# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 04:30:27 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N-{8-[(2R,6S)-2,6-dimethylmorpholin-4-yl]octyl}formamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN(CCCCCCCCNC=O)C[C@H](C)O1
#
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
 MF2  MF2  N-{8-[(2R,6S)-2,6-dimethylmorpholin-4-yl]octyl}formamide  ligand  49  19  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MF2
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
 MF2  C2    C  CH2   0  -0.283   1.0029  -0.4374   3.9473
 MF2  C3    C  CH1   0   0.037   1.5274   0.2236   5.2125
 MF2  O4    O  O2    0  -0.497   0.5924   0.0931   6.2663
 MF2  C7    C  CH3   0  -0.686  -1.5964   0.4220   7.1216
 MF2  C8    C  CH3   0  -0.687   2.8371  -0.3837   5.6703
 MF2  C10   C  CH2   0  -0.437  -0.0975   0.1231   1.1041
 MF2  C11   C  CH2   0  -0.416  -0.6708  -0.4374  -0.1911
 MF2  C12   C  CH2   0  -0.413  -0.0291   0.1665  -1.4334
 MF2  C13   C  CH2   0  -0.413  -0.5993  -0.3831  -2.7342
 MF2  C14   C  CH2   0  -0.417   0.0325   0.2411  -3.9717
 MF2  C15   C  CH2   0  -0.472  -0.5488  -0.2990  -5.2712
 MF2  C16   C  CH2   0  -0.236   0.0828   0.3508  -6.4911
 MF2  N1    N  NT    0  -0.437  -0.2869   0.1129   3.5794
 MF2  C5    C  CH1   0   0.035  -0.6787   0.6174   5.9334
 MF2  C6    C  CH2   0  -0.277  -1.2187  -0.0495   4.6775
 MF2  N17   N  NH1   0  -0.595  -0.4953  -0.1736  -7.7127
 MF2  C18   C  C1    0   0.249  -0.0510   0.1386  -8.9308
 MF2  O19   O  O     0  -0.503   0.8893   0.8817  -9.1646
 MF2  H21   H  HCH2  0   0.187   0.9478  -1.5308   4.1041
 MF2  H22   H  HCH2  0   0.238   1.7234  -0.2663   3.1444
 MF2  H3    H  HCH1  0   0.197   1.6807   1.2920   4.9928
 MF2  H71   H  HCH3  0   0.239  -1.2074   0.9260   8.0070
 MF2  H72   H  HCH3  0   0.230  -2.5805   0.8398   6.9082
 MF2  H73   H  HCH3  0   0.226  -1.7224  -0.6361   7.3571
 MF2  H81   H  HCH3  0   0.239   3.2140   0.1229   6.5590
 MF2  H82   H  HCH3  0   0.226   2.7234  -1.4442   5.9014
 MF2  H83   H  HCH3  0   0.231   3.5905  -0.2875   4.8884
 MF2  H91   H  HCH2  0   0.187  -0.7408  -1.5389   2.3275
 MF2  H92   H  HCH2  0   0.225  -1.8592  -0.1869   2.2688
 MF2  H101  H  HCH2  0   0.214  -0.1967   1.2130   1.1104
 MF2  H102  H  HCH2  0   0.218   0.9755  -0.0886   1.1397
 MF2  H111  H  HCH2  0   0.212  -0.5447  -1.5255  -0.2078
 MF2  H112  H  HCH2  0   0.210  -1.7514  -0.2583  -0.2200
 MF2  H121  H  HCH2  0   0.209  -0.1583   1.2543  -1.4128
 MF2  H122  H  HCH2  0   0.210   1.0519  -0.0089  -1.4066
 MF2  H131  H  HCH2  0   0.211  -0.4609  -1.4694  -2.7635
 MF2  H132  H  HCH2  0   0.210  -1.6817  -0.2154  -2.7562
 MF2  H141  H  HCH2  0   0.215  -0.1008   1.3277  -3.9371
 MF2  H142  H  HCH2  0   0.216   1.1136   0.0674  -3.9549
 MF2  H151  H  HCH2  0   0.230  -0.4022  -1.3826  -5.3180
 MF2  H152  H  HCH2  0   0.229  -1.6303  -0.1280  -5.2851
 MF2  H161  H  HCH2  0   0.232  -0.0561   1.4354  -6.4464
 MF2  H162  H  HCH2  0   0.234   1.1609   0.1708  -6.4912
 MF2  H5    H  HCH1  0   0.197  -0.5835   1.6945   5.7232
 MF2  H61   H  HCH2  0   0.186  -1.4289  -1.1133   4.8919
 MF2  H62   H  HCH2  0   0.236  -2.1697   0.4206   4.4137
 MF2  HNH   H  HNH1  0   0.406  -1.2949  -0.7829  -7.6458
 MF2  H18   H  H     0   0.203  -0.6293  -0.3556  -9.7264
 MF2  C9    C  CH2   0  -0.253  -0.7960  -0.4360   2.3357

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
 MF2  C2   C3    single  1.521  0.020  1.521
 MF2  C2   N1    single  1.450  0.020  1.450
 MF2  C2   H21   single  0.970  0.020  1.090
 MF2  C2   H22   single  0.970  0.020  1.090
 MF2  C3   O4    single  1.415  0.020  1.415
 MF2  C3   C8    single  1.515  0.020  1.515
 MF2  C3   H3    single  0.970  0.020  1.090
 MF2  O4   C5    single  1.415  0.020  1.415
 MF2  C7   C5    single  1.514  0.020  1.514
 MF2  C7   H71   single  0.970  0.020  1.090
 MF2  C7   H72   single  0.970  0.020  1.090
 MF2  C7   H73   single  0.970  0.020  1.090
 MF2  C8   H81   single  0.970  0.020  1.090
 MF2  C8   H82   single  0.970  0.020  1.090
 MF2  C8   H83   single  0.970  0.020  1.090
 MF2  C9   C10   single  1.522  0.020  1.522
 MF2  C9   N1    single  1.452  0.020  1.452
 MF2  C9   H91   single  0.970  0.020  1.090
 MF2  C9   H92   single  0.970  0.020  1.090
 MF2  C10  C11   single  1.523  0.020  1.523
 MF2  C10  H101  single  0.970  0.020  1.090
 MF2  C10  H102  single  0.970  0.020  1.090
 MF2  C11  C12   single  1.523  0.020  1.523
 MF2  C11  H111  single  0.970  0.020  1.090
 MF2  C11  H112  single  0.970  0.020  1.090
 MF2  C12  C13   single  1.523  0.020  1.523
 MF2  C12  H121  single  0.970  0.020  1.090
 MF2  C12  H122  single  0.970  0.020  1.090
 MF2  C13  C14   single  1.523  0.020  1.523
 MF2  C13  H131  single  0.970  0.020  1.090
 MF2  C13  H132  single  0.970  0.020  1.090
 MF2  C14  C15   single  1.523  0.020  1.523
 MF2  C14  H141  single  0.970  0.020  1.090
 MF2  C14  H142  single  0.970  0.020  1.090
 MF2  C15  C16   single  1.520  0.020  1.520
 MF2  C15  H151  single  0.970  0.020  1.090
 MF2  C15  H152  single  0.970  0.020  1.090
 MF2  C16  N17   single  1.450  0.020  1.450
 MF2  C16  H161  single  0.970  0.020  1.090
 MF2  C16  H162  single  0.970  0.020  1.090
 MF2  N1   C6    single  1.449  0.020  1.449
 MF2  C5   C6    single  1.521  0.020  1.521
 MF2  C5   H5    single  0.970  0.020  1.090
 MF2  C6   H61   single  0.970  0.020  1.090
 MF2  C6   H62   single  0.970  0.020  1.090
 MF2  N17  C18   single  1.334  0.020  1.334
 MF2  N17  HNH   single  0.860  0.020  1.020
 MF2  C18  O19   double  1.221  0.020  1.221
 MF2  C18  H18   single  0.930  0.020  1.080

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
 MF2  H22   C2   H21   106.97  3.000
 MF2  H22   C2   N1    109.93  3.000
 MF2  H21   C2   N1    111.52  3.000
 MF2  H22   C2   C3    108.42  3.000
 MF2  H21   C2   C3    109.20  3.000
 MF2  N1    C2   C3    110.67  3.000
 MF2  H3    C3   C8    109.20  3.000
 MF2  H3    C3   O4    109.27  3.000
 MF2  C8    C3   O4    108.02  3.000
 MF2  H3    C3   C2    107.67  3.000
 MF2  C8    C3   C2    112.05  3.000
 MF2  O4    C3   C2    110.59  3.000
 MF2  C5    O4   C3    112.60  3.000
 MF2  H73   C7   H72   108.03  3.000
 MF2  H73   C7   H71   108.31  3.000
 MF2  H72   C7   H71   107.69  3.000
 MF2  H73   C7   C5    111.37  3.000
 MF2  H72   C7   C5    110.12  3.000
 MF2  H71   C7   C5    111.18  3.000
 MF2  H83   C8   H82   108.04  3.000
 MF2  H83   C8   H81   107.75  3.000
 MF2  H82   C8   H81   108.36  3.000
 MF2  H83   C8   C3    110.21  3.000
 MF2  H82   C8   C3    111.31  3.000
 MF2  H81   C8   C3    111.04  3.000
 MF2  H102  C10  H101  106.34  3.000
 MF2  H102  C10  C11   109.00  3.000
 MF2  H101  C10  C11   109.71  3.000
 MF2  H102  C10  C9    110.65  3.000
 MF2  H101  C10  C9    108.63  3.000
 MF2  C11   C10  C9    112.34  3.000
 MF2  H112  C11  H111  105.99  3.000
 MF2  H112  C11  C12   109.22  3.000
 MF2  H111  C11  C12   109.45  3.000
 MF2  H112  C11  C10   109.48  3.000
 MF2  H111  C11  C10   109.57  3.000
 MF2  C12   C11  C10   112.90  3.000
 MF2  H122  C12  H121  105.96  3.000
 MF2  H122  C12  C13   109.42  3.000
 MF2  H121  C12  C13   109.28  3.000
 MF2  H122  C12  C11   109.41  3.000
 MF2  H121  C12  C11   109.19  3.000
 MF2  C13   C12  C11   113.32  3.000
 MF2  H132  C13  H131  106.02  3.000
 MF2  H132  C13  C14   109.31  3.000
 MF2  H131  C13  C14   109.40  3.000
 MF2  H132  C13  C12   109.38  3.000
 MF2  H131  C13  C12   109.48  3.000
 MF2  C14   C13  C12   113.00  3.000
 MF2  H142  C14  H141  106.08  3.000
 MF2  H142  C14  C15   109.50  3.000
 MF2  H141  C14  C15   109.42  3.000
 MF2  H142  C14  C13   109.39  3.000
 MF2  H141  C14  C13   109.29  3.000
 MF2  C15   C14  C13   112.93  3.000
 MF2  H152  C15  H151  106.64  3.000
 MF2  H152  C15  C16   109.48  3.000
 MF2  H151  C15  C16   109.47  3.000
 MF2  H152  C15  C14   109.42  3.000
 MF2  H151  C15  C14   109.67  3.000
 MF2  C16   C15  C14   112.01  3.000
 MF2  H162  C16  H161  106.76  3.000
 MF2  H162  C16  N17   109.49  3.000
 MF2  H161  C16  N17   110.02  3.000
 MF2  H162  C16  C15   109.85  3.000
 MF2  H161  C16  C15   109.77  3.000
 MF2  N17   C16  C15   110.85  3.000
 MF2  C6    N1   C9    112.41  3.000
 MF2  C6    N1   C2    109.71  3.000
 MF2  C9    N1   C2    112.70  3.000
 MF2  H5    C5   C6    107.57  3.000
 MF2  H5    C5   C7    109.17  3.000
 MF2  C6    C5   C7    112.10  3.000
 MF2  H5    C5   O4    109.24  3.000
 MF2  C6    C5   O4    110.54  3.000
 MF2  C7    C5   O4    108.18  3.000
 MF2  H62   C6   H61   107.16  3.000
 MF2  H62   C6   C5    108.64  3.000
 MF2  H61   C6   C5    109.23  3.000
 MF2  H62   C6   N1    109.17  3.000
 MF2  H61   C6   N1    112.15  3.000
 MF2  C5    C6   N1    110.38  3.000
 MF2  HNH   N17  C18   117.81  3.000
 MF2  HNH   N17  C16   118.64  3.000
 MF2  C18   N17  C16   123.51  3.000
 MF2  H18   C18  O19   122.64  3.000
 MF2  H18   C18  N17   112.34  3.000
 MF2  O19   C18  N17   125.02  3.000
 MF2  H92   C9   H91   106.00  3.000
 MF2  H92   C9   N1    107.89  3.000
 MF2  H91   C9   N1    111.50  3.000
 MF2  H92   C9   C10   108.23  3.000
 MF2  H91   C9   C10   109.74  3.000
 MF2  N1    C9   C10   113.16  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
 MF2  CONST_01  O19  C18  N17  C16     0.00   0.0  0
 MF2  CONST_02  HNH  N17  C18  O19   180.00   0.0  0
 MF2  Var_01    C5   C6   N1   C2     57.33  30.0  1
 MF2  Var_02    C6   N1   C2   C3    -57.06  30.0  1
 MF2  Var_03    C10  C9   N1   C2    -75.29  30.0  1
 MF2  Var_04    N1   C9   C10  C11  -178.48  30.0  1
 MF2  Var_05    C12  C11  C10  C9    177.08  30.0  3
 MF2  Var_06    C13  C12  C11  C10  -179.77  30.0  3
 MF2  Var_07    C14  C13  C12  C11   179.12  30.0  3
 MF2  Var_08    C15  C14  C13  C12  -179.40  30.0  3
 MF2  Var_09    C16  C15  C14  C13   179.24  30.0  3
 MF2  Var_10    N17  C16  C15  C14  -179.57  30.0  3
 MF2  Var_11    C18  N17  C16  C15  -174.24  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
 MF2  chir_01  C3  C2  O4  C8  negativ
 MF2  chir_02  C5  O4  C7  C6  positiv

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
 MF2  plan-1  C16  0.020
 MF2  plan-1  N17  0.020
 MF2  plan-1  C18  0.020
 MF2  plan-1  O19  0.020
 MF2  plan-1  HNH  0.020
 MF2  plan-1  H18  0.020

