  C3'   110.57  3.000
 IMH  HO'2  O2'  C2'   107.40  3.000
 IMH  H1'   C1'  C9    108.46  3.000
 IMH  H1'   C1'  C2'   109.29  3.000
 IMH  C9    C1'  C2'   111.42  3.000
 IMH  H1'   C1'  N4'   111.11  3.000
 IMH  C9    C1'  N4'   111.09  3.000
 IMH  C2'   C1'  N4'   105.46  3.000
 IMH  C4    C9   C8    105.62  3.000
 IMH  C4    C9   C1'   126.80  3.000
 IMH  C8    C9   C1'   127.58  3.000
 IMH  H8    C8   N7    120.52  3.000
 IMH  H8    C8   C9    128.82  3.000
 IMH  N7    C8   C9    110.66  3.000
 IMH  HN7   N7   C5    127.17  3.000
 IMH  HN7   N7   C8    124.23  3.000
 IMH  C5    N7   C8    108.61  3.000
 IMH  C4    C5   C6    117.58  3.000
 IMH  C4    C5   N7    107.64  3.000
 IMH  C6    C5   N7    134.79  3.000
 IMH  N1    C6   O6    115.71  3.000
 IMH  N1    C6   C5    119.22  3.000
 IMH  O6    C6   C5    125.06  3.000
 IMH  HO6   O6   C6    112.42  3.000
 IMH  C2    N1   C6    118.76  3.000
 IMH  H2    C2   N3    116.95  3.000
 IMH  H2    C2   N1    115.45  3.000
 IMH  N3    C2   N1    127.60  3.000
 IMH  C4    N3   C2    114.44  3.000
 IMH  N3    C4   C5    122.40  3.000
 IMH  N3    C4   C9    130.12  3.000
 IMH  C5    C4   C9    107.48  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
 IMH  CONST_01  C5   N7  C8  C9     0.00  0.0  0
 IMH  CONST_02  N7   C5  C4  C9     0.00  0.0  0
 IMH  CONST_03  C6   C5  C4  C9   180.00  0.0  0
 IMH  CONST_04  C2   N3  C4  C9   180.00  0.0  0
 IMH  CONST_05  C5   C4  C9  C8     0.00  0.0  0
 IMH  CONST_06  N3   C4  C9  C8   180.00  0.0  0
 IMH  CONST_07  C6   C5  N7  C8   180.00  0.0  0
 IMH  CONST_08  C4   C5  N7  C8     0.00  0.0  0
 IMH  CONST_09  C4   C9  C8  N7     0.00  0.0  0
 IMH  CONST_10  N1   C6  C5  N7   180.00  0.0  0
 IMH  CONST_11  N3   C4  C5  N7   180.00  0.0  0
 IMH  CONST_12  C2   N1  C6  C5     0.00  0.0  0
 IMH  CONST_13  C2   N3  C4  C5     0.00  0.0  0
 IMH  CONST_14  N3   C4  C5  C6     0.00  0.0  0
 IMH  CONST_15  N3   C2  N1  C6     0.00  0.0  0
 IMH  CONST_16  C4   C5  C6  N1     0.00  0.0  0
 IMH  CONST_17  C4   N3  C2  N1     0.00  0.0  0
 IMH  CONST_18  N7   C8  C9  C1'  180.00  0.0  0
 IMH  CONST_19  C5   C4  C9  C1'  180.00  0.0  0
 IMH  CONST_20  N3   C4  C9  C1'    0.00  0.0  0
 IMH  CONST_21  O6   C6  C5  N7     0.00  0.0  0
 IMH  CONST_22  C4   C5  C6  O6   180.00  0.0  0
 IMH  CONST_23  C2   N1  C6  O6   180.00  0.0  0
 IMH  CONST_24  H8   C8  C9  C1'    0.00  0.0  0
 IMH  CONST_25  HN7  N7  C8  C9   180.00  0.0  0
 IMH  CONST_26  H2   C2  N1  C6   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
 IMH  chir_01  C4'  C5'  N4'  C3'  negativ
 IMH  chir_02  C3'  O3'  C4'  C2'  positiv
 IMH  chir_03  C2'  O2'  C3'  C1'  positiv
 IMH  chir_04  C1'  N4'  C2'  C9   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
 IMH  plan-1  C1'  0.020
 IMH  plan-1  C9   0.020
 IMH  plan-1  C8   0.020
 IMH  plan-1  N7   0.020
 IMH  plan-1  C5   0.020
 IMH  plan-1  C6   0.020
 IMH  plan-1  O6   0.020
 IMH  plan-1  N1   0.020
 IMH  plan-1  C2   0.020
 IMH  plan-1  N3   0.020
 IMH  plan-1  C4   0.020
 IMH  plan-1  H8   0.020
 IMH  plan-1  HN7  0.020
 IMH  plan-1  H2   0.020

