# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 23:11:24 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CCOc2c(Cl)cc(C(=O)N[C@@H](Cc3ccccc3)C(O)=O)c(O)c2Cl)CC1
#
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
 JBG  JBG  N-{3,5-dichloro-2-hydroxy-4-[2-(4-methylpiperazin-1-yl)ethoxy]benzene-1-carbonyl}-L-phenylalanine  ligand  59  33  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JBG
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
 JBG  C2    C   CH2    0  -0.279   5.9673   1.9007  -1.2889
 JBG  C3    C   CH2    0  -0.288   5.2863   1.7553   0.0575
 JBG  C11   C   CR6    0   0.510   1.3077  -0.6578   0.4223
 JBG  C12   C   CR6    0  -0.176   0.7952   0.0942  -0.6378
 JBG  C13   C   CR16   0  -0.266  -0.5558   0.1069  -0.9040
 JBG  C14   C   CR6    0  -0.208  -1.4497  -0.6228  -0.1232
 JBG  C15   C   CR6    0   0.433  -0.9565  -1.3873   0.9525
 JBG  C16   C   CR6    0  -0.276   0.4201  -1.3820   1.2039
 JBG  C20   C   C      0   0.665  -2.9202  -0.6197  -0.3490
 JBG  C23   C   CH1    0  -0.217  -4.8201   0.3426  -1.5735
 JBG  C24   C   C      0   0.428  -5.0502   0.5544  -3.0892
 JBG  C27   C   CH2    0  -0.513  -5.3428   1.5802  -0.8116
 JBG  C28   C   CR6    0   0.140  -5.0449   1.5199   0.6572
 JBG  C29   C   CR16   0  -0.293  -5.9210   0.8889   1.5365
 JBG  C30   C   CR16   0  -0.244  -5.6125   0.7619   2.8828
 JBG  N1    N   NT     0  -0.412   7.3284   1.4092  -1.2321
 JBG  N4    N   NT     0  -0.414   5.3003   0.3704   0.4861
 JBG  C5    C   CH2    0  -0.285   6.6650  -0.1153   0.5518
 JBG  C6    C   CH2    0  -0.282   7.3464   0.0282  -0.7956
 JBG  C7    C   CH2    0  -0.306   4.5919   0.1529   1.7275
 JBG  C8    C   CH2    0  -0.190   3.0923   0.2871   1.6056
 JBG  O9    O   O2     0  -0.460   2.6251  -0.6918   0.6668
 JBG  C10   C   CH3    0  -0.517   8.0177   1.5882  -2.4878
 JBG  CL17  CL  CL     0  -0.068   1.0238  -2.3284   2.5077
 JBG  CL18  CL  CL     0  -0.086   1.8874   0.9924  -1.6299
 JBG  O19   O   OH1    0  -0.611  -1.7375  -2.1049   1.7387
 JBG  O21   O   O      0  -0.543  -3.6459  -1.3220   0.3764
 JBG  N22   N   NH1    0  -0.648  -3.4131   0.1405  -1.3173
 JBG  O25   O   OC    -1  -0.599  -6.2358   0.5214  -3.4576
 JBG  O26   O   O      0  -0.592  -4.0401   0.7767  -3.7840
 JBG  C31   C   CR16   0  -0.271  -4.4120   1.2609   3.3729
 JBG  C32   C   CR16   0  -0.236  -3.5342   1.9003   2.5084
 JBG  C33   C   CR16   0  -0.309  -3.8534   2.0335   1.1636
 JBG  H1    H   HCH2   0   0.186   5.3705   1.3683  -2.0508
 JBG  H2    H   HCH2   0   0.233   5.9804   2.9562  -1.5719
 JBG  H3    H   HCH2   0   0.190   5.7842   2.4113   0.7933
 JBG  H4    H   HCH2   0   0.234   4.2581   2.1053  -0.0411
 JBG  H5    H   HCR6   0   0.279  -0.8999   0.7031  -1.7376
 JBG  H6    H   HCH1   0   0.258  -5.3704  -0.5377  -1.2386
 JBG  H7    H   HCH2   0   0.244  -4.8866   2.4744  -1.2462
 JBG  H8    H   HCH2   0   0.253  -6.4178   1.6515  -0.9839
 JBG  H9    H   HCR6   0   0.240  -6.8548   0.4857   1.1612
 JBG  H10   H   HCR6   0   0.248  -6.3087   0.2698   3.5506
 JBG  H13   H   HCH2   0   0.189   7.2564   0.4200   1.3150
 JBG  H14   H   HCH2   0   0.236   6.6558  -1.1705   0.8353
 JBG  H15   H   HCH2   0   0.187   6.8506  -0.6377  -1.5240
 JBG  H16   H   HCH2   0   0.234   8.3833  -0.3061  -0.7087
 JBG  H17   H   HCH2   0   0.244   4.8187  -0.8561   2.0828
 JBG  H18   H   HCH2   0   0.210   4.9148   0.8410   2.5274
 JBG  H19   H   HCH2   0   0.242   2.6418   0.1142   2.5872
 JBG  H20   H   HCH2   0   0.235   2.7941   1.2870   1.2784
 JBG  H21   H   HCH3   0   0.232   8.0294   2.6452  -2.7595
 JBG  H22   H   HCH3   0   0.231   9.0526   1.2541  -2.3981
 JBG  H23   H   HCH3   0   0.190   7.5571   1.0352  -3.3216
 JBG  H24   H   HOH1   0   0.484  -2.6691  -1.9576   1.3887
 JBG  H25   H   HNH1   0   0.399  -2.8098   0.6136  -1.9731
 JBG  H27   H   HCR6   0   0.248  -4.1668   1.1585   4.4224
 JBG  H28   H   HCR6   0   0.247  -2.5992   2.2993   2.8808
 JBG  H29   H   HCR6   0   0.243  -3.1643   2.5422   0.4994

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
 JBG  C2    C3   single    1.516  0.020  1.516
 JBG  C2    N1   single    1.448  0.020  1.448
 JBG  C3    N4   single    1.450  0.020  1.450
 JBG  C7    C8   single    1.511  0.020  1.511
 JBG  C7    N4   single    1.446  0.020  1.446
 JBG  C8    O9   single    1.435  0.020  1.435
 JBG  N4    C5   single    1.450  0.020  1.450
 JBG  C10   N1   single    1.444  0.020  1.444
 JBG  N1    C6   single    1.448  0.020  1.448
 JBG  O9    C11  single    1.340  0.020  1.340
 JBG  C5    C6   single    1.517  0.020  1.517
 JBG  CL18  C12  single    1.727  0.020  1.727
 JBG  O26   C24  deloc     1.246  0.020  1.246
 JBG  C11   C12  aromatic  1.397  0.020  1.397
 JBG  C11   C16  aromatic  1.387  0.020  1.387
 JBG  C12   C13  aromatic  1.377  0.020  1.377
 JBG  CL17  C16  single    1.721  0.020  1.721
 JBG  O25   C24  deloc     1.242  0.020  1.242
 JBG  C16   C15  aromatic  1.399  0.020  1.399
 JBG  C24   C23  single    1.548  0.020  1.548
 JBG  C13   C14  aromatic  1.393  0.020  1.393
 JBG  C15   C14  aromatic  1.409  0.020  1.409
 JBG  C15   O19  single    1.320  0.020  1.320
 JBG  C14   C20  single    1.488  0.020  1.488
 JBG  N22   C20  single    1.326  0.020  1.326
 JBG  N22   C23  single    1.444  0.020  1.444
 JBG  C20   O21  double    1.243  0.020  1.243
 JBG  C23   C27  single    1.544  0.020  1.544
 JBG  C27   C28  single    1.500  0.020  1.500
 JBG  C29   C28  aromatic  1.392  0.020  1.392
 JBG  C29   C30  aromatic  1.387  0.020  1.387
 JBG  C28   C33  aromatic  1.393  0.020  1.393
 JBG  C30   C31  aromatic  1.389  0.020  1.389
 JBG  C33   C32  aromatic  1.389  0.020  1.389
 JBG  C31   C32  aromatic  1.388  0.020  1.388
 JBG  C2    H1   single    0.970  0.020  1.090
 JBG  C2    H2   single    0.970  0.020  1.090
 JBG  C3    H3   single    0.970  0.020  1.090
 JBG  C3    H4   single    0.970  0.020  1.090
 JBG  C13   H5   single    0.930  0.020  1.080
 JBG  C23   H6   single    0.970  0.020  1.090
 JBG  C27   H7   single    0.970  0.020  1.090
 JBG  C27   H8   single    0.970  0.020  1.090
 JBG  C29   H9   single    0.930  0.020  1.080
 JBG  C30   H10  single    0.930  0.020  1.080
 JBG  C5    H13  single    0.970  0.020  1.090
 JBG  C5    H14  single    0.970  0.020  1.090
 JBG  C6    H15  single    0.970  0.020  1.090
 JBG  C6    H16  single    0.970  0.020  1.090
 JBG  C7    H17  single    0.970  0.020  1.090
 JBG  C7    H18  single    0.970  0.020  1.090
 JBG  C8    H19  single    0.970  0.020  1.090
 JBG  C8    H20  single    0.970  0.020  1.090
 JBG  C10   H21  single    0.970  0.020  1.090
 JBG  C10   H22  single    0.970  0.020  1.090
 JBG  C10   H23  single    0.970  0.020  1.090
 JBG  O19   H24  single    0.850  0.020  0.980
 JBG  N22   H25  single    0.860  0.020  1.020
 JBG  C31   H27  single    0.930  0.020  1.080
 JBG  C32   H28  single    0.930  0.020  1.080
 JBG  C33   H29  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
 JBG  H2    C2   H1   107.06  3.000
 JBG  H2    C2   N1   109.07  3.000
 JBG  H1    C2   N1   111.80  3.000
 JBG  H2    C2   C3   109.14  3.000
 JBG  H1    C2   C3   108.89  3.000
 JBG  N1    C2   C3   110.78  3.000
 JBG  H4    C3   H3   107.14  3.000
 JBG  H4    C3   N4   110.02  3.000
 JBG  H3    C3   N4   111.47  3.000
 JBG  H4    C3   C2   108.21  3.000
 JBG  H3    C3   C2   109.41  3.000
 JBG  N4    C3   C2   110.48  3.000
 JBG  O9    C11  C16  120.87  3.000
 JBG  C16   C11  C12  118.29  3.000
 JBG  O9    C11  C12  120.83  3.000
 JBG  CL18  C12  C13  120.31  3.000
 JBG  C13   C12  C11  120.76  3.000
 JBG  CL18  C12  C11  118.93  3.000
 JBG  H5    C13  C14  121.11  3.000
 JBG  H5    C13  C12  117.80  3.000
 JBG  C14   C13  C12  121.09  3.000
 JBG  C20   C14  C15  117.58  3.000
 JBG  C20   C14  C13  123.23  3.000
 JBG  C15   C14  C13  119.18  3.000
 JBG  O19   C15  C16  118.49  3.000
 JBG  O19   C15  C14  122.86  3.000
 JBG  C16   C15  C14  118.65  3.000
 JBG  CL17  C16  C15  118.64  3.000
 JBG  C15   C16  C11  122.03  3.000
 JBG  CL17  C16  C11  119.33  3.000
 JBG  N22   C20  O21  122.19  3.000
 JBG  O21   C20  C14  119.16  3.000
 JBG  N22   C20  C14  118.65  3.000
 JBG  H6    C23  N22  108.91  3.000
 JBG  H6    C23  C27  108.93  3.000
 JBG  N22   C23  C27  110.75  3.000
 JBG  H6    C23  C24  109.65  3.000
 JBG  C27   C23  C24  108.85  3.000
 JBG  N22   C23  C24  109.73  3.000
 JBG  O26   C24  O25  127.82  3.000
 JBG  O25   C24  C23  115.39  3.000
 JBG  O26   C24  C23  116.75  3.000
 JBG  H8    C27  H7   107.14  3.000
 JBG  H8    C27  C28  110.67  3.000
 JBG  H7    C27  C28  109.82  3.000
 JBG  H8    C27  C23  107.94  3.000
 JBG  H7    C27  C23  108.54  3.000
 JBG  C28   C27  C23  112.56  3.000
 JBG  C33   C28  C29  118.41  3.000
 JBG  C33   C28  C27  120.74  3.000
 JBG  C29   C28  C27  120.77  3.000
 JBG  H9    C29  C30  119.57  3.000
 JBG  H9    C29  C28  119.47  3.000
 JBG  C30   C29  C28  120.96  3.000
 JBG  H10   C30  C31  120.07  3.000
 JBG  H10   C30  C29  119.81  3.000
 JBG  C31   C30  C29  120.11  3.000
 JBG  C10   N1   C6   111.99  3.000
 JBG  C6    N1   C2   110.31  3.000
 JBG  C10   N1   C2   111.87  3.000
 JBG  C7    N4   C5   111.83  3.000
 JBG  C5    N4   C3   110.03  3.000
 JBG  C7    N4   C3   113.14  3.000
 JBG  H14   C5   H13  107.06  3.000
 JBG  H14   C5   C6   109.01  3.000
 JBG  H13   C5   C6   109.12  3.000
 JBG  H14   C5   N4   109.11  3.000
 JBG  H13   C5   N4   111.90  3.000
 JBG  C6    C5   N4   110.54  3.000
 JBG  H16   C6   H15  107.09  3.000
 JBG  H16   C6   C5   109.07  3.000
 JBG  H15   C6   C5   109.10  3.000
 JBG  H16   C6   N1   109.11  3.000
 JBG  H15   C6   N1   111.75  3.000
 JBG  C5    C6   N1   110.63  3.000
 JBG  H18   C7   H17  106.21  3.000
 JBG  H18   C7   C8   107.07  3.000
 JBG  H17   C7   C8   108.31  3.000
 JBG  H18   C7   N4   112.65  3.000
 JBG  H17   C7   N4   108.44  3.000
 JBG  C8    C7   N4   113.82  3.000
 JBG  H20   C8   H19  107.51  3.000
 JBG  H20   C8   O9   109.83  3.000
 JBG  H19   C8   O9   110.20  3.000
 JBG  H20   C8   C7   112.09  3.000
 JBG  H19   C8   C7   108.81  3.000
 JBG  O9    C8   C7   108.39  3.000
 JBG  C8    O9   C11  114.97  3.000
 JBG  H23   C10  H22  107.77  3.000
 JBG  H23   C10  H21  107.60  3.000
 JBG  H22   C10  H21  107.87  3.000
 JBG  H23   C10  N1   113.36  3.000
 JBG  H22   C10  N1   110.08  3.000
 JBG  H21   C10  N1   109.98  3.000
 JBG  H24   O19  C15  105.13  3.000
 JBG  H25   N22  C23  113.68  3.000
 JBG  H25   N22  C20  121.41  3.000
 JBG  C23   N22  C20  124.88  3.000
 JBG  H27   C31  C32  120.28  3.000
 JBG  H27   C31  C30  120.24  3.000
 JBG  C32   C31  C30  119.48  3.000
 JBG  H28   C32  C33  119.75  3.000
 JBG  H28   C32  C31  120.11  3.000
 JBG  C33   C32  C31  120.13  3.000
 JBG  H29   C33  C32  119.50  3.000
 JBG  H29   C33  C28  119.61  3.000
 JBG  C32   C33  C28  120.89  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
 JBG  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 JBG  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 JBG  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 JBG  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 JBG  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 JBG  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 JBG  CONST_07  C31   C30  C29  C28     0.00   0.0  0
 JBG  CONST_08  C31   C32  C33  C28     0.00   0.0  0
 JBG  CONST_09  C32   C33  C28  C29     0.00   0.0  0
 JBG  CONST_10  C32   C31  C30  C29     0.00   0.0  0
 JBG  CONST_11  C33   C28  C29  C30     0.00   0.0  0
 JBG  CONST_12  C33   C32  C31  C30     0.00   0.0  0
 JBG  CONST_13  O19   C15  C16  C11   180.00   0.0  0
 JBG  CONST_14  CL17  C16  C11  C12   180.00   0.0  0
 JBG  CONST_15  C20   C14  C13  C12   180.00   0.0  0
 JBG  CONST_16  O9    C11  C12  C13   180.00   0.0  0
 JBG  CONST_17  O19   C15  C14  C13   180.00   0.0  0
 JBG  CONST_18  CL18  C12  C13  C14   180.00   0.0  0
 JBG  CONST_19  CL17  C16  C15  C14   180.00   0.0  0
 JBG  CONST_20  O9    C11  C16  C15   180.00   0.0  0
 JBG  CONST_21  CL18  C12  C11  C16   180.00   0.0  0
 JBG  CONST_22  C20   C14  C15  C16   180.00   0.0  0
 JBG  CONST_23  C30   C29  C28  C27   180.00   0.0  0
 JBG  CONST_24  C32   C33  C28  C27   180.00   0.0  0
 JBG  CONST_25  H5    C13  C12  C11   180.00   0.0  0
 JBG  CONST_26  H10   C30  C29  C28   180.00   0.0  0
 JBG  CONST_27  H28   C32  C33  C28   180.00   0.0  0
 JBG  CONST_28  H29   C33  C28  C29   180.00   0.0  0
 JBG  CONST_29  H27   C31  C30  C29   180.00   0.0  0
 JBG  CONST_30  H9    C29  C30  C31   180.00   0.0  0
 JBG  CONST_31  C23   N22  C20  C14   180.00   0.0  0
 JBG  CONST_32  H25   N22  C20  C14     0.00   0.0  0
 JBG  CONST_33  O21   C20  N22  C23     0.00   0.0  0
 JBG  Var_01    C5    N4   C3   C2     57.70  30.0  1
 JBG  Var_02    C5    C6   N1   C2    -57.04  30.0  1
 JBG  Var_03    C6    N1   C2   C3     57.07  30.0  1
 JBG  Var_04    C6    C5   N4   C3    -57.79  30.0  1
 JBG  Var_05    N4    C3   C2   N1    -57.63  30.0  1
 JBG  Var_06    N4    C5   C6   N1     57.69  30.0  1
 JBG  Var_07    C8    C7   N4   C3     70.78  30.0  1
 JBG  Var_08    N22   C20  C14  C13    -1.83  30.0  2
 JBG  Var_09    C29   C28  C27  C23   -87.47  30.0  2
 JBG  Var_10    H21   C10  N1   C2     58.50  30.0  3
 JBG  Var_11    C7    C8   O9   C11  -177.78  30.0  1
 JBG  Var_12    O9    C8   C7   N4     60.53  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JBG  chir_01  C23  C24  N22  C27  negativ

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
 JBG  plan-1  C11   0.020
 JBG  plan-1  C12   0.020
 JBG  plan-1  C13   0.020
 JBG  plan-1  C14   0.020
 JBG  plan-1  C15   0.020
 JBG  plan-1  C16   0.020
 JBG  plan-1  C20   0.020
 JBG  plan-1  O9    0.020
 JBG  plan-1  CL17  0.020
 JBG  plan-1  CL18  0.020
 JBG  plan-1  O19   0.020
 JBG  plan-1  H5    0.020
 JBG  plan-2  C27   0.020
 JBG  plan-2  C28   0.020
 JBG  plan-2  C29   0.020
 JBG  plan-2  C30   0.020
 JBG  plan-2  C31   0.020
 JBG  plan-2  C32   0.020
 JBG  plan-2  C33   0.020
 JBG  plan-2  H9    0.020
 JBG  plan-2  H10   0.020
 JBG  plan-2  H27   0.020
 JBG  plan-2  H28   0.020
 JBG  plan-2  H29   0.020
 JBG  plan-3  C14   0.020
 JBG  plan-3  C20   0.020
 JBG  plan-3  C23   0.020
 JBG  plan-3  O21   0.020
 JBG  plan-3  N22   0.020
 JBG  plan-3  H25   0.020
 JBG  plan-4  C23   0.020
 JBG  plan-4  C24   0.020
 JBG  plan-4  O25   0.020
 JBG  plan-4  O26   0.020

