# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 16:16:32 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-(3-tert-butyl-1H-pyrazol-5-yl)-3-{4-chloro-3-[(pyridin-3-yloxy)methyl]phenyl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1cc([nH]n1)NC(=O)Nc2ccc(Cl)c(COc3cccnc3)c2
#
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
 L09  L09  1-(3-tert-butyl-1H-pyrazol-5-yl)-3-{4-chloro-3-[(pyridin-3-yloxy)methyl]phenyl}urea  ligand  50  28  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_L09
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
 L09  C1    C   CH3   0  -0.636  -1.1949   0.9647   8.3444
 L09  C2    C   CT    0  -0.189  -0.1351   1.0187   7.2451
 L09  C3    C   CH3   0  -0.633   0.2340   2.4824   6.9752
 L09  C4    C   CH3   0  -0.633   1.1161   0.2614   7.7058
 L09  C5    C   CR5   0   0.324  -0.6481   0.4015   5.9698
 L09  C6    C   CR15  0  -0.528   0.0404   0.3185   4.7371
 L09  C7    C   CR5   0   0.633  -0.8483  -0.3123   3.8924
 L09  N8    N   NH1   0  -0.785  -0.8116  -0.6769   2.5620
 L09  C9    C   C     0   0.735   0.2815  -0.5276   1.7502
 L09  O10   O   O     0  -0.485   1.3526  -0.1144   2.1489
 L09  N11   N   NH1   0  -0.793   0.0311  -0.8966   0.4564
 L09  C12   C   CR6   0   0.417   0.9436  -0.8386  -0.5993
 L09  C13   C   CR16  0  -0.319   2.3077  -1.0702  -0.4414
 L09  C14   C   CR16  0  -0.190   3.1391  -1.0268  -1.5481
 L09  C15   C   CR6   0  -0.120   2.6194  -0.7687  -2.8035
 L09  CL16  CL  CL    0  -0.128   3.6926  -0.7291  -4.1676
 L09  C17   C   CR6   0   0.135   1.2579  -0.5473  -2.9896
 L09  C18   C   CH2   0  -0.198   0.7298  -0.2683  -4.3683
 L09  O19   O   O2    0  -0.477  -0.6576  -0.0405  -4.2940
 L09  C20   C   CR6   0   0.338  -1.3249   0.2483  -5.4263
 L09  C21   C   CR16  0  -0.255  -2.6912   0.4929  -5.3091
 L09  C22   C   CR16  0  -0.306  -3.4100   0.7952  -6.4483
 L09  C23   C   CR16  0  -0.090  -2.7463   0.8447  -7.6688
 L09  N24   N   N     0  -0.388  -1.4488   0.6118  -7.7836
 L09  C25   C   CR16  0  -0.183  -0.7479   0.3195  -6.6928
 L09  C26   C   CR16  0  -0.427   0.4361  -0.5821  -1.8730
 L09  N27   N   NR15  0  -0.513  -1.9521  -0.5648   4.6201
 L09  N28   N   N     0  -0.307  -1.8469  -0.1353   5.8840
 L09  H1C1  H   HCH3  0   0.224  -0.8054   1.4197   9.2568
 L09  H1C2  H   HCH3  0   0.224  -2.0964   1.5078   8.0586
 L09  H1C3  H   HCH3  0   0.225  -1.4850  -0.0598   8.5788
 L09  H3C1  H   HCH3  0   0.227  -0.6324   3.0512   6.6325
 L09  H3C2  H   HCH3  0   0.226   0.6071   2.9566   7.8854
 L09  H3C3  H   HCH3  0   0.227   1.0122   2.5697   6.2152
 L09  H4C1  H   HCH3  0   0.227   0.8912  -0.7856   7.9162
 L09  H4C2  H   HCH3  0   0.227   1.9030   0.2886   6.9499
 L09  H4C3  H   HCH3  0   0.226   1.5165   0.7086   8.6184
 L09  H6    H   HCR5  0   0.263   1.0274   0.6729   4.5061
 L09  H8    H   HNH1  0   0.420  -1.6546  -1.0791   2.1800
 L09  H11   H   HNH1  0   0.416  -0.9303  -1.0419   0.1874
 L09  H13   H   HCR6  0   0.280   2.7323  -1.2974   0.5234
 L09  H14   H   HCR6  0   0.284   4.1988  -1.2052  -1.4261
 L09  H181  H   HCH2  0   0.256   1.2429   0.6053  -4.7882
 L09  H182  H   HCH2  0   0.257   0.9485  -1.1193  -5.0249
 L09  H21   H   HCR6  0   0.283  -3.1701   0.4472  -4.3389
 L09  H22   H   HCR6  0   0.275  -4.4724   0.9895  -6.3941
 L09  H23   H   HCR6  0   0.263  -3.2848   1.0810  -8.5792
 L09  H25   H   HCR6  0   0.279   0.3101   0.1376  -6.8432
 L09  H26   H   HCR6  0   0.276  -0.6248  -0.4023  -1.9870
 L09  H27   H   HNR5  0   0.416  -2.7984  -1.0177   4.3137

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
 L09  C1   C2    single    1.528  0.020  1.528
 L09  C1   H1C1  single    0.970  0.020  1.090
 L09  C1   H1C2  single    0.970  0.020  1.090
 L09  C1   H1C3  single    0.970  0.020  1.090
 L09  C2   C3    single    1.533  0.020  1.533
 L09  C2   C4    single    1.533  0.020  1.533
 L09  C2   C5    single    1.507  0.020  1.507
 L09  C3   H3C1  single    0.970  0.020  1.090
 L09  C3   H3C2  single    0.970  0.020  1.090
 L09  C3   H3C3  single    0.970  0.020  1.090
 L09  C4   H4C1  single    0.970  0.020  1.090
 L09  C4   H4C2  single    0.970  0.020  1.090
 L09  C4   H4C3  single    0.970  0.020  1.090
 L09  C5   C6    aromatic  1.414  0.020  1.414
 L09  C5   N28   aromatic  1.316  0.020  1.316
 L09  C6   C7    aromatic  1.379  0.020  1.379
 L09  C6   H6    single    0.930  0.020  1.080
 L09  C7   N8    single    1.380  0.020  1.380
 L09  C7   N27   aromatic  1.346  0.020  1.346
 L09  N8   C9    single    1.370  0.020  1.370
 L09  N8   H8    single    0.860  0.020  1.020
 L09  C9   O10   double    1.215  0.020  1.215
 L09  C9   N11   single    1.369  0.020  1.369
 L09  N11  C12   single    1.397  0.020  1.397
 L09  N11  H11   single    0.860  0.020  1.020
 L09  C12  C13   aromatic  1.393  0.020  1.393
 L09  C12  C26   aromatic  1.395  0.020  1.395
 L09  C13  C14   aromatic  1.385  0.020  1.385
 L09  C13  H13   single    0.930  0.020  1.080
 L09  C14  C15   aromatic  1.383  0.020  1.383
 L09  C14  H14   single    0.930  0.020  1.080
 L09  C15  CL16  single    1.736  0.020  1.736
 L09  C15  C17   aromatic  1.392  0.020  1.392
 L09  C17  C18   single    1.503  0.020  1.503
 L09  C17  C26   aromatic  1.387  0.020  1.387
 L09  C18  O19   single    1.408  0.020  1.408
 L09  C18  H181  single    0.970  0.020  1.090
 L09  C18  H182  single    0.970  0.020  1.090
 L09  O19  C20   single    1.346  0.020  1.346
 L09  C20  C21   aromatic  1.393  0.020  1.393
 L09  C20  C25   aromatic  1.394  0.020  1.394
 L09  C21  C22   aromatic  1.381  0.020  1.381
 L09  C21  H21   single    0.930  0.020  1.080
 L09  C22  C23   aromatic  1.390  0.020  1.390
 L09  C22  H22   single    0.930  0.020  1.080
 L09  C23  N24   aromatic  1.323  0.020  1.323
 L09  C23  H23   single    0.930  0.020  1.080
 L09  N24  C25   aromatic  1.329  0.020  1.329
 L09  C25  H25   single    0.930  0.020  1.080
 L09  C26  H26   single    0.930  0.020  1.080
 L09  N27  N28   aromatic  1.339  0.020  1.339
 L09  N27  H27   single    0.860  0.020  1.020

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
 L09  H1C3  C1   H1C2  107.72  3.000
 L09  H1C3  C1   H1C1  107.88  3.000
 L09  H1C2  C1   H1C1  107.85  3.000
 L09  H1C3  C1   C2    111.86  3.000
 L09  H1C2  C1   C2    111.54  3.000
 L09  H1C1  C1   C2    109.83  3.000
 L09  C5    C2   C4    109.26  3.000
 L09  C5    C2   C3    108.90  3.000
 L09  C4    C2   C3    109.14  3.000
 L09  C5    C2   C1    111.00  3.000
 L09  C4    C2   C1    109.41  3.000
 L09  C3    C2   C1    109.10  3.000
 L09  H3C3  C3   H3C2  107.58  3.000
 L09  H3C3  C3   H3C1  107.80  3.000
 L09  H3C2  C3   H3C1  107.86  3.000
 L09  H3C3  C3   C2    111.75  3.000
 L09  H3C2  C3   C2    110.49  3.000
 L09  H3C1  C3   C2    111.20  3.000
 L09  H4C3  C4   H4C2  107.71  3.000
 L09  H4C3  C4   H4C1  107.89  3.000
 L09  H4C2  C4   H4C1  107.81  3.000
 L09  H4C3  C4   C2    110.37  3.000
 L09  H4C2  C4   C2    111.58  3.000
 L09  H4C1  C4   C2    111.32  3.000
 L09  N28   C5   C6    111.26  3.000
 L09  N28   C5   C2    122.16  3.000
 L09  C6    C5   C2    126.58  3.000
 L09  H6    C6   C7    127.70  3.000
 L09  H6    C6   C5    127.99  3.000
 L09  C7    C6   C5    104.31  3.000
 L09  N27   C7   N8    119.57  3.000
 L09  N27   C7   C6    106.45  3.000
 L09  N8    C7   C6    133.98  3.000
 L09  H8    N8   C9    119.07  3.000
 L09  H8    N8   C7    116.61  3.000
 L09  C9    N8   C7    124.32  3.000
 L09  N11   C9   O10   124.27  3.000
 L09  N11   C9   N8    112.64  3.000
 L09  O10   C9   N8    123.10  3.000
 L09  H11   N11  C12   115.29  3.000
 L09  H11   N11  C9    117.72  3.000
 L09  C12   N11  C9    125.73  3.000
 L09  C26   C12  C13   119.38  3.000
 L09  C26   C12  N11   117.39  3.000
 L09  C13   C12  N11   123.19  3.000
 L09  H13   C13  C14   119.03  3.000
 L09  H13   C13  C12   121.48  3.000
 L09  C14   C13  C12   119.49  3.000
 L09  H14   C14  C15   120.10  3.000
 L09  H14   C14  C13   119.53  3.000
 L09  C15   C14  C13   120.37  3.000
 L09  C17   C15  CL16  119.74  3.000
 L09  C17   C15  C14   121.24  3.000
 L09  CL16  C15  C14   119.02  3.000
 L09  C26   C17  C18   122.35  3.000
 L09  C26   C17  C15   117.91  3.000
 L09  C18   C17  C15   119.73  3.000
 L09  H182  C18  H181  107.19  3.000
 L09  H182  C18  O19   110.71  3.000
 L09  H181  C18  O19   110.63  3.000
 L09  H182  C18  C17   109.58  3.000
 L09  H181  C18  C17   109.56  3.000
 L09  O19   C18  C17   109.14  3.000
 L09  C20   O19  C18   118.62  3.000
 L09  C25   C20  C21   118.26  3.000
 L09  C25   C20  O19   124.78  3.000
 L09  C21   C20  O19   116.96  3.000
 L09  H21   C21  C22   121.22  3.000
 L09  H21   C21  C20   120.12  3.000
 L09  C22   C21  C20   118.67  3.000
 L09  H22   C22  C23   120.44  3.000
 L09  H22   C22  C21   120.63  3.000
 L09  C23   C22  C21   118.92  3.000
 L09  H23   C23  N24   116.92  3.000
 L09  H23   C23  C22   120.53  3.000
 L09  N24   C23  C22   122.55  3.000
 L09  C25   N24  C23   118.98  3.000
 L09  H25   C25  N24   115.96  3.000
 L09  H25   C25  C20   121.44  3.000
 L09  N24   C25  C20   122.61  3.000
 L09  H26   C26  C17   119.47  3.000
 L09  H26   C26  C12   118.92  3.000
 L09  C17   C26  C12   121.61  3.000
 L09  H27   N27  N28   119.81  3.000
 L09  H27   N27  C7    127.49  3.000
 L09  N28   N27  C7    112.69  3.000
 L09  N27   N28  C5    105.30  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
 L09  CONST_01  N27   C7   C6   C5       0.00   0.0  0
 L09  CONST_02  C7    N27  N28  C5       0.00   0.0  0
 L09  CONST_03  N27   N28  C5   C6       0.00   0.0  0
 L09  CONST_04  N28   N27  C7   C6       0.00   0.0  0
 L09  CONST_05  N28   C5   C6   C7       0.00   0.0  0
 L09  CONST_06  C15   C14  C13  C12      0.00   0.0  0
 L09  CONST_07  C15   C17  C26  C12      0.00   0.0  0
 L09  CONST_08  C17   C26  C12  C13      0.00   0.0  0
 L09  CONST_09  C17   C15  C14  C13      0.00   0.0  0
 L09  CONST_10  C26   C12  C13  C14      0.00   0.0  0
 L09  CONST_11  C26   C17  C15  C14      0.00   0.0  0
 L09  CONST_12  C23   C22  C21  C20      0.00   0.0  0
 L09  CONST_13  C23   N24  C25  C20      0.00   0.0  0
 L09  CONST_14  N24   C25  C20  C21      0.00   0.0  0
 L09  CONST_15  N24   C23  C22  C21      0.00   0.0  0
 L09  CONST_16  C25   C20  C21  C22      0.00   0.0  0
 L09  CONST_17  C25   N24  C23  C22      0.00   0.0  0
 L09  CONST_18  C7    C6   C5   C2     180.00   0.0  0
 L09  CONST_19  N27   N28  C5   C2     180.00   0.0  0
 L09  CONST_20  N8    C7   C6   C5     180.00   0.0  0
 L09  CONST_21  N28   N27  C7   N8     180.00   0.0  0
 L09  CONST_22  C14   C13  C12  N11    180.00   0.0  0
 L09  CONST_23  C17   C26  C12  N11    180.00   0.0  0
 L09  CONST_24  C18   C17  C26  C12    180.00   0.0  0
 L09  CONST_25  CL16  C15  C14  C13    180.00   0.0  0
 L09  CONST_26  C18   C17  C15  C14    180.00   0.0  0
 L09  CONST_27  C26   C17  C15  CL16   180.00   0.0  0
 L09  CONST_28  C22   C21  C20  O19    180.00   0.0  0
 L09  CONST_29  N24   C25  C20  O19    180.00   0.0  0
 L09  CONST_30  H27   N27  N28  C5     180.00   0.0  0
 L09  CONST_31  H14   C14  C13  C12    180.00   0.0  0
 L09  CONST_32  H26   C26  C12  C13    180.00   0.0  0
 L09  CONST_33  H13   C13  C14  C15    180.00   0.0  0
 L09  CONST_34  H22   C22  C21  C20    180.00   0.0  0
 L09  CONST_35  H25   C25  C20  C21    180.00   0.0  0
 L09  CONST_36  H23   C23  C22  C21    180.00   0.0  0
 L09  CONST_37  H21   C21  C22  C23    180.00   0.0  0
 L09  CONST_38  H6    C6   C7   N27    180.00   0.0  0
 L09  CONST_39  C9    N8   C7   C6       0.00   0.0  0
 L09  CONST_40  N27   C7   N8   C9     180.00   0.0  0
 L09  CONST_43  H8    N8   C7   C6     180.00   0.0  0
 L09  CONST_45  O10   C9   N8   C7       0.00   0.0  0
 L09  CONST_46  C12   N11  C9   O10      0.00   0.0  0
 L09  CONST_47  N11   C9   N8   C7     180.00   0.0  0
 L09  CONST_48  C12   N11  C9   N8     180.00   0.0  0
 L09  Var_01    C6    C5   C2   C1     177.68  30.0  2
 L09  Var_02    O19   C18  C17  C15   -178.26  30.0  2
 L09  Var_03    C21   C20  O19  C18   -178.78  30.0  2
 L09  Var_04    H1C1  C1   C2   C5    -179.77  30.0  3
 L09  Var_05    H3C1  C3   C2   C5      60.10  30.0  3
 L09  Var_06    H4C1  C4   C2   C5     -61.48  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
 L09  plan-1  C2    0.020
 L09  plan-1  C5    0.020
 L09  plan-1  C6    0.020
 L09  plan-1  C7    0.020
 L09  plan-1  N8    0.020
 L09  plan-1  N27   0.020
 L09  plan-1  N28   0.020
 L09  plan-1  H6    0.020
 L09  plan-1  H27   0.020
 L09  plan-2  N11   0.020
 L09  plan-2  C12   0.020
 L09  plan-2  C13   0.020
 L09  plan-2  C14   0.020
 L09  plan-2  C15   0.020
 L09  plan-2  CL16  0.020
 L09  plan-2  C17   0.020
 L09  plan-2  C18   0.020
 L09  plan-2  C26   0.020
 L09  plan-2  H13   0.020
 L09  plan-2  H14   0.020
 L09  plan-2  H26   0.020
 L09  plan-3  O19   0.020
 L09  plan-3  C20   0.020
 L09  plan-3  C21   0.020
 L09  plan-3  C22   0.020
 L09  plan-3  C23   0.020
 L09  plan-3  N24   0.020
 L09  plan-3  C25   0.020
 L09  plan-3  H21   0.020
 L09  plan-3  H22   0.020
 L09  plan-3  H23   0.020
 L09  plan-3  H25   0.020
 L09  plan-4  C7    0.020
 L09  plan-4  N8    0.020
 L09  plan-4  C9    0.020
 L09  plan-4  O10   0.020
 L09  plan-4  N11   0.020
 L09  plan-4  C12   0.020
 L09  plan-4  H8    0.020
 L09  plan-4  H11   0.020

