# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:25:34 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (3~{R})-3-(piperidin-1-ylmethyl)-2,3-dihydro-1~{H}-pyrrolo[1,2-a]quinazolin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N=C2[C@H](CCN2c3ccccc13)CN4CCCCC4
#
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
 5XM  5XM  (3~{R})-3-(piperidin-1-ylmethyl)-2,3-dihydro-1~{H}-pyrrolo[1,2-a]quinazolin-5-one  ligand  42  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5XM
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
 5XM  CAQ  C  CH2   0  -0.286   3.7252   0.8694   0.7721
 5XM  CAR  C  CH2   0  -0.434   4.5101  -0.2449   1.4472
 5XM  CAS  C  CH2   0  -0.440   5.2228  -1.1019   0.4079
 5XM  CAT  C  CH2   0  -0.438   4.2236  -1.5916  -0.6333
 5XM  CAU  C  CH2   0  -0.268   3.4472  -0.4297  -1.2341
 5XM  NAP  N  NT    0  -0.400   2.7879   0.3386  -0.1980
 5XM  CAO  C  CH2   0  -0.272   1.9002   1.3569  -0.7101
 5XM  CAN  C  CH1   0  -0.366   0.6714   1.5541   0.1727
 5XM  CAM  C  CH2   0  -0.475  -0.0830   2.8618  -0.0754
 5XM  CAL  C  CH2   0  -0.290  -1.5269   2.5479   0.3007
 5XM  NAG  N  NR6   0  -0.581  -1.6034   1.1099   0.0628
 5XM  CAH  C  CR6   0   0.536  -0.3976   0.5185  -0.0337
 5XM  NAI  N  N     0  -0.469  -0.1900  -0.7362  -0.2665
 5XM  CAJ  C  CR6   0   0.430  -1.2644  -1.5768  -0.4216
 5XM  OAK  O  O     0  -0.464  -1.0980  -2.7603  -0.6811
 5XM  CAE  C  CR66  0  -0.166  -2.6128  -1.0061  -0.2536
 5XM  CAD  C  CR66  0   0.438  -2.7553   0.3639  -0.0047
 5XM  CAC  C  CR16  0  -0.332  -4.0217   0.9287   0.1669
 5XM  CAB  C  CR16  0  -0.241  -5.1345   0.1169   0.0835
 5XM  CAA  C  CR16  0  -0.257  -5.0090  -1.2507  -0.1696
 5XM  CAF  C  CR16  0  -0.285  -3.7563  -1.8031  -0.3352
 5XM  H1   H  HCH2  0   0.232   3.1727   1.4396   1.5240
 5XM  H2   H  HCH2  0   0.181   4.4304   1.5788   0.2995
 5XM  H3   H  HCH2  0   0.226   5.2224   0.1899   2.1520
 5XM  H4   H  HCH2  0   0.214   3.8209  -0.8664   2.0266
 5XM  H5   H  HCH2  0   0.208   6.0013  -0.5073  -0.0824
 5XM  H6   H  HCH2  0   0.229   5.7269  -1.9460   0.8838
 5XM  H7   H  HCH2  0   0.226   4.7295  -2.1424  -1.4294
 5XM  H8   H  HCH2  0   0.214   3.5158  -2.2814  -0.1634
 5XM  H9   H  HCH2  0   0.177   4.1343   0.1928  -1.8365
 5XM  H10  H  HCH2  0   0.229   2.6835  -0.8127  -1.9146
 5XM  H12  H  HCH2  0   0.222   2.4094   2.3285  -0.8177
 5XM  H13  H  HCH2  0   0.240   1.5661   1.0811  -1.7132
 5XM  H14  H  HCH1  0   0.295   0.9710   1.5014   1.2269
 5XM  H15  H  HCH2  0   0.273   0.3192   3.6935   0.4989
 5XM  H16  H  HCH2  0   0.259  -0.0268   3.1280  -1.1336
 5XM  H17  H  HCH2  0   0.270  -1.7472   2.7629   1.3483
 5XM  H18  H  HCH2  0   0.275  -2.2491   3.0762  -0.3196
 5XM  H19  H  HCR6  0   0.287  -4.1360   1.9855   0.3661
 5XM  H20  H  HCR6  0   0.273  -6.1162   0.5511   0.2190
 5XM  H21  H  HCR6  0   0.265  -5.8912  -1.8728  -0.2347
 5XM  H22  H  HCR6  0   0.266  -3.6465  -2.8620  -0.5276

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
 5XM  CAS  CAT  single    1.524  0.020  1.524
 5XM  CAS  CAR  single    1.524  0.020  1.524
 5XM  CAT  CAU  single    1.521  0.020  1.521
 5XM  CAR  CAQ  single    1.521  0.020  1.521
 5XM  CAU  NAP  single    1.449  0.020  1.449
 5XM  CAQ  NAP  single    1.450  0.020  1.450
 5XM  NAP  CAO  single    1.445  0.020  1.445
 5XM  CAO  CAN  single    1.526  0.020  1.526
 5XM  CAM  CAL  single    1.525  0.020  1.525
 5XM  CAM  CAN  single    1.530  0.020  1.530
 5XM  CAL  NAG  single    1.460  0.020  1.460
 5XM  CAN  CAH  single    1.503  0.020  1.503
 5XM  CAH  NAG  single    1.346  0.020  1.346
 5XM  CAH  NAI  double    1.293  0.020  1.293
 5XM  NAG  CAD  single    1.374  0.020  1.374
 5XM  CAC  CAD  aromatic  1.397  0.020  1.397
 5XM  CAC  CAB  aromatic  1.380  0.020  1.380
 5XM  CAD  CAE  aromatic  1.400  0.020  1.400
 5XM  NAI  CAJ  single    1.373  0.020  1.373
 5XM  CAB  CAA  aromatic  1.396  0.020  1.396
 5XM  CAE  CAJ  single    1.474  0.020  1.474
 5XM  CAE  CAF  aromatic  1.396  0.020  1.396
 5XM  CAJ  OAK  double    1.223  0.020  1.223
 5XM  CAA  CAF  aromatic  1.379  0.020  1.379
 5XM  CAQ  H1   single    0.970  0.020  1.090
 5XM  CAQ  H2   single    0.970  0.020  1.090
 5XM  CAR  H3   single    0.970  0.020  1.090
 5XM  CAR  H4   single    0.970  0.020  1.090
 5XM  CAS  H5   single    0.970  0.020  1.090
 5XM  CAS  H6   single    0.970  0.020  1.090
 5XM  CAT  H7   single    0.970  0.020  1.090
 5XM  CAT  H8   single    0.970  0.020  1.090
 5XM  CAU  H9   single    0.970  0.020  1.090
 5XM  CAU  H10  single    0.970  0.020  1.090
 5XM  CAO  H12  single    0.970  0.020  1.090
 5XM  CAO  H13  single    0.970  0.020  1.090
 5XM  CAN  H14  single    0.970  0.020  1.090
 5XM  CAM  H15  single    0.970  0.020  1.090
 5XM  CAM  H16  single    0.970  0.020  1.090
 5XM  CAL  H17  single    0.970  0.020  1.090
 5XM  CAL  H18  single    0.970  0.020  1.090
 5XM  CAC  H19  single    0.930  0.020  1.080
 5XM  CAB  H20  single    0.930  0.020  1.080
 5XM  CAA  H21  single    0.930  0.020  1.080
 5XM  CAF  H22  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
 5XM  H2   CAQ  H1   106.34  3.000
 5XM  H2   CAQ  NAP  111.17  3.000
 5XM  H1   CAQ  NAP  108.93  3.000
 5XM  H2   CAQ  CAR  109.30  3.000
 5XM  H1   CAQ  CAR  109.73  3.000
 5XM  NAP  CAQ  CAR  111.25  3.000
 5XM  H4   CAR  H3   107.17  3.000
 5XM  H4   CAR  CAS  109.65  3.000
 5XM  H3   CAR  CAS  111.04  3.000
 5XM  H4   CAR  CAQ  109.03  3.000
 5XM  H3   CAR  CAQ  109.34  3.000
 5XM  CAS  CAR  CAQ  110.53  3.000
 5XM  H6   CAS  H5   106.64  3.000
 5XM  H6   CAS  CAT  110.61  3.000
 5XM  H5   CAS  CAT  109.55  3.000
 5XM  H6   CAS  CAR  110.69  3.000
 5XM  H5   CAS  CAR  109.41  3.000
 5XM  CAT  CAS  CAR  109.88  3.000
 5XM  H8   CAT  H7   107.14  3.000
 5XM  H8   CAT  CAU  108.72  3.000
 5XM  H7   CAT  CAU  109.50  3.000
 5XM  H8   CAT  CAS  109.46  3.000
 5XM  H7   CAT  CAS  110.87  3.000
 5XM  CAU  CAT  CAS  111.04  3.000
 5XM  H10  CAU  H9   107.01  3.000
 5XM  H10  CAU  NAP  108.26  3.000
 5XM  H9   CAU  NAP  111.95  3.000
 5XM  H10  CAU  CAT  109.58  3.000
 5XM  H9   CAU  CAT  109.15  3.000
 5XM  NAP  CAU  CAT  110.79  3.000
 5XM  CAO  NAP  CAU  113.57  3.000
 5XM  CAO  NAP  CAQ  112.12  3.000
 5XM  CAU  NAP  CAQ  112.25  3.000
 5XM  H13  CAO  H12  105.91  3.000
 5XM  H13  CAO  CAN  108.52  3.000
 5XM  H12  CAO  CAN  108.34  3.000
 5XM  H13  CAO  NAP  109.60  3.000
 5XM  H12  CAO  NAP  111.84  3.000
 5XM  CAN  CAO  NAP  112.38  3.000
 5XM  H14  CAN  CAH  107.05  3.000
 5XM  H14  CAN  CAM  109.36  3.000
 5XM  CAH  CAN  CAM  102.47  3.000
 5XM  H14  CAN  CAO  109.26  3.000
 5XM  CAH  CAN  CAO  113.85  3.000
 5XM  CAM  CAN  CAO  114.44  3.000
 5XM  H16  CAM  H15  107.82  3.000
 5XM  H16  CAM  CAL  109.74  3.000
 5XM  H15  CAM  CAL  112.17  3.000
 5XM  H16  CAM  CAN  109.87  3.000
 5XM  H15  CAM  CAN  112.67  3.000
 5XM  CAL  CAM  CAN  104.53  3.000
 5XM  H18  CAL  H17  108.49  3.000
 5XM  H18  CAL  NAG  110.52  3.000
 5XM  H17  CAL  NAG  109.86  3.000
 5XM  H18  CAL  CAM  112.81  3.000
 5XM  H17  CAL  CAM  112.78  3.000
 5XM  NAG  CAL  CAM  102.26  3.000
 5XM  CAD  NAG  CAH  120.58  3.000
 5XM  CAD  NAG  CAL  125.94  3.000
 5XM  CAH  NAG  CAL  113.42  3.000
 5XM  NAI  CAH  NAG  125.66  3.000
 5XM  NAI  CAH  CAN  125.40  3.000
 5XM  NAG  CAH  CAN  108.94  3.000
 5XM  CAJ  NAI  CAH  119.26  3.000
 5XM  CAE  CAJ  OAK  121.56  3.000
 5XM  OAK  CAJ  NAI  120.66  3.000
 5XM  CAE  CAJ  NAI  117.78  3.000
 5XM  CAF  CAE  CAD  119.06  3.000
 5XM  CAF  CAE  CAJ  121.44  3.000
 5XM  CAD  CAE  CAJ  119.50  3.000
 5XM  CAC  CAD  CAE  120.65  3.000
 5XM  CAE  CAD  NAG  117.05  3.000
 5XM  CAC  CAD  NAG  122.30  3.000
 5XM  H19  CAC  CAB  120.05  3.000
 5XM  H19  CAC  CAD  120.90  3.000
 5XM  CAB  CAC  CAD  119.06  3.000
 5XM  H20  CAB  CAA  119.82  3.000
 5XM  H20  CAB  CAC  119.21  3.000
 5XM  CAA  CAB  CAC  120.97  3.000
 5XM  H21  CAA  CAF  120.22  3.000
 5XM  H21  CAA  CAB  120.06  3.000
 5XM  CAF  CAA  CAB  119.71  3.000
 5XM  H22  CAF  CAA  120.37  3.000
 5XM  H22  CAF  CAE  119.08  3.000
 5XM  CAA  CAF  CAE  120.55  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
 5XM  CONST_01  CAB  CAC  CAD  CAE    0.00   0.0  0
 5XM  CONST_02  CAB  CAA  CAF  CAE    0.00   0.0  0
 5XM  CONST_03  CAA  CAB  CAC  CAD    0.00   0.0  0
 5XM  CONST_04  CAA  CAF  CAE  CAD    0.00   0.0  0
 5XM  CONST_05  CAF  CAE  CAD  CAC    0.00   0.0  0
 5XM  CONST_06  CAF  CAA  CAB  CAC    0.00   0.0  0
 5XM  CONST_07  CAL  NAG  CAH  CAN    0.00   0.0  0
 5XM  CONST_08  CAD  NAG  CAH  CAN  180.00   0.0  0
 5XM  CONST_09  CAJ  NAI  CAH  CAN  180.00   0.0  0
 5XM  CONST_10  NAI  CAH  NAG  CAL  180.00   0.0  0
 5XM  CONST_11  CAJ  NAI  CAH  NAG    0.00   0.0  0
 5XM  CONST_12  CAD  NAG  CAH  NAI    0.00   0.0  0
 5XM  CONST_13  H19  CAC  CAD  NAG    0.00   0.0  0
 5XM  CONST_14  H22  CAF  CAE  CAJ    0.00   0.0  0
 5XM  CONST_15  H21  CAA  CAF  CAE  180.00   0.0  0
 5XM  CONST_16  H20  CAB  CAC  CAD  180.00   0.0  0
 5XM  Var_01    CAT  CAS  CAR  CAQ  -53.37  30.0  1
 5XM  Var_02    CAT  CAU  NAP  CAQ   58.74  30.0  1
 5XM  Var_03    CAU  CAT  CAS  CAR   53.59  30.0  1
 5XM  Var_04    CAU  NAP  CAQ  CAR  -59.08  30.0  1
 5XM  Var_05    NAP  CAU  CAT  CAS  -55.98  30.0  1
 5XM  Var_06    NAP  CAQ  CAR  CAS   56.09  30.0  1
 5XM  Var_07    NAG  CAL  CAM  CAN  -26.97  30.0  1
 5XM  Var_08    CAH  NAG  CAL  CAM   16.53  30.0  1
 5XM  Var_09    CAN  CAO  NAP  CAQ  -86.17  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
 5XM  chir_01  CAN  CAO  CAM  CAH  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
 5XM  plan-1  CAN  0.020
 5XM  plan-1  CAL  0.020
 5XM  plan-1  NAG  0.020
 5XM  plan-1  CAH  0.020
 5XM  plan-1  NAI  0.020
 5XM  plan-1  CAJ  0.020
 5XM  plan-1  OAK  0.020
 5XM  plan-1  CAE  0.020
 5XM  plan-1  CAD  0.020
 5XM  plan-1  CAC  0.020
 5XM  plan-1  CAB  0.020
 5XM  plan-1  CAA  0.020
 5XM  plan-1  CAF  0.020
 5XM  plan-1  H19  0.020
 5XM  plan-1  H20  0.020
 5XM  plan-1  H21  0.020
 5XM  plan-1  H22  0.020

