# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:19:36 2021
#   Inital geometry file: a 106 line input string
#   Ligand name: 5-[(4-bromo-2-fluorophenyl)amino]-4-fluoro-N-(2-hydroxyethoxy)-1-methyl-1H-benzimidazole-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2c(F)c(Nc3ccc(Br)cc3F)c(cc12)C(=O)NOCCO
#
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
 QO7  QO7  5-[(4-bromo-2-fluorophenyl)amino]-4-fluoro-N-(2-hydroxyethoxy)-1-methyl-1H-benzimidazole-6-carboxamide  ligand  42  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QO7
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
 QO7  C13   C   CR6   0   0.229  65.4471  -25.0140   6.3119
 QO7  C14   C   CR6   0   0.473  66.3088  -25.9682   6.8567
 QO7  C15   C   CR16  0  -0.374  66.8904  -25.8479   8.0975
 QO7  C16   C   CR6   0  -0.133  66.6068  -24.7176   8.8515
 QO7  C17   C   CR16  0  -0.238  65.7535  -23.7441   8.3582
 QO7  C18   C   CR16  0  -0.305  65.1810  -23.8966   7.1052
 QO7  C03   C   CR15  0   0.117  63.7019  -20.3990   2.0812
 QO7  C05   C   CR56  0  -0.048  64.2775  -22.0819   3.2128
 QO7  C06   C   CR56  0   0.377  62.9539  -22.3138   2.8113
 QO7  C07   C   CR16  0  -0.348  62.2541  -23.4696   3.1351
 QO7  C08   C   CR6   0  -0.106  62.9146  -24.3918   3.9248
 QO7  C09   C   CR6   0   0.095  64.2499  -24.2091   4.3364
 QO7  C10   C   CR6   0   0.531  64.9213  -23.0603   3.9602
 QO7  C25   C   CH2   0  -0.191  61.2648  -24.0009   6.8422
 QO7  C26   C   CH2   0  -0.173  60.1213  -24.6137   7.6314
 QO7  F11   F   F     0  -0.290  66.1946  -22.8876   4.3145
 QO7  F20   F   F     0  -0.317  66.5768  -27.0633   6.1195
 QO7  N02   N   NR5   0  -0.506  62.6135  -21.2063   2.0851
 QO7  N04   N   N     0  -0.456  64.7210  -20.8768   2.7397
 QO7  N12   N   NH1   0  -0.778  64.8921  -25.2185   5.0727
 QO7  N23   N   NH1   0  -0.335  61.8236  -25.8267   5.5356
 QO7  O22   O   O     0  -0.456  61.9545  -26.5042   3.4035
 QO7  O24   O   O2    0  -0.374  62.2573  -24.9633   6.4964
 QO7  O27   O   OH1   0  -0.672  59.2518  -23.5578   7.9694
 QO7  BR19  BR  BR    0  -0.052  67.3931  -24.5155  10.5552
 QO7  H1    H   HCR6  0   0.297  67.5505  -26.6287   8.4523
 QO7  H2    H   HCR6  0   0.280  65.5181  -22.8617   8.9375
 QO7  H3    H   HCR6  0   0.279  64.5062  -23.1302   6.7495
 QO7  H4    H   HCH3  0   0.265  61.1508  -21.7201   0.6818
 QO7  H5    H   HCH3  0   0.265  60.5373  -20.9733   2.1702
 QO7  H6    H   HCH3  0   0.275  61.3704  -19.9883   0.9617
 QO7  H7    H   HCR5  0   0.297  63.6890  -19.4497   1.5652
 QO7  H8    H   HCR6  0   0.290  61.2365  -23.6382   2.8074
 QO7  H9    H   HCH2  0   0.247  61.7973  -23.2666   7.4493
 QO7  H10   H   HCH2  0   0.228  60.8900  -23.4967   5.9453
 QO7  H11   H   HCH2  0   0.203  59.6144  -25.3745   7.0245
 QO7  H12   H   HCH2  0   0.205  60.5226  -25.1176   8.5196
 QO7  H13   H   HNH1  0   0.404  65.2079  -26.0229   4.5543
 QO7  H14   H   HNH1  0   0.415  61.5074  -26.7277   5.8727
 QO7  H15   H   HOH1  0   0.460  58.5038  -23.9255   8.4477
 QO7  C21   C   C     0   0.451  62.2140  -25.6738   4.2566
 QO7  C01   C   CH3   0  -0.532  61.3443  -20.9632   1.4400

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
 QO7  C03  N04   aromatic  1.304  0.020  1.304
 QO7  C03  N02   aromatic  1.355  0.020  1.355
 QO7  N04  C05   aromatic  1.368  0.020  1.368
 QO7  C01  N02   single    1.444  0.020  1.444
 QO7  N02  C06   aromatic  1.367  0.020  1.367
 QO7  C05  C06   aromatic  1.402  0.020  1.402
 QO7  C05  C10   aromatic  1.389  0.020  1.389
 QO7  C06  C07   aromatic  1.389  0.020  1.389
 QO7  F11  C10   single    1.333  0.020  1.333
 QO7  C10  C09   aromatic  1.383  0.020  1.383
 QO7  C07  C08   aromatic  1.382  0.020  1.382
 QO7  C09  C08   aromatic  1.409  0.020  1.409
 QO7  C09  N12   single    1.405  0.020  1.405
 QO7  C08  C21   single    1.498  0.020  1.498
 QO7  N12  C13   single    1.373  0.020  1.373
 QO7  C25  O24   single    1.425  0.020  1.425
 QO7  C25  C26   single    1.519  0.020  1.519
 QO7  O24  N23   single    1.363  0.020  1.363
 QO7  C21  N23   single    1.346  0.020  1.346
 QO7  C21  O22   double    1.218  0.020  1.218
 QO7  C13  C18   aromatic  1.396  0.020  1.396
 QO7  C13  C14   aromatic  1.396  0.020  1.396
 QO7  C18  C17   aromatic  1.386  0.020  1.386
 QO7  C26  O27   single    1.409  0.020  1.409
 QO7  F20  C14   single    1.347  0.020  1.347
 QO7  C14  C15   aromatic  1.376  0.020  1.376
 QO7  C17  C16   aromatic  1.385  0.020  1.385
 QO7  C15  C16   aromatic  1.388  0.020  1.388
 QO7  C16  BR19  single    1.887  0.020  1.887
 QO7  C15  H1    single    0.930  0.020  1.080
 QO7  C17  H2    single    0.930  0.020  1.080
 QO7  C18  H3    single    0.930  0.020  1.080
 QO7  C01  H4    single    0.970  0.020  1.090
 QO7  C01  H5    single    0.970  0.020  1.090
 QO7  C01  H6    single    0.970  0.020  1.090
 QO7  C03  H7    single    0.930  0.020  1.080
 QO7  C07  H8    single    0.930  0.020  1.080
 QO7  C25  H9    single    0.970  0.020  1.090
 QO7  C25  H10   single    0.970  0.020  1.090
 QO7  C26  H11   single    0.970  0.020  1.090
 QO7  C26  H12   single    0.970  0.020  1.090
 QO7  N12  H13   single    0.890  0.020  1.040
 QO7  N23  H14   single    0.890  0.020  1.040
 QO7  O27  H15   single    0.850  0.020  0.980

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
 QO7  N12   C13  C18  123.72  3.000
 QO7  C18   C13  C14  116.29  3.000
 QO7  N12   C13  C14  119.98  3.000
 QO7  F20   C14  C15  118.72  3.000
 QO7  C15   C14  C13  123.58  3.000
 QO7  F20   C14  C13  117.70  3.000
 QO7  H1    C15  C16  122.28  3.000
 QO7  H1    C15  C14  119.37  3.000
 QO7  C16   C15  C14  118.35  3.000
 QO7  BR19  C16  C17  120.19  3.000
 QO7  BR19  C16  C15  119.50  3.000
 QO7  C17   C16  C15  120.31  3.000
 QO7  H2    C17  C18  118.96  3.000
 QO7  H2    C17  C16  121.11  3.000
 QO7  C18   C17  C16  119.93  3.000
 QO7  H3    C18  C17  118.50  3.000
 QO7  H3    C18  C13  119.95  3.000
 QO7  C17   C18  C13  121.55  3.000
 QO7  H7    C03  N04  124.92  3.000
 QO7  H7    C03  N02  121.00  3.000
 QO7  N04   C03  N02  114.08  3.000
 QO7  N04   C05  C10  130.99  3.000
 QO7  C10   C05  C06  118.35  3.000
 QO7  N04   C05  C06  110.64  3.000
 QO7  N02   C06  C07  132.23  3.000
 QO7  C07   C06  C05  123.11  3.000
 QO7  N02   C06  C05  104.66  3.000
 QO7  H8    C07  C08  121.22  3.000
 QO7  H8    C07  C06  122.18  3.000
 QO7  C08   C07  C06  116.58  3.000
 QO7  C09   C08  C07  122.22  3.000
 QO7  C09   C08  C21  119.30  3.000
 QO7  C07   C08  C21  118.30  3.000
 QO7  N12   C09  C10  121.17  3.000
 QO7  N12   C09  C08  119.54  3.000
 QO7  C10   C09  C08  119.23  3.000
 QO7  F11   C10  C09  119.94  3.000
 QO7  C09   C10  C05  120.43  3.000
 QO7  F11   C10  C05  119.63  3.000
 QO7  H10   C25  H9   108.23  3.000
 QO7  H10   C25  O24  110.52  3.000
 QO7  H9    C25  O24  104.45  3.000
 QO7  H10   C25  C26  110.71  3.000
 QO7  H9    C25  C26  110.48  3.000
 QO7  O24   C25  C26  112.21  3.000
 QO7  H12   C26  H11  107.36  3.000
 QO7  H12   C26  O27  112.06  3.000
 QO7  H11   C26  O27  111.55  3.000
 QO7  H12   C26  C25  109.30  3.000
 QO7  H11   C26  C25  109.89  3.000
 QO7  O27   C26  C25  106.67  3.000
 QO7  C06   N02  C03  106.50  3.000
 QO7  C06   N02  C01  126.32  3.000
 QO7  C03   N02  C01  127.18  3.000
 QO7  C05   N04  C03  104.12  3.000
 QO7  H13   N12  C09  116.56  3.000
 QO7  H13   N12  C13  117.16  3.000
 QO7  C09   N12  C13  123.42  3.000
 QO7  H14   N23  O24  115.37  3.000
 QO7  H14   N23  C21  120.53  3.000
 QO7  O24   N23  C21  120.38  3.000
 QO7  N23   O24  C25  112.17  3.000
 QO7  H15   O27  C26  108.24  3.000
 QO7  O22   C21  N23  121.74  3.000
 QO7  O22   C21  C08  121.85  3.000
 QO7  N23   C21  C08  116.32  3.000
 QO7  H6    C01  H5   108.76  3.000
 QO7  H6    C01  H4   108.77  3.000
 QO7  H5    C01  H4   109.21  3.000
 QO7  H6    C01  N02  109.06  3.000
 QO7  H5    C01  N02  110.51  3.000
 QO7  H4    C01  N02  110.50  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
 QO7  CONST_01  C16   C17  C18  C13     0.00   0.0  0
 QO7  CONST_02  C16   C15  C14  C13     0.00   0.0  0
 QO7  CONST_03  C17   C18  C13  C14     0.00   0.0  0
 QO7  CONST_04  C17   C16  C15  C14     0.00   0.0  0
 QO7  CONST_05  C18   C13  C14  C15     0.00   0.0  0
 QO7  CONST_06  C18   C17  C16  C15     0.00   0.0  0
 QO7  CONST_07  C06   C05  N04  C03     0.00   0.0  0
 QO7  CONST_08  C10   C05  N04  C03   180.00   0.0  0
 QO7  CONST_09  C05   C06  N02  C03     0.00   0.0  0
 QO7  CONST_10  C07   C06  N02  C03   180.00   0.0  0
 QO7  CONST_11  N02   C03  N04  C05     0.00   0.0  0
 QO7  CONST_12  C08   C07  C06  C05     0.00   0.0  0
 QO7  CONST_13  C08   C09  C10  C05     0.00   0.0  0
 QO7  CONST_14  N04   C03  N02  C06     0.00   0.0  0
 QO7  CONST_15  C09   C10  C05  C06     0.00   0.0  0
 QO7  CONST_16  C09   C08  C07  C06     0.00   0.0  0
 QO7  CONST_17  N04   C05  C06  C07   180.00   0.0  0
 QO7  CONST_18  C10   C05  C06  C07     0.00   0.0  0
 QO7  CONST_19  C10   C09  C08  C07     0.00   0.0  0
 QO7  CONST_20  N02   C06  C07  C08   180.00   0.0  0
 QO7  CONST_21  N04   C05  C10  C09   180.00   0.0  0
 QO7  CONST_22  N02   C06  C05  C10   180.00   0.0  0
 QO7  CONST_23  N04   C05  C06  N02     0.00   0.0  0
 QO7  CONST_24  BR19  C16  C15  C14   180.00   0.0  0
 QO7  CONST_25  N12   C13  C14  C15   180.00   0.0  0
 QO7  CONST_26  F20   C14  C15  C16   180.00   0.0  0
 QO7  CONST_27  N12   C13  C18  C17   180.00   0.0  0
 QO7  CONST_28  F20   C14  C13  C18   180.00   0.0  0
 QO7  CONST_29  BR19  C16  C17  C18   180.00   0.0  0
 QO7  CONST_30  C06   C07  C08  C21   180.00   0.0  0
 QO7  CONST_31  C10   C09  C08  C21   180.00   0.0  0
 QO7  CONST_32  N04   C03  N02  C01   180.00   0.0  0
 QO7  CONST_33  C05   C06  N02  C01   180.00   0.0  0
 QO7  CONST_34  C07   C06  N02  C01     0.00   0.0  0
 QO7  CONST_35  N12   C09  C10  C05   180.00   0.0  0
 QO7  CONST_36  F11   C10  C05  C06   180.00   0.0  0
 QO7  CONST_37  N12   C09  C08  C07   180.00   0.0  0
 QO7  CONST_38  F11   C10  C09  C08   180.00   0.0  0
 QO7  CONST_39  N04   C05  C10  F11     0.00   0.0  0
 QO7  CONST_40  H2    C17  C18  C13   180.00   0.0  0
 QO7  CONST_41  H1    C15  C14  C13   180.00   0.0  0
 QO7  CONST_42  H3    C18  C13  C14   180.00   0.0  0
 QO7  CONST_43  H7    C03  N04  C05   180.00   0.0  0
 QO7  CONST_44  H8    C07  C06  C05   180.00   0.0  0
 QO7  CONST_45  O24   N23  C21  C08     0.00   0.0  0
 QO7  CONST_46  H14   N23  C21  C08   180.00   0.0  0
 QO7  CONST_47  O24   N23  C21  O22   180.00   0.0  0
 QO7  Var_01    C10   C09  N12  C13    59.77  30.0  2
 QO7  Var_02    C09   N12  C13  C14  -166.29  30.0  2
 QO7  Var_03    N23   C21  C08  C07  -110.00  30.0  2
 QO7  Var_04    H4    C01  N02  C03   117.38  30.0  2
 QO7  Var_05    O27   C26  C25  O24   176.98  30.0  3
 QO7  Var_06    H9    C25  O24  N23  -168.77  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
 QO7  plan-1  C13   0.020
 QO7  plan-1  C14   0.020
 QO7  plan-1  C15   0.020
 QO7  plan-1  C16   0.020
 QO7  plan-1  C17   0.020
 QO7  plan-1  C18   0.020
 QO7  plan-1  F20   0.020
 QO7  plan-1  N12   0.020
 QO7  plan-1  BR19  0.020
 QO7  plan-1  H1    0.020
 QO7  plan-1  H2    0.020
 QO7  plan-1  H3    0.020
 QO7  plan-2  C03   0.020
 QO7  plan-2  C05   0.020
 QO7  plan-2  C06   0.020
 QO7  plan-2  C07   0.020
 QO7  plan-2  C08   0.020
 QO7  plan-2  C09   0.020
 QO7  plan-2  C10   0.020
 QO7  plan-2  F11   0.020
 QO7  plan-2  N02   0.020
 QO7  plan-2  N04   0.020
 QO7  plan-2  N12   0.020
 QO7  plan-2  H7    0.020
 QO7  plan-2  H8    0.020
 QO7  plan-2  C21   0.020
 QO7  plan-2  C01   0.020
 QO7  plan-3  C08   0.020
 QO7  plan-3  N23   0.020
 QO7  plan-3  O22   0.020
 QO7  plan-3  O24   0.020
 QO7  plan-3  H14   0.020
 QO7  plan-3  C21   0.020

