# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 04:01:27 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: 2-{[2-ethoxy-4-(4-hydroxypiperidin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1cc(ccc1Nc2ncc3N(C)C(=O)c4ccccc4N(C)c3n2)N5CCC(O)CC5
#
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
 4WG  4WG  2-{[2-ethoxy-4-(4-hydroxypiperidin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one  ligand  65  35  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4WG
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
 4WG  C1   C  CH2   0  -0.184   2.9605   3.5922  -0.1539
 4WG  C2   C  CR6   0   0.354   2.4938   1.2451   0.0013
 4WG  C3   C  CR16  0  -0.473   3.8277   0.8943  -0.0603
 4WG  C4   C  CR6   0   0.371   4.2324  -0.4497   0.0023
 4WG  C5   C  CR16  0  -0.376   3.2436  -1.4157   0.1428
 4WG  C6   C  CR16  0  -0.302   1.8979  -1.0631   0.2258
 4WG  C7   C  CR6   0   0.238   1.4916   0.2588   0.1522
 4WG  C8   C  CR6   0   0.606  -0.9961   0.0611   0.3668
 4WG  C11  C  CR6   0   0.479  -3.2442   0.2989   0.6210
 4WG  C12  C  CR6   0   0.301  -5.3553   0.8248  -0.3043
 4WG  C15  C  CR16  0  -0.255  -7.2529   0.2723  -2.2948
 4WG  C16  C  CR16  0  -0.285  -6.8872  -0.6984  -1.3821
 4WG  C17  C  CR6   0  -0.104  -5.9470  -0.4427  -0.3829
 4WG  C18  C  C     0   0.551  -5.7804  -1.5096   0.6437
 4WG  C21  C  CH2   0  -0.315   5.9887  -2.1033   0.3030
 4WG  C23  C  CH1   0   0.067   8.2881  -1.6711  -0.6020
 4WG  C24  C  CH2   0  -0.461   7.8329  -0.2675  -0.9535
 4WG  O1   O  O     0  -0.471  -6.7376  -2.1997   0.9592
 4WG  N4   N  NT    0  -0.560  -4.5684  -1.6935   1.2198
 4WG  C10  C  CR6   0   0.147  -3.3812  -1.0895   0.7699
 4WG  C9   C  CR16  0  -0.027  -2.2178  -1.8161   0.6142
 4WG  N1   N  N     0  -0.474  -1.0291  -1.2655   0.4022
 4WG  C14  C  CR16  0  -0.249  -6.6966   1.5391  -2.1874
 4WG  C13  C  CR16  0  -0.301  -5.7582   1.8114  -1.2074
 4WG  N3   N  NT    0  -0.570  -4.3644   1.1172   0.6571
 4WG  C20  C  CH3   0  -0.561  -4.1385   2.5112   1.0031
 4WG  N2   N  N     0  -0.486  -2.0696   0.8576   0.4440
 4WG  N    N  NH1   0  -0.761   0.1779   0.7222   0.2254
 4WG  O    O  O2    0  -0.490   2.0403   2.5140  -0.0532
 4WG  C    C  CH3   0  -0.681   2.1673   4.8759  -0.2097
 4WG  N5   N  NT    0  -0.511   5.5998  -0.7498  -0.0416
 4WG  C25  C  CH2   0  -0.310   6.3328  -0.2361  -1.1939
 4WG  O2   O  OH1   0  -0.674   9.6756  -1.6386  -0.3431
 4WG  C22  C  CH2   0  -0.474   7.4822  -2.1771   0.5858
 4WG  H1   H  HCH2  0   0.227   3.6330   3.5936   0.7102
 4WG  H2   H  HCH2  0   0.226   3.5746   3.4817  -1.0536
 4WG  H3   H  HCR6  0   0.283   4.5831   1.6649  -0.1286
 4WG  H4   H  HCR6  0   0.260   3.4902  -2.4673   0.1845
 4WG  H5   H  HCR6  0   0.283   1.1596  -1.8403   0.3333
 4WG  H6   H  HCR6  0   0.262  -7.9761   0.0512  -3.0678
 4WG  H7   H  HCR6  0   0.264  -7.3460  -1.6768  -1.4308
 4WG  H8   H  HCH3  0   0.265  -5.3179  -2.6236   2.9430
 4WG  H9   H  HCH3  0   0.251  -4.4312  -3.7107   1.8694
 4WG  H10  H  HCH3  0   0.257  -3.5609  -2.5179   2.8461
 4WG  H11  H  HCH2  0   0.252   5.4427  -2.4141   1.1942
 4WG  H12  H  HCH2  0   0.207   5.7343  -2.8193  -0.4958
 4WG  H13  H  HCH1  0   0.188   8.0730  -2.3257  -1.4618
 4WG  H14  H  HCH2  0   0.225   8.0838   0.4152  -0.1355
 4WG  H15  H  HCH2  0   0.242   8.3455   0.0886  -1.8503
 4WG  H16  H  HCR6  0   0.286  -2.2368  -2.8982   0.6934
 4WG  H17  H  HCR6  0   0.268  -6.9825   2.3222  -2.8773
 4WG  H18  H  HCR6  0   0.279  -5.3292   2.8019  -1.1599
 4WG  H19  H  HCH3  0   0.267  -3.5244   2.5546   1.8990
 4WG  H20  H  HCH3  0   0.240  -3.6398   3.0892   0.2227
 4WG  H21  H  HCH3  0   0.260  -5.0982   2.9724   1.2263
 4WG  H22  H  HNH1  0   0.406   0.0733   1.7249   0.1959
 4WG  H23  H  HCH3  0   0.239   2.8514   5.7209  -0.2791
 4WG  H24  H  HCH3  0   0.236   1.5128   4.9017  -1.0808
 4WG  H25  H  HCH3  0   0.236   1.5613   5.0073   0.6868
 4WG  H26  H  HCH2  0   0.255   6.0277   0.7889  -1.3955
 4WG  H27  H  HCH2  0   0.212   6.0882  -0.8201  -2.0955
 4WG  H28  H  HOH1  0   0.447   9.9622  -2.5311  -0.1252
 4WG  H29  H  HCH2  0   0.225   7.7207  -1.5765   1.4691
 4WG  H30  H  HCH2  0   0.240   7.7443  -3.2142   0.8141
 4WG  C19  C  CH3   0  -0.549  -4.4660  -2.6977   2.2720

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
 4WG  C    C1   single    1.510  0.020  1.510
 4WG  C19  N4   single    1.458  0.020  1.458
 4WG  N1   C9   aromatic  1.327  0.020  1.327
 4WG  N1   C8   aromatic  1.327  0.020  1.327
 4WG  C9   C10  aromatic  1.380  0.020  1.380
 4WG  C1   O    single    1.421  0.020  1.421
 4WG  O    C2   single    1.349  0.020  1.349
 4WG  C8   N    single    1.355  0.020  1.355
 4WG  C8   N2   aromatic  1.339  0.020  1.339
 4WG  N4   C10  single    1.406  0.020  1.406
 4WG  N4   C18  single    1.354  0.020  1.354
 4WG  N    C7   single    1.395  0.020  1.395
 4WG  C10  C11  aromatic  1.403  0.020  1.403
 4WG  C2   C7   aromatic  1.414  0.020  1.414
 4WG  C2   C3   aromatic  1.381  0.020  1.381
 4WG  O1   C18  double    1.221  0.020  1.221
 4WG  C7   C6   aromatic  1.385  0.020  1.385
 4WG  C18  C17  single    1.490  0.020  1.490
 4WG  N2   C11  aromatic  1.313  0.020  1.313
 4WG  C11  N3   single    1.388  0.020  1.388
 4WG  C3   C4   aromatic  1.405  0.020  1.405
 4WG  C17  C16  aromatic  1.396  0.020  1.396
 4WG  C17  C12  aromatic  1.401  0.020  1.401
 4WG  C6   C5   aromatic  1.394  0.020  1.394
 4WG  N3   C12  single    1.411  0.020  1.411
 4WG  N3   C20  single    1.454  0.020  1.454
 4WG  C16  C15  aromatic  1.382  0.020  1.382
 4WG  C12  C13  aromatic  1.397  0.020  1.397
 4WG  C4   C5   aromatic  1.389  0.020  1.389
 4WG  C4   N5   single    1.401  0.020  1.401
 4WG  C15  C14  aromatic  1.388  0.020  1.388
 4WG  N5   C21  single    1.450  0.020  1.450
 4WG  N5   C25  single    1.459  0.020  1.459
 4WG  C21  C22  single    1.522  0.020  1.522
 4WG  C13  C14  aromatic  1.384  0.020  1.384
 4WG  C25  C24  single    1.520  0.020  1.520
 4WG  C22  C23  single    1.522  0.020  1.522
 4WG  C24  C23  single    1.517  0.020  1.517
 4WG  C23  O2   single    1.412  0.020  1.412
 4WG  C1   H1   single    0.970  0.020  1.090
 4WG  C1   H2   single    0.970  0.020  1.090
 4WG  C3   H3   single    0.930  0.020  1.080
 4WG  C5   H4   single    0.930  0.020  1.080
 4WG  C6   H5   single    0.930  0.020  1.080
 4WG  C15  H6   single    0.930  0.020  1.080
 4WG  C16  H7   single    0.930  0.020  1.080
 4WG  C19  H8   single    0.970  0.020  1.090
 4WG  C19  H9   single    0.970  0.020  1.090
 4WG  C19  H10  single    0.970  0.020  1.090
 4WG  C21  H11  single    0.970  0.020  1.090
 4WG  C21  H12  single    0.970  0.020  1.090
 4WG  C23  H13  single    0.970  0.020  1.090
 4WG  C24  H14  single    0.970  0.020  1.090
 4WG  C24  H15  single    0.970  0.020  1.090
 4WG  C9   H16  single    0.930  0.020  1.080
 4WG  C14  H17  single    0.930  0.020  1.080
 4WG  C13  H18  single    0.930  0.020  1.080
 4WG  C20  H19  single    0.970  0.020  1.090
 4WG  C20  H20  single    0.970  0.020  1.090
 4WG  C20  H21  single    0.970  0.020  1.090
 4WG  N    H22  single    0.860  0.020  1.020
 4WG  C    H23  single    0.970  0.020  1.090
 4WG  C    H24  single    0.970  0.020  1.090
 4WG  C    H25  single    0.970  0.020  1.090
 4WG  C25  H26  single    0.970  0.020  1.090
 4WG  C25  H27  single    0.970  0.020  1.090
 4WG  O2   H28  single    0.850  0.020  0.980
 4WG  C22  H29  single    0.970  0.020  1.090
 4WG  C22  H30  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
 4WG  H2   C1   H1   107.71  3.000
 4WG  H2   C1   C    110.49  3.000
 4WG  H1   C1   C    110.53  3.000
 4WG  H2   C1   O    110.17  3.000
 4WG  H1   C1   O    110.05  3.000
 4WG  C    C1   O    107.91  3.000
 4WG  O    C2   C7   114.97  3.000
 4WG  C7   C2   C3   120.82  3.000
 4WG  O    C2   C3   124.21  3.000
 4WG  H3   C3   C4   118.90  3.000
 4WG  H3   C3   C2   119.78  3.000
 4WG  C4   C3   C2   121.29  3.000
 4WG  N5   C4   C5   123.30  3.000
 4WG  N5   C4   C3   118.99  3.000
 4WG  C5   C4   C3   117.68  3.000
 4WG  H4   C5   C6   117.65  3.000
 4WG  H4   C5   C4   121.19  3.000
 4WG  C6   C5   C4   121.15  3.000
 4WG  H5   C6   C7   119.53  3.000
 4WG  H5   C6   C5   119.02  3.000
 4WG  C7   C6   C5   121.44  3.000
 4WG  N    C7   C6   126.20  3.000
 4WG  C6   C7   C2   117.61  3.000
 4WG  N    C7   C2   116.19  3.000
 4WG  N    C8   N2   114.23  3.000
 4WG  N2   C8   N1   124.96  3.000
 4WG  N    C8   N1   120.80  3.000
 4WG  N2   C11  N3   118.35  3.000
 4WG  N3   C11  C10  120.12  3.000
 4WG  N2   C11  C10  121.53  3.000
 4WG  N3   C12  C13  119.77  3.000
 4WG  C13  C12  C17  118.75  3.000
 4WG  N3   C12  C17  121.48  3.000
 4WG  H6   C15  C14  120.67  3.000
 4WG  H6   C15  C16  120.37  3.000
 4WG  C14  C15  C16  118.95  3.000
 4WG  H7   C16  C17  118.93  3.000
 4WG  H7   C16  C15  119.57  3.000
 4WG  C17  C16  C15  121.50  3.000
 4WG  C18  C17  C16  115.94  3.000
 4WG  C16  C17  C12  119.37  3.000
 4WG  C18  C17  C12  124.19  3.000
 4WG  N4   C18  O1   120.97  3.000
 4WG  O1   C18  C17  119.66  3.000
 4WG  N4   C18  C17  119.36  3.000
 4WG  H12  C21  H11  106.94  3.000
 4WG  H12  C21  C22  109.25  3.000
 4WG  H11  C21  C22  109.01  3.000
 4WG  H12  C21  N5   111.85  3.000
 4WG  H11  C21  N5   109.03  3.000
 4WG  C22  C21  N5   110.66  3.000
 4WG  H13  C23  C22  107.95  3.000
 4WG  H13  C23  O2   110.40  3.000
 4WG  C22  C23  O2   112.64  3.000
 4WG  H13  C23  C24  108.08  3.000
 4WG  O2   C23  C24  108.42  3.000
 4WG  C22  C23  C24  109.24  3.000
 4WG  H15  C24  H14  107.61  3.000
 4WG  H15  C24  C25  109.05  3.000
 4WG  H14  C24  C25  109.37  3.000
 4WG  H15  C24  C23  110.55  3.000
 4WG  H14  C24  C23  109.59  3.000
 4WG  C25  C24  C23  110.61  3.000
 4WG  C10  N4   C19  117.87  3.000
 4WG  C10  N4   C18  124.13  3.000
 4WG  C19  N4   C18  117.60  3.000
 4WG  C9   C10  N4   121.44  3.000
 4WG  N4   C10  C11  122.79  3.000
 4WG  C9   C10  C11  115.25  3.000
 4WG  H16  C9   N1   116.17  3.000
 4WG  H16  C9   C10  120.12  3.000
 4WG  N1   C9   C10  123.68  3.000
 4WG  C9   N1   C8   116.17  3.000
 4WG  H17  C14  C13  119.23  3.000
 4WG  H17  C14  C15  120.36  3.000
 4WG  C13  C14  C15  120.41  3.000
 4WG  H18  C13  C14  118.73  3.000
 4WG  H18  C13  C12  120.30  3.000
 4WG  C14  C13  C12  120.96  3.000
 4WG  C20  N3   C12  118.03  3.000
 4WG  C20  N3   C11  116.49  3.000
 4WG  C12  N3   C11  115.27  3.000
 4WG  H21  C20  H20  108.97  3.000
 4WG  H21  C20  H19  108.20  3.000
 4WG  H20  C20  H19  108.06  3.000
 4WG  H21  C20  N3   108.55  3.000
 4WG  H20  C20  N3   114.11  3.000
 4WG  H19  C20  N3   108.80  3.000
 4WG  C11  N2   C8   118.16  3.000
 4WG  H22  N    C8   113.48  3.000
 4WG  H22  N    C7   115.24  3.000
 4WG  C8   N    C7   131.26  3.000
 4WG  C2   O    C1   119.93  3.000
 4WG  H25  C    H24  108.70  3.000
 4WG  H25  C    H23  107.94  3.000
 4WG  H24  C    H23  107.93  3.000
 4WG  H25  C    C1   111.35  3.000
 4WG  H24  C    C1   111.41  3.000
 4WG  H23  C    C1   109.39  3.000
 4WG  C25  N5   C21  112.43  3.000
 4WG  C25  N5   C4   116.09  3.000
 4WG  C21  N5   C4   117.03  3.000
 4WG  H27  C25  H26  106.59  3.000
 4WG  H27  C25  N5   110.37  3.000
 4WG  H26  C25  N5   109.70  3.000
 4WG  H27  C25  C24  109.73  3.000
 4WG  H26  C25  C24  109.00  3.000
 4WG  N5   C25  C24  111.33  3.000
 4WG  H28  O2   C23  108.23  3.000
 4WG  H30  C22  H29  107.44  3.000
 4WG  H30  C22  C23  110.56  3.000
 4WG  H29  C22  C23  109.40  3.000
 4WG  H30  C22  C21  108.66  3.000
 4WG  H29  C22  C21  109.71  3.000
 4WG  C23  C22  C21  111.00  3.000
 4WG  H10  C19  H9   108.79  3.000
 4WG  H10  C19  H8   108.38  3.000
 4WG  H9   C19  H8   108.44  3.000
 4WG  H10  C19  N4   109.01  3.000
 4WG  H9   C19  N4   112.05  3.000
 4WG  H8   C19  N4   110.09  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
 4WG  CONST_01  C5   C6   C7   C2      0.00   0.0  0
 4WG  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 4WG  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 4WG  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 4WG  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 4WG  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 4WG  CONST_07  C10  C9   N1   C8      0.00   0.0  0
 4WG  CONST_08  N1   C8   N2   C11     0.00   0.0  0
 4WG  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 4WG  CONST_10  C13  C14  C15  C16     0.00   0.0  0
 4WG  CONST_11  C14  C15  C16  C17     0.00   0.0  0
 4WG  CONST_12  N2   C8   N1   C9      0.00   0.0  0
 4WG  CONST_13  N5   C4   C3   C2    180.00   0.0  0
 4WG  CONST_14  N5   C4   C5   C6    180.00   0.0  0
 4WG  CONST_15  N    C7   C2   C3    180.00   0.0  0
 4WG  CONST_16  O    C2   C3   C4    180.00   0.0  0
 4WG  CONST_17  N    C7   C6   C5    180.00   0.0  0
 4WG  CONST_18  O    C2   C7   C6    180.00   0.0  0
 4WG  CONST_19  N    C8   N2   C11   180.00   0.0  0
 4WG  CONST_20  N    C8   N1   C9    180.00   0.0  0
 4WG  CONST_21  H5   C6   C7   C2    180.00   0.0  0
 4WG  CONST_22  H4   C5   C4   C3    180.00   0.0  0
 4WG  CONST_23  H3   C3   C4   C5    180.00   0.0  0
 4WG  CONST_24  H16  C9   N1   C8    180.00   0.0  0
 4WG  CONST_25  H17  C14  C13  C12   180.00   0.0  0
 4WG  CONST_26  H18  C13  C14  C15   180.00   0.0  0
 4WG  CONST_27  H6   C15  C16  C17   180.00   0.0  0
 4WG  CONST_28  H7   C16  C15  C14   180.00   0.0  0
 4WG  Var_01    C21  N5   C4   C3    167.48  30.0  2
 4WG  Var_02    C22  C21  N5   C4   -164.29  30.0  1
 4WG  Var_03    C24  C25  N5   C4    163.78  30.0  1
 4WG  Var_04    N5   C21  C22  C23   -56.65  30.0  1
 4WG  Var_05    N5   C25  C24  C23    56.12  30.0  1
 4WG  Var_06    C8   N    C7   C2    179.99  30.0  3
 4WG  Var_07    N1   C8   N    C7     -3.06  30.0  1
 4WG  Var_08    C7   C2   O    C1    177.68  30.0  2
 4WG  Var_09    C    C1   O    C2    179.42  30.0  1
 4WG  Var_10    H23  C    C1   O     179.54  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
 4WG  chir_01  C23  C22  C24  O2  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
 4WG  plan-1  C2   0.020
 4WG  plan-1  C3   0.020
 4WG  plan-1  C4   0.020
 4WG  plan-1  C5   0.020
 4WG  plan-1  C6   0.020
 4WG  plan-1  C7   0.020
 4WG  plan-1  N    0.020
 4WG  plan-1  O    0.020
 4WG  plan-1  N5   0.020
 4WG  plan-1  H3   0.020
 4WG  plan-1  H4   0.020
 4WG  plan-1  H5   0.020
 4WG  plan-2  C12  0.020
 4WG  plan-2  C15  0.020
 4WG  plan-2  C16  0.020
 4WG  plan-2  C17  0.020
 4WG  plan-2  C18  0.020
 4WG  plan-2  C14  0.020
 4WG  plan-2  C13  0.020
 4WG  plan-2  N3   0.020
 4WG  plan-2  H6   0.020
 4WG  plan-2  H7   0.020
 4WG  plan-2  H17  0.020
 4WG  plan-2  H18  0.020
 4WG  plan-3  C8   0.020
 4WG  plan-3  C11  0.020
 4WG  plan-3  N4   0.020
 4WG  plan-3  C10  0.020
 4WG  plan-3  C9   0.020
 4WG  plan-3  N1   0.020
 4WG  plan-3  N3   0.020
 4WG  plan-3  N2   0.020
 4WG  plan-3  N    0.020
 4WG  plan-3  H16  0.020
 4WG  plan-4  C17  0.020
 4WG  plan-4  C18  0.020
 4WG  plan-4  O1   0.020
 4WG  plan-4  N4   0.020
 4WG  plan-4  C10  0.020
 4WG  plan-4  C19  0.020

