# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 08:22:33 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (5R)-5-(2-cyclohexylethyl)-5-(cyclohexylmethyl)-2-imino-3-methyl-imidazolidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N)N[C@](CCC2CCCCC2)(CC3CCCCC3)C1=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
 BDX  BDX  (5R)-5-(2-cyclohexylethyl)-5-(cyclohexylmethyl)-2-imino-3-methyl-imidazolidin-4-one  ligand  56  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BDX
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
 BDX  C1    C  C     0   0.609  -0.8505  -2.0418   0.8477
 BDX  N1    N  NT    0  -0.512  -0.7182  -2.0505  -0.5447
 BDX  O1    O  O     0  -0.451  -0.3561  -0.5234  -2.2085
 BDX  C2    C  C     0   0.550  -0.4835  -0.8092  -1.0375
 BDX  N2    N  NH1   0  -0.679  -0.5986  -0.7691   1.2417
 BDX  C3    C  CT    0  -0.001  -0.3810   0.1441   0.1440
 BDX  N3    N  N     0  -0.686  -1.1414  -3.0904   1.5030
 BDX  C4    C  CH2   0  -0.405   1.0293   0.7584   0.1800
 BDX  C5    C  CH1   0  -0.228  -2.8871   0.9203   0.3366
 BDX  C6    C  CH2   0  -0.417  -3.6828   2.2085   0.5698
 BDX  C7    C  CH2   0  -0.431  -5.1530   1.9343   0.8669
 BDX  C8    C  CH2   0  -0.429  -5.7981   1.1090  -0.2404
 BDX  C9    C  CH2   0  -0.426  -5.0154  -0.1753  -0.4852
 BDX  C10   C  CH2   0  -0.427  -3.5454   0.1107  -0.7814
 BDX  C11   C  CH2   0  -0.401  -1.4226   1.2746   0.0784
 BDX  C12   C  CH2   0  -0.425   2.1686  -0.2533   0.1867
 BDX  C13   C  CH1   0  -0.224   3.5434   0.3655   0.4389
 BDX  C14   C  CH2   0  -0.412   4.6023  -0.7300   0.5761
 BDX  C15   C  CH2   0  -0.431   5.9970  -0.1620   0.8188
 BDX  C16   C  CH2   0  -0.429   6.3904   0.8241  -0.2751
 BDX  C17   C  CH2   0  -0.428   5.3480   1.9289  -0.4095
 BDX  C18   C  CH2   0  -0.424   3.9545   1.3550  -0.6518
 BDX  C19   C  CH3   0  -0.531  -0.8993  -3.2215  -1.3655
 BDX  HN2   H  HNH1  0   0.400  -0.7615  -0.4627   2.1863
 BDX  HN3   H  H     0   0.336  -1.1844  -2.8965   2.4967
 BDX  H4    H  HCH2  0   0.239   1.1200   1.4374  -0.6711
 BDX  H4A   H  HCH2  0   0.238   1.0890   1.3834   1.0771
 BDX  H5    H  HCH1  0   0.212  -2.9408   0.3295   1.2601
 BDX  H6    H  HCH2  0   0.225  -3.2342   2.7748   1.3912
 BDX  H6A   H  HCH2  0   0.207  -3.6039   2.8417  -0.3221
 BDX  H7    H  HCH2  0   0.208  -5.2330   1.3936   1.8163
 BDX  H7A   H  HCH2  0   0.225  -5.6893   2.8770   1.0020
 BDX  H8    H  HCH2  0   0.225  -6.8369   0.8801   0.0103
 BDX  H8A   H  HCH2  0   0.207  -5.8223   1.6984  -1.1638
 BDX  H9    H  HCH2  0   0.209  -5.0855  -0.8171   0.3996
 BDX  H9A   H  HCH2  0   0.226  -5.4574  -0.7384  -1.3111
 BDX  H10   H  HCH2  0   0.209  -3.4676   0.6694  -1.7215
 BDX  H10A  H  HCH2  0   0.226  -3.0313  -0.8386  -0.9415
 BDX  H11   H  HCH2  0   0.240  -1.1196   2.0190   0.8223
 BDX  H11A  H  HCH2  0   0.236  -1.3240   1.7704  -0.8922
 BDX  H12   H  HCH2  0   0.227   1.9831  -0.9996   0.9650
 BDX  H12A  H  HCH2  0   0.217   2.2004  -0.7954  -0.7655
 BDX  H13   H  HCH1  0   0.204   3.5010   0.9128   1.3918
 BDX  H14   H  HCH2  0   0.221   4.3292  -1.4107   1.3878
 BDX  H14A  H  HCH2  0   0.203   4.6092  -1.3316  -0.3412
 BDX  H15   H  HCH2  0   0.207   6.0156   0.3470   1.7890
 BDX  H15A  H  HCH2  0   0.224   6.7269  -0.9731   0.8812
 BDX  H16   H  HCH2  0   0.224   7.3744   1.2519  -0.0669
 BDX  H16A  H  HCH2  0   0.206   6.4774   0.2912  -1.2285
 BDX  H17   H  HCH2  0   0.207   5.3372   2.5286   0.5075
 BDX  H17A  H  HCH2  0   0.224   5.6166   2.6108  -1.2203
 BDX  H18   H  HCH2  0   0.203   3.9369   0.8402  -1.6209
 BDX  H18A  H  HCH2  0   0.229   3.2299   2.1700  -0.7220
 BDX  H19   H  HCH3  0   0.266  -0.8845  -4.0987  -0.7267
 BDX  H19A  H  HCH3  0   0.250  -1.8525  -3.1869  -1.8935
 BDX  H19B  H  HCH3  0   0.256  -0.0955  -3.2982  -2.0947

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
 BDX  C1   N1    single  1.399  0.020  1.399
 BDX  C1   N2    single  1.356  0.020  1.356
 BDX  C1   N3    double  1.270  0.020  1.270
 BDX  N1   C2    single  1.356  0.020  1.356
 BDX  N1   C19   single  1.441  0.020  1.441
 BDX  O1   C2    double  1.212  0.020  1.212
 BDX  C2   C3    single  1.522  0.020  1.522
 BDX  N2   C3    single  1.444  0.020  1.444
 BDX  C3   C4    single  1.539  0.020  1.539
 BDX  C3   C11   single  1.539  0.020  1.539
 BDX  C4   C12   single  1.524  0.020  1.524
 BDX  C5   C6    single  1.532  0.020  1.532
 BDX  C5   C10   single  1.529  0.020  1.529
 BDX  C5   C11   single  1.529  0.020  1.529
 BDX  C6   C7    single  1.525  0.020  1.525
 BDX  C7   C8    single  1.524  0.020  1.524
 BDX  C8   C9    single  1.524  0.020  1.524
 BDX  C9   C10   single  1.527  0.020  1.527
 BDX  C12  C13   single  1.529  0.020  1.529
 BDX  C13  C14   single  1.530  0.020  1.530
 BDX  C13  C18   single  1.529  0.020  1.529
 BDX  C14  C15   single  1.525  0.020  1.525
 BDX  C15  C16   single  1.524  0.020  1.524
 BDX  C16  C17   single  1.525  0.020  1.525
 BDX  C17  C18   single  1.526  0.020  1.526
 BDX  N2   HN2   single  0.860  0.020  1.020
 BDX  N3   HN3   single  0.890  0.020  1.040
 BDX  C4   H4    single  0.970  0.020  1.090
 BDX  C4   H4A   single  0.970  0.020  1.090
 BDX  C5   H5    single  0.970  0.020  1.090
 BDX  C6   H6    single  0.970  0.020  1.090
 BDX  C6   H6A   single  0.970  0.020  1.090
 BDX  C7   H7    single  0.970  0.020  1.090
 BDX  C7   H7A   single  0.970  0.020  1.090
 BDX  C8   H8    single  0.970  0.020  1.090
 BDX  C8   H8A   single  0.970  0.020  1.090
 BDX  C9   H9    single  0.970  0.020  1.090
 BDX  C9   H9A   single  0.970  0.020  1.090
 BDX  C10  H10   single  0.970  0.020  1.090
 BDX  C10  H10A  single  0.970  0.020  1.090
 BDX  C11  H11   single  0.970  0.020  1.090
 BDX  C11  H11A  single  0.970  0.020  1.090
 BDX  C12  H12   single  0.970  0.020  1.090
 BDX  C12  H12A  single  0.970  0.020  1.090
 BDX  C13  H13   single  0.970  0.020  1.090
 BDX  C14  H14   single  0.970  0.020  1.090
 BDX  C14  H14A  single  0.970  0.020  1.090
 BDX  C15  H15   single  0.970  0.020  1.090
 BDX  C15  H15A  single  0.970  0.020  1.090
 BDX  C16  H16   single  0.970  0.020  1.090
 BDX  C16  H16A  single  0.970  0.020  1.090
 BDX  C17  H17   single  0.970  0.020  1.090
 BDX  C17  H17A  single  0.970  0.020  1.090
 BDX  C18  H18   single  0.970  0.020  1.090
 BDX  C18  H18A  single  0.970  0.020  1.090
 BDX  C19  H19   single  0.970  0.020  1.090
 BDX  C19  H19A  single  0.970  0.020  1.090
 BDX  C19  H19B  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
 BDX  N3    C1   N2    131.87  3.000
 BDX  N3    C1   N1    122.01  3.000
 BDX  N2    C1   N1    106.11  3.000
 BDX  C19   N1   C2    123.95  3.000
 BDX  C19   N1   C1    124.06  3.000
 BDX  C2    N1   C1    111.87  3.000
 BDX  C3    C2   O1    126.54  3.000
 BDX  C3    C2   N1    107.64  3.000
 BDX  O1    C2   N1    125.81  3.000
 BDX  HN2   N2   C3    123.04  3.000
 BDX  HN2   N2   C1    121.91  3.000
 BDX  C3    N2   C1    113.61  3.000
 BDX  C11   C3   C4    109.16  3.000
 BDX  C11   C3   N2    113.26  3.000
 BDX  C4    C3   N2    111.88  3.000
 BDX  C11   C3   C2    112.44  3.000
 BDX  C4    C3   C2    109.27  3.000
 BDX  N2    C3   C2    100.59  3.000
 BDX  HN3   N3   C1    110.95  3.000
 BDX  H4A   C4   H4    106.20  3.000
 BDX  H4A   C4   C12   109.55  3.000
 BDX  H4    C4   C12   110.73  3.000
 BDX  H4A   C4   C3    107.28  3.000
 BDX  H4    C4   C3    107.82  3.000
 BDX  C12   C4   C3    114.86  3.000
 BDX  H5    C5   C11   108.28  3.000
 BDX  H5    C5   C10   108.00  3.000
 BDX  C11   C5   C10   114.31  3.000
 BDX  H5    C5   C6    107.41  3.000
 BDX  C11   C5   C6    109.17  3.000
 BDX  C10   C5   C6    109.44  3.000
 BDX  H6A   C6   H6    106.40  3.000
 BDX  H6A   C6   C7    109.37  3.000
 BDX  H6    C6   C7    110.01  3.000
 BDX  H6A   C6   C5    108.93  3.000
 BDX  H6    C6   C5    109.67  3.000
 BDX  C7    C6   C5    112.29  3.000
 BDX  H7A   C7   H7    106.43  3.000
 BDX  H7A   C7   C8    110.43  3.000
 BDX  H7    C7   C8    109.35  3.000
 BDX  H7A   C7   C6    110.01  3.000
 BDX  H7    C7   C6    109.15  3.000
 BDX  C8    C7   C6    111.34  3.000
 BDX  H8A   C8   H8    106.56  3.000
 BDX  H8A   C8   C9    109.23  3.000
 BDX  H8    C8   C9    110.40  3.000
 BDX  H8A   C8   C7    109.28  3.000
 BDX  H8    C8   C7    110.43  3.000
 BDX  C9    C8   C7    110.84  3.000
 BDX  H9A   C9   H9    106.42  3.000
 BDX  H9A   C9   C10   109.84  3.000
 BDX  H9    C9   C10   109.15  3.000
 BDX  H9A   C9   C8    110.36  3.000
 BDX  H9    C9   C8    109.34  3.000
 BDX  C10   C9   C8    111.58  3.000
 BDX  H10A  C10  H10   106.50  3.000
 BDX  H10A  C10  C9    108.61  3.000
 BDX  H10   C10  C9    109.28  3.000
 BDX  H10A  C10  C5    111.40  3.000
 BDX  H10   C10  C5    109.06  3.000
 BDX  C9    C10  C5    111.83  3.000
 BDX  H11A  C11  H11   105.64  3.000
 BDX  H11A  C11  C5    109.95  3.000
 BDX  H11   C11  C5    107.93  3.000
 BDX  H11A  C11  C3    108.04  3.000
 BDX  H11   C11  C3    106.45  3.000
 BDX  C5    C11  C3    118.11  3.000
 BDX  H12A  C12  H12   106.59  3.000
 BDX  H12A  C12  C13   108.51  3.000
 BDX  H12   C12  C13   108.13  3.000
 BDX  H12A  C12  C4    110.26  3.000
 BDX  H12   C12  C4    109.22  3.000
 BDX  C13   C12  C4    113.86  3.000
 BDX  H13   C13  C18   107.85  3.000
 BDX  H13   C13  C14   107.78  3.000
 BDX  C18   C13  C14   109.95  3.000
 BDX  H13   C13  C12   108.05  3.000
 BDX  C18   C13  C12   112.71  3.000
 BDX  C14   C13  C12   110.33  3.000
 BDX  H14A  C14  H14   106.30  3.000
 BDX  H14A  C14  C15   109.36  3.000
 BDX  H14   C14  C15   109.99  3.000
 BDX  H14A  C14  C13   108.79  3.000
 BDX  H14   C14  C13   109.83  3.000
 BDX  C15   C14  C13   112.37  3.000
 BDX  H15A  C15  H15   106.43  3.000
 BDX  H15A  C15  C16   110.40  3.000
 BDX  H15   C15  C16   109.30  3.000
 BDX  H15A  C15  C14   110.08  3.000
 BDX  H15   C15  C14   109.23  3.000
 BDX  C16   C15  C14   111.26  3.000
 BDX  H16A  C16  H16   106.54  3.000
 BDX  H16A  C16  C17   109.27  3.000
 BDX  H16   C16  C17   110.40  3.000
 BDX  H16A  C16  C15   109.29  3.000
 BDX  H16   C16  C15   110.42  3.000
 BDX  C17   C16  C15   110.83  3.000
 BDX  H17A  C17  H17   106.37  3.000
 BDX  H17A  C17  C18   109.95  3.000
 BDX  H17   C17  C18   109.24  3.000
 BDX  H17A  C17  C16   110.46  3.000
 BDX  H17   C17  C16   109.24  3.000
 BDX  C18   C17  C16   111.45  3.000
 BDX  H18A  C18  H18   106.40  3.000
 BDX  H18A  C18  C17   109.58  3.000
 BDX  H18   C18  C17   109.34  3.000
 BDX  H18A  C18  C13   110.50  3.000
 BDX  H18   C18  C13   108.79  3.000
 BDX  C17   C18  C13   112.06  3.000
 BDX  H19B  C19  H19A  108.88  3.000
 BDX  H19B  C19  H19   109.11  3.000
 BDX  H19A  C19  H19   108.82  3.000
 BDX  H19B  C19  N1    110.25  3.000
 BDX  H19A  C19  N1    111.09  3.000
 BDX  H19   C19  N1    108.65  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
 BDX  CONST_01  C3   C2   N1   C1      0.00   0.0  0
 BDX  CONST_02  C3   N2   C1   N1      0.00   0.0  0
 BDX  CONST_03  N2   C1   N1   C2      0.00   0.0  0
 BDX  CONST_04  O1   C2   N1   C1    180.00   0.0  0
 BDX  CONST_05  N3   C1   N1   C2    180.00   0.0  0
 BDX  CONST_06  C19  N1   C1   N2    180.00   0.0  0
 BDX  CONST_07  C19  N1   C2   C3    180.00   0.0  0
 BDX  CONST_08  N3   C1   N2   C3    180.00   0.0  0
 BDX  CONST_09  HN2  N2   C1   N1    180.00   0.0  0
 BDX  CONST_10  C19  N1   C2   O1      0.00   0.0  0
 BDX  CONST_11  C19  N1   C1   N3      0.00   0.0  0
 BDX  CONST_12  HN3  N3   C1   N1    180.00   0.0  0
 BDX  Var_01    C8   C7   C6   C5    -55.83  30.0  1
 BDX  Var_02    C8   C9   C10  C5     56.27  30.0  1
 BDX  Var_03    C9   C8   C7   C6     54.59  30.0  1
 BDX  Var_04    C10  C9   C8   C7    -54.97  30.0  1
 BDX  Var_05    C16  C15  C14  C13   -55.60  30.0  1
 BDX  Var_06    C16  C17  C18  C13    55.77  30.0  1
 BDX  Var_07    C17  C16  C15  C14    55.11  30.0  1
 BDX  Var_08    C18  C17  C16  C15   -55.33  30.0  1
 BDX  Var_09    C13  C12  C4   C3   -171.08  30.0  3
 BDX  Var_10    H19  C19  N1   C1    -14.86  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 BDX  chir_01  C3   N2   C2   C11  negativ
 BDX  chir_02  C5   C6   C10  C11  negativ
 BDX  chir_03  C13  C12  C14  C18  negativ

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
 BDX  plan-1  C1   0.020
 BDX  plan-1  N1   0.020
 BDX  plan-1  O1   0.020
 BDX  plan-1  C2   0.020
 BDX  plan-1  N2   0.020
 BDX  plan-1  C3   0.020
 BDX  plan-1  N3   0.020
 BDX  plan-1  C19  0.020
 BDX  plan-1  HN2  0.020
 BDX  plan-1  HN3  0.020

