# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 10:37:30 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-[4-(2-{[(4-chlorophenyl)carbonyl]amino}ethyl)phenoxy]-2-methylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(Oc1ccc(CCNC(=O)c2ccc(Cl)cc2)cc1)C(O)=O
#
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
 PEM  PEM  '2-[4-(2-{[(4-chlorophenyl)carbonyl]amino}ethyl)phenoxy]-2-methylpropanoic acid'  ligand  45  25  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PEM
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
 PEM  C1    C   CR6   0  -0.014   0.7991  -4.2157   8.5307
 PEM  C2    C   CR16  0  -0.276   1.3722  -4.1266   9.7962
 PEM  C3    C   CR16  0  -0.198   1.2768  -2.9610  10.5375
 PEM  C4    C   CR6   0  -0.040   0.6199  -1.8672   9.9929
 PEM  C5    C   CR16  0  -0.200   0.0635  -1.9230   8.7249
 PEM  C6    C   CR16  0  -0.289   0.1552  -3.1008   7.9996
 PEM  CL    CL  CL    0  -0.117   0.5002  -0.4044  10.9084
 PEM  C7    C   C     0   0.523   0.9515  -5.4892   7.7613
 PEM  O1    O   O     0  -0.485   1.9419  -6.1951   7.9001
 PEM  N1    N   NH1   0  -0.634  -0.0608  -5.7977   6.9384
 PEM  C8    C   CH2   0  -0.295   0.0165  -6.8375   5.9359
 PEM  C9    C   CH2   0  -0.536   0.9657  -6.4852   4.7796
 PEM  C10   C   CR6   0   0.377   0.2428  -2.3877   3.6423
 PEM  C11   C   CR16  0  -0.336  -0.6215  -3.4022   3.2277
 PEM  C12   C   CR16  0  -0.285  -0.3652  -4.7216   3.5543
 PEM  C13   C   CR6   0   0.110   0.7529  -5.0765   4.3073
 PEM  C14   C   CR16  0  -0.302   1.6121  -4.0587   4.6972
 PEM  C15   C   CR16  0  -0.352   1.3767  -2.7279   4.3718
 PEM  C16   C   CT    0   0.078   0.4250   0.0272   3.8628
 PEM  C17   C   CH3   0  -0.680   0.2286   0.0514   5.3776
 PEM  C18   C   CH3   0  -0.665  -0.3534   1.1836   3.2285
 PEM  C19   C   C     0   0.529   1.8784   0.1887   3.4105
 PEM  O3    O   OH1   0  -0.583   2.5640   0.9907   4.2090
 PEM  O4    O   O     0  -0.425   2.3231  -0.3092   2.4100
 PEM  H21   H   HCR6  0   0.272   1.8921  -4.9773  10.2158
 PEM  H31   H   HCR6  0   0.286   1.7129  -2.9052  11.5254
 PEM  H51   H   HCR6  0   0.287  -0.4332  -1.0598   8.3032
 PEM  HC6   H   HCR6  0   0.262  -0.2575  -3.1205   6.9981
 PEM  HN1   H   HNH1  0   0.407  -0.8523  -5.1785   6.8924
 PEM  HC81  H   HCH2  0   0.257  -0.9942  -6.9807   5.5562
 PEM  HC82  H   HCH2  0   0.257   0.3220  -7.7793   6.3935
 PEM  HC91  H   HCH2  0   0.251   1.9991  -6.6146   5.1048
 PEM  HC92  H   HCH2  0   0.258   0.7960  -7.2038   3.9743
 PEM  H11   H   HCR6  0   0.261  -1.5007  -3.1452   2.6497
 PEM  H12   H   HCR6  0   0.251  -1.0606  -5.4870   3.2291
 PEM  H14   H   HCR6  0   0.253   2.4908  -4.2997   5.2841
 PEM  H15   H   HCR6  0   0.272   2.0885  -1.9920   4.7178
 PEM  H171  H   HCH3  0   0.259   0.4487   1.0416   5.7722
 PEM  H172  H   HCH3  0   0.254  -0.8159  -0.1682   5.6016
 PEM  H173  H   HCH3  0   0.252   0.8475  -0.6636   5.9159
 PEM  H181  H   HCH3  0   0.255  -0.2644   1.1737   2.1421
 PEM  H182  H   HCH3  0   0.248   0.0117   2.1410   3.5961
 PEM  H183  H   HCH3  0   0.259  -1.4084   1.1008   3.4904
 PEM  HO3   H   HOH1  0   0.487   3.4571   1.1299   3.8577
 PEM  O2    O   O2    0  -0.489  -0.1149  -1.1369   3.2638

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
 PEM  C1   C2    aromatic  1.392  0.020  1.392
 PEM  C1   C6    aromatic  1.393  0.020  1.393
 PEM  C1   C7    single    1.496  0.020  1.496
 PEM  C2   C3    aromatic  1.385  0.020  1.385
 PEM  C2   H21   single    0.930  0.020  1.080
 PEM  C3   C4    aromatic  1.387  0.020  1.387
 PEM  C3   H31   single    0.930  0.020  1.080
 PEM  C4   C5    aromatic  1.386  0.020  1.386
 PEM  C4   CL    single    1.730  0.020  1.730
 PEM  C5   C6    aromatic  1.386  0.020  1.386
 PEM  C5   H51   single    0.930  0.020  1.080
 PEM  C6   HC6   single    0.930  0.020  1.080
 PEM  C7   O1    double    1.224  0.020  1.224
 PEM  C7   N1    single    1.341  0.020  1.341
 PEM  N1   C8    single    1.446  0.020  1.446
 PEM  N1   HN1   single    0.860  0.020  1.020
 PEM  C8   C9    single    1.537  0.020  1.537
 PEM  C8   HC81  single    0.970  0.020  1.090
 PEM  C8   HC82  single    0.970  0.020  1.090
 PEM  C9   C13   single    1.501  0.020  1.501
 PEM  C9   HC91  single    0.970  0.020  1.090
 PEM  C9   HC92  single    0.970  0.020  1.090
 PEM  C10  C11   aromatic  1.396  0.020  1.396
 PEM  C10  C15   aromatic  1.391  0.020  1.391
 PEM  C10  O2    single    1.355  0.020  1.355
 PEM  C11  C12   aromatic  1.383  0.020  1.383
 PEM  C11  H11   single    0.930  0.020  1.080
 PEM  C12  C13   aromatic  1.394  0.020  1.394
 PEM  C12  H12   single    0.930  0.020  1.080
 PEM  C13  C14   aromatic  1.388  0.020  1.388
 PEM  C14  C15   aromatic  1.390  0.020  1.390
 PEM  C14  H14   single    0.930  0.020  1.080
 PEM  C15  H15   single    0.930  0.020  1.080
 PEM  O2   C16   single    1.416  0.020  1.416
 PEM  C16  C17   single    1.528  0.020  1.528
 PEM  C16  C18   single    1.531  0.020  1.531
 PEM  C16  C19   single    1.531  0.020  1.531
 PEM  C17  H171  single    0.970  0.020  1.090
 PEM  C17  H172  single    0.970  0.020  1.090
 PEM  C17  H173  single    0.970  0.020  1.090
 PEM  C18  H181  single    0.970  0.020  1.090
 PEM  C18  H182  single    0.970  0.020  1.090
 PEM  C18  H183  single    0.970  0.020  1.090
 PEM  C19  O3    single    1.323  0.020  1.323
 PEM  C19  O4    double    1.203  0.020  1.203
 PEM  O3   HO3   single    0.850  0.020  0.980

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
 PEM  C7    C1   C6    122.18  3.000
 PEM  C7    C1   C2    118.70  3.000
 PEM  C6    C1   C2    119.07  3.000
 PEM  H21   C2   C3    119.18  3.000
 PEM  H21   C2   C1    120.01  3.000
 PEM  C3    C2   C1    120.81  3.000
 PEM  H31   C3   C4    120.60  3.000
 PEM  H31   C3   C2    120.31  3.000
 PEM  C4    C3   C2    119.09  3.000
 PEM  CL    C4   C5    119.38  3.000
 PEM  CL    C4   C3    119.45  3.000
 PEM  C5    C4   C3    121.17  3.000
 PEM  H51   C5   C6    120.30  3.000
 PEM  H51   C5   C4    120.60  3.000
 PEM  C6    C5   C4    119.10  3.000
 PEM  HC6   C6   C5    118.29  3.000
 PEM  HC6   C6   C1    120.94  3.000
 PEM  C5    C6   C1    120.74  3.000
 PEM  N1    C7   O1    123.22  3.000
 PEM  N1    C7   C1    115.77  3.000
 PEM  O1    C7   C1    121.01  3.000
 PEM  HN1   N1   C8    116.93  3.000
 PEM  HN1   N1   C7    118.72  3.000
 PEM  C8    N1   C7    123.40  3.000
 PEM  HC82  C8   HC81  107.02  3.000
 PEM  HC82  C8   C9    109.91  3.000
 PEM  HC81  C8   C9    109.93  3.000
 PEM  HC82  C8   N1    110.18  3.000
 PEM  HC81  C8   N1    106.66  3.000
 PEM  C9    C8   N1    112.93  3.000
 PEM  HC92  C9   HC91  106.78  3.000
 PEM  HC92  C9   C13   111.31  3.000
 PEM  HC91  C9   C13   109.85  3.000
 PEM  HC92  C9   C8    107.93  3.000
 PEM  HC91  C9   C8    109.48  3.000
 PEM  C13   C9   C8    111.36  3.000
 PEM  O2    C10  C15   125.99  3.000
 PEM  O2    C10  C11   115.12  3.000
 PEM  C15   C10  C11   118.88  3.000
 PEM  H11   C11  C12   120.18  3.000
 PEM  H11   C11  C10   119.26  3.000
 PEM  C12   C11  C10   120.56  3.000
 PEM  H12   C12  C13   119.80  3.000
 PEM  H12   C12  C11   118.93  3.000
 PEM  C13   C12  C11   121.27  3.000
 PEM  C14   C13  C12   117.49  3.000
 PEM  C14   C13  C9    120.80  3.000
 PEM  C12   C13  C9    121.51  3.000
 PEM  H14   C14  C15   118.49  3.000
 PEM  H14   C14  C13   119.41  3.000
 PEM  C15   C14  C13   122.10  3.000
 PEM  H15   C15  C14   117.74  3.000
 PEM  H15   C15  C10   122.58  3.000
 PEM  C14   C15  C10   119.68  3.000
 PEM  C19   C16  C18   106.30  3.000
 PEM  C19   C16  C17   114.42  3.000
 PEM  C18   C16  C17   109.47  3.000
 PEM  C19   C16  O2    108.89  3.000
 PEM  C18   C16  O2    104.58  3.000
 PEM  C17   C16  O2    112.54  3.000
 PEM  H173  C17  H172  108.11  3.000
 PEM  H173  C17  H171  107.67  3.000
 PEM  H172  C17  H171  107.61  3.000
 PEM  H173  C17  C16   114.02  3.000
 PEM  H172  C17  C16   108.88  3.000
 PEM  H171  C17  C16   110.36  3.000
 PEM  H183  C18  H182  108.07  3.000
 PEM  H183  C18  H181  108.53  3.000
 PEM  H182  C18  H181  108.49  3.000
 PEM  H183  C18  C16   109.58  3.000
 PEM  H182  C18  C16   110.71  3.000
 PEM  H181  C18  C16   111.37  3.000
 PEM  O4    C19  O3    124.15  3.000
 PEM  O4    C19  C16   123.59  3.000
 PEM  O3    C19  C16   112.18  3.000
 PEM  HO3   O3   C19   110.21  3.000
 PEM  C16   O2   C10   122.69  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
 PEM  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 PEM  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 PEM  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 PEM  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PEM  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 PEM  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PEM  CONST_07  C13   C12  C11  C10     0.00   0.0  0
 PEM  CONST_08  C13   C14  C15  C10     0.00   0.0  0
 PEM  CONST_09  C14   C15  C10  C11     0.00   0.0  0
 PEM  CONST_10  C14   C13  C12  C11     0.00   0.0  0
 PEM  CONST_11  C15   C10  C11  C12     0.00   0.0  0
 PEM  CONST_12  C15   C14  C13  C12     0.00   0.0  0
 PEM  CONST_13  CL    C4   C3   C2    180.00   0.0  0
 PEM  CONST_14  C7    C1   C2   C3    180.00   0.0  0
 PEM  CONST_15  C7    C1   C6   C5    180.00   0.0  0
 PEM  CONST_16  CL    C4   C5   C6    180.00   0.0  0
 PEM  CONST_17  C11   C12  C13  C9    180.00   0.0  0
 PEM  CONST_18  C15   C14  C13  C9    180.00   0.0  0
 PEM  CONST_19  O2    C10  C11  C12   180.00   0.0  0
 PEM  CONST_20  O2    C10  C15  C14   180.00   0.0  0
 PEM  CONST_21  H31   C3   C2   C1    180.00   0.0  0
 PEM  CONST_22  H51   C5   C6   C1    180.00   0.0  0
 PEM  CONST_23  HC6   C6   C1   C2    180.00   0.0  0
 PEM  CONST_24  H21   C2   C3   C4    180.00   0.0  0
 PEM  CONST_25  H12   C12  C11  C10   180.00   0.0  0
 PEM  CONST_26  H14   C14  C15  C10   180.00   0.0  0
 PEM  CONST_27  H15   C15  C10  C11   180.00   0.0  0
 PEM  CONST_28  H11   C11  C12  C13   180.00   0.0  0
 PEM  CONST_29  C8    N1   C7   C1    180.00   0.0  0
 PEM  CONST_30  HN1   N1   C7   C1      0.00   0.0  0
 PEM  CONST_31  C8    N1   C7   O1      0.00   0.0  0
 PEM  CONST_32  HO3   O3   C19  C16   180.00   0.0  0
 PEM  Var_01    O1    C7   C1   C2    -30.68  30.0  2
 PEM  Var_02    C12   C13  C9   C8    -73.83  30.0  2
 PEM  Var_03    C13   C9   C8   N1    -45.03  30.0  3
 PEM  Var_04    C17   C16  O2   C10   -55.93  30.0  3
 PEM  Var_05    C9    C8   N1   C7    -69.30  30.0  3
 PEM  Var_06    O3    C19  C16  O2   -161.08  30.0  3
 PEM  Var_07    H171  C17  C16  O2   -167.36  30.0  3
 PEM  Var_08    H181  C18  C16  O2    -57.10  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
 PEM  plan-1  C1   0.020
 PEM  plan-1  C2   0.020
 PEM  plan-1  C3   0.020
 PEM  plan-1  C4   0.020
 PEM  plan-1  C5   0.020
 PEM  plan-1  C6   0.020
 PEM  plan-1  CL   0.020
 PEM  plan-1  C7   0.020
 PEM  plan-1  H21  0.020
 PEM  plan-1  H31  0.020
 PEM  plan-1  H51  0.020
 PEM  plan-1  HC6  0.020
 PEM  plan-2  C9   0.020
 PEM  plan-2  C10  0.020
 PEM  plan-2  C11  0.020
 PEM  plan-2  C12  0.020
 PEM  plan-2  C13  0.020
 PEM  plan-2  C14  0.020
 PEM  plan-2  C15  0.020
 PEM  plan-2  H11  0.020
 PEM  plan-2  H12  0.020
 PEM  plan-2  H14  0.020
 PEM  plan-2  H15  0.020
 PEM  plan-2  O2   0.020
 PEM  plan-3  C1   0.020
 PEM  plan-3  C7   0.020
 PEM  plan-3  O1   0.020
 PEM  plan-3  N1   0.020
 PEM  plan-3  C8   0.020
 PEM  plan-3  HN1  0.020
 PEM  plan-4  C16  0.020
 PEM  plan-4  C19  0.020
 PEM  plan-4  O3   0.020
 PEM  plan-4  O4   0.020
 PEM  plan-4  HO3  0.020

