# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 06:23:27 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: N,N~2~-bis[(4-methoxyphenyl)methyl]glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNCC(=O)NCc2ccc(OC)cc2)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
 98C  98C  "N,N~2~-bis[(4-methoxyphenyl)methyl]glycinamide"
  ligand  45  23  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_98C
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
 98C  O1   O  O     0  -0.488   -7.3580  13.0129  -5.4053
 98C  C1   C  C     0   0.537   -7.8022  13.8253  -4.6085
 98C  N1   N  NH1   0  -0.617   -7.0433  14.5004  -3.7265
 98C  C2   C  CH2   0  -0.389   -5.6200  14.3078  -3.5392
 98C  C3   C  CR6   0   0.097   -5.3170  13.5188  -2.2917
 98C  C4   C  CR16  0  -0.274   -5.2709  12.1248  -2.3075
 98C  C5   C  CR16  0  -0.329   -5.0470  11.4010  -1.1513
 98C  C6   C  CR6   0   0.368   -4.8656  12.0606   0.0676
 98C  O2   O  O2    0  -0.467   -4.6594  11.2810   1.1461
 98C  C7   C  CH3   0  -0.439   -4.4872  11.9019   2.4028
 98C  C8   C  CR16  0  -0.368   -4.9050  13.4519   0.0991
 98C  C9   C  CR16  0  -0.280   -5.1282  14.1605  -1.0762
 98C  C10  C  CH2   0  -0.419   -9.2744  14.2120  -4.5554
 98C  N2   N  NH1   0  -0.577  -10.1484  13.1550  -5.0032
 98C  C11  C  CH2   0  -0.381  -10.1296  11.9342  -4.2032
 98C  C12  C  CR6   0   0.067  -10.0429  12.1298  -2.7095
 98C  C13  C  CR16  0  -0.278  -11.0987  12.6774  -1.9784
 98C  C14  C  CR16  0  -0.329  -10.9871  12.9097  -0.6207
 98C  C15  C  CR6   0   0.367   -9.7995  12.6039   0.0522
 98C  O3   O  O2    0  -0.469   -9.7733  12.8714   1.3729
 98C  C16  C  CH3   0  -0.436   -8.5925  12.5833   2.0919
 98C  C17  C  CR16  0  -0.374   -8.7381  12.0558  -0.6599
 98C  C18  C  CR16  0  -0.282   -8.8753  11.8289  -2.0253
 98C  H1   H  HNH1  0   0.397   -7.5081  15.0924  -3.0561
 98C  H2   H  HCH2  0   0.263   -5.2243  13.8066  -4.4206
 98C  H3   H  HCH2  0   0.263   -5.1438  15.2884  -3.4833
 98C  H4   H  HCR6  0   0.252   -5.4129  11.5942  -3.2417
 98C  H5   H  HCR6  0   0.260   -5.0109  10.3189  -1.1823
 98C  H6   H  HCH3  0   0.258   -4.3455  11.1024   3.1260
 98C  H7   H  HCH3  0   0.228   -3.6084  12.5519   2.4229
 98C  H8   H  HCH3  0   0.229   -5.3639  12.4874   2.6938
 98C  H9   H  HCR6  0   0.276   -4.7623  14.0003   1.0204
 98C  H10  H  HCR6  0   0.253   -5.1528  15.2436  -1.0323
 98C  H11  H  HCH2  0   0.279   -9.4053  15.0647  -5.2294
 98C  H12  H  HCH2  0   0.224   -9.5077  14.5847  -3.5481
 98C  H13  H  HNH1  0   0.358  -11.0896  13.5206  -5.0459
 98C  H15  H  HCH2  0   0.248  -11.0325  11.3760  -4.4595
 98C  H16  H  HCH2  0   0.234   -9.2875  11.3149  -4.5203
 98C  H17  H  HCR6  0   0.247  -12.0273  12.9287  -2.4794
 98C  H18  H  HCR6  0   0.256  -11.8174  13.3315  -0.0673
 98C  H19  H  HCH3  0   0.257   -8.7803  12.8674   3.1245
 98C  H20  H  HCH3  0   0.225   -8.3420  11.5192   2.0607
 98C  H21  H  HCH3  0   0.224   -7.7355  13.1533   1.7209
 98C  H22  H  HCR6  0   0.279   -7.7993  11.8056  -0.1838
 98C  H23  H  HCR6  0   0.250   -8.0354  11.4070  -2.5648

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
 98C  O1   C1   double    1.221  0.020  1.221
 98C  N2   C10  single    1.443  0.020  1.443
 98C  N2   C11  single    1.460  0.020  1.460
 98C  C1   C10  single    1.523  0.020  1.523
 98C  C1   N1   single    1.345  0.020  1.345
 98C  C11  C12  single    1.509  0.020  1.509
 98C  N1   C2   single    1.448  0.020  1.448
 98C  C2   C3   single    1.507  0.020  1.507
 98C  C12  C13  aromatic  1.396  0.020  1.396
 98C  C12  C18  aromatic  1.386  0.020  1.386
 98C  C4   C3   aromatic  1.395  0.020  1.395
 98C  C4   C5   aromatic  1.382  0.020  1.382
 98C  C3   C9   aromatic  1.387  0.020  1.387
 98C  C13  C14  aromatic  1.382  0.020  1.382
 98C  C18  C17  aromatic  1.391  0.020  1.391
 98C  C5   C6   aromatic  1.398  0.020  1.398
 98C  C9   C8   aromatic  1.390  0.020  1.390
 98C  C14  C15  aromatic  1.399  0.020  1.399
 98C  C17  C15  aromatic  1.391  0.020  1.391
 98C  C6   C8   aromatic  1.392  0.020  1.392
 98C  C6   O2   single    1.347  0.020  1.347
 98C  C15  O3   single    1.348  0.020  1.348
 98C  O2   C7   single    1.412  0.020  1.412
 98C  O3   C16  single    1.412  0.020  1.412
 98C  N1   H1   single    0.860  0.020  1.020
 98C  C2   H2   single    0.970  0.020  1.090
 98C  C2   H3   single    0.970  0.020  1.090
 98C  C4   H4   single    0.930  0.020  1.080
 98C  C5   H5   single    0.930  0.020  1.080
 98C  C7   H6   single    0.970  0.020  1.090
 98C  C7   H7   single    0.970  0.020  1.090
 98C  C7   H8   single    0.970  0.020  1.090
 98C  C8   H9   single    0.930  0.020  1.080
 98C  C9   H10  single    0.930  0.020  1.080
 98C  C10  H11  single    0.970  0.020  1.090
 98C  C10  H12  single    0.970  0.020  1.090
 98C  N2   H13  single    0.890  0.020  1.040
 98C  C11  H15  single    0.970  0.020  1.090
 98C  C11  H16  single    0.970  0.020  1.090
 98C  C13  H17  single    0.930  0.020  1.080
 98C  C14  H18  single    0.930  0.020  1.080
 98C  C16  H19  single    0.970  0.020  1.090
 98C  C16  H20  single    0.970  0.020  1.090
 98C  C16  H21  single    0.970  0.020  1.090
 98C  C17  H22  single    0.930  0.020  1.080
 98C  C18  H23  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
 98C  C10  C1   N1   113.26  3.000
 98C  N1   C1   O1   123.80  3.000
 98C  C10  C1   O1   122.90  3.000
 98C  H1   N1   C2   116.44  3.000
 98C  H1   N1   C1   118.08  3.000
 98C  C2   N1   C1   124.92  3.000
 98C  H3   C2   H2   107.25  3.000
 98C  H3   C2   C3   109.89  3.000
 98C  H2   C2   C3   110.87  3.000
 98C  H3   C2   N1   108.41  3.000
 98C  H2   C2   N1   108.28  3.000
 98C  C3   C2   N1   111.98  3.000
 98C  C9   C3   C4   117.88  3.000
 98C  C9   C3   C2   120.70  3.000
 98C  C4   C3   C2   121.37  3.000
 98C  H4   C4   C5   119.07  3.000
 98C  H4   C4   C3   119.65  3.000
 98C  C5   C4   C3   121.28  3.000
 98C  H5   C5   C6   119.48  3.000
 98C  H5   C5   C4   120.30  3.000
 98C  C6   C5   C4   120.22  3.000
 98C  C8   C6   O2   124.38  3.000
 98C  O2   C6   C5   116.43  3.000
 98C  C8   C6   C5   119.18  3.000
 98C  C7   O2   C6   118.48  3.000
 98C  H8   C7   H7   108.74  3.000
 98C  H8   C7   H6   108.73  3.000
 98C  H7   C7   H6   108.67  3.000
 98C  H8   C7   O2   111.99  3.000
 98C  H7   C7   O2   112.08  3.000
 98C  H6   C7   O2   106.52  3.000
 98C  H9   C8   C9   118.87  3.000
 98C  H9   C8   C6   121.48  3.000
 98C  C9   C8   C6   119.65  3.000
 98C  H10  C9   C8   118.59  3.000
 98C  H10  C9   C3   119.63  3.000
 98C  C8   C9   C3   121.78  3.000
 98C  H12  C10  H11  105.94  3.000
 98C  H12  C10  N2   113.85  3.000
 98C  H11  C10  N2   107.88  3.000
 98C  H12  C10  C1   108.86  3.000
 98C  H11  C10  C1   106.97  3.000
 98C  N2   C10  C1   112.87  3.000
 98C  H13  N2   C11  109.74  3.000
 98C  H13  N2   C10  108.20  3.000
 98C  C11  N2   C10  115.77  3.000
 98C  H16  C11  H15  106.23  3.000
 98C  H16  C11  C12  108.46  3.000
 98C  H15  C11  C12  110.25  3.000
 98C  H16  C11  N2   108.97  3.000
 98C  H15  C11  N2   106.75  3.000
 98C  C12  C11  N2   115.77  3.000
 98C  C18  C12  C13  117.62  3.000
 98C  C18  C12  C11  120.59  3.000
 98C  C13  C12  C11  121.72  3.000
 98C  H17  C13  C14  118.95  3.000
 98C  H17  C13  C12  119.77  3.000
 98C  C14  C13  C12  121.29  3.000
 98C  H18  C14  C15  119.35  3.000
 98C  H18  C14  C13  120.36  3.000
 98C  C15  C14  C13  120.29  3.000
 98C  C17  C15  O3   124.42  3.000
 98C  O3   C15  C14  116.39  3.000
 98C  C17  C15  C14  119.20  3.000
 98C  C16  O3   C15  118.33  3.000
 98C  H21  C16  H20  108.53  3.000
 98C  H21  C16  H19  108.74  3.000
 98C  H20  C16  H19  108.72  3.000
 98C  H21  C16  O3   112.09  3.000
 98C  H20  C16  O3   112.06  3.000
 98C  H19  C16  O3   106.60  3.000
 98C  H22  C17  C18  118.67  3.000
 98C  H22  C17  C15  121.88  3.000
 98C  C18  C17  C15  119.45  3.000
 98C  H23  C18  C17  118.41  3.000
 98C  H23  C18  C12  119.44  3.000
 98C  C17  C18  C12  122.15  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
 98C  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 98C  CONST_02  C6   C8   C9   C3      0.00   0.0  0
 98C  CONST_03  C8   C9   C3   C4      0.00   0.0  0
 98C  CONST_04  C8   C6   C5   C4      0.00   0.0  0
 98C  CONST_05  C9   C3   C4   C5      0.00   0.0  0
 98C  CONST_06  C9   C8   C6   C5      0.00   0.0  0
 98C  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 98C  CONST_08  C15  C17  C18  C12     0.00   0.0  0
 98C  CONST_09  C17  C18  C12  C13     0.00   0.0  0
 98C  CONST_10  C17  C15  C14  C13     0.00   0.0  0
 98C  CONST_11  C18  C12  C13  C14     0.00   0.0  0
 98C  CONST_12  C18  C17  C15  C14     0.00   0.0  0
 98C  CONST_13  C5   C4   C3   C2    180.00   0.0  0
 98C  CONST_14  C8   C9   C3   C2    180.00   0.0  0
 98C  CONST_15  O2   C6   C5   C4    180.00   0.0  0
 98C  CONST_16  C9   C8   C6   O2    180.00   0.0  0
 98C  CONST_17  C14  C13  C12  C11   180.00   0.0  0
 98C  CONST_18  C17  C18  C12  C11   180.00   0.0  0
 98C  CONST_19  O3   C15  C14  C13   180.00   0.0  0
 98C  CONST_20  C18  C17  C15  O3    180.00   0.0  0
 98C  CONST_21  H5   C5   C4   C3    180.00   0.0  0
 98C  CONST_22  H9   C8   C9   C3    180.00   0.0  0
 98C  CONST_23  H10  C9   C3   C4    180.00   0.0  0
 98C  CONST_24  H9   C8   C6   C5    180.00   0.0  0
 98C  CONST_25  H4   C4   C5   C6    180.00   0.0  0
 98C  CONST_26  H10  C9   C8   C6    180.00   0.0  0
 98C  CONST_27  H5   C5   C6   C8    180.00   0.0  0
 98C  CONST_28  H4   C4   C3   C9    180.00   0.0  0
 98C  CONST_29  H18  C14  C13  C12   180.00   0.0  0
 98C  CONST_30  H22  C17  C18  C12   180.00   0.0  0
 98C  CONST_31  H23  C18  C12  C13   180.00   0.0  0
 98C  CONST_32  H22  C17  C15  C14   180.00   0.0  0
 98C  CONST_33  H17  C13  C14  C15   180.00   0.0  0
 98C  CONST_34  H23  C18  C17  C15   180.00   0.0  0
 98C  CONST_35  H18  C14  C15  C17   180.00   0.0  0
 98C  CONST_36  H17  C13  C12  C18   180.00   0.0  0
 98C  CONST_37  C2   N1   C1   O1      0.00   0.0  0
 98C  CONST_38  C10  C1   N1   C2    180.00   0.0  0
 98C  CONST_39  H1   N1   C1   O1    180.00   0.0  0
 98C  CONST_40  H1   N1   C1   C10     0.00   0.0  0
 98C  Var_01    C4   C3   C2   N1     87.76  30.0  2
 98C  Var_02    C9   C3   C2   N1    -89.60  30.0  2
 98C  Var_03    C7   O2   C6   C5   -179.24  30.0  2
 98C  Var_04    C8   C6   O2   C7      0.86  30.0  2
 98C  Var_05    C13  C12  C11  N2     68.61  30.0  2
 98C  Var_06    C18  C12  C11  N2   -108.16  30.0  2
 98C  Var_07    C16  O3   C15  C14  -179.77  30.0  2
 98C  Var_08    C17  C15  O3   C16     0.18  30.0  2
 98C  Var_09    H2   C2   C3   C4    -33.30  30.0  2
 98C  Var_10    H3   C2   C3   C4   -151.69  30.0  2
 98C  Var_11    H2   C2   C3   C9    149.33  30.0  2
 98C  Var_12    H3   C2   C3   C9     30.94  30.0  2
 98C  Var_13    H15  C11  C12  C13   -52.67  30.0  2
 98C  Var_14    H16  C11  C12  C13  -168.60  30.0  2
 98C  Var_15    H15  C11  C12  C18   130.56  30.0  2
 98C  Var_16    H16  C11  C12  C18    14.63  30.0  2
 98C  Var_17    C3   C2   N1   C1   -103.63  30.0  3
 98C  Var_18    C12  C11  N2   C10    39.46  30.0  3
 98C  Var_19    H1   N1   C2   C3     67.55  30.0  1
 98C  Var_20    H6   C7   O2   C6    179.52  30.0  3
 98C  Var_21    H7   C7   O2   C6    -61.75  30.0  3
 98C  Var_22    H8   C7   O2   C6     60.77  30.0  3
 98C  Var_23    H13  N2   C11  C12   -83.34  30.0  1
 98C  Var_24    H19  C16  O3   C15  -179.87  30.0  3
 98C  Var_25    H20  C16  O3   C15   -61.05  30.0  3
 98C  Var_26    H21  C16  O3   C15    61.26  30.0  3
 98C  Var_27    N2   C10  C1   O1     28.40  30.0  3
 98C  Var_28    C11  N2   C10  C1     63.15  30.0  1
 98C  Var_29    N2   C10  C1   N1   -153.79  30.0  3
 98C  Var_30    H11  C10  C1   O1    -90.10  30.0  3
 98C  Var_31    H12  C10  C1   O1    155.83  30.0  3
 98C  Var_32    H13  N2   C10  C1   -173.24  30.0  1
 98C  Var_33    H2   C2   N1   C1     18.92  30.0  3
 98C  Var_34    H3   C2   N1   C1    134.96  30.0  3
 98C  Var_35    H11  C10  C1   N1     87.71  30.0  3
 98C  Var_36    H12  C10  C1   N1    -26.35  30.0  3
 98C  Var_37    H15  C11  N2   C10   162.60  30.0  3
 98C  Var_38    H16  C11  N2   C10   -83.06  30.0  3
 98C  Var_39    H11  C10  N2   C11  -178.88  30.0  3
 98C  Var_40    H12  C10  N2   C11   -61.61  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
 98C  plan-1  C2   0.020
 98C  plan-1  C3   0.020
 98C  plan-1  C4   0.020
 98C  plan-1  C5   0.020
 98C  plan-1  C6   0.020
 98C  plan-1  O2   0.020
 98C  plan-1  C8   0.020
 98C  plan-1  C9   0.020
 98C  plan-1  H4   0.020
 98C  plan-1  H5   0.020
 98C  plan-1  H9   0.020
 98C  plan-1  H10  0.020
 98C  plan-2  C11  0.020
 98C  plan-2  C12  0.020
 98C  plan-2  C13  0.020
 98C  plan-2  C14  0.020
 98C  plan-2  C15  0.020
 98C  plan-2  O3   0.020
 98C  plan-2  C17  0.020
 98C  plan-2  C18  0.020
 98C  plan-2  H17  0.020
 98C  plan-2  H18  0.020
 98C  plan-2  H22  0.020
 98C  plan-2  H23  0.020
 98C  plan-3  O1   0.020
 98C  plan-3  C1   0.020
 98C  plan-3  N1   0.020
 98C  plan-3  C2   0.020
 98C  plan-3  C10  0.020
 98C  plan-3  H1   0.020

