# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 16:33:54 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 4-[(7R,7aS)-7-hydroxy-1,3-dioxotetrahydro-1H-pyrrolo[1,2-c]imidazol-2(3H)-yl]naphthalene-1-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCN2[C@@H]1C(=O)N(C2=O)c3ccc(C#N)c4ccccc34
#
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
 LG7  LG7  4-[(7R,7aS)-7-hydroxy-1,3-dioxotetrahydro-1H-pyrrolo[1,2-c]imidazol-2(3H)-yl]naphthalene-1-carbonitrile  ligand  36  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LG7
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
 LG7  C13  C  CR16  0  -0.279   5.6342   2.8064   3.1896
 LG7  C18  C  CR16  0  -0.239   3.3988   6.7564   5.3960
 LG7  C17  C  CR16  0  -0.320   4.6820   6.2832   5.3947
 LG7  C16  C  CR66  0   0.144   5.0169   5.1238   4.6625
 LG7  C15  C  CR6   0  -0.009   6.3358   4.5884   4.6396
 LG7  C19  C  CR16  0  -0.248   2.3928   6.0899   4.6708
 LG7  C20  C  CR16  0  -0.324   2.6872   4.9659   3.9497
 LG7  C21  C  CR66  0   0.123   4.0057   4.4571   3.9227
 LG7  C22  C  CSP   0   0.028   7.3752   5.2352   5.3722
 LG7  C12  C  CR6   0   0.314   4.3576   3.2958   3.1883
 LG7  O1   O  OH1   0  -0.663   0.2820   3.3165   1.7858
 LG7  C2   C  CH1   0   0.056   0.4605   2.4017   0.7322
 LG7  C3   C  CH2   0  -0.532  -0.2293   1.0633   0.9997
 LG7  C4   C  CH2   0  -0.270   0.6489   0.3797   2.0589
 LG7  N5   N  NR5   0  -0.490   1.9543   1.0134   1.8634
 LG7  C6   C  CR15  0  -0.254   1.9233   1.9719   0.7742
 LG7  C7   C  CR5   0   0.548   2.9281   3.0170   1.1929
 LG7  O8   O  O     0  -0.406   3.3001   3.9830   0.5805
 LG7  N9   N  NR5   0  -0.685   3.3722   2.6231   2.4325
 LG7  C10  C  CR5   0   0.706   2.7099   1.4701   2.8889
 LG7  O11  O  O     0  -0.455   2.8215   1.0148   4.0008
 LG7  C14  C  CR16  0  -0.272   6.6361   3.4547   3.9248
 LG7  N23  N  NS    0  -0.239   8.2159   5.7555   5.9638
 LG7  H13  H  HCR6  0   0.290   5.8775   1.9191   2.6214
 LG7  H18  H  HCR6  0   0.274   3.1540   7.6463   5.9600
 LG7  H17  H  HCR6  0   0.265   5.4441   6.8007   5.9630
 LG7  H19  H  HCR6  0   0.271   1.3803   6.4696   4.6863
 LG7  H20  H  HCR6  0   0.266   1.9030   4.4628   3.4010
 LG7  HO1  H  HOH1  0   0.467  -0.6493   3.5544   1.8424
 LG7  H2   H  HCH1  0   0.257   0.1853   2.8254  -0.2378
 LG7  H31  H  HCH2  0   0.260  -0.2422   0.4774   0.0789
 LG7  H32  H  HCH2  0   0.277  -1.2629   1.1819   1.3252
 LG7  H41  H  HCH2  0   0.255   0.2917   0.5636   3.0723
 LG7  H42  H  HCH2  0   0.262   0.7063  -0.6971   1.9095
 LG7  H6   H  HCR5  0   0.327   2.2235   1.5303  -0.1800
 LG7  H14  H  HCR6  0   0.295   7.6430   3.0617   3.9193

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
 LG7  C13  C14  aromatic  1.402  0.020  1.402
 LG7  C13  C12  aromatic  1.367  0.020  1.367
 LG7  C13  H13  single    0.930  0.020  1.080
 LG7  C18  C17  aromatic  1.368  0.020  1.368
 LG7  C18  C19  aromatic  1.408  0.020  1.408
 LG7  C18  H18  single    0.930  0.020  1.080
 LG7  C17  C16  aromatic  1.412  0.020  1.412
 LG7  C17  H17  single    0.930  0.020  1.080
 LG7  C16  C15  aromatic  1.424  0.020  1.424
 LG7  C16  C21  aromatic  1.419  0.020  1.419
 LG7  C15  C14  aromatic  1.373  0.020  1.373
 LG7  C15  C22  single    1.427  0.020  1.427
 LG7  C19  C20  aromatic  1.367  0.020  1.367
 LG7  C19  H19  single    0.930  0.020  1.080
 LG7  C20  C21  aromatic  1.414  0.020  1.414
 LG7  C20  H20  single    0.930  0.020  1.080
 LG7  C21  C12  aromatic  1.418  0.020  1.418
 LG7  C22  N23  triple    1.152  0.020  1.152
 LG7  C12  N9   single    1.412  0.020  1.412
 LG7  O1   C2   single    1.407  0.020  1.407
 LG7  O1   HO1  single    0.850  0.020  0.980
 LG7  C2   C3   single    1.529  0.020  1.529
 LG7  C2   C6   single    1.525  0.020  1.525
 LG7  C2   H2   single    0.970  0.020  1.090
 LG7  C3   C4   single    1.536  0.020  1.536
 LG7  C3   H31  single    0.970  0.020  1.090
 LG7  C3   H32  single    0.970  0.020  1.090
 LG7  C4   N5   single    1.464  0.020  1.464
 LG7  C4   H41  single    0.970  0.020  1.090
 LG7  C4   H42  single    0.970  0.020  1.090
 LG7  N5   C10  single    1.353  0.020  1.353
 LG7  N5   C6   single    1.451  0.020  1.451
 LG7  C6   C7   single    1.509  0.020  1.509
 LG7  C6   H6   single    0.970  0.020  1.090
 LG7  C7   N9   single    1.374  0.020  1.374
 LG7  C7   O8   double    1.203  0.020  1.203
 LG7  N9   C10  single    1.406  0.020  1.406
 LG7  C10  O11  double    1.207  0.020  1.207
 LG7  C14  H14  single    0.930  0.020  1.080

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
 LG7  H13  C13  C14  119.63  3.000
 LG7  H13  C13  C12  120.22  3.000
 LG7  C14  C13  C12  120.15  3.000
 LG7  H18  C18  C19  119.77  3.000
 LG7  H18  C18  C17  119.84  3.000
 LG7  C19  C18  C17  120.40  3.000
 LG7  H17  C17  C16  119.87  3.000
 LG7  H17  C17  C18  119.65  3.000
 LG7  C16  C17  C18  120.49  3.000
 LG7  C21  C16  C15  118.37  3.000
 LG7  C21  C16  C17  119.15  3.000
 LG7  C15  C16  C17  122.48  3.000
 LG7  C14  C15  C22  118.83  3.000
 LG7  C22  C15  C16  119.75  3.000
 LG7  C14  C15  C16  121.42  3.000
 LG7  H19  C19  C20  119.85  3.000
 LG7  H19  C19  C18  119.69  3.000
 LG7  C20  C19  C18  120.46  3.000
 LG7  H20  C20  C21  119.95  3.000
 LG7  H20  C20  C19  119.60  3.000
 LG7  C21  C20  C19  120.45  3.000
 LG7  C12  C21  C20  122.41  3.000
 LG7  C12  C21  C16  118.53  3.000
 LG7  C20  C21  C16  119.05  3.000
 LG7  N23  C22  C15  180.00  3.000
 LG7  N9   C12  C21  119.60  3.000
 LG7  N9   C12  C13  118.78  3.000
 LG7  C21  C12  C13  121.62  3.000
 LG7  HO1  O1   C2   109.11  3.000
 LG7  H2   C2   C6   112.02  3.000
 LG7  H2   C2   C3   112.38  3.000
 LG7  C6   C2   C3   100.44  3.000
 LG7  H2   C2   O1   112.36  3.000
 LG7  C6   C2   O1   106.52  3.000
 LG7  C3   C2   O1   112.39  3.000
 LG7  H32  C3   H31  107.41  3.000
 LG7  H32  C3   C4   112.61  3.000
 LG7  H31  C3   C4   110.46  3.000
 LG7  H32  C3   C2   112.63  3.000
 LG7  H31  C3   C2   109.12  3.000
 LG7  C4   C3   C2   104.61  3.000
 LG7  H42  C4   H41  108.16  3.000
 LG7  H42  C4   N5   111.27  3.000
 LG7  H41  C4   N5   110.07  3.000
 LG7  H42  C4   C3   112.06  3.000
 LG7  H41  C4   C3   112.24  3.000
 LG7  N5   C4   C3   103.00  3.000
 LG7  C10  N5   C6   110.97  3.000
 LG7  C6   N5   C4   111.53  3.000
 LG7  C10  N5   C4   122.87  3.000
 LG7  H6   C6   C7   109.82  3.000
 LG7  H6   C6   N5   112.48  3.000
 LG7  C7   C6   N5   103.59  3.000
 LG7  H6   C6   C2   110.68  3.000
 LG7  C7   C6   C2   116.81  3.000
 LG7  N5   C6   C2   103.14  3.000
 LG7  N9   C7   O8   126.12  3.000
 LG7  O8   C7   C6   128.38  3.000
 LG7  N9   C7   C6   105.48  3.000
 LG7  C10  N9   C7   112.06  3.000
 LG7  C10  N9   C12  123.07  3.000
 LG7  C7   N9   C12  124.86  3.000
 LG7  O11  C10  N9   124.41  3.000
 LG7  O11  C10  N5   128.51  3.000
 LG7  N9   C10  N5   107.09  3.000
 LG7  H14  C14  C15  120.43  3.000
 LG7  H14  C14  C13  119.67  3.000
 LG7  C15  C14  C13  119.90  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
 LG7  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 LG7  CONST_02  C16  C21  C12  C13     0.00   0.0  0
 LG7  CONST_03  C20  C21  C12  C13   180.00   0.0  0
 LG7  CONST_04  C15  C16  C17  C18   180.00   0.0  0
 LG7  CONST_05  C21  C16  C17  C18     0.00   0.0  0
 LG7  CONST_06  C21  C20  C19  C18     0.00   0.0  0
 LG7  CONST_07  C20  C19  C18  C17     0.00   0.0  0
 LG7  CONST_08  C14  C15  C16  C17   180.00   0.0  0
 LG7  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 LG7  CONST_10  C12  C21  C16  C17   180.00   0.0  0
 LG7  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 LG7  CONST_12  C19  C20  C21  C16     0.00   0.0  0
 LG7  CONST_13  C20  C21  C16  C15   180.00   0.0  0
 LG7  CONST_14  C12  C21  C16  C15     0.00   0.0  0
 LG7  CONST_15  C12  C13  C14  C15     0.00   0.0  0
 LG7  CONST_16  C12  C21  C20  C19   180.00   0.0  0
 LG7  CONST_17  C14  C15  C16  C21     0.00   0.0  0
 LG7  CONST_18  C14  C13  C12  C21     0.00   0.0  0
 LG7  CONST_19  N9   C12  C21  C16   180.00   0.0  0
 LG7  CONST_20  N9   C12  C21  C20     0.00   0.0  0
 LG7  CONST_21  C14  C13  C12  N9    180.00   0.0  0
 LG7  CONST_22  C6   C7   N9   C12   180.00   0.0  0
 LG7  CONST_23  N5   C10  N9   C12   180.00   0.0  0
 LG7  CONST_25  C7   N9   C10  N5      0.00   0.0  0
 LG7  CONST_26  N9   C10  N5   C6      0.00   0.0  0
 LG7  CONST_27  C10  N9   C7   C6      0.00   0.0  0
 LG7  CONST_28  C22  C15  C14  C13   180.00   0.0  0
 LG7  CONST_29  C22  C15  C16  C17     0.00   0.0  0
 LG7  CONST_30  C22  C15  C16  C21   180.00   0.0  0
 LG7  CONST_31  O8   C7   N9   C12     0.00   0.0  0
 LG7  CONST_32  O11  C10  N9   C12     0.00   0.0  0
 LG7  CONST_34  O11  C10  N5   C6    180.00   0.0  0
 LG7  CONST_35  O11  C10  N9   C7    180.00   0.0  0
 LG7  CONST_36  C10  N9   C7   O8    180.00   0.0  0
 LG7  CONST_37  H20  C20  C19  C18   180.00   0.0  0
 LG7  CONST_38  H19  C19  C18  C17   180.00   0.0  0
 LG7  CONST_39  H18  C18  C17  C16   180.00   0.0  0
 LG7  CONST_40  H14  C14  C15  C16   180.00   0.0  0
 LG7  CONST_41  H17  C17  C16  C15     0.00   0.0  0
 LG7  CONST_42  H13  C13  C14  C15   180.00   0.0  0
 LG7  Var_01    C7   N9   C12  C13  -100.41  30.0  2
 LG7  Var_02    N5   C4   C3   C2    -24.05  30.0  1
 LG7  Var_03    C10  N5   C4   C3    134.09  30.0  1

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
 LG7  chir_01  C2  O1  C3  C6  positiv
 LG7  chir_02  C6  N5  C2  C7  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
 LG7  plan-1  C13  0.020
 LG7  plan-1  C18  0.020
 LG7  plan-1  C17  0.020
 LG7  plan-1  C16  0.020
 LG7  plan-1  C15  0.020
 LG7  plan-1  C19  0.020
 LG7  plan-1  C20  0.020
 LG7  plan-1  C21  0.020
 LG7  plan-1  C22  0.020
 LG7  plan-1  C12  0.020
 LG7  plan-1  N9   0.020
 LG7  plan-1  C14  0.020
 LG7  plan-1  N23  0.020
 LG7  plan-1  H13  0.020
 LG7  plan-1  H18  0.020
 LG7  plan-1  H17  0.020
 LG7  plan-1  H19  0.020
 LG7  plan-1  H20  0.020
 LG7  plan-1  H14  0.020
 LG7  plan-2  C12  0.020
 LG7  plan-2  C4   0.020
 LG7  plan-2  N5   0.020
 LG7  plan-2  C6   0.020
 LG7  plan-2  C7   0.020
 LG7  plan-2  O8   0.020
 LG7  plan-2  N9   0.020
 LG7  plan-2  C10  0.020
 LG7  plan-2  O11  0.020

