# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 08:55:59 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2c(CN3C[C@H](O)[C@@H](CO)C3)c[nH]c2C(=O)N1
#
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
 IM5  IM5  2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one  ligand  37  20  .  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_IM5
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
 IM5  N1    N  NR16  0  -0.716   3.8280   0.9250  -0.6448
 IM5  C2    C  CR6   0   0.632   2.7599   1.7243  -0.3267
 IM5  N2    N  NH2   0  -0.842   2.8641   3.0252  -0.6940
 IM5  N3    N  N     0  -0.502   1.6798   1.2839   0.2427
 IM5  C4    C  CR56  0   0.172   1.6640  -0.0526   0.5021
 IM5  C5    C  CR56  0   0.122   2.7202  -0.9088   0.2078
 IM5  C6    C  CR6   0   0.510   3.9113  -0.4426  -0.4056
 IM5  O6    O  O     0  -0.490   4.9076  -1.0844  -0.7126
 IM5  N7    N  NR15  0  -0.655   2.3781  -2.1676   0.6122
 IM5  C8    C  CR15  0  -0.051   1.1390  -2.1236   1.1497
 IM5  C9    C  CR5   0  -0.049   0.6485  -0.8351   1.1097
 IM5  N1'   N  NT    0  -0.412  -1.5736  -0.0292   0.4935
 IM5  C10   C  CH2   0  -0.362  -0.6852  -0.3691   1.5846
 IM5  C2'   C  CH2   0  -0.295  -1.9310  -1.1398  -0.3629
 IM5  C3'   C  CH1   0   0.042  -3.0640  -0.5868  -1.2269
 IM5  O3'   O  OH1   0  -0.677  -2.6144   0.0227  -2.4184
 IM5  C4'   C  CH1   0  -0.308  -3.7086   0.4902  -0.3309
 IM5  C5'   C  CH2   0  -0.155  -5.1730   0.2127  -0.0611
 IM5  O5'   O  OH1   0  -0.673  -5.6676   1.2106   0.8040
 IM5  C6'   C  CH2   0  -0.262  -2.8486   0.4996   0.9367
 IM5  HN1   H  HNR6  0   0.420   4.6288   1.3443  -1.0990
 IM5  HN2   H  HNH2  0   0.402   3.7788   3.4323  -0.8004
 IM5  HN2A  H  HNH2  0   0.400   2.1776   3.6444  -0.2957
 IM5  H8    H  HCR5  0   0.286   0.6698  -3.0172   1.5308
 IM5  H10   H  HCH2  0   0.201  -1.1294  -1.1431   2.2355
 IM5  H10A  H  HCH2  0   0.236  -0.5640   0.5221   2.2078
 IM5  H2'   H  HCH2  0   0.241  -1.0815  -1.4981  -0.9488
 IM5  H2'A  H  HCH2  0   0.186  -2.3090  -1.9992   0.2207
 IM5  H3'   H  HCH1  0   0.212  -3.7788  -1.3887  -1.4564
 IM5  HO3'  H  HOH1  0   0.447  -2.2428  -0.6639  -2.9804
 IM5  H4'   H  HCH1  0   0.251  -3.6227   1.4535  -0.8424
 IM5  H5'   H  HCH2  0   0.206  -5.7242   0.1952  -1.0114
 IM5  H5'A  H  HCH2  0   0.190  -5.2753  -0.7884   0.3814
 IM5  HO5'  H  HOH1  0   0.454  -6.5730   0.9871   1.0372
 IM5  H6'   H  HCH2  0   0.187  -3.3068  -0.1434   1.7104
 IM5  H6'A  H  HCH2  0   0.236  -2.7327   1.4950   1.3700
 IM5  HN7   H  HNR5  0   0.414   2.9478  -2.9921   0.5211

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
 IM5  C2   N1    single    1.371  0.020  1.371
 IM5  N1   C6    single    1.391  0.020  1.391
 IM5  N1   HN1   single    0.860  0.020  1.020
 IM5  N2   C2    single    1.356  0.020  1.356
 IM5  N3   C2    double    1.298  0.020  1.298
 IM5  N2   HN2   single    0.890  0.020  1.040
 IM5  N2   HN2A  single    0.890  0.020  1.040
 IM5  N3   C4    single    1.362  0.020  1.362
 IM5  C9   C4    aromatic  1.419  0.020  1.419
 IM5  C4   C5    aromatic  1.391  0.020  1.391
 IM5  C5   N7    aromatic  1.366  0.020  1.366
 IM5  C5   C6    single    1.419  0.020  1.419
 IM5  C6   O6    double    1.224  0.020  1.224
 IM5  C8   N7    aromatic  1.351  0.020  1.351
 IM5  C9   C8    aromatic  1.379  0.020  1.379
 IM5  C8   H8    single    0.930  0.020  1.080
 IM5  C10  C9    single    1.490  0.020  1.490
 IM5  C10  N1'   single    1.447  0.020  1.447
 IM5  N1'  C2'   single    1.447  0.020  1.447
 IM5  N1'  C6'   single    1.450  0.020  1.450
 IM5  C10  H10   single    0.970  0.020  1.090
 IM5  C10  H10A  single    0.970  0.020  1.090
 IM5  C2'  C3'   single    1.528  0.020  1.528
 IM5  C2'  H2'   single    0.970  0.020  1.090
 IM5  C2'  H2'A  single    0.970  0.020  1.090
 IM5  O3'  C3'   single    1.412  0.020  1.412
 IM5  C3'  C4'   single    1.542  0.020  1.542
 IM5  C3'  H3'   single    0.970  0.020  1.090
 IM5  O3'  HO3'  single    0.850  0.020  0.980
 IM5  C6'  C4'   single    1.532  0.020  1.532
 IM5  C4'  C5'   single    1.515  0.020  1.515
 IM5  C4'  H4'   single    0.970  0.020  1.090
 IM5  C5'  O5'   single    1.410  0.020  1.410
 IM5  C5'  H5'   single    0.970  0.020  1.090
 IM5  C5'  H5'A  single    0.970  0.020  1.090
 IM5  O5'  HO5'  single    0.850  0.020  0.980
 IM5  C6'  H6'   single    0.970  0.020  1.090
 IM5  C6'  H6'A  single    0.970  0.020  1.090
 IM5  N7   HN7   single    0.860  0.020  1.020

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
 IM5  HN1   N1   C6   115.94  3.000
 IM5  HN1   N1   C2   118.63  3.000
 IM5  C6    N1   C2   125.43  3.000
 IM5  N3    C2   N2   120.55  3.000
 IM5  N3    C2   N1   123.51  3.000
 IM5  N2    C2   N1   115.88  3.000
 IM5  HN2A  N2   HN2  114.37  3.000
 IM5  HN2A  N2   C2   115.51  3.000
 IM5  HN2   N2   C2   119.10  3.000
 IM5  C4    N3   C2   115.23  3.000
 IM5  C9    C4   C5   107.14  3.000
 IM5  C5    C4   N3   123.71  3.000
 IM5  C9    C4   N3   129.14  3.000
 IM5  N7    C5   C6   129.89  3.000
 IM5  C6    C5   C4   121.78  3.000
 IM5  N7    C5   C4   108.33  3.000
 IM5  O6    C6   C5   128.28  3.000
 IM5  O6    C6   N1   121.40  3.000
 IM5  C5    C6   N1   110.32  3.000
 IM5  HN7   N7   C8   125.58  3.000
 IM5  HN7   N7   C5   125.91  3.000
 IM5  C8    N7   C5   108.51  3.000
 IM5  H8    C8   C9   129.01  3.000
 IM5  H8    C8   N7   120.82  3.000
 IM5  C9    C8   N7   110.18  3.000
 IM5  C10   C9   C8   126.94  3.000
 IM5  C10   C9   C4   127.20  3.000
 IM5  C8    C9   C4   105.85  3.000
 IM5  C6'   N1'  C2'  104.10  3.000
 IM5  C6'   N1'  C10  113.27  3.000
 IM5  C2'   N1'  C10  114.67  3.000
 IM5  H10A  C10  H10  106.24  3.000
 IM5  H10A  C10  N1'  107.82  3.000
 IM5  H10   C10  N1'  111.22  3.000
 IM5  H10A  C10  C9   109.69  3.000
 IM5  H10   C10  C9   109.18  3.000
 IM5  N1'   C10  C9   112.48  3.000
 IM5  H2'A  C2'  H2'  107.10  3.000
 IM5  H2'A  C2'  C3'  109.05  3.000
 IM5  H2'   C2'  C3'  113.08  3.000
 IM5  H2'A  C2'  N1'  111.63  3.000
 IM5  H2'   C2'  N1'  112.14  3.000
 IM5  C3'   C2'  N1'  103.88  3.000
 IM5  H3'   C3'  C4'  111.05  3.000
 IM5  H3'   C3'  O3'  110.24  3.000
 IM5  C4'   C3'  O3'  108.78  3.000
 IM5  H3'   C3'  C2'  109.65  3.000
 IM5  C4'   C3'  C2'  103.54  3.000
 IM5  O3'   C3'  C2'  113.41  3.000
 IM5  HO3'  O3'  C3'  107.94  3.000
 IM5  H4'   C4'  C6'  109.72  3.000
 IM5  H4'   C4'  C5'  108.69  3.000
 IM5  C6'   C4'  C5'  113.36  3.000
 IM5  H4'   C4'  C3'  108.09  3.000
 IM5  C5'   C4'  C3'  112.32  3.000
 IM5  C6'   C4'  C3'  104.50  3.000
 IM5  H5'A  C5'  H5'  106.68  3.000
 IM5  H5'A  C5'  O5'  111.39  3.000
 IM5  H5'   C5'  O5'  111.46  3.000
 IM5  H5'A  C5'  C4'  109.18  3.000
 IM5  H5'   C5'  C4'  109.51  3.000
 IM5  O5'   C5'  C4'  108.59  3.000
 IM5  HO5'  O5'  C5'  108.34  3.000
 IM5  H6'A  C6'  H6'  107.25  3.000
 IM5  H6'A  C6'  C4'  113.18  3.000
 IM5  H6'   C6'  C4'  110.05  3.000
 IM5  H6'A  C6'  N1'  111.13  3.000
 IM5  H6'   C6'  N1'  111.49  3.000
 IM5  C4'   C6'  N1'  103.80  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
 IM5  CONST_01  N7    C8   C9   C4     0.00   0.0  0
 IM5  CONST_02  C8    N7   C5   C4     0.00   0.0  0
 IM5  CONST_03  C8    C9   C4   C5     0.00   0.0  0
 IM5  CONST_04  C9    C8   N7   C5     0.00   0.0  0
 IM5  CONST_05  C9    C4   C5   N7     0.00   0.0  0
 IM5  CONST_06  C4    N3   C2   N1     0.00   0.0  0
 IM5  CONST_07  C5    C6   N1   C2     0.00   0.0  0
 IM5  CONST_08  C6    N1   C2   N3     0.00   0.0  0
 IM5  CONST_09  C10   C9   C4   N3     0.00   0.0  0
 IM5  CONST_10  C10   C9   C4   C5   180.00   0.0  0
 IM5  CONST_11  C10   C9   C8   N7   180.00   0.0  0
 IM5  CONST_12  O6    C6   N1   C2   180.00   0.0  0
 IM5  CONST_13  C6    N1   C2   N2   180.00   0.0  0
 IM5  CONST_14  C4    N3   C2   N2   180.00   0.0  0
 IM5  CONST_15  H8    C8   C9   C4   180.00   0.0  0
 IM5  CONST_16  HN7   N7   C5   C4   180.00   0.0  0
 IM5  CONST_17  HN1   N1   C2   N3   180.00   0.0  0
 IM5  CONST_19  HN2A  N2   C2   N1   180.00   0.0  0
 IM5  Var_01    C4'   C6'  N1'  C2'  -42.79  30.0  1
 IM5  Var_02    C6'   N1'  C2'  C3'   44.67  30.0  1
 IM5  Var_03    N1'   C10  C9   C4    70.62  30.0  3
 IM5  Var_04    C2'   N1'  C10  C9    64.08  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
 IM5  chir_01  C3'  C2'  O3'  C4'  positiv
 IM5  chir_02  C4'  C3'  C6'  C5'  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
 IM5  plan-1  N1    0.020
 IM5  plan-1  C2    0.020
 IM5  plan-1  N2    0.020
 IM5  plan-1  N3    0.020
 IM5  plan-1  C4    0.020
 IM5  plan-1  C5    0.020
 IM5  plan-1  C6    0.020
 IM5  plan-1  O6    0.020
 IM5  plan-1  N7    0.020
 IM5  plan-1  C8    0.020
 IM5  plan-1  C9    0.020
 IM5  plan-1  C10   0.020
 IM5  plan-1  HN1   0.020
 IM5  plan-1  HN2   0.020
 IM5  plan-1  HN2A  0.020
 IM5  plan-1  H8    0.020
 IM5  plan-1  HN7   0.020

