# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:15:36 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: 2-methoxy-6-{[{2-[(4-methoxybenzyl)carbamoyl]benzyl}(methyl)amino]methyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNC(=O)c2ccccc2CN(C)Cc3cccc(OC)c3C(O)=O)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
 JDX  JDX  '2-methoxy-6-{[{2-[(4-methoxybenzyl)carbamoyl]benzyl}(methyl)amino]methyl}benzoic acid'  ligand  60  33  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JDX
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
 JDX  C15   C  CR16   0  -0.258   0.9347  -5.0705  -0.9557
 JDX  C16   C  CR16   0  -0.246  -0.3854  -5.4747  -1.0716
 JDX  C14   C  CR16   0  -0.260   1.2429  -3.9516  -0.1933
 JDX  C17   C  CR16   0  -0.298  -1.3851  -4.7489  -0.4363
 JDX  C23   C  CR16   0  -0.331  -5.0439   0.7429   0.0020
 JDX  C6    C  CR16   0  -0.285   2.9067   1.4740  -0.1667
 JDX  C10   C  CR16   0  -0.288   4.4258   0.2006   1.1624
 JDX  C24   C  CR16   0  -0.247  -5.4525   1.9115  -0.6138
 JDX  C7    C  CR16   0  -0.332   3.9687   2.0325  -0.8539
 JDX  C9    C  CR16   0  -0.372   5.5069   0.7535   0.4844
 JDX  C13   C  CR6    0  -0.080   0.2433  -3.2356   0.4594
 JDX  C30   C  CR6    0  -0.132  -2.7667   1.5408   0.0575
 JDX  C5    C  CR6    0   0.029   3.1179   0.5498   0.8577
 JDX  C18   C  CR6    0   0.110  -1.0935  -3.6284   0.3333
 JDX  C22   C  CR6    0   0.059  -3.7053   0.5548   0.3503
 JDX  C25   C  CR16   0  -0.403  -4.5311   2.9113  -0.8995
 JDX  C29   C  CR6    0   0.361  -3.1930   2.7203  -0.5681
 JDX  C8    C  CR6    0   0.370   5.2811   1.6784  -0.5316
 JDX  C2    C  C      0   0.502   0.6605  -2.1325   1.3862
 JDX  C4    C  CH2    0  -0.346   1.9543  -0.0624   1.5857
 JDX  C19   C  CH2    0  -0.370  -2.2142  -2.8271   0.9405
 JDX  C21   C  CH2    0  -0.330  -3.3108  -0.7286   1.0342
 JDX  N3    N  NH1    0  -0.604   1.4251  -1.1856   0.8314
 JDX  N20   N  NT     0  -0.373  -2.4145  -1.5643   0.2494
 JDX  O33   O  O      0  -0.584  -0.5045   1.2534  -0.5241
 JDX  O1    O  O      0  -0.501   0.3965  -2.1778   2.5817
 JDX  O32   O  OC    -1  -0.606  -1.0392   1.4880   1.6388
 JDX  O28   O  O2     0  -0.467  -2.2322   3.6450  -0.7959
 JDX  C20   C  CH3    0  -0.518  -2.8847  -1.7677  -1.1027
 JDX  O11   O  O2     0  -0.472   6.2552   2.2765  -1.2464
 JDX  H15   H  HCR6   0   0.258   1.7235  -5.6231  -1.4491
 JDX  H16   H  HCR6   0   0.258  -0.6406  -6.3469  -1.6594
 JDX  H14   H  HCR6   0   0.259   2.2765  -3.6461  -0.0885
 JDX  H17   H  HCR6   0   0.253  -2.4191  -5.0538  -0.5476
 JDX  H23   H  HCR6   0   0.235  -5.7653  -0.0367   0.2165
 JDX  H24   H  HCR6   0   0.248  -6.4926   2.0561  -0.8769
 JDX  H6    H  HCR6   0   0.274   1.8895   1.7449  -0.4275
 JDX  H7    H  HCR6   0   0.257   3.7924   2.7505  -1.6459
 JDX  H10   H  HCR6   0   0.250   4.6185  -0.5156   1.9529
 JDX  H9    H  HCR6   0   0.275   6.5076   0.4533   0.7639
 JDX  H25   H  HCR6   0   0.269  -4.8727   3.8216  -1.3735
 JDX  H41C  H  HCH2   0   0.242   2.2767  -0.4288   2.5608
 JDX  H42C  H  HCH2   0   0.272   1.1638   0.6736   1.7437
 JDX  H191  H  HCH2   0   0.209  -3.1325  -3.4397   0.9350
 JDX  H192  H  HCH2   0   0.253  -1.9924  -2.6110   1.9862
 JDX  H211  H  HCH2   0   0.243  -2.8062  -0.5028   1.9768
 JDX  H212  H  HCH2   0   0.199  -4.2361  -1.2726   1.2920
 JDX  H3    H  HNH1   0   0.397   1.3969  -1.0865  -0.1711
 JDX  H271  H  HCH3   0   0.222  -3.3186   5.4250  -0.7531
 JDX  H272  H  HCH3   0   0.255  -1.6922   5.4670  -1.4559
 JDX  H273  H  HCH3   0   0.222  -3.0297   4.7549  -2.3723
 JDX  H121  H  HCH3   0   0.227   7.8788   2.2026   0.0613
 JDX  H122  H  HCH3   0   0.227   7.8005   0.8820  -1.1246
 JDX  H123  H  HCH3   0   0.258   8.2127   2.5234  -1.6492
 JDX  H201  H  HCH3   0   0.181  -3.8704  -2.2596  -1.1542
 JDX  H202  H  HCH3   0   0.242  -2.9579  -0.8162  -1.6267
 JDX  H203  H  HCH3   0   0.236  -2.1783  -2.3864  -1.6554
 JDX  C31   C  C      0   0.419  -1.2933   1.3995   0.4229
 JDX  C27   C  CH3    0  -0.433  -2.6025   4.8775  -1.3728
 JDX  C12   C  CH3    0  -0.436   7.5991   1.9443  -0.9635

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
 JDX  C15  C16   aromatic  1.385  0.020  1.385
 JDX  C15  C14   aromatic  1.389  0.020  1.389
 JDX  C16  C17   aromatic  1.389  0.020  1.389
 JDX  C14  C13   aromatic  1.392  0.020  1.392
 JDX  C17  C18   aromatic  1.390  0.020  1.390
 JDX  C23  C24   aromatic  1.383  0.020  1.383
 JDX  C23  C22   aromatic  1.396  0.020  1.396
 JDX  C6   C7    aromatic  1.383  0.020  1.383
 JDX  C6   C5    aromatic  1.396  0.020  1.396
 JDX  C10  C9    aromatic  1.391  0.020  1.391
 JDX  C10  C5    aromatic  1.388  0.020  1.388
 JDX  C24  C25   aromatic  1.389  0.020  1.389
 JDX  C7   C8    aromatic  1.397  0.020  1.397
 JDX  C9   C8    aromatic  1.392  0.020  1.392
 JDX  C13  C18   aromatic  1.399  0.020  1.399
 JDX  C13  C2    single    1.500  0.020  1.500
 JDX  C30  C22   aromatic  1.392  0.020  1.392
 JDX  C30  C29   aromatic  1.402  0.020  1.402
 JDX  C30  C31   single    1.525  0.020  1.525
 JDX  C5   C4    single    1.503  0.020  1.503
 JDX  C18  C19   single    1.506  0.020  1.506
 JDX  C22  C21   single    1.507  0.020  1.507
 JDX  C25  C29   aromatic  1.392  0.020  1.392
 JDX  C29  O28   single    1.353  0.020  1.353
 JDX  C8   O11   single    1.348  0.020  1.348
 JDX  C2   N3    single    1.338  0.020  1.338
 JDX  C2   O1    double    1.225  0.020  1.225
 JDX  C31  O33   deloc     1.241  0.020  1.241
 JDX  C31  O32   deloc     1.245  0.020  1.245
 JDX  C27  O28   single    1.410  0.020  1.410
 JDX  C12  O11   single    1.413  0.020  1.413
 JDX  C4   N3    single    1.453  0.020  1.453
 JDX  C19  N20   single    1.453  0.020  1.453
 JDX  C21  N20   single    1.455  0.020  1.455
 JDX  N20  C20   single    1.446  0.020  1.446
 JDX  C15  H15   single    0.930  0.020  1.080
 JDX  C16  H16   single    0.930  0.020  1.080
 JDX  C14  H14   single    0.930  0.020  1.080
 JDX  C17  H17   single    0.930  0.020  1.080
 JDX  C23  H23   single    0.930  0.020  1.080
 JDX  C24  H24   single    0.930  0.020  1.080
 JDX  C6   H6    single    0.930  0.020  1.080
 JDX  C7   H7    single    0.930  0.020  1.080
 JDX  C10  H10   single    0.930  0.020  1.080
 JDX  C9   H9    single    0.930  0.020  1.080
 JDX  C25  H25   single    0.930  0.020  1.080
 JDX  C4   H41C  single    0.970  0.020  1.090
 JDX  C4   H42C  single    0.970  0.020  1.090
 JDX  C19  H191  single    0.970  0.020  1.090
 JDX  C19  H192  single    0.970  0.020  1.090
 JDX  C21  H211  single    0.970  0.020  1.090
 JDX  C21  H212  single    0.970  0.020  1.090
 JDX  N3   H3    single    0.860  0.020  1.020
 JDX  C27  H271  single    0.970  0.020  1.090
 JDX  C27  H272  single    0.970  0.020  1.090
 JDX  C27  H273  single    0.970  0.020  1.090
 JDX  C12  H121  single    0.970  0.020  1.090
 JDX  C12  H122  single    0.970  0.020  1.090
 JDX  C12  H123  single    0.970  0.020  1.090
 JDX  C20  H201  single    0.970  0.020  1.090
 JDX  C20  H202  single    0.970  0.020  1.090
 JDX  C20  H203  single    0.970  0.020  1.090

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
 JDX  H15   C15  C14   120.00  3.000
 JDX  H15   C15  C16   120.49  3.000
 JDX  C14   C15  C16   119.50  3.000
 JDX  H16   C16  C17   119.98  3.000
 JDX  H16   C16  C15   120.35  3.000
 JDX  C17   C16  C15   119.67  3.000
 JDX  H14   C14  C13   119.66  3.000
 JDX  H14   C14  C15   119.50  3.000
 JDX  C13   C14  C15   120.83  3.000
 JDX  H17   C17  C18   118.92  3.000
 JDX  H17   C17  C16   119.52  3.000
 JDX  C18   C17  C16   121.56  3.000
 JDX  H23   C23  C22   119.48  3.000
 JDX  H23   C23  C24   119.96  3.000
 JDX  C22   C23  C24   120.56  3.000
 JDX  H6    C6   C5    118.94  3.000
 JDX  H6    C6   C7    120.00  3.000
 JDX  C5    C6   C7    121.06  3.000
 JDX  H10   C10  C5    119.60  3.000
 JDX  H10   C10  C9    118.69  3.000
 JDX  C5    C10  C9    121.71  3.000
 JDX  H24   C24  C25   119.41  3.000
 JDX  H24   C24  C23   120.34  3.000
 JDX  C25   C24  C23   120.25  3.000
 JDX  H7    C7   C8    119.31  3.000
 JDX  H7    C7   C6    120.40  3.000
 JDX  C8    C7   C6    120.29  3.000
 JDX  H9    C9   C8    121.53  3.000
 JDX  H9    C9   C10   118.88  3.000
 JDX  C8    C9   C10   119.59  3.000
 JDX  C2    C13  C18   121.86  3.000
 JDX  C2    C13  C14   117.92  3.000
 JDX  C18   C13  C14   119.97  3.000
 JDX  C31   C30  C29   118.62  3.000
 JDX  C31   C30  C22   122.37  3.000
 JDX  C29   C30  C22   119.00  3.000
 JDX  C4    C5   C10   121.39  3.000
 JDX  C4    C5   C6    120.53  3.000
 JDX  C10   C5   C6    118.06  3.000
 JDX  C19   C18  C13   121.70  3.000
 JDX  C19   C18  C17   119.74  3.000
 JDX  C13   C18  C17   118.46  3.000
 JDX  C21   C22  C30   121.47  3.000
 JDX  C21   C22  C23   118.62  3.000
 JDX  C30   C22  C23   119.90  3.000
 JDX  H25   C25  C29   121.57  3.000
 JDX  H25   C25  C24   119.10  3.000
 JDX  C29   C25  C24   119.34  3.000
 JDX  O28   C29  C25   123.29  3.000
 JDX  O28   C29  C30   115.75  3.000
 JDX  C25   C29  C30   120.95  3.000
 JDX  O11   C8   C9    124.36  3.000
 JDX  O11   C8   C7    116.36  3.000
 JDX  C9    C8   C7    119.28  3.000
 JDX  O1    C2   N3    123.65  3.000
 JDX  O1    C2   C13   121.05  3.000
 JDX  N3    C2   C13   115.04  3.000
 JDX  H42C  C4   H41C  108.13  3.000
 JDX  H42C  C4   N3    109.43  3.000
 JDX  H41C  C4   N3    108.20  3.000
 JDX  H42C  C4   C5    110.86  3.000
 JDX  H41C  C4   C5    109.94  3.000
 JDX  N3    C4   C5    110.21  3.000
 JDX  H192  C19  H191  106.49  3.000
 JDX  H192  C19  N20   108.17  3.000
 JDX  H191  C19  N20   111.41  3.000
 JDX  H192  C19  C18   109.92  3.000
 JDX  H191  C19  C18   108.77  3.000
 JDX  N20   C19  C18   111.92  3.000
 JDX  H212  C21  H211  106.71  3.000
 JDX  H212  C21  N20   111.05  3.000
 JDX  H211  C21  N20   107.43  3.000
 JDX  H212  C21  C22   107.83  3.000
 JDX  H211  C21  C22   109.65  3.000
 JDX  N20   C21  C22   113.93  3.000
 JDX  H3    N3   C4    116.79  3.000
 JDX  H3    N3   C2    117.79  3.000
 JDX  C4    N3   C2    122.69  3.000
 JDX  C20   N20  C21   112.63  3.000
 JDX  C20   N20  C19   111.55  3.000
 JDX  C21   N20  C19   109.11  3.000
 JDX  C27   O28  C29   118.67  3.000
 JDX  H203  C20  H202  107.20  3.000
 JDX  H203  C20  H201  107.61  3.000
 JDX  H202  C20  H201  107.90  3.000
 JDX  H203  C20  N20   110.08  3.000
 JDX  H202  C20  N20   110.43  3.000
 JDX  H201  C20  N20   113.39  3.000
 JDX  C12   O11  C8    118.48  3.000
 JDX  O32   C31  O33   128.58  3.000
 JDX  O32   C31  C30   115.13  3.000
 JDX  O33   C31  C30   116.25  3.000
 JDX  H273  C27  H272  108.53  3.000
 JDX  H273  C27  H271  108.54  3.000
 JDX  H272  C27  H271  108.66  3.000
 JDX  H273  C27  O28   112.23  3.000
 JDX  H272  C27  O28   106.57  3.000
 JDX  H271  C27  O28   112.18  3.000
 JDX  H123  C12  H122  108.70  3.000
 JDX  H123  C12  H121  108.72  3.000
 JDX  H122  C12  H121  108.70  3.000
 JDX  H123  C12  O11   106.58  3.000
 JDX  H122  C12  O11   111.98  3.000
 JDX  H121  C12  O11   112.05  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
 JDX  CONST_01  C18   C17  C16  C15     0.00   0.0  0
 JDX  CONST_02  C18   C13  C14  C15     0.00   0.0  0
 JDX  CONST_03  C13   C14  C15  C16     0.00   0.0  0
 JDX  CONST_04  C13   C18  C17  C16     0.00   0.0  0
 JDX  CONST_05  C17   C16  C15  C14     0.00   0.0  0
 JDX  CONST_06  C17   C18  C13  C14     0.00   0.0  0
 JDX  CONST_07  C29   C25  C24  C23     0.00   0.0  0
 JDX  CONST_08  C29   C30  C22  C23     0.00   0.0  0
 JDX  CONST_09  C9    C8   C7   C6      0.00   0.0  0
 JDX  CONST_10  C9    C10  C5   C6      0.00   0.0  0
 JDX  CONST_11  C7    C8   C9   C10     0.00   0.0  0
 JDX  CONST_12  C7    C6   C5   C10     0.00   0.0  0
 JDX  CONST_13  C30   C22  C23  C24     0.00   0.0  0
 JDX  CONST_14  C30   C29  C25  C24     0.00   0.0  0
 JDX  CONST_15  C8    C7   C6   C5      0.00   0.0  0
 JDX  CONST_16  C8    C9   C10  C5      0.00   0.0  0
 JDX  CONST_17  C25   C24  C23  C22     0.00   0.0  0
 JDX  CONST_18  C25   C29  C30  C22     0.00   0.0  0
 JDX  CONST_19  C2    C13  C14  C15   180.00   0.0  0
 JDX  CONST_20  C19   C18  C17  C16   180.00   0.0  0
 JDX  CONST_21  C19   C18  C13  C14   180.00   0.0  0
 JDX  CONST_22  C2    C13  C18  C17   180.00   0.0  0
 JDX  CONST_23  C31   C30  C22  C23   180.00   0.0  0
 JDX  CONST_24  O11   C8   C7   C6    180.00   0.0  0
 JDX  CONST_25  O11   C8   C9   C10   180.00   0.0  0
 JDX  CONST_26  C21   C22  C23  C24   180.00   0.0  0
 JDX  CONST_27  O28   C29  C25  C24   180.00   0.0  0
 JDX  CONST_28  C4    C5   C6   C7    180.00   0.0  0
 JDX  CONST_29  C4    C5   C10  C9    180.00   0.0  0
 JDX  CONST_30  O28   C29  C30  C22   180.00   0.0  0
 JDX  CONST_31  C31   C30  C29  C25   180.00   0.0  0
 JDX  CONST_32  C21   C22  C30  C29   180.00   0.0  0
 JDX  CONST_33  H17   C17  C16  C15   180.00   0.0  0
 JDX  CONST_34  H14   C14  C15  C16   180.00   0.0  0
 JDX  CONST_35  H16   C16  C15  C14   180.00   0.0  0
 JDX  CONST_36  H15   C15  C16  C17   180.00   0.0  0
 JDX  CONST_37  H25   C25  C24  C23   180.00   0.0  0
 JDX  CONST_38  H10   C10  C5   C6    180.00   0.0  0
 JDX  CONST_39  H6    C6   C5   C10   180.00   0.0  0
 JDX  CONST_40  H9    C9   C8   C7    180.00   0.0  0
 JDX  CONST_41  H7    C7   C8   C9    180.00   0.0  0
 JDX  CONST_42  H23   C23  C22  C30   180.00   0.0  0
 JDX  CONST_43  H24   C24  C23  C22   180.00   0.0  0
 JDX  CONST_44  C4    N3   C2   C13   180.00   0.0  0
 JDX  CONST_46  O1    C2   N3   C4      0.00   0.0  0
 JDX  Var_01    N3    C2   C13  C14    56.74  30.0  2
 JDX  Var_02    N20   C19  C18  C17  -106.07  30.0  2
 JDX  Var_03    N20   C21  C22  C23   115.00  30.0  2
 JDX  Var_04    N3    C4   C5   C6     82.90  30.0  2
 JDX  Var_05    O33   C31  C30  C22   110.78  30.0  2
 JDX  Var_06    C2    N3   C4   C5    160.68  30.0  3
 JDX  Var_07    C21   N20  C19  C18  -168.64  30.0  3
 JDX  Var_08    C19   N20  C21  C22  -174.13  30.0  3
 JDX  Var_09    H271  C27  O28  C29    60.56  30.0  3
 JDX  Var_10    H121  C12  O11  C8    -61.69  30.0  3
 JDX  Var_11    H201  C20  N20  C19    62.97  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
 JDX  plan-1  C15  0.020
 JDX  plan-1  C16  0.020
 JDX  plan-1  C14  0.020
 JDX  plan-1  C17  0.020
 JDX  plan-1  C13  0.020
 JDX  plan-1  C18  0.020
 JDX  plan-1  C2   0.020
 JDX  plan-1  C19  0.020
 JDX  plan-1  H15  0.020
 JDX  plan-1  H16  0.020
 JDX  plan-1  H14  0.020
 JDX  plan-1  H17  0.020
 JDX  plan-2  C23  0.020
 JDX  plan-2  C24  0.020
 JDX  plan-2  C30  0.020
 JDX  plan-2  C22  0.020
 JDX  plan-2  C25  0.020
 JDX  plan-2  C29  0.020
 JDX  plan-2  C21  0.020
 JDX  plan-2  O28  0.020
 JDX  plan-2  H23  0.020
 JDX  plan-2  H24  0.020
 JDX  plan-2  H25  0.020
 JDX  plan-2  C31  0.020
 JDX  plan-3  C6   0.020
 JDX  plan-3  C10  0.020
 JDX  plan-3  C7   0.020
 JDX  plan-3  C9   0.020
 JDX  plan-3  C5   0.020
 JDX  plan-3  C8   0.020
 JDX  plan-3  C4   0.020
 JDX  plan-3  O11  0.020
 JDX  plan-3  H6   0.020
 JDX  plan-3  H7   0.020
 JDX  plan-3  H10  0.020
 JDX  plan-3  H9   0.020
 JDX  plan-4  C13  0.020
 JDX  plan-4  C2   0.020
 JDX  plan-4  C4   0.020
 JDX  plan-4  N3   0.020
 JDX  plan-4  O1   0.020
 JDX  plan-4  H3   0.020
 JDX  plan-5  C30  0.020
 JDX  plan-5  O33  0.020
 JDX  plan-5  O32  0.020
 JDX  plan-5  C31  0.020

