# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:44:13 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-[(2-azanyl-4-chloranyl-phenyl)carbamoylamino]-4-methyl-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C(O)=O)c(NC(=O)Nc2ccc(Cl)cc2N)c1
#
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
 5LP  5LP  '2-[(2-azanyl-4-chloranyl-phenyl)carbamoylamino]-4-methyl-benzoic acid'  ligand  36  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5LP
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
 5LP  N    N   NH1   0  -0.813  -1.3411   0.3431  -0.3265
 5LP  C2   C   CR16  0  -0.301  -5.0207  -1.5820   0.2389
 5LP  C3   C   CR16  0  -0.250  -4.9665  -0.2442  -0.0782
 5LP  C4   C   CR6   0  -0.213  -3.7493   0.4192  -0.2710
 5LP  O    O   O     0  -0.474  -2.7582   2.5241  -0.8212
 5LP  C11  C   CR6   0  -0.033   4.9782   0.0704  -0.4165
 5LP  C10  C   CR16  0  -0.262   4.1974  -0.6011  -1.3446
 5LP  C9   C   CR16  0  -0.277   2.8357  -0.3423  -1.3511
 5LP  C12  C   CR16  0  -0.297   4.4409   0.9666   0.4872
 5LP  C13  C   CR6   0   0.283   3.0630   1.2144   0.4884
 5LP  C8   C   CR6   0   0.267   2.2625   0.5446  -0.4539
 5LP  C7   C   C     0   0.727  -0.0614  -0.1417  -0.2142
 5LP  O2   O   O     0  -0.494   0.2333  -1.2841   0.0867
 5LP  C6   C   CR6   0   0.412  -2.5431  -0.3130  -0.1347
 5LP  O1   O   OH1   0  -0.587  -4.9655   2.3803  -0.6716
 5LP  C14  C   CR16  0  -0.376  -2.6209  -1.6733   0.1865
 5LP  C1   C   CR6   0   0.122  -3.8380  -2.3097   0.3748
 5LP  H1   H   HNH1  0   0.423  -1.4592   1.3237  -0.5665
 5LP  H2   H   HCR6  0   0.254  -5.9789  -2.0648   0.3812
 5LP  H3   H   HNH2  0   0.389   3.0720   2.3733   2.1510
 5LP  H4   H   HNH2  0   0.382   1.5442   1.9984   1.5818
 5LP  H5   H   HCR6  0   0.270  -5.8936   0.3009  -0.1827
 5LP  H6   H   HCH3  0   0.257  -4.0576  -3.8774   1.8152
 5LP  H7   H   HCH3  0   0.250  -4.6885  -4.2779   0.2273
 5LP  H8   H   HCH3  0   0.249  -2.9438  -4.2649   0.5079
 5LP  H9   H   HCR6  0   0.273   4.6344  -1.2964  -2.0469
 5LP  H10  H   HCR6  0   0.270   2.2046  -0.8355  -2.0789
 5LP  H11  H   HCR6  0   0.281   5.0770   1.4696   1.2044
 5LP  H12  H   HNH1  0   0.406   0.5903   1.7489  -0.7252
 5LP  H13  H   HOH1  0   0.491  -4.9022   3.3203  -0.8971
 5LP  H14  H   HCR6  0   0.285  -1.7137  -2.2448   0.2922
 5LP  C5   C   C     0   0.583  -3.7540   1.8533  -0.6109
 5LP  C    C   CH3   0  -0.723  -3.8798  -3.7615   0.7442
 5LP  N1   N   NH1   0  -0.790   0.8783   0.8136  -0.4778
 5LP  N2   N   NH2   0  -0.850   2.5151   2.1312   1.3477
 5LP  CL   CL  CL    0  -0.134   6.6887  -0.2219  -0.3829

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
 5LP  CL   C11  single    1.736  0.020  1.736
 5LP  C12  C11  aromatic  1.382  0.020  1.382
 5LP  C12  C13  aromatic  1.400  0.020  1.400
 5LP  N2   C13  single    1.371  0.020  1.371
 5LP  C11  C10  aromatic  1.386  0.020  1.386
 5LP  C13  C8   aromatic  1.406  0.020  1.406
 5LP  C10  C9   aromatic  1.386  0.020  1.386
 5LP  C8   C9   aromatic  1.386  0.020  1.386
 5LP  C8   N1   single    1.410  0.020  1.410
 5LP  N1   C7   single    1.366  0.020  1.366
 5LP  O    C5   double    1.219  0.020  1.219
 5LP  C7   N    single    1.373  0.020  1.373
 5LP  C7   O2   double    1.218  0.020  1.218
 5LP  C5   O1   single    1.323  0.020  1.323
 5LP  C5   C4   single    1.474  0.020  1.474
 5LP  N    C6   single    1.383  0.020  1.383
 5LP  C6   C4   aromatic  1.418  0.020  1.418
 5LP  C6   C14  aromatic  1.400  0.020  1.400
 5LP  C4   C3   aromatic  1.400  0.020  1.400
 5LP  C14  C1   aromatic  1.386  0.020  1.386
 5LP  C3   C2   aromatic  1.376  0.020  1.376
 5LP  C1   C2   aromatic  1.395  0.020  1.395
 5LP  C1   C    single    1.499  0.020  1.499
 5LP  N    H1   single    0.860  0.020  1.020
 5LP  C2   H2   single    0.930  0.020  1.080
 5LP  N2   H3   single    0.890  0.020  1.040
 5LP  N2   H4   single    0.890  0.020  1.040
 5LP  C3   H5   single    0.930  0.020  1.080
 5LP  C    H6   single    0.970  0.020  1.090
 5LP  C    H7   single    0.970  0.020  1.090
 5LP  C    H8   single    0.970  0.020  1.090
 5LP  C10  H9   single    0.930  0.020  1.080
 5LP  C9   H10  single    0.930  0.020  1.080
 5LP  C12  H11  single    0.930  0.020  1.080
 5LP  N1   H12  single    0.860  0.020  1.020
 5LP  O1   H13  single    0.850  0.020  0.980
 5LP  C14  H14  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
 5LP  H1   N    C6   112.92  3.000
 5LP  H1   N    C7   117.92  3.000
 5LP  C6   N    C7   129.15  3.000
 5LP  H2   C2   C1   120.33  3.000
 5LP  H2   C2   C3   119.93  3.000
 5LP  C1   C2   C3   119.74  3.000
 5LP  H5   C3   C4   119.59  3.000
 5LP  H5   C3   C2   118.62  3.000
 5LP  C4   C3   C2   121.79  3.000
 5LP  C6   C4   C5   121.84  3.000
 5LP  C6   C4   C3   118.82  3.000
 5LP  C5   C4   C3   119.35  3.000
 5LP  C12  C11  C10  122.21  3.000
 5LP  C10  C11  CL   119.11  3.000
 5LP  C12  C11  CL   118.68  3.000
 5LP  H9   C10  C9   120.96  3.000
 5LP  H9   C10  C11  121.26  3.000
 5LP  C9   C10  C11  117.78  3.000
 5LP  H10  C9   C8   119.07  3.000
 5LP  H10  C9   C10  119.41  3.000
 5LP  C8   C9   C10  121.52  3.000
 5LP  H11  C12  C13  119.70  3.000
 5LP  H11  C12  C11  120.41  3.000
 5LP  C13  C12  C11  119.88  3.000
 5LP  C8   C13  C12  118.39  3.000
 5LP  C8   C13  N2   120.73  3.000
 5LP  C12  C13  N2   120.82  3.000
 5LP  N1   C8   C13  118.64  3.000
 5LP  N1   C8   C9   121.14  3.000
 5LP  C13  C8   C9   120.22  3.000
 5LP  O2   C7   N1   122.51  3.000
 5LP  O2   C7   N    125.25  3.000
 5LP  N1   C7   N    112.24  3.000
 5LP  C14  C6   C4   118.47  3.000
 5LP  C14  C6   N    122.76  3.000
 5LP  C4   C6   N    118.77  3.000
 5LP  H13  O1   C5   109.73  3.000
 5LP  H14  C14  C1   118.85  3.000
 5LP  H14  C14  C6   119.42  3.000
 5LP  C1   C14  C6   121.73  3.000
 5LP  C14  C1   C    120.17  3.000
 5LP  C    C1   C2   120.37  3.000
 5LP  C14  C1   C2   119.45  3.000
 5LP  O1   C5   O    121.41  3.000
 5LP  O1   C5   C4   113.66  3.000
 5LP  O    C5   C4   124.93  3.000
 5LP  H8   C    H7   108.41  3.000
 5LP  H8   C    H6   107.69  3.000
 5LP  H7   C    H6   107.10  3.000
 5LP  H8   C    C1   111.74  3.000
 5LP  H7   C    C1   111.28  3.000
 5LP  H6   C    C1   110.43  3.000
 5LP  H12  N1   C7   119.95  3.000
 5LP  H12  N1   C8   117.44  3.000
 5LP  C7   N1   C8   122.59  3.000
 5LP  H4   N2   H3   112.29  3.000
 5LP  H4   N2   C13  116.28  3.000
 5LP  H3   N2   C13  116.09  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
 5LP  CONST_01  C6   C4   C3   C2      0.00   0.0  0
 5LP  CONST_02  C6   C14  C1   C2      0.00   0.0  0
 5LP  CONST_03  C14  C6   C4   C3      0.00   0.0  0
 5LP  CONST_04  C14  C1   C2   C3      0.00   0.0  0
 5LP  CONST_05  C1   C14  C6   C4      0.00   0.0  0
 5LP  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 5LP  CONST_07  C8   C13  C12  C11     0.00   0.0  0
 5LP  CONST_08  C8   C9   C10  C11     0.00   0.0  0
 5LP  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 5LP  CONST_10  C13  C8   C9   C10     0.00   0.0  0
 5LP  CONST_11  C12  C11  C10  C9      0.00   0.0  0
 5LP  CONST_12  C12  C13  C8   C9      0.00   0.0  0
 5LP  CONST_13  C3   C4   C6   N     180.00   0.0  0
 5LP  CONST_14  C1   C14  C6   N     180.00   0.0  0
 5LP  CONST_15  C5   C4   C3   C2    180.00   0.0  0
 5LP  CONST_16  C11  C12  C13  N2    180.00   0.0  0
 5LP  CONST_17  C9   C8   C13  N2    180.00   0.0  0
 5LP  CONST_18  C    C1   C2   C3    180.00   0.0  0
 5LP  CONST_19  C14  C6   C4   C5    180.00   0.0  0
 5LP  CONST_20  C6   C14  C1   C     180.00   0.0  0
 5LP  CONST_21  C13  C12  C11  CL    180.00   0.0  0
 5LP  CONST_22  C9   C10  C11  CL    180.00   0.0  0
 5LP  CONST_23  N1   C8   C9   C10   180.00   0.0  0
 5LP  CONST_24  N1   C8   C13  C12   180.00   0.0  0
 5LP  CONST_25  H14  C14  C1   C2    180.00   0.0  0
 5LP  CONST_26  H2   C2   C3   C4    180.00   0.0  0
 5LP  CONST_27  H10  C9   C10  C11   180.00   0.0  0
 5LP  CONST_28  H11  C12  C11  C10   180.00   0.0  0
 5LP  CONST_29  H9   C10  C11  C12   180.00   0.0  0
 5LP  CONST_30  H5   C3   C4   C6    180.00   0.0  0
 5LP  CONST_31  C7   N    C6   C4    180.00   0.0  0
 5LP  CONST_34  C14  C6   N    C7      0.00   0.0  0
 5LP  CONST_35  H1   N    C6   C4      0.00   0.0  0
 5LP  CONST_39  O2   C7   N1   C8      0.00   0.0  0
 5LP  CONST_40  C6   N    C7   O2      0.00   0.0  0
 5LP  CONST_41  C8   N1   C7   N     180.00   0.0  0
 5LP  CONST_42  C6   N    C7   N1    180.00   0.0  0
 5LP  CONST_43  H13  O1   C5   C4    180.00   0.0  0
 5LP  Var_01    O    C5   C4   C3   -178.76  30.0  2
 5LP  Var_02    H6   C    C1   C2    -78.32  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
 5LP  plan-1  C11  0.020
 5LP  plan-1  C10  0.020
 5LP  plan-1  C9   0.020
 5LP  plan-1  C12  0.020
 5LP  plan-1  C13  0.020
 5LP  plan-1  C8   0.020
 5LP  plan-1  H9   0.020
 5LP  plan-1  H10  0.020
 5LP  plan-1  H11  0.020
 5LP  plan-1  N1   0.020
 5LP  plan-1  N2   0.020
 5LP  plan-1  CL   0.020
 5LP  plan-2  C4   0.020
 5LP  plan-2  O    0.020
 5LP  plan-2  O1   0.020
 5LP  plan-2  H13  0.020
 5LP  plan-2  C5   0.020
 5LP  plan-3  N    0.020
 5LP  plan-3  C2   0.020
 5LP  plan-3  C3   0.020
 5LP  plan-3  C4   0.020
 5LP  plan-3  C6   0.020
 5LP  plan-3  C14  0.020
 5LP  plan-3  C1   0.020
 5LP  plan-3  H2   0.020
 5LP  plan-3  H5   0.020
 5LP  plan-3  H14  0.020
 5LP  plan-3  C5   0.020
 5LP  plan-3  C    0.020
 5LP  plan-4  N    0.020
 5LP  plan-4  C8   0.020
 5LP  plan-4  C7   0.020
 5LP  plan-4  O2   0.020
 5LP  plan-4  C6   0.020
 5LP  plan-4  H1   0.020
 5LP  plan-4  H12  0.020
 5LP  plan-4  N1   0.020
 5LP  plan-5  C13  0.020
 5LP  plan-5  H3   0.020
 5LP  plan-5  H4   0.020
 5LP  plan-5  N2   0.020

