# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:42:40 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-[(2,6-dichloro-3-methylphenyl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Cl)c(Nc2ccccc2C(O)=O)c1Cl
#
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
 JMS  JMS  '2-[(2,6-dichloro-3-methylphenyl)amino]benzoic acid'  ligand  29  19  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JMS
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
 JMS  OXT  O   OC    -1  -0.599  -1.2252  -0.8257   2.5121
 JMS  C7   C   C      0   0.372  -0.9513  -1.0719   1.3228
 JMS  OH   O   O      0  -0.577   0.0013  -1.7438   0.8889
 JMS  C1   C   CR6    0  -0.065  -1.9318  -0.5618   0.2758
 JMS  C6   C   CR16   0  -0.299  -3.2892  -0.7946   0.4890
 JMS  C5   C   CR16   0  -0.268  -4.2445  -0.5330  -0.4814
 JMS  C4   C   CR16   0  -0.269  -3.8441   0.0100  -1.6956
 JMS  C3   C   CR16   0  -0.328  -2.5096   0.3111  -1.9056
 JMS  C2   C   CR6    0   0.305  -1.5470   0.0310  -0.9331
 JMS  N    N   NH1    0  -0.783  -0.2272   0.3871  -1.2308
 JMS  C1B  C   CR6    0   0.529   0.7615   0.6982  -0.3256
 JMS  C2B  C   CR6    0  -0.193   2.0464   0.1495  -0.4381
 JMS  CL1  CL  CL     0  -0.124   2.3220  -1.0103  -1.6984
 JMS  C3B  C   CR6    0   0.164   3.0969   0.4711   0.4113
 JMS  C7B  C   CH3    0  -0.722   4.4574  -0.1362   0.2530
 JMS  C4B  C   CR16   0  -0.358   2.8362   1.3701   1.4421
 JMS  C5B  C   CR16   0  -0.197   1.5866   1.9446   1.5879
 JMS  C6B  C   CR6    0  -0.131   0.5738   1.6319   0.6994
 JMS  CL2  CL  CL     0  -0.111  -0.9284   2.4800   0.8340
 JMS  H2   H   HCR6   0   0.242  -3.5975  -1.2255   1.4337
 JMS  H3   H   HCR6   0   0.243  -5.2879  -0.7506  -0.2928
 JMS  H4   H   HCR6   0   0.248  -4.5714   0.2242  -2.4686
 JMS  H5   H   HCR6   0   0.253  -2.1997   0.7819  -2.8315
 JMS  H6   H   HNH1   0   0.386   0.0877   0.1317  -2.1531
 JMS  H7   H   HCH3   0   0.250   4.8818   0.0796  -0.7285
 JMS  H8   H   HCH3   0   0.251   5.1395   0.2529   1.0069
 JMS  H9   H   HCH3   0   0.251   4.4274  -1.2218   0.3573
 JMS  H10  H   HCR6   0   0.258   3.6279   1.6336   2.1314
 JMS  H11  H   HCR6   0   0.274   1.4067   2.6614   2.3776

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
 JMS  CL2  C6B  single    1.730  0.020  1.730
 JMS  C5B  C4B  aromatic  1.383  0.020  1.383
 JMS  C5B  C6B  aromatic  1.383  0.020  1.383
 JMS  C4B  C3B  aromatic  1.392  0.020  1.392
 JMS  C6B  C1B  aromatic  1.399  0.020  1.399
 JMS  C3B  C7B  single    1.498  0.020  1.498
 JMS  C3B  C2B  aromatic  1.389  0.020  1.389
 JMS  C1B  N    single    1.376  0.020  1.376
 JMS  C1B  C2B  aromatic  1.402  0.020  1.402
 JMS  N    C2   single    1.399  0.020  1.399
 JMS  C2B  CL1  single    1.735  0.020  1.735
 JMS  C3   C2   aromatic  1.397  0.020  1.397
 JMS  C3   C4   aromatic  1.384  0.020  1.384
 JMS  OH   C7   deloc     1.244  0.020  1.244
 JMS  C2   C1   aromatic  1.400  0.020  1.400
 JMS  C4   C5   aromatic  1.389  0.020  1.389
 JMS  C1   C7   single    1.522  0.020  1.522
 JMS  C1   C6   aromatic  1.394  0.020  1.394
 JMS  C7   OXT  deloc     1.245  0.020  1.245
 JMS  C5   C6   aromatic  1.387  0.020  1.387
 JMS  C6   H2   single    0.930  0.020  1.080
 JMS  C5   H3   single    0.930  0.020  1.080
 JMS  C4   H4   single    0.930  0.020  1.080
 JMS  C3   H5   single    0.930  0.020  1.080
 JMS  N    H6   single    0.860  0.020  1.020
 JMS  C7B  H7   single    0.970  0.020  1.090
 JMS  C7B  H8   single    0.970  0.020  1.090
 JMS  C7B  H9   single    0.970  0.020  1.090
 JMS  C4B  H10  single    0.930  0.020  1.080
 JMS  C5B  H11  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
 JMS  C1   C7   OH   115.74  3.000
 JMS  C1   C7   OXT  116.67  3.000
 JMS  OH   C7   OXT  127.49  3.000
 JMS  C2   C1   C6   118.06  3.000
 JMS  C6   C1   C7   117.78  3.000
 JMS  C2   C1   C7   123.96  3.000
 JMS  H2   C6   C5   119.30  3.000
 JMS  H2   C6   C1   118.49  3.000
 JMS  C5   C6   C1   122.18  3.000
 JMS  H3   C5   C4   120.58  3.000
 JMS  H3   C5   C6   120.29  3.000
 JMS  C4   C5   C6   119.14  3.000
 JMS  H4   C4   C3   119.76  3.000
 JMS  H4   C4   C5   120.52  3.000
 JMS  C3   C4   C5   119.71  3.000
 JMS  H5   C3   C2   119.01  3.000
 JMS  H5   C3   C4   119.98  3.000
 JMS  C2   C3   C4   121.01  3.000
 JMS  N    C2   C3   116.80  3.000
 JMS  C3   C2   C1   119.78  3.000
 JMS  N    C2   C1   123.41  3.000
 JMS  H6   N    C1B  115.78  3.000
 JMS  H6   N    C2   115.16  3.000
 JMS  C1B  N    C2   126.54  3.000
 JMS  C6B  C1B  C2B  116.30  3.000
 JMS  C2B  C1B  N    121.15  3.000
 JMS  C6B  C1B  N    122.43  3.000
 JMS  C3B  C2B  CL1  118.62  3.000
 JMS  CL1  C2B  C1B  117.76  3.000
 JMS  C3B  C2B  C1B  123.62  3.000
 JMS  C4B  C3B  C7B  120.66  3.000
 JMS  C7B  C3B  C2B  121.90  3.000
 JMS  C4B  C3B  C2B  117.44  3.000
 JMS  H9   C7B  H8   107.86  3.000
 JMS  H9   C7B  H7   107.07  3.000
 JMS  H8   C7B  H7   107.98  3.000
 JMS  H9   C7B  C3B  111.61  3.000
 JMS  H8   C7B  C3B  110.55  3.000
 JMS  H7   C7B  C3B  111.60  3.000
 JMS  H10  C4B  C5B  119.51  3.000
 JMS  H10  C4B  C3B  119.46  3.000
 JMS  C5B  C4B  C3B  121.03  3.000
 JMS  H11  C5B  C6B  119.81  3.000
 JMS  H11  C5B  C4B  120.17  3.000
 JMS  C6B  C5B  C4B  120.00  3.000
 JMS  CL2  C6B  C5B  118.35  3.000
 JMS  C5B  C6B  C1B  121.55  3.000
 JMS  CL2  C6B  C1B  120.04  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
 JMS  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 JMS  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 JMS  CONST_03  C3   C2   C1   C6     0.00   0.0  0
 JMS  CONST_04  C3   C4   C5   C6     0.00   0.0  0
 JMS  CONST_05  C2   C3   C4   C5     0.00   0.0  0
 JMS  CONST_06  C2   C1   C6   C5     0.00   0.0  0
 JMS  CONST_07  C4B  C5B  C6B  C1B    0.00   0.0  0
 JMS  CONST_08  C4B  C3B  C2B  C1B    0.00   0.0  0
 JMS  CONST_09  C5B  C4B  C3B  C2B    0.00   0.0  0
 JMS  CONST_10  C5B  C6B  C1B  C2B    0.00   0.0  0
 JMS  CONST_11  C6B  C5B  C4B  C3B    0.00   0.0  0
 JMS  CONST_12  C6B  C1B  C2B  C3B    0.00   0.0  0
 JMS  CONST_13  C3   C2   C1   C7   180.00   0.0  0
 JMS  CONST_14  C5   C6   C1   C7   180.00   0.0  0
 JMS  CONST_15  N    C2   C1   C6   180.00   0.0  0
 JMS  CONST_16  N    C2   C3   C4   180.00   0.0  0
 JMS  CONST_17  C5B  C6B  C1B  N    180.00   0.0  0
 JMS  CONST_18  C3B  C2B  C1B  N    180.00   0.0  0
 JMS  CONST_19  C7B  C3B  C2B  C1B  180.00   0.0  0
 JMS  CONST_20  CL2  C6B  C1B  C2B  180.00   0.0  0
 JMS  CONST_21  C4B  C3B  C2B  CL1  180.00   0.0  0
 JMS  CONST_22  C6B  C1B  C2B  CL1  180.00   0.0  0
 JMS  CONST_23  C5B  C4B  C3B  C7B  180.00   0.0  0
 JMS  CONST_24  CL2  C6B  C5B  C4B  180.00   0.0  0
 JMS  CONST_25  H5   C3   C2   C1   180.00   0.0  0
 JMS  CONST_26  H3   C5   C6   C1   180.00   0.0  0
 JMS  CONST_27  H4   C4   C5   C6   180.00   0.0  0
 JMS  CONST_28  H2   C6   C5   C4   180.00   0.0  0
 JMS  CONST_29  H11  C5B  C6B  C1B  180.00   0.0  0
 JMS  CONST_30  H10  C4B  C3B  C2B  180.00   0.0  0
 JMS  Var_01    C1B  N    C2   C1   -26.04  30.0  2
 JMS  Var_02    C6B  C1B  N    C2   -50.44  30.0  2
 JMS  Var_03    C2   C1   C7   OXT  137.98  30.0  3
 JMS  Var_04    H7   C7B  C3B  C2B   59.15  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
 JMS  plan-1  C7   0.020
 JMS  plan-1  C1   0.020
 JMS  plan-1  C6   0.020
 JMS  plan-1  C5   0.020
 JMS  plan-1  C4   0.020
 JMS  plan-1  C3   0.020
 JMS  plan-1  C2   0.020
 JMS  plan-1  N    0.020
 JMS  plan-1  H2   0.020
 JMS  plan-1  H3   0.020
 JMS  plan-1  H4   0.020
 JMS  plan-1  H5   0.020
 JMS  plan-2  N    0.020
 JMS  plan-2  C1B  0.020
 JMS  plan-2  C2B  0.020
 JMS  plan-2  CL1  0.020
 JMS  plan-2  C3B  0.020
 JMS  plan-2  C7B  0.020
 JMS  plan-2  C4B  0.020
 JMS  plan-2  C5B  0.020
 JMS  plan-2  C6B  0.020
 JMS  plan-2  CL2  0.020
 JMS  plan-2  H10  0.020
 JMS  plan-2  H11  0.020
 JMS  plan-3  OXT  0.020
 JMS  plan-3  C7   0.020
 JMS  plan-3  OH   0.020
 JMS  plan-3  C1   0.020

