# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:37:22 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 1-(2-chlorobenzyl)-N-hydroxy-4-phenyl-1H-pyrrole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1cn(Cc2ccccc2Cl)cc1c3ccccc3
#
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
 YU7  YU7  1-(2-chlorobenzyl)-N-hydroxy-4-phenyl-1H-pyrrole-3-carboxamide  ligand  38  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YU7
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
 YU7  CL    CL  CL    0  -0.117  -2.4868  -1.5185  -1.3575
 YU7  C10   C   CR6   0  -0.094  -3.3898  -0.1423  -0.8135
 YU7  C9    C   CR16  0  -0.200  -4.3151   0.4258  -1.6737
 YU7  C8    C   CR16  0  -0.271  -5.0528   1.5231  -1.2515
 YU7  C7    C   CR16  0  -0.231  -4.8629   2.0410   0.0206
 YU7  C6    C   CR16  0  -0.313  -3.9301   1.4590   0.8671
 YU7  C5    C   CR6   0   0.177  -3.1768   0.3596   0.4688
 YU7  C4    C   CH2   0  -0.376  -2.1723  -0.2439   1.4086
 YU7  N2    N   NR5   0  -0.421  -0.8082  -0.0575   0.9460
 YU7  C3    C   CR15  0  -0.002  -0.2844   1.1097   0.5064
 YU7  C11   C   CR15  0  -0.061   0.1529  -1.0206   0.9303
 YU7  C12   C   CR5   0   0.016   1.3281  -0.4716   0.4785
 YU7  C2    C   CR5   0  -0.232   1.0421   0.8994   0.1996
 YU7  C1    C   C     0   0.424   1.9991   1.9512  -0.1846
 YU7  N1    N   NH1   0  -0.376   1.4921   2.8393  -1.0693
 YU7  O2    O   OH1   0  -0.544   2.1424   4.0161  -1.2911
 YU7  O1    O   O     0  -0.466   3.1430   2.0067   0.2347
 YU7  C13   C   CR6   0   0.069   2.5727  -1.2151   0.2600
 YU7  C18   C   CR16  0  -0.321   2.9969  -2.1700   1.1862
 YU7  C17   C   CR16  0  -0.241   4.1527  -2.9078   0.9707
 YU7  C16   C   CR16  0  -0.272   4.9121  -2.6990  -0.1726
 YU7  C15   C   CR16  0  -0.243   4.5004  -1.7507  -1.1013
 YU7  C14   C   CR16  0  -0.315   3.3427  -1.0181  -0.8881
 YU7  H9    H   HCR6  0   0.283  -4.4618   0.0156  -2.6636
 YU7  H8    H   HCR6  0   0.272  -5.7758   1.9679  -1.9219
 YU7  H7    H   HCR6  0   0.267  -5.4355   2.8957   0.3545
 YU7  H6    H   HCR6  0   0.269  -3.7784   1.8632   1.8604
 YU7  H41C  H   HCH2  0   0.293  -2.2857   0.2011   2.3981
 YU7  H42C  H   HCH2  0   0.288  -2.3373  -1.3158   1.5190
 YU7  H3    H   HCR5  0   0.303  -0.8707   2.0151   0.4830
 YU7  H11   H   HCR5  0   0.291  -0.0760  -2.0393   1.2006
 YU7  H1    H   HNH1  0   0.415   0.5215   2.8306  -1.3490
 YU7  H18   H   HCR6  0   0.246   2.4239  -2.3270   2.0921
 YU7  H14   H   HCR6  0   0.243   3.0220  -0.3054  -1.6374
 YU7  H17   H   HCR6  0   0.254   4.4647  -3.6405   1.7039
 YU7  H16   H   HCR6  0   0.254   5.8164  -3.2697  -0.3392
 YU7  H15   H   HCR6  0   0.254   5.0800  -1.5862  -2.0007
 YU7  H2    H   HOH1  0   0.477   2.6425   3.8966  -2.1084

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
 YU7  CL   C10   single    1.734  0.020  1.734
 YU7  C10  C9    aromatic  1.385  0.020  1.385
 YU7  C10  C5    aromatic  1.393  0.020  1.393
 YU7  C9   C8    aromatic  1.388  0.020  1.388
 YU7  C8   C7    aromatic  1.387  0.020  1.387
 YU7  C7   C6    aromatic  1.388  0.020  1.388
 YU7  C6   C5    aromatic  1.391  0.020  1.391
 YU7  C5   C4    single    1.502  0.020  1.502
 YU7  C4   N2    single    1.452  0.020  1.452
 YU7  N2   C3    aromatic  1.353  0.020  1.353
 YU7  N2   C11   aromatic  1.361  0.020  1.361
 YU7  C3   C2    aromatic  1.378  0.020  1.378
 YU7  C11  C12   aromatic  1.374  0.020  1.374
 YU7  C12  C2    aromatic  1.428  0.020  1.428
 YU7  C12  C13   single    1.466  0.020  1.466
 YU7  C2   C1    single    1.473  0.020  1.473
 YU7  C1   N1    single    1.352  0.020  1.352
 YU7  C1   O1    double    1.220  0.020  1.220
 YU7  N1   O2    single    1.363  0.020  1.363
 YU7  C13  C18   aromatic  1.396  0.020  1.396
 YU7  C13  C14   aromatic  1.396  0.020  1.396
 YU7  C18  C17   aromatic  1.388  0.020  1.388
 YU7  C17  C16   aromatic  1.388  0.020  1.388
 YU7  C16  C15   aromatic  1.390  0.020  1.390
 YU7  C15  C14   aromatic  1.387  0.020  1.387
 YU7  O2   H2    single    0.850  0.020  0.980
 YU7  C9   H9    single    0.930  0.020  1.080
 YU7  C8   H8    single    0.930  0.020  1.080
 YU7  C7   H7    single    0.930  0.020  1.080
 YU7  C6   H6    single    0.930  0.020  1.080
 YU7  C4   H41C  single    0.970  0.020  1.090
 YU7  C4   H42C  single    0.970  0.020  1.090
 YU7  C3   H3    single    0.930  0.020  1.080
 YU7  C11  H11   single    0.930  0.020  1.080
 YU7  N1   H1    single    0.890  0.020  1.040
 YU7  C18  H18   single    0.930  0.020  1.080
 YU7  C14  H14   single    0.930  0.020  1.080
 YU7  C17  H17   single    0.930  0.020  1.080
 YU7  C16  H16   single    0.930  0.020  1.080
 YU7  C15  H15   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
 YU7  C5    C10  C9    121.72  3.000
 YU7  C5    C10  CL    119.68  3.000
 YU7  C9    C10  CL    118.60  3.000
 YU7  H9    C9   C8    120.40  3.000
 YU7  H9    C9   C10   120.23  3.000
 YU7  C8    C9   C10   119.37  3.000
 YU7  H8    C8   C7    120.44  3.000
 YU7  H8    C8   C9    119.46  3.000
 YU7  C7    C8   C9    120.10  3.000
 YU7  H7    C7   C6    119.93  3.000
 YU7  H7    C7   C8    120.39  3.000
 YU7  C6    C7   C8    119.68  3.000
 YU7  H6    C6   C5    118.80  3.000
 YU7  H6    C6   C7    119.81  3.000
 YU7  C5    C6   C7    121.39  3.000
 YU7  C4    C5   C6    120.03  3.000
 YU7  C4    C5   C10   122.23  3.000
 YU7  C6    C5   C10   117.74  3.000
 YU7  H42C  C4   H41C  107.06  3.000
 YU7  H42C  C4   N2    107.49  3.000
 YU7  H41C  C4   N2    109.52  3.000
 YU7  H42C  C4   C5    110.93  3.000
 YU7  H41C  C4   C5    109.52  3.000
 YU7  N2    C4   C5    112.17  3.000
 YU7  C11   N2   C3    109.48  3.000
 YU7  C11   N2   C4    125.19  3.000
 YU7  C3    N2   C4    125.30  3.000
 YU7  H3    C3   C2    130.28  3.000
 YU7  H3    C3   N2    121.38  3.000
 YU7  C2    C3   N2    108.27  3.000
 YU7  H11   C11  C12   129.90  3.000
 YU7  H11   C11  N2    121.05  3.000
 YU7  C12   C11  N2    108.98  3.000
 YU7  C13   C12  C2    128.89  3.000
 YU7  C13   C12  C11   124.94  3.000
 YU7  C2    C12  C11   106.05  3.000
 YU7  C1    C2   C12   127.32  3.000
 YU7  C1    C2   C3    125.08  3.000
 YU7  C12   C2   C3    107.22  3.000
 YU7  O1    C1   N1    123.14  3.000
 YU7  O1    C1   C2    123.52  3.000
 YU7  N1    C1   C2    113.33  3.000
 YU7  H1    N1   O2    114.89  3.000
 YU7  H1    N1   C1    122.40  3.000
 YU7  O2    N1   C1    119.65  3.000
 YU7  H2    O2   N1    106.14  3.000
 YU7  C14   C13  C18   118.32  3.000
 YU7  C14   C13  C12   121.27  3.000
 YU7  C18   C13  C12   120.39  3.000
 YU7  H18   C18  C17   119.55  3.000
 YU7  H18   C18  C13   119.55  3.000
 YU7  C17   C18  C13   120.90  3.000
 YU7  H17   C17  C16   120.13  3.000
 YU7  H17   C17  C18   119.64  3.000
 YU7  C16   C17  C18   120.22  3.000
 YU7  H16   C16  C15   120.30  3.000
 YU7  H16   C16  C17   120.30  3.000
 YU7  C15   C16  C17   119.40  3.000
 YU7  H15   C15  C14   119.63  3.000
 YU7  H15   C15  C16   120.02  3.000
 YU7  C14   C15  C16   120.34  3.000
 YU7  H14   C14  C15   119.25  3.000
 YU7  H14   C14  C13   119.91  3.000
 YU7  C15   C14  C13   120.81  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
 YU7  CONST_01  C7   C8   C9   C10    0.00   0.0  0
 YU7  CONST_02  C7   C6   C5   C10    0.00   0.0  0
 YU7  CONST_03  C6   C5   C10  C9     0.00   0.0  0
 YU7  CONST_04  C6   C7   C8   C9     0.00   0.0  0
 YU7  CONST_05  C5   C10  C9   C8     0.00   0.0  0
 YU7  CONST_06  C5   C6   C7   C8     0.00   0.0  0
 YU7  CONST_07  C12  C2   C3   N2     0.00   0.0  0
 YU7  CONST_08  C2   C12  C11  N2     0.00   0.0  0
 YU7  CONST_09  C13  C12  C11  N2   180.00   0.0  0
 YU7  CONST_10  C12  C11  N2   C3     0.00   0.0  0
 YU7  CONST_11  C11  C12  C2   C3     0.00   0.0  0
 YU7  CONST_12  C13  C12  C2   C3   180.00   0.0  0
 YU7  CONST_13  C2   C3   N2   C11    0.00   0.0  0
 YU7  CONST_16  C17  C18  C13  C12  180.00   0.0  0
 YU7  CONST_17  C15  C14  C13  C12  180.00   0.0  0
 YU7  CONST_20  C16  C17  C18  C13    0.00   0.0  0
 YU7  CONST_21  C16  C15  C14  C13    0.00   0.0  0
 YU7  CONST_22  C15  C14  C13  C18    0.00   0.0  0
 YU7  CONST_23  C15  C16  C17  C18    0.00   0.0  0
 YU7  CONST_24  C14  C13  C18  C17    0.00   0.0  0
 YU7  CONST_25  C14  C15  C16  C17    0.00   0.0  0
 YU7  CONST_26  C8   C9   C10  CL   180.00   0.0  0
 YU7  CONST_27  C6   C5   C10  CL   180.00   0.0  0
 YU7  CONST_28  C4   C5   C10  C9   180.00   0.0  0
 YU7  CONST_29  C4   C5   C6   C7   180.00   0.0  0
 YU7  CONST_30  C2   C3   N2   C4   180.00   0.0  0
 YU7  CONST_31  C12  C11  N2   C4   180.00   0.0  0
 YU7  CONST_32  C1   C2   C3   N2   180.00   0.0  0
 YU7  CONST_33  C1   C2   C12  C11  180.00   0.0  0
 YU7  CONST_34  C13  C12  C2   C1     0.00   0.0  0
 YU7  CONST_35  H8   C8   C9   C10  180.00   0.0  0
 YU7  CONST_36  H6   C6   C5   C10  180.00   0.0  0
 YU7  CONST_37  H7   C7   C8   C9   180.00   0.0  0
 YU7  CONST_38  H9   C9   C8   C7   180.00   0.0  0
 YU7  CONST_39  H11  C11  N2   C3   180.00   0.0  0
 YU7  CONST_40  H3   C3   N2   C11  180.00   0.0  0
 YU7  CONST_41  H18  C18  C13  C12    0.00   0.0  0
 YU7  CONST_42  H14  C14  C13  C12    0.00   0.0  0
 YU7  CONST_43  H17  C17  C18  C13  180.00   0.0  0
 YU7  CONST_44  H15  C15  C14  C13  180.00   0.0  0
 YU7  CONST_45  H16  C16  C17  C18  180.00   0.0  0
 YU7  CONST_46  O2   N1   C1   C2   180.00   0.0  0
 YU7  CONST_47  H1   N1   C1   C2     0.00   0.0  0
 YU7  Var_01    N2   C4   C5   C10   67.13  30.0  2
 YU7  Var_02    C3   N2   C4   C5    47.66  30.0  2
 YU7  Var_03    N1   C1   C2   C3   -43.71  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
 YU7  plan-1  C4   0.020
 YU7  plan-1  N2   0.020
 YU7  plan-1  C3   0.020
 YU7  plan-1  C11  0.020
 YU7  plan-1  C12  0.020
 YU7  plan-1  C2   0.020
 YU7  plan-1  C1   0.020
 YU7  plan-1  C13  0.020
 YU7  plan-1  H3   0.020
 YU7  plan-1  H11  0.020
 YU7  plan-2  CL   0.020
 YU7  plan-2  C10  0.020
 YU7  plan-2  C9   0.020
 YU7  plan-2  C8   0.020
 YU7  plan-2  C7   0.020
 YU7  plan-2  C6   0.020
 YU7  plan-2  C5   0.020
 YU7  plan-2  C4   0.020
 YU7  plan-2  H9   0.020
 YU7  plan-2  H8   0.020
 YU7  plan-2  H7   0.020
 YU7  plan-2  H6   0.020
 YU7  plan-3  C12  0.020
 YU7  plan-3  C13  0.020
 YU7  plan-3  C18  0.020
 YU7  plan-3  C17  0.020
 YU7  plan-3  C16  0.020
 YU7  plan-3  C15  0.020
 YU7  plan-3  C14  0.020
 YU7  plan-3  H18  0.020
 YU7  plan-3  H14  0.020
 YU7  plan-3  H17  0.020
 YU7  plan-3  H16  0.020
 YU7  plan-3  H15  0.020
 YU7  plan-4  C2   0.020
 YU7  plan-4  C1   0.020
 YU7  plan-4  N1   0.020
 YU7  plan-4  O2   0.020
 YU7  plan-4  O1   0.020
 YU7  plan-4  H1   0.020

