# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 12:35:00 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: N-(6-acetamidohexyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCCCCCNC(C)=O
#
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
 5D4  5D4  N-(6-acetamidohexyl)ethanamide  ligand  34  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5D4
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
 5D4  O1    O  O     0  -0.515   5.8348  -1.3388  -0.0238
 5D4  C8    C  C     0   0.520   5.6113  -0.1338   0.0006
 5D4  C9    C  CH3   0  -0.777   6.7256   0.8831   0.0129
 5D4  N1    N  NH1   0  -0.634   4.3685   0.3674   0.0171
 5D4  C7    C  CH2   0  -0.233   3.1798  -0.4599   0.0067
 5D4  C6    C  CH2   0  -0.476   1.9273   0.4016   0.0183
 5D4  C5    C  CH2   0  -0.417   0.6572  -0.4385   0.0066
 5D4  C4    C  CH2   0  -0.417  -0.6081   0.4098   0.0160
 5D4  C3    C  CH2   0  -0.476  -1.8772  -0.4316   0.0032
 5D4  C2    C  CH2   0  -0.233  -3.1317   0.4272   0.0121
 5D4  N     N  NH1   0  -0.633  -4.3177  -0.4038  -0.0020
 5D4  C1    C  C     0   0.520  -5.5624   0.0925   0.0207
 5D4  O     O  O     0  -0.515  -5.7906   1.2962   0.0566
 5D4  C     C  CH3   0  -0.777  -6.6728  -0.9289   0.0001
 5D4  H91C  H  HCH3  0   0.264   7.3452   0.7553  -0.8746
 5D4  H92C  H  HCH3  0   0.247   6.3753   1.9130   0.0412
 5D4  H93C  H  HCH3  0   0.264   7.3640   0.7130   0.8798
 5D4  H1    H  HNH1  0   0.400   4.2492   1.3670   0.0372
 5D4  H71C  H  HCH2  0   0.229   3.1789  -1.1005  -0.8802
 5D4  H72C  H  HCH2  0   0.230   3.1795  -1.1240   0.8762
 5D4  H61C  H  HCH2  0   0.230   1.9326   1.0431   0.9056
 5D4  H62C  H  HCH2  0   0.230   1.9333   1.0671  -0.8512
 5D4  H51C  H  HCH2  0   0.219   0.6548  -1.0848  -0.8775
 5D4  H52C  H  HCH2  0   0.219   0.6533  -1.1065   0.8745
 5D4  H41C  H  HCH2  0   0.219  -0.6066   1.0551   0.9009
 5D4  H42C  H  HCH2  0   0.219  -0.6038   1.0786  -0.8512
 5D4  H31C  H  HCH2  0   0.230  -1.8804  -1.0739  -0.8836
 5D4  H32C  H  HCH2  0   0.230  -1.8834  -1.0965   0.8730
 5D4  H21C  H  HCH2  0   0.230  -3.1354   1.0666   0.8997
 5D4  H22C  H  HCH2  0   0.229  -3.1304   1.0924  -0.8566
 5D4  H     H  HNH1  0   0.400  -4.1951  -1.4026  -0.0359
 5D4  HC1   H  HCH3  0   0.247  -6.3187  -1.9575  -0.0323
 5D4  HC2   H  HCH3  0   0.264  -7.2949  -0.8074   0.8867
 5D4  HC3   H  HCH3  0   0.264  -7.3095  -0.7571  -0.8676

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
 5D4  O1  C8    double  1.226  0.020  1.226
 5D4  C8  C9    single  1.509  0.020  1.509
 5D4  C8  N1    single  1.340  0.020  1.340
 5D4  N1  C7    single  1.448  0.020  1.448
 5D4  C7  C6    single  1.520  0.020  1.520
 5D4  C6  C5    single  1.523  0.020  1.523
 5D4  C5  C4    single  1.523  0.020  1.523
 5D4  C4  C3    single  1.523  0.020  1.523
 5D4  C3  C2    single  1.520  0.020  1.520
 5D4  C2  N     single  1.448  0.020  1.448
 5D4  N   C1    single  1.340  0.020  1.340
 5D4  C1  O     double  1.226  0.020  1.226
 5D4  C1  C     single  1.509  0.020  1.509
 5D4  C9  H91C  single  0.970  0.020  1.090
 5D4  C9  H92C  single  0.970  0.020  1.090
 5D4  C9  H93C  single  0.970  0.020  1.090
 5D4  N1  H1    single  0.860  0.020  1.020
 5D4  C7  H71C  single  0.970  0.020  1.090
 5D4  C7  H72C  single  0.970  0.020  1.090
 5D4  C6  H61C  single  0.970  0.020  1.090
 5D4  C6  H62C  single  0.970  0.020  1.090
 5D4  C5  H51C  single  0.970  0.020  1.090
 5D4  C5  H52C  single  0.970  0.020  1.090
 5D4  C4  H41C  single  0.970  0.020  1.090
 5D4  C4  H42C  single  0.970  0.020  1.090
 5D4  C3  H31C  single  0.970  0.020  1.090
 5D4  C3  H32C  single  0.970  0.020  1.090
 5D4  C2  H21C  single  0.970  0.020  1.090
 5D4  C2  H22C  single  0.970  0.020  1.090
 5D4  N   H     single  0.860  0.020  1.020
 5D4  C   HC1   single  0.970  0.020  1.090
 5D4  C   HC2   single  0.970  0.020  1.090
 5D4  C   HC3   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
 5D4  N1    C8  C9    115.64  3.000
 5D4  N1    C8  O1    122.48  3.000
 5D4  C9    C8  O1    121.88  3.000
 5D4  H93C  C9  H92C  108.40  3.000
 5D4  H93C  C9  H91C  107.24  3.000
 5D4  H92C  C9  H91C  108.37  3.000
 5D4  H93C  C9  C8    109.51  3.000
 5D4  H92C  C9  C8    113.60  3.000
 5D4  H91C  C9  C8    109.52  3.000
 5D4  H1    N1  C7    118.03  3.000
 5D4  H1    N1  C8    118.78  3.000
 5D4  C7    N1  C8    123.19  3.000
 5D4  H72C  C7  H71C  106.78  3.000
 5D4  H72C  C7  C6    109.74  3.000
 5D4  H71C  C7  C6    109.71  3.000
 5D4  H72C  C7  N1    109.95  3.000
 5D4  H71C  C7  N1    109.93  3.000
 5D4  C6    C7  N1    110.64  3.000
 5D4  H62C  C6  H61C  106.70  3.000
 5D4  H62C  C6  C5    109.50  3.000
 5D4  H61C  C6  C5    109.48  3.000
 5D4  H62C  C6  C7    109.50  3.000
 5D4  H61C  C6  C7    109.52  3.000
 5D4  C5    C6  C7    111.99  3.000
 5D4  H52C  C5  H51C  106.25  3.000
 5D4  H52C  C5  C4    109.38  3.000
 5D4  H51C  C5  C4    109.38  3.000
 5D4  H52C  C5  C6    109.48  3.000
 5D4  H51C  C5  C6    109.49  3.000
 5D4  C4    C5  C6    112.67  3.000
 5D4  H42C  C4  H41C  106.26  3.000
 5D4  H42C  C4  C3    109.51  3.000
 5D4  H41C  C4  C3    109.48  3.000
 5D4  H42C  C4  C5    109.39  3.000
 5D4  H41C  C4  C5    109.39  3.000
 5D4  C3    C4  C5    112.61  3.000
 5D4  H32C  C3  H31C  106.69  3.000
 5D4  H32C  C3  C2    109.49  3.000
 5D4  H31C  C3  C2    109.50  3.000
 5D4  H32C  C3  C4    109.49  3.000
 5D4  H31C  C3  C4    109.47  3.000
 5D4  C2    C3  C4    112.06  3.000
 5D4  H22C  C2  H21C  106.79  3.000
 5D4  H22C  C2  N     110.00  3.000
 5D4  H21C  C2  N     109.91  3.000
 5D4  H22C  C2  C3    109.74  3.000
 5D4  H21C  C2  C3    109.74  3.000
 5D4  N     C2  C3    110.58  3.000
 5D4  H     N   C1    118.75  3.000
 5D4  H     N   C2    118.02  3.000
 5D4  C1    N   C2    123.23  3.000
 5D4  C     C1  O     121.88  3.000
 5D4  C     C1  N     115.63  3.000
 5D4  O     C1  N     122.48  3.000
 5D4  HC3   C   HC2   107.26  3.000
 5D4  HC3   C   HC1   108.38  3.000
 5D4  HC2   C   HC1   108.38  3.000
 5D4  HC3   C   C1    109.52  3.000
 5D4  HC2   C   C1    109.48  3.000
 5D4  HC1   C   C1    113.63  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
 5D4  CONST_01  C7    N1  C8  O1     0.00   0.0  0
 5D4  CONST_02  C7    N1  C8  C9   180.00   0.0  0
 5D4  CONST_03  O     C1  N   C2     0.00   0.0  0
 5D4  CONST_04  C     C1  N   C2   180.00   0.0  0
 5D4  CONST_05  H1    N1  C8  O1   180.00   0.0  0
 5D4  CONST_06  H     N   C1  O    180.00   0.0  0
 5D4  Var_01    C6    C7  N1  C8  -179.51  30.0  3
 5D4  Var_02    C5    C6  C7  N1   179.95  30.0  3
 5D4  Var_03    C4    C5  C6  C7  -179.92  30.0  3
 5D4  Var_04    C3    C4  C5  C6   179.95  30.0  3
 5D4  Var_05    C2    C3  C4  C5  -179.98  30.0  3
 5D4  Var_06    N     C2  C3  C4   179.93  30.0  3
 5D4  Var_07    C1    N   C2  C3   179.04  30.0  3
 5D4  Var_08    H91C  C9  C8  O1    59.05  30.0  3
 5D4  Var_09    HC1   C   C1  N     -0.07  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
 5D4  plan-1  O1  0.020
 5D4  plan-1  C8  0.020
 5D4  plan-1  C9  0.020
 5D4  plan-1  N1  0.020
 5D4  plan-1  C7  0.020
 5D4  plan-1  H1  0.020
 5D4  plan-2  C2  0.020
 5D4  plan-2  N   0.020
 5D4  plan-2  C1  0.020
 5D4  plan-2  O   0.020
 5D4  plan-2  C   0.020
 5D4  plan-2  H   0.020

