# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 17:51:48 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  44  25  .  2021-08-19  2022-09-22
;
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  -0.015   0.8666  -4.2288   8.6060
 PEM  C2    C   CR16   0  -0.276   1.4190  -4.1814   9.8831
 PEM  C3    C   CR16   0  -0.199   1.3773  -3.0171  10.6312
 PEM  C4    C   CR6    0  -0.041   0.7973  -1.8828  10.0818
 PEM  C5    C   CR16   0  -0.199   0.2628  -1.8979   8.8033
 PEM  C6    C   CR16   0  -0.291   0.2978  -3.0751   8.0722
 PEM  CL    CL  CL     0  -0.117   0.7502  -0.4202  11.0044
 PEM  C7    C   C      0   0.521   0.9686  -5.5015   7.8262
 PEM  O1    O   O      0  -0.485   1.9155  -6.2612   7.9831
 PEM  N1    N   NH1    0  -0.633  -0.0355  -5.7462   6.9722
 PEM  C8    C   CH2    0  -0.294   0.0145  -6.7779   5.9598
 PEM  C9    C   CH2    0  -0.534   0.9601  -6.4291   4.8000
 PEM  C10   C   CR6    0   0.381   0.1611  -2.3514   3.6086
 PEM  C11   C   CR16   0  -0.349  -0.6411  -3.4022   3.1518
 PEM  C12   C   CR16   0  -0.286  -0.3596  -4.7123   3.4963
 PEM  C13   C   CR6    0   0.105   0.7288  -5.0303   4.3068
 PEM  C14   C   CR16   0  -0.306   1.5313  -3.9810   4.7353
 PEM  C15   C   CR16   0  -0.357   1.2677  -2.6588   4.3989
 PEM  C16   C   CT     0   0.083   0.3959   0.0654   3.7417
 PEM  C17   C   CH3    0  -0.665   0.1397   0.2189   5.2375
 PEM  C18   C   CH3    0  -0.673  -0.3062   1.1962   2.9932
 PEM  C19   C   C      0   0.401   1.8999   0.1185   3.3433
 PEM  O3    O   OC    -1  -0.597   2.6551   0.7255   4.1257
 PEM  O4    O   O      0  -0.594   2.1988  -0.4000   2.2548
 PEM  H21   H   HCR6   0   0.271   1.8808  -5.0637  10.3057
 PEM  H31   H   HCR6   0   0.285   1.7972  -2.9931  11.6274
 PEM  H51   H   HCR6   0   0.286  -0.1699  -1.0033   8.3768
 PEM  HC6   H   HCR6   0   0.265  -0.0939  -3.0638   7.0624
 PEM  HN1   H   HNH1   0   0.406  -0.7899  -5.0840   6.9077
 PEM  HC81  H   HCH2   0   0.254  -1.0012  -6.9012   5.5856
 PEM  HC82  H   HCH2   0   0.255   0.3076  -7.7275   6.4089
 PEM  HC91  H   HCH2   0   0.248   1.9943  -6.5425   5.1304
 PEM  HC92  H   HCH2   0   0.253   0.8008  -7.1617   4.0050
 PEM  H11   H   HCR6   0   0.251  -1.4972  -3.1789   2.5264
 PEM  H12   H   HCR6   0   0.244  -1.0119  -5.5004   3.1369
 PEM  H14   H   HCR6   0   0.246   2.3878  -4.1911   5.3663
 PEM  H15   H   HCR6   0   0.269   1.9283  -1.8944   4.7814
 PEM  H171  H   HCH3   0   0.234   0.4745   1.1976   5.5752
 PEM  H172  H   HCH3   0   0.221  -0.9292   0.1447   5.4482
 PEM  H173  H   HCH3   0   0.230   0.6537  -0.5255   5.8450
 PEM  H181  H   HCH3   0   0.235  -0.1716   1.0994   1.9155
 PEM  H182  H   HCH3   0   0.229   0.1041   2.1580   3.3002
 PEM  H183  H   HCH3   0   0.231  -1.3766   1.2044   3.2089
 PEM  O2    O   O2     0  -0.495  -0.2323  -1.1214   3.2389

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  1.399  0.020  1.399
 PEM  C10  C15   aromatic  1.394  0.020  1.394
 PEM  C10  O2    single    1.343  0.020  1.343
 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  1.389  0.020  1.389
 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    1.434  0.020  1.434
 PEM  C16  C17   single    1.525  0.020  1.525
 PEM  C16  C18   single    1.527  0.020  1.527
 PEM  C16  C19   single    1.557  0.020  1.557
 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    deloc     1.245  0.020  1.245
 PEM  C19  O4    deloc     1.242  0.020  1.242

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    122.19  3.000
 PEM  C7    C1   C2    118.69  3.000
 PEM  C6    C1   C2    119.04  3.000
 PEM  H21   C2   C3    119.19  3.000
 PEM  H21   C2   C1    120.00  3.000
 PEM  C3    C2   C1    120.82  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    119.39  3.000
 PEM  CL    C4   C3    119.43  3.000
 PEM  C5    C4   C3    121.18  3.000
 PEM  H51   C5   C6    120.30  3.000
 PEM  H51   C5   C4    120.61  3.000
 PEM  C6    C5   C4    119.09  3.000
 PEM  HC6   C6   C5    118.28  3.000
 PEM  HC6   C6   C1    120.91  3.000
 PEM  C5    C6   C1    120.77  3.000
 PEM  N1    C7   O1    123.21  3.000
 PEM  N1    C7   C1    115.86  3.000
 PEM  O1    C7   C1    120.92  3.000
 PEM  HN1   N1   C8    116.79  3.000
 PEM  HN1   N1   C7    118.84  3.000
 PEM  C8    N1   C7    123.38  3.000
 PEM  HC82  C8   HC81  107.07  3.000
 PEM  HC82  C8   C9    110.07  3.000
 PEM  HC81  C8   C9    109.89  3.000
 PEM  HC82  C8   N1    110.01  3.000
 PEM  HC81  C8   N1    106.79  3.000
 PEM  C9    C8   N1    112.81  3.000
 PEM  HC92  C9   HC91  106.78  3.000
 PEM  HC92  C9   C13   111.30  3.000
 PEM  HC91  C9   C13   110.02  3.000
 PEM  HC92  C9   C8    107.89  3.000
 PEM  HC91  C9   C8    109.33  3.000
 PEM  C13   C9   C8    111.39  3.000
 PEM  O2    C10  C15   126.18  3.000
 PEM  O2    C10  C11   115.48  3.000
 PEM  C15   C10  C11   118.34  3.000
 PEM  H11   C11  C12   119.98  3.000
 PEM  H11   C11  C10   119.13  3.000
 PEM  C12   C11  C10   120.89  3.000
 PEM  H12   C12  C13   119.78  3.000
 PEM  H12   C12  C11   118.90  3.000
 PEM  C13   C12  C11   121.32  3.000
 PEM  C14   C13  C12   117.27  3.000
 PEM  C14   C13  C9    120.91  3.000
 PEM  C12   C13  C9    121.60  3.000
 PEM  H14   C14  C15   118.36  3.000
 PEM  H14   C14  C13   119.31  3.000
 PEM  C15   C14  C13   122.32  3.000
 PEM  H15   C15  C14   118.13  3.000
 PEM  H15   C15  C10   122.02  3.000
 PEM  C14   C15  C10   119.84  3.000
 PEM  C19   C16  C18   107.07  3.000
 PEM  C19   C16  C17   114.19  3.000
 PEM  C18   C16  C17   109.21  3.000
 PEM  C19   C16  O2    111.21  3.000
 PEM  C18   C16  O2    103.86  3.000
 PEM  C17   C16  O2    110.71  3.000
 PEM  H173  C17  H172  107.92  3.000
 PEM  H173  C17  H171  107.24  3.000
 PEM  H172  C17  H171  107.61  3.000
 PEM  H173  C17  C16   113.50  3.000
 PEM  H172  C17  C16   110.29  3.000
 PEM  H171  C17  C16   110.07  3.000
 PEM  H183  C18  H182  107.87  3.000
 PEM  H183  C18  H181  108.47  3.000
 PEM  H182  C18  H181  108.07  3.000
 PEM  H183  C18  C16   111.07  3.000
 PEM  H182  C18  C16   110.02  3.000
 PEM  H181  C18  C16   111.22  3.000
 PEM  O4    C19  O3    127.46  3.000
 PEM  O4    C19  C16   116.26  3.000
 PEM  O3    C19  C16   116.21  3.000
 PEM  C16   O2   C10   122.22  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  Var_01    O1    C7   C1   C2    -30.26  30.0  2
 PEM  Var_02    C12   C13  C9   C8    -76.81  30.0  2
 PEM  Var_03    C13   C9   C8   N1    -47.36  30.0  3
 PEM  Var_04    C17   C16  O2   C10   -66.38  30.0  3
 PEM  Var_05    C9    C8   N1   C7    -72.24  30.0  3
 PEM  Var_06    O3    C19  C16  O2   -150.74  30.0  3
 PEM  Var_07    H171  C17  C16  O2   -170.59  30.0  3
 PEM  Var_08    H181  C18  C16  O2    -59.99  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
 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

