# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 21:37:38 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-chloranyl-3-[2-(5-methyl-1-phenyl-benzimidazol-2-yl)ethyl]chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2n(c(CCC3=COc4ccc(Cl)cc4C3=O)nc2c1)c5ccccc5
#
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
 DL0  DL0  6-chloranyl-3-[2-(5-methyl-1-phenyl-benzimidazol-2-yl)ethyl]chromen-4-one  ligand  49  30  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DL0
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
 DL0  C12  C   CH2   0  -0.503   0.0554   1.0860  -0.6392
 DL0  C13  C   CH2   0  -0.540   0.7538   0.9661   0.7255
 DL0  C14  C   CR5   0   0.428   2.2280   0.8358   0.5737
 DL0  C20  C   CR16  0  -0.311   6.5100  -0.2565  -0.2277
 DL0  C10  C   CR6   0   0.429  -2.2762   0.2077  -0.0708
 DL0  C9   C   CR6   0  -0.148  -1.4195   1.3031  -0.5009
 DL0  C8   C   CR16  0   0.027  -1.9673   2.5009  -0.7719
 DL0  O7   O   O     0  -0.424  -3.2666   2.7940  -0.6693
 DL0  C4   C   CR66  0   0.380  -4.1323   1.8397  -0.2733
 DL0  C5   C   CR66  0  -0.123  -3.7022   0.5532   0.0344
 DL0  C6   C   CR16  0  -0.246  -4.6456  -0.3969   0.4378
 DL0  C3   C   CR16  0  -0.330  -5.4764   2.1954  -0.1864
 DL0  C2   C   CR16  0  -0.202  -6.3955   1.2514   0.2122
 DL0  C1   C   CR6   0  -0.036  -5.9711  -0.0436   0.5214
 DL0  CL   CL  CL    0  -0.115  -7.1441  -1.2150   1.0180
 DL0  N15  N   NR5   0  -0.636   2.8338  -0.3393   0.2145
 DL0  C16  C   CR56  0   0.307   4.1798  -0.0742   0.0949
 DL0  C19  C   CR16  0  -0.289   5.2717  -0.8727  -0.2188
 DL0  C21  C   CR6   0   0.082   6.6762   1.1107   0.0695
 DL0  C29  C   CH3   0  -0.723   8.0515   1.7160   0.0268
 DL0  C22  C   CR16  0  -0.390   5.5701   1.8833   0.3883
 DL0  C17  C   CR56  0   0.154   4.3097   1.2850   0.4005
 DL0  N18  N   N     0  -0.474   3.0768   1.8199   0.6906
 DL0  C23  C   CR6   0   0.275   2.2244  -1.6063   0.0381
 DL0  C24  C   CR16  0  -0.264   2.1385  -2.1535  -1.2355
 DL0  C25  C   CR16  0  -0.258   1.5595  -3.4030  -1.4034
 DL0  C26  C   CR16  0  -0.243   1.0625  -4.0958  -0.3073
 DL0  C27  C   CR16  0  -0.253   1.1515  -3.5413   0.9623
 DL0  C28  C   CR16  0  -0.256   1.7416  -2.2986   1.1400
 DL0  H1   H   HCH2  0   0.266   0.4981   1.9145  -1.1954
 DL0  H2   H   HCH2  0   0.264   0.2283   0.1802  -1.2241
 DL0  H3   H   HCH2  0   0.274   0.5618   1.8652   1.3112
 DL0  H4   H   HCH2  0   0.279   0.3417   0.1219   1.2785
 DL0  H5   H   HCR6  0   0.247   7.3858  -0.8470  -0.4696
 DL0  H6   H   HCR6  0   0.307  -1.3938   3.3550  -1.1078
 DL0  H7   H   HCR6  0   0.290  -4.3195  -1.4005   0.6757
 DL0  H8   H   HCR6  0   0.297  -5.7906   3.2010  -0.4322
 DL0  H9   H   HCR6  0   0.297  -7.4417   1.5150   0.2840
 DL0  H10  H   HCR6  0   0.264   5.1673  -1.9260  -0.4461
 DL0  H11  H   HCH3  0   0.243   8.4538   1.7127  -0.9881
 DL0  H12  H   HCH3  0   0.242   8.0424   2.7481   0.3746
 DL0  H13  H   HCH3  0   0.242   8.7533   1.1601   0.6504
 DL0  H14  H   HCR6  0   0.246   5.6786   2.9358   0.6232
 DL0  H15  H   HCR6  0   0.274   2.5199  -1.6055  -2.0879
 DL0  H16  H   HCR6  0   0.265   1.4908  -3.8318  -2.3943
 DL0  H17  H   HCR6  0   0.263   0.6059  -5.0672  -0.4440
 DL0  H18  H   HCR6  0   0.264   0.7713  -4.0799   1.8202
 DL0  H19  H   HCR6  0   0.273   1.8307  -1.8680   2.1293
 DL0  O11  O   O     0  -0.412  -1.8533  -0.9096   0.1822

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
 DL0  C20  C19  aromatic  1.383  0.020  1.383
 DL0  C20  C21  aromatic  1.409  0.020  1.409
 DL0  C19  C16  aromatic  1.389  0.020  1.389
 DL0  C29  C21  single    1.503  0.020  1.503
 DL0  C21  C22  aromatic  1.386  0.020  1.386
 DL0  C26  C27  aromatic  1.388  0.020  1.388
 DL0  C26  C25  aromatic  1.389  0.020  1.389
 DL0  C27  C28  aromatic  1.387  0.020  1.387
 DL0  C25  C24  aromatic  1.387  0.020  1.387
 DL0  C28  C23  aromatic  1.388  0.020  1.388
 DL0  C16  N15  aromatic  1.377  0.020  1.377
 DL0  C16  C17  aromatic  1.399  0.020  1.399
 DL0  C24  C23  aromatic  1.389  0.020  1.389
 DL0  C23  N15  single    1.417  0.020  1.417
 DL0  C22  C17  aromatic  1.395  0.020  1.395
 DL0  N15  C14  aromatic  1.370  0.020  1.370
 DL0  C17  N18  aromatic  1.375  0.020  1.375
 DL0  C14  N18  aromatic  1.305  0.020  1.305
 DL0  C14  C13  single    1.488  0.020  1.488
 DL0  C13  C12  single    1.538  0.020  1.538
 DL0  C12  C9   single    1.497  0.020  1.497
 DL0  C8   O7   single    1.336  0.020  1.336
 DL0  C8   C9   double    1.345  0.020  1.345
 DL0  O7   C4   single    1.348  0.020  1.348
 DL0  C9   C10  single    1.456  0.020  1.456
 DL0  C4   C3   aromatic  1.393  0.020  1.393
 DL0  C4   C5   aromatic  1.391  0.020  1.391
 DL0  C10  C5   single    1.471  0.020  1.471
 DL0  C10  O11  double    1.221  0.020  1.221
 DL0  C3   C2   aromatic  1.376  0.020  1.376
 DL0  C5   C6   aromatic  1.398  0.020  1.398
 DL0  C2   C1   aromatic  1.397  0.020  1.397
 DL0  C6   C1   aromatic  1.374  0.020  1.374
 DL0  C1   CL   single    1.731  0.020  1.731
 DL0  C12  H1   single    0.970  0.020  1.090
 DL0  C12  H2   single    0.970  0.020  1.090
 DL0  C13  H3   single    0.970  0.020  1.090
 DL0  C13  H4   single    0.970  0.020  1.090
 DL0  C20  H5   single    0.930  0.020  1.080
 DL0  C8   H6   single    0.930  0.020  1.080
 DL0  C6   H7   single    0.930  0.020  1.080
 DL0  C3   H8   single    0.930  0.020  1.080
 DL0  C2   H9   single    0.930  0.020  1.080
 DL0  C19  H10  single    0.930  0.020  1.080
 DL0  C29  H11  single    0.970  0.020  1.090
 DL0  C29  H12  single    0.970  0.020  1.090
 DL0  C29  H13  single    0.970  0.020  1.090
 DL0  C22  H14  single    0.930  0.020  1.080
 DL0  C24  H15  single    0.930  0.020  1.080
 DL0  C25  H16  single    0.930  0.020  1.080
 DL0  C26  H17  single    0.930  0.020  1.080
 DL0  C27  H18  single    0.930  0.020  1.080
 DL0  C28  H19  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
 DL0  H2   C12  H1   107.00  3.000
 DL0  H2   C12  C9   109.02  3.000
 DL0  H1   C12  C9   109.67  3.000
 DL0  H2   C12  C13  109.80  3.000
 DL0  H1   C12  C13  109.09  3.000
 DL0  C9   C12  C13  112.13  3.000
 DL0  H4   C13  H3   107.43  3.000
 DL0  H4   C13  C14  111.01  3.000
 DL0  H3   C13  C14  107.55  3.000
 DL0  H4   C13  C12  109.81  3.000
 DL0  H3   C13  C12  109.42  3.000
 DL0  C14  C13  C12  111.49  3.000
 DL0  N18  C14  N15  112.51  3.000
 DL0  N18  C14  C13  124.71  3.000
 DL0  N15  C14  C13  122.69  3.000
 DL0  H5   C20  C21  118.72  3.000
 DL0  H5   C20  C19  118.83  3.000
 DL0  C21  C20  C19  122.45  3.000
 DL0  C5   C10  C9   114.51  3.000
 DL0  C5   C10  O11  122.40  3.000
 DL0  C9   C10  O11  123.09  3.000
 DL0  C8   C9   C10  119.35  3.000
 DL0  C10  C9   C12  119.86  3.000
 DL0  C8   C9   C12  120.79  3.000
 DL0  H6   C8   O7   111.47  3.000
 DL0  H6   C8   C9   123.35  3.000
 DL0  O7   C8   C9   125.18  3.000
 DL0  C4   O7   C8   119.47  3.000
 DL0  C3   C4   C5   121.38  3.000
 DL0  C5   C4   O7   121.41  3.000
 DL0  C3   C4   O7   117.21  3.000
 DL0  C6   C5   C4   118.92  3.000
 DL0  C6   C5   C10  121.00  3.000
 DL0  C4   C5   C10  120.08  3.000
 DL0  H7   C6   C1   121.06  3.000
 DL0  H7   C6   C5   119.37  3.000
 DL0  C1   C6   C5   119.57  3.000
 DL0  H8   C3   C2   120.62  3.000
 DL0  H8   C3   C4   120.22  3.000
 DL0  C2   C3   C4   119.16  3.000
 DL0  H9   C2   C1   120.33  3.000
 DL0  H9   C2   C3   119.88  3.000
 DL0  C1   C2   C3   119.79  3.000
 DL0  CL   C1   C2   119.01  3.000
 DL0  CL   C1   C6   119.81  3.000
 DL0  C2   C1   C6   121.18  3.000
 DL0  C23  N15  C16  125.57  3.000
 DL0  C23  N15  C14  127.55  3.000
 DL0  C16  N15  C14  106.85  3.000
 DL0  C17  C16  C19  122.34  3.000
 DL0  C17  C16  N15  105.00  3.000
 DL0  C19  C16  N15  132.65  3.000
 DL0  H10  C19  C16  122.08  3.000
 DL0  H10  C19  C20  121.23  3.000
 DL0  C16  C19  C20  116.69  3.000
 DL0  C22  C21  C29  120.80  3.000
 DL0  C22  C21  C20  119.68  3.000
 DL0  C29  C21  C20  119.52  3.000
 DL0  H13  C29  H12  107.80  3.000
 DL0  H13  C29  H11  107.03  3.000
 DL0  H12  C29  H11  107.63  3.000
 DL0  H13  C29  C21  111.53  3.000
 DL0  H12  C29  C21  111.40  3.000
 DL0  H11  C29  C21  111.24  3.000
 DL0  H14  C22  C17  120.33  3.000
 DL0  H14  C22  C21  120.74  3.000
 DL0  C17  C22  C21  118.93  3.000
 DL0  N18  C17  C22  130.17  3.000
 DL0  N18  C17  C16  109.92  3.000
 DL0  C22  C17  C16  119.90  3.000
 DL0  C17  N18  C14  105.72  3.000
 DL0  C28  C23  C24  120.66  3.000
 DL0  C24  C23  N15  119.54  3.000
 DL0  C28  C23  N15  119.79  3.000
 DL0  H15  C24  C25  120.50  3.000
 DL0  H15  C24  C23  120.05  3.000
 DL0  C25  C24  C23  119.45  3.000
 DL0  H16  C25  C26  120.16  3.000
 DL0  H16  C25  C24  119.63  3.000
 DL0  C26  C25  C24  120.21  3.000
 DL0  H17  C26  C27  120.08  3.000
 DL0  H17  C26  C25  119.94  3.000
 DL0  C27  C26  C25  119.97  3.000
 DL0  H18  C27  C28  119.60  3.000
 DL0  H18  C27  C26  120.25  3.000
 DL0  C28  C27  C26  120.15  3.000
 DL0  H19  C28  C27  120.56  3.000
 DL0  H19  C28  C23  119.89  3.000
 DL0  C27  C28  C23  119.54  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
 DL0  CONST_01  C19  C16  N15  C14   180.00   0.0  0
 DL0  CONST_02  C17  C16  N15  C14     0.00   0.0  0
 DL0  CONST_05  C16  C17  N18  C14     0.00   0.0  0
 DL0  CONST_06  C22  C17  N18  C14   180.00   0.0  0
 DL0  CONST_07  N15  C16  C19  C20   180.00   0.0  0
 DL0  CONST_08  C17  C16  C19  C20     0.00   0.0  0
 DL0  CONST_09  C17  C22  C21  C20     0.00   0.0  0
 DL0  CONST_10  C1   C2   C3   C4      0.00   0.0  0
 DL0  CONST_11  C1   C6   C5   C4      0.00   0.0  0
 DL0  CONST_12  C2   C3   C4   C5      0.00   0.0  0
 DL0  CONST_13  C2   C1   C6   C5      0.00   0.0  0
 DL0  CONST_14  C3   C4   C5   C6      0.00   0.0  0
 DL0  CONST_15  C3   C2   C1   C6      0.00   0.0  0
 DL0  CONST_16  C22  C17  C16  N15   180.00   0.0  0
 DL0  CONST_17  N18  C17  C16  N15     0.00   0.0  0
 DL0  CONST_18  C27  C28  C23  N15   180.00   0.0  0
 DL0  CONST_19  C25  C24  C23  N15   180.00   0.0  0
 DL0  CONST_20  C17  N18  C14  N15     0.00   0.0  0
 DL0  CONST_21  C21  C20  C19  C16     0.00   0.0  0
 DL0  CONST_24  N18  C14  N15  C16     0.00   0.0  0
 DL0  CONST_25  C21  C22  C17  C16     0.00   0.0  0
 DL0  CONST_26  C22  C21  C20  C19     0.00   0.0  0
 DL0  CONST_27  C23  N15  C16  C19     0.00   0.0  0
 DL0  CONST_28  C22  C17  C16  C19     0.00   0.0  0
 DL0  CONST_29  N18  C17  C16  C19   180.00   0.0  0
 DL0  CONST_30  N18  C17  C22  C21   180.00   0.0  0
 DL0  CONST_31  C23  N15  C16  C17   180.00   0.0  0
 DL0  CONST_32  C23  N15  C14  N18   180.00   0.0  0
 DL0  CONST_33  C26  C27  C28  C23     0.00   0.0  0
 DL0  CONST_34  C26  C25  C24  C23     0.00   0.0  0
 DL0  CONST_35  C27  C26  C25  C24     0.00   0.0  0
 DL0  CONST_36  C27  C28  C23  C24     0.00   0.0  0
 DL0  CONST_37  C28  C27  C26  C25     0.00   0.0  0
 DL0  CONST_38  C28  C23  C24  C25     0.00   0.0  0
 DL0  CONST_39  C16  N15  C14  C13   180.00   0.0  0
 DL0  CONST_40  C23  N15  C14  C13     0.00   0.0  0
 DL0  CONST_41  C17  N18  C14  C13   180.00   0.0  0
 DL0  CONST_42  CL   C1   C6   C5    180.00   0.0  0
 DL0  CONST_43  CL   C1   C2   C3    180.00   0.0  0
 DL0  CONST_44  C29  C21  C20  C19   180.00   0.0  0
 DL0  CONST_45  C17  C22  C21  C29   180.00   0.0  0
 DL0  CONST_46  H14  C22  C21  C20   180.00   0.0  0
 DL0  CONST_47  H7   C6   C5   C10     0.00   0.0  0
 DL0  CONST_48  H8   C3   C4   O7      0.00   0.0  0
 DL0  CONST_49  H9   C2   C3   C4    180.00   0.0  0
 DL0  CONST_50  H10  C19  C16  N15     0.00   0.0  0
 DL0  CONST_51  H19  C28  C23  N15     0.00   0.0  0
 DL0  CONST_52  H15  C24  C23  N15     0.00   0.0  0
 DL0  CONST_53  H5   C20  C19  C16   180.00   0.0  0
 DL0  CONST_54  H18  C27  C28  C23   180.00   0.0  0
 DL0  CONST_55  H16  C25  C24  C23   180.00   0.0  0
 DL0  CONST_56  H17  C26  C25  C24   180.00   0.0  0
 DL0  Var_01    O7   C8   C9   C10     0.64  30.0  1
 DL0  Var_02    C4   C5   C10  C9      0.29  30.0  1
 DL0  Var_03    C3   C4   O7   C8   -179.81  30.0  1
 DL0  Var_04    C5   C10  C9   C8     -0.54  30.0  1
 DL0  Var_05    N15  C14  C13  C12   -78.00  30.0  2
 DL0  Var_06    C9   C12  C13  C14  -176.46  30.0  3
 DL0  Var_07    H11  C29  C21  C20    65.68  30.0  2

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
 DL0  plan-1  N15  0.020
 DL0  plan-1  C23  0.020
 DL0  plan-1  C24  0.020
 DL0  plan-1  C25  0.020
 DL0  plan-1  C26  0.020
 DL0  plan-1  C27  0.020
 DL0  plan-1  C28  0.020
 DL0  plan-1  H15  0.020
 DL0  plan-1  H16  0.020
 DL0  plan-1  H17  0.020
 DL0  plan-1  H18  0.020
 DL0  plan-1  H19  0.020
 DL0  plan-2  C13  0.020
 DL0  plan-2  C14  0.020
 DL0  plan-2  C20  0.020
 DL0  plan-2  N15  0.020
 DL0  plan-2  C16  0.020
 DL0  plan-2  C19  0.020
 DL0  plan-2  C21  0.020
 DL0  plan-2  C29  0.020
 DL0  plan-2  C22  0.020
 DL0  plan-2  C17  0.020
 DL0  plan-2  N18  0.020
 DL0  plan-2  C23  0.020
 DL0  plan-2  H5   0.020
 DL0  plan-2  H10  0.020
 DL0  plan-2  H14  0.020
 DL0  plan-3  C10  0.020
 DL0  plan-3  O7   0.020
 DL0  plan-3  C4   0.020
 DL0  plan-3  C5   0.020
 DL0  plan-3  C6   0.020
 DL0  plan-3  C3   0.020
 DL0  plan-3  C2   0.020
 DL0  plan-3  C1   0.020
 DL0  plan-3  CL   0.020
 DL0  plan-3  H7   0.020
 DL0  plan-3  H8   0.020
 DL0  plan-3  H9   0.020
 DL0  plan-4  C10  0.020
 DL0  plan-4  C9   0.020
 DL0  plan-4  C5   0.020
 DL0  plan-4  O11  0.020

