# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:55:32 2021
#   Inital geometry file: a 136 line input string
#   Ligand name: 5-chloranyl-3,3-dimethyl-2-[5-[1-(1-methylpyrazol-4-yl)carbonylazetidin-3-yl]oxypyridin-3-yl]isoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)C(=O)N2CC(C2)Oc3cncc(c3)N4C(=O)c5ccc(Cl)cc5C4(C)C
#
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
 O4W  O4W  5-chloranyl-3,3-dimethyl-2-[5-[1-(1-methylpyrazol-4-yl)carbonylazetidin-3-yl]oxypyridin-3-yl]isoindol-1-one  ligand  54  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O4W
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
 O4W  C1   C   CR6   0  -0.026  -22.3379  31.5545  37.3651
 O4W  C2   C   CR56  0   0.159  -23.0561  32.4277  35.2894
 O4W  C3   C   CR16  0  -0.295  -23.3576  32.1033  36.5992
 O4W  C4   C   CR56  0  -0.067  -21.7913  32.2110  34.7759
 O4W  C5   C   CR16  0  -0.219  -21.0589  31.3317  36.8591
 O4W  C6   C   CR16  0  -0.302  -20.7774  31.6633  35.5435
 O4W  C7   C   CR5   0   0.528  -21.7681  32.6461  33.3678
 O4W  O12  O   O     0  -0.456  -20.8431  32.5996  32.5809
 O4W  C14  C   CR6   0   0.255  -23.4003  33.5772  31.8326
 O4W  C15  C   CR6   0   0.303  -24.1179  33.1524  29.5984
 O4W  C16  C   CR16  0  -0.283  -23.7331  32.6634  30.8382
 O4W  C8   C   CR5   0   0.040  -23.9549  33.0346  34.2439
 O4W  C32  C   CH3   0  -0.508  -28.5043  25.6612  24.6670
 O4W  N9   N   NR5   0  -0.638  -23.0179  33.1231  33.1095
 O4W  CL1  CL  CL    0  -0.110  -22.6661  31.1304  39.0097
 O4W  C11  C   CH3   0  -0.637  -25.1291  32.1167  33.9121
 O4W  C13  C   CH3   0  -0.636  -24.4472  34.4139  34.6742
 O4W  C17  C   CR16  0  -0.136  -24.1482  34.5378  29.4144
 O4W  C18  C   CR16  0  -0.096  -23.4468  34.9325  31.5484
 O4W  N19  N   N     0  -0.383  -23.8194  35.3956  30.3609
 O4W  O20  O   O2    0  -0.469  -24.4745  32.3965  28.5460
 O4W  C21  C   C     0  -0.074  -24.3754  30.9995  28.6667
 O4W  C22  C   C     0  -0.269  -25.4569  30.3076  29.5293
 O4W  C23  C   C     0  -0.290  -24.9659  30.2947  27.4385
 O4W  N24  N   N     0  -0.478  -25.9487  29.6786  28.3192
 O4W  C25  C   C     0   0.476  -26.8058  28.6523  28.2274
 O4W  O26  O   O     0  -0.500  -27.3647  28.2112  29.2282
 O4W  C27  C   CR5   0  -0.290  -27.0561  28.0854  26.8978
 O4W  C28  C   CR15  0  -0.059  -26.6717  28.4745  25.5968
 O4W  N29  N   N     0  -0.275  -27.1551  27.6514  24.6911
 O4W  N30  N   NR5   0  -0.266  -27.8431  26.7343  25.3720
 O4W  C31  C   CR15  0   0.095  -27.8180  26.9489  26.6881
 O4W  H1   H   HCR6  0   0.285  -24.3426  32.2662  37.0178
 O4W  H2   H   HCR6  0   0.289  -20.2938  30.9027  37.4912
 O4W  H3   H   HCR6  0   0.274  -19.7888  31.4956  35.1366
 O4W  H4   H   HCR6  0   0.298  -23.6830  31.6046  31.0575
 O4W  H5   H   HCH3  0   0.266  -27.7742  25.0456  24.1462
 O4W  H6   H   HCH3  0   0.263  -29.0419  25.0473  25.3830
 O4W  H7   H   HCH3  0   0.266  -29.2103  26.0684  23.9468
 O4W  H8   H   HCH3  0   0.253  -25.7783  32.0102  34.7813
 O4W  H9   H   HCH3  0   0.248  -25.7298  32.5356  33.1036
 O4W  H10  H   HCH3  0   0.246  -24.7855  31.1254  33.6161
 O4W  H11  H   HCH3  0   0.251  -25.0658  34.3260  35.5676
 O4W  H12  H   HCH3  0   0.247  -23.6142  35.0801  34.8986
 O4W  H13  H   HCH3  0   0.249  -25.0603  34.8713  33.8970
 O4W  H14  H   HCR6  0   0.278  -24.4509  34.9422  28.4541
 O4W  H15  H   HCR6  0   0.275  -23.1746  35.6610  32.3034
 O4W  H16  H   H     0   0.288  -23.3518  30.7019  28.9076
 O4W  H17  H   H     0   0.262  -26.1723  30.9792  30.0103
 O4W  H18  H   H     0   0.260  -25.0696  29.6062  30.2709
 O4W  H19  H   H     0   0.271  -24.2918  29.5908  26.9485
 O4W  H20  H   H     0   0.269  -25.3876  30.9739  26.6948
 O4W  H21  H   HCR5  0   0.269  -26.0832  29.3210  25.2798
 O4W  H22  H   HCR5  0   0.302  -28.3273  26.3024  27.3839

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
 O4W  C32  N30  single    1.444  0.020  1.444
 O4W  N29  N30  aromatic  1.333  0.020  1.333
 O4W  N29  C28  aromatic  1.316  0.020  1.316
 O4W  N30  C31  aromatic  1.334  0.020  1.334
 O4W  C28  C27  aromatic  1.411  0.020  1.411
 O4W  C31  C27  aromatic  1.384  0.020  1.384
 O4W  C27  C25  single    1.467  0.020  1.467
 O4W  C23  N24  single    1.456  0.020  1.456
 O4W  C23  C21  single    1.534  0.020  1.534
 O4W  C25  N24  single    1.340  0.020  1.340
 O4W  C25  O26  double    1.228  0.020  1.228
 O4W  N24  C22  single    1.450  0.020  1.450
 O4W  O20  C21  single    1.406  0.020  1.406
 O4W  O20  C15  single    1.344  0.020  1.344
 O4W  C21  C22  single    1.547  0.020  1.547
 O4W  C17  C15  aromatic  1.398  0.020  1.398
 O4W  C17  N19  aromatic  1.319  0.020  1.319
 O4W  C15  C16  aromatic  1.387  0.020  1.387
 O4W  N19  C18  aromatic  1.328  0.020  1.328
 O4W  C16  C14  aromatic  1.391  0.020  1.391
 O4W  C18  C14  aromatic  1.386  0.020  1.386
 O4W  C14  N9   single    1.408  0.020  1.408
 O4W  O12  C7   double    1.215  0.020  1.215
 O4W  N9   C7   single    1.363  0.020  1.363
 O4W  N9   C8   single    1.474  0.020  1.474
 O4W  C7   C4   single    1.474  0.020  1.474
 O4W  C11  C8   single    1.527  0.020  1.527
 O4W  C8   C13  single    1.526  0.020  1.526
 O4W  C8   C2   single    1.506  0.020  1.506
 O4W  C4   C2   aromatic  1.382  0.020  1.382
 O4W  C4   C6   aromatic  1.385  0.020  1.385
 O4W  C2   C3   aromatic  1.383  0.020  1.383
 O4W  C6   C5   aromatic  1.386  0.020  1.386
 O4W  C3   C1   aromatic  1.388  0.020  1.388
 O4W  C5   C1   aromatic  1.393  0.020  1.393
 O4W  C1   CL1  single    1.730  0.020  1.730
 O4W  C3   H1   single    0.930  0.020  1.080
 O4W  C5   H2   single    0.930  0.020  1.080
 O4W  C6   H3   single    0.930  0.020  1.080
 O4W  C16  H4   single    0.930  0.020  1.080
 O4W  C32  H5   single    0.970  0.020  1.090
 O4W  C32  H6   single    0.970  0.020  1.090
 O4W  C32  H7   single    0.970  0.020  1.090
 O4W  C11  H8   single    0.970  0.020  1.090
 O4W  C11  H9   single    0.970  0.020  1.090
 O4W  C11  H10  single    0.970  0.020  1.090
 O4W  C13  H11  single    0.970  0.020  1.090
 O4W  C13  H12  single    0.970  0.020  1.090
 O4W  C13  H13  single    0.970  0.020  1.090
 O4W  C17  H14  single    0.930  0.020  1.080
 O4W  C18  H15  single    0.930  0.020  1.080
 O4W  C21  H16  single    0.970  0.020  1.090
 O4W  C22  H17  single    0.970  0.020  1.090
 O4W  C22  H18  single    0.970  0.020  1.090
 O4W  C23  H19  single    0.970  0.020  1.090
 O4W  C23  H20  single    0.970  0.020  1.090
 O4W  C28  H21  single    0.930  0.020  1.080
 O4W  C31  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
 O4W  CL1  C1   C5   118.70  3.000
 O4W  CL1  C1   C3   118.81  3.000
 O4W  C5   C1   C3   122.48  3.000
 O4W  C8   C2   C4   110.57  3.000
 O4W  C4   C2   C3   120.98  3.000
 O4W  C8   C2   C3   128.45  3.000
 O4W  H1   C3   C2   121.96  3.000
 O4W  H1   C3   C1   120.96  3.000
 O4W  C2   C3   C1   117.07  3.000
 O4W  C7   C4   C6   129.41  3.000
 O4W  C6   C4   C2   121.74  3.000
 O4W  C7   C4   C2   108.85  3.000
 O4W  H2   C5   C6   120.42  3.000
 O4W  H2   C5   C1   120.04  3.000
 O4W  C6   C5   C1   119.54  3.000
 O4W  H3   C6   C5   120.36  3.000
 O4W  H3   C6   C4   121.45  3.000
 O4W  C5   C6   C4   118.19  3.000
 O4W  N9   C7   O12  126.07  3.000
 O4W  N9   C7   C4   105.66  3.000
 O4W  O12  C7   C4   128.26  3.000
 O4W  C18  C14  N9   120.70  3.000
 O4W  N9   C14  C16  120.09  3.000
 O4W  C18  C14  C16  119.21  3.000
 O4W  O20  C15  C17  116.66  3.000
 O4W  C17  C15  C16  118.23  3.000
 O4W  O20  C15  C16  125.12  3.000
 O4W  H4   C16  C15  122.60  3.000
 O4W  H4   C16  C14  119.13  3.000
 O4W  C15  C16  C14  118.28  3.000
 O4W  C13  C8   C11  110.88  3.000
 O4W  C13  C8   N9   111.58  3.000
 O4W  C11  C8   N9   110.96  3.000
 O4W  C13  C8   C2   111.15  3.000
 O4W  C11  C8   C2   111.56  3.000
 O4W  N9   C8   C2   100.31  3.000
 O4W  H7   C32  H6   109.09  3.000
 O4W  H7   C32  H5   109.30  3.000
 O4W  H6   C32  H5   109.15  3.000
 O4W  H7   C32  N30  110.01  3.000
 O4W  H6   C32  N30  108.96  3.000
 O4W  H5   C32  N30  110.30  3.000
 O4W  C8   N9   C14  123.00  3.000
 O4W  C8   N9   C7   114.60  3.000
 O4W  C14  N9   C7   122.27  3.000
 O4W  H10  C11  H9   108.76  3.000
 O4W  H10  C11  H8   108.38  3.000
 O4W  H9   C11  H8   107.49  3.000
 O4W  H10  C11  C8   111.30  3.000
 O4W  H9   C11  C8   110.71  3.000
 O4W  H8   C11  C8   110.08  3.000
 O4W  H13  C13  H12  108.66  3.000
 O4W  H13  C13  H11  107.39  3.000
 O4W  H12  C13  H11  108.32  3.000
 O4W  H13  C13  C8   111.06  3.000
 O4W  H12  C13  C8   111.34  3.000
 O4W  H11  C13  C8   109.95  3.000
 O4W  H14  C17  N19  117.53  3.000
 O4W  H14  C17  C15  119.46  3.000
 O4W  N19  C17  C15  123.01  3.000
 O4W  H15  C18  N19  117.32  3.000
 O4W  H15  C18  C14  120.41  3.000
 O4W  N19  C18  C14  122.27  3.000
 O4W  C18  N19  C17  119.00  3.000
 O4W  C21  O20  C15  118.23  3.000
 O4W  H16  C21  C23  114.33  3.000
 O4W  H16  C21  C22  114.22  3.000
 O4W  C23  C21  C22   88.39  3.000
 O4W  H16  C21  O20  110.83  3.000
 O4W  C22  C21  O20  116.30  3.000
 O4W  C23  C21  O20  111.14  3.000
 O4W  H18  C22  H17  109.15  3.000
 O4W  H18  C22  N24  114.11  3.000
 O4W  H17  C22  N24  114.33  3.000
 O4W  H18  C22  C21  114.72  3.000
 O4W  H17  C22  C21  115.36  3.000
 O4W  N24  C22  C21   88.04  3.000
 O4W  H20  C23  H19  109.51  3.000
 O4W  H20  C23  N24  114.48  3.000
 O4W  H19  C23  N24  114.56  3.000
 O4W  H20  C23  C21  114.09  3.000
 O4W  H19  C23  C21  114.72  3.000
 O4W  N24  C23  C21   88.28  3.000
 O4W  C25  N24  C23  135.57  3.000
 O4W  C25  N24  C22  127.32  3.000
 O4W  C23  N24  C22   95.29  3.000
 O4W  C27  C25  O26  121.47  3.000
 O4W  O26  C25  N24  120.68  3.000
 O4W  C27  C25  N24  117.85  3.000
 O4W  C31  C27  C28  103.69  3.000
 O4W  C31  C27  C25  123.27  3.000
 O4W  C28  C27  C25  133.04  3.000
 O4W  H21  C28  N29  119.28  3.000
 O4W  H21  C28  C27  129.49  3.000
 O4W  N29  C28  C27  111.22  3.000
 O4W  N30  N29  C28  105.57  3.000
 O4W  C31  N30  N29  112.55  3.000
 O4W  C31  N30  C32  127.58  3.000
 O4W  N29  N30  C32  119.87  3.000
 O4W  H22  C31  N30  122.12  3.000
 O4W  H22  C31  C27  130.90  3.000
 O4W  N30  C31  C27  106.98  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
 O4W  CONST_01  C4   C2   C3   C1     0.00   0.0  0
 O4W  CONST_02  C4   C6   C5   C1     0.00   0.0  0
 O4W  CONST_03  C5   C6   C4   C2     0.00   0.0  0
 O4W  CONST_04  C5   C1   C3   C2     0.00   0.0  0
 O4W  CONST_05  C6   C4   C2   C3     0.00   0.0  0
 O4W  CONST_06  C6   C5   C1   C3     0.00   0.0  0
 O4W  CONST_07  C17  C15  C16  C14    0.00   0.0  0
 O4W  CONST_08  C17  N19  C18  C14    0.00   0.0  0
 O4W  CONST_09  C18  N19  C17  C15    0.00   0.0  0
 O4W  CONST_10  C18  C14  C16  C15    0.00   0.0  0
 O4W  CONST_11  N19  C17  C15  C16    0.00   0.0  0
 O4W  CONST_12  N19  C18  C14  C16    0.00   0.0  0
 O4W  CONST_13  N30  N29  C28  C27    0.00   0.0  0
 O4W  CONST_14  N29  N30  C31  C27    0.00   0.0  0
 O4W  CONST_15  C31  N30  N29  C28    0.00   0.0  0
 O4W  CONST_16  N30  C31  C27  C28    0.00   0.0  0
 O4W  CONST_17  C31  C27  C28  N29    0.00   0.0  0
 O4W  CONST_18  N9   C14  C16  C15  180.00   0.0  0
 O4W  CONST_19  N19  C18  C14  N9   180.00   0.0  0
 O4W  CONST_20  C14  N9   C7   C4   180.00   0.0  0
 O4W  CONST_21  C8   N9   C7   C4     0.00   0.0  0
 O4W  CONST_22  CL1  C1   C3   C2   180.00   0.0  0
 O4W  CONST_23  CL1  C1   C5   C6   180.00   0.0  0
 O4W  CONST_24  O20  C15  C16  C14  180.00   0.0  0
 O4W  CONST_25  C28  N29  N30  C32  180.00   0.0  0
 O4W  CONST_26  C27  C31  N30  C32  180.00   0.0  0
 O4W  CONST_27  O20  C15  C17  N19  180.00   0.0  0
 O4W  CONST_28  N29  C28  C27  C25  180.00   0.0  0
 O4W  CONST_29  N30  C31  C27  C25  180.00   0.0  0
 O4W  CONST_30  C27  C25  N24  C22  180.00   0.0  0
 O4W  CONST_31  C27  C25  N24  C23    0.00   0.0  0
 O4W  CONST_32  C14  N9   C7   O12    0.00   0.0  0
 O4W  CONST_33  C8   N9   C7   O12  180.00   0.0  0
 O4W  CONST_34  H3   C6   C5   C1   180.00   0.0  0
 O4W  CONST_35  H2   C5   C1   C3   180.00   0.0  0
 O4W  CONST_36  H1   C3   C2   C4   180.00   0.0  0
 O4W  CONST_37  H14  C17  C15  C16  180.00   0.0  0
 O4W  CONST_38  H15  C18  C14  C16  180.00   0.0  0
 O4W  CONST_39  H4   C16  C14  N9     0.00   0.0  0
 O4W  CONST_40  H22  C31  C27  C28  180.00   0.0  0
 O4W  CONST_41  H21  C28  N29  N30  180.00   0.0  0
 O4W  CONST_42  O26  C25  N24  C22    0.00   0.0  0
 O4W  CONST_43  O26  C25  N24  C23  180.00   0.0  0
 O4W  Var_01    C16  C14  N9   C7    78.75  30.0  2
 O4W  Var_02    C22  N24  C23  C21    0.20  30.0  1
 O4W  Var_03    C11  C8   C2   C3   -62.93  30.0  1
 O4W  Var_04    C28  C27  C25  N24   -7.30  30.0  2
 O4W  Var_05    H8   C11  C8   C2    65.40  30.0  3
 O4W  Var_06    H11  C13  C8   C2   -63.89  30.0  3
 O4W  Var_07    H5   C32  N30  N29   62.60  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
 O4W  chir_01  C21  C23  O20  C22  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
 O4W  plan-1  C32  0.020
 O4W  plan-1  C25  0.020
 O4W  plan-1  C27  0.020
 O4W  plan-1  C28  0.020
 O4W  plan-1  N29  0.020
 O4W  plan-1  N30  0.020
 O4W  plan-1  C31  0.020
 O4W  plan-1  H21  0.020
 O4W  plan-1  H22  0.020
 O4W  plan-2  C14  0.020
 O4W  plan-2  C15  0.020
 O4W  plan-2  C16  0.020
 O4W  plan-2  N9   0.020
 O4W  plan-2  C17  0.020
 O4W  plan-2  C18  0.020
 O4W  plan-2  N19  0.020
 O4W  plan-2  O20  0.020
 O4W  plan-2  H4   0.020
 O4W  plan-2  H14  0.020
 O4W  plan-2  H15  0.020
 O4W  plan-3  C22  0.020
 O4W  plan-3  C23  0.020
 O4W  plan-3  N24  0.020
 O4W  plan-3  C25  0.020
 O4W  plan-3  O26  0.020
 O4W  plan-3  C27  0.020
 O4W  plan-4  C1   0.020
 O4W  plan-4  C2   0.020
 O4W  plan-4  C3   0.020
 O4W  plan-4  C4   0.020
 O4W  plan-4  C5   0.020
 O4W  plan-4  C6   0.020
 O4W  plan-4  C7   0.020
 O4W  plan-4  O12  0.020
 O4W  plan-4  C14  0.020
 O4W  plan-4  C8   0.020
 O4W  plan-4  N9   0.020
 O4W  plan-4  CL1  0.020
 O4W  plan-4  H1   0.020
 O4W  plan-4  H2   0.020
 O4W  plan-4  H3   0.020

