# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 14:16:32 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: 6-(cycloprop-2-en-1-ylmethoxy)-2-[6-(cyclopropylmethyl)-5-oxo-3,4,5,6-tetrahydro-2,6-naphthyridin-2(1H)-yl]-7-methoxyquinazolin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2N=C(NC(=O)c2cc1OCC3C=C3)N4CCC5=C(C4)C=CN(CC6CC6)C5=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
 LZR  LZR  6-(cycloprop-2-en-1-ylmethoxy)-2-[6-(cyclopropylmethyl)-5-oxo-3,4,5,6-tetrahydro-2,6-naphthyridin-2(1H)-yl]-7-methoxyquinazolin-4(3H)-one  ligand  59  33  .  2022-07-25  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_LZR
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
 LZR  O29   O  O     0  -0.507   5.8138  -1.8031   0.0779
 LZR  C26   C  CR6   0   0.570   5.4038  -0.6586   0.2597
 LZR  N28   N  NR6   0  -0.514   6.2716   0.4215   0.2544
 LZR  C30   C  CH2   0  -0.345   7.6937   0.2035  -0.0240
 LZR  C31   C  CH1   0  -0.243   8.0254   0.4136  -1.4751
 LZR  C32   C  CH2   0  -0.492   9.2157  -0.2841  -2.0576
 LZR  C33   C  CH2   0  -0.480   7.8327  -0.6883  -2.4705
 LZR  C27   C  CR16  0   0.053   5.8457   1.6969   0.4408
 LZR  C23   C  CR16  0  -0.433   4.5442   1.9974   0.6437
 LZR  C19   C  CR6   0   0.171   3.5989   0.9397   0.6609
 LZR  C22   C  CR6   0  -0.175   4.0109  -0.3467   0.4975
 LZR  C20   C  CH2   0  -0.487   3.0418  -1.4847   0.5617
 LZR  C15   C  CH2   0  -0.335   2.1547   1.3133   0.8380
 LZR  N12   N  NT    0  -0.531   1.2657   0.1772   0.7552
 LZR  C16   C  CH2   0  -0.324   1.7843  -1.0682   1.2976
 LZR  C7    C  CR6   0   0.784  -0.0592   0.3085   0.5060
 LZR  N3    N  N     0  -0.550  -0.8338  -0.7333   0.4979
 LZR  C1    C  CR66  0   0.280  -2.1563  -0.5511   0.2192
 LZR  C2    C  CR66  0  -0.124  -2.7163   0.6968  -0.0664
 LZR  C5    C  CR16  0  -0.436  -4.0888   0.8258  -0.3451
 LZR  C6    C  CR6   0   0.532  -1.8560   1.8558  -0.0484
 LZR  O11   O  O     0  -0.470  -2.1959   3.0092  -0.2623
 LZR  N10   N  NR16  0  -0.760  -0.5383   1.5666   0.2560
 LZR  C4    C  CR16  0  -0.481  -2.9994  -1.6788   0.2150
 LZR  C8    C  CR6   0   0.334  -4.3425  -1.5543  -0.0597
 LZR  O13   O  O2    0  -0.454  -5.2130  -2.5679  -0.0854
 LZR  C17   C  CH3   0  -0.441  -4.7381  -3.8726   0.1904
 LZR  C9    C  CR6   0   0.317  -4.9055  -0.2749  -0.3440
 LZR  O14   O  O2    0  -0.466  -6.2287  -0.2736  -0.5848
 LZR  C18   C  CH2   0  -0.186  -6.8578   0.9692  -0.8667
 LZR  C21   C  CH1   0  -0.274  -8.3218   0.7029  -1.0822
 LZR  C24   C  C1    0  -0.229  -9.3542   1.6449  -0.5450
 LZR  C25   C  C1    0  -0.217  -9.2453   0.5253   0.0823
 LZR  H301  H  HCH2  0   0.273   8.2565   0.8997   0.5992
 LZR  H302  H  HCH2  0   0.269   7.9558  -0.8026   0.2969
 LZR  H27   H  HCR6  0   0.305   6.6124   2.4583   0.4168
 LZR  H31   H  HCH1  0   0.262   7.8412   1.4217  -1.8349
 LZR  H32   H  HCH2  0   0.254   9.8298   0.2608  -2.7624
 LZR  H33   H  HCH2  0   0.251   7.4511  -1.6342  -2.1097
 LZR  H23   H  HCR6  0   0.271   4.2429   3.0251   0.7873
 LZR  H151  H  HCH2  0   0.279   2.0423   1.8511   1.7890
 LZR  H152  H  HCH2  0   0.281   1.9359   2.0290   0.0417
 LZR  H201  H  HCH2  0   0.255   2.7906  -1.8368  -0.4437
 LZR  H202  H  HCH2  0   0.255   3.4890  -2.3332   1.0825
 LZR  H161  H  HCH2  0   0.284   1.0176  -1.8304   1.2122
 LZR  H162  H  HCH2  0   0.248   2.0041  -0.9327   2.3625
 LZR  H10   H  HNR6  0   0.434   0.0694   2.3710   0.3159
 LZR  H4    H  HCR6  0   0.282  -2.5560  -2.6397   0.4380
 LZR  H5    H  HCR6  0   0.285  -4.4781   1.8118  -0.5588
 LZR  H171  H  HCH3  0   0.233  -3.9757  -4.1864  -0.5266
 LZR  H172  H  HCH3  0   0.234  -4.3269  -3.9484   1.1998
 LZR  H173  H  HCH3  0   0.265  -5.5953  -4.5352   0.1064
 LZR  H181  H  HCH2  0   0.219  -6.7154   1.6681  -0.0336
 LZR  H182  H  HCH2  0   0.225  -6.4117   1.4203  -1.7616
 LZR  H21   H  HCH1  0   0.233  -8.5326   0.1649  -2.0084
 LZR  H24   H  H     0   0.258  -9.8206   2.6061  -0.6764
 LZR  H25   H  H     0   0.258  -9.5551  -0.1442   0.8660
 LZR  H34   H  HCH2  0   0.247   9.7688  -0.9595  -1.4161
 LZR  H35   H  HCH2  0   0.251   7.4955  -0.4169  -3.4625

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
 LZR  O29  C26   double    1.229  0.020  1.229
 LZR  C26  N28   single    1.386  0.020  1.386
 LZR  C26  C22   single    1.447  0.020  1.447
 LZR  N28  C30   single    1.465  0.020  1.465
 LZR  N28  C27   single    1.358  0.020  1.358
 LZR  C30  C31   single    1.503  0.020  1.503
 LZR  C31  C32   single    1.498  0.020  1.498
 LZR  C31  C33   single    1.497  0.020  1.497
 LZR  C32  C33   single    1.499  0.020  1.499
 LZR  C27  C23   double    1.351  0.020  1.351
 LZR  C23  C19   single    1.419  0.020  1.419
 LZR  C19  C22   double    1.361  0.020  1.361
 LZR  C19  C15   single    1.502  0.020  1.502
 LZR  C22  C20   single    1.496  0.020  1.496
 LZR  C20  C16   single    1.515  0.020  1.515
 LZR  C15  N12   single    1.445  0.020  1.445
 LZR  N12  C16   single    1.454  0.020  1.454
 LZR  N12  C7    single    1.354  0.020  1.354
 LZR  C7   N3    double    1.298  0.020  1.298
 LZR  C7   N10   single    1.369  0.020  1.369
 LZR  N3   C1    single    1.364  0.020  1.364
 LZR  C1   C2    aromatic  1.397  0.020  1.397
 LZR  C1   C4    aromatic  1.408  0.020  1.408
 LZR  C2   C5    aromatic  1.406  0.020  1.406
 LZR  C2   C6    single    1.443  0.020  1.443
 LZR  C5   C9    aromatic  1.371  0.020  1.371
 LZR  C6   O11   double    1.221  0.020  1.221
 LZR  C6   N10   single    1.383  0.020  1.383
 LZR  C4   C8    aromatic  1.377  0.020  1.377
 LZR  C8   O13   single    1.336  0.020  1.336
 LZR  C8   C9    aromatic  1.426  0.020  1.426
 LZR  O13  C17   single    1.416  0.020  1.416
 LZR  C9   O14   single    1.345  0.020  1.345
 LZR  O14  C18   single    1.421  0.020  1.421
 LZR  C18  C21   single    1.504  0.020  1.504
 LZR  C21  C24   single    1.497  0.020  1.497
 LZR  C21  C25   single    1.497  0.020  1.497
 LZR  C24  C25   double    1.288  0.020  1.288
 LZR  C30  H301  single    0.970  0.020  1.090
 LZR  C30  H302  single    0.970  0.020  1.090
 LZR  C27  H27   single    0.930  0.020  1.080
 LZR  C31  H31   single    0.970  0.020  1.090
 LZR  C32  H32   single    0.970  0.020  1.090
 LZR  C33  H33   single    0.970  0.020  1.090
 LZR  C23  H23   single    0.930  0.020  1.080
 LZR  C15  H151  single    0.970  0.020  1.090
 LZR  C15  H152  single    0.970  0.020  1.090
 LZR  C20  H201  single    0.970  0.020  1.090
 LZR  C20  H202  single    0.970  0.020  1.090
 LZR  C16  H161  single    0.970  0.020  1.090
 LZR  C16  H162  single    0.970  0.020  1.090
 LZR  N10  H10   single    0.860  0.020  1.020
 LZR  C4   H4    single    0.930  0.020  1.080
 LZR  C5   H5    single    0.930  0.020  1.080
 LZR  C17  H171  single    0.970  0.020  1.090
 LZR  C17  H172  single    0.970  0.020  1.090
 LZR  C17  H173  single    0.970  0.020  1.090
 LZR  C18  H181  single    0.970  0.020  1.090
 LZR  C18  H182  single    0.970  0.020  1.090
 LZR  C21  H21   single    0.970  0.020  1.090
 LZR  C24  H24   single    0.930  0.020  1.080
 LZR  C25  H25   single    0.930  0.020  1.080
 LZR  C32  H34   single    0.970  0.020  1.090
 LZR  C33  H35   single    0.970  0.020  1.090

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
 LZR  C22   C26  N28   115.82  3.000
 LZR  C22   C26  O29   123.10  3.000
 LZR  N28   C26  O29   121.08  3.000
 LZR  C27   N28  C30   118.06  3.000
 LZR  C27   N28  C26   122.37  3.000
 LZR  C30   N28  C26   119.51  3.000
 LZR  H302  C30  H301  107.30  3.000
 LZR  H302  C30  C31   111.15  3.000
 LZR  H301  C30  C31   110.39  3.000
 LZR  H302  C30  N28   108.38  3.000
 LZR  H301  C30  N28   107.29  3.000
 LZR  C31   C30  N28   112.13  3.000
 LZR  H31   C31  C33   116.16  3.000
 LZR  H31   C31  C32   116.00  3.000
 LZR  C33   C31  C32    60.06  3.000
 LZR  H31   C31  C30   114.34  3.000
 LZR  C33   C31  C30   120.69  3.000
 LZR  C32   C31  C30   119.06  3.000
 LZR  H34   C32  H32   114.19  3.000
 LZR  H34   C32  C33   117.78  3.000
 LZR  H32   C32  C33   118.69  3.000
 LZR  H34   C32  C31   117.77  3.000
 LZR  H32   C32  C31   118.02  3.000
 LZR  C33   C32  C31    59.96  3.000
 LZR  H35   C33  H33   114.52  3.000
 LZR  H35   C33  C32   118.18  3.000
 LZR  H33   C33  C32   117.99  3.000
 LZR  H35   C33  C31   117.70  3.000
 LZR  H33   C33  C31   117.84  3.000
 LZR  C32   C33  C31    59.98  3.000
 LZR  H27   C27  C23   122.00  3.000
 LZR  H27   C27  N28   115.87  3.000
 LZR  C23   C27  N28   122.13  3.000
 LZR  H23   C23  C19   121.45  3.000
 LZR  H23   C23  C27   120.00  3.000
 LZR  C19   C23  C27   118.55  3.000
 LZR  C15   C19  C22   122.71  3.000
 LZR  C15   C19  C23   117.17  3.000
 LZR  C22   C19  C23   120.11  3.000
 LZR  C20   C22  C19   121.19  3.000
 LZR  C20   C22  C26   117.81  3.000
 LZR  C19   C22  C26   121.00  3.000
 LZR  H202  C20  H201  106.40  3.000
 LZR  H202  C20  C16   108.78  3.000
 LZR  H201  C20  C16   110.13  3.000
 LZR  H202  C20  C22   110.26  3.000
 LZR  H201  C20  C22   110.73  3.000
 LZR  C16   C20  C22   110.44  3.000
 LZR  H152  C15  H151  106.84  3.000
 LZR  H152  C15  N12   110.49  3.000
 LZR  H151  C15  N12   111.82  3.000
 LZR  H152  C15  C19   105.63  3.000
 LZR  H151  C15  C19   108.80  3.000
 LZR  N12   C15  C19   112.91  3.000
 LZR  C7    N12  C16   120.03  3.000
 LZR  C7    N12  C15   122.42  3.000
 LZR  C16   N12  C15   115.63  3.000
 LZR  H162  C16  H161  107.77  3.000
 LZR  H162  C16  N12   109.16  3.000
 LZR  H161  C16  N12   108.69  3.000
 LZR  H162  C16  C20   109.85  3.000
 LZR  H161  C16  C20   110.81  3.000
 LZR  N12   C16  C20   110.50  3.000
 LZR  N10   C7   N3    121.83  3.000
 LZR  N10   C7   N12   117.70  3.000
 LZR  N3    C7   N12   120.47  3.000
 LZR  C1    N3   C7    118.21  3.000
 LZR  C4    C1   C2    118.34  3.000
 LZR  C4    C1   N3    118.32  3.000
 LZR  C2    C1   N3    123.35  3.000
 LZR  C6    C2   C5    120.69  3.000
 LZR  C6    C2   C1    118.40  3.000
 LZR  C5    C2   C1    120.90  3.000
 LZR  H5    C5   C9    121.19  3.000
 LZR  H5    C5   C2    118.30  3.000
 LZR  C9    C5   C2    120.51  3.000
 LZR  N10   C6   O11   120.08  3.000
 LZR  N10   C6   C2    113.75  3.000
 LZR  O11   C6   C2    126.17  3.000
 LZR  H10   N10  C6    114.83  3.000
 LZR  H10   N10  C7    120.69  3.000
 LZR  C6    N10  C7    124.45  3.000
 LZR  H4    C4   C8    121.44  3.000
 LZR  H4    C4   C1    117.74  3.000
 LZR  C8    C4   C1    120.82  3.000
 LZR  C9    C8   O13   114.80  3.000
 LZR  C9    C8   C4    120.40  3.000
 LZR  O13   C8   C4    124.80  3.000
 LZR  C17   O13  C8    118.48  3.000
 LZR  H173  C17  H172  109.02  3.000
 LZR  H173  C17  H171  108.94  3.000
 LZR  H172  C17  H171  108.89  3.000
 LZR  H173  C17  O13   106.40  3.000
 LZR  H172  C17  O13   111.73  3.000
 LZR  H171  C17  O13   111.78  3.000
 LZR  O14   C9   C8    115.14  3.000
 LZR  O14   C9   C5    125.82  3.000
 LZR  C8    C9   C5    119.03  3.000
 LZR  C18   O14  C9    118.16  3.000
 LZR  H182  C18  H181  107.75  3.000
 LZR  H182  C18  C21   110.60  3.000
 LZR  H181  C18  C21   110.37  3.000
 LZR  H182  C18  O14   109.97  3.000
 LZR  H181  C18  O14   110.43  3.000
 LZR  C21   C18  O14   107.73  3.000
 LZR  H21   C21  C25   118.85  3.000
 LZR  H21   C21  C24   118.77  3.000
 LZR  C25   C21  C24    50.96  3.000
 LZR  H21   C21  C18   113.38  3.000
 LZR  C25   C21  C18   120.68  3.000
 LZR  C24   C21  C18   120.57  3.000
 LZR  H24   C24  C25   150.73  3.000
 LZR  H24   C24  C21   144.76  3.000
 LZR  C25   C24  C21    64.50  3.000
 LZR  H25   C25  C24   150.58  3.000
 LZR  H25   C25  C21   144.87  3.000
 LZR  C24   C25  C21    64.54  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
 LZR  CONST_01  C9    C5   C2   C1      0.00   0.0  0
 LZR  CONST_02  C9    C8   C4   C1      0.00   0.0  0
 LZR  CONST_03  C8    C4   C1   C2      0.00   0.0  0
 LZR  CONST_04  C8    C9   C5   C2      0.00   0.0  0
 LZR  CONST_05  C4    C1   C2   C5      0.00   0.0  0
 LZR  CONST_06  C4    C8   C9   C5      0.00   0.0  0
 LZR  CONST_07  C22   C26  N28  C27     0.00   0.0  0
 LZR  CONST_08  N3    C7   N12  C15   180.00   0.0  0
 LZR  CONST_09  N10   C7   N12  C15     0.00   0.0  0
 LZR  CONST_10  C1    N3   C7   N12   180.00   0.0  0
 LZR  CONST_11  C6    N10  C7   N12   180.00   0.0  0
 LZR  CONST_12  N3    C7   N12  C16     0.00   0.0  0
 LZR  CONST_13  N10   C7   N12  C16   180.00   0.0  0
 LZR  CONST_14  C2    C6   N10  C7      0.00   0.0  0
 LZR  CONST_15  C6    N10  C7   N3      0.00   0.0  0
 LZR  CONST_16  N10   C7   N3   C1      0.00   0.0  0
 LZR  CONST_17  O13   C8   C4   C1    180.00   0.0  0
 LZR  CONST_18  O14   C9   C5   C2    180.00   0.0  0
 LZR  CONST_19  O13   C8   C9   C5    180.00   0.0  0
 LZR  CONST_20  O14   C9   C8   C4    180.00   0.0  0
 LZR  CONST_21  C27   N28  C26  O29   180.00   0.0  0
 LZR  CONST_22  C22   C26  N28  C30   180.00   0.0  0
 LZR  CONST_23  O11   C6   N10  C7    180.00   0.0  0
 LZR  CONST_24  H4    C4   C1   N3      0.00   0.0  0
 LZR  CONST_25  H5    C5   C2   C1    180.00   0.0  0
 LZR  CONST_26  H10   N10  C7   N12     0.00   0.0  0
 LZR  CONST_27  C30   N28  C26  O29     0.00   0.0  0
 LZR  Var_01    C16   C20  C22  C26   159.21  30.0  1
 LZR  Var_02    N12   C15  C19  C23   176.23  30.0  1
 LZR  Var_03    C16   N12  C15  C19    35.00  30.0  1
 LZR  Var_04    N12   C16  C20  C22    50.46  30.0  1
 LZR  Var_05    C15   N12  C16  C20   -60.33  30.0  1
 LZR  Var_06    C31   C30  N28  C26    94.65  30.0  3
 LZR  Var_07    C32   C31  C30  N28  -154.61  30.0  3
 LZR  Var_08    C33   C32  C31  C30   110.72  30.0  1
 LZR  Var_09    C25   C24  C21  C18  -106.50  30.0  1
 LZR  Var_10    H33   C33  C32  C31  -107.68  30.0  1
 LZR  Var_11    H25   C25  C24  C21  -178.96  30.0  1
 LZR  Var_12    C9    C8   O13  C17  -179.79  30.0  1
 LZR  Var_13    C21   C18  O14  C9   -179.42  30.0  3
 LZR  Var_14    C24   C21  C18  O14   140.12  30.0  3
 LZR  Var_15    H171  C17  O13  C8    -60.58  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
 LZR  chir_01  C31  C30  C32  C33  both
 LZR  chir_02  C21  C18  C24  C25  both

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
 LZR  plan-1  C15  0.020
 LZR  plan-1  N12  0.020
 LZR  plan-1  C16  0.020
 LZR  plan-1  C7   0.020
 LZR  plan-1  N3   0.020
 LZR  plan-1  C1   0.020
 LZR  plan-1  C2   0.020
 LZR  plan-1  C5   0.020
 LZR  plan-1  C6   0.020
 LZR  plan-1  O11  0.020
 LZR  plan-1  N10  0.020
 LZR  plan-1  C4   0.020
 LZR  plan-1  C8   0.020
 LZR  plan-1  O13  0.020
 LZR  plan-1  C9   0.020
 LZR  plan-1  O14  0.020
 LZR  plan-1  H10  0.020
 LZR  plan-1  H4   0.020
 LZR  plan-1  H5   0.020
 LZR  plan-2  O29  0.020
 LZR  plan-2  C26  0.020
 LZR  plan-2  N28  0.020
 LZR  plan-2  C30  0.020
 LZR  plan-2  C27  0.020
 LZR  plan-2  C23  0.020
 LZR  plan-2  C19  0.020
 LZR  plan-2  C22  0.020
 LZR  plan-2  C20  0.020
 LZR  plan-2  C15  0.020
 LZR  plan-2  H27  0.020
 LZR  plan-2  H23  0.020

