# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:52:02 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 1-{3-[(2-ethylpyridin-3-yl)oxy]-5-(pyridin-2-ylsulfanyl)pyridin-2-yl}-3-methylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ncccc1Oc2cc(Sc3ccccn3)cnc2NC(=O)NC
#
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
 3LZ  3LZ  1-{3-[(2-ethylpyridin-3-yl)oxy]-5-(pyridin-2-ylsulfanyl)pyridin-2-yl}-3-methylurea  ligand  46  27  .  2021-08-04  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3LZ
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
 3LZ  C18  C  CR16  0  -0.318  -3.1922   2.0097   2.1770
 3LZ  N5   N  N     0  -0.418   0.3871  -2.2721   0.7028
 3LZ  C14  C  CR16  0  -0.333   5.8247   1.0364  -1.8967
 3LZ  C13  C  CR16  0  -0.147   6.3571   1.2853  -0.6365
 3LZ  C12  C  CR16  0  -0.300   5.5895   1.0264   0.4831
 3LZ  C17  C  CR16  0  -0.230  -2.2465   1.2336   1.5224
 3LZ  C15  C  CR16  0  -0.067   4.5373   0.5359  -1.9696
 3LZ  C11  C  CR6   0   0.078   4.3041   0.5218   0.2876
 3LZ  C22  C  CH2   0  -0.494  -2.7987   2.4999  -2.0148
 3LZ  C6   C  CR16  0  -0.052   1.5202  -1.7500   1.1528
 3LZ  C1   C  CR6   0  -0.220   1.8290  -0.4032   1.0674
 3LZ  C4   C  CR6   0   0.474  -0.5132  -1.4786   0.1514
 3LZ  C19  C  CR16  0  -0.094  -3.9418   2.9042   1.4359
 3LZ  C21  C  CR6   0   0.186  -2.8992   2.3229  -0.5269
 3LZ  C2   C  CR16  0  -0.134   0.8928   0.4438   0.4798
 3LZ  C3   C  CR6   0   0.158  -0.2814  -0.0966   0.0167
 3LZ  O8   O  O2    0  -0.514  -1.2202   0.6793  -0.6051
 3LZ  C9   C  CR6   0   0.273  -2.1033   1.3948   0.1561
 3LZ  S10  S  S2    0   0.076   3.3341   0.2075   1.7418
 3LZ  N16  N  N     0  -0.395   3.7874   0.2818  -0.8995
 3LZ  N20  N  N     0  -0.408  -3.7954   3.0523   0.1238
 3LZ  C23  C  CH3   0  -0.664  -3.6100   1.4510  -2.7758
 3LZ  C24  C  C     0   0.732  -2.3025  -3.1821   0.0328
 3LZ  O25  O  O     0  -0.498  -1.9419  -3.8551   0.9800
 3LZ  N26  N  NH1   0  -0.668  -3.3564  -3.5013  -0.7420
 3LZ  C27  C  CH3   0  -0.508  -4.1618  -4.6669  -0.4683
 3LZ  H1   H  HCR6  0   0.276  -3.3393   1.9150   3.2438
 3LZ  H3   H  HCR6  0   0.280   7.3591   1.6787  -0.5267
 3LZ  H4   H  HCR6  0   0.281   5.9730   1.2101   1.4782
 3LZ  H5   H  HCR6  0   0.294  -1.6448   0.5277   2.0802
 3LZ  H6   H  HCR6  0   0.270   4.0819   0.3272  -2.9309
 3LZ  H7   H  HCH2  0   0.250  -3.1750   3.4938  -2.2595
 3LZ  H8   H  HCH2  0   0.246  -1.7566   2.4657  -2.3373
 3LZ  H9   H  HCR6  0   0.279   2.2257  -2.4426   1.5980
 3LZ  H10  H  HCR6  0   0.262  -4.6867   3.5288   1.9153
 3LZ  H11  H  HCR6  0   0.303   1.0767   1.5071   0.3899
 3LZ  H13  H  HCH3  0   0.239  -3.5166   1.6002  -3.8515
 3LZ  H14  H  HCH3  0   0.223  -3.2724   0.4380  -2.5547
 3LZ  H15  H  HCH3  0   0.231  -4.6678   1.5142  -2.5193
 3LZ  H16  H  HNH1  0   0.401  -3.5902  -2.9448  -1.5467
 3LZ  H17  H  HCH3  0   0.237  -3.5791  -5.5871  -0.5215
 3LZ  H18  H  HCH3  0   0.238  -4.6310  -4.6149   0.5146
 3LZ  H19  H  HCH3  0   0.252  -4.9473  -4.7188  -1.2164
 3LZ  N7   N  NH1   0  -0.762  -1.6873  -1.9944  -0.3475
 3LZ  H2   H  HCR6  0   0.274   6.3916   1.2256  -2.7972
 3LZ  H12  H  HNH1  0   0.411  -2.1892  -1.3956  -0.9853

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
 3LZ  O25  C24  double    1.217  0.020  1.217
 3LZ  C24  N7   single    1.391  0.020  1.391
 3LZ  C24  N26  single    1.346  0.020  1.346
 3LZ  C27  N26  single    1.443  0.020  1.443
 3LZ  N7   C4   single    1.376  0.020  1.376
 3LZ  C19  N20  aromatic  1.329  0.020  1.329
 3LZ  C19  C18  aromatic  1.383  0.020  1.383
 3LZ  N20  C21  aromatic  1.326  0.020  1.326
 3LZ  C18  C17  aromatic  1.388  0.020  1.388
 3LZ  C22  C21  single    1.502  0.020  1.502
 3LZ  C22  C23  single    1.529  0.020  1.529
 3LZ  C21  C9   aromatic  1.400  0.020  1.400
 3LZ  C17  C9   aromatic  1.383  0.020  1.383
 3LZ  C9   O8   single    1.368  0.020  1.368
 3LZ  O8   C3   single    1.367  0.020  1.367
 3LZ  C4   C3   aromatic  1.408  0.020  1.408
 3LZ  C4   N5   aromatic  1.321  0.020  1.321
 3LZ  C3   C2   aromatic  1.373  0.020  1.373
 3LZ  N5   C6   aromatic  1.326  0.020  1.326
 3LZ  C2   C1   aromatic  1.393  0.020  1.393
 3LZ  C6   C1   aromatic  1.384  0.020  1.384
 3LZ  C1   S10  single    1.759  0.020  1.759
 3LZ  C13  C12  aromatic  1.382  0.020  1.382
 3LZ  C13  C14  aromatic  1.391  0.020  1.391
 3LZ  C12  C11  aromatic  1.395  0.020  1.395
 3LZ  C14  C15  aromatic  1.383  0.020  1.383
 3LZ  C11  S10  single    1.776  0.020  1.776
 3LZ  C11  N16  aromatic  1.317  0.020  1.317
 3LZ  C15  N16  aromatic  1.331  0.020  1.331
 3LZ  C18  H1   single    0.930  0.020  1.080
 3LZ  C14  H2   single    0.930  0.020  1.080
 3LZ  C13  H3   single    0.930  0.020  1.080
 3LZ  C12  H4   single    0.930  0.020  1.080
 3LZ  C17  H5   single    0.930  0.020  1.080
 3LZ  C15  H6   single    0.930  0.020  1.080
 3LZ  C22  H7   single    0.970  0.020  1.090
 3LZ  C22  H8   single    0.970  0.020  1.090
 3LZ  C6   H9   single    0.930  0.020  1.080
 3LZ  C19  H10  single    0.930  0.020  1.080
 3LZ  C2   H11  single    0.930  0.020  1.080
 3LZ  N7   H12  single    0.860  0.020  1.020
 3LZ  C23  H13  single    0.970  0.020  1.090
 3LZ  C23  H14  single    0.970  0.020  1.090
 3LZ  C23  H15  single    0.970  0.020  1.090
 3LZ  N26  H16  single    0.860  0.020  1.020
 3LZ  C27  H17  single    0.970  0.020  1.090
 3LZ  C27  H18  single    0.970  0.020  1.090
 3LZ  C27  H19  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
 3LZ  H1   C18  C19  120.79  3.000
 3LZ  H1   C18  C17  120.61  3.000
 3LZ  C19  C18  C17  118.60  3.000
 3LZ  C4   N5   C6   119.18  3.000
 3LZ  H2   C14  C15  120.51  3.000
 3LZ  H2   C14  C13  121.53  3.000
 3LZ  C15  C14  C13  117.96  3.000
 3LZ  H3   C13  C12  120.02  3.000
 3LZ  H3   C13  C14  120.77  3.000
 3LZ  C12  C13  C14  119.21  3.000
 3LZ  H4   C12  C11  121.13  3.000
 3LZ  H4   C12  C13  121.08  3.000
 3LZ  C11  C12  C13  117.79  3.000
 3LZ  H5   C17  C9   121.84  3.000
 3LZ  H5   C17  C18  120.04  3.000
 3LZ  C9   C17  C18  118.12  3.000
 3LZ  H6   C15  N16  116.07  3.000
 3LZ  H6   C15  C14  120.49  3.000
 3LZ  N16  C15  C14  123.44  3.000
 3LZ  N16  C11  S10  119.44  3.000
 3LZ  N16  C11  C12  123.64  3.000
 3LZ  S10  C11  C12  116.91  3.000
 3LZ  H8   C22  H7   106.97  3.000
 3LZ  H8   C22  C23  109.76  3.000
 3LZ  H7   C22  C23  109.29  3.000
 3LZ  H8   C22  C21  110.67  3.000
 3LZ  H7   C22  C21  107.86  3.000
 3LZ  C23  C22  C21  112.13  3.000
 3LZ  H9   C6   C1   120.11  3.000
 3LZ  H9   C6   N5   116.34  3.000
 3LZ  C1   C6   N5   123.55  3.000
 3LZ  S10  C1   C2   121.73  3.000
 3LZ  S10  C1   C6   120.34  3.000
 3LZ  C2   C1   C6   117.89  3.000
 3LZ  N7   C4   C3   118.28  3.000
 3LZ  C3   C4   N5   121.17  3.000
 3LZ  N7   C4   N5   120.52  3.000
 3LZ  H10  C19  N20  116.64  3.000
 3LZ  H10  C19  C18  120.56  3.000
 3LZ  N20  C19  C18  122.80  3.000
 3LZ  N20  C21  C9   120.62  3.000
 3LZ  C9   C21  C22  121.55  3.000
 3LZ  N20  C21  C22  117.81  3.000
 3LZ  H11  C2   C3   120.24  3.000
 3LZ  H11  C2   C1   121.21  3.000
 3LZ  C3   C2   C1   118.55  3.000
 3LZ  O8   C3   C2   121.15  3.000
 3LZ  C2   C3   C4   119.66  3.000
 3LZ  O8   C3   C4   119.17  3.000
 3LZ  C9   O8   C3   119.14  3.000
 3LZ  O8   C9   C21  116.24  3.000
 3LZ  O8   C9   C17  123.75  3.000
 3LZ  C21  C9   C17  120.01  3.000
 3LZ  C1   S10  C11  102.41  3.000
 3LZ  C11  N16  C15  117.96  3.000
 3LZ  C21  N20  C19  119.85  3.000
 3LZ  H15  C23  H14  107.85  3.000
 3LZ  H15  C23  H13  107.90  3.000
 3LZ  H14  C23  H13  107.50  3.000
 3LZ  H15  C23  C22  110.98  3.000
 3LZ  H14  C23  C22  111.85  3.000
 3LZ  H13  C23  C22  110.60  3.000
 3LZ  N26  C24  O25  123.29  3.000
 3LZ  N26  C24  N7   113.04  3.000
 3LZ  O25  C24  N7   123.66  3.000
 3LZ  H16  N26  C27  117.96  3.000
 3LZ  H16  N26  C24  120.74  3.000
 3LZ  C27  N26  C24  121.28  3.000
 3LZ  H19  C27  H18  108.18  3.000
 3LZ  H19  C27  H17  108.21  3.000
 3LZ  H18  C27  H17  108.31  3.000
 3LZ  H19  C27  N26  108.16  3.000
 3LZ  H18  C27  N26  111.88  3.000
 3LZ  H17  C27  N26  111.97  3.000
 3LZ  H12  N7   C24  117.38  3.000
 3LZ  H12  N7   C4   115.55  3.000
 3LZ  C24  N7   C4   126.76  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
 3LZ  CONST_01  C21  N20  C19  C18     0.00   0.0  0
 3LZ  CONST_02  C21  C9   C17  C18     0.00   0.0  0
 3LZ  CONST_03  C2   C3   C4   N5      0.00   0.0  0
 3LZ  CONST_04  C2   C1   C6   N5      0.00   0.0  0
 3LZ  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 3LZ  CONST_06  C11  N16  C15  C14     0.00   0.0  0
 3LZ  CONST_07  N16  C11  C12  C13     0.00   0.0  0
 3LZ  CONST_08  N16  C15  C14  C13     0.00   0.0  0
 3LZ  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 3LZ  CONST_10  C15  N16  C11  C12     0.00   0.0  0
 3LZ  CONST_11  N20  C19  C18  C17     0.00   0.0  0
 3LZ  CONST_12  N20  C21  C9   C17     0.00   0.0  0
 3LZ  CONST_13  C3   C4   N5   C6      0.00   0.0  0
 3LZ  CONST_14  C3   C2   C1   C6      0.00   0.0  0
 3LZ  CONST_15  C4   C3   C2   C1      0.00   0.0  0
 3LZ  CONST_16  C4   N5   C6   C1      0.00   0.0  0
 3LZ  CONST_17  C9   C21  N20  C19     0.00   0.0  0
 3LZ  CONST_18  C9   C17  C18  C19     0.00   0.0  0
 3LZ  CONST_19  O8   C9   C17  C18   180.00   0.0  0
 3LZ  CONST_20  O8   C3   C4   N5    180.00   0.0  0
 3LZ  CONST_21  S10  C1   C6   N5    180.00   0.0  0
 3LZ  CONST_22  S10  C11  C12  C13   180.00   0.0  0
 3LZ  CONST_23  C22  C21  C9   C17   180.00   0.0  0
 3LZ  CONST_24  S10  C11  N16  C15   180.00   0.0  0
 3LZ  CONST_25  C19  N20  C21  C22   180.00   0.0  0
 3LZ  CONST_26  N7   C4   N5   C6    180.00   0.0  0
 3LZ  CONST_27  O8   C3   C2   C1    180.00   0.0  0
 3LZ  CONST_28  N7   C4   C3   C2    180.00   0.0  0
 3LZ  CONST_29  S10  C1   C2   C3    180.00   0.0  0
 3LZ  CONST_30  N20  C21  C9   O8    180.00   0.0  0
 3LZ  CONST_31  H4   C12  C13  C14   180.00   0.0  0
 3LZ  CONST_32  H6   C15  C14  C13   180.00   0.0  0
 3LZ  CONST_33  H2   C14  C13  C12   180.00   0.0  0
 3LZ  CONST_34  H10  C19  C18  C17   180.00   0.0  0
 3LZ  CONST_35  H3   C13  C14  C15   180.00   0.0  0
 3LZ  CONST_36  H11  C2   C1   C6    180.00   0.0  0
 3LZ  CONST_37  H9   C6   N5   C4    180.00   0.0  0
 3LZ  CONST_38  H5   C17  C18  C19   180.00   0.0  0
 3LZ  CONST_39  H1   C18  C17  C9    180.00   0.0  0
 3LZ  CONST_43  O25  C24  N7   C4      0.00   0.0  0
 3LZ  CONST_44  N26  C24  N7   C4    180.00   0.0  0
 3LZ  CONST_45  C27  N26  C24  O25     0.00   0.0  0
 3LZ  CONST_46  C27  N26  C24  N7    180.00   0.0  0
 3LZ  CONST_47  H16  N26  C24  O25   180.00   0.0  0
 3LZ  Var_01    C2   C1   S10  C11   -76.14  30.0  3
 3LZ  Var_02    N16  C11  S10  C1      0.46  30.0  1
 3LZ  Var_03    C23  C22  C21  C9     82.17  30.0  3
 3LZ  Var_04    H13  C23  C22  C21  -179.79  30.0  3
 3LZ  Var_05    H17  C27  N26  C24   -60.99  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
 3LZ  plan-1  C14  0.020
 3LZ  plan-1  C13  0.020
 3LZ  plan-1  C12  0.020
 3LZ  plan-1  C15  0.020
 3LZ  plan-1  C11  0.020
 3LZ  plan-1  S10  0.020
 3LZ  plan-1  N16  0.020
 3LZ  plan-1  H3   0.020
 3LZ  plan-1  H4   0.020
 3LZ  plan-1  H6   0.020
 3LZ  plan-1  H2   0.020
 3LZ  plan-2  N5   0.020
 3LZ  plan-2  C6   0.020
 3LZ  plan-2  C1   0.020
 3LZ  plan-2  C4   0.020
 3LZ  plan-2  C2   0.020
 3LZ  plan-2  C3   0.020
 3LZ  plan-2  O8   0.020
 3LZ  plan-2  S10  0.020
 3LZ  plan-2  H9   0.020
 3LZ  plan-2  H11  0.020
 3LZ  plan-2  N7   0.020
 3LZ  plan-3  C18  0.020
 3LZ  plan-3  C17  0.020
 3LZ  plan-3  C22  0.020
 3LZ  plan-3  C19  0.020
 3LZ  plan-3  C21  0.020
 3LZ  plan-3  O8   0.020
 3LZ  plan-3  C9   0.020
 3LZ  plan-3  N20  0.020
 3LZ  plan-3  H1   0.020
 3LZ  plan-3  H5   0.020
 3LZ  plan-3  H10  0.020
 3LZ  plan-4  C4   0.020
 3LZ  plan-4  C24  0.020
 3LZ  plan-4  O25  0.020
 3LZ  plan-4  N26  0.020
 3LZ  plan-4  C27  0.020
 3LZ  plan-4  H16  0.020
 3LZ  plan-4  N7   0.020
 3LZ  plan-4  H12  0.020

