# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:46:59 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-{2-chloro-4-[(6,7-dimethoxyquinolin-4-yl)oxy]phenyl}-3-[(3E)-5-methylisoxazol-3(2H)-ylidene]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2nccc(Oc3ccc(NC(=O)N=C4NOC(=C4)C)c(Cl)c3)c2cc1OC
#
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
 AV9  AV9  1-{2-chloro-4-[(6,7-dimethoxyquinolin-4-yl)oxy]phenyl}-3-[(3E)-5-methylisoxazol-3(2H)-ylidene]urea  ligand  51  32  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AV9
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
 AV9  C1    C   CR6   0   0.330   6.9102  -0.4697   0.1588
 AV9  C2    C   CR16  0  -0.452   6.2560  -0.8633   1.2937
 AV9  C3    C   CR66  0   0.203   4.8475  -0.7615   1.3964
 AV9  C4    C   CR66  0  -0.007   4.1217  -0.2429   0.3026
 AV9  C5    C   CR16  0  -0.458   4.8064   0.1642  -0.8684
 AV9  C6    C   CR6   0   0.343   6.1669   0.0572  -0.9483
 AV9  N7    N   N     0  -0.451   4.2612  -1.1695   2.5449
 AV9  C8    C   CR16  0  -0.091   2.9591  -1.0720   2.6276
 AV9  C9    C   CR16  0  -0.426   2.1274  -0.5763   1.6120
 AV9  C10   C   CR6   0   0.436   2.7166  -0.1598   0.4430
 AV9  O11   O   O2    0  -0.506   2.0472   0.3405  -0.6157
 AV9  C12   C   CR6   0   0.291   0.6742   0.4075  -0.5691
 AV9  C13   C   CR16  0  -0.259   0.0682   1.5807  -0.1603
 AV9  C15   C   CR6   0   0.449  -2.1241   0.5799  -0.5460
 AV9  C16   C   CR16  0  -0.320  -1.4714  -0.5844  -0.9657
 AV9  C17   C   CR16  0  -0.285  -0.0903  -0.6732  -0.9704
 AV9  O25   O   O     0  -0.312  -8.9690  -0.7672  -0.2130
 AV9  C11   C   CR6   0  -0.142  -1.3137   1.6546  -0.1519
 AV9  N28   N   NH1   0  -0.766  -3.4981   0.7299  -0.5400
 AV9  O33   O   O2    0  -0.459   6.9138   0.4105  -2.0032
 AV9  O34   O   O2    0  -0.455   8.2323  -0.5274  -0.0333
 AV9  C35   C   C     0   0.635  -4.4669  -0.2517  -0.5033
 AV9  O36   O   O     0  -0.509  -4.1930  -1.4447  -0.5025
 AV9  N37   N   N     0  -0.590  -5.6990   0.3272  -0.4714
 AV9  C38   C   CR5   0   0.556  -6.7568  -0.4354  -0.3912
 AV9  C30   C   CR5   0   0.471  -8.3666  -1.9631  -0.1583
 AV9  C43   C   CR15  0  -0.557  -7.0261  -1.8413  -0.2694
 AV9  N21   N   NR15  0  -0.363  -7.9794   0.1395  -0.4267
 AV9  CL4   CL  CL    0  -0.108  -2.0461   3.1374   0.3713
 AV9  C49   C   CH3   0  -0.442   6.2581   0.9581  -3.1303
 AV9  C53   C   CH3   0  -0.440   9.0370  -1.0369   1.0134
 AV9  H2    H   HCR6  0   0.284   6.7862  -1.2638   2.1467
 AV9  H5    H   HCR6  0   0.289   4.2417   0.5622  -1.6991
 AV9  H8    H   HCR6  0   0.262   2.5031  -1.4028   3.5546
 AV9  H9    H   HCR6  0   0.286   1.0590  -0.5360   1.7709
 AV9  H13   H   HCR6  0   0.298   0.6612   2.4314   0.1487
 AV9  H17   H   HCR6  0   0.283   0.3845  -1.5859  -1.3060
 AV9  H16   H   HCR6  0   0.290  -2.0480  -1.4306  -1.3001
 AV9  H28   H   HNH1  0   0.395  -3.8564   1.6688  -0.4589
 AV9  H21   H   HNR5  0   0.441  -8.2254   1.0898  -0.1872
 AV9  H491  H   HCH3  0   0.232   5.7246   1.8790  -2.8807
 AV9  H492  H   HCH3  0   0.264   7.0334   1.1852  -3.8575
 AV9  H493  H   HCH3  0   0.232   5.5525   0.2503  -3.5734
 AV9  H531  H   HCH3  0   0.265  10.0630  -1.0047   0.6567
 AV9  H532  H   HCH3  0   0.233   8.9561  -0.4289   1.9181
 AV9  H533  H   HCH3  0   0.233   8.7773  -2.0701   1.2570
 AV9  H43   H   HCR5  0   0.304  -6.3117  -2.6416  -0.2512
 AV9  H401  H   HCH3  0   0.280  -9.8381  -3.0673   0.9077
 AV9  H402  H   HCH3  0   0.281  -9.9352  -3.2221  -0.8464
 AV9  H403  H   HCH3  0   0.276  -8.6464  -4.0438   0.0405
 AV9  C40   C   CH3   0  -0.746  -9.2462  -3.1390  -0.0052

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
 AV9  C1   C2    aromatic  1.368  0.020  1.368
 AV9  C1   C6    aromatic  1.434  0.020  1.434
 AV9  C1   O34   single    1.337  0.020  1.337
 AV9  C2   C3    aromatic  1.416  0.020  1.416
 AV9  C3   C4    aromatic  1.411  0.020  1.411
 AV9  C3   N7    aromatic  1.353  0.020  1.353
 AV9  C4   C5    aromatic  1.416  0.020  1.416
 AV9  C4   C10   aromatic  1.415  0.020  1.415
 AV9  C5   C6    aromatic  1.367  0.020  1.367
 AV9  C6   O33   single    1.340  0.020  1.340
 AV9  N7   C8    aromatic  1.308  0.020  1.308
 AV9  C8   C9    aromatic  1.403  0.020  1.403
 AV9  C9   C10   aromatic  1.374  0.020  1.374
 AV9  C10  O11   single    1.349  0.020  1.349
 AV9  O11  C12   single    1.375  0.020  1.375
 AV9  C12  C13   aromatic  1.382  0.020  1.382
 AV9  C12  C17   aromatic  1.383  0.020  1.383
 AV9  C13  C11   aromatic  1.384  0.020  1.384
 AV9  C15  C16   aromatic  1.399  0.020  1.399
 AV9  C15  N28   single    1.382  0.020  1.382
 AV9  C15  C11   aromatic  1.403  0.020  1.403
 AV9  C16  C17   aromatic  1.384  0.020  1.384
 AV9  O25  C30   single    1.340  0.020  1.340
 AV9  O25  N21   single    1.359  0.020  1.359
 AV9  N28  C35   single    1.380  0.020  1.380
 AV9  O33  C49   single    1.414  0.020  1.414
 AV9  O34  C53   single    1.415  0.020  1.415
 AV9  C11  CL4   single    1.735  0.020  1.735
 AV9  C35  O36   double    1.224  0.020  1.224
 AV9  C35  N37   single    1.362  0.020  1.362
 AV9  N37  C38   double    1.306  0.020  1.306
 AV9  C38  C43   single    1.437  0.020  1.437
 AV9  C38  N21   single    1.352  0.020  1.352
 AV9  C40  C30   single    1.476  0.020  1.476
 AV9  C43  C30   double    1.351  0.020  1.351
 AV9  C2   H2    single    0.930  0.020  1.080
 AV9  C5   H5    single    0.930  0.020  1.080
 AV9  C8   H8    single    0.930  0.020  1.080
 AV9  C9   H9    single    0.930  0.020  1.080
 AV9  C13  H13   single    0.930  0.020  1.080
 AV9  C17  H17   single    0.930  0.020  1.080
 AV9  C16  H16   single    0.930  0.020  1.080
 AV9  N28  H28   single    0.860  0.020  1.020
 AV9  N21  H21   single    0.890  0.020  1.040
 AV9  C49  H491  single    0.970  0.020  1.090
 AV9  C49  H492  single    0.970  0.020  1.090
 AV9  C49  H493  single    0.970  0.020  1.090
 AV9  C53  H531  single    0.970  0.020  1.090
 AV9  C53  H532  single    0.970  0.020  1.090
 AV9  C53  H533  single    0.970  0.020  1.090
 AV9  C43  H43   single    0.930  0.020  1.080
 AV9  C40  H401  single    0.970  0.020  1.090
 AV9  C40  H402  single    0.970  0.020  1.090
 AV9  C40  H403  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
 AV9  O34   C1   C6    114.67  3.000
 AV9  O34   C1   C2    125.43  3.000
 AV9  C6    C1   C2    119.90  3.000
 AV9  H2    C2   C3    117.21  3.000
 AV9  H2    C2   C1    121.78  3.000
 AV9  C3    C2   C1    121.02  3.000
 AV9  N7    C3   C4    123.10  3.000
 AV9  N7    C3   C2    118.10  3.000
 AV9  C4    C3   C2    118.80  3.000
 AV9  C10   C4   C5    123.06  3.000
 AV9  C10   C4   C3    117.09  3.000
 AV9  C5    C4   C3    119.85  3.000
 AV9  H5    C5   C6    120.27  3.000
 AV9  H5    C5   C4    119.27  3.000
 AV9  C6    C5   C4    120.47  3.000
 AV9  O33   C6   C5    125.46  3.000
 AV9  O33   C6   C1    114.57  3.000
 AV9  C5    C6   C1    119.97  3.000
 AV9  C8    N7   C3    117.55  3.000
 AV9  H8    C8   C9    118.50  3.000
 AV9  H8    C8   N7    116.72  3.000
 AV9  C9    C8   N7    124.79  3.000
 AV9  H9    C9   C10   122.53  3.000
 AV9  H9    C9   C8    119.51  3.000
 AV9  C10   C9   C8    117.96  3.000
 AV9  O11   C10  C9    124.58  3.000
 AV9  O11   C10  C4    115.90  3.000
 AV9  C9    C10  C4    119.52  3.000
 AV9  C12   O11  C10   119.14  3.000
 AV9  C17   C12  C13   120.44  3.000
 AV9  C17   C12  O11   120.25  3.000
 AV9  C13   C12  O11   119.27  3.000
 AV9  H13   C13  C11   120.23  3.000
 AV9  H13   C13  C12   120.77  3.000
 AV9  C11   C13  C12   119.00  3.000
 AV9  N28   C15  C11   119.34  3.000
 AV9  C11   C15  C16   116.90  3.000
 AV9  N28   C15  C16   123.73  3.000
 AV9  H16   C16  C17   118.86  3.000
 AV9  H16   C16  C15   119.81  3.000
 AV9  C17   C16  C15   121.33  3.000
 AV9  H17   C17  C16   119.54  3.000
 AV9  H17   C17  C12   120.42  3.000
 AV9  C16   C17  C12   120.03  3.000
 AV9  N21   O25  C30   105.93  3.000
 AV9  CL4   C11  C15   119.72  3.000
 AV9  CL4   C11  C13   117.97  3.000
 AV9  C15   C11  C13   122.30  3.000
 AV9  H28   N28  C35   114.26  3.000
 AV9  H28   N28  C15   117.05  3.000
 AV9  C35   N28  C15   128.38  3.000
 AV9  C49   O33  C6    118.11  3.000
 AV9  C53   O34  C1    118.13  3.000
 AV9  N37   C35  O36   128.09  3.000
 AV9  N37   C35  N28   109.48  3.000
 AV9  O36   C35  N28   122.43  3.000
 AV9  C38   N37  C35   119.07  3.000
 AV9  N21   C38  C43   104.41  3.000
 AV9  N21   C38  N37   118.85  3.000
 AV9  C43   C38  N37   136.74  3.000
 AV9  C43   C30  C40   132.19  3.000
 AV9  C43   C30  O25   111.24  3.000
 AV9  C40   C30  O25   116.56  3.000
 AV9  H43   C43  C30   126.32  3.000
 AV9  H43   C43  C38   127.34  3.000
 AV9  C30   C43  C38   106.34  3.000
 AV9  H21   N21  C38   127.88  3.000
 AV9  H21   N21  O25   114.39  3.000
 AV9  C38   N21  O25   111.76  3.000
 AV9  H493  C49  H492  108.94  3.000
 AV9  H493  C49  H491  108.84  3.000
 AV9  H492  C49  H491  108.96  3.000
 AV9  H493  C49  O33   111.81  3.000
 AV9  H492  C49  O33   106.46  3.000
 AV9  H491  C49  O33   111.74  3.000
 AV9  H533  C53  H532  108.89  3.000
 AV9  H533  C53  H531  109.00  3.000
 AV9  H532  C53  H531  108.97  3.000
 AV9  H533  C53  O34   111.72  3.000
 AV9  H532  C53  O34   111.71  3.000
 AV9  H531  C53  O34   106.46  3.000
 AV9  H403  C40  H402  108.54  3.000
 AV9  H403  C40  H401  108.61  3.000
 AV9  H402  C40  H401  107.93  3.000
 AV9  H403  C40  C30   109.80  3.000
 AV9  H402  C40  C30   110.92  3.000
 AV9  H401  C40  C30   110.97  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
 AV9  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 AV9  CONST_02  N7    C3   C2   C1   180.00   0.0  0
 AV9  CONST_03  C4    C5   C6   C1     0.00   0.0  0
 AV9  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 AV9  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 AV9  CONST_06  C10   C4   C3   C2   180.00   0.0  0
 AV9  CONST_07  C8    N7   C3   C2   180.00   0.0  0
 AV9  CONST_08  C6    C1   C2   C3     0.00   0.0  0
 AV9  CONST_09  C6    C5   C4   C3     0.00   0.0  0
 AV9  CONST_10  C9    C10  C4   C3     0.00   0.0  0
 AV9  CONST_11  C9    C8   N7   C3     0.00   0.0  0
 AV9  CONST_12  C8    N7   C3   C4     0.00   0.0  0
 AV9  CONST_13  C8    C9   C10  C4     0.00   0.0  0
 AV9  CONST_14  N7    C3   C4   C5   180.00   0.0  0
 AV9  CONST_15  C9    C10  C4   C5   180.00   0.0  0
 AV9  CONST_16  C10   C4   C5   C6   180.00   0.0  0
 AV9  CONST_17  C10   C4   C3   N7     0.00   0.0  0
 AV9  CONST_18  C10   C9   C8   N7     0.00   0.0  0
 AV9  CONST_19  C15   C11  C13  C12    0.00   0.0  0
 AV9  CONST_20  C15   C16  C17  C12    0.00   0.0  0
 AV9  CONST_21  C16   C17  C12  C13    0.00   0.0  0
 AV9  CONST_22  C16   C15  C11  C13    0.00   0.0  0
 AV9  CONST_23  C11   C13  C12  C17    0.00   0.0  0
 AV9  CONST_24  C11   C15  C16  C17    0.00   0.0  0
 AV9  CONST_25  C43   C38  N21  O25    0.00   0.0  0
 AV9  CONST_26  O33   C6   C1   C2   180.00   0.0  0
 AV9  CONST_27  O34   C1   C2   C3   180.00   0.0  0
 AV9  CONST_28  O11   C10  C4   C3   180.00   0.0  0
 AV9  CONST_29  O33   C6   C5   C4   180.00   0.0  0
 AV9  CONST_30  O11   C10  C4   C5     0.00   0.0  0
 AV9  CONST_31  O34   C1   C6   C5   180.00   0.0  0
 AV9  CONST_32  O11   C10  C9   C8   180.00   0.0  0
 AV9  CONST_33  C11   C13  C12  O11  180.00   0.0  0
 AV9  CONST_34  C16   C17  C12  O11  180.00   0.0  0
 AV9  CONST_35  CL4   C11  C13  C12  180.00   0.0  0
 AV9  CONST_36  N28   C15  C11  C13  180.00   0.0  0
 AV9  CONST_37  CL4   C11  C15  C16  180.00   0.0  0
 AV9  CONST_38  N28   C15  C16  C17  180.00   0.0  0
 AV9  CONST_39  N37   C38  N21  O25  180.00   0.0  0
 AV9  CONST_40  H5    C5   C6   C1   180.00   0.0  0
 AV9  CONST_41  H8    C8   N7   C3   180.00   0.0  0
 AV9  CONST_42  H2    C2   C3   C4   180.00   0.0  0
 AV9  CONST_43  H9    C9   C10  C4   180.00   0.0  0
 AV9  CONST_44  H16   C16  C17  C12  180.00   0.0  0
 AV9  CONST_45  H17   C17  C12  C13  180.00   0.0  0
 AV9  CONST_46  H13   C13  C11  C15  180.00   0.0  0
 AV9  CONST_50  C43   C38  N37  C35    0.00   0.0  0
 AV9  CONST_51  N21   C38  N37  C35  180.00   0.0  0
 AV9  CONST_53  O36   C35  N28  C15    0.00   0.0  0
 AV9  CONST_54  C38   N37  C35  O36    0.00   0.0  0
 AV9  CONST_55  N37   C35  N28  C15  180.00   0.0  0
 AV9  CONST_56  C38   N37  C35  N28  180.00   0.0  0
 AV9  Var_01    C13   C12  O11  C10   94.68  30.0  2
 AV9  Var_02    H401  C40  C30  O25  -59.13  30.0  3
 AV9  Var_03    H531  C53  O34  C1   179.61  30.0  3
 AV9  Var_04    H491  C49  O33  C6    60.44  30.0  3

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
 AV9  plan-1  O11  0.020
 AV9  plan-1  C12  0.020
 AV9  plan-1  C13  0.020
 AV9  plan-1  C15  0.020
 AV9  plan-1  C16  0.020
 AV9  plan-1  C17  0.020
 AV9  plan-1  C11  0.020
 AV9  plan-1  N28  0.020
 AV9  plan-1  CL4  0.020
 AV9  plan-1  H13  0.020
 AV9  plan-1  H17  0.020
 AV9  plan-1  H16  0.020
 AV9  plan-2  C1   0.020
 AV9  plan-2  C2   0.020
 AV9  plan-2  C3   0.020
 AV9  plan-2  C4   0.020
 AV9  plan-2  C5   0.020
 AV9  plan-2  C6   0.020
 AV9  plan-2  N7   0.020
 AV9  plan-2  C8   0.020
 AV9  plan-2  C9   0.020
 AV9  plan-2  C10  0.020
 AV9  plan-2  O11  0.020
 AV9  plan-2  O33  0.020
 AV9  plan-2  O34  0.020
 AV9  plan-2  H2   0.020
 AV9  plan-2  H5   0.020
 AV9  plan-2  H8   0.020
 AV9  plan-2  H9   0.020
 AV9  plan-3  C15  0.020
 AV9  plan-3  O25  0.020
 AV9  plan-3  N28  0.020
 AV9  plan-3  C35  0.020
 AV9  plan-3  O36  0.020
 AV9  plan-3  N37  0.020
 AV9  plan-3  C38  0.020
 AV9  plan-3  C30  0.020
 AV9  plan-3  C43  0.020
 AV9  plan-3  N21  0.020
 AV9  plan-3  H28  0.020
 AV9  plan-3  H21  0.020
 AV9  plan-3  H43  0.020
 AV9  plan-3  C40  0.020

