# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:29:37 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 5-[2-cyclopropyl-6-(3,5-dimethyl-1,2-oxazol-4-yl)-1H-benzimidazol-4-yl]-6-methylquinoline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(C)c1c2cc3[nH]c(nc3c(c2)c4c(C)ccc5ncccc45)C6CC6
#
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
 JW4  JW4  5-[2-cyclopropyl-6-(3,5-dimethyl-1,2-oxazol-4-yl)-1H-benzimidazol-4-yl]-6-methylquinoline  ligand  52  30  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JW4
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
 JW4  C01  C  CR6   0   0.039  -2.0352  -0.2141   0.1305
 JW4  C02  C  CR16  0  -0.372  -1.8032  -1.5827   0.2298
 JW4  C03  C  CR56  0   0.369  -0.5053  -2.0192   0.0231
 JW4  C04  C  CR56  0   0.116   0.5537  -1.1508  -0.2855
 JW4  C05  C  CR6   0  -0.068   0.3215   0.2219  -0.3844
 JW4  C06  C  CR16  0  -0.371  -0.9748   0.6628  -0.1637
 JW4  C07  C  CR6   0   0.055   1.4204   1.1634  -0.6981
 JW4  C08  C  CR5   0  -0.190  -3.3832   0.3226   0.3313
 JW4  C09  C  CR5   0   0.249  -4.2907   0.0527   1.3996
 JW4  N10  N  N     0  -0.183  -5.3892   0.7348   1.2607
 JW4  O11  O  O     0  -0.346  -5.2509   1.4587   0.1115
 JW4  C12  C  CR5   0   0.415  -4.0605   1.2147  -0.4410
 JW4  C13  C  CH3   0  -0.762  -3.7354   1.9034  -1.7105
 JW4  C14  C  CH3   0  -0.749  -4.0929  -0.8544   2.5616
 JW4  N15  N  NR15  0  -0.737   0.0652  -3.2641   0.0405
 JW4  C16  C  CR5   0   0.506   1.3881  -3.1128  -0.2446
 JW4  N17  N  N     0  -0.476   1.7161  -1.8619  -0.4442
 JW4  C18  C  CH1   0  -0.396   2.3335  -4.2292  -0.3125
 JW4  C19  C  CH2   0  -0.476   1.8875  -5.5981  -0.7569
 JW4  C20  C  CH2   0  -0.475   2.2470  -5.3715   0.6688
 JW4  C21  C  CR66  0   0.063   1.9542   1.9835   0.3332
 JW4  C22  C  CR66  0   0.185   2.9984   2.8975   0.0404
 JW4  C23  C  CR16  0  -0.293   3.4944   2.9636  -1.2783
 JW4  C24  C  CR16  0  -0.298   2.9697   2.1587  -2.2495
 JW4  C25  C  CR6   0   0.051   1.9247   1.2444  -1.9793
 JW4  C26  C  CR16  0  -0.206   1.5051   1.9313   1.6737
 JW4  C27  C  CR16  0  -0.325   2.0694   2.7557   2.6051
 JW4  C28  C  CR16  0  -0.088   3.0917   3.6380   2.2004
 JW4  N29  N  N     0  -0.431   3.5440   3.7098   0.9778
 JW4  C30  C  CH3   0  -0.744   1.3877   0.3901  -3.0901
 JW4  H1   H  HCR6  0   0.260  -2.6065  -2.2778   0.4366
 JW4  H2   H  HCR6  0   0.248  -1.1738   1.7271  -0.2050
 JW4  H3   H  HCH3  0   0.273  -4.5891   1.9004  -2.3878
 JW4  H4   H  HCH3  0   0.272  -3.4487   2.9423  -1.5394
 JW4  H5   H  HCH3  0   0.263  -2.9040   1.4050  -2.2051
 JW4  H6   H  HCH3  0   0.257  -3.0944  -0.7306   2.9797
 JW4  H7   H  HCH3  0   0.265  -4.8258  -0.6534   3.3405
 JW4  H8   H  HCH3  0   0.260  -4.1944  -1.8989   2.2644
 JW4  H9   H  HNR5  0   0.422  -0.4143  -4.1299   0.2329
 JW4  H11  H  HCH1  0   0.282   3.3261  -3.9170  -0.6098
 JW4  H12  H  HCH2  0   0.261   0.8438  -5.7364  -1.0101
 JW4  H13  H  HCH2  0   0.274   2.5720  -6.1543  -1.3829
 JW4  H14  H  HCH2  0   0.273   3.1831  -5.7692   1.0370
 JW4  H15  H  HCH2  0   0.262   1.4534  -5.3471   1.4047
 JW4  H16  H  HCR6  0   0.259   4.2917   3.6615  -1.4998
 JW4  H17  H  HCR6  0   0.256   3.3569   2.2214  -3.2592
 JW4  H18  H  HCR6  0   0.269   0.7212   1.2405   1.9560
 JW4  H19  H  HCR6  0   0.271   1.7489   2.7399   3.6374
 JW4  H20  H  HCR6  0   0.263   3.5449   4.3018   2.9293
 JW4  H21  H  HCH3  0   0.255   1.7018  -0.6487  -2.9739
 JW4  H22  H  HCH3  0   0.246   0.2975   0.3936  -3.1114
 JW4  H23  H  HCH3  0   0.249   1.7443   0.7366  -4.0589

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
 JW4  C13  C12  single    1.480  0.020  1.480
 JW4  C30  C25  single    1.501  0.020  1.501
 JW4  C24  C25  aromatic  1.415  0.020  1.415
 JW4  C24  C23  aromatic  1.366  0.020  1.366
 JW4  C25  C07  aromatic  1.379  0.020  1.379
 JW4  C12  O11  aromatic  1.335  0.020  1.335
 JW4  C12  C08  aromatic  1.361  0.020  1.361
 JW4  O11  N10  aromatic  1.365  0.020  1.365
 JW4  C23  C22  aromatic  1.411  0.020  1.411
 JW4  C07  C05  single    1.481  0.020  1.481
 JW4  C07  C21  aromatic  1.422  0.020  1.422
 JW4  C06  C05  aromatic  1.387  0.020  1.387
 JW4  C06  C01  aromatic  1.407  0.020  1.407
 JW4  C08  C01  single    1.465  0.020  1.465
 JW4  C08  C09  aromatic  1.427  0.020  1.427
 JW4  N10  C09  aromatic  1.300  0.020  1.300
 JW4  C22  C21  aromatic  1.418  0.020  1.418
 JW4  C22  N29  aromatic  1.355  0.020  1.355
 JW4  C05  C04  aromatic  1.396  0.020  1.396
 JW4  C01  C02  aromatic  1.392  0.020  1.392
 JW4  C21  C26  aromatic  1.415  0.020  1.415
 JW4  N29  C28  aromatic  1.306  0.020  1.306
 JW4  C09  C14  single    1.487  0.020  1.487
 JW4  C04  C03  aromatic  1.404  0.020  1.404
 JW4  C04  N17  aromatic  1.372  0.020  1.372
 JW4  C02  C03  aromatic  1.385  0.020  1.385
 JW4  C03  N15  aromatic  1.369  0.020  1.369
 JW4  N17  C16  aromatic  1.309  0.020  1.309
 JW4  C26  C27  aromatic  1.366  0.020  1.366
 JW4  C28  C27  aromatic  1.410  0.020  1.410
 JW4  C16  N15  aromatic  1.362  0.020  1.362
 JW4  C16  C18  single    1.464  0.020  1.464
 JW4  C18  C20  single    1.508  0.020  1.508
 JW4  C18  C19  single    1.507  0.020  1.507
 JW4  C20  C19  single    1.488  0.020  1.488
 JW4  C02  H1   single    0.930  0.020  1.080
 JW4  C06  H2   single    0.930  0.020  1.080
 JW4  C13  H3   single    0.970  0.020  1.090
 JW4  C13  H4   single    0.970  0.020  1.090
 JW4  C13  H5   single    0.970  0.020  1.090
 JW4  C14  H6   single    0.970  0.020  1.090
 JW4  C14  H7   single    0.970  0.020  1.090
 JW4  C14  H8   single    0.970  0.020  1.090
 JW4  N15  H9   single    0.860  0.020  1.020
 JW4  C18  H11  single    0.970  0.020  1.090
 JW4  C19  H12  single    0.970  0.020  1.090
 JW4  C19  H13  single    0.970  0.020  1.090
 JW4  C20  H14  single    0.970  0.020  1.090
 JW4  C20  H15  single    0.970  0.020  1.090
 JW4  C23  H16  single    0.930  0.020  1.080
 JW4  C24  H17  single    0.930  0.020  1.080
 JW4  C26  H18  single    0.930  0.020  1.080
 JW4  C27  H19  single    0.930  0.020  1.080
 JW4  C28  H20  single    0.930  0.020  1.080
 JW4  C30  H21  single    0.970  0.020  1.090
 JW4  C30  H22  single    0.970  0.020  1.090
 JW4  C30  H23  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
 JW4  C08  C01  C06  119.59  3.000
 JW4  C08  C01  C02  120.26  3.000
 JW4  C06  C01  C02  120.15  3.000
 JW4  H1   C02  C03  121.45  3.000
 JW4  H1   C02  C01  121.44  3.000
 JW4  C03  C02  C01  117.10  3.000
 JW4  N15  C03  C04  104.53  3.000
 JW4  N15  C03  C02  132.46  3.000
 JW4  C04  C03  C02  123.01  3.000
 JW4  N17  C04  C05  129.98  3.000
 JW4  N17  C04  C03  110.12  3.000
 JW4  C05  C04  C03  119.90  3.000
 JW4  C07  C05  C06  121.69  3.000
 JW4  C06  C05  C04  117.18  3.000
 JW4  C07  C05  C04  121.12  3.000
 JW4  H2   C06  C05  118.54  3.000
 JW4  H2   C06  C01  118.80  3.000
 JW4  C05  C06  C01  122.65  3.000
 JW4  C25  C07  C21  120.18  3.000
 JW4  C21  C07  C05  119.45  3.000
 JW4  C25  C07  C05  120.37  3.000
 JW4  C12  C08  C09  103.43  3.000
 JW4  C09  C08  C01  128.20  3.000
 JW4  C12  C08  C01  128.36  3.000
 JW4  C14  C09  N10  121.04  3.000
 JW4  C14  C09  C08  127.98  3.000
 JW4  N10  C09  C08  110.97  3.000
 JW4  O11  N10  C09  106.41  3.000
 JW4  C12  O11  N10  109.99  3.000
 JW4  C13  C12  O11  117.76  3.000
 JW4  O11  C12  C08  109.20  3.000
 JW4  C13  C12  C08  133.04  3.000
 JW4  H5   C13  H4   107.85  3.000
 JW4  H5   C13  H3   108.35  3.000
 JW4  H4   C13  H3   107.81  3.000
 JW4  H5   C13  C12  110.15  3.000
 JW4  H4   C13  C12  111.48  3.000
 JW4  H3   C13  C12  111.07  3.000
 JW4  H8   C14  H7   108.01  3.000
 JW4  H8   C14  H6   107.38  3.000
 JW4  H7   C14  H6   108.76  3.000
 JW4  H8   C14  C09  111.03  3.000
 JW4  H7   C14  C09  110.91  3.000
 JW4  H6   C14  C09  110.64  3.000
 JW4  H9   N15  C16  126.68  3.000
 JW4  H9   N15  C03  125.80  3.000
 JW4  C16  N15  C03  107.52  3.000
 JW4  C18  C16  N17  124.04  3.000
 JW4  C18  C16  N15  123.52  3.000
 JW4  N17  C16  N15  112.44  3.000
 JW4  C16  N17  C04  105.39  3.000
 JW4  H11  C18  C20  116.73  3.000
 JW4  H11  C18  C19  116.91  3.000
 JW4  C20  C18  C19   59.13  3.000
 JW4  H11  C18  C16  112.64  3.000
 JW4  C19  C18  C16  121.01  3.000
 JW4  C20  C18  C16  120.67  3.000
 JW4  H13  C19  H12  114.14  3.000
 JW4  H13  C19  C20  118.69  3.000
 JW4  H12  C19  C20  118.46  3.000
 JW4  H13  C19  C18  116.78  3.000
 JW4  H12  C19  C18  118.06  3.000
 JW4  C20  C19  C18   60.49  3.000
 JW4  H15  C20  H14  114.30  3.000
 JW4  H15  C20  C19  118.53  3.000
 JW4  H14  C20  C19  118.64  3.000
 JW4  H15  C20  C18  117.85  3.000
 JW4  H14  C20  C18  116.76  3.000
 JW4  C19  C20  C18   60.38  3.000
 JW4  C26  C21  C22  116.94  3.000
 JW4  C26  C21  C07  123.16  3.000
 JW4  C22  C21  C07  119.89  3.000
 JW4  N29  C22  C23  118.49  3.000
 JW4  N29  C22  C21  122.68  3.000
 JW4  C23  C22  C21  118.82  3.000
 JW4  H16  C23  C24  121.15  3.000
 JW4  H16  C23  C22  118.72  3.000
 JW4  C24  C23  C22  120.13  3.000
 JW4  H17  C24  C25  118.66  3.000
 JW4  H17  C24  C23  119.42  3.000
 JW4  C25  C24  C23  121.93  3.000
 JW4  C30  C25  C24  119.40  3.000
 JW4  C24  C25  C07  119.04  3.000
 JW4  C30  C25  C07  121.56  3.000
 JW4  H18  C26  C27  120.44  3.000
 JW4  H18  C26  C21  120.04  3.000
 JW4  C27  C26  C21  119.52  3.000
 JW4  H19  C27  C28  119.89  3.000
 JW4  H19  C27  C26  121.32  3.000
 JW4  C28  C27  C26  118.79  3.000
 JW4  H20  C28  N29  116.79  3.000
 JW4  H20  C28  C27  119.53  3.000
 JW4  N29  C28  C27  123.68  3.000
 JW4  C28  N29  C22  118.38  3.000
 JW4  H23  C30  H22  108.00  3.000
 JW4  H23  C30  H21  107.66  3.000
 JW4  H22  C30  H21  107.03  3.000
 JW4  H23  C30  C25  111.12  3.000
 JW4  H22  C30  C25  111.74  3.000
 JW4  H21  C30  C25  111.10  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
 JW4  CONST_01  C07  C05  C06  C01  180.00   0.0  0
 JW4  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 JW4  CONST_03  O11  C12  C08  C01  180.00   0.0  0
 JW4  CONST_04  N10  C09  C08  C01  180.00   0.0  0
 JW4  CONST_05  C04  C03  C02  C01    0.00   0.0  0
 JW4  CONST_06  N15  C03  C02  C01  180.00   0.0  0
 JW4  CONST_07  C05  C06  C01  C02    0.00   0.0  0
 JW4  CONST_10  C05  C04  C03  C02    0.00   0.0  0
 JW4  CONST_11  N17  C04  C03  C02  180.00   0.0  0
 JW4  CONST_12  C16  N15  C03  C02  180.00   0.0  0
 JW4  CONST_13  C07  C05  C04  C03  180.00   0.0  0
 JW4  CONST_14  C06  C05  C04  C03    0.00   0.0  0
 JW4  CONST_15  C16  N17  C04  C03    0.00   0.0  0
 JW4  CONST_16  C06  C01  C02  C03    0.00   0.0  0
 JW4  CONST_17  C08  C01  C02  C03  180.00   0.0  0
 JW4  CONST_18  N17  C16  N15  C03    0.00   0.0  0
 JW4  CONST_21  C16  N15  C03  C04    0.00   0.0  0
 JW4  CONST_22  N15  C16  N17  C04    0.00   0.0  0
 JW4  CONST_23  C24  C25  C07  C05  180.00   0.0  0
 JW4  CONST_24  C22  C21  C07  C05  180.00   0.0  0
 JW4  CONST_25  C26  C21  C07  C05    0.00   0.0  0
 JW4  CONST_26  C08  C01  C06  C05  180.00   0.0  0
 JW4  CONST_27  N15  C03  C04  C05  180.00   0.0  0
 JW4  CONST_28  C16  N17  C04  C05  180.00   0.0  0
 JW4  CONST_31  N17  C04  C05  C06  180.00   0.0  0
 JW4  CONST_34  C23  C24  C25  C07    0.00   0.0  0
 JW4  CONST_35  N17  C04  C05  C07    0.00   0.0  0
 JW4  CONST_36  C23  C22  C21  C07    0.00   0.0  0
 JW4  CONST_37  N29  C22  C21  C07  180.00   0.0  0
 JW4  CONST_38  C27  C26  C21  C07  180.00   0.0  0
 JW4  CONST_39  N10  O11  C12  C08    0.00   0.0  0
 JW4  CONST_40  O11  N10  C09  C08    0.00   0.0  0
 JW4  CONST_41  O11  C12  C08  C09    0.00   0.0  0
 JW4  CONST_42  C12  O11  N10  C09    0.00   0.0  0
 JW4  CONST_43  C12  C08  C09  N10    0.00   0.0  0
 JW4  CONST_44  N17  C04  C03  N15    0.00   0.0  0
 JW4  CONST_45  C24  C25  C07  C21    0.00   0.0  0
 JW4  CONST_46  C24  C23  C22  C21    0.00   0.0  0
 JW4  CONST_47  C28  N29  C22  C21    0.00   0.0  0
 JW4  CONST_48  C28  C27  C26  C21    0.00   0.0  0
 JW4  CONST_49  C25  C24  C23  C22    0.00   0.0  0
 JW4  CONST_50  C25  C07  C21  C22    0.00   0.0  0
 JW4  CONST_51  C27  C26  C21  C22    0.00   0.0  0
 JW4  CONST_52  C27  C28  N29  C22    0.00   0.0  0
 JW4  CONST_53  C26  C21  C22  C23  180.00   0.0  0
 JW4  CONST_54  C28  N29  C22  C23  180.00   0.0  0
 JW4  CONST_55  N29  C22  C23  C24  180.00   0.0  0
 JW4  CONST_56  C26  C21  C07  C25  180.00   0.0  0
 JW4  CONST_57  N29  C22  C21  C26    0.00   0.0  0
 JW4  CONST_58  N29  C28  C27  C26    0.00   0.0  0
 JW4  CONST_59  C18  C16  N15  C03  180.00   0.0  0
 JW4  CONST_60  C18  C16  N17  C04  180.00   0.0  0
 JW4  CONST_61  C13  C12  C08  C01    0.00   0.0  0
 JW4  CONST_62  C14  C09  C08  C01    0.00   0.0  0
 JW4  CONST_63  C30  C25  C07  C05    0.00   0.0  0
 JW4  CONST_64  C13  C12  C08  C09  180.00   0.0  0
 JW4  CONST_65  C13  C12  O11  N10  180.00   0.0  0
 JW4  CONST_66  C14  C09  N10  O11  180.00   0.0  0
 JW4  CONST_67  C14  C09  C08  C12  180.00   0.0  0
 JW4  CONST_68  C30  C25  C07  C21  180.00   0.0  0
 JW4  CONST_69  C30  C25  C24  C23  180.00   0.0  0
 JW4  CONST_70  H2   C06  C01  C02  180.00   0.0  0
 JW4  CONST_71  H9   N15  C03  C02    0.00   0.0  0
 JW4  CONST_72  H1   C02  C03  C04  180.00   0.0  0
 JW4  CONST_73  H17  C24  C25  C07  180.00   0.0  0
 JW4  CONST_74  H18  C26  C21  C07    0.00   0.0  0
 JW4  CONST_75  H16  C23  C22  C21  180.00   0.0  0
 JW4  CONST_76  H19  C27  C26  C21  180.00   0.0  0
 JW4  CONST_77  H20  C28  N29  C22  180.00   0.0  0
 JW4  Var_01    C20  C18  C16  N15  -38.95  30.0  2
 JW4  Var_02    C19  C20  C18  C16  110.07  30.0  1
 JW4  Var_03    H21  C30  C25  C07  -72.58  30.0  2
 JW4  Var_04    H3   C13  C12  C08  136.60  30.0  2
 JW4  Var_05    H6   C14  C09  C08   43.65  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
 JW4  chir_01  C18  C16  C20  C19  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
 JW4  plan-1  C01  0.020
 JW4  plan-1  C08  0.020
 JW4  plan-1  C09  0.020
 JW4  plan-1  N10  0.020
 JW4  plan-1  O11  0.020
 JW4  plan-1  C12  0.020
 JW4  plan-1  C13  0.020
 JW4  plan-1  C14  0.020
 JW4  plan-2  C01  0.020
 JW4  plan-2  C02  0.020
 JW4  plan-2  C03  0.020
 JW4  plan-2  C04  0.020
 JW4  plan-2  C05  0.020
 JW4  plan-2  C06  0.020
 JW4  plan-2  C07  0.020
 JW4  plan-2  C08  0.020
 JW4  plan-2  N15  0.020
 JW4  plan-2  C16  0.020
 JW4  plan-2  N17  0.020
 JW4  plan-2  C18  0.020
 JW4  plan-2  H1   0.020
 JW4  plan-2  H2   0.020
 JW4  plan-2  H9   0.020
 JW4  plan-3  C05  0.020
 JW4  plan-3  C07  0.020
 JW4  plan-3  C21  0.020
 JW4  plan-3  C22  0.020
 JW4  plan-3  C23  0.020
 JW4  plan-3  C24  0.020
 JW4  plan-3  C25  0.020
 JW4  plan-3  C26  0.020
 JW4  plan-3  C27  0.020
 JW4  plan-3  C28  0.020
 JW4  plan-3  N29  0.020
 JW4  plan-3  C30  0.020
 JW4  plan-3  H16  0.020
 JW4  plan-3  H17  0.020
 JW4  plan-3  H18  0.020
 JW4  plan-3  H19  0.020
 JW4  plan-3  H20  0.020

