# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 06:11:25 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: N-[3-(dimethylnitroryl)propyl]dodecanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC(=O)NCCC[N+](C)(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
 LDM  LDM  N-[3-(dimethylnitroryl)propyl]dodecanamide  ligand  57  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LDM
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
 LDM  N1    N  NT     1  -0.075   -8.1916  -0.4807   0.0348
 LDM  O1    O  O     -1  -0.689   -8.1486  -1.2321  -1.0887
 LDM  C1    C  CH2    0  -0.271   -7.0220   0.4574   0.0890
 LDM  C3    C  CH2    0  -0.230   -4.5655   0.7900  -0.0278
 LDM  C4    C  C      0   0.562   -2.1156   0.8077  -0.0676
 LDM  C5    C  CH2    0  -0.586   -0.8746  -0.0635  -0.0875
 LDM  C7    C  CH2    0  -0.416    1.6460  -0.1999  -0.0926
 LDM  C8    C  CH2    0  -0.413    2.9631   0.5654  -0.0863
 LDM  C10   C  CH2    0  -0.412    5.5028   0.4260  -0.0490
 LDM  C11   C  CH2    0  -0.412    6.7287  -0.4788  -0.0269
 LDM  C12   C  CH2    0  -0.412    8.0437   0.2903   0.0001
 LDM  CM1   C  CH3    0  -0.527   -8.2055  -1.3606   1.2333
 LDM  CM2   C  CH3    0  -0.517   -9.4317   0.3388   0.0419
 LDM  C2    C  CH2    0  -0.509   -5.6827  -0.2426  -0.0173
 LDM  C9    C  CH2    0  -0.412    4.1871  -0.3421  -0.0695
 LDM  N2    N  NH1    0  -0.649   -3.2777   0.1336  -0.0855
 LDM  C14   C  CH2    0  -0.419   10.5865   0.1519   0.0532
 LDM  C15   C  CH3    0  -0.663   11.8012  -0.7660   0.0800
 LDM  O2    O  O      0  -0.504   -2.0749   2.0303  -0.0322
 LDM  C6    C  CH2    0  -0.410    0.4290   0.7178  -0.0978
 LDM  C13   C  CH2    0  -0.406    9.2695  -0.6145   0.0252
 LDM  H1C1  H  HCH2   0   0.250   -7.0838   1.0345   1.0145
 LDM  H1C2  H  HCH2   0   0.265   -7.1539   1.1474  -0.7455
 LDM  H3C1  H  HCH2   0   0.232   -4.6252   1.4141   0.8685
 LDM  H3C2  H  HCH2   0   0.234   -4.6856   1.4585  -0.8852
 LDM  H5C1  H  HCH2   0   0.262   -0.9246  -0.7242  -0.9594
 LDM  H5C2  H  HCH2   0   0.262   -0.9059  -0.7263   0.7841
 LDM  H7C1  H  HCH2   0   0.210    1.6116  -0.8592  -0.9671
 LDM  H7C2  H  HCH2   0   0.210    1.6036  -0.8568   0.7836
 LDM  H8C1  H  HCH2   0   0.207    2.9927   1.2283   0.7858
 LDM  H8C2  H  HCH2   0   0.208    3.0080   1.2192  -0.9646
 LDM  H101  H  HCH2   0   0.206    5.5240   1.0851   0.8263
 LDM  H102  H  HCH2   0   0.206    5.5536   1.0841  -0.9239
 LDM  H111  H  HCH2   0   0.206    6.7105  -1.1365  -0.9033
 LDM  H112  H  HCH2   0   0.206    6.6761  -1.1384   0.8468
 LDM  H121  H  HCH2   0   0.206    8.0610   0.9491   0.8758
 LDM  H122  H  HCH2   0   0.206    8.0975   0.9490  -0.8742
 LDM  HM11  H  HCH3   0   0.244   -8.1987  -0.7757   2.1519
 LDM  HM12  H  HCH3   0   0.267   -9.1062  -1.9671   1.1908
 LDM  HM13  H  HCH3   0   0.269   -7.3362  -2.0097   1.2026
 LDM  HM21  H  HCH3   0   0.264   -9.4282   0.9682  -0.8441
 LDM  HM22  H  HCH3   0   0.265  -10.2835  -0.3353   0.0068
 LDM  HM23  H  HCH3   0   0.244   -9.4912   0.9592   0.9351
 LDM  H2C1  H  HCH2   0   0.252   -5.6555  -0.8385  -0.9300
 LDM  H2C2  H  HCH2   0   0.248   -5.5330  -0.9194   0.8277
 LDM  H9C1  H  HCH2   0   0.207    4.1632  -1.0005  -0.9452
 LDM  H9C2  H  HCH2   0   0.206    4.1375  -1.0005   0.8052
 LDM  H2    H  HNH1   0   0.400   -3.2552  -0.8732  -0.1036
 LDM  H141  H  HCH2   0   0.210   10.6039   0.8101   0.9277
 LDM  H142  H  HCH2   0   0.210   10.6411   0.8088  -0.8207
 LDM  H151  H  HCH3   0   0.225   12.7341  -0.2012   0.0965
 LDM  H152  H  HCH3   0   0.215   11.7878  -1.4079   0.9628
 LDM  H153  H  HCH3   0   0.216   11.8230  -1.4142  -0.7982
 LDM  H6C1  H  HCH2   0   0.219    0.4729   1.3783   0.7722
 LDM  H6C2  H  HCH2   0   0.219    0.4683   1.3658  -0.9776
 LDM  H131  H  HCH2   0   0.206    9.2525  -1.2730  -0.8509
 LDM  H132  H  HCH2   0   0.205    9.2157  -1.2738   0.8991

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
 LDM  N1   O1    single  1.352  0.020  1.352
 LDM  N1   C1    single  1.500  0.020  1.500
 LDM  N1   CM1   single  1.487  0.020  1.487
 LDM  N1   CM2   single  1.486  0.020  1.486
 LDM  C1   C2    single  1.515  0.020  1.515
 LDM  C1   H1C1  single  0.970  0.020  1.090
 LDM  C1   H1C2  single  0.970  0.020  1.090
 LDM  C3   C2    single  1.521  0.020  1.521
 LDM  C3   N2    single  1.447  0.020  1.447
 LDM  C3   H3C1  single  0.970  0.020  1.090
 LDM  C3   H3C2  single  0.970  0.020  1.090
 LDM  C4   C5    single  1.516  0.020  1.516
 LDM  C4   N2    single  1.344  0.020  1.344
 LDM  C4   O2    double  1.224  0.020  1.224
 LDM  C5   C6    single  1.520  0.020  1.520
 LDM  C5   H5C1  single  0.970  0.020  1.090
 LDM  C5   H5C2  single  0.970  0.020  1.090
 LDM  C7   C8    single  1.523  0.020  1.523
 LDM  C7   C6    single  1.524  0.020  1.524
 LDM  C7   H7C1  single  0.970  0.020  1.090
 LDM  C7   H7C2  single  0.970  0.020  1.090
 LDM  C8   C9    single  1.524  0.020  1.524
 LDM  C8   H8C1  single  0.970  0.020  1.090
 LDM  C8   H8C2  single  0.970  0.020  1.090
 LDM  C10  C11   single  1.524  0.020  1.524
 LDM  C10  C9    single  1.524  0.020  1.524
 LDM  C10  H101  single  0.970  0.020  1.090
 LDM  C10  H102  single  0.970  0.020  1.090
 LDM  C11  C12   single  1.524  0.020  1.524
 LDM  C11  H111  single  0.970  0.020  1.090
 LDM  C11  H112  single  0.970  0.020  1.090
 LDM  C12  C13   single  1.524  0.020  1.524
 LDM  C12  H121  single  0.970  0.020  1.090
 LDM  C12  H122  single  0.970  0.020  1.090
 LDM  CM1  HM11  single  0.970  0.020  1.090
 LDM  CM1  HM12  single  0.970  0.020  1.090
 LDM  CM1  HM13  single  0.970  0.020  1.090
 LDM  CM2  HM21  single  0.970  0.020  1.090
 LDM  CM2  HM22  single  0.970  0.020  1.090
 LDM  CM2  HM23  single  0.970  0.020  1.090
 LDM  C2   H2C1  single  0.970  0.020  1.090
 LDM  C2   H2C2  single  0.970  0.020  1.090
 LDM  C9   H9C1  single  0.970  0.020  1.090
 LDM  C9   H9C2  single  0.970  0.020  1.090
 LDM  N2   H2    single  0.860  0.020  1.020
 LDM  C14  C15   single  1.523  0.020  1.523
 LDM  C14  C13   single  1.524  0.020  1.524
 LDM  C14  H141  single  0.970  0.020  1.090
 LDM  C14  H142  single  0.970  0.020  1.090
 LDM  C15  H151  single  0.970  0.020  1.090
 LDM  C15  H152  single  0.970  0.020  1.090
 LDM  C15  H153  single  0.970  0.020  1.090
 LDM  C6   H6C1  single  0.970  0.020  1.090
 LDM  C6   H6C2  single  0.970  0.020  1.090
 LDM  C13  H131  single  0.970  0.020  1.090
 LDM  C13  H132  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
 LDM  CM2   N1   CM1   108.34  3.000
 LDM  CM2   N1   C1    107.79  3.000
 LDM  CM1   N1   C1    110.38  3.000
 LDM  CM2   N1   O1    109.68  3.000
 LDM  CM1   N1   O1    109.95  3.000
 LDM  C1    N1   O1    110.65  3.000
 LDM  H1C2  C1   H1C1  107.89  3.000
 LDM  H1C2  C1   C2    110.21  3.000
 LDM  H1C1  C1   C2    110.70  3.000
 LDM  H1C2  C1   N1    105.88  3.000
 LDM  H1C1  C1   N1    108.47  3.000
 LDM  C2    C1   N1    113.44  3.000
 LDM  H3C2  C3   H3C1  106.72  3.000
 LDM  H3C2  C3   N2    110.11  3.000
 LDM  H3C1  C3   N2    109.89  3.000
 LDM  H3C2  C3   C2    109.85  3.000
 LDM  H3C1  C3   C2    109.97  3.000
 LDM  N2    C3   C2    110.25  3.000
 LDM  O2    C4   N2    122.03  3.000
 LDM  O2    C4   C5    123.17  3.000
 LDM  N2    C4   C5    114.80  3.000
 LDM  H5C2  C5   H5C1  105.49  3.000
 LDM  H5C2  C5   C6    109.94  3.000
 LDM  H5C1  C5   C6    110.11  3.000
 LDM  H5C2  C5   C4    108.29  3.000
 LDM  H5C1  C5   C4    108.64  3.000
 LDM  C6    C5   C4    114.00  3.000
 LDM  H7C2  C7   H7C1  106.04  3.000
 LDM  H7C2  C7   C6    109.44  3.000
 LDM  H7C1  C7   C6    109.54  3.000
 LDM  H7C2  C7   C8    109.35  3.000
 LDM  H7C1  C7   C8    109.43  3.000
 LDM  C6    C7   C8    112.82  3.000
 LDM  H8C2  C8   H8C1  106.01  3.000
 LDM  H8C2  C8   C9    109.35  3.000
 LDM  H8C1  C8   C9    109.26  3.000
 LDM  H8C2  C8   C7    109.38  3.000
 LDM  H8C1  C8   C7    109.30  3.000
 LDM  C9    C8   C7    113.29  3.000
 LDM  H102  C10  H101  105.99  3.000
 LDM  H102  C10  C9    109.39  3.000
 LDM  H101  C10  C9    109.31  3.000
 LDM  H102  C10  C11   109.32  3.000
 LDM  H101  C10  C11   109.26  3.000
 LDM  C9    C10  C11   113.31  3.000
 LDM  H112  C11  H111  105.99  3.000
 LDM  H112  C11  C12   109.34  3.000
 LDM  H111  C11  C12   109.36  3.000
 LDM  H112  C11  C10   109.29  3.000
 LDM  H111  C11  C10   109.35  3.000
 LDM  C12   C11  C10   113.26  3.000
 LDM  H122  C12  H121  105.99  3.000
 LDM  H122  C12  C13   109.30  3.000
 LDM  H121  C12  C13   109.33  3.000
 LDM  H122  C12  C11   109.37  3.000
 LDM  H121  C12  C11   109.34  3.000
 LDM  C13   C12  C11   113.25  3.000
 LDM  HM13  CM1  HM12  109.20  3.000
 LDM  HM13  CM1  HM11  109.88  3.000
 LDM  HM12  CM1  HM11  109.75  3.000
 LDM  HM13  CM1  N1    108.88  3.000
 LDM  HM12  CM1  N1    107.85  3.000
 LDM  HM11  CM1  N1    111.23  3.000
 LDM  HM23  CM2  HM22  109.69  3.000
 LDM  HM23  CM2  HM21  109.81  3.000
 LDM  HM22  CM2  HM21  109.60  3.000
 LDM  HM23  CM2  N1    111.31  3.000
 LDM  HM22  CM2  N1    108.17  3.000
 LDM  HM21  CM2  N1    108.22  3.000
 LDM  H2C2  C2   H2C1  107.78  3.000
 LDM  H2C2  C2   C3    108.97  3.000
 LDM  H2C1  C2   C3    110.29  3.000
 LDM  H2C2  C2   C1    110.67  3.000
 LDM  H2C1  C2   C1    109.47  3.000
 LDM  C3    C2   C1    109.64  3.000
 LDM  H9C2  C9   H9C1  106.01  3.000
 LDM  H9C2  C9   C10   109.34  3.000
 LDM  H9C1  C9   C10   109.42  3.000
 LDM  H9C2  C9   C8    109.29  3.000
 LDM  H9C1  C9   C8    109.36  3.000
 LDM  C10   C9   C8    113.18  3.000
 LDM  H2    N2   C4    118.84  3.000
 LDM  H2    N2   C3    118.31  3.000
 LDM  C4    N2   C3    122.81  3.000
 LDM  H142  C14  H141  106.03  3.000
 LDM  H142  C14  C13   109.28  3.000
 LDM  H141  C14  C13   109.32  3.000
 LDM  H142  C14  C15   109.63  3.000
 LDM  H141  C14  C15   109.62  3.000
 LDM  C13   C14  C15   112.74  3.000
 LDM  H153  C15  H152  107.55  3.000
 LDM  H153  C15  H151  107.61  3.000
 LDM  H152  C15  H151  107.62  3.000
 LDM  H153  C15  C14   111.08  3.000
 LDM  H152  C15  C14   111.03  3.000
 LDM  H151  C15  C14   111.74  3.000
 LDM  H6C2  C6   H6C1  106.31  3.000
 LDM  H6C2  C6   C7    109.32  3.000
 LDM  H6C1  C6   C7    109.21  3.000
 LDM  H6C2  C6   C5    109.93  3.000
 LDM  H6C1  C6   C5    109.85  3.000
 LDM  C7    C6   C5    112.04  3.000
 LDM  H132  C13  H131  105.97  3.000
 LDM  H132  C13  C14   109.28  3.000
 LDM  H131  C13  C14   109.28  3.000
 LDM  H132  C13  C12   109.32  3.000
 LDM  H131  C13  C12   109.34  3.000
 LDM  C14   C13  C12   113.38  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
 LDM  CONST_01  C5    C4   N2   C3    180.00   0.0  0
 LDM  CONST_02  O2    C4   N2   C3      0.00   0.0  0
 LDM  CONST_03  H2    N2   C4   C5      0.00   0.0  0
 LDM  Var_01    C3    C2   C1   N1    177.01  30.0  3
 LDM  Var_02    C2    C1   N1   O1    -55.74  30.0  3
 LDM  Var_03    N2    C3   C2   C1    178.16  30.0  1
 LDM  Var_04    C7    C6   C5   C4    178.98  30.0  3
 LDM  Var_05    C2    C3   N2   C4   -178.03  30.0  1
 LDM  Var_06    C8    C7   C6   C5   -179.33  30.0  1
 LDM  Var_07    C10   C9   C8   C7   -179.42  30.0  3
 LDM  Var_08    C11   C10  C9   C8    179.78  30.0  1
 LDM  Var_09    C13   C12  C11  C10   179.88  30.0  3
 LDM  Var_10    C14   C13  C12  C11  -179.95  30.0  3
 LDM  Var_11    C9    C10  C11  C12  -179.73  30.0  1
 LDM  Var_12    C15   C14  C13  C12   179.92  30.0  1
 LDM  Var_13    C6    C7   C8   C9    179.53  30.0  1
 LDM  Var_14    C6    C5   C4   N2    178.72  30.0  3
 LDM  Var_15    HM11  CM1  N1   O1    177.66  30.0  3
 LDM  Var_16    HM21  CM2  N1   O1    -58.98  30.0  3
 LDM  Var_17    H151  C15  C14  C13   179.81  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
 LDM  plan-1  C3  0.020
 LDM  plan-1  C4  0.020
 LDM  plan-1  C5  0.020
 LDM  plan-1  N2  0.020
 LDM  plan-1  O2  0.020
 LDM  plan-1  H2  0.020

