# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:54:52 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: ~{N}-[3-[3-(aminomethyl)phenyl]phenyl]-3-methyl-butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC(=O)Nc1cccc(c1)c2cccc(CN)c2
#
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
 E8B  E8B  ~{N}-[3-[3-(aminomethyl)phenyl]phenyl]-3-methyl-butanamide  ligand  43  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E8B
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
 E8B  N1   N  NH2   0  -0.795  -6.0400  -1.3527  -1.1037
 E8B  C4   C  CH2   0  -0.333  -5.9415   0.0947  -1.1466
 E8B  C7   C  CR6   0   0.102  -4.7496   0.6134  -0.3806
 E8B  C8   C  CR16  0  -0.356  -3.5825  -0.1339  -0.2683
 E8B  C10  C  CR6   0   0.107  -2.4632   0.3586   0.4035
 E8B  C13  C  CR16  0  -0.227  -3.6863   2.3835   0.8689
 E8B  C15  C  CR16  0  -0.317  -4.7924   1.8775   0.2014
 E8B  C17  C  CR6   0   0.108  -1.2377  -0.4597   0.5157
 E8B  C20  C  CR6   0   0.403   1.1902  -0.6103   0.5512
 E8B  C21  C  CR16  0  -0.327   1.1048  -1.9898   0.7413
 E8B  O30  O  O     0  -0.472   3.9474  -1.4316   1.0832
 E8B  C29  C  C     0   0.540   3.6583  -0.3046   0.7187
 E8B  C31  C  CH2   0  -0.562   4.7073   0.7715   0.5496
 E8B  C34  C  CH1   0  -0.238   5.8914   0.3102  -0.3040
 E8B  C40  C  CH3   0  -0.657   5.4560  -0.0283  -1.7259
 E8B  C36  C  CH3   0  -0.653   6.9759   1.3813  -0.3086
 E8B  N27  N  NH1   0  -0.747   2.3915   0.0973   0.4393
 E8B  C18  C  CR16  0  -0.428   0.0162   0.1364   0.4381
 E8B  C23  C  CR16  0  -0.231  -0.1480  -2.5830   0.8172
 E8B  C25  C  CR16  0  -0.329  -1.3112  -1.8401   0.7090
 E8B  C11  C  CR16  0  -0.327  -2.5263   1.6316   0.9722
 E8B  H1   H  HNH2  0   0.344  -6.3041  -1.6483  -0.1722
 E8B  H2   H  HNH2  0   0.356  -6.7868  -1.6546  -1.7156
 E8B  H4   H  HCH2  0   0.243  -5.8317   0.3900  -2.1946
 E8B  H5   H  HCH2  0   0.215  -6.8390   0.6142  -0.7843
 E8B  H6   H  HCR6  0   0.245  -3.5465  -1.1148  -0.7254
 E8B  H7   H  HCR6  0   0.255  -3.7338   3.3632   1.3268
 E8B  H8   H  HCR6  0   0.249  -5.6988   2.4687   0.1386
 E8B  H9   H  HCR6  0   0.279   1.9893  -2.5982   0.8265
 E8B  H10  H  HCH2  0   0.248   4.2809   1.6843   0.1235
 E8B  H11  H  HCH2  0   0.276   5.0618   1.0338   1.5517
 E8B  H12  H  HCH1  0   0.230   6.3055  -0.5922   0.1554
 E8B  H13  H  HCH3  0   0.217   5.0219   0.8437  -2.2211
 E8B  H14  H  HCH3  0   0.232   6.3071  -0.3577  -2.3241
 E8B  H15  H  HCH3  0   0.230   4.7156  -0.8297  -1.7523
 E8B  H16  H  HCH3  0   0.228   7.3110   1.6157   0.7030
 E8B  H17  H  HCH3  0   0.230   7.8467   1.0533  -0.8782
 E8B  H18  H  HCH3  0   0.217   6.6139   2.3068  -0.7624
 E8B  H19  H  HNH1  0   0.415   2.2855   1.0661   0.1812
 E8B  H20  H  HCR6  0   0.267   0.0900   1.2053   0.2703
 E8B  H21  H  HCR6  0   0.259  -0.2107  -3.6527   0.9697
 E8B  H22  H  HCR6  0   0.253  -2.2725  -2.3297   0.7968
 E8B  H23  H  HCR6  0   0.252  -1.6801   2.0263   1.5207

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
 E8B  C40  C34  single    1.525  0.020  1.525
 E8B  O30  C29  double    1.219  0.020  1.219
 E8B  C34  C31  single    1.531  0.020  1.531
 E8B  C34  C36  single    1.524  0.020  1.524
 E8B  C31  C29  single    1.512  0.020  1.512
 E8B  C13  C15  aromatic  1.387  0.020  1.387
 E8B  C13  C11  aromatic  1.386  0.020  1.386
 E8B  C29  N27  single    1.358  0.020  1.358
 E8B  C15  C7   aromatic  1.392  0.020  1.392
 E8B  C11  C10  aromatic  1.396  0.020  1.396
 E8B  N1   C4   single    1.451  0.020  1.451
 E8B  C7   C4   single    1.509  0.020  1.509
 E8B  C7   C8   aromatic  1.390  0.020  1.390
 E8B  N27  C20  single    1.399  0.020  1.399
 E8B  C10  C8   aromatic  1.395  0.020  1.395
 E8B  C10  C17  single    1.478  0.020  1.478
 E8B  C18  C20  aromatic  1.396  0.020  1.396
 E8B  C18  C17  aromatic  1.391  0.020  1.391
 E8B  C20  C21  aromatic  1.395  0.020  1.395
 E8B  C17  C25  aromatic  1.396  0.020  1.396
 E8B  C21  C23  aromatic  1.388  0.020  1.388
 E8B  C25  C23  aromatic  1.384  0.020  1.384
 E8B  N1   H1   single    0.890  0.020  1.040
 E8B  N1   H2   single    0.890  0.020  1.040
 E8B  C4   H4   single    0.970  0.020  1.090
 E8B  C4   H5   single    0.970  0.020  1.090
 E8B  C8   H6   single    0.930  0.020  1.080
 E8B  C13  H7   single    0.930  0.020  1.080
 E8B  C15  H8   single    0.930  0.020  1.080
 E8B  C21  H9   single    0.930  0.020  1.080
 E8B  C31  H10  single    0.970  0.020  1.090
 E8B  C31  H11  single    0.970  0.020  1.090
 E8B  C34  H12  single    0.970  0.020  1.090
 E8B  C40  H13  single    0.970  0.020  1.090
 E8B  C40  H14  single    0.970  0.020  1.090
 E8B  C40  H15  single    0.970  0.020  1.090
 E8B  C36  H16  single    0.970  0.020  1.090
 E8B  C36  H17  single    0.970  0.020  1.090
 E8B  C36  H18  single    0.970  0.020  1.090
 E8B  N27  H19  single    0.860  0.020  1.020
 E8B  C18  H20  single    0.930  0.020  1.080
 E8B  C23  H21  single    0.930  0.020  1.080
 E8B  C25  H22  single    0.930  0.020  1.080
 E8B  C11  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
 E8B  H2   N1   H1   106.08  3.000
 E8B  H2   N1   C4   109.26  3.000
 E8B  H1   N1   C4   109.63  3.000
 E8B  H5   C4   H4   105.68  3.000
 E8B  H5   C4   C7   108.39  3.000
 E8B  H4   C4   C7   108.31  3.000
 E8B  H5   C4   N1   113.98  3.000
 E8B  H4   C4   N1   107.71  3.000
 E8B  C7   C4   N1   112.42  3.000
 E8B  C15  C7   C8   118.68  3.000
 E8B  C8   C7   C4   121.29  3.000
 E8B  C15  C7   C4   120.00  3.000
 E8B  H6   C8   C10  119.76  3.000
 E8B  H6   C8   C7   118.73  3.000
 E8B  C10  C8   C7   121.51  3.000
 E8B  C11  C10  C17  120.77  3.000
 E8B  C17  C10  C8   120.42  3.000
 E8B  C11  C10  C8   118.81  3.000
 E8B  H7   C13  C11  119.74  3.000
 E8B  H7   C13  C15  119.91  3.000
 E8B  C11  C13  C15  120.34  3.000
 E8B  H8   C15  C13  119.71  3.000
 E8B  H8   C15  C7   119.78  3.000
 E8B  C13  C15  C7   120.51  3.000
 E8B  C25  C17  C18  118.63  3.000
 E8B  C25  C17  C10  120.96  3.000
 E8B  C18  C17  C10  120.41  3.000
 E8B  C18  C20  N27  116.43  3.000
 E8B  C18  C20  C21  119.24  3.000
 E8B  N27  C20  C21  124.31  3.000
 E8B  H9   C21  C23  119.69  3.000
 E8B  H9   C21  C20  121.28  3.000
 E8B  C23  C21  C20  119.03  3.000
 E8B  N27  C29  C31  114.42  3.000
 E8B  N27  C29  O30  123.79  3.000
 E8B  C31  C29  O30  121.79  3.000
 E8B  H11  C31  H10  106.43  3.000
 E8B  H11  C31  C34  109.40  3.000
 E8B  H10  C31  C34  109.62  3.000
 E8B  H11  C31  C29  107.02  3.000
 E8B  H10  C31  C29  111.53  3.000
 E8B  C34  C31  C29  112.61  3.000
 E8B  H12  C34  C36  108.15  3.000
 E8B  H12  C34  C40  108.45  3.000
 E8B  C36  C34  C40  110.87  3.000
 E8B  H12  C34  C31  107.89  3.000
 E8B  C36  C34  C31  109.89  3.000
 E8B  C40  C34  C31  111.46  3.000
 E8B  H15  C40  H14  107.11  3.000
 E8B  H15  C40  H13  107.80  3.000
 E8B  H14  C40  H13  107.60  3.000
 E8B  H15  C40  C34  112.28  3.000
 E8B  H14  C40  C34  110.82  3.000
 E8B  H13  C40  C34  111.03  3.000
 E8B  H18  C36  H17  107.59  3.000
 E8B  H18  C36  H16  107.75  3.000
 E8B  H17  C36  H16  107.67  3.000
 E8B  H18  C36  C34  111.15  3.000
 E8B  H17  C36  C34  110.99  3.000
 E8B  H16  C36  C34  111.51  3.000
 E8B  H19  N27  C29  115.79  3.000
 E8B  H19  N27  C20  114.61  3.000
 E8B  C29  N27  C20  129.42  3.000
 E8B  H20  C18  C20  118.85  3.000
 E8B  H20  C18  C17  119.51  3.000
 E8B  C20  C18  C17  121.63  3.000
 E8B  H21  C23  C25  119.51  3.000
 E8B  H21  C23  C21  118.84  3.000
 E8B  C25  C23  C21  121.64  3.000
 E8B  H22  C25  C23  119.81  3.000
 E8B  H22  C25  C17  120.35  3.000
 E8B  C23  C25  C17  119.83  3.000
 E8B  H23  C11  C13  119.60  3.000
 E8B  H23  C11  C10  120.24  3.000
 E8B  C13  C11  C10  120.14  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
 E8B  CONST_01  C11  C13  C15  C7      0.00   0.0  0
 E8B  CONST_02  C11  C10  C8   C7      0.00   0.0  0
 E8B  CONST_03  C17  C10  C8   C7    180.00   0.0  0
 E8B  CONST_04  C13  C15  C7   C8      0.00   0.0  0
 E8B  CONST_05  C13  C11  C10  C8      0.00   0.0  0
 E8B  CONST_08  C15  C13  C11  C10     0.00   0.0  0
 E8B  CONST_09  C15  C7   C8   C10     0.00   0.0  0
 E8B  CONST_10  C20  C18  C17  C10   180.00   0.0  0
 E8B  CONST_11  C23  C25  C17  C10   180.00   0.0  0
 E8B  CONST_12  C17  C10  C11  C13   180.00   0.0  0
 E8B  CONST_13  C21  C20  C18  C17     0.00   0.0  0
 E8B  CONST_14  C21  C23  C25  C17     0.00   0.0  0
 E8B  CONST_15  C25  C17  C18  C20     0.00   0.0  0
 E8B  CONST_16  C25  C23  C21  C20     0.00   0.0  0
 E8B  CONST_17  C23  C21  C20  C18     0.00   0.0  0
 E8B  CONST_19  C23  C25  C17  C18     0.00   0.0  0
 E8B  CONST_21  C13  C15  C7   C4    180.00   0.0  0
 E8B  CONST_22  C10  C8   C7   C4    180.00   0.0  0
 E8B  CONST_23  N27  C20  C18  C17   180.00   0.0  0
 E8B  CONST_24  C23  C21  C20  N27   180.00   0.0  0
 E8B  CONST_25  H7   C13  C15  C7    180.00   0.0  0
 E8B  CONST_26  H8   C15  C7   C8    180.00   0.0  0
 E8B  CONST_27  H23  C11  C10  C8    180.00   0.0  0
 E8B  CONST_28  H20  C18  C17  C10     0.00   0.0  0
 E8B  CONST_29  H22  C25  C17  C10     0.00   0.0  0
 E8B  CONST_30  H6   C8   C7   C15   180.00   0.0  0
 E8B  CONST_31  H21  C23  C25  C17   180.00   0.0  0
 E8B  CONST_32  H9   C21  C20  C18   180.00   0.0  0
 E8B  CONST_33  C29  N27  C20  C21     0.00   0.0  0
 E8B  CONST_34  C18  C20  N27  C29   180.00   0.0  0
 E8B  CONST_35  H19  N27  C20  C21   180.00   0.0  0
 E8B  CONST_36  O30  C29  N27  C20     0.00   0.0  0
 E8B  CONST_37  C31  C29  N27  C20   180.00   0.0  0
 E8B  Var_01    C15  C7   C4   N1   -151.02  30.0  1
 E8B  Var_02    H1   N1   C4   C7     70.62  30.0  3
 E8B  Var_03    C34  C31  C29  O30    50.63  30.0  1
 E8B  Var_04    C40  C34  C31  C29    62.83  30.0  2
 E8B  Var_05    H13  C40  C34  C31    60.61  30.0  3
 E8B  Var_06    H16  C36  C34  C31    57.59  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
 E8B  plan-1  C4   0.020
 E8B  plan-1  C7   0.020
 E8B  plan-1  C8   0.020
 E8B  plan-1  C10  0.020
 E8B  plan-1  C13  0.020
 E8B  plan-1  C15  0.020
 E8B  plan-1  C17  0.020
 E8B  plan-1  C11  0.020
 E8B  plan-1  H6   0.020
 E8B  plan-1  H7   0.020
 E8B  plan-1  H8   0.020
 E8B  plan-1  H23  0.020
 E8B  plan-2  C10  0.020
 E8B  plan-2  C17  0.020
 E8B  plan-2  C20  0.020
 E8B  plan-2  C21  0.020
 E8B  plan-2  N27  0.020
 E8B  plan-2  C18  0.020
 E8B  plan-2  C23  0.020
 E8B  plan-2  C25  0.020
 E8B  plan-2  H9   0.020
 E8B  plan-2  H20  0.020
 E8B  plan-2  H21  0.020
 E8B  plan-2  H22  0.020
 E8B  plan-3  C20  0.020
 E8B  plan-3  O30  0.020
 E8B  plan-3  C29  0.020
 E8B  plan-3  C31  0.020
 E8B  plan-3  N27  0.020
 E8B  plan-3  H19  0.020

