# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 19:13:23 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 7-({[(1R,2S)-2,3-dihydroxy-1-(hydroxymethyl)propyl]amino}methyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](CO)NCc1c[nH]c2C(=O)NC=Nc12
#
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
 229  229  7-({[(1R,2S)-2,3-dihydroxy-1-(hydroxymethyl)propyl]amino}methyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one  ligand  35  19  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_229
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
 229  O4    O  OH1   0  -0.682   3.3488  -4.3431   0.1110
 229  C11   C  CH2   0  -0.178   2.3392  -3.5545   0.7138
 229  C6    C  CH1   0   0.010   1.5813  -4.4624   1.6693
 229  O3    O  OH1   0  -0.678   2.4380  -5.0113   2.6488
 229  C8    C  CH1   0  -0.123   0.4313  -3.7563   2.4011
 229  C3    C  CH2   0  -0.153   0.9324  -2.7024   3.3821
 229  O2    O  OH1   0  -0.676  -0.1845  -2.1977   4.0877
 229  N2    N  NH1   0  -0.604  -0.4604  -3.1181   1.4475
 229  C10   C  CH2   0  -0.362  -1.2539  -4.0324   0.6395
 229  C4    C  CR5   0  -0.048  -2.1117  -3.2711  -0.3119
 229  C1    C  CR56  0   0.158  -1.6839  -2.5992  -1.4840
 229  N4    N  N     0  -0.433  -0.4354  -2.5280  -2.0355
 229  C7    C  CR16  0   0.121  -0.3693  -1.8523  -3.1277
 229  N3    N  NR16  0  -0.661  -1.4242  -1.2361  -3.7285
 229  C9    C  CR15  0  -0.051  -3.4660  -3.0373  -0.2223
 229  N1    N  NR15  0  -0.651  -3.8748  -2.2733  -1.2649
 229  C2    C  CR56  0   0.146  -2.8018  -1.9950  -2.0512
 229  C5    C  CR6   0   0.518  -2.7308  -1.2435  -3.2599
 229  O1    O  O     0  -0.484  -3.6390  -0.6713  -3.8456
 229  HO4   H  HOH1  0   0.458   3.9221  -3.7653  -0.3998
 229  H111  H  HCH2  0   0.194   2.7751  -2.7101   1.2623
 229  H112  H  HCH2  0   0.219   1.6454  -3.1448  -0.0277
 229  H6    H  HCH1  0   0.212   1.1497  -5.2773   1.0681
 229  HO3   H  HOH1  0   0.447   3.1914  -5.3981   2.1905
 229  H8    H  HCH1  0   0.214  -0.0892  -4.5326   2.9922
 229  H31   H  HCH2  0   0.195   1.4441  -1.9027   2.8329
 229  H32   H  HCH2  0   0.209   1.6601  -3.1518   4.0638
 229  HO2   H  HOH1  0   0.457   0.0937  -1.4126   4.5668
 229  HN2   H  HNH1  0   0.345  -1.0992  -2.5221   1.9599
 229  H101  H  HCH2  0   0.216  -1.8782  -4.7039   1.2483
 229  H102  H  HCH2  0   0.233  -0.5820  -4.6738   0.0654
 229  H7    H  HCR6  0   0.290   0.5760  -1.7389  -3.6427
 229  HN3   H  HNR6  0   0.429  -1.2472  -0.7337  -4.5880
 229  H9    H  HCR5  0   0.290  -4.1681  -3.3714   0.5254
 229  HN1   H  HNR5  0   0.419  -4.8209  -1.9708  -1.4303

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
 229  O4   C11   single  1.416  0.020  1.416
 229  O4   HO4   single  0.850  0.020  0.980
 229  C11  C6    single  1.520  0.020  1.520
 229  C11  H111  single  0.970  0.020  1.090
 229  C11  H112  single  0.970  0.020  1.090
 229  C6   C8    single  1.535  0.020  1.535
 229  C6   O3    single  1.412  0.020  1.412
 229  C6   H6    single  0.970  0.020  1.090
 229  O3   HO3   single  0.850  0.020  0.980
 229  C8   C3    single  1.525  0.020  1.525
 229  C8   N2    single  1.453  0.020  1.453
 229  C8   H8    single  0.970  0.020  1.090
 229  C3   O2    single  1.414  0.020  1.414
 229  C3   H31   single  0.970  0.020  1.090
 229  C3   H32   single  0.970  0.020  1.090
 229  O2   HO2   single  0.850  0.020  0.980
 229  N2   C10   single  1.456  0.020  1.456
 229  N2   HN2   single  0.890  0.020  1.040
 229  C10  C4    single  1.490  0.020  1.490
 229  C10  H101  single  0.970  0.020  1.090
 229  C10  H102  single  0.970  0.020  1.090
 229  C4   C1    single  1.417  0.020  1.417
 229  C4   C9    double  1.377  0.020  1.377
 229  C1   N4    single  1.367  0.020  1.367
 229  C1   C2    double  1.392  0.020  1.392
 229  N4   C7    double  1.286  0.020  1.286
 229  C7   N3    single  1.361  0.020  1.361
 229  C7   H7    single  0.930  0.020  1.080
 229  N3   C5    single  1.388  0.020  1.388
 229  N3   HN3   single  0.860  0.020  1.020
 229  C9   N1    single  1.356  0.020  1.356
 229  C9   H9    single  0.930  0.020  1.080
 229  N1   C2    single  1.359  0.020  1.359
 229  N1   HN1   single  0.860  0.020  1.020
 229  C2   C5    single  1.425  0.020  1.425
 229  C5   O1    double  1.223  0.020  1.223

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
 229  HO4   O4   C11   108.47  3.000
 229  H112  C11  H111  107.60  3.000
 229  H112  C11  C6    109.46  3.000
 229  H111  C11  C6    110.09  3.000
 229  H112  C11  O4    111.83  3.000
 229  H111  C11  O4    110.99  3.000
 229  C6    C11  O4    106.88  3.000
 229  H6    C6   C8    107.89  3.000
 229  H6    C6   O3    109.20  3.000
 229  C8    C6   O3    107.61  3.000
 229  H6    C6   C11   107.12  3.000
 229  O3    C6   C11   111.44  3.000
 229  C8    C6   C11   113.47  3.000
 229  HO3   O3   C6    107.50  3.000
 229  H8    C8   N2    111.73  3.000
 229  H8    C8   C3    107.22  3.000
 229  N2    C8   C3    108.68  3.000
 229  H8    C8   C6    106.53  3.000
 229  N2    C8   C6    110.42  3.000
 229  C3    C8   C6    112.24  3.000
 229  H32   C3   H31   107.54  3.000
 229  H32   C3   O2    111.17  3.000
 229  H31   C3   O2    110.98  3.000
 229  H32   C3   C8    109.61  3.000
 229  H31   C3   C8    109.58  3.000
 229  O2    C3   C8    107.95  3.000
 229  HO2   O2   C3    108.16  3.000
 229  HN2   N2   C10   107.86  3.000
 229  HN2   N2   C8    108.27  3.000
 229  C10   N2   C8    115.02  3.000
 229  H102  C10  H101  106.35  3.000
 229  H102  C10  C4    108.59  3.000
 229  H101  C10  C4    109.78  3.000
 229  H102  C10  N2    108.99  3.000
 229  H101  C10  N2    112.67  3.000
 229  C4    C10  N2    110.32  3.000
 229  C9    C4   C1    105.67  3.000
 229  C9    C4   C10   127.68  3.000
 229  C1    C4   C10   126.62  3.000
 229  C2    C1   N4    123.14  3.000
 229  C2    C1   C4    107.49  3.000
 229  N4    C1   C4    129.36  3.000
 229  C7    N4   C1    114.64  3.000
 229  H7    C7   N3    114.79  3.000
 229  H7    C7   N4    120.26  3.000
 229  N3    C7   N4    124.95  3.000
 229  HN3   N3   C5    117.02  3.000
 229  HN3   N3   C7    117.67  3.000
 229  C5    N3   C7    125.30  3.000
 229  H9    C9   N1    120.76  3.000
 229  H9    C9   C4    129.23  3.000
 229  N1    C9   C4    110.01  3.000
 229  HN1   N1   C2    125.82  3.000
 229  HN1   N1   C9    125.37  3.000
 229  C2    N1   C9    108.80  3.000
 229  C5    C2   N1    129.65  3.000
 229  C5    C2   C1    122.32  3.000
 229  N1    C2   C1    108.03  3.000
 229  O1    C5   C2    128.02  3.000
 229  O1    C5   N3    122.34  3.000
 229  C2    C5   N3    109.64  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
 229  CONST_01  N3   C7   N4   C1     0.00   0.0  0
 229  CONST_02  C5   N3   C7   N4     0.00   0.0  0
 229  CONST_03  C2   C5   N3   C7     0.00   0.0  0
 229  CONST_04  O1   C5   N3   C7   180.00   0.0  0
 229  CONST_05  H7   C7   N4   C1   180.00   0.0  0
 229  CONST_06  HN3  N3   C7   N4   180.00   0.0  0
 229  Var_01    C1   C4   C10  N2    73.77  30.0  3
 229  Var_02    C4   C10  N2   C8  -179.15  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
 229  chir_01  C6  C11  C8  O3  positiv
 229  chir_02  C8  N2   C6  C3  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
 229  plan-1  C10  0.020
 229  plan-1  C4   0.020
 229  plan-1  C1   0.020
 229  plan-1  N4   0.020
 229  plan-1  C7   0.020
 229  plan-1  N3   0.020
 229  plan-1  C9   0.020
 229  plan-1  N1   0.020
 229  plan-1  C2   0.020
 229  plan-1  C5   0.020
 229  plan-1  O1   0.020
 229  plan-1  H7   0.020
 229  plan-1  HN3  0.020
 229  plan-1  H9   0.020
 229  plan-1  HN1  0.020

