# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:16:13 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: N-[(1R,2R,3E)-2-hydroxy-1-(hydroxymethyl)heptadec-3-en-1-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCC/C=C/[C@@H](O)[C@@H](CO)NC(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
 2ED  2ED  N-[(1R,2R,3E)-2-hydroxy-1-(hydroxymethyl)heptadec-3-en-1-yl]acetamide  ligand  63  24  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2ED
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
 2ED  O2    O  O     0  -0.503    3.3978   1.6903   0.7744
 2ED  O3    O  OH1   0  -0.669    7.9018   1.1901  -1.0499
 2ED  O1    O  OH1   0  -0.657    6.5471  -1.3711  -0.6370
 2ED  C1    C  CH1   0  -0.140    6.0731   0.7737   0.4632
 2ED  C2    C  CH1   0   0.003    6.1156  -0.7687   0.5544
 2ED  C3    C  C1    0  -0.236    4.7861  -1.2733   1.0362
 2ED  C4    C  C1    0  -0.220    3.9523  -2.0534   0.3587
 2ED  C5    C  CH2   0  -0.479    2.5846  -2.4311   0.8348
 2ED  C6    C  CH2   0  -0.416    1.4970  -1.6427   0.1026
 2ED  C18   C  C     0   0.545    3.8908   1.6120  -0.3415
 2ED  C19   C  CH3   0  -0.778    3.1027   1.9594  -1.5802
 2ED  N     N  NH1   0  -0.633    5.1550   1.2052  -0.5666
 2ED  C     C  CH2   0  -0.161    7.4320   1.4275   0.2574
 2ED  HO3   H  HOH1  0   0.459    8.5751   1.8465  -1.2479
 2ED  HO1   H  HOH1  0   0.441    5.9200  -1.1566  -1.3365
 2ED  H1    H  HCH1  0   0.267    5.7018   1.1405   1.4228
 2ED  H2    H  HCH1  0   0.242    6.8739  -1.0163   1.3072
 2ED  H3    H  H     0   0.235    4.4896  -0.9091   2.0166
 2ED  H4    H  H     0   0.225    4.2254  -2.4214  -0.6268
 2ED  H5    H  HCH2  0   0.223    2.4192  -3.5027   0.6819
 2ED  H5A   H  HCH2  0   0.224    2.4966  -2.2488   1.9099
 2ED  H6    H  HCH2  0   0.221    1.6529  -0.5771   0.2954
 2ED  H6A   H  HCH2  0   0.211    1.6095  -1.7762  -0.9787
 2ED  H19   H  HCH3  0   0.263    2.6390   2.9376  -1.4602
 2ED  H19A  H  HCH3  0   0.247    3.6980   1.9637  -2.4917
 2ED  H19B  H  HCH3  0   0.263    2.2991   1.2320  -1.7019
 2ED  HN    H  HNH1  0   0.395    5.5107   1.2512  -1.5082
 2ED  H     H  HCH2  0   0.204    8.1227   1.0378   1.0165
 2ED  HA    H  HCH2  0   0.220    7.3192   2.5008   0.4479
 2ED  C10   C  CH2   0  -0.413    0.0856  -2.0350   0.5214
 2ED  C11   C  CH2   0  -0.411   -0.9833  -1.1541  -0.1125
 2ED  C12   C  CH2   0  -0.412   -2.4032  -1.5184   0.3050
 2ED  C13   C  CH2   0  -0.412   -3.4447  -0.5403  -0.2242
 2ED  C14   C  CH2   0  -0.412   -4.8715  -0.8823   0.1875
 2ED  C15   C  CH2   0  -0.411   -5.8846   0.1681  -0.2510
 2ED  C16   C  CH2   0  -0.411   -7.3164  -0.1593   0.1543
 2ED  C17   C  CH2   0  -0.411   -8.3093   0.9339  -0.2213
 2ED  C181  C  CH2   0  -0.406   -9.7439   0.6119   0.1774
 2ED  C191  C  CH2   0  -0.418  -10.7283   1.7249  -0.1613
 2ED  C20   C  CH3   0  -0.663  -12.1600   1.3902   0.2333
 2ED  H17   H  HCH2  0   0.209   -0.0951  -3.0840   0.2631
 2ED  H18   H  HCH2  0   0.207    0.0014  -1.9717   1.6123
 2ED  H191  H  HCH2  0   0.206   -0.7888  -0.1100   0.1573
 2ED  H20   H  HCH2  0   0.207   -0.8995  -1.2035  -1.2038
 2ED  H21   H  HCH2  0   0.207   -2.6389  -2.5315  -0.0382
 2ED  H22   H  HCH2  0   0.205   -2.4627  -1.5470   1.3989
 2ED  H23   H  HCH2  0   0.205   -3.2000   0.4660   0.1340
 2ED  H24   H  HCH2  0   0.207   -3.3817  -0.4944  -1.3171
 2ED  H25   H  HCH2  0   0.207   -5.1502  -1.8573  -0.2268
 2ED  H26   H  HCH2  0   0.205   -4.9180  -0.9921   1.2769
 2ED  H27   H  HCH2  0   0.205   -5.6012   1.1363   0.1767
 2ED  H28   H  HCH2  0   0.206   -5.8335   0.2926  -1.3384
 2ED  H29   H  HCH2  0   0.206   -7.6212  -1.1042  -0.3090
 2ED  H30   H  HCH2  0   0.205   -7.3581  -0.3265   1.2365
 2ED  H31   H  HCH2  0   0.205   -8.0037   1.8737   0.2521
 2ED  H32   H  HCH2  0   0.206   -8.2633   1.1117  -1.3015
 2ED  H33   H  HCH2  0   0.206  -10.0609  -0.3140  -0.3156
 2ED  H34   H  HCH2  0   0.205   -9.7857   0.4095   1.2536
 2ED  H35   H  HCH2  0   0.210  -10.4144   2.6471   0.3378
 2ED  H36   H  HCH2  0   0.209  -10.6835   1.9331  -1.2348
 2ED  H37   H  HCH3  0   0.226  -12.8457   2.2012  -0.0151
 2ED  H38   H  HCH3  0   0.216  -12.5102   0.4937  -0.2819
 2ED  H39   H  HCH3  0   0.215  -12.2417   1.2052   1.3062

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
 2ED  O2    C18   double  1.222  0.020  1.222
 2ED  O3    C     single  1.409  0.020  1.409
 2ED  O3    HO3   single  0.850  0.020  0.980
 2ED  O1    C2    single  1.403  0.020  1.403
 2ED  O1    HO1   single  0.850  0.020  0.980
 2ED  C1    C2    single  1.546  0.020  1.546
 2ED  C1    N     single  1.446  0.020  1.446
 2ED  C1    C     single  1.522  0.020  1.522
 2ED  C1    H1    single  0.970  0.020  1.090
 2ED  C2    C3    single  1.501  0.020  1.501
 2ED  C2    H2    single  0.970  0.020  1.090
 2ED  C3    C4    double  1.328  0.020  1.328
 2ED  C3    H3    single  0.930  0.020  1.080
 2ED  C4    C5    single  1.497  0.020  1.497
 2ED  C4    H4    single  0.930  0.020  1.080
 2ED  C5    C6    single  1.530  0.020  1.530
 2ED  C5    H5    single  0.970  0.020  1.090
 2ED  C5    H5A   single  0.970  0.020  1.090
 2ED  C6    H6    single  0.970  0.020  1.090
 2ED  C6    H6A   single  0.970  0.020  1.090
 2ED  C18   C19   single  1.509  0.020  1.509
 2ED  C18   N     single  1.347  0.020  1.347
 2ED  C19   H19   single  0.970  0.020  1.090
 2ED  C19   H19A  single  0.970  0.020  1.090
 2ED  C19   H19B  single  0.970  0.020  1.090
 2ED  N     HN    single  0.860  0.020  1.020
 2ED  C     H     single  0.970  0.020  1.090
 2ED  C     HA    single  0.970  0.020  1.090
 2ED  C6    C10   single  1.524  0.020  1.524
 2ED  C10   C11   single  1.523  0.020  1.523
 2ED  C11   C12   single  1.524  0.020  1.524
 2ED  C12   C13   single  1.524  0.020  1.524
 2ED  C13   C14   single  1.524  0.020  1.524
 2ED  C14   C15   single  1.524  0.020  1.524
 2ED  C15   C16   single  1.524  0.020  1.524
 2ED  C16   C17   single  1.524  0.020  1.524
 2ED  C17   C181  single  1.523  0.020  1.523
 2ED  C181  C191  single  1.524  0.020  1.524
 2ED  C191  C20   single  1.522  0.020  1.522
 2ED  C10   H17   single  0.970  0.020  1.090
 2ED  C10   H18   single  0.970  0.020  1.090
 2ED  C11   H191  single  0.970  0.020  1.090
 2ED  C11   H20   single  0.970  0.020  1.090
 2ED  C12   H21   single  0.970  0.020  1.090
 2ED  C12   H22   single  0.970  0.020  1.090
 2ED  C13   H23   single  0.970  0.020  1.090
 2ED  C13   H24   single  0.970  0.020  1.090
 2ED  C14   H25   single  0.970  0.020  1.090
 2ED  C14   H26   single  0.970  0.020  1.090
 2ED  C15   H27   single  0.970  0.020  1.090
 2ED  C15   H28   single  0.970  0.020  1.090
 2ED  C16   H29   single  0.970  0.020  1.090
 2ED  C16   H30   single  0.970  0.020  1.090
 2ED  C17   H31   single  0.970  0.020  1.090
 2ED  C17   H32   single  0.970  0.020  1.090
 2ED  C181  H33   single  0.970  0.020  1.090
 2ED  C181  H34   single  0.970  0.020  1.090
 2ED  C191  H35   single  0.970  0.020  1.090
 2ED  C191  H36   single  0.970  0.020  1.090
 2ED  C20   H37   single  0.970  0.020  1.090
 2ED  C20   H38   single  0.970  0.020  1.090
 2ED  C20   H39   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
 2ED  HO3   O3    C     108.04  3.000
 2ED  HO1   O1    C2    108.71  3.000
 2ED  H1    C1    C     106.15  3.000
 2ED  H1    C1    N     108.04  3.000
 2ED  C     C1    N     110.03  3.000
 2ED  H1    C1    C2    107.01  3.000
 2ED  C     C1    C2    114.33  3.000
 2ED  N     C1    C2    110.94  3.000
 2ED  H2    C2    C3    108.43  3.000
 2ED  H2    C2    C1    106.55  3.000
 2ED  C3    C2    C1    109.26  3.000
 2ED  H2    C2    O1    105.86  3.000
 2ED  C3    C2    O1    113.61  3.000
 2ED  C1    C2    O1    112.75  3.000
 2ED  H3    C3    C4    119.06  3.000
 2ED  H3    C3    C2    114.73  3.000
 2ED  C4    C3    C2    126.14  3.000
 2ED  H4    C4    C5    115.63  3.000
 2ED  H4    C4    C3    120.26  3.000
 2ED  C5    C4    C3    124.04  3.000
 2ED  H5A   C5    H5    106.74  3.000
 2ED  H5A   C5    C6    109.11  3.000
 2ED  H5    C5    C6    109.27  3.000
 2ED  H5A   C5    C4    110.13  3.000
 2ED  H5    C5    C4    109.91  3.000
 2ED  C6    C5    C4    111.56  3.000
 2ED  C10   C6    H6A   109.59  3.000
 2ED  C10   C6    H6    109.53  3.000
 2ED  H6A   C6    H6    106.14  3.000
 2ED  C10   C6    C5    113.22  3.000
 2ED  H6A   C6    C5    109.67  3.000
 2ED  H6    C6    C5    108.43  3.000
 2ED  N     C18   C19   115.00  3.000
 2ED  N     C18   O2    123.39  3.000
 2ED  C19   C18   O2    121.61  3.000
 2ED  H19B  C19   H19A  108.18  3.000
 2ED  H19B  C19   H19   107.31  3.000
 2ED  H19A  C19   H19   108.75  3.000
 2ED  H19B  C19   C18   108.84  3.000
 2ED  H19A  C19   C18   113.75  3.000
 2ED  H19   C19   C18   109.80  3.000
 2ED  HN    N     C18   118.27  3.000
 2ED  HN    N     C1    117.07  3.000
 2ED  C18   N     C1    124.56  3.000
 2ED  HA    C     H     106.99  3.000
 2ED  HA    C     C1    107.78  3.000
 2ED  H     C     C1    108.41  3.000
 2ED  HA    C     O3    111.13  3.000
 2ED  H     C     O3    111.83  3.000
 2ED  C1    C     O3    110.53  3.000
 2ED  H18   C10   H17   106.11  3.000
 2ED  H18   C10   C11   109.08  3.000
 2ED  H17   C10   C11   109.87  3.000
 2ED  H18   C10   C6    109.27  3.000
 2ED  H17   C10   C6    109.55  3.000
 2ED  C11   C10   C6    112.75  3.000
 2ED  H20   C11   H191  105.94  3.000
 2ED  H20   C11   C12   109.47  3.000
 2ED  H191  C11   C12   109.01  3.000
 2ED  H20   C11   C10   109.55  3.000
 2ED  H191  C11   C10   108.91  3.000
 2ED  C12   C11   C10   113.67  3.000
 2ED  H22   C12   H21   106.07  3.000
 2ED  H22   C12   C13   109.05  3.000
 2ED  H21   C12   C13   109.75  3.000
 2ED  H22   C12   C11   109.28  3.000
 2ED  H21   C12   C11   109.62  3.000
 2ED  C13   C12   C11   112.85  3.000
 2ED  H24   C13   H23   105.95  3.000
 2ED  H24   C13   C14   109.44  3.000
 2ED  H23   C13   C14   109.08  3.000
 2ED  H24   C13   C12   109.51  3.000
 2ED  H23   C13   C12   108.86  3.000
 2ED  C14   C13   C12   113.71  3.000
 2ED  H26   C14   H25   106.02  3.000
 2ED  H26   C14   C15   109.08  3.000
 2ED  H25   C14   C15   109.60  3.000
 2ED  H26   C14   C13   109.32  3.000
 2ED  H25   C14   C13   109.62  3.000
 2ED  C15   C14   C13   112.95  3.000
 2ED  H28   C15   H27   105.95  3.000
 2ED  H28   C15   C16   109.40  3.000
 2ED  H27   C15   C16   109.21  3.000
 2ED  H28   C15   C14   109.45  3.000
 2ED  H27   C15   C14   108.96  3.000
 2ED  C16   C15   C14   113.58  3.000
 2ED  H30   C16   H29   105.99  3.000
 2ED  H30   C16   C17   109.15  3.000
 2ED  H29   C16   C17   109.46  3.000
 2ED  H30   C16   C15   109.35  3.000
 2ED  H29   C16   C15   109.53  3.000
 2ED  C17   C16   C15   113.12  3.000
 2ED  H32   C17   H31   105.96  3.000
 2ED  H32   C17   C181  109.38  3.000
 2ED  H31   C17   C181  109.32  3.000
 2ED  H32   C17   C16   109.40  3.000
 2ED  H31   C17   C16   109.09  3.000
 2ED  C181  C17   C16   113.42  3.000
 2ED  H34   C181  H33   105.95  3.000
 2ED  H34   C181  C191  109.18  3.000
 2ED  H33   C181  C191  109.28  3.000
 2ED  H34   C181  C17   109.39  3.000
 2ED  H33   C181  C17   109.46  3.000
 2ED  C191  C181  C17   113.31  3.000
 2ED  H36   C191  H35   105.98  3.000
 2ED  H36   C191  C20   109.54  3.000
 2ED  H35   C191  C20   109.68  3.000
 2ED  H36   C191  C181  109.30  3.000
 2ED  H35   C191  C181  109.19  3.000
 2ED  C20   C191  C181  112.91  3.000
 2ED  H39   C20   H38   107.49  3.000
 2ED  H39   C20   H37   107.63  3.000
 2ED  H38   C20   H37   107.55  3.000
 2ED  H39   C20   C191  111.24  3.000
 2ED  H38   C20   C191  111.09  3.000
 2ED  H37   C20   C191  111.64  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
 2ED  CONST_01  C1    N     C18   O2       0.00   0.0  0
 2ED  CONST_02  C19   C18   N     C1     180.00   0.0  0
 2ED  CONST_03  HN    N     C18   O2     180.00   0.0  0
 2ED  Var_01    C5    C4    C3    C2    -174.36   0.0  2
 2ED  Var_02    C6    C5    C4    C3     103.68  30.0  3
 2ED  Var_03    C10   C6    C5    C4     177.85  30.0  3
 2ED  Var_04    C11   C10   C6    C5     174.47  30.0  3
 2ED  Var_05    C12   C11   C10   C6    -179.34  30.0  3
 2ED  Var_06    C13   C12   C11   C10    174.11  30.0  3
 2ED  Var_07    C14   C13   C12   C11   -179.72  30.0  3
 2ED  Var_08    C15   C14   C13   C12    175.18  30.0  3
 2ED  Var_09    C16   C15   C14   C13   -179.96  30.0  3
 2ED  Var_10    C17   C16   C15   C14    176.82  30.0  3
 2ED  Var_11    C181  C17   C16   C15    179.84  30.0  3
 2ED  Var_12    C191  C181  C17   C16    178.25  30.0  3
 2ED  Var_13    C20   C191  C181  C17    179.65  30.0  3
 2ED  Var_14    H19   C19   C18   O2      50.73  30.0  3
 2ED  Var_15    H37   C20   C191  C181   179.81  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
 2ED  chir_01  C1  C2  N   C   positiv
 2ED  chir_02  C2  O1  C1  C3  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
 2ED  plan-1  O2   0.020
 2ED  plan-1  C1   0.020
 2ED  plan-1  C18  0.020
 2ED  plan-1  C19  0.020
 2ED  plan-1  N    0.020
 2ED  plan-1  HN   0.020
 2ED  plan-2  C2   0.020
 2ED  plan-2  C3   0.020
 2ED  plan-2  C4   0.020
 2ED  plan-2  C5   0.020
 2ED  plan-2  H3   0.020
 2ED  plan-2  H4   0.020

