# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 08:55:04 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: [2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methyl-(3-oxidanyl-1,2-oxazol-4-yl)azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C[NH2+]c2conc2O)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
 OJQ  OJQ  '[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methyl-(3-oxidanyl-1,2-oxazol-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_OJQ
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
 OJQ  C3    C  CR6   0   0.282  -0.9653   2.4343   0.0620
 OJQ  C4    C  CR6   0   0.060  -0.3754   1.2024   0.3155
 OJQ  C5    C  CR6   0  -0.057   1.0162   1.1041   0.2671
 OJQ  C6    C  CR16  0  -0.122   1.7275   2.2574  -0.0271
 OJQ  C2    C  CR6   0   0.153  -0.1660   3.5449  -0.2339
 OJQ  N     N  NT2   1  -0.765  -2.1429  -0.3098  -0.5295
 OJQ  CA    C  CR5   0  -0.011  -3.0190  -1.4159  -0.2836
 OJQ  C     C  CR5   0   0.508  -4.2135  -1.4001   0.4817
 OJQ  O     O  OH1   0  -0.591  -4.6961  -0.3218   1.0607
 OJQ  CB    C  CR15  0   0.156  -2.8985  -2.6973  -0.6846
 OJQ  OG    O  O     0  -0.304  -3.9187  -3.3907  -0.2141
 OJQ  ND    N  N     0  -0.192  -4.7485  -2.5830   0.5198
 OJQ  C2A   C  CH3   0  -0.779  -0.7815   4.8801  -0.5172
 OJQ  C4A   C  CH2   0  -0.413  -1.2591   0.0371   0.6440
 OJQ  C5A   C  CH2   0  -0.219   1.6920  -0.2122   0.5331
 OJQ  N1    N  N     0  -0.398   1.1497   3.4287  -0.2685
 OJQ  O1    O  OH1   0  -0.631  -2.3094   2.4815   0.1071
 OJQ  O1P   O  OH1   0  -0.726   5.4077  -0.6078   0.2324
 OJQ  O2P   O  OH1   0  -0.736   3.7774  -1.5885  -1.5134
 OJQ  O3P   O  O     0  -0.703   3.7354  -2.5603   0.8022
 OJQ  O4P   O  O2    0  -0.590   3.0987  -0.0570   0.4267
 OJQ  P     P  P     0   1.458   4.0003  -1.3244   0.0449
 OJQ  H6    H  HCR6  0   0.269   2.8078   2.2450  -0.0761
 OJQ  H1    H  HNT2  0   0.489  -1.5646  -0.4996  -1.3520
 OJQ  H4    H  HOH1  0   0.503  -5.5230  -0.5089   1.5271
 OJQ  HB1   H  HCR5  0   0.348  -2.1648  -3.2137  -1.2856
 OJQ  H2A3  H  HCH3  0   0.264  -1.3856   5.2376   0.3199
 OJQ  H2A1  H  HCH3  0   0.276  -0.0006   5.6138  -0.7008
 OJQ  H2A2  H  HCH3  0   0.262  -1.4245   4.8526  -1.4005
 OJQ  H4A   H  HCH2  0   0.336  -0.7102  -0.8672   0.8893
 OJQ  H2    H  HCH2  0   0.346  -1.9214   0.2566   1.4802
 OJQ  H5A2  H  HCH2  0   0.278   1.4454  -0.5709   1.5358
 OJQ  H5A1  H  HCH2  0   0.256   1.3226  -0.9584  -0.1784
 OJQ  H3    H  HOH1  0   0.501  -2.6583   3.3415  -0.1569
 OJQ  H5    H  HOH1  0   0.507   6.1666  -1.2011   0.1460
 OJQ  H7    H  HOH1  0   0.498   3.9850  -0.8503  -2.1024
 OJQ  H12   H  HNT2  0   0.488  -2.6908   0.5203  -0.7877

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
 OJQ  O    C     single    1.316  0.020  1.316
 OJQ  C    ND    aromatic  1.299  0.020  1.299
 OJQ  C    CA    aromatic  1.419  0.020  1.419
 OJQ  ND   OG    aromatic  1.371  0.020  1.371
 OJQ  CA   N     single    1.432  0.020  1.432
 OJQ  CA   CB    aromatic  1.348  0.020  1.348
 OJQ  N    C4A   single    1.509  0.020  1.509
 OJQ  C2A  C2    single    1.497  0.020  1.497
 OJQ  OG   CB    aromatic  1.320  0.020  1.320
 OJQ  O1   C3    single    1.346  0.020  1.346
 OJQ  O3P  P     double    1.473  0.020  1.473
 OJQ  C2   C3    aromatic  1.400  0.020  1.400
 OJQ  C2   N1    aromatic  1.321  0.020  1.321
 OJQ  C3   C4    aromatic  1.389  0.020  1.389
 OJQ  N1   C6    aromatic  1.328  0.020  1.328
 OJQ  O4P  P     single    1.601  0.020  1.601
 OJQ  O4P  C5A   single    1.419  0.020  1.419
 OJQ  C4   C4A   single    1.499  0.020  1.499
 OJQ  C4   C5    aromatic  1.396  0.020  1.396
 OJQ  C6   C5    aromatic  1.386  0.020  1.386
 OJQ  C5   C5A   single    1.503  0.020  1.503
 OJQ  P    O1P   single    1.590  0.020  1.590
 OJQ  P    O2P   single    1.596  0.020  1.596
 OJQ  C6   H6    single    0.930  0.020  1.080
 OJQ  N    H1    single    0.890  0.020  1.040
 OJQ  O    H4    single    0.850  0.020  0.980
 OJQ  CB   HB1   single    0.930  0.020  1.080
 OJQ  C2A  H2A3  single    0.970  0.020  1.090
 OJQ  C2A  H2A1  single    0.970  0.020  1.090
 OJQ  C2A  H2A2  single    0.970  0.020  1.090
 OJQ  C4A  H4A   single    0.970  0.020  1.090
 OJQ  C4A  H2    single    0.970  0.020  1.090
 OJQ  C5A  H5A2  single    0.970  0.020  1.090
 OJQ  C5A  H5A1  single    0.970  0.020  1.090
 OJQ  O1   H3    single    0.850  0.020  0.980
 OJQ  O1P  H5    single    0.850  0.020  0.980
 OJQ  O2P  H7    single    0.850  0.020  0.980
 OJQ  N    H12   single    0.890  0.020  1.040

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
 OJQ  O1    C3   C2    123.34  3.000
 OJQ  C2    C3   C4    119.97  3.000
 OJQ  O1    C3   C4    116.69  3.000
 OJQ  C4A   C4   C5    122.73  3.000
 OJQ  C5    C4   C3    118.65  3.000
 OJQ  C4A   C4   C3    118.62  3.000
 OJQ  C5A   C5   C6    122.36  3.000
 OJQ  C5A   C5   C4    120.24  3.000
 OJQ  C6    C5   C4    117.40  3.000
 OJQ  H6    C6   N1    115.87  3.000
 OJQ  H6    C6   C5    120.83  3.000
 OJQ  N1    C6   C5    123.29  3.000
 OJQ  N1    C2   C2A   118.87  3.000
 OJQ  N1    C2   C3    120.29  3.000
 OJQ  C2A   C2   C3    120.84  3.000
 OJQ  H12   N    H1    104.43  3.000
 OJQ  H12   N    C4A   108.78  3.000
 OJQ  H1    N    C4A   109.67  3.000
 OJQ  H12   N    CA    109.93  3.000
 OJQ  H1    N    CA    109.90  3.000
 OJQ  C4A   N    CA    113.71  3.000
 OJQ  CB    CA   C     104.26  3.000
 OJQ  CB    CA   N     128.93  3.000
 OJQ  C     CA   N     126.80  3.000
 OJQ  ND    C    O     125.62  3.000
 OJQ  ND    C    CA    110.64  3.000
 OJQ  O     C    CA    123.74  3.000
 OJQ  H4    O    C     111.54  3.000
 OJQ  HB1   CB   OG    118.18  3.000
 OJQ  HB1   CB   CA    132.90  3.000
 OJQ  OG    CB   CA    108.92  3.000
 OJQ  ND    OG   CB    110.43  3.000
 OJQ  OG    ND   C     105.75  3.000
 OJQ  H2A2  C2A  H2A1  107.65  3.000
 OJQ  H2A2  C2A  H2A3  107.59  3.000
 OJQ  H2A1  C2A  H2A3  107.80  3.000
 OJQ  H2A2  C2A  C2    111.86  3.000
 OJQ  H2A1  C2A  C2    109.78  3.000
 OJQ  H2A3  C2A  C2    111.97  3.000
 OJQ  H2    C4A  H4A   107.56  3.000
 OJQ  H2    C4A  N     106.69  3.000
 OJQ  H4A   C4A  N     106.28  3.000
 OJQ  H2    C4A  C4    111.72  3.000
 OJQ  H4A   C4A  C4    113.51  3.000
 OJQ  N     C4A  C4    110.70  3.000
 OJQ  H5A1  C5A  H5A2  107.23  3.000
 OJQ  H5A1  C5A  O4P   111.11  3.000
 OJQ  H5A2  C5A  O4P   109.16  3.000
 OJQ  H5A1  C5A  C5    109.26  3.000
 OJQ  H5A2  C5A  C5    110.38  3.000
 OJQ  O4P   C5A  C5    109.67  3.000
 OJQ  C2    N1   C6    120.40  3.000
 OJQ  H3    O1   C3    112.53  3.000
 OJQ  H5    O1P  P     114.04  3.000
 OJQ  H7    O2P  P     116.00  3.000
 OJQ  P     O4P  C5A   119.30  3.000
 OJQ  O4P   P    O3P   116.11  3.000
 OJQ  O4P   P    O2P   106.57  3.000
 OJQ  O3P   P    O2P   109.75  3.000
 OJQ  O2P   P    O1P   108.25  3.000
 OJQ  O4P   P    O1P    96.52  3.000
 OJQ  O3P   P    O1P   118.45  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
 OJQ  CONST_01  C6    N1   C2   C3      0.00   0.0  0
 OJQ  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 OJQ  CONST_03  N1    C2   C3   C4      0.00   0.0  0
 OJQ  CONST_04  N1    C6   C5   C4      0.00   0.0  0
 OJQ  CONST_05  C2    C3   C4   C5      0.00   0.0  0
 OJQ  CONST_06  C2    N1   C6   C5      0.00   0.0  0
 OJQ  CONST_07  OG    ND   C    CA      0.00   0.0  0
 OJQ  CONST_08  ND    OG   CB   CA      0.00   0.0  0
 OJQ  CONST_09  CB    OG   ND   C       0.00   0.0  0
 OJQ  CONST_10  OG    CB   CA   C       0.00   0.0  0
 OJQ  CONST_11  ND    C    CA   CB      0.00   0.0  0
 OJQ  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 OJQ  CONST_13  C2A   C2   C3   C4    180.00   0.0  0
 OJQ  CONST_14  O1    C3   C4   C5    180.00   0.0  0
 OJQ  CONST_15  C2A   C2   N1   C6    180.00   0.0  0
 OJQ  CONST_16  C4A   C4   C5   C6    180.00   0.0  0
 OJQ  CONST_17  C4A   C4   C3   C2    180.00   0.0  0
 OJQ  CONST_18  ND    C    CA   N     180.00   0.0  0
 OJQ  CONST_19  OG    CB   CA   N     180.00   0.0  0
 OJQ  CONST_20  OG    ND   C    O     180.00   0.0  0
 OJQ  CONST_21  CB    CA   C    O     180.00   0.0  0
 OJQ  CONST_22  N1    C6   C5   C5A   180.00   0.0  0
 OJQ  CONST_23  O1    C3   C2   N1    180.00   0.0  0
 OJQ  CONST_24  H6    C6   C5   C4    180.00   0.0  0
 OJQ  CONST_25  HB1   CB   CA   C     180.00   0.0  0
 OJQ  Var_01    N     C4A  C4   C3     64.30  30.0  2
 OJQ  Var_02    CA    N    C4A  C4   -179.85  30.0  2
 OJQ  Var_03    O4P   C5A  C5   C4   -179.97  30.0  2
 OJQ  Var_04    C4A   N    CA   C      76.61  30.0  2
 OJQ  Var_05    H2A3  C2A  C2   C3     59.02  30.0  2
 OJQ  Var_06    O3P   P    O4P  C5A   -48.02  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
 OJQ  plan-1  N    0.020
 OJQ  plan-1  CA   0.020
 OJQ  plan-1  C    0.020
 OJQ  plan-1  O    0.020
 OJQ  plan-1  CB   0.020
 OJQ  plan-1  OG   0.020
 OJQ  plan-1  ND   0.020
 OJQ  plan-1  HB1  0.020
 OJQ  plan-2  C3   0.020
 OJQ  plan-2  C4   0.020
 OJQ  plan-2  C5   0.020
 OJQ  plan-2  C6   0.020
 OJQ  plan-2  C2   0.020
 OJQ  plan-2  C2A  0.020
 OJQ  plan-2  C4A  0.020
 OJQ  plan-2  C5A  0.020
 OJQ  plan-2  N1   0.020
 OJQ  plan-2  O1   0.020
 OJQ  plan-2  H6   0.020

