# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:49:16 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: 2-methoxy-6-{[({6-[(4-methoxybenzyl)carbamoyl]-1,3-benzodioxol-5-yl}methyl)(methyl)amino]methyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNC(=O)c2cc3OCOc3cc2CN(C)Cc4cccc(OC)c4C(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
 FYM  FYM  '2-methoxy-6-{[({6-[(4-methoxybenzyl)carbamoyl]-1,3-benzodioxol-5-yl}methyl)(methyl)amino]methyl}benzoic acid'  ligand  63  36  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FYM
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
 FYM  C1    C  C1     0  -0.247   5.5756   2.2452   0.7997
 FYM  C2    C  C1     0  -0.331   5.1224   1.1864   0.0351
 FYM  C3    C  C1     0  -0.289  -2.7776   2.0363   0.2835
 FYM  C4    C  C1     0  -0.289  -4.3272   1.1412  -1.2953
 FYM  C5    C  C1     0  -0.402   4.6912   3.2273   1.2282
 FYM  C6    C  C1     0  -0.332  -3.8247   2.5301   1.0391
 FYM  C7    C  C1     0  -0.372  -5.3936   1.6359  -0.5515
 FYM  C8    C  CR16   0  -0.353  -1.3182  -3.3208  -0.5132
 FYM  C9    C  CR16   0  -0.392   1.3362  -4.2415  -0.2774
 FYM  C10   C  CR6    0  -0.100  -0.2446  -2.5597  -1.0045
 FYM  C11   C  C      0  -0.133   2.8742   2.0588   0.1128
 FYM  C12   C  C      0   0.023  -3.0114   1.3319  -0.8992
 FYM  C13   C  C      0   0.058   3.7757   1.0910  -0.3220
 FYM  C14   C  CR6    0   0.101   1.0721  -3.0073  -0.8874
 FYM  C15   C  CR56   0   0.300  -1.0267  -4.5272   0.0702
 FYM  C16   C  CR56   0   0.311   0.2741  -4.9805   0.1814
 FYM  C17   C  C      0   0.371  -5.1453   2.3344   0.6270
 FYM  C18   C  C      0   0.363   3.3461   3.1278   0.8868
 FYM  C20   C  C      0   0.420   1.3923   2.0191  -0.2413
 FYM  C21   C  CH2    0   0.067  -1.0806  -6.5857   0.8909
 FYM  C22   C  CH3    0  -0.518   2.8341  -1.3388   0.8297
 FYM  C23   C  CH3    0  -0.435  -7.4548   2.6814   1.0482
 FYM  C24   C  CH3    0  -0.433   2.8270   5.1580   2.0098
 FYM  C25   C  CH2    0  -0.343  -1.8622   0.7798  -1.6938
 FYM  C26   C  CH2    0  -0.327   3.3413  -0.0756  -1.1701
 FYM  C27   C  CH2    0  -0.375   2.2366  -2.1640  -1.3385
 FYM  N28   N  NH1    0  -0.611  -1.4024  -0.4678  -1.1075
 FYM  N29   N  NT     0  -0.372   2.4161  -0.9851  -0.5083
 FYM  O30   O  O      0  -0.584   0.6155   1.7420   0.6863
 FYM  O31   O  O      0  -0.500  -0.2265  -1.1354  -2.9143
 FYM  O32   O  OC    -1  -0.605   1.1213   2.3139  -1.4204
 FYM  O33   O  O      0  -0.487  -1.8702  -5.4346   0.6211
 FYM  O34   O  O      0  -0.485   0.2810  -6.1821   0.8058
 FYM  O35   O  O2     0  -0.472  -6.1030   2.8521   1.4219
 FYM  O36   O  O2     0  -0.468   2.4184   4.0445   1.2469
 FYM  H1    H  H      0   0.248   6.6215   2.3163   1.0696
 FYM  H2    H  H      0   0.235   5.8155   0.4203  -0.2914
 FYM  H5    H  H      0   0.269   5.0655   4.0528   1.8184
 FYM  H3    H  H      0   0.279  -1.7537   2.1883   0.6088
 FYM  H6    H  H      0   0.256  -3.6285   3.0755   1.9544
 FYM  H4    H  H      0   0.250  -4.5408   0.6005  -2.2098
 FYM  H7    H  H      0   0.275  -6.4005   1.4655  -0.9075
 FYM  H8    H  HCR6   0   0.276  -2.3399  -2.9788  -0.6122
 FYM  H9    H  HCR6   0   0.272   2.3553  -4.5895  -0.1648
 FYM  H251  H  HCH2   0   0.240  -2.1790   0.5810  -2.7186
 FYM  H252  H  HCH2   0   0.274  -1.0356   1.4922  -1.7263
 FYM  H261  H  HCH2   0   0.242   2.8502   0.2851  -2.0776
 FYM  H262  H  HCH2   0   0.199   4.2520  -0.6073  -1.4950
 FYM  H271  H  HCH2   0   0.211   3.1447  -2.7919  -1.3448
 FYM  H272  H  HCH2   0   0.255   2.0822  -1.8355  -2.3662
 FYM  H28   H  HNH1   0   0.397  -1.4660  -0.5540  -0.1057
 FYM  H211  H  HCH2   0   0.247  -1.2940  -6.9544   1.8936
 FYM  H212  H  HCH2   0   0.234  -1.2846  -7.3607   0.1440
 FYM  H221  H  HCH3   0   0.241   2.8607  -0.4554   1.4651
 FYM  H222  H  HCH3   0   0.236   2.1187  -2.0328   1.2704
 FYM  H223  H  HCH3   0   0.181   3.8269  -1.8172   0.8665
 FYM  H231  H  HCH3   0   0.227  -7.6775   3.1522   0.0868
 FYM  H232  H  HCH3   0   0.227  -7.7358   1.6261   0.9953
 FYM  H233  H  HCH3   0   0.258  -8.0527   3.1621   1.8186
 FYM  H241  H  HCH3   0   0.222   3.2542   4.8645   2.9729
 FYM  H242  H  HCH3   0   0.222   3.5574   5.7770   1.4805
 FYM  H243  H  HCH3   0   0.255   1.9349   5.7527   2.1929
 FYM  C19   C  C      0   0.513  -0.5865  -1.3082  -1.7569

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
 FYM  C1   C2    aromatic  1.382  0.020  1.382
 FYM  C1   C5    aromatic  1.389  0.020  1.389
 FYM  C2   C13   aromatic  1.396  0.020  1.396
 FYM  C3   C6    aromatic  1.382  0.020  1.382
 FYM  C3   C12   aromatic  1.396  0.020  1.396
 FYM  C4   C7    aromatic  1.391  0.020  1.391
 FYM  C4   C12   aromatic  1.387  0.020  1.387
 FYM  C5   C18   aromatic  1.391  0.020  1.391
 FYM  C6   C17   aromatic  1.397  0.020  1.397
 FYM  C7   C17   aromatic  1.392  0.020  1.392
 FYM  C8   C10   aromatic  1.405  0.020  1.405
 FYM  C8   C15   aromatic  1.371  0.020  1.371
 FYM  C9   C14   aromatic  1.402  0.020  1.402
 FYM  C9   C16   aromatic  1.373  0.020  1.373
 FYM  C10  C14   aromatic  1.396  0.020  1.396
 FYM  C10  C19   single    1.500  0.020  1.500
 FYM  C11  C13   aromatic  1.392  0.020  1.392
 FYM  C11  C18   aromatic  1.402  0.020  1.402
 FYM  C11  C20   single    1.524  0.020  1.524
 FYM  C12  C25   single    1.502  0.020  1.502
 FYM  C13  C26   single    1.506  0.020  1.506
 FYM  C14  C27   single    1.507  0.020  1.507
 FYM  C15  C16   aromatic  1.382  0.020  1.382
 FYM  C15  O33   single    1.356  0.020  1.356
 FYM  C16  O34   single    1.354  0.020  1.354
 FYM  C17  O35   single    1.348  0.020  1.348
 FYM  C18  O36   single    1.353  0.020  1.353
 FYM  C19  N28   single    1.339  0.020  1.339
 FYM  C19  O31   double    1.224  0.020  1.224
 FYM  C20  O30   deloc     1.241  0.020  1.241
 FYM  C20  O32   deloc     1.245  0.020  1.245
 FYM  C21  O33   single    1.422  0.020  1.422
 FYM  C21  O34   single    1.423  0.020  1.423
 FYM  C22  N29   single    1.446  0.020  1.446
 FYM  C23  O35   single    1.413  0.020  1.413
 FYM  C24  O36   single    1.410  0.020  1.410
 FYM  C25  N28   single    1.453  0.020  1.453
 FYM  C26  N29   single    1.456  0.020  1.456
 FYM  C27  N29   single    1.453  0.020  1.453
 FYM  C1   H1    single    0.930  0.020  1.080
 FYM  C2   H2    single    0.930  0.020  1.080
 FYM  C5   H5    single    0.930  0.020  1.080
 FYM  C3   H3    single    0.930  0.020  1.080
 FYM  C6   H6    single    0.930  0.020  1.080
 FYM  C4   H4    single    0.930  0.020  1.080
 FYM  C7   H7    single    0.930  0.020  1.080
 FYM  C8   H8    single    0.930  0.020  1.080
 FYM  C9   H9    single    0.930  0.020  1.080
 FYM  C25  H251  single    0.970  0.020  1.090
 FYM  C25  H252  single    0.970  0.020  1.090
 FYM  C26  H261  single    0.970  0.020  1.090
 FYM  C26  H262  single    0.970  0.020  1.090
 FYM  C27  H271  single    0.970  0.020  1.090
 FYM  C27  H272  single    0.970  0.020  1.090
 FYM  N28  H28   single    0.860  0.020  1.020
 FYM  C21  H211  single    0.970  0.020  1.090
 FYM  C21  H212  single    0.970  0.020  1.090
 FYM  C22  H221  single    0.970  0.020  1.090
 FYM  C22  H222  single    0.970  0.020  1.090
 FYM  C22  H223  single    0.970  0.020  1.090
 FYM  C23  H231  single    0.970  0.020  1.090
 FYM  C23  H232  single    0.970  0.020  1.090
 FYM  C23  H233  single    0.970  0.020  1.090
 FYM  C24  H241  single    0.970  0.020  1.090
 FYM  C24  H242  single    0.970  0.020  1.090
 FYM  C24  H243  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
 FYM  H1    C1   C5    119.45  3.000
 FYM  H1    C1   C2    120.33  3.000
 FYM  C5    C1   C2    120.22  3.000
 FYM  H2    C2   C13   119.44  3.000
 FYM  H2    C2   C1    119.90  3.000
 FYM  C13   C2   C1    120.66  3.000
 FYM  H3    C3   C12   118.86  3.000
 FYM  H3    C3   C6    120.05  3.000
 FYM  C12   C3   C6    121.08  3.000
 FYM  H4    C4   C12   119.77  3.000
 FYM  H4    C4   C7    118.52  3.000
 FYM  C12   C4   C7    121.71  3.000
 FYM  H5    C5   C18   121.54  3.000
 FYM  H5    C5   C1    119.17  3.000
 FYM  C18   C5   C1    119.29  3.000
 FYM  H6    C6   C17   119.40  3.000
 FYM  H6    C6   C3    120.30  3.000
 FYM  C17   C6   C3    120.31  3.000
 FYM  H7    C7   C17   121.58  3.000
 FYM  H7    C7   C4    118.80  3.000
 FYM  C17   C7   C4    119.62  3.000
 FYM  H8    C8   C15   121.18  3.000
 FYM  H8    C8   C10   121.23  3.000
 FYM  C15   C8   C10   117.58  3.000
 FYM  H9    C9   C16   121.36  3.000
 FYM  H9    C9   C14   120.36  3.000
 FYM  C16   C9   C14   118.28  3.000
 FYM  C19   C10  C14   121.65  3.000
 FYM  C19   C10  C8    116.96  3.000
 FYM  C14   C10  C8    121.19  3.000
 FYM  C20   C11  C18   118.39  3.000
 FYM  C20   C11  C13   122.61  3.000
 FYM  C18   C11  C13   118.99  3.000
 FYM  C25   C12  C4    121.60  3.000
 FYM  C25   C12  C3    120.35  3.000
 FYM  C4    C12  C3    118.04  3.000
 FYM  C26   C13  C11   121.83  3.000
 FYM  C26   C13  C2    118.36  3.000
 FYM  C11   C13  C2    119.81  3.000
 FYM  C27   C14  C10   121.64  3.000
 FYM  C27   C14  C9    118.52  3.000
 FYM  C10   C14  C9    119.77  3.000
 FYM  O33   C15  C16   109.47  3.000
 FYM  O33   C15  C8    129.00  3.000
 FYM  C16   C15  C8    121.52  3.000
 FYM  O34   C16  C15   109.45  3.000
 FYM  O34   C16  C9    128.89  3.000
 FYM  C15   C16  C9    121.64  3.000
 FYM  O35   C17  C7    124.41  3.000
 FYM  O35   C17  C6    116.35  3.000
 FYM  C7    C17  C6    119.24  3.000
 FYM  O36   C18  C11   115.65  3.000
 FYM  O36   C18  C5    123.31  3.000
 FYM  C11   C18  C5    121.03  3.000
 FYM  O32   C20  O30   128.63  3.000
 FYM  O32   C20  C11   115.18  3.000
 FYM  O30   C20  C11   116.14  3.000
 FYM  H212  C21  H211  110.59  3.000
 FYM  H212  C21  O34   109.76  3.000
 FYM  H211  C21  O34   109.78  3.000
 FYM  H212  C21  O33   109.88  3.000
 FYM  H211  C21  O33   109.87  3.000
 FYM  O34   C21  O33   106.89  3.000
 FYM  H223  C22  H222  107.54  3.000
 FYM  H223  C22  H221  108.10  3.000
 FYM  H222  C22  H221  107.26  3.000
 FYM  H223  C22  N29   113.42  3.000
 FYM  H222  C22  N29   109.89  3.000
 FYM  H221  C22  N29   110.41  3.000
 FYM  H233  C23  H232  108.64  3.000
 FYM  H233  C23  H231  108.70  3.000
 FYM  H232  C23  H231  108.71  3.000
 FYM  H233  C23  O35   106.58  3.000
 FYM  H232  C23  O35   112.05  3.000
 FYM  H231  C23  O35   112.05  3.000
 FYM  H243  C24  H242  108.64  3.000
 FYM  H243  C24  H241  108.60  3.000
 FYM  H242  C24  H241  108.49  3.000
 FYM  H243  C24  O36   106.57  3.000
 FYM  H242  C24  O36   112.24  3.000
 FYM  H241  C24  O36   112.19  3.000
 FYM  H252  C25  H251  108.11  3.000
 FYM  H252  C25  N28   109.43  3.000
 FYM  H251  C25  N28   108.33  3.000
 FYM  H252  C25  C12   110.80  3.000
 FYM  H251  C25  C12   109.99  3.000
 FYM  N28   C25  C12   110.13  3.000
 FYM  H262  C26  H261  106.58  3.000
 FYM  H262  C26  N29   110.92  3.000
 FYM  H261  C26  N29   107.33  3.000
 FYM  H262  C26  C13   107.52  3.000
 FYM  H261  C26  C13   109.97  3.000
 FYM  N29   C26  C13   114.27  3.000
 FYM  H272  C27  H271  106.41  3.000
 FYM  H272  C27  N29   108.16  3.000
 FYM  H271  C27  N29   111.29  3.000
 FYM  H272  C27  C14   109.97  3.000
 FYM  H271  C27  C14   108.61  3.000
 FYM  N29   C27  C14   112.24  3.000
 FYM  H28   N28  C25   117.05  3.000
 FYM  H28   N28  C19   117.83  3.000
 FYM  C25   N28  C19   122.40  3.000
 FYM  C27   N29  C26   109.00  3.000
 FYM  C27   N29  C22   111.47  3.000
 FYM  C26   N29  C22   112.93  3.000
 FYM  C21   O33  C15   105.87  3.000
 FYM  C21   O34  C16   105.93  3.000
 FYM  C23   O35  C17   118.51  3.000
 FYM  C24   O36  C18   118.70  3.000
 FYM  O31   C19  N28   123.29  3.000
 FYM  O31   C19  C10   121.67  3.000
 FYM  N28   C19  C10   114.79  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
 FYM  CONST_01  C11   C13  C2   C1      0.00   0.0  0
 FYM  CONST_02  C11   C18  C5   C1      0.00   0.0  0
 FYM  CONST_03  C18   C5   C1   C2      0.00   0.0  0
 FYM  CONST_04  C18   C11  C13  C2      0.00   0.0  0
 FYM  CONST_05  C7    C17  C6   C3      0.00   0.0  0
 FYM  CONST_06  C7    C4   C12  C3      0.00   0.0  0
 FYM  CONST_07  C6    C17  C7   C4      0.00   0.0  0
 FYM  CONST_08  C6    C3   C12  C4      0.00   0.0  0
 FYM  CONST_09  C13   C2   C1   C5      0.00   0.0  0
 FYM  CONST_10  C13   C11  C18  C5      0.00   0.0  0
 FYM  CONST_11  C9    C14  C10  C8      0.00   0.0  0
 FYM  CONST_12  C9    C16  C15  C8      0.00   0.0  0
 FYM  CONST_13  C16   C15  C8   C10     0.00   0.0  0
 FYM  CONST_14  C16   C9   C14  C10     0.00   0.0  0
 FYM  CONST_15  C17   C6   C3   C12     0.00   0.0  0
 FYM  CONST_16  C17   C7   C4   C12     0.00   0.0  0
 FYM  CONST_17  C15   C16  C9   C14     0.00   0.0  0
 FYM  CONST_18  C15   C8   C10  C14     0.00   0.0  0
 FYM  CONST_19  C26   C13  C2   C1    180.00   0.0  0
 FYM  CONST_20  O36   C18  C5   C1    180.00   0.0  0
 FYM  CONST_21  C20   C11  C13  C2    180.00   0.0  0
 FYM  CONST_22  O35   C17  C6   C3    180.00   0.0  0
 FYM  CONST_23  O35   C17  C7   C4    180.00   0.0  0
 FYM  CONST_24  C20   C11  C18  C5    180.00   0.0  0
 FYM  CONST_25  C25   C12  C3   C6    180.00   0.0  0
 FYM  CONST_26  C25   C12  C4   C7    180.00   0.0  0
 FYM  CONST_27  C27   C14  C10  C8    180.00   0.0  0
 FYM  CONST_28  C19   C10  C14  C9    180.00   0.0  0
 FYM  CONST_29  O36   C18  C11  C13   180.00   0.0  0
 FYM  CONST_30  C19   C10  C8   C15   180.00   0.0  0
 FYM  CONST_31  C27   C14  C9   C16   180.00   0.0  0
 FYM  CONST_32  C26   C13  C11  C18   180.00   0.0  0
 FYM  CONST_33  H5    C5   C1   C2    180.00   0.0  0
 FYM  CONST_34  H4    C4   C12  C3    180.00   0.0  0
 FYM  CONST_35  H3    C3   C12  C4    180.00   0.0  0
 FYM  CONST_36  H2    C2   C1   C5    180.00   0.0  0
 FYM  CONST_37  H7    C7   C17  C6    180.00   0.0  0
 FYM  CONST_38  H6    C6   C17  C7    180.00   0.0  0
 FYM  CONST_39  H9    C9   C14  C10   180.00   0.0  0
 FYM  CONST_40  H1    C1   C2   C13   180.00   0.0  0
 FYM  CONST_41  H8    C8   C10  C14   180.00   0.0  0
 FYM  CONST_42  C25   N28  C19  C10   180.00   0.0  0
 FYM  CONST_44  O31   C19  N28  C25     0.00   0.0  0
 FYM  Var_01    O34   C21  O33  C15    15.01  30.0  1
 FYM  Var_02    O33   C21  O34  C16   -15.07  30.0  1
 FYM  Var_03    N29   C26  C13  C2    115.38  30.0  2
 FYM  Var_04    N28   C25  C12  C3     80.37  30.0  2
 FYM  Var_05    N28   C19  C10  C8     53.15  30.0  2
 FYM  Var_06    N29   C27  C14  C9   -108.78  30.0  2
 FYM  Var_07    O30   C20  C11  C13   108.98  30.0  2
 FYM  Var_08    C19   N28  C25  C12   165.85  30.0  3
 FYM  Var_09    C22   N29  C26  C13   -46.76  30.0  3
 FYM  Var_10    H231  C23  O35  C17   -61.58  30.0  3
 FYM  Var_11    H241  C24  O36  C18   -60.77  30.0  3
 FYM  Var_12    H221  C22  N29  C26    62.92  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
 FYM  plan-1  C1   0.020
 FYM  plan-1  C2   0.020
 FYM  plan-1  C5   0.020
 FYM  plan-1  C11  0.020
 FYM  plan-1  C13  0.020
 FYM  plan-1  C18  0.020
 FYM  plan-1  C20  0.020
 FYM  plan-1  C26  0.020
 FYM  plan-1  O36  0.020
 FYM  plan-1  H1   0.020
 FYM  plan-1  H2   0.020
 FYM  plan-1  H5   0.020
 FYM  plan-2  C3   0.020
 FYM  plan-2  C4   0.020
 FYM  plan-2  C6   0.020
 FYM  plan-2  C7   0.020
 FYM  plan-2  C12  0.020
 FYM  plan-2  C17  0.020
 FYM  plan-2  C25  0.020
 FYM  plan-2  O35  0.020
 FYM  plan-2  H3   0.020
 FYM  plan-2  H6   0.020
 FYM  plan-2  H4   0.020
 FYM  plan-2  H7   0.020
 FYM  plan-3  C8   0.020
 FYM  plan-3  C9   0.020
 FYM  plan-3  C10  0.020
 FYM  plan-3  C14  0.020
 FYM  plan-3  C15  0.020
 FYM  plan-3  C16  0.020
 FYM  plan-3  C27  0.020
 FYM  plan-3  O33  0.020
 FYM  plan-3  O34  0.020
 FYM  plan-3  H8   0.020
 FYM  plan-3  H9   0.020
 FYM  plan-3  C19  0.020
 FYM  plan-4  C10  0.020
 FYM  plan-4  C25  0.020
 FYM  plan-4  N28  0.020
 FYM  plan-4  O31  0.020
 FYM  plan-4  H28  0.020
 FYM  plan-4  C19  0.020
 FYM  plan-5  C11  0.020
 FYM  plan-5  C20  0.020
 FYM  plan-5  O30  0.020
 FYM  plan-5  O32  0.020

