# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 01:00:38 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylidene-[(4~{R})-3-oxidanylidene-1,2-oxazolidin-4-yl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=[NH+][C@@H]2CONC2=O)c1O
#
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
 L7N  L7N  (~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylidene-[(4~{R})-3-oxidanylidene-1,2-oxazolidin-4-yl]azanium  ligand  37  22  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L7N
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
 L7N  C3    C  CR6   0   0.350  -0.8781   2.2538  -0.2343
 L7N  C4    C  CR6   0   0.015  -0.3275   0.9746  -0.0932
 L7N  C5    C  CR6   0  -0.040   1.0649   0.8611   0.1216
 L7N  C6    C  CR16  0  -0.118   1.7939   2.0282   0.1842
 L7N  C2    C  CR6   0   0.155  -0.0431   3.3833  -0.1408
 L7N  N     N  NC1   1  -0.510  -2.3847  -0.2970  -0.3893
 L7N  CA    C  CH1   0  -0.334  -3.1230  -1.5304  -0.3532
 L7N  C     C  C     0   0.575  -3.8256  -1.6956   1.0041
 L7N  O     O  O     0  -0.434  -3.3429  -1.4712   2.0903
 L7N  CB    C  CH2   0  -0.144  -4.3016  -1.5722  -1.3143
 L7N  OG    O  O2    0  -0.373  -5.2482  -2.3893  -0.6352
 L7N  ND    N  NH1   0  -0.355  -5.0656  -2.0909   0.7046
 L7N  C2A   C  CH3   0  -0.787  -0.6135   4.7605  -0.2699
 L7N  C4A   C  C1    0   0.149  -1.1220  -0.2218  -0.1553
 L7N  C5A   C  CH2   0  -0.229   1.7122  -0.4877   0.2719
 L7N  N1    N  N     0  -0.378   1.2467   3.2389   0.0605
 L7N  O1    O  OH1   0  -0.619  -2.1846   2.3561  -0.4517
 L7N  O1P   O  OH1   0  -0.724   5.4134  -0.8355   0.7079
 L7N  O2P   O  OH1   0  -0.735   4.2454  -1.3689  -1.5331
 L7N  O3P   O  O     0  -0.701   3.7367  -2.8502   0.4313
 L7N  O4P   O  O2    0  -0.591   3.0988  -0.3221   0.5070
 L7N  P     P  P     0   1.457   4.1150  -1.4777   0.0531
 L7N  H6    H  HCR6  0   0.282   2.8628   2.0100   0.3409
 L7N  HA    H  HCH1  0   0.360  -2.4336  -2.3660  -0.4947
 L7N  HB2   H  HCH2  0   0.263  -4.7051  -0.5670  -1.4814
 L7N  HB1   H  HCH2  0   0.296  -4.0798  -2.0424  -2.2681
 L7N  H3    H  HNH1  0   0.443  -5.7373  -2.5235   1.3243
 L7N  H2A2  H  HCH3  0   0.271  -1.3788   4.9586   0.4842
 L7N  H2A1  H  HCH3  0   0.285   0.1762   5.4956  -0.1398
 L7N  H2A3  H  HCH3  0   0.271  -1.0612   4.9243  -1.2532
 L7N  H4A   H  H     0   0.345  -0.6309  -1.1749  -0.0029
 L7N  H5A2  H  HCH2  0   0.284   1.2704  -1.0278   1.1136
 L7N  H5A1  H  HCH2  0   0.271   1.5292  -1.0787  -0.6316
 L7N  H2    H  HOH1  0   0.517  -2.4848   3.2700  -0.5477
 L7N  H4    H  HOH1  0   0.508   6.2033  -1.3904   0.6496
 L7N  H5    H  HOH1  0   0.499   4.5464  -0.5172  -1.8783
 L7N  H1    H  HNC1  0   0.472  -2.9125   0.5621  -0.5335

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
 L7N  O    C     double    1.210  0.020  1.210
 L7N  ND   C     single    1.335  0.020  1.335
 L7N  ND   OG    single    1.385  0.020  1.385
 L7N  C    CA    single    1.537  0.020  1.537
 L7N  C2A  C2    single    1.496  0.020  1.496
 L7N  OG   CB    single    1.423  0.020  1.423
 L7N  O1   C3    single    1.328  0.020  1.328
 L7N  O3P  P     double    1.473  0.020  1.473
 L7N  N    CA    single    1.438  0.020  1.438
 L7N  N    C4A   double    1.286  0.020  1.286
 L7N  C2   C3    aromatic  1.408  0.020  1.408
 L7N  C2   N1    aromatic  1.313  0.020  1.313
 L7N  CA   CB    single    1.521  0.020  1.521
 L7N  C3   C4    aromatic  1.400  0.020  1.400
 L7N  N1   C6    aromatic  1.334  0.020  1.334
 L7N  O4P  P     single    1.604  0.020  1.604
 L7N  O4P  C5A   single    1.416  0.020  1.416
 L7N  C4   C4A   single    1.438  0.020  1.438
 L7N  C4   C5    aromatic  1.413  0.020  1.413
 L7N  C6   C5    aromatic  1.377  0.020  1.377
 L7N  P    O2P   single    1.595  0.020  1.595
 L7N  P    O1P   single    1.590  0.020  1.590
 L7N  C5   C5A   single    1.504  0.020  1.504
 L7N  C6   H6    single    0.930  0.020  1.080
 L7N  CA   HA    single    0.970  0.020  1.090
 L7N  CB   HB2   single    0.970  0.020  1.090
 L7N  CB   HB1   single    0.970  0.020  1.090
 L7N  ND   H3    single    0.890  0.020  1.040
 L7N  C2A  H2A2  single    0.970  0.020  1.090
 L7N  C2A  H2A1  single    0.970  0.020  1.090
 L7N  C2A  H2A3  single    0.970  0.020  1.090
 L7N  C4A  H4A   single    0.930  0.020  1.080
 L7N  C5A  H5A2  single    0.970  0.020  1.090
 L7N  C5A  H5A1  single    0.970  0.020  1.090
 L7N  O1   H2    single    0.850  0.020  0.980
 L7N  O1P  H4    single    0.850  0.020  0.980
 L7N  O2P  H5    single    0.850  0.020  0.980
 L7N  N    H1    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
 L7N  O1    C3   C2    122.17  3.000
 L7N  C2    C3   C4    119.55  3.000
 L7N  O1    C3   C4    118.27  3.000
 L7N  C4A   C4   C5    118.96  3.000
 L7N  C5    C4   C3    118.43  3.000
 L7N  C4A   C4   C3    122.60  3.000
 L7N  C5A   C5   C6    121.85  3.000
 L7N  C5A   C5   C4    120.75  3.000
 L7N  C6    C5   C4    117.40  3.000
 L7N  H6    C6   N1    115.75  3.000
 L7N  H6    C6   C5    121.05  3.000
 L7N  N1    C6   C5    123.20  3.000
 L7N  N1    C2   C2A   119.26  3.000
 L7N  N1    C2   C3    120.30  3.000
 L7N  C2A   C2   C3    120.44  3.000
 L7N  H1    N    C4A   119.02  3.000
 L7N  H1    N    CA    117.45  3.000
 L7N  C4A   N    CA    123.34  3.000
 L7N  HA    CA   CB    112.71  3.000
 L7N  HA    CA   C     108.70  3.000
 L7N  CB    CA   C     101.58  3.000
 L7N  HA    CA   N     109.19  3.000
 L7N  CB    CA   N     113.92  3.000
 L7N  C     CA   N     110.43  3.000
 L7N  ND    C    O     128.82  3.000
 L7N  ND    C    CA    104.96  3.000
 L7N  O     C    CA    126.19  3.000
 L7N  HB1   CB   HB2   109.77  3.000
 L7N  HB1   CB   OG    107.84  3.000
 L7N  HB2   CB   OG    110.77  3.000
 L7N  HB1   CB   CA    114.10  3.000
 L7N  HB2   CB   CA    110.87  3.000
 L7N  OG    CB   CA    103.28  3.000
 L7N  ND    OG   CB    104.49  3.000
 L7N  H3    ND   OG    114.40  3.000
 L7N  H3    ND   C     127.30  3.000
 L7N  OG    ND   C     113.78  3.000
 L7N  H2A3  C2A  H2A1  107.70  3.000
 L7N  H2A3  C2A  H2A2  107.88  3.000
 L7N  H2A1  C2A  H2A2  107.68  3.000
 L7N  H2A3  C2A  C2    111.82  3.000
 L7N  H2A1  C2A  C2    109.59  3.000
 L7N  H2A2  C2A  C2    111.99  3.000
 L7N  H4A   C4A  N     114.79  3.000
 L7N  H4A   C4A  C4    118.40  3.000
 L7N  N     C4A  C4    126.81  3.000
 L7N  H5A1  C5A  H5A2  107.52  3.000
 L7N  H5A1  C5A  O4P   111.33  3.000
 L7N  H5A2  C5A  O4P   109.00  3.000
 L7N  H5A1  C5A  C5    109.25  3.000
 L7N  H5A2  C5A  C5    110.25  3.000
 L7N  O4P   C5A  C5    109.46  3.000
 L7N  C2    N1   C6    121.11  3.000
 L7N  H2    O1   C3    113.24  3.000
 L7N  H4    O1P  P     114.24  3.000
 L7N  H5    O2P  P     116.14  3.000
 L7N  P     O4P  C5A   119.27  3.000
 L7N  O4P   P    O3P   115.84  3.000
 L7N  O4P   P    O2P   106.49  3.000
 L7N  O3P   P    O2P   109.87  3.000
 L7N  O2P   P    O1P   108.38  3.000
 L7N  O4P   P    O1P    96.30  3.000
 L7N  O3P   P    O1P   118.71  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
 L7N  CONST_01  C6    N1   C2   C3      0.00   0.0  0
 L7N  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 L7N  CONST_03  N1    C2   C3   C4      0.00   0.0  0
 L7N  CONST_04  N1    C6   C5   C4      0.00   0.0  0
 L7N  CONST_05  C2    C3   C4   C5      0.00   0.0  0
 L7N  CONST_06  C2    N1   C6   C5      0.00   0.0  0
 L7N  CONST_07  OG    ND   C    CA      0.00   0.0  0
 L7N  CONST_08  C5A   C5   C4   C3    180.00   0.0  0
 L7N  CONST_09  C2A   C2   C3   C4    180.00   0.0  0
 L7N  CONST_10  O1    C3   C4   C5    180.00   0.0  0
 L7N  CONST_11  C2A   C2   N1   C6    180.00   0.0  0
 L7N  CONST_12  C4A   C4   C5   C6    180.00   0.0  0
 L7N  CONST_13  C4A   C4   C3   C2    180.00   0.0  0
 L7N  CONST_14  N1    C6   C5   C5A   180.00   0.0  0
 L7N  CONST_15  O1    C3   C2   N1    180.00   0.0  0
 L7N  CONST_16  OG    ND   C    O     180.00   0.0  0
 L7N  CONST_17  H6    C6   C5   C4    180.00   0.0  0
 L7N  CONST_19  CA    N    C4A  C4    180.00   0.0  0
 L7N  CONST_20  H1    N    C4A  C4      0.00   0.0  0
 L7N  CONST_21  H4A   C4A  N    CA      0.00   0.0  0
 L7N  Var_01    HB2   CB   OG   ND    -84.27  30.0  1
 L7N  Var_02    N     C4A  C4   C3      2.77  30.0  2
 L7N  Var_03    O4P   C5A  C5   C4   -178.64  30.0  2
 L7N  Var_04    H2A2  C2A  C2   C3     58.82  30.0  2
 L7N  Var_05    O3P   P    O4P  C5A   -47.45  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
 L7N  chir_01  CA  C  N  CB  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
 L7N  plan-1  C3   0.020
 L7N  plan-1  C4   0.020
 L7N  plan-1  C5   0.020
 L7N  plan-1  C6   0.020
 L7N  plan-1  C2   0.020
 L7N  plan-1  C2A  0.020
 L7N  plan-1  C4A  0.020
 L7N  plan-1  C5A  0.020
 L7N  plan-1  N1   0.020
 L7N  plan-1  O1   0.020
 L7N  plan-1  H6   0.020
 L7N  plan-2  CA   0.020
 L7N  plan-2  C    0.020
 L7N  plan-2  O    0.020
 L7N  plan-2  OG   0.020
 L7N  plan-2  ND   0.020
 L7N  plan-2  H3   0.020
 L7N  plan-3  C4   0.020
 L7N  plan-3  N    0.020
 L7N  plan-3  CA   0.020
 L7N  plan-3  C4A  0.020
 L7N  plan-3  H4A  0.020
 L7N  plan-3  H1   0.020

