# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:19:54 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C[C@@H](C)NC[C@H](O)c2ccc(O)c(NC=O)c2)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
 H98  H98  ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide  ligand  49  25  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H98
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
 H98  C1   C  CH3   0  -0.664  -1.2081   3.7342  -1.1667
 H98  C2   C  CH1   0  -0.051  -1.7406   2.3356  -0.8900
 H98  C3   C  CH2   0  -0.505  -3.1849   2.4221  -0.3800
 H98  C4   C  CR6   0   0.083  -3.8286   1.0796  -0.1721
 H98  C5   C  CR16  0  -0.282  -4.2587   0.3185  -1.2618
 H98  C6   C  CR16  0  -0.327  -4.8206  -0.9321  -1.0934
 H98  C7   C  CR6   0   0.366  -4.9720  -1.4687   0.1882
 H98  C8   C  CR16  0  -0.371  -4.5527  -0.7261   1.2868
 H98  C9   C  CR16  0  -0.301  -3.9895   0.5327   1.0942
 H98  O1   O  O2    0  -0.473  -5.5305  -2.6936   0.2606
 H98  C10  C  CH3   0  -0.435  -5.6832  -3.2905   1.5321
 H98  N1   N  NH1   0  -0.631  -0.9242   1.6492   0.1040
 H98  C11  C  CH2   0  -0.301   0.3876   1.2185  -0.3429
 H98  C12  C  CH1   0  -0.008   1.2430   0.9088   0.8904
 H98  C13  C  CR6   0   0.087   2.6705   0.6465   0.4914
 H98  C14  C  CR16  0  -0.371   3.0564  -0.6541   0.1798
 H98  C15  C  CR6   0   0.306   4.3440  -0.9383  -0.2627
 H98  C16  C  CR6   0   0.283   5.2670   0.1132  -0.3798
 H98  C17  C  CR16  0  -0.359   4.8851   1.4059  -0.0598
 H98  C18  C  CR16  0  -0.315   3.5928   1.6755   0.3684
 H98  O2   O  OH1   0  -0.638   6.5084  -0.2100  -0.8023
 H98  N2   N  NH1   0  -0.695   4.8014  -2.2217  -0.5856
 H98  C19  C  C1    0   0.242   4.0951  -3.3556  -0.7700
 H98  O3   O  O     0  -0.468   2.8913  -3.4889  -0.6680
 H98  O4   O  OH1   0  -0.682   1.1665   1.9879   1.7860
 H98  H1   H  HCH3  0   0.229  -1.8289   4.2302  -1.9135
 H98  H2   H  HCH3  0   0.221  -1.2205   4.3367  -0.2569
 H98  H3   H  HCH3  0   0.234  -0.1884   3.7225  -1.5515
 H98  H4   H  HCH1  0   0.204  -1.7545   1.7776  -1.8402
 H98  H5   H  HCH2  0   0.240  -3.1915   2.9914   0.5543
 H98  H6   H  HCH2  0   0.247  -3.7636   3.0011  -1.1044
 H98  H7   H  HCR6  0   0.248  -4.1537   0.7136  -2.2657
 H98  H8   H  HCR6  0   0.260  -5.1495  -1.5035  -1.9528
 H98  H9   H  HCR6  0   0.277  -4.6569  -1.1004   2.2961
 H98  H10  H  HCR6  0   0.254  -3.6738   1.0964   1.9647
 H98  H11  H  HCH3  0   0.227  -4.7227  -3.4357   2.0338
 H98  H12  H  HCH3  0   0.227  -6.3357  -2.7050   2.1856
 H98  H13  H  HCH3  0   0.259  -6.1398  -4.2629   1.3646
 H98  H14  H  HNH1  0   0.361  -1.4285   0.8343   0.4378
 H98  H16  H  HCH2  0   0.222   0.3630   0.3461  -1.0095
 H98  H17  H  HCH2  0   0.235   0.8644   2.0299  -0.8976
 H98  H18  H  HCH1  0   0.210   0.8428  -0.0073   1.3557
 H98  H19  H  HCR6  0   0.272   2.3388  -1.4530   0.2896
 H98  H20  H  HCR6  0   0.272   5.6041   2.2124  -0.1489
 H98  H21  H  HCR6  0   0.252   3.3166   2.6938   0.6060
 H98  H22  H  HOH1  0   0.483   7.0733   0.5701  -0.8307
 H98  H23  H  HNH1  0   0.420   5.7949  -2.3114  -0.7368
 H98  H24  H  H     0   0.220   4.7607  -4.1885  -1.0371
 H98  H25  H  HOH1  0   0.436   0.2701   2.3400   1.6556

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
 H98  O2   C16  single    1.350  0.020  1.350
 H98  O3   C19  double    1.215  0.020  1.215
 H98  N2   C19  single    1.349  0.020  1.349
 H98  N2   C15  single    1.400  0.020  1.400
 H98  C16  C15  aromatic  1.404  0.020  1.404
 H98  C16  C17  aromatic  1.385  0.020  1.385
 H98  C15  C14  aromatic  1.391  0.020  1.391
 H98  C17  C18  aromatic  1.388  0.020  1.388
 H98  C14  C13  aromatic  1.392  0.020  1.392
 H98  C18  C13  aromatic  1.387  0.020  1.387
 H98  C13  C12  single    1.505  0.020  1.505
 H98  C12  C11  single    1.533  0.020  1.533
 H98  C12  O4   single    1.404  0.020  1.404
 H98  C11  N1   single    1.451  0.020  1.451
 H98  N1   C2   single    1.458  0.020  1.458
 H98  C1   C2   single    1.522  0.020  1.522
 H98  C2   C3   single    1.534  0.020  1.534
 H98  C3   C4   single    1.503  0.020  1.503
 H98  C5   C4   aromatic  1.397  0.020  1.397
 H98  C5   C6   aromatic  1.381  0.020  1.381
 H98  C4   C9   aromatic  1.389  0.020  1.389
 H98  C6   C7   aromatic  1.398  0.020  1.398
 H98  C10  O1   single    1.413  0.020  1.413
 H98  C9   C8   aromatic  1.392  0.020  1.392
 H98  C7   C8   aromatic  1.391  0.020  1.391
 H98  C7   O1   single    1.348  0.020  1.348
 H98  C1   H1   single    0.970  0.020  1.090
 H98  C1   H2   single    0.970  0.020  1.090
 H98  C1   H3   single    0.970  0.020  1.090
 H98  C2   H4   single    0.970  0.020  1.090
 H98  C3   H5   single    0.970  0.020  1.090
 H98  C3   H6   single    0.970  0.020  1.090
 H98  C5   H7   single    0.930  0.020  1.080
 H98  C6   H8   single    0.930  0.020  1.080
 H98  C8   H9   single    0.930  0.020  1.080
 H98  C9   H10  single    0.930  0.020  1.080
 H98  C10  H11  single    0.970  0.020  1.090
 H98  C10  H12  single    0.970  0.020  1.090
 H98  C10  H13  single    0.970  0.020  1.090
 H98  N1   H14  single    0.890  0.020  1.040
 H98  C11  H16  single    0.970  0.020  1.090
 H98  C11  H17  single    0.970  0.020  1.090
 H98  C12  H18  single    0.970  0.020  1.090
 H98  C14  H19  single    0.930  0.020  1.080
 H98  C17  H20  single    0.930  0.020  1.080
 H98  C18  H21  single    0.930  0.020  1.080
 H98  O2   H22  single    0.850  0.020  0.980
 H98  N2   H23  single    0.860  0.020  1.020
 H98  C19  H24  single    0.930  0.020  1.080
 H98  O4   H25  single    0.850  0.020  0.980

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
 H98  H3   C1   H2   108.11  3.000
 H98  H3   C1   H1   107.20  3.000
 H98  H2   C1   H1   108.26  3.000
 H98  H3   C1   C2   112.44  3.000
 H98  H2   C1   C2   110.60  3.000
 H98  H1   C1   C2   110.08  3.000
 H98  H4   C2   N1   110.88  3.000
 H98  H4   C2   C3   107.65  3.000
 H98  N1   C2   C3   109.09  3.000
 H98  H4   C2   C1   108.24  3.000
 H98  C3   C2   C1   109.76  3.000
 H98  N1   C2   C1   111.14  3.000
 H98  H6   C3   H5   106.69  3.000
 H98  H6   C3   C4   109.76  3.000
 H98  H5   C3   C4   110.12  3.000
 H98  H6   C3   C2   107.94  3.000
 H98  H5   C3   C2   108.59  3.000
 H98  C4   C3   C2   113.50  3.000
 H98  C9   C4   C5   117.45  3.000
 H98  C9   C4   C3   121.83  3.000
 H98  C5   C4   C3   120.69  3.000
 H98  H7   C5   C6   118.84  3.000
 H98  H7   C5   C4   119.60  3.000
 H98  C6   C5   C4   121.56  3.000
 H98  H8   C6   C7   119.48  3.000
 H98  H8   C6   C5   120.29  3.000
 H98  C7   C6   C5   120.23  3.000
 H98  O1   C7   C8   124.59  3.000
 H98  O1   C7   C6   116.29  3.000
 H98  C8   C7   C6   119.12  3.000
 H98  H9   C8   C9   118.75  3.000
 H98  H9   C8   C7   121.56  3.000
 H98  C9   C8   C7   119.69  3.000
 H98  H10  C9   C8   118.47  3.000
 H98  H10  C9   C4   119.58  3.000
 H98  C8   C9   C4   121.94  3.000
 H98  C10  O1   C7   118.48  3.000
 H98  H13  C10  H12  108.68  3.000
 H98  H13  C10  H11  108.71  3.000
 H98  H12  C10  H11  108.73  3.000
 H98  H13  C10  O1   106.53  3.000
 H98  H12  C10  O1   112.10  3.000
 H98  H11  C10  O1   111.97  3.000
 H98  H14  N1   C11  108.19  3.000
 H98  H14  N1   C2   108.90  3.000
 H98  C11  N1   C2   115.84  3.000
 H98  H17  C11  H16  106.95  3.000
 H98  H17  C11  C12  108.36  3.000
 H98  H16  C11  C12  109.90  3.000
 H98  H17  C11  N1   109.30  3.000
 H98  H16  C11  N1   113.74  3.000
 H98  C12  C11  N1   108.46  3.000
 H98  H18  C12  O4   110.46  3.000
 H98  H18  C12  C13  108.14  3.000
 H98  O4   C12  C13  110.77  3.000
 H98  H18  C12  C11  107.75  3.000
 H98  O4   C12  C11  109.12  3.000
 H98  C13  C12  C11  110.56  3.000
 H98  C18  C13  C14  119.27  3.000
 H98  C18  C13  C12  121.65  3.000
 H98  C14  C13  C12  119.02  3.000
 H98  H19  C14  C15  119.77  3.000
 H98  H19  C14  C13  118.98  3.000
 H98  C15  C14  C13  121.25  3.000
 H98  N2   C15  C16  116.90  3.000
 H98  C16  C15  C14  118.82  3.000
 H98  N2   C15  C14  124.27  3.000
 H98  O2   C16  C17  123.30  3.000
 H98  C17  C16  C15  119.88  3.000
 H98  O2   C16  C15  116.82  3.000
 H98  H20  C17  C18  119.90  3.000
 H98  H20  C17  C16  119.49  3.000
 H98  C18  C17  C16  120.61  3.000
 H98  H21  C18  C17  119.24  3.000
 H98  H21  C18  C13  120.60  3.000
 H98  C17  C18  C13  120.15  3.000
 H98  H22  O2   C16  110.75  3.000
 H98  H23  N2   C19  114.87  3.000
 H98  H23  N2   C15  115.96  3.000
 H98  C19  N2   C15  129.13  3.000
 H98  H24  C19  O3   122.48  3.000
 H98  H24  C19  N2   110.68  3.000
 H98  O3   C19  N2   126.83  3.000
 H98  H25  O4   C12  104.07  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
 H98  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 H98  CONST_02  C7   C8   C9   C4     0.00   0.0  0
 H98  CONST_03  C8   C9   C4   C5     0.00   0.0  0
 H98  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 H98  CONST_05  C9   C4   C5   C6     0.00   0.0  0
 H98  CONST_06  C9   C8   C7   C6     0.00   0.0  0
 H98  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 H98  CONST_08  C16  C17  C18  C13    0.00   0.0  0
 H98  CONST_09  C17  C16  C15  C14    0.00   0.0  0
 H98  CONST_10  C17  C18  C13  C14    0.00   0.0  0
 H98  CONST_11  C18  C17  C16  C15    0.00   0.0  0
 H98  CONST_12  C18  C13  C14  C15    0.00   0.0  0
 H98  CONST_13  C6   C5   C4   C3   180.00   0.0  0
 H98  CONST_14  C8   C9   C4   C3   180.00   0.0  0
 H98  CONST_15  O1   C7   C6   C5   180.00   0.0  0
 H98  CONST_16  O1   C7   C8   C9   180.00   0.0  0
 H98  CONST_17  C15  C14  C13  C12  180.00   0.0  0
 H98  CONST_18  C17  C18  C13  C12  180.00   0.0  0
 H98  CONST_19  N2   C15  C14  C13  180.00   0.0  0
 H98  CONST_20  O2   C16  C15  C14  180.00   0.0  0
 H98  CONST_21  N2   C15  C16  C17  180.00   0.0  0
 H98  CONST_22  O2   C16  C17  C18  180.00   0.0  0
 H98  CONST_23  H8   C6   C5   C4   180.00   0.0  0
 H98  CONST_24  H9   C8   C9   C4   180.00   0.0  0
 H98  CONST_25  H10  C9   C4   C5   180.00   0.0  0
 H98  CONST_26  H7   C5   C6   C7   180.00   0.0  0
 H98  CONST_27  H20  C17  C18  C13  180.00   0.0  0
 H98  CONST_28  H21  C18  C13  C14  180.00   0.0  0
 H98  CONST_29  H19  C14  C15  C16  180.00   0.0  0
 H98  CONST_30  C19  N2   C15  C14    0.00   0.0  0
 H98  CONST_31  C19  N2   C15  C16  180.00   0.0  0
 H98  CONST_32  H23  N2   C15  C14  180.00   0.0  0
 H98  CONST_33  O3   C19  N2   C15    0.00   0.0  0
 H98  CONST_34  H24  C19  N2   C15  180.00   0.0  0
 H98  Var_01    C5   C4   C3   C2   -75.03  30.0  2
 H98  Var_02    H11  C10  O1   C7   -60.85  30.0  3
 H98  Var_03    C12  C11  N1   C2   163.44  30.0  2

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
 H98  chir_01  C2   N1  C1   C3   positiv
 H98  chir_02  C12  O4  C11  C13  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
 H98  plan-1  C3   0.020
 H98  plan-1  C4   0.020
 H98  plan-1  C5   0.020
 H98  plan-1  C6   0.020
 H98  plan-1  C7   0.020
 H98  plan-1  C8   0.020
 H98  plan-1  C9   0.020
 H98  plan-1  O1   0.020
 H98  plan-1  H7   0.020
 H98  plan-1  H8   0.020
 H98  plan-1  H9   0.020
 H98  plan-1  H10  0.020
 H98  plan-2  C12  0.020
 H98  plan-2  C13  0.020
 H98  plan-2  C14  0.020
 H98  plan-2  C15  0.020
 H98  plan-2  C16  0.020
 H98  plan-2  C17  0.020
 H98  plan-2  C18  0.020
 H98  plan-2  O2   0.020
 H98  plan-2  N2   0.020
 H98  plan-2  H19  0.020
 H98  plan-2  H20  0.020
 H98  plan-2  H21  0.020
 H98  plan-3  C15  0.020
 H98  plan-3  N2   0.020
 H98  plan-3  C19  0.020
 H98  plan-3  O3   0.020
 H98  plan-3  H23  0.020
 H98  plan-3  H24  0.020

