# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 20:58:48 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 3-[3-[5-(1-oxa-4$l^{4}-azacyclohex-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl]-1-phenyl-urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccccc1)Nc2c[nH]nc2c3[nH]c4ccc(C[NH]5CCOCC5)cc4n3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 L0E  L0E  3-[3-[5-(1-oxa-4$l^{4}-azacyclohex-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl]-1-phenyl-urea  ligand  55  31  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L0E
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
 L0E  O1   O  O     0  -0.512  6.7781  28.3044   7.3572
 L0E  C2   C  C     0   0.661  6.3387  28.8523   6.3568
 L0E  N3   N  NH1   0  -0.783  5.4361  29.8681   6.4086
 L0E  C4   C  CR5   0   0.123  4.9929  30.4629   7.5749
 L0E  C5   C  CR15  0  -0.019  5.2548  30.2081   8.9045
 L0E  N6   N  NR15  0  -0.415  4.5476  31.1289   9.5964
 L0E  N8   N  N     0  -0.272  3.8537  31.9500   8.8455
 L0E  C9   C  CR5   0   0.104  4.1076  31.5654   7.6020
 L0E  C10  C  CR5   0   0.530  3.5413  32.2147   6.4464
 L0E  N11  N  N     0  -0.540  3.7344  31.7827   5.2246
 L0E  C12  C  CR56  0   0.205  3.0625  32.6621   4.4194
 L0E  C13  C  CR16  0  -0.368  2.9296  32.6821   3.0361
 L0E  C14  C  CR6   0   0.088  2.1916  33.7066   2.4608
 L0E  C15  C  CH2   0  -0.430  2.0319  33.7603   0.9740
 L0E  N16  N  NT1   1  -0.525  3.1031  34.5586   0.2730
 L0E  C18  C  CH2   0  -0.351  4.4708  33.9835   0.4226
 L0E  C19  C  CH2   0  -0.201  5.4625  34.8108  -0.3731
 L0E  O20  O  O2    0  -0.464  5.4505  36.1556   0.0334
 L0E  C21  C  CH2   0  -0.205  4.1804  36.7272  -0.1596
 L0E  C22  C  CH2   0  -0.344  3.1163  36.0031   0.6439
 L0E  C23  C  CR16  0  -0.305  1.5696  34.6771   3.2678
 L0E  C24  C  CR16  0  -0.299  1.6835  34.6695   4.6460
 L0E  C25  C  CR56  0   0.321  2.4437  33.6508   5.2049
 L0E  N26  N  NR15  0  -0.709  2.7706  33.3309   6.4938
 L0E  N28  N  NH1   0  -0.764  6.7218  28.4672   5.1015
 L0E  C29  C  CR6   0   0.270  6.3522  29.0541   3.8749
 L0E  C30  C  CR16  0  -0.281  5.7492  28.2723   2.8927
 L0E  C31  C  CR16  0  -0.254  5.4176  28.8287   1.6664
 L0E  C32  C  CR16  0  -0.264  5.6669  30.1719   1.4156
 L0E  C33  C  CR16  0  -0.255  6.2654  30.9521   2.3953
 L0E  C34  C  CR16  0  -0.276  6.6203  30.3967   3.6158
 L0E  H7   H  HNR5  0   0.431  4.5145  31.2210  10.5995
 L0E  H17  H  HNT1  0   0.469  2.8598  34.5021  -0.7192
 L0E  H27  H  HNR5  0   0.427  2.5093  33.8343   7.3277
 L0E  H35  H  HNH1  0   0.448  5.0213  30.2560   5.5642
 L0E  H36  H  HCR5  0   0.302  5.8625  29.4732   9.3988
 L0E  H37  H  HCR6  0   0.264  3.3902  31.9060   2.4359
 L0E  H38  H  HCH2  0   0.322  2.0750  32.7665   0.5310
 L0E  H39  H  HCH2  0   0.325  1.0879  34.2183   0.6829
 L0E  H40  H  HCH2  0   0.303  4.4448  32.9579   0.0559
 L0E  H41  H  HCH2  0   0.304  4.7142  33.9877   1.4843
 L0E  H42  H  HCH2  0   0.238  5.2459  34.7209  -1.4465
 L0E  H43  H  HCH2  0   0.280  6.4625  34.4136  -0.2025
 L0E  H44  H  HCH2  0   0.237  3.9085  36.7291  -1.2241
 L0E  H45  H  HCH2  0   0.281  4.2202  37.7636   0.1739
 L0E  H46  H  HCH2  0   0.313  2.1301  36.4149   0.4362
 L0E  H47  H  HCH2  0   0.305  3.3181  36.0672   1.7120
 L0E  H48  H  HCR6  0   0.268  0.9747  35.4513   2.7989
 L0E  H49  H  HCR6  0   0.277  1.1963  35.4212   5.2518
 L0E  H50  H  HNH1  0   0.408  7.2071  27.5833   5.0649
 L0E  H51  H  HCR6  0   0.269  5.5385  27.2293   3.0930
 L0E  H52  H  HCR6  0   0.264  4.9538  28.2122   0.9075
 L0E  H53  H  HCR6  0   0.261  5.4037  30.6005   0.4569
 L0E  H54  H  HCR6  0   0.259  6.4835  31.9957   2.2067
 L0E  H55  H  HCR6  0   0.278  7.1195  31.0041   4.3601

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
 L0E  C2   O1   double    1.222  0.020  1.222
 L0E  N28  C2   single    1.368  0.020  1.368
 L0E  C2   N3   single    1.360  0.020  1.360
 L0E  H35  N3   single    0.860  0.020  1.020
 L0E  N3   C4   single    1.382  0.020  1.382
 L0E  C9   C4   aromatic  1.414  0.020  1.414
 L0E  C4   C5   aromatic  1.379  0.020  1.379
 L0E  C5   H36  single    0.930  0.020  1.080
 L0E  C5   N6   aromatic  1.352  0.020  1.352
 L0E  N8   N6   aromatic  1.311  0.020  1.311
 L0E  N6   H7   single    0.860  0.020  1.020
 L0E  C9   N8   aromatic  1.326  0.020  1.326
 L0E  C10  C9   single    1.441  0.020  1.441
 L0E  N11  C10  aromatic  1.310  0.020  1.310
 L0E  C10  N26  aromatic  1.357  0.020  1.357
 L0E  C12  N11  aromatic  1.369  0.020  1.369
 L0E  C13  C12  aromatic  1.390  0.020  1.390
 L0E  C12  C25  aromatic  1.406  0.020  1.406
 L0E  C14  C13  aromatic  1.388  0.020  1.388
 L0E  H37  C13  single    0.930  0.020  1.080
 L0E  C15  C14  single    1.496  0.020  1.496
 L0E  C14  C23  aromatic  1.407  0.020  1.407
 L0E  N16  C15  single    1.509  0.020  1.509
 L0E  H38  C15  single    0.970  0.020  1.090
 L0E  H39  C15  single    0.970  0.020  1.090
 L0E  H17  N16  single    0.890  0.020  1.040
 L0E  N16  C18  single    1.491  0.020  1.491
 L0E  N16  C22  single    1.491  0.020  1.491
 L0E  C19  C18  single    1.517  0.020  1.517
 L0E  H41  C18  single    0.970  0.020  1.090
 L0E  C18  H40  single    0.970  0.020  1.090
 L0E  H43  C19  single    0.970  0.020  1.090
 L0E  C19  H42  single    0.970  0.020  1.090
 L0E  C19  O20  single    1.405  0.020  1.405
 L0E  C21  O20  single    1.406  0.020  1.406
 L0E  H45  C21  single    0.970  0.020  1.090
 L0E  C21  H44  single    0.970  0.020  1.090
 L0E  C21  C22  single    1.517  0.020  1.517
 L0E  C22  H46  single    0.970  0.020  1.090
 L0E  C22  H47  single    0.970  0.020  1.090
 L0E  H48  C23  single    0.930  0.020  1.080
 L0E  C23  C24  aromatic  1.383  0.020  1.383
 L0E  C24  H49  single    0.930  0.020  1.080
 L0E  C24  C25  aromatic  1.389  0.020  1.389
 L0E  C25  N26  aromatic  1.368  0.020  1.368
 L0E  N26  H27  single    0.860  0.020  1.020
 L0E  C29  N28  single    1.409  0.020  1.409
 L0E  H50  N28  single    0.860  0.020  1.020
 L0E  C30  C29  aromatic  1.393  0.020  1.393
 L0E  C34  C29  aromatic  1.393  0.020  1.393
 L0E  C31  C30  aromatic  1.387  0.020  1.387
 L0E  C30  H51  single    0.930  0.020  1.080
 L0E  H52  C31  single    0.930  0.020  1.080
 L0E  C32  C31  aromatic  1.389  0.020  1.389
 L0E  H53  C32  single    0.930  0.020  1.080
 L0E  C32  C33  aromatic  1.388  0.020  1.388
 L0E  H54  C33  single    0.930  0.020  1.080
 L0E  C33  C34  aromatic  1.387  0.020  1.387
 L0E  C34  H55  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
 L0E  N28  C2   N3   115.55  3.000
 L0E  N3   C2   O1   122.84  3.000
 L0E  N28  C2   O1   121.61  3.000
 L0E  H35  N3   C4   113.92  3.000
 L0E  C4   N3   C2   124.50  3.000
 L0E  H35  N3   C2   121.58  3.000
 L0E  C9   C4   C5   104.15  3.000
 L0E  C5   C4   N3   132.32  3.000
 L0E  C9   C4   N3   123.53  3.000
 L0E  H36  C5   N6   121.77  3.000
 L0E  N6   C5   C4   105.57  3.000
 L0E  H36  C5   C4   132.66  3.000
 L0E  H7   N6   N8   119.69  3.000
 L0E  H7   N6   C5   126.09  3.000
 L0E  N8   N6   C5   114.22  3.000
 L0E  C9   N8   N6   104.72  3.000
 L0E  C10  C9   N8   123.08  3.000
 L0E  C10  C9   C4   125.58  3.000
 L0E  N8   C9   C4   111.34  3.000
 L0E  N26  C10  N11  112.79  3.000
 L0E  N26  C10  C9   124.44  3.000
 L0E  N11  C10  C9   122.76  3.000
 L0E  C12  N11  C10  105.33  3.000
 L0E  C25  C12  C13  120.25  3.000
 L0E  C25  C12  N11  109.83  3.000
 L0E  C13  C12  N11  129.92  3.000
 L0E  H37  C13  C14  121.68  3.000
 L0E  H37  C13  C12  120.02  3.000
 L0E  C14  C13  C12  118.31  3.000
 L0E  C23  C14  C15  119.87  3.000
 L0E  C23  C14  C13  120.43  3.000
 L0E  C15  C14  C13  119.69  3.000
 L0E  H39  C15  H38  108.03  3.000
 L0E  H39  C15  N16  105.59  3.000
 L0E  H38  C15  N16  105.41  3.000
 L0E  H39  C15  C14  111.91  3.000
 L0E  H38  C15  C14  111.55  3.000
 L0E  N16  C15  C14  113.89  3.000
 L0E  H17  N16  C22  107.26  3.000
 L0E  C22  N16  C18  109.91  3.000
 L0E  H17  N16  C18  107.10  3.000
 L0E  C22  N16  C15  113.78  3.000
 L0E  C18  N16  C15  113.61  3.000
 L0E  H17  N16  C15  104.63  3.000
 L0E  H41  C18  H40  109.70  3.000
 L0E  H40  C18  C19  110.64  3.000
 L0E  H41  C18  C19  111.29  3.000
 L0E  H40  C18  N16  107.91  3.000
 L0E  H41  C18  N16  107.53  3.000
 L0E  C19  C18  N16  109.67  3.000
 L0E  H43  C19  H42  107.70  3.000
 L0E  H42  C19  O20  111.06  3.000
 L0E  H43  C19  O20  108.15  3.000
 L0E  O20  C19  C18  111.39  3.000
 L0E  H42  C19  C18  109.81  3.000
 L0E  H43  C19  C18  108.61  3.000
 L0E  C21  O20  C19  110.92  3.000
 L0E  H45  C21  H44  107.70  3.000
 L0E  H44  C21  C22  109.90  3.000
 L0E  H45  C21  C22  108.51  3.000
 L0E  C22  C21  O20  111.52  3.000
 L0E  H44  C21  O20  110.93  3.000
 L0E  H45  C21  O20  108.16  3.000
 L0E  H47  C22  H46  109.43  3.000
 L0E  H47  C22  C21  111.18  3.000
 L0E  H46  C22  C21  110.72  3.000
 L0E  H47  C22  N16  107.61  3.000
 L0E  H46  C22  N16  108.11  3.000
 L0E  C21  C22  N16  109.68  3.000
 L0E  H48  C23  C24  118.73  3.000
 L0E  C24  C23  C14  122.10  3.000
 L0E  H48  C23  C14  119.17  3.000
 L0E  H49  C24  C25  122.08  3.000
 L0E  C25  C24  C23  116.76  3.000
 L0E  H49  C24  C23  121.15  3.000
 L0E  N26  C25  C24  132.98  3.000
 L0E  N26  C25  C12  104.88  3.000
 L0E  C24  C25  C12  122.13  3.000
 L0E  H27  N26  C25  126.92  3.000
 L0E  H27  N26  C10  125.91  3.000
 L0E  C25  N26  C10  107.17  3.000
 L0E  H50  N28  C29  117.35  3.000
 L0E  H50  N28  C2   114.50  3.000
 L0E  C29  N28  C2   127.45  3.000
 L0E  C34  C29  C30  119.54  3.000
 L0E  C34  C29  N28  120.85  3.000
 L0E  C30  C29  N28  119.58  3.000
 L0E  H51  C30  C31  120.23  3.000
 L0E  H51  C30  C29  119.64  3.000
 L0E  C31  C30  C29  120.13  3.000
 L0E  H52  C31  C32  120.08  3.000
 L0E  C32  C31  C30  120.31  3.000
 L0E  H52  C31  C30  119.61  3.000
 L0E  H53  C32  C33  120.49  3.000
 L0E  C33  C32  C31  119.57  3.000
 L0E  H53  C32  C31  119.94  3.000
 L0E  H54  C33  C34  119.20  3.000
 L0E  C34  C33  C32  120.41  3.000
 L0E  H54  C33  C32  120.37  3.000
 L0E  H55  C34  C33  119.88  3.000
 L0E  H55  C34  C29  120.10  3.000
 L0E  C33  C34  C29  120.02  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
 L0E  CONST_01  N6   N8   C9   C4     0.00   0.0  0
 L0E  CONST_02  N11  C10  C9   C4     0.00   0.0  0
 L0E  CONST_03  N26  C10  C9   C4   180.00   0.0  0
 L0E  CONST_04  N8   N6   C5   C4     0.00   0.0  0
 L0E  CONST_05  N8   C9   C4   C5     0.00   0.0  0
 L0E  CONST_06  C10  C9   C4   C5   180.00   0.0  0
 L0E  CONST_07  C9   N8   N6   C5     0.00   0.0  0
 L0E  CONST_08  C9   C4   C5   N6     0.00   0.0  0
 L0E  CONST_09  C10  C9   N8   N6   180.00   0.0  0
 L0E  CONST_10  N11  C10  C9   N8   180.00   0.0  0
 L0E  CONST_11  N26  C10  C9   N8     0.00   0.0  0
 L0E  CONST_12  C12  N11  C10  C9   180.00   0.0  0
 L0E  CONST_13  C25  N26  C10  C9   180.00   0.0  0
 L0E  CONST_14  C13  C12  N11  C10  180.00   0.0  0
 L0E  CONST_15  C25  C12  N11  C10    0.00   0.0  0
 L0E  CONST_16  C12  C25  N26  C10    0.00   0.0  0
 L0E  CONST_17  C24  C25  N26  C10  180.00   0.0  0
 L0E  CONST_18  C25  N26  C10  N11    0.00   0.0  0
 L0E  CONST_19  C14  C13  C12  N11  180.00   0.0  0
 L0E  CONST_20  C24  C25  C12  N11  180.00   0.0  0
 L0E  CONST_21  N26  C25  C12  N11    0.00   0.0  0
 L0E  CONST_22  N26  C10  N11  C12    0.00   0.0  0
 L0E  CONST_23  C23  C14  C13  C12    0.00   0.0  0
 L0E  CONST_24  C23  C24  C25  C12    0.00   0.0  0
 L0E  CONST_25  C24  C25  C12  C13    0.00   0.0  0
 L0E  CONST_26  N26  C25  C12  C13  180.00   0.0  0
 L0E  CONST_27  C24  C23  C14  C13    0.00   0.0  0
 L0E  CONST_28  C25  C12  C13  C14    0.00   0.0  0
 L0E  CONST_29  C25  C24  C23  C14    0.00   0.0  0
 L0E  CONST_30  N26  C25  C24  C23  180.00   0.0  0
 L0E  CONST_31  C32  C31  C30  C29    0.00   0.0  0
 L0E  CONST_32  C32  C33  C34  C29    0.00   0.0  0
 L0E  CONST_33  C33  C34  C29  C30    0.00   0.0  0
 L0E  CONST_34  C33  C32  C31  C30    0.00   0.0  0
 L0E  CONST_35  C34  C29  C30  C31    0.00   0.0  0
 L0E  CONST_36  C34  C33  C32  C31    0.00   0.0  0
 L0E  CONST_37  N8   C9   C4   N3   180.00   0.0  0
 L0E  CONST_38  C10  C9   C4   N3     0.00   0.0  0
 L0E  CONST_39  N6   C5   C4   N3   180.00   0.0  0
 L0E  CONST_40  C15  C14  C13  C12  180.00   0.0  0
 L0E  CONST_41  C24  C23  C14  C15  180.00   0.0  0
 L0E  CONST_42  C31  C30  C29  N28  180.00   0.0  0
 L0E  CONST_43  C33  C34  C29  N28  180.00   0.0  0
 L0E  CONST_44  H7   N6   C5   C4   180.00   0.0  0
 L0E  CONST_45  H36  C5   N6   N8   180.00   0.0  0
 L0E  CONST_46  H27  N26  C10  C9     0.00   0.0  0
 L0E  CONST_47  H37  C13  C12  N11    0.00   0.0  0
 L0E  CONST_48  H49  C24  C25  C12  180.00   0.0  0
 L0E  CONST_49  H48  C23  C14  C13  180.00   0.0  0
 L0E  CONST_50  H52  C31  C30  C29  180.00   0.0  0
 L0E  CONST_51  H54  C33  C34  C29  180.00   0.0  0
 L0E  CONST_52  H55  C34  C29  C30  180.00   0.0  0
 L0E  CONST_53  H53  C32  C31  C30  180.00   0.0  0
 L0E  CONST_54  H51  C30  C31  C32  180.00   0.0  0
 L0E  CONST_57  C9   C4   N3   C2   180.00   0.0  0
 L0E  CONST_58  C5   C4   N3   C2     0.00   0.0  0
 L0E  CONST_59  H35  N3   C4   C5   180.00   0.0  0
 L0E  CONST_61  C29  N28  C2   O1   180.00   0.0  0
 L0E  CONST_62  C4   N3   C2   O1     0.00   0.0  0
 L0E  CONST_63  C29  N28  C2   N3     0.00   0.0  0
 L0E  CONST_64  N28  C2   N3   C4   180.00   0.0  0
 L0E  Var_01    O20  C19  C18  N16   57.53  30.0  1
 L0E  Var_02    O20  C21  C22  N16  -57.16  30.0  1
 L0E  Var_03    C22  C21  O20  C19   60.45  30.0  1
 L0E  Var_04    N16  C15  C14  C13  -90.37  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
 L0E  chir_01  N16  C15  C18  C22  positiv

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
 L0E  plan-1  N3   0.020
 L0E  plan-1  C4   0.020
 L0E  plan-1  C5   0.020
 L0E  plan-1  N6   0.020
 L0E  plan-1  N8   0.020
 L0E  plan-1  C9   0.020
 L0E  plan-1  C10  0.020
 L0E  plan-1  H7   0.020
 L0E  plan-1  H36  0.020
 L0E  plan-2  N28  0.020
 L0E  plan-2  C29  0.020
 L0E  plan-2  C30  0.020
 L0E  plan-2  C31  0.020
 L0E  plan-2  C32  0.020
 L0E  plan-2  C33  0.020
 L0E  plan-2  C34  0.020
 L0E  plan-2  H51  0.020
 L0E  plan-2  H52  0.020
 L0E  plan-2  H53  0.020
 L0E  plan-2  H54  0.020
 L0E  plan-2  H55  0.020
 L0E  plan-3  C9   0.020
 L0E  plan-3  C10  0.020
 L0E  plan-3  N11  0.020
 L0E  plan-3  C12  0.020
 L0E  plan-3  C13  0.020
 L0E  plan-3  C14  0.020
 L0E  plan-3  C15  0.020
 L0E  plan-3  C23  0.020
 L0E  plan-3  C24  0.020
 L0E  plan-3  C25  0.020
 L0E  plan-3  N26  0.020
 L0E  plan-3  H27  0.020
 L0E  plan-3  H37  0.020
 L0E  plan-3  H48  0.020
 L0E  plan-3  H49  0.020
 L0E  plan-4  O1   0.020
 L0E  plan-4  C2   0.020
 L0E  plan-4  N3   0.020
 L0E  plan-4  C4   0.020
 L0E  plan-4  N28  0.020
 L0E  plan-4  C29  0.020
 L0E  plan-4  H35  0.020
 L0E  plan-4  H50  0.020

