# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 17:27:05 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 1-deoxy-1-[(5-nitroso-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H](O)CNC1=C(N=O)C(=O)NC(=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
 LMZ  LMZ  1-deoxy-1-[(5-nitroso-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)amino]-D-ribitol  ligand  34  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LMZ
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
 LMZ  N1    N  NR16  0  -0.752   1.4119  -0.2151  -2.0635
 LMZ  C2    C  CR6   0   0.692   1.9193  -0.4377  -3.3318
 LMZ  N3    N  NR16  0  -0.728   1.0084  -0.3216  -4.3358
 LMZ  C4    C  CR6   0   0.550  -0.3425   0.0028  -4.2249
 LMZ  C5    C  CR6   0  -0.114  -0.7938   0.2188  -2.8678
 LMZ  C6    C  CR6   0   0.724   0.1257   0.0906  -1.7905
 LMZ  N7    N  NH1   0  -0.635  -0.2461   0.2597  -0.5433
 LMZ  C8    C  CH2   0  -0.315   0.6016   0.2068   0.6320
 LMZ  C9    C  CH1   0  -0.033  -0.2886   0.0447   1.8662
 LMZ  O9    O  OH1   0  -0.654  -1.3396   0.9837   1.8459
 LMZ  C10   C  CH1   0  -0.029   0.5391   0.1535   3.1607
 LMZ  O10   O  OH1   0  -0.654   1.8438  -0.3578   3.0129
 LMZ  C11   C  CH1   0  -0.016  -0.1532  -0.5109   4.3680
 LMZ  O11   O  OH1   0  -0.654  -1.5483  -0.3451   4.3833
 LMZ  C12   C  CH2   0  -0.160   0.4892  -0.0330   5.6608
 LMZ  O12   O  OH1   0  -0.671  -0.0187  -0.7893   6.7335
 LMZ  N5    N  N     0  -0.051  -2.0487   0.5501  -2.4778
 LMZ  O52   O  O     0  -0.395  -2.9317   0.6913  -3.3085
 LMZ  O4    O  OC    0  -0.436  -1.0170   0.0784  -5.2300
 LMZ  O2    O  OC    0  -0.449   3.0832  -0.7111  -3.5038
 LMZ  HN1   H  HNR6  0   0.457   2.0884  -0.2857  -1.3149
 LMZ  HN3   H  HNR6  0   0.431   1.3578  -0.4801  -5.2728
 LMZ  HN7   H  HNH1  0   0.416  -1.2107   0.5449  -0.4185
 LMZ  H81   H  HCH2  0   0.274   1.2060   1.1182   0.7001
 LMZ  H82   H  HCH2  0   0.270   1.2810  -0.6425   0.5617
 LMZ  H9    H  HCH1  0   0.263  -0.7687  -0.9375   1.8076
 LMZ  HO9   H  HOH1  0   0.453  -0.9679   1.8720   1.9084
 LMZ  H10   H  HCH1  0   0.239   0.6757   1.2249   3.3636
 LMZ  HO10  H  HOH1  0   0.452   1.7994  -1.3182   2.9400
 LMZ  H11   H  HCH1  0   0.232   0.0040  -1.5935   4.2753
 LMZ  HO11  H  HOH1  0   0.442  -1.7545   0.5955   4.3675
 LMZ  H121  H  HCH2  0   0.193   0.2734   1.0398   5.7807
 LMZ  H122  H  HCH2  0   0.205   1.5774  -0.1304   5.5758
 LMZ  HO12  H  HOH1  0   0.455   0.4472  -0.5232   7.5309

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
 LMZ  N1   C2    aromatic  1.384  0.020  1.384
 LMZ  N1   C6    aromatic  1.350  0.020  1.350
 LMZ  N1   HN1   single    0.860  0.020  1.020
 LMZ  C2   N3    aromatic  1.361  0.020  1.361
 LMZ  C2   O2    double    1.208  0.020  1.208
 LMZ  N3   C4    aromatic  1.394  0.020  1.394
 LMZ  N3   HN3   single    0.860  0.020  1.020
 LMZ  C4   C5    aromatic  1.446  0.020  1.446
 LMZ  C4   O4    double    1.213  0.020  1.213
 LMZ  C5   C6    aromatic  1.422  0.020  1.422
 LMZ  C5   N5    single    1.355  0.020  1.355
 LMZ  C6   N7    single    1.312  0.020  1.312
 LMZ  N7   C8    single    1.450  0.020  1.450
 LMZ  N7   HN7   single    0.860  0.020  1.020
 LMZ  C8   C9    single    1.530  0.020  1.530
 LMZ  C8   H81   single    0.970  0.020  1.090
 LMZ  C8   H82   single    0.970  0.020  1.090
 LMZ  C9   O9    single    1.410  0.020  1.410
 LMZ  C9   C10   single    1.540  0.020  1.540
 LMZ  C9   H9    single    0.970  0.020  1.090
 LMZ  O9   HO9   single    0.850  0.020  0.980
 LMZ  C10  O10   single    1.409  0.020  1.409
 LMZ  C10  C11   single    1.542  0.020  1.542
 LMZ  C10  H10   single    0.970  0.020  1.090
 LMZ  O10  HO10  single    0.850  0.020  0.980
 LMZ  C11  O11   single    1.405  0.020  1.405
 LMZ  C11  C12   single    1.521  0.020  1.521
 LMZ  C11  H11   single    0.970  0.020  1.090
 LMZ  O11  HO11  single    0.850  0.020  0.980
 LMZ  C12  O12   single    1.407  0.020  1.407
 LMZ  C12  H121  single    0.970  0.020  1.090
 LMZ  C12  H122  single    0.970  0.020  1.090
 LMZ  O12  HO12  single    0.850  0.020  0.980
 LMZ  N5   O52   double    1.220  0.020  1.220

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
 LMZ  HN1   N1   C6    120.22  3.000
 LMZ  HN1   N1   C2    114.96  3.000
 LMZ  C6    N1   C2    124.82  3.000
 LMZ  O2    C2   N3    124.01  3.000
 LMZ  O2    C2   N1    121.34  3.000
 LMZ  N3    C2   N1    114.65  3.000
 LMZ  HN3   N3   C4    116.39  3.000
 LMZ  HN3   N3   C2    116.01  3.000
 LMZ  C4    N3   C2    127.60  3.000
 LMZ  O4    C4   C5    126.50  3.000
 LMZ  O4    C4   N3    119.18  3.000
 LMZ  C5    C4   N3    114.32  3.000
 LMZ  N5    C5   C6    113.75  3.000
 LMZ  N5    C5   C4    126.54  3.000
 LMZ  C6    C5   C4    119.70  3.000
 LMZ  N7    C6   C5    121.67  3.000
 LMZ  N7    C6   N1    119.43  3.000
 LMZ  C5    C6   N1    118.90  3.000
 LMZ  HN7   N7   C8    117.83  3.000
 LMZ  HN7   N7   C6    115.02  3.000
 LMZ  C8    N7   C6    126.86  3.000
 LMZ  H82   C8   H81   107.96  3.000
 LMZ  H82   C8   C9    109.40  3.000
 LMZ  H81   C8   C9    111.03  3.000
 LMZ  H82   C8   N7    109.91  3.000
 LMZ  H81   C8   N7    110.03  3.000
 LMZ  C9    C8   N7    108.51  3.000
 LMZ  H9    C9   C10   110.12  3.000
 LMZ  H9    C9   O9    105.66  3.000
 LMZ  C10   C9   O9    111.45  3.000
 LMZ  H9    C9   C8    107.88  3.000
 LMZ  C10   C9   C8    110.96  3.000
 LMZ  O9    C9   C8    110.59  3.000
 LMZ  HO9   O9   C9    108.97  3.000
 LMZ  H10   C10  C11   109.34  3.000
 LMZ  H10   C10  O10   104.96  3.000
 LMZ  C11   C10  O10   109.96  3.000
 LMZ  H10   C10  C9    106.91  3.000
 LMZ  C11   C10  C9    112.72  3.000
 LMZ  O10   C10  C9    112.56  3.000
 LMZ  HO10  O10  C10   109.07  3.000
 LMZ  H11   C11  C12   108.74  3.000
 LMZ  H11   C11  O11   105.04  3.000
 LMZ  C12   C11  O11   111.91  3.000
 LMZ  H11   C11  C10   107.12  3.000
 LMZ  C12   C11  C10   109.91  3.000
 LMZ  O11   C11  C10   113.79  3.000
 LMZ  HO11  O11  C11   109.13  3.000
 LMZ  H122  C12  H121  106.85  3.000
 LMZ  H122  C12  O12   111.70  3.000
 LMZ  H121  C12  O12   111.71  3.000
 LMZ  H122  C12  C11   109.00  3.000
 LMZ  H121  C12  C11   108.42  3.000
 LMZ  O12   C12  C11   109.07  3.000
 LMZ  HO12  O12  C12   107.98  3.000
 LMZ  O52   N5   C5    120.16  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
 LMZ  CONST_01  C4   N3  C2  N1     0.00   0.0  0
 LMZ  CONST_02  C4   C5  C6  N1     0.00   0.0  0
 LMZ  CONST_03  C5   C6  N1  C2     0.00   0.0  0
 LMZ  CONST_04  C5   C4  N3  C2     0.00   0.0  0
 LMZ  CONST_05  C6   N1  C2  N3     0.00   0.0  0
 LMZ  CONST_06  C6   C5  C4  N3     0.00   0.0  0
 LMZ  CONST_07  N5   C5  C6  N1   180.00   0.0  0
 LMZ  CONST_08  N7   C6  N1  C2   180.00   0.0  0
 LMZ  CONST_09  O4   C4  N3  C2   180.00   0.0  0
 LMZ  CONST_10  N5   C5  C4  N3   180.00   0.0  0
 LMZ  CONST_11  O2   C2  N3  C4   180.00   0.0  0
 LMZ  CONST_12  N7   C6  C5  C4   180.00   0.0  0
 LMZ  CONST_13  O2   C2  N1  C6   180.00   0.0  0
 LMZ  CONST_14  O4   C4  C5  C6   180.00   0.0  0
 LMZ  CONST_15  HN3  N3  C2  N1   180.00   0.0  0
 LMZ  CONST_16  HN1  N1  C2  N3   180.00   0.0  0
 LMZ  CONST_17  C8   N7  C6  N1     0.00   0.0  0
 LMZ  CONST_18  C8   N7  C6  C5   180.00   0.0  0
 LMZ  CONST_19  HN7  N7  C6  N1   180.00   0.0  0
 LMZ  Var_01    C9   C8  N7  C6  -163.42  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
 LMZ  chir_01  C9   C8   O9   C10  positiv
 LMZ  chir_02  C10  O10  C9   C11  negativ
 LMZ  chir_03  C11  O11  C10  C12  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
 LMZ  plan-1  N1   0.020
 LMZ  plan-1  C2   0.020
 LMZ  plan-1  N3   0.020
 LMZ  plan-1  C4   0.020
 LMZ  plan-1  C5   0.020
 LMZ  plan-1  C6   0.020
 LMZ  plan-1  N7   0.020
 LMZ  plan-1  N5   0.020
 LMZ  plan-1  O4   0.020
 LMZ  plan-1  O2   0.020
 LMZ  plan-1  HN1  0.020
 LMZ  plan-1  HN3  0.020
 LMZ  plan-2  C5   0.020
 LMZ  plan-2  N5   0.020
 LMZ  plan-2  O52  0.020
 LMZ  plan-3  C6   0.020
 LMZ  plan-3  N7   0.020
 LMZ  plan-3  C8   0.020
 LMZ  plan-3  HN7  0.020

