# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:26:55 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (1~{R},9~{S})-5-(3-oxidanylpropyl)-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCC1=CC=C2[C@H]3CNC[C@H](C3)CN2C1=O
#
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
 MXQ  MXQ  (1~{R},9~{S})-5-(3-oxidanylpropyl)-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one  ligand  38  18  .  2021-08-14  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MXQ
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
 MXQ  C2    C  CR6   0   0.541  -0.6352  -0.5637   0.3391
 MXQ  N3    N  NR6   0  -0.561   0.6855  -0.3573  -0.0610
 MXQ  C4    C  CH2   0  -0.269   1.4632  -1.5935  -0.2468
 MXQ  C5    C  CH1   0  -0.296   2.9288  -1.3922  -0.6073
 MXQ  C6    C  CH2   0  -0.288   3.8205  -1.1763   0.6122
 MXQ  C8    C  CH2   0  -0.268   3.5452   1.1982   0.4390
 MXQ  C9    C  CH1   0  -0.367   2.6235   1.0157  -0.7718
 MXQ  C10   C  CH2   0  -0.442   3.0562  -0.2133  -1.5588
 MXQ  C11   C  CR6   0   0.456   1.1977   0.8790  -0.3182
 MXQ  C12   C  CR16  0  -0.423   0.4145   1.9831  -0.1569
 MXQ  C14   C  CR6   0  -0.108  -1.4510   0.6099   0.5165
 MXQ  C15   C  CH2   0  -0.497  -2.8862   0.4214   0.9047
 MXQ  C16   C  CH2   0  -0.451  -3.7655   0.0398  -0.2879
 MXQ  C17   C  CH2   0  -0.141  -5.2128  -0.1500   0.1209
 MXQ  O1    O  O     0  -0.521  -1.0414  -1.7128   0.5219
 MXQ  N7    N  NH1   0  -0.597   3.4409   0.0411   1.3011
 MXQ  C13   C  CR16  0  -0.166  -0.9163   1.8382   0.2728
 MXQ  O18   O  OH1   0  -0.675  -5.9771  -0.4684  -1.0232
 MXQ  HC4B  H  HCH2  0   0.257   1.3782  -2.1882   0.6630
 MXQ  HC4A  H  HCH2  0   0.259   0.9771  -2.1628  -1.0412
 MXQ  HC5   H  HCH1  0   0.264   3.2548  -2.3142  -1.0947
 MXQ  HC6B  H  HCH2  0   0.237   3.7144  -2.0192   1.2988
 MXQ  HC6A  H  HCH2  0   0.204   4.8694  -1.1671   0.2724
 MXQ  HC8B  H  HCH2  0   0.208   4.5662   1.3713   0.0606
 MXQ  HC8A  H  HCH2  0   0.243   3.2540   2.0902   0.9965
 MXQ  HC9   H  HCH1  0   0.274   2.6880   1.9133  -1.3897
 MXQ  H10B  H  HCH2  0   0.250   4.0867  -0.0952  -1.9023
 MXQ  H10A  H  HCH2  0   0.250   2.4353  -0.3521  -2.4479
 MXQ  HC12  H  HCR6  0   0.261   0.8275   2.9593  -0.3668
 MXQ  H15B  H  HCH2  0   0.234  -2.9699  -0.3439   1.6807
 MXQ  H15A  H  HCH2  0   0.236  -3.2593   1.3515   1.3419
 MXQ  H16B  H  HCH2  0   0.225  -3.7006   0.8251  -1.0470
 MXQ  H16A  H  HCH2  0   0.231  -3.3904  -0.8805  -0.7430
 MXQ  H17B  H  HCH2  0   0.188  -5.2747  -0.9442   0.8772
 MXQ  H17A  H  HCH2  0   0.188  -5.5765   0.7694   0.5992
 MXQ  HN7   H  HNH1  0   0.358   4.0147   0.1692   2.1237
 MXQ  HC13  H  HCR6  0   0.256  -1.5298   2.7231   0.4006
 MXQ  HO18  H  HOH1  0   0.452  -6.8948  -0.5622  -0.7529

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
 MXQ  C17  O18   single  1.412  0.020  1.412
 MXQ  C17  C16   single  1.516  0.020  1.516
 MXQ  C16  C15   single  1.530  0.020  1.530
 MXQ  C10  C9    single  1.522  0.020  1.522
 MXQ  C10  C5    single  1.520  0.020  1.520
 MXQ  C12  C13   single  1.406  0.020  1.406
 MXQ  C12  C11   double  1.363  0.020  1.363
 MXQ  C13  C14   double  1.362  0.020  1.362
 MXQ  C15  C14   single  1.499  0.020  1.499
 MXQ  C9   C11   single  1.502  0.020  1.502
 MXQ  C9   C8    single  1.533  0.020  1.533
 MXQ  C11  N3    single  1.363  0.020  1.363
 MXQ  C14  C2    single  1.440  0.020  1.440
 MXQ  N3   C2    single  1.395  0.020  1.395
 MXQ  N3   C4    single  1.472  0.020  1.472
 MXQ  C2   O1    double  1.232  0.020  1.232
 MXQ  C4   C5    single  1.523  0.020  1.523
 MXQ  C5   C6    single  1.526  0.020  1.526
 MXQ  C8   N7    single  1.447  0.020  1.447
 MXQ  C6   N7    single  1.449  0.020  1.449
 MXQ  C4   HC4B  single  0.970  0.020  1.090
 MXQ  C4   HC4A  single  0.970  0.020  1.090
 MXQ  C5   HC5   single  0.970  0.020  1.090
 MXQ  C6   HC6B  single  0.970  0.020  1.090
 MXQ  C6   HC6A  single  0.970  0.020  1.090
 MXQ  C8   HC8B  single  0.970  0.020  1.090
 MXQ  C8   HC8A  single  0.970  0.020  1.090
 MXQ  C9   HC9   single  0.970  0.020  1.090
 MXQ  C10  H10B  single  0.970  0.020  1.090
 MXQ  C10  H10A  single  0.970  0.020  1.090
 MXQ  C12  HC12  single  0.930  0.020  1.080
 MXQ  C15  H15B  single  0.970  0.020  1.090
 MXQ  C15  H15A  single  0.970  0.020  1.090
 MXQ  C16  H16B  single  0.970  0.020  1.090
 MXQ  C16  H16A  single  0.970  0.020  1.090
 MXQ  C17  H17B  single  0.970  0.020  1.090
 MXQ  C17  H17A  single  0.970  0.020  1.090
 MXQ  N7   HN7   single  0.890  0.020  1.040
 MXQ  C13  HC13  single  0.930  0.020  1.080
 MXQ  O18  HO18  single  0.850  0.020  0.980

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
 MXQ  O1    C2   C14   123.69  3.000
 MXQ  O1    C2   N3    119.51  3.000
 MXQ  C14   C2   N3    116.80  3.000
 MXQ  C11   N3   C4    122.65  3.000
 MXQ  C4    N3   C2    114.32  3.000
 MXQ  C11   N3   C2    122.96  3.000
 MXQ  HC4A  C4   HC4B  106.74  3.000
 MXQ  HC4A  C4   C5    108.98  3.000
 MXQ  HC4B  C4   C5    110.16  3.000
 MXQ  HC4A  C4   N3    107.13  3.000
 MXQ  HC4B  C4   N3    108.15  3.000
 MXQ  C5    C4   N3    115.30  3.000
 MXQ  HC5   C5   C10   110.50  3.000
 MXQ  HC5   C5   C6    107.55  3.000
 MXQ  C10   C5   C6    109.96  3.000
 MXQ  HC5   C5   C4    106.33  3.000
 MXQ  C6    C5   C4    113.07  3.000
 MXQ  C10   C5   C4    109.35  3.000
 MXQ  HC6A  C6   HC6B  107.01  3.000
 MXQ  HC6A  C6   N7    112.86  3.000
 MXQ  HC6B  C6   N7    108.90  3.000
 MXQ  HC6A  C6   C5    108.10  3.000
 MXQ  HC6B  C6   C5    109.66  3.000
 MXQ  N7    C6   C5    110.22  3.000
 MXQ  HC8A  C8   HC8B  107.10  3.000
 MXQ  HC8A  C8   N7    109.27  3.000
 MXQ  HC8B  C8   N7    113.38  3.000
 MXQ  HC8A  C8   C9    109.90  3.000
 MXQ  HC8B  C8   C9    107.73  3.000
 MXQ  N7    C8   C9    109.40  3.000
 MXQ  HC9   C9   C11   107.56  3.000
 MXQ  HC9   C9   C10   110.76  3.000
 MXQ  C11   C9   C10   110.63  3.000
 MXQ  HC9   C9   C8    108.29  3.000
 MXQ  C11   C9   C8    110.06  3.000
 MXQ  C10   C9   C8    109.49  3.000
 MXQ  H10A  C10  H10B  107.08  3.000
 MXQ  H10A  C10  C9    111.20  3.000
 MXQ  H10B  C10  C9    110.08  3.000
 MXQ  H10A  C10  C5    111.28  3.000
 MXQ  H10B  C10  C5    111.08  3.000
 MXQ  C9    C10  C5    106.18  3.000
 MXQ  C12   C11  C9    120.48  3.000
 MXQ  C9    C11  N3    119.75  3.000
 MXQ  C12   C11  N3    119.77  3.000
 MXQ  HC12  C12  C13   120.94  3.000
 MXQ  HC12  C12  C11   119.28  3.000
 MXQ  C13   C12  C11   119.77  3.000
 MXQ  C13   C14  C15   122.40  3.000
 MXQ  C15   C14  C2    118.16  3.000
 MXQ  C13   C14  C2    119.38  3.000
 MXQ  H15A  C15  H15B  106.59  3.000
 MXQ  H15A  C15  C16   109.13  3.000
 MXQ  H15B  C15  C16   109.56  3.000
 MXQ  H15A  C15  C14   108.87  3.000
 MXQ  H15B  C15  C14   110.20  3.000
 MXQ  C16   C15  C14   112.32  3.000
 MXQ  H16A  C16  H16B  107.17  3.000
 MXQ  H16A  C16  C17   109.54  3.000
 MXQ  H16B  C16  C17   109.49  3.000
 MXQ  H16A  C16  C15   109.71  3.000
 MXQ  H16B  C16  C15   109.13  3.000
 MXQ  C17   C16  C15   111.70  3.000
 MXQ  H17A  C17  H17B  106.66  3.000
 MXQ  H17A  C17  O18   111.24  3.000
 MXQ  H17B  C17  O18   111.37  3.000
 MXQ  H17A  C17  C16   109.19  3.000
 MXQ  H17B  C17  C16   109.27  3.000
 MXQ  O18   C17  C16   109.05  3.000
 MXQ  HN7   N7   C8    110.03  3.000
 MXQ  HN7   N7   C6    110.15  3.000
 MXQ  C8    N7   C6    111.70  3.000
 MXQ  HC13  C13  C14   119.53  3.000
 MXQ  HC13  C13  C12   119.18  3.000
 MXQ  C14   C13  C12   121.29  3.000
 MXQ  HO18  O18  C17   108.11  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
 MXQ  CONST_01  C14  C2   N3   C4    180.00   0.0  0
 MXQ  CONST_02  C14  C2   N3   C11     0.00   0.0  0
 MXQ  CONST_03  O1   C2   N3   C4      0.00   0.0  0
 MXQ  CONST_04  O1   C2   N3   C11   180.00   0.0  0
 MXQ  Var_01    C5   C4   N3   C2   -176.71  30.0  1
 MXQ  Var_02    C8   N7   C6   C5    -59.03  30.0  3
 MXQ  Var_03    C9   C8   N7   C6     59.80  30.0  3
 MXQ  Var_04    C16  C15  C14  C2    -79.19  30.0  1
 MXQ  Var_05    C17  C16  C15  C14   179.88  30.0  2
 MXQ  Var_06    O18  C17  C16  C15   178.62  30.0  2

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
 MXQ  chir_01  C5  C10  C4   C6   positiv
 MXQ  chir_02  C9  C8   C11  C10  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
 MXQ  plan-1  C2    0.020
 MXQ  plan-1  N3    0.020
 MXQ  plan-1  C4    0.020
 MXQ  plan-1  C9    0.020
 MXQ  plan-1  C11   0.020
 MXQ  plan-1  C12   0.020
 MXQ  plan-1  C14   0.020
 MXQ  plan-1  C15   0.020
 MXQ  plan-1  O1    0.020
 MXQ  plan-1  C13   0.020
 MXQ  plan-1  HC12  0.020
 MXQ  plan-1  HC13  0.020

