# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 00:14:41 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (4R)-4-{[(S)-tert-butoxy(hydroxy)methyl]amino}-5-[(1S)-cyclohex-2-en-1-ylselanyl]pentane-1,1-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)O[C@H](O)N[C@H](CCC(O)O)C[Se][C@H]1CCCC=C1
#
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
 4WM  4WM  (4R)-4-{[(S)-tert-butoxy(hydroxy)methyl]amino}-5-[(1S)-cyclohex-2-en-1-ylselanyl]pentane-1,1-diol  ligand  53  22  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4WM
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
 4WM  N    N   NH1   0  -0.640   1.1843  -0.0355  -0.8602
 4WM  O4   O   OH1   0  -0.661   0.1634  -1.6017   0.6435
 4WM  C12  C   CH1   0   0.438   1.3203  -1.1986  -0.0443
 4WM  O3   O   O2    0  -0.518   1.7572  -2.2085  -0.8959
 4WM  C13  C   CT    0   0.179   2.7450  -3.1347  -0.4278
 4WM  C16  C   CH3   0  -0.658   2.8296  -4.1822  -1.5311
 4WM  C15  C   CH3   0  -0.659   4.0943  -2.4346  -0.2707
 4WM  C14  C   CH3   0  -0.664   2.3403  -3.8052   0.8847
 4WM  C8   C   CH1   0  -0.091   0.8073   1.2338  -0.2671
 4WM  C9   C   CH2   0  -0.444   1.8415   1.6943   0.7644
 4WM  C10  C   CH2   0  -0.498   3.2493   1.8002   0.1943
 4WM  C11  C   CH1   0   0.267   4.2424   2.3778   1.1887
 4WM  O2   O   OH1   0  -0.661   4.3305   1.6207   2.3653
 4WM  O1   O   OH1   0  -0.670   5.4753   2.4784   0.5362
 4WM  C7   C   CH2   0  -0.582  -0.5913   1.3241   0.3632
 4WM  SE   SE  SE    0   0.019  -1.9955   0.8381  -0.9196
 4WM  C2   C   CH1   0  -0.425  -3.5122   0.7834   0.3463
 4WM  C3   C   C1    0  -0.194  -3.4556  -0.4606   1.1778
 4WM  C4   C   C1    0  -0.229  -4.5170  -1.2313   1.4097
 4WM  C5   C   CH2   0  -0.473  -5.8966  -0.9137   0.9205
 4WM  C6   C   CH2   0  -0.447  -6.0001   0.5290   0.4402
 4WM  C1   C   CH2   0  -0.435  -4.8119   0.8837  -0.4476
 4WM  H1   H   HNH1  0   0.358   0.6790  -0.2337  -1.7148
 4WM  H4   H   HCH1  0   0.192   2.0446  -0.9943   0.7506
 4WM  H5   H   HCH3  0   0.232   3.0902  -3.7284  -2.4887
 4WM  H6   H   HCH3  0   0.224   3.5936  -4.9226  -1.2942
 4WM  H7   H   HCH3  0   0.232   1.8796  -4.7067  -1.6471
 4WM  H8   H   HCH3  0   0.219   4.0809  -1.6837   0.5219
 4WM  H9   H   HCH3  0   0.234   4.8651  -3.1604  -0.0077
 4WM  H10  H   HCH3  0   0.234   4.3950  -1.9461  -1.1987
 4WM  H11  H   HCH3  0   0.233   1.3573  -4.2704   0.8072
 4WM  H12  H   HCH3  0   0.230   3.0627  -4.5849   1.1302
 4WM  H13  H   HCH3  0   0.229   2.3222  -3.1085   1.7240
 4WM  H14  H   HCH1  0   0.247   0.8383   1.9542  -1.0920
 4WM  H15  H   HCH2  0   0.241   1.5285   2.6753   1.1339
 4WM  H16  H   HCH2  0   0.229   1.8277   1.0324   1.6349
 4WM  H17  H   HCH2  0   0.232   3.6046   0.8214  -0.1457
 4WM  H18  H   HCH2  0   0.236   3.2308   2.4443  -0.6894
 4WM  H19  H   HOH1  0   0.439   4.5083   0.7015   2.1325
 4WM  H20  H   HOH1  0   0.453   6.0750   2.9989   1.0815
 4WM  H21  H   HCH2  0   0.267  -0.6679   0.6697   1.2322
 4WM  H22  H   HCH2  0   0.264  -0.7702   2.3505   0.6901
 4WM  H23  H   HCH1  0   0.279  -3.4003   1.6676   0.9839
 4WM  H24  H   H     0   0.242  -2.4986  -0.7323   1.6118
 4WM  H26  H   H     0   0.240  -4.3916  -2.1320   2.0015
 4WM  H28  H   HCH2  0   0.237  -6.1681  -1.6024   0.1118
 4WM  H29  H   HCH2  0   0.242  -6.6184  -1.1033   1.7195
 4WM  H30  H   HCH2  0   0.240  -6.9338   0.6818  -0.1041
 4WM  H31  H   HCH2  0   0.225  -6.0218   1.2020   1.3025
 4WM  H32  H   HCH2  0   0.247  -4.9200   1.8887  -0.8590
 4WM  H33  H   HCH2  0   0.230  -4.7915   0.1912  -1.2967
 4WM  H2   H   HCH1  0   0.199   3.8979   3.3640   1.5242
 4WM  H3   H   HOH1  0   0.438  -0.5661  -1.6696   0.0138

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
 4WM  C1   C2   single  1.526  0.020  1.526
 4WM  C1   C6   single  1.525  0.020  1.525
 4WM  C2   SE   single  1.976  0.020  1.976
 4WM  C2   C3   single  1.497  0.020  1.497
 4WM  C6   C5   single  1.524  0.020  1.524
 4WM  SE   C7   single  1.963  0.020  1.963
 4WM  C5   C4   single  1.498  0.020  1.498
 4WM  C4   C3   double  1.332  0.020  1.332
 4WM  C7   C8   single  1.537  0.020  1.537
 4WM  O4   C12  single  1.405  0.020  1.405
 4WM  C8   N    single  1.451  0.020  1.451
 4WM  C8   C9   single  1.532  0.020  1.532
 4WM  C12  N    single  1.427  0.020  1.427
 4WM  C12  O3   single  1.391  0.020  1.391
 4WM  C9   C10  single  1.523  0.020  1.523
 4WM  O3   C13  single  1.433  0.020  1.433
 4WM  C16  C13  single  1.524  0.020  1.524
 4WM  C10  C11  single  1.519  0.020  1.519
 4WM  C13  C14  single  1.528  0.020  1.528
 4WM  C13  C15  single  1.528  0.020  1.528
 4WM  C11  O2   single  1.402  0.020  1.402
 4WM  C11  O1   single  1.399  0.020  1.399
 4WM  N    H1   single  0.890  0.020  1.040
 4WM  O4   H3   single  0.850  0.020  0.980
 4WM  C12  H4   single  0.970  0.020  1.090
 4WM  C16  H5   single  0.970  0.020  1.090
 4WM  C16  H6   single  0.970  0.020  1.090
 4WM  C16  H7   single  0.970  0.020  1.090
 4WM  C15  H8   single  0.970  0.020  1.090
 4WM  C15  H9   single  0.970  0.020  1.090
 4WM  C15  H10  single  0.970  0.020  1.090
 4WM  C14  H11  single  0.970  0.020  1.090
 4WM  C14  H12  single  0.970  0.020  1.090
 4WM  C14  H13  single  0.970  0.020  1.090
 4WM  C8   H14  single  0.970  0.020  1.090
 4WM  C9   H15  single  0.970  0.020  1.090
 4WM  C9   H16  single  0.970  0.020  1.090
 4WM  C10  H17  single  0.970  0.020  1.090
 4WM  C10  H18  single  0.970  0.020  1.090
 4WM  O2   H19  single  0.850  0.020  0.980
 4WM  O1   H20  single  0.850  0.020  0.980
 4WM  C7   H21  single  0.970  0.020  1.090
 4WM  C7   H22  single  0.970  0.020  1.090
 4WM  C2   H23  single  0.970  0.020  1.090
 4WM  C3   H24  single  0.930  0.020  1.080
 4WM  C4   H26  single  0.930  0.020  1.080
 4WM  C5   H28  single  0.970  0.020  1.090
 4WM  C5   H29  single  0.970  0.020  1.090
 4WM  C6   H30  single  0.970  0.020  1.090
 4WM  C6   H31  single  0.970  0.020  1.090
 4WM  C1   H32  single  0.970  0.020  1.090
 4WM  C1   H33  single  0.970  0.020  1.090
 4WM  C11  H2   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
 4WM  H1   N    C8   112.74  3.000
 4WM  H1   N    C12  111.76  3.000
 4WM  C8   N    C12  120.27  3.000
 4WM  H3   O4   C12  108.84  3.000
 4WM  H4   C12  O3   111.85  3.000
 4WM  H4   C12  O4   104.06  3.000
 4WM  O3   C12  O4   110.48  3.000
 4WM  H4   C12  N    109.03  3.000
 4WM  O3   C12  N    105.76  3.000
 4WM  O4   C12  N    115.80  3.000
 4WM  C13  O3   C12  119.06  3.000
 4WM  C14  C13  C15  110.27  3.000
 4WM  C15  C13  C16  109.90  3.000
 4WM  C14  C13  C16  109.57  3.000
 4WM  C15  C13  O3   110.26  3.000
 4WM  C14  C13  O3   112.43  3.000
 4WM  C16  C13  O3   104.25  3.000
 4WM  H7   C16  H6   107.86  3.000
 4WM  H7   C16  H5   108.33  3.000
 4WM  H6   C16  H5   107.81  3.000
 4WM  H7   C16  C13  111.04  3.000
 4WM  H6   C16  C13  110.40  3.000
 4WM  H5   C16  C13  111.27  3.000
 4WM  H10  C15  H9   107.95  3.000
 4WM  H10  C15  H8   108.23  3.000
 4WM  H9   C15  H8   106.94  3.000
 4WM  H10  C15  C13  111.16  3.000
 4WM  H9   C15  C13  110.11  3.000
 4WM  H8   C15  C13  112.26  3.000
 4WM  H13  C14  H12  107.12  3.000
 4WM  H13  C14  H11  108.20  3.000
 4WM  H12  C14  H11  107.94  3.000
 4WM  H13  C14  C13  112.63  3.000
 4WM  H12  C14  C13  109.36  3.000
 4WM  H11  C14  C13  111.40  3.000
 4WM  H14  C8   C7   107.21  3.000
 4WM  H14  C8   C9   106.88  3.000
 4WM  C7   C8   C9   108.70  3.000
 4WM  H14  C8   N    105.08  3.000
 4WM  C9   C8   N    111.28  3.000
 4WM  C7   C8   N    117.10  3.000
 4WM  H16  C9   H15  105.68  3.000
 4WM  H16  C9   C10  110.60  3.000
 4WM  H15  C9   C10  109.19  3.000
 4WM  H16  C9   C8   110.22  3.000
 4WM  H15  C9   C8   107.69  3.000
 4WM  C10  C9   C8   113.15  3.000
 4WM  H18  C10  H17  106.32  3.000
 4WM  H18  C10  C11  108.42  3.000
 4WM  H17  C10  C11  109.32  3.000
 4WM  H18  C10  C9   109.14  3.000
 4WM  H17  C10  C9   110.73  3.000
 4WM  C11  C10  C9   112.69  3.000
 4WM  H2   C11  O1   110.78  3.000
 4WM  H2   C11  O2   104.39  3.000
 4WM  O1   C11  O2   112.03  3.000
 4WM  H2   C11  C10  109.67  3.000
 4WM  O1   C11  C10  107.34  3.000
 4WM  O2   C11  C10  112.64  3.000
 4WM  H19  O2   C11  108.88  3.000
 4WM  H20  O1   C11  108.87  3.000
 4WM  H22  C7   H21  108.31  3.000
 4WM  H22  C7   SE   108.13  3.000
 4WM  H21  C7   SE   108.78  3.000
 4WM  H22  C7   C8   109.10  3.000
 4WM  H21  C7   C8   110.82  3.000
 4WM  SE   C7   C8   111.62  3.000
 4WM  C2   SE   C7    97.89  3.000
 4WM  H23  C2   C1   109.67  3.000
 4WM  H23  C2   C3   110.09  3.000
 4WM  C1   C2   C3   112.06  3.000
 4WM  H23  C2   SE   105.78  3.000
 4WM  C3   C2   SE   110.47  3.000
 4WM  C1   C2   SE   108.57  3.000
 4WM  H24  C3   C4   119.21  3.000
 4WM  H24  C3   C2   117.60  3.000
 4WM  C4   C3   C2   123.18  3.000
 4WM  H26  C4   C5   117.43  3.000
 4WM  H26  C4   C3   118.90  3.000
 4WM  C5   C4   C3   123.67  3.000
 4WM  H29  C5   H28  105.46  3.000
 4WM  H29  C5   C6   110.47  3.000
 4WM  H28  C5   C6   110.20  3.000
 4WM  H29  C5   C4   109.43  3.000
 4WM  H28  C5   C4   109.63  3.000
 4WM  C6   C5   C4   111.48  3.000
 4WM  H31  C6   H30  106.85  3.000
 4WM  H31  C6   C1   109.34  3.000
 4WM  H30  C6   C1   110.10  3.000
 4WM  H31  C6   C5   109.59  3.000
 4WM  H30  C6   C5   110.35  3.000
 4WM  C1   C6   C5   110.53  3.000
 4WM  H33  C1   H32  106.96  3.000
 4WM  H33  C1   C6   108.57  3.000
 4WM  H32  C1   C6   110.89  3.000
 4WM  H33  C1   C2   110.22  3.000
 4WM  H32  C1   C2   109.94  3.000
 4WM  C6   C1   C2   110.20  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
 4WM  Var_01  C5   C6   C1   C2   -62.55  30.0  1
 4WM  Var_02  C5   C4   C3   C2    -2.84  30.0  1
 4WM  Var_03  C6   C5   C4   C3   -14.00  30.0  1
 4WM  Var_04  C1   C6   C5   C4    45.89  30.0  1
 4WM  Var_05  H21  C7   SE   C2    48.20  30.0  3
 4WM  Var_06  C16  C13  O3   C12  172.53  30.0  3
 4WM  Var_07  C11  C10  C9   C8   174.76  30.0  3
 4WM  Var_08  O2   C11  C10  C9    58.71  30.0  3
 4WM  Var_09  H5   C16  C13  O3    57.89  30.0  3
 4WM  Var_10  H11  C14  C13  O3    53.80  30.0  3
 4WM  Var_11  H8   C15  C13  O3    66.44  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
 4WM  chir_01  C12  O4  N   O3  positiv
 4WM  chir_02  C8   N   C7  C9  negativ
 4WM  chir_03  C2   SE  C3  C1  positiv

