# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 01:24:39 2021
#   Inital geometry file: a 133 line input string
#   Ligand name: 4-[[[4-(aminomethyl)phenyl]carbamoyl-(4-oxidanylbutyl)amino]methyl]-~{N}-oxidanyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(NC(=O)N(CCCCO)Cc2ccc(cc2)C(=O)NO)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
 N28  N28  4-[[[4-(aminomethyl)phenyl]carbamoyl-(4-oxidanylbutyl)amino]methyl]-~{N}-oxidanyl-benzamide  ligand  54  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N28
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
 N28  N1   N  NH2   0  -0.793  -5.8220  -15.4574  11.7844
 N28  C1   C  CH2   0  -0.339  -4.9186  -14.3484  11.5288
 N28  C2   C  CR6   0   0.079  -5.0253  -13.8517  10.1098
 N28  C3   C  CR16  0  -0.304  -4.9359  -12.4951   9.8192
 N28  C4   C  CR16  0  -0.324  -4.9896  -12.0344   8.5126
 N28  C5   C  CR6   0   0.355  -5.1573  -12.9223   7.4527
 N28  N2   N  NH1   0  -0.787  -5.2719  -12.3916   6.1609
 N28  C6   C  C     0   0.724  -4.7288  -12.9504   5.0272
 N28  O1   O  O     0  -0.517  -4.1368  -14.0189   5.0516
 N28  N3   N  NT    0  -0.493  -4.9051  -12.2266   3.8848
 N28  C7   C  CH2   0  -0.326  -4.3794  -12.7205   2.6199
 N28  C8   C  CH2   0  -0.423  -5.4458  -13.3452   1.7259
 N28  C9   C  CH2   0  -0.448  -6.0718  -14.6073   2.3054
 N28  C10  C  CH2   0  -0.156  -7.0998  -15.2503   1.3953
 N28  O2   O  OH1   0  -0.675  -8.1907  -14.3698   1.2206
 N28  C11  C  CH2   0  -0.398  -5.6640  -10.9981   3.8455
 N28  C12  C  CR6   0   0.048  -4.9648   -9.8025   4.4555
 N28  C13  C  CR16  0  -0.273  -5.7197   -8.7065   4.8662
 N28  C14  C  CR16  0  -0.250  -5.1095   -7.5891   5.4080
 N28  C15  C  CR6   0  -0.070  -3.7242   -7.5383   5.5442
 N28  C16  C  C     0   0.504  -3.1265   -6.3124   6.1508
 N28  O3   O  O     0  -0.461  -3.7592   -5.5796   6.8897
 N28  N4   N  NH1   0  -0.386  -1.8311   -6.1027   5.8306
 N28  O4   O  OH1   0  -0.539  -1.2409   -4.9348   6.2101
 N28  C17  C  CR16  0  -0.264  -2.9683   -8.6387   5.1475
 N28  C18  C  CR16  0  -0.267  -3.5840   -9.7585   4.6094
 N28  C19  C  CR16  0  -0.277  -5.2721  -14.2841   7.7335
 N28  C20  C  CR16  0  -0.285  -5.1991  -14.7310   9.0435
 N28  H1   H  HNH2  0   0.352  -5.6473  -15.8271  12.7098
 N28  H27  H  HNH2  0   0.343  -6.7763  -15.1197  11.7933
 N28  H4   H  HCH2  0   0.237  -3.8985  -14.7048  11.7018
 N28  H3   H  HCH2  0   0.213  -5.0551  -13.4968  12.2088
 N28  H5   H  HCR6  0   0.249  -4.8189  -11.7777  10.6231
 N28  H6   H  HCR6  0   0.253  -4.9065  -10.9708   8.3188
 N28  H7   H  HNH1  0   0.411  -5.5404  -11.4212   6.1403
 N28  H9   H  HCH2  0   0.256  -3.5888  -13.4396   2.8234
 N28  H8   H  HCH2  0   0.251  -3.9150  -11.8796   2.0986
 N28  H11  H  HCH2  0   0.227  -4.9746  -13.5789   0.7659
 N28  H10  H  HCH2  0   0.226  -6.2209  -12.6044   1.5103
 N28  H12  H  HCH2  0   0.223  -5.2908  -15.3484   2.4948
 N28  H13  H  HCH2  0   0.223  -6.5360  -14.3944   3.2725
 N28  H15  H  HCH2  0   0.201  -7.4231  -16.1996   1.8415
 N28  H14  H  HCH2  0   0.187  -6.6285  -15.4979   0.4344
 N28  H16  H  HOH1  0   0.452  -8.8189  -14.7869   0.6249
 N28  H17  H  HCH2  0   0.303  -5.8725  -10.7738   2.7977
 N28  H18  H  HCH2  0   0.278  -6.6490  -11.1285   4.3046
 N28  H19  H  HCR6  0   0.262  -6.7987   -8.7303   4.7682
 N28  H20  H  HCR6  0   0.265  -5.7142   -6.7509   5.7275
 N28  H21  H  HNH1  0   0.419  -1.4046   -6.5309   5.0217
 N28  H22  H  HOH1  0   0.480  -0.7245   -5.1413   6.9996
 N28  H23  H  HCR6  0   0.265  -1.8936   -8.6541   5.2764
 N28  H24  H  HCR6  0   0.265  -2.9757  -10.6062   4.3208
 N28  H25  H  HCR6  0   0.260  -5.4323  -14.9980   6.9399
 N28  H26  H  HCR6  0   0.246  -5.2990  -15.7905   9.2415

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
 N28  O2   C10  single    1.413  0.020  1.413
 N28  C8   C9   single    1.523  0.020  1.523
 N28  C8   C7   single    1.525  0.020  1.525
 N28  C10  C9   single    1.516  0.020  1.516
 N28  C7   N3   single    1.456  0.020  1.456
 N28  C11  N3   single    1.445  0.020  1.445
 N28  C11  C12  single    1.513  0.020  1.513
 N28  N3   C6   single    1.364  0.020  1.364
 N28  C13  C12  aromatic  1.393  0.020  1.393
 N28  C13  C14  aromatic  1.384  0.020  1.384
 N28  O4   N4   single    1.362  0.020  1.362
 N28  C12  C18  aromatic  1.390  0.020  1.390
 N28  C14  C15  aromatic  1.393  0.020  1.393
 N28  C18  C17  aromatic  1.387  0.020  1.387
 N28  C15  C17  aromatic  1.393  0.020  1.393
 N28  C15  C16  single    1.493  0.020  1.493
 N28  N4   C16  single    1.351  0.020  1.351
 N28  C16  O3   double    1.218  0.020  1.218
 N28  O1   C6   double    1.222  0.020  1.222
 N28  C6   N2   single    1.376  0.020  1.376
 N28  N2   C5   single    1.401  0.020  1.401
 N28  C5   C19  aromatic  1.395  0.020  1.395
 N28  C5   C4   aromatic  1.393  0.020  1.393
 N28  C19  C20  aromatic  1.386  0.020  1.386
 N28  C4   C3   aromatic  1.386  0.020  1.386
 N28  C20  C2   aromatic  1.393  0.020  1.393
 N28  C3   C2   aromatic  1.390  0.020  1.390
 N28  C2   C1   single    1.507  0.020  1.507
 N28  N1   C1   single    1.453  0.020  1.453
 N28  N1   H1   single    0.890  0.020  1.040
 N28  N1   H27  single    0.890  0.020  1.040
 N28  C1   H4   single    0.970  0.020  1.090
 N28  C1   H3   single    0.970  0.020  1.090
 N28  C3   H5   single    0.930  0.020  1.080
 N28  C4   H6   single    0.930  0.020  1.080
 N28  N2   H7   single    0.860  0.020  1.020
 N28  C7   H9   single    0.970  0.020  1.090
 N28  C7   H8   single    0.970  0.020  1.090
 N28  C8   H11  single    0.970  0.020  1.090
 N28  C8   H10  single    0.970  0.020  1.090
 N28  C9   H12  single    0.970  0.020  1.090
 N28  C9   H13  single    0.970  0.020  1.090
 N28  C10  H15  single    0.970  0.020  1.090
 N28  C10  H14  single    0.970  0.020  1.090
 N28  O2   H16  single    0.850  0.020  0.980
 N28  C11  H17  single    0.970  0.020  1.090
 N28  C11  H18  single    0.970  0.020  1.090
 N28  C13  H19  single    0.930  0.020  1.080
 N28  C14  H20  single    0.930  0.020  1.080
 N28  N4   H21  single    0.890  0.020  1.040
 N28  O4   H22  single    0.850  0.020  0.980
 N28  C17  H23  single    0.930  0.020  1.080
 N28  C18  H24  single    0.930  0.020  1.080
 N28  C19  H25  single    0.930  0.020  1.080
 N28  C20  H26  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
 N28  H27  N1   H1   106.06  3.000
 N28  H27  N1   C1   109.45  3.000
 N28  H1   N1   C1   109.41  3.000
 N28  H3   C1   H4   105.69  3.000
 N28  H3   C1   C2   108.58  3.000
 N28  H4   C1   C2   108.80  3.000
 N28  H3   C1   N1   113.93  3.000
 N28  H4   C1   N1   107.65  3.000
 N28  C2   C1   N1   111.91  3.000
 N28  C20  C2   C3   117.64  3.000
 N28  C3   C2   C1   120.92  3.000
 N28  C20  C2   C1   121.43  3.000
 N28  H5   C3   C4   118.90  3.000
 N28  H5   C3   C2   119.85  3.000
 N28  C4   C3   C2   121.25  3.000
 N28  H6   C4   C5   119.90  3.000
 N28  H6   C4   C3   119.44  3.000
 N28  C5   C4   C3   120.66  3.000
 N28  C19  C5   N2   123.26  3.000
 N28  C19  C5   C4   118.62  3.000
 N28  N2   C5   C4   118.03  3.000
 N28  H7   N2   C6   118.67  3.000
 N28  H7   N2   C5   113.93  3.000
 N28  C6   N2   C5   125.00  3.000
 N28  N3   C6   O1   122.92  3.000
 N28  O1   C6   N2   122.01  3.000
 N28  N3   C6   N2   115.07  3.000
 N28  C11  N3   C7   117.03  3.000
 N28  C11  N3   C6   122.82  3.000
 N28  C7   N3   C6   120.07  3.000
 N28  H8   C7   H9   106.79  3.000
 N28  H8   C7   C8   109.43  3.000
 N28  H9   C7   C8   110.31  3.000
 N28  H8   C7   N3   107.87  3.000
 N28  H9   C7   N3   108.90  3.000
 N28  C8   C7   N3   113.31  3.000
 N28  H10  C8   H11  106.07  3.000
 N28  H10  C8   C9   110.18  3.000
 N28  H11  C8   C9   109.49  3.000
 N28  H10  C8   C7   109.49  3.000
 N28  H11  C8   C7   107.49  3.000
 N28  C9   C8   C7   113.80  3.000
 N28  H13  C9   H12  106.38  3.000
 N28  H13  C9   C10  109.00  3.000
 N28  H12  C9   C10  107.51  3.000
 N28  H13  C9   C8   110.46  3.000
 N28  H12  C9   C8   109.51  3.000
 N28  C10  C9   C8   113.68  3.000
 N28  H14  C10  H15  106.68  3.000
 N28  H14  C10  O2   111.32  3.000
 N28  H15  C10  O2   111.21  3.000
 N28  H14  C10  C9   109.26  3.000
 N28  H15  C10  C9   108.82  3.000
 N28  O2   C10  C9   109.48  3.000
 N28  H16  O2   C10  108.12  3.000
 N28  H18  C11  H17  104.78  3.000
 N28  H18  C11  C12  109.92  3.000
 N28  H17  C11  C12  108.23  3.000
 N28  H18  C11  N3   111.11  3.000
 N28  H17  C11  N3   107.53  3.000
 N28  C12  C11  N3   114.72  3.000
 N28  C18  C12  C13  118.74  3.000
 N28  C18  C12  C11  121.91  3.000
 N28  C13  C12  C11  119.35  3.000
 N28  H19  C13  C14  119.48  3.000
 N28  H19  C13  C12  119.72  3.000
 N28  C14  C13  C12  120.80  3.000
 N28  H20  C14  C15  119.92  3.000
 N28  H20  C14  C13  119.66  3.000
 N28  C15  C14  C13  120.42  3.000
 N28  C17  C15  C16  123.18  3.000
 N28  C16  C15  C14  117.90  3.000
 N28  C17  C15  C14  118.89  3.000
 N28  N4   C16  O3   123.27  3.000
 N28  O3   C16  C15  122.19  3.000
 N28  N4   C16  C15  114.53  3.000
 N28  H21  N4   O4   113.81  3.000
 N28  H21  N4   C16  121.95  3.000
 N28  O4   N4   C16  118.84  3.000
 N28  H22  O4   N4   106.02  3.000
 N28  H23  C17  C18  118.40  3.000
 N28  H23  C17  C15  121.07  3.000
 N28  C18  C17  C15  120.51  3.000
 N28  H24  C18  C17  119.10  3.000
 N28  H24  C18  C12  120.26  3.000
 N28  C17  C18  C12  120.64  3.000
 N28  H25  C19  C20  119.30  3.000
 N28  H25  C19  C5   120.66  3.000
 N28  C20  C19  C5   120.04  3.000
 N28  H26  C20  C19  118.92  3.000
 N28  H26  C20  C2   119.30  3.000
 N28  C19  C20  C2   121.77  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
 N28  CONST_01  C5   C19  C20  C2      0.00   0.0  0
 N28  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 N28  CONST_03  C19  C5   C4   C3      0.00   0.0  0
 N28  CONST_04  C19  C20  C2   C3      0.00   0.0  0
 N28  CONST_05  C20  C19  C5   C4      0.00   0.0  0
 N28  CONST_06  C20  C2   C3   C4      0.00   0.0  0
 N28  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 N28  CONST_08  C15  C17  C18  C12     0.00   0.0  0
 N28  CONST_09  C17  C18  C12  C13     0.00   0.0  0
 N28  CONST_10  C17  C15  C14  C13     0.00   0.0  0
 N28  CONST_11  C18  C12  C13  C14     0.00   0.0  0
 N28  CONST_12  C18  C17  C15  C14     0.00   0.0  0
 N28  CONST_13  C19  C20  C2   C1    180.00   0.0  0
 N28  CONST_14  C4   C3   C2   C1    180.00   0.0  0
 N28  CONST_15  N2   C5   C4   C3    180.00   0.0  0
 N28  CONST_16  C20  C19  C5   N2    180.00   0.0  0
 N28  CONST_17  C14  C13  C12  C11   180.00   0.0  0
 N28  CONST_18  C17  C18  C12  C11   180.00   0.0  0
 N28  CONST_19  C16  C15  C14  C13   180.00   0.0  0
 N28  CONST_20  C18  C17  C15  C16   180.00   0.0  0
 N28  CONST_21  H25  C19  C20  C2    180.00   0.0  0
 N28  CONST_22  H6   C4   C3   C2    180.00   0.0  0
 N28  CONST_23  H26  C20  C2   C3    180.00   0.0  0
 N28  CONST_24  H5   C3   C4   C5    180.00   0.0  0
 N28  CONST_25  H20  C14  C13  C12   180.00   0.0  0
 N28  CONST_26  H23  C17  C18  C12   180.00   0.0  0
 N28  CONST_27  H24  C18  C12  C13   180.00   0.0  0
 N28  CONST_28  H19  C13  C14  C15   180.00   0.0  0
 N28  CONST_32  O1   C6   N2   C5      0.00   0.0  0
 N28  CONST_33  O4   N4   C16  C15   180.00   0.0  0
 N28  CONST_34  N3   C6   N2   C5    180.00   0.0  0
 N28  CONST_36  C7   N3   C6   O1      0.00   0.0  0
 N28  CONST_37  C11  N3   C6   O1    180.00   0.0  0
 N28  CONST_38  O4   N4   C16  O3      0.00   0.0  0
 N28  CONST_39  C7   N3   C6   N2    180.00   0.0  0
 N28  CONST_40  C11  N3   C6   N2      0.00   0.0  0
 N28  Var_01    C20  C2   C1   N1    -38.54  30.0  2
 N28  Var_02    C13  C12  C11  N3   -159.37  30.0  2
 N28  Var_03    N4   C16  C15  C14  -157.35  30.0  2
 N28  Var_04    C12  C11  N3   C6     74.44  30.0  3
 N28  Var_05    H1   N1   C1   C2    173.73  30.0  3
 N28  Var_06    C8   C7   N3   C6    102.03  30.0  2
 N28  Var_07    C9   C8   C7   N3    -64.82  30.0  1
 N28  Var_08    C10  C9   C8   C7   -178.17  30.0  3
 N28  Var_09    O2   C10  C9   C8    -63.89  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
 N28  plan-1  C1   0.020
 N28  plan-1  C2   0.020
 N28  plan-1  C3   0.020
 N28  plan-1  C4   0.020
 N28  plan-1  C5   0.020
 N28  plan-1  N2   0.020
 N28  plan-1  C19  0.020
 N28  plan-1  C20  0.020
 N28  plan-1  H5   0.020
 N28  plan-1  H6   0.020
 N28  plan-1  H25  0.020
 N28  plan-1  H26  0.020
 N28  plan-2  C11  0.020
 N28  plan-2  C12  0.020
 N28  plan-2  C13  0.020
 N28  plan-2  C14  0.020
 N28  plan-2  C15  0.020
 N28  plan-2  C16  0.020
 N28  plan-2  C17  0.020
 N28  plan-2  C18  0.020
 N28  plan-2  H19  0.020
 N28  plan-2  H20  0.020
 N28  plan-2  H23  0.020
 N28  plan-2  H24  0.020
 N28  plan-3  C5   0.020
 N28  plan-3  N2   0.020
 N28  plan-3  C6   0.020
 N28  plan-3  O1   0.020
 N28  plan-3  N3   0.020
 N28  plan-3  C7   0.020
 N28  plan-3  C11  0.020
 N28  plan-3  H7   0.020
 N28  plan-4  C15  0.020
 N28  plan-4  C16  0.020
 N28  plan-4  O3   0.020
 N28  plan-4  N4   0.020
 N28  plan-4  O4   0.020
 N28  plan-4  H21  0.020

