# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 17:48:59 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-N'-[(pyridin-3-yl)methyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1cccnc1)Nc2ccc(CN3C(=O)c4ccccc4C3=O)cc2
#
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
 BWA  BWA  N-{4-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]phenyl}-N'-[(pyridin-3-yl)methyl]urea  ligand  47  29  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BWA
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
 BWA  C1   C  CR6   0   0.366  -0.8505  -1.1931   0.0833
 BWA  C3   C  C     0   0.750  -3.0284  -0.1585   0.6854
 BWA  C11  C  CR16  0  -0.286   1.2070  -1.9673  -0.9284
 BWA  C12  C  CR16  0  -0.339  -0.1346  -1.6469  -1.0288
 BWA  C13  C  CR16  0  -0.083  -7.5782  -0.1273   0.5021
 BWA  C15  C  CR16  0  -0.065  -8.9483   0.5544  -1.1789
 BWA  C16  C  CR16  0  -0.319  -8.0096   1.4646  -1.6431
 BWA  C17  C  CR16  0  -0.167  -6.7987   1.5614  -0.9771
 BWA  C20  C  CR5   0   0.584   4.6058  -0.5735  -1.1003
 BWA  C21  C  CR56  0  -0.025   5.3761   0.6739  -0.8835
 BWA  C22  C  CR56  0  -0.024   5.3682   0.9502   0.4737
 BWA  C23  C  CR5   0   0.584   4.5920  -0.1144   1.1521
 BWA  C24  C  CR16  0  -0.296   6.0222   1.4912  -1.7857
 BWA  C25  C  CR16  0  -0.240   6.6708   2.6144  -1.2749
 BWA  C26  C  CR16  0  -0.241   6.6625   2.8922   0.0889
 BWA  C27  C  CR16  0  -0.297   6.0060   2.0568   0.9914
 BWA  N2   N  NH1   0  -0.787  -2.2035  -0.9229  -0.1039
 BWA  N4   N  NH1   0  -0.683  -4.2820  -0.0248   0.1950
 BWA  O5   O  O     0  -0.522  -2.6803   0.3528   1.7400
 BWA  C6   C  CH2   0  -0.304  -5.2673   0.7907   0.8775
 BWA  C7   C  CR6   0  -0.050  -6.5661   0.7490   0.1269
 BWA  C8   C  CR16  0  -0.301  -0.1825  -1.0811   1.3049
 BWA  C9   C  CR16  0  -0.288   1.1650  -1.4005   1.3858
 BWA  C10  C  CR6   0   0.124   1.8839  -1.8416   0.2809
 BWA  N14  N  N     0  -0.402  -8.7423  -0.2283  -0.1265
 BWA  N19  N  NR5   0  -0.585   4.1844  -0.9855   0.1539
 BWA  O29  O  O     0  -0.401   4.3467  -0.2324   2.3261
 BWA  H1   H  HCR6  0   0.254   1.7306  -2.3182  -1.8089
 BWA  H2   H  HCR6  0   0.267  -0.6373  -1.7507  -1.9837
 BWA  H3   H  HCR6  0   0.263  -7.4355  -0.7753   1.3620
 BWA  H4   H  HCR6  0   0.267  -9.9067   0.4568  -1.6766
 BWA  H5   H  HCR6  0   0.274  -8.2265   2.0823  -2.5035
 BWA  H6   H  HCR6  0   0.274  -6.0445   2.2647  -1.3093
 BWA  H7   H  HCH2  0   0.288   3.5973  -2.5415   1.3739
 BWA  H8   H  HCH2  0   0.288   3.6395  -2.9148  -0.3390
 BWA  H9   H  HCR6  0   0.276   6.0296   1.2750  -2.8457
 BWA  H10  H  HCR6  0   0.279   7.1899   3.2832  -1.9480
 BWA  H11  H  HCR6  0   0.279   7.1736   3.7730   0.4535
 BWA  H12  H  HCR6  0   0.276   6.0002   2.2739   2.0511
 BWA  H13  H  HNH1  0   0.408  -2.5717  -1.2217  -0.9937
 BWA  H14  H  HNH1  0   0.403  -4.5288  -0.4199  -0.6981
 BWA  H15  H  HCH2  0   0.256  -5.4199   0.4243   1.8952
 BWA  H16  H  HCH2  0   0.255  -4.9219   1.8249   0.9576
 BWA  H17  H  HCR6  0   0.273  -0.7001  -0.7583   2.1927
 BWA  H18  H  HCR6  0   0.252   1.6603  -1.3100   2.3449
 BWA  C18  C  CH2   0  -0.431   3.3519  -2.1539   0.3856
 BWA  O28  O  O     0  -0.400   4.3755  -1.1436  -2.1368

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
 BWA  C15  C16  aromatic  1.387  0.020  1.387
 BWA  C15  N14  aromatic  1.328  0.020  1.328
 BWA  C16  C17  aromatic  1.385  0.020  1.385
 BWA  N14  C13  aromatic  1.327  0.020  1.327
 BWA  C17  C7   aromatic  1.390  0.020  1.390
 BWA  C13  C7   aromatic  1.390  0.020  1.390
 BWA  C7   C6   single    1.501  0.020  1.501
 BWA  N4   C6   single    1.450  0.020  1.450
 BWA  N4   C3   single    1.353  0.020  1.353
 BWA  N2   C3   single    1.374  0.020  1.374
 BWA  N2   C1   single    1.392  0.020  1.392
 BWA  C12  C11  aromatic  1.383  0.020  1.383
 BWA  C12  C1   aromatic  1.398  0.020  1.398
 BWA  C3   O5   double    1.223  0.020  1.223
 BWA  C11  C10  aromatic  1.392  0.020  1.392
 BWA  C1   C8   aromatic  1.397  0.020  1.397
 BWA  C10  C18  single    1.504  0.020  1.504
 BWA  C10  C9   aromatic  1.390  0.020  1.390
 BWA  C8   C9   aromatic  1.387  0.020  1.387
 BWA  O29  C23  double    1.205  0.020  1.205
 BWA  C18  N19  single    1.453  0.020  1.453
 BWA  C23  N19  single    1.386  0.020  1.386
 BWA  C23  C22  single    1.482  0.020  1.482
 BWA  N19  C20  single    1.386  0.020  1.386
 BWA  C22  C27  aromatic  1.378  0.020  1.378
 BWA  C22  C21  aromatic  1.385  0.020  1.385
 BWA  C20  O28  double    1.205  0.020  1.205
 BWA  C20  C21  single    1.482  0.020  1.482
 BWA  C27  C26  aromatic  1.394  0.020  1.394
 BWA  C21  C24  aromatic  1.378  0.020  1.378
 BWA  C26  C25  aromatic  1.392  0.020  1.392
 BWA  C24  C25  aromatic  1.394  0.020  1.394
 BWA  C11  H1   single    0.930  0.020  1.080
 BWA  C12  H2   single    0.930  0.020  1.080
 BWA  C13  H3   single    0.930  0.020  1.080
 BWA  C15  H4   single    0.930  0.020  1.080
 BWA  C16  H5   single    0.930  0.020  1.080
 BWA  C17  H6   single    0.930  0.020  1.080
 BWA  C18  H7   single    0.970  0.020  1.090
 BWA  C18  H8   single    0.970  0.020  1.090
 BWA  C24  H9   single    0.930  0.020  1.080
 BWA  C25  H10  single    0.930  0.020  1.080
 BWA  C26  H11  single    0.930  0.020  1.080
 BWA  C27  H12  single    0.930  0.020  1.080
 BWA  N2   H13  single    0.860  0.020  1.020
 BWA  N4   H14  single    0.860  0.020  1.020
 BWA  C6   H15  single    0.970  0.020  1.090
 BWA  C6   H16  single    0.970  0.020  1.090
 BWA  C8   H17  single    0.930  0.020  1.080
 BWA  C9   H18  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
 BWA  C8   C1   N2   124.53  3.000
 BWA  C8   C1   C12  118.47  3.000
 BWA  N2   C1   C12  116.97  3.000
 BWA  O5   C3   N4   122.36  3.000
 BWA  O5   C3   N2   123.86  3.000
 BWA  N4   C3   N2   113.78  3.000
 BWA  H1   C11  C10  120.05  3.000
 BWA  H1   C11  C12  119.02  3.000
 BWA  C10  C11  C12  120.93  3.000
 BWA  H2   C12  C11  119.45  3.000
 BWA  H2   C12  C1   119.61  3.000
 BWA  C11  C12  C1   120.94  3.000
 BWA  H3   C13  N14  116.42  3.000
 BWA  H3   C13  C7   119.61  3.000
 BWA  N14  C13  C7   123.97  3.000
 BWA  H4   C15  N14  116.61  3.000
 BWA  H4   C15  C16  120.23  3.000
 BWA  N14  C15  C16  123.16  3.000
 BWA  H5   C16  C17  121.20  3.000
 BWA  H5   C16  C15  120.36  3.000
 BWA  C17  C16  C15  118.45  3.000
 BWA  H6   C17  C7   120.42  3.000
 BWA  H6   C17  C16  120.43  3.000
 BWA  C7   C17  C16  119.16  3.000
 BWA  O28  C20  N19  125.43  3.000
 BWA  O28  C20  C21  128.55  3.000
 BWA  N19  C20  C21  106.02  3.000
 BWA  C24  C21  C22  121.73  3.000
 BWA  C24  C21  C20  130.32  3.000
 BWA  C22  C21  C20  107.95  3.000
 BWA  C27  C22  C23  130.34  3.000
 BWA  C27  C22  C21  121.71  3.000
 BWA  C23  C22  C21  107.96  3.000
 BWA  O29  C23  N19  125.46  3.000
 BWA  N19  C23  C22  106.01  3.000
 BWA  O29  C23  C22  128.53  3.000
 BWA  H9   C24  C25  121.12  3.000
 BWA  H9   C24  C21  121.75  3.000
 BWA  C25  C24  C21  117.13  3.000
 BWA  H10  C25  C26  119.29  3.000
 BWA  H10  C25  C24  119.56  3.000
 BWA  C26  C25  C24  121.14  3.000
 BWA  H11  C26  C27  119.49  3.000
 BWA  H11  C26  C25  119.34  3.000
 BWA  C27  C26  C25  121.17  3.000
 BWA  H12  C27  C26  121.09  3.000
 BWA  H12  C27  C22  121.78  3.000
 BWA  C26  C27  C22  117.13  3.000
 BWA  H13  N2   C3   116.91  3.000
 BWA  H13  N2   C1   114.58  3.000
 BWA  C3   N2   C1   127.89  3.000
 BWA  H14  N4   C6   118.13  3.000
 BWA  H14  N4   C3   120.64  3.000
 BWA  C6   N4   C3   120.98  3.000
 BWA  H16  C6   H15  107.05  3.000
 BWA  H16  C6   C7   109.66  3.000
 BWA  H15  C6   C7   109.62  3.000
 BWA  H16  C6   N4   110.61  3.000
 BWA  H15  C6   N4   110.17  3.000
 BWA  C7   C6   N4   109.70  3.000
 BWA  C6   C7   C17  121.72  3.000
 BWA  C6   C7   C13  120.83  3.000
 BWA  C17  C7   C13  117.44  3.000
 BWA  H17  C8   C9   119.19  3.000
 BWA  H17  C8   C1   121.00  3.000
 BWA  C9   C8   C1   119.81  3.000
 BWA  H18  C9   C10  119.59  3.000
 BWA  H18  C9   C8   118.46  3.000
 BWA  C10  C9   C8   121.94  3.000
 BWA  C9   C10  C18  121.01  3.000
 BWA  C9   C10  C11  117.90  3.000
 BWA  C18  C10  C11  121.09  3.000
 BWA  C15  N14  C13  117.82  3.000
 BWA  C23  N19  C20  112.06  3.000
 BWA  C20  N19  C18  123.89  3.000
 BWA  C23  N19  C18  123.98  3.000
 BWA  H8   C18  H7   107.18  3.000
 BWA  H8   C18  N19  107.71  3.000
 BWA  H7   C18  N19  107.55  3.000
 BWA  H8   C18  C10  110.88  3.000
 BWA  H7   C18  C10  110.90  3.000
 BWA  N19  C18  C10  112.39  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
 BWA  CONST_01  C10  C11  C12  C1      0.00   0.0  0
 BWA  CONST_02  C10  C9   C8   C1      0.00   0.0  0
 BWA  CONST_03  C8   C1   C12  C11     0.00   0.0  0
 BWA  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 BWA  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 BWA  CONST_06  C9   C8   C1   C12     0.00   0.0  0
 BWA  CONST_07  C16  C15  N14  C13     0.00   0.0  0
 BWA  CONST_08  C16  C17  C7   C13     0.00   0.0  0
 BWA  CONST_09  C7   C17  C16  C15     0.00   0.0  0
 BWA  CONST_10  C7   C13  N14  C15     0.00   0.0  0
 BWA  CONST_11  N14  C15  C16  C17     0.00   0.0  0
 BWA  CONST_12  N14  C13  C7   C17     0.00   0.0  0
 BWA  CONST_13  C26  C27  C22  C21     0.00   0.0  0
 BWA  CONST_14  C26  C25  C24  C21     0.00   0.0  0
 BWA  CONST_15  C25  C26  C27  C22     0.00   0.0  0
 BWA  CONST_16  C25  C24  C21  C22     0.00   0.0  0
 BWA  CONST_17  C27  C22  C21  C24     0.00   0.0  0
 BWA  CONST_18  C27  C26  C25  C24     0.00   0.0  0
 BWA  CONST_19  C23  N19  C20  C21     0.00   0.0  0
 BWA  CONST_20  N2   C1   C12  C11   180.00   0.0  0
 BWA  CONST_21  C18  C10  C11  C12   180.00   0.0  0
 BWA  CONST_22  C6   C7   C17  C16   180.00   0.0  0
 BWA  CONST_23  C8   C9   C10  C18   180.00   0.0  0
 BWA  CONST_24  C9   C8   C1   N2    180.00   0.0  0
 BWA  CONST_25  N14  C13  C7   C6    180.00   0.0  0
 BWA  CONST_26  C21  C20  N19  C18   180.00   0.0  0
 BWA  CONST_27  O28  C20  N19  C23   180.00   0.0  0
 BWA  CONST_28  H1   C11  C12  C1    180.00   0.0  0
 BWA  CONST_29  H18  C9   C8   C1    180.00   0.0  0
 BWA  CONST_30  H17  C8   C1   C12   180.00   0.0  0
 BWA  CONST_31  H4   C15  N14  C13   180.00   0.0  0
 BWA  CONST_32  H6   C17  C7   C13   180.00   0.0  0
 BWA  CONST_33  H3   C13  N14  C15   180.00   0.0  0
 BWA  CONST_34  H9   C24  C21  C20     0.00   0.0  0
 BWA  CONST_35  H12  C27  C22  C21   180.00   0.0  0
 BWA  CONST_36  H10  C25  C24  C21   180.00   0.0  0
 BWA  CONST_37  H11  C26  C27  C22   180.00   0.0  0
 BWA  CONST_38  H5   C16  C17  C7    180.00   0.0  0
 BWA  CONST_39  H2   C12  C1   C8    180.00   0.0  0
 BWA  CONST_42  O28  C20  N19  C18     0.00   0.0  0
 BWA  CONST_43  H13  N2   C1   C12     0.00   0.0  0
 BWA  CONST_44  O5   C3   N2   C1      0.00   0.0  0
 BWA  CONST_45  N4   C3   N2   C1    180.00   0.0  0
 BWA  CONST_46  C6   N4   C3   O5      0.00   0.0  0
 BWA  CONST_47  C6   N4   C3   N2    180.00   0.0  0
 BWA  CONST_48  H14  N4   C3   O5    180.00   0.0  0
 BWA  Var_01    N19  C18  C10  C11    91.15  30.0  2
 BWA  Var_02    C10  C18  N19  C20   -86.98  30.0  2
 BWA  Var_03    N4   C6   C7   C13    96.70  30.0  2
 BWA  Var_04    C7   C6   N4   C3   -179.39  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
 BWA  plan-1  C1   0.020
 BWA  plan-1  C11  0.020
 BWA  plan-1  C12  0.020
 BWA  plan-1  N2   0.020
 BWA  plan-1  C8   0.020
 BWA  plan-1  C9   0.020
 BWA  plan-1  C10  0.020
 BWA  plan-1  H1   0.020
 BWA  plan-1  H2   0.020
 BWA  plan-1  H17  0.020
 BWA  plan-1  H18  0.020
 BWA  plan-1  C18  0.020
 BWA  plan-2  C13  0.020
 BWA  plan-2  C15  0.020
 BWA  plan-2  C16  0.020
 BWA  plan-2  C17  0.020
 BWA  plan-2  C6   0.020
 BWA  plan-2  C7   0.020
 BWA  plan-2  N14  0.020
 BWA  plan-2  H3   0.020
 BWA  plan-2  H4   0.020
 BWA  plan-2  H5   0.020
 BWA  plan-2  H6   0.020
 BWA  plan-3  C20  0.020
 BWA  plan-3  C21  0.020
 BWA  plan-3  C22  0.020
 BWA  plan-3  C23  0.020
 BWA  plan-3  C24  0.020
 BWA  plan-3  C25  0.020
 BWA  plan-3  C26  0.020
 BWA  plan-3  C27  0.020
 BWA  plan-3  N19  0.020
 BWA  plan-3  O29  0.020
 BWA  plan-3  H9   0.020
 BWA  plan-3  H10  0.020
 BWA  plan-3  H11  0.020
 BWA  plan-3  H12  0.020
 BWA  plan-3  C18  0.020
 BWA  plan-3  O28  0.020
 BWA  plan-4  C1   0.020
 BWA  plan-4  C3   0.020
 BWA  plan-4  N2   0.020
 BWA  plan-4  N4   0.020
 BWA  plan-4  O5   0.020
 BWA  plan-4  C6   0.020
 BWA  plan-4  H13  0.020
 BWA  plan-4  H14  0.020

