# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 05:57:38 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: N-(2-hydroxyethyl)icosanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCCCCCC(=O)NCCO
#
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
 A9M  A9M  N-(2-hydroxyethyl)icosanamide  ligand  70  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A9M
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
 A9M  C1    C  C     0   0.559   -9.1996  -0.3178  -0.4337
 A9M  O1    O  O     0  -0.506   -9.3025  -1.4190  -0.9586
 A9M  C2    C  CH2   0  -0.584   -7.8780   0.4143  -0.3249
 A9M  C3    C  CH2   0  -0.413   -6.6614  -0.4990  -0.2877
 A9M  C4    C  CH2   0  -0.415   -5.3641   0.2981  -0.2335
 A9M  C5    C  CH2   0  -0.413   -4.1165  -0.5755  -0.1966
 A9M  C6    C  CH2   0  -0.412   -2.8293   0.2393  -0.1678
 A9M  C7    C  CH2   0  -0.413   -1.5660  -0.6118  -0.1264
 A9M  C8    C  CH2   0  -0.412   -0.2911   0.2227  -0.1160
 A9M  C9    C  CH2   0  -0.412    0.9844  -0.6095  -0.0688
 A9M  C10   C  CH2   0  -0.412    2.2486   0.2413  -0.0739
 A9M  C11   C  CH2   0  -0.412    3.5336  -0.5753  -0.0188
 A9M  C12   C  CH2   0  -0.412    4.7890   0.2886  -0.0310
 A9M  C13   C  CH2   0  -0.412    6.0815  -0.5158   0.0294
 A9M  C14   C  CH2   0  -0.412    7.3297   0.3583   0.0131
 A9M  C15   C  CH2   0  -0.412    8.6278  -0.4366   0.0771
 A9M  C16   C  CH2   0  -0.411    9.8708   0.4451   0.0590
 A9M  C17   C  CH2   0  -0.412   11.1732  -0.3429   0.1219
 A9M  C18   C  CH2   0  -0.406   12.4116   0.5447   0.1062
 A9M  C19   C  CH2   0  -0.419   13.7188  -0.2365   0.1637
 A9M  C20   C  CH3   0  -0.663   14.9446   0.6667   0.1475
 A9M  C22   C  CH2   0  -0.178  -12.4413   0.4095   1.1355
 A9M  C23   C  CH2   0  -0.292  -11.6220  -0.0912  -0.0332
 A9M  OAC   O  OH1   0  -0.674  -12.4210   1.8212   1.1262
 A9M  NAX   N  NH1   0  -0.637  -10.2505   0.3511   0.0708
 A9M  H2    H  HCH2  0   0.266   -7.8063   1.0819  -1.1914
 A9M  H2A   H  HCH2  0   0.249   -7.8836   1.0672   0.5525
 A9M  H3    H  HCH2  0   0.220   -6.7212  -1.1607   0.5820
 A9M  H3A   H  HCH2  0   0.222   -6.6555  -1.1454  -1.1686
 A9M  H4    H  HCH2  0   0.210   -5.3123   0.9633  -1.1030
 A9M  H4A   H  HCH2  0   0.210   -5.3729   0.9519   0.6459
 A9M  H5    H  HCH2  0   0.208   -4.1551  -1.2303   0.6812
 A9M  H5A   H  HCH2  0   0.208   -4.1089  -1.2378  -1.0694
 A9M  H6    H  HCH2  0   0.207   -2.7959   0.8912  -1.0482
 A9M  H6A   H  HCH2  0   0.207   -2.8432   0.9069   0.7012
 A9M  H7    H  HCH2  0   0.206   -1.5888  -1.2554   0.7603
 A9M  H7A   H  HCH2  0   0.206   -1.5522  -1.2861  -0.9902
 A9M  H8    H  HCH2  0   0.206   -0.2718   0.8627  -1.0057
 A9M  H8A   H  HCH2  0   0.206   -0.3109   0.9024   0.7434
 A9M  H9    H  HCH2  0   0.206    0.9738  -1.2417   0.8264
 A9M  H9A   H  HCH2  0   0.206    1.0042  -1.2950  -0.9235
 A9M  H10   H  HCH2  0   0.206    2.2573   0.8692  -0.9722
 A9M  H10A  H  HCH2  0   0.206    2.2225   0.9323   0.7764
 A9M  H11   H  HCH2  0   0.206    3.5301  -1.1995   0.8820
 A9M  H11A  H  HCH2  0   0.206    3.5615  -1.2683  -0.8672
 A9M  H12   H  HCH2  0   0.206    4.7911   0.9100  -0.9339
 A9M  H12A  H  HCH2  0   0.206    4.7564   0.9852   0.8144
 A9M  H13   H  HCH2  0   0.206    6.0827  -1.1347   0.9339
 A9M  H13A  H  HCH2  0   0.206    6.1160  -1.2136  -0.8149
 A9M  H14   H  HCH2  0   0.206    7.3271   0.9757  -0.8925
 A9M  H14A  H  HCH2  0   0.206    7.2914   1.0583   0.8554
 A9M  H15   H  HCH2  0   0.206    8.6328  -1.0527   0.9835
 A9M  H15A  H  HCH2  0   0.206    8.6677  -1.1370  -0.7647
 A9M  H16   H  HCH2  0   0.206    9.8637   1.0617  -0.8472
 A9M  H16A  H  HCH2  0   0.206    9.8293   1.1455   0.9007
 A9M  H17   H  HCH2  0   0.206   11.1809  -0.9613   1.0268
 A9M  H17A  H  HCH2  0   0.206   11.2168  -1.0411  -0.7216
 A9M  H18   H  HCH2  0   0.205   12.4013   1.1659  -0.7969
 A9M  H18A  H  HCH2  0   0.206   12.3690   1.2412   0.9514
 A9M  H19   H  HCH2  0   0.210   13.7306  -0.8568   1.0656
 A9M  H19A  H  HCH2  0   0.210   13.7630  -0.9306  -0.6815
 A9M  H20   H  HCH3  0   0.225   15.8708   0.0920   0.1864
 A9M  H20A  H  HCH3  0   0.215   14.9717   1.2750  -0.7587
 A9M  H20B  H  HCH3  0   0.216   14.9418   1.3477   1.0006
 A9M  H22   H  HCH2  0   0.210  -13.4602   0.0167   1.0349
 A9M  H22A  H  HCH2  0   0.209  -12.0270   0.0063   2.0667
 A9M  H23   H  HCH2  0   0.249  -11.6506  -1.1800  -0.0376
 A9M  H23A  H  HCH2  0   0.237  -12.0712   0.2459  -0.9740
 A9M  HOAC  H  HOH1  0   0.459  -12.7568   2.1377   1.9692
 A9M  HNAX  H  HNH1  0   0.394  -10.0975   1.2817   0.4260

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
 A9M  C1   O1    double  1.224  0.020  1.224
 A9M  C1   C2    single  1.515  0.020  1.515
 A9M  C1   NAX   single  1.344  0.020  1.344
 A9M  C2   C3    single  1.522  0.020  1.522
 A9M  C3   C4    single  1.524  0.020  1.524
 A9M  C4   C5    single  1.524  0.020  1.524
 A9M  C5   C6    single  1.524  0.020  1.524
 A9M  C6   C7    single  1.524  0.020  1.524
 A9M  C7   C8    single  1.524  0.020  1.524
 A9M  C8   C9    single  1.524  0.020  1.524
 A9M  C9   C10   single  1.524  0.020  1.524
 A9M  C10  C11   single  1.524  0.020  1.524
 A9M  C11  C12   single  1.524  0.020  1.524
 A9M  C12  C13   single  1.524  0.020  1.524
 A9M  C13  C14   single  1.524  0.020  1.524
 A9M  C14  C15   single  1.523  0.020  1.523
 A9M  C15  C16   single  1.524  0.020  1.524
 A9M  C16  C17   single  1.524  0.020  1.524
 A9M  C17  C18   single  1.524  0.020  1.524
 A9M  C18  C19   single  1.524  0.020  1.524
 A9M  C19  C20   single  1.523  0.020  1.523
 A9M  C22  C23   single  1.513  0.020  1.513
 A9M  C22  OAC   single  1.412  0.020  1.412
 A9M  C23  NAX   single  1.445  0.020  1.445
 A9M  C2   H2    single  0.970  0.020  1.090
 A9M  C2   H2A   single  0.970  0.020  1.090
 A9M  C3   H3    single  0.970  0.020  1.090
 A9M  C3   H3A   single  0.970  0.020  1.090
 A9M  C4   H4    single  0.970  0.020  1.090
 A9M  C4   H4A   single  0.970  0.020  1.090
 A9M  C5   H5    single  0.970  0.020  1.090
 A9M  C5   H5A   single  0.970  0.020  1.090
 A9M  C6   H6    single  0.970  0.020  1.090
 A9M  C6   H6A   single  0.970  0.020  1.090
 A9M  C7   H7    single  0.970  0.020  1.090
 A9M  C7   H7A   single  0.970  0.020  1.090
 A9M  C8   H8    single  0.970  0.020  1.090
 A9M  C8   H8A   single  0.970  0.020  1.090
 A9M  C9   H9    single  0.970  0.020  1.090
 A9M  C9   H9A   single  0.970  0.020  1.090
 A9M  C10  H10   single  0.970  0.020  1.090
 A9M  C10  H10A  single  0.970  0.020  1.090
 A9M  C11  H11   single  0.970  0.020  1.090
 A9M  C11  H11A  single  0.970  0.020  1.090
 A9M  C12  H12   single  0.970  0.020  1.090
 A9M  C12  H12A  single  0.970  0.020  1.090
 A9M  C13  H13   single  0.970  0.020  1.090
 A9M  C13  H13A  single  0.970  0.020  1.090
 A9M  C14  H14   single  0.970  0.020  1.090
 A9M  C14  H14A  single  0.970  0.020  1.090
 A9M  C15  H15   single  0.970  0.020  1.090
 A9M  C15  H15A  single  0.970  0.020  1.090
 A9M  C16  H16   single  0.970  0.020  1.090
 A9M  C16  H16A  single  0.970  0.020  1.090
 A9M  C17  H17   single  0.970  0.020  1.090
 A9M  C17  H17A  single  0.970  0.020  1.090
 A9M  C18  H18   single  0.970  0.020  1.090
 A9M  C18  H18A  single  0.970  0.020  1.090
 A9M  C19  H19   single  0.970  0.020  1.090
 A9M  C19  H19A  single  0.970  0.020  1.090
 A9M  C20  H20   single  0.970  0.020  1.090
 A9M  C20  H20A  single  0.970  0.020  1.090
 A9M  C20  H20B  single  0.970  0.020  1.090
 A9M  C22  H22   single  0.970  0.020  1.090
 A9M  C22  H22A  single  0.970  0.020  1.090
 A9M  C23  H23   single  0.970  0.020  1.090
 A9M  C23  H23A  single  0.970  0.020  1.090
 A9M  OAC  HOAC  single  0.850  0.020  0.980
 A9M  NAX  HNAX  single  0.860  0.020  1.020

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
 A9M  NAX   C1   C2    114.50  3.000
 A9M  NAX   C1   O1    122.88  3.000
 A9M  C2    C1   O1    122.61  3.000
 A9M  H2A   C2   H2    105.72  3.000
 A9M  H2A   C2   C3    110.05  3.000
 A9M  H2    C2   C3    109.42  3.000
 A9M  H2A   C2   C1    109.98  3.000
 A9M  H2    C2   C1    107.13  3.000
 A9M  C3    C2   C1    114.15  3.000
 A9M  H3A   C3   H3    106.45  3.000
 A9M  H3A   C3   C4    109.48  3.000
 A9M  H3    C3   C4    109.55  3.000
 A9M  H3A   C3   C2    109.86  3.000
 A9M  H3    C3   C2    109.80  3.000
 A9M  C4    C3   C2    111.57  3.000
 A9M  H4A   C4   H4    105.96  3.000
 A9M  H4A   C4   C5    109.22  3.000
 A9M  H4    C4   C5    109.18  3.000
 A9M  H4A   C4   C3    109.50  3.000
 A9M  H4    C4   C3    109.24  3.000
 A9M  C5    C4   C3    113.46  3.000
 A9M  H5A   C5   H5    106.09  3.000
 A9M  H5A   C5   C6    109.42  3.000
 A9M  H5    C5   C6    109.52  3.000
 A9M  H5A   C5   C4    109.44  3.000
 A9M  H5    C5   C4    109.46  3.000
 A9M  C6    C5   C4    112.68  3.000
 A9M  H6A   C6   H6    105.96  3.000
 A9M  H6A   C6   C7    109.22  3.000
 A9M  H6    C6   C7    109.19  3.000
 A9M  H6A   C6   C5    109.27  3.000
 A9M  H6    C6   C5    109.19  3.000
 A9M  C7    C6   C5    113.72  3.000
 A9M  H7A   C7   H7    106.06  3.000
 A9M  H7A   C7   C8    109.38  3.000
 A9M  H7    C7   C8    109.48  3.000
 A9M  H7A   C7   C6    109.43  3.000
 A9M  H7    C7   C6    109.44  3.000
 A9M  C8    C7   C6    112.83  3.000
 A9M  H8A   C8   H8    105.94  3.000
 A9M  H8A   C8   C9    109.24  3.000
 A9M  H8    C8   C9    109.23  3.000
 A9M  H8A   C8   C7    109.26  3.000
 A9M  H8    C8   C7    109.20  3.000
 A9M  C9    C8   C7    113.67  3.000
 A9M  H9A   C9   H9    106.05  3.000
 A9M  H9A   C9   C10   109.37  3.000
 A9M  H9    C9   C10   109.44  3.000
 A9M  H9A   C9   C8    109.43  3.000
 A9M  H9    C9   C8    109.41  3.000
 A9M  C10   C9   C8    112.92  3.000
 A9M  H10A  C10  H10   105.95  3.000
 A9M  H10A  C10  C11   109.27  3.000
 A9M  H10   C10  C11   109.27  3.000
 A9M  H10A  C10  C9    109.25  3.000
 A9M  H10   C10  C9    109.22  3.000
 A9M  C11   C10  C9    113.60  3.000
 A9M  H11A  C11  H11   106.03  3.000
 A9M  H11A  C11  C12   109.35  3.000
 A9M  H11   C11  C12   109.40  3.000
 A9M  H11A  C11  C10   109.42  3.000
 A9M  H11   C11  C10   109.41  3.000
 A9M  C12   C11  C10   113.00  3.000
 A9M  H12A  C12  H12   105.97  3.000
 A9M  H12A  C12  C13   109.28  3.000
 A9M  H12   C12  C13   109.29  3.000
 A9M  H12A  C12  C11   109.25  3.000
 A9M  H12   C12  C11   109.24  3.000
 A9M  C13   C12  C11   113.53  3.000
 A9M  H13A  C13  H13   106.04  3.000
 A9M  H13A  C13  C14   109.34  3.000
 A9M  H13   C13  C14   109.37  3.000
 A9M  H13A  C13  C12   109.42  3.000
 A9M  H13   C13  C12   109.38  3.000
 A9M  C14   C13  C12   113.05  3.000
 A9M  H14A  C14  H14   105.97  3.000
 A9M  H14A  C14  C15   109.32  3.000
 A9M  H14   C14  C15   109.31  3.000
 A9M  H14A  C14  C13   109.24  3.000
 A9M  H14   C14  C13   109.27  3.000
 A9M  C15   C14  C13   113.47  3.000
 A9M  H15A  C15  H15   106.01  3.000
 A9M  H15A  C15  C16   109.32  3.000
 A9M  H15   C15  C16   109.35  3.000
 A9M  H15A  C15  C14   109.40  3.000
 A9M  H15   C15  C14   109.38  3.000
 A9M  C16   C15  C14   113.12  3.000
 A9M  H16A  C16  H16   105.97  3.000
 A9M  H16A  C16  C17   109.34  3.000
 A9M  H16   C16  C17   109.31  3.000
 A9M  H16A  C16  C15   109.26  3.000
 A9M  H16   C16  C15   109.27  3.000
 A9M  C17   C16  C15   113.42  3.000
 A9M  H17A  C17  H17   106.01  3.000
 A9M  H17A  C17  C18   109.32  3.000
 A9M  H17   C17  C18   109.35  3.000
 A9M  H17A  C17  C16   109.38  3.000
 A9M  H17   C17  C16   109.39  3.000
 A9M  C18   C17  C16   113.15  3.000
 A9M  H18A  C18  H18   105.95  3.000
 A9M  H18A  C18  C19   109.27  3.000
 A9M  H18   C18  C19   109.25  3.000
 A9M  H18A  C18  C17   109.31  3.000
 A9M  H18   C18  C17   109.32  3.000
 A9M  C19   C18  C17   113.46  3.000
 A9M  H19A  C19  H19   106.05  3.000
 A9M  H19A  C19  C20   109.60  3.000
 A9M  H19   C19  C20   109.65  3.000
 A9M  H19A  C19  C18   109.31  3.000
 A9M  H19   C19  C18   109.32  3.000
 A9M  C20   C19  C18   112.71  3.000
 A9M  H20B  C20  H20A  107.53  3.000
 A9M  H20B  C20  H20   107.64  3.000
 A9M  H20A  C20  H20   107.59  3.000
 A9M  H20B  C20  C19   111.08  3.000
 A9M  H20A  C20  C19   111.06  3.000
 A9M  H20   C20  C19   111.76  3.000
 A9M  H22A  C22  H22   107.31  3.000
 A9M  H22A  C22  OAC   111.59  3.000
 A9M  H22   C22  OAC   111.77  3.000
 A9M  H22A  C22  C23   109.27  3.000
 A9M  H22   C22  C23   108.29  3.000
 A9M  OAC   C22  C23   108.55  3.000
 A9M  H23A  C23  H23   107.06  3.000
 A9M  H23A  C23  NAX   110.91  3.000
 A9M  H23   C23  NAX   109.34  3.000
 A9M  H23A  C23  C22   109.85  3.000
 A9M  H23   C23  C22   108.65  3.000
 A9M  NAX   C23  C22   110.93  3.000
 A9M  HOAC  OAC  C22   108.57  3.000
 A9M  HNAX  NAX  C23   116.88  3.000
 A9M  HNAX  NAX  C1    118.25  3.000
 A9M  C23   NAX  C1    124.25  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
 A9M  CONST_01  C23   NAX  C1   O1      0.00   0.0  0
 A9M  CONST_02  C23   NAX  C1   C2    180.00   0.0  0
 A9M  CONST_03  HNAX  NAX  C1   O1    180.00   0.0  0
 A9M  Var_01    C4    C3   C2   C1    177.75  30.0  3
 A9M  Var_02    C22   C23  NAX  C1    151.31  30.0  1
 A9M  Var_03    C3    C2   C1   O1    -27.35  30.0  3
 A9M  Var_04    C5    C4   C3   C2   -179.93  30.0  3
 A9M  Var_05    C6    C5   C4   C3    178.97  30.0  3
 A9M  Var_06    C7    C6   C5   C4    179.83  30.0  3
 A9M  Var_07    C8    C7   C6   C5    179.27  30.0  3
 A9M  Var_08    C9    C8   C7   C6    179.76  30.0  3
 A9M  Var_09    C10   C9   C8   C7    179.39  30.0  3
 A9M  Var_10    C11   C10  C9   C8    179.67  30.0  3
 A9M  Var_11    C12   C11  C10  C9    179.73  30.0  3
 A9M  Var_12    C13   C12  C11  C10   179.77  30.0  3
 A9M  Var_13    C14   C13  C12  C11   179.86  30.0  3
 A9M  Var_14    C15   C14  C13  C12   179.84  30.0  3
 A9M  Var_15    C16   C15  C14  C13   179.94  30.0  3
 A9M  Var_16    C17   C16  C15  C14  -179.97  30.0  3
 A9M  Var_17    C18   C17  C16  C15  -179.88  30.0  3
 A9M  Var_18    C19   C18  C17  C16  -179.79  30.0  3
 A9M  Var_19    C20   C19  C18  C17  -179.99  30.0  3
 A9M  Var_20    NAX   C23  C22  OAC    60.74  30.0  3
 A9M  Var_21    H20   C20  C19  C18  -179.85  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
 A9M  plan-1  C1    0.020
 A9M  plan-1  O1    0.020
 A9M  plan-1  C2    0.020
 A9M  plan-1  C23   0.020
 A9M  plan-1  NAX   0.020
 A9M  plan-1  HNAX  0.020

