# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 15:46:34 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: [4-[(~{Z})-[(2~{S},5~{S})-5-(azanyloxymethyl)-3,6-bis(oxidanylidene)piperazin-2-yl]methoxyiminomethyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(\C=N/OC[C@@H]2NC(=O)[C@H](CON)NC2=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
 LUH  LUH  '[4-[(~{Z})-[(2~{S},5~{S})-5-(azanyloxymethyl)-3,6-bis(oxidanylidene)piperazin-2-yl]methoxyiminomethyl]-6-methyl-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate'  ligand  49  29  .  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_LUH
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
 LUH  OAG  O  OH1   0  -0.728  -6.9157  -0.2269  -0.7646
 LUH  PBC  P  P     0   1.468  -5.9298   0.7064   0.0650
 LUH  OAH  O  OH1   0  -0.742  -5.6609   2.0309  -0.7847
 LUH  OAE  O  O     0  -0.706  -6.3071   1.0724   1.4411
 LUH  OAT  O  O2    0  -0.590  -4.6306  -0.2152  -0.0937
 LUH  CAK  C  CH2   0  -0.203  -3.4057   0.1934   0.4984
 LUH  CAX  C  CR6   0  -0.066  -2.3538  -0.8490   0.2468
 LUH  CAJ  C  CR16  0  -0.132  -2.6257  -2.0419  -0.3936
 LUH  NAO  N  N     0  -0.402  -1.7023  -2.9746  -0.6200
 LUH  CAW  C  CR6   0   0.143  -0.4567  -2.7755  -0.2343
 LUH  CAA  C  CH3   0  -0.722   0.5604  -3.8386  -0.5105
 LUH  CAY  C  CR6   0   0.270  -0.0761  -1.5926   0.4241
 LUH  OAF  O  OH1   0  -0.633   1.1979  -1.5101   0.8330
 LUH  CAZ  C  CR6   0   0.025  -1.0352  -0.6109   0.6687
 LUH  CAI  C  C1    0  -0.155  -0.7485   0.6232   1.4208
 LUH  NAN  N  N     0  -0.044   0.2133   1.4435   1.2974
 LUH  OAS  O  O2    0  -0.436   1.0739   1.1106   0.2881
 LUH  CAM  C  CH2   0  -0.138   2.2006   1.9761   0.2728
 LUH  CBB  C  CH1   0  -0.233   2.9467   1.7235  -1.0494
 LUH  CAV  C  C     0   0.525   4.3492   2.2678  -0.8714
 LUH  OAD  O  O     0  -0.480   4.5239   3.4729  -0.7871
 LUH  N    N  NH1   0  -0.622   5.3330   1.3676  -0.7880
 LUH  NAQ  N  NH1   0  -0.632   2.9218   0.3483  -1.4864
 LUH  C    C  C     0   0.540   3.8987  -0.5585  -1.3587
 LUH  O    O  O     0  -0.476   3.7842  -1.7203  -1.7089
 LUH  CA   C  CH1   0  -0.253   5.1980  -0.0723  -0.7475
 LUH  CB   C  CH2   0  -0.108   5.3430  -0.6468   0.6566
 LUH  OAR  O  O2    0  -0.429   4.1924  -0.2867   1.3774
 LUH  NAB  N  NH2   0  -0.531   4.2656  -0.7984   2.6886
 LUH  H1   H  HOH1  0   0.506  -7.8482   0.0154  -0.6857
 LUH  H2   H  HOH1  0   0.498  -5.4590   1.9062  -1.7221
 LUH  H3   H  HCH2  0   0.264  -3.0852   1.1535   0.0817
 LUH  H4   H  HCH2  0   0.264  -3.5424   0.3336   1.5755
 LUH  H5   H  HCR6  0   0.264  -3.6227  -2.2683  -0.7477
 LUH  H6   H  HCH3  0   0.251   1.4130  -3.4400  -1.0629
 LUH  H7   H  HCH3  0   0.249   0.9549  -4.2667   0.4128
 LUH  H8   H  HCH3  0   0.247   0.1103  -4.6395  -1.0929
 LUH  H9   H  HOH1  0   0.477   1.5182  -0.5978   0.7389
 LUH  H10  H  H     0   0.297  -1.4504   0.9142   2.1957
 LUH  H11  H  HCH2  0   0.267   1.8779   3.0169   0.3113
 LUH  H12  H  HCH2  0   0.251   2.8362   1.7717   1.1359
 LUH  H13  H  HCH1  0   0.318   2.4713   2.3160  -1.8331
 LUH  H14  H  HNH1  0   0.413   6.2651   1.7332  -0.6456
 LUH  H15  H  HNH1  0   0.410   2.0749   0.0310  -1.9373
 LUH  H16  H  HCH1  0   0.320   6.0041  -0.4960  -1.3500
 LUH  H17  H  HCH2  0   0.225   5.4485  -1.7343   0.5821
 LUH  H18  H  HCH2  0   0.233   6.2534  -0.2527   1.1227
 LUH  H19  H  HNH2  0   0.371   4.0122  -0.0147   3.2807
 LUH  H20  H  HNH2  0   0.363   3.4962  -1.4574   2.7568

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
 LUH  OAE  PBC  double    1.473  0.020  1.473
 LUH  OAH  PBC  single    1.596  0.020  1.596
 LUH  PBC  OAT  single    1.601  0.020  1.601
 LUH  PBC  OAG  single    1.591  0.020  1.591
 LUH  OAD  CAV  double    1.221  0.020  1.221
 LUH  OAT  CAK  single    1.421  0.020  1.421
 LUH  CAI  NAN  double    1.270  0.020  1.270
 LUH  CAI  CAZ  single    1.473  0.020  1.473
 LUH  NAN  OAS  single    1.367  0.020  1.367
 LUH  CAV  CBB  single    1.515  0.020  1.515
 LUH  CAV  N    single    1.336  0.020  1.336
 LUH  CBB  CAM  single    1.539  0.020  1.539
 LUH  CBB  NAQ  single    1.443  0.020  1.443
 LUH  OAF  CAY  single    1.341  0.020  1.341
 LUH  CAM  OAS  single    1.421  0.020  1.421
 LUH  CAZ  CAY  aromatic  1.394  0.020  1.394
 LUH  CAZ  CAX  aromatic  1.405  0.020  1.405
 LUH  CAK  CAX  single    1.502  0.020  1.502
 LUH  N    CA   single    1.447  0.020  1.447
 LUH  CAY  CAW  aromatic  1.406  0.020  1.406
 LUH  CAX  CAJ  aromatic  1.381  0.020  1.381
 LUH  NAQ  C    single    1.339  0.020  1.339
 LUH  CAW  CAA  single    1.497  0.020  1.497
 LUH  CAW  NAO  aromatic  1.319  0.020  1.319
 LUH  CAJ  NAO  aromatic  1.332  0.020  1.332
 LUH  CA   C    single    1.516  0.020  1.516
 LUH  CA   CB   single    1.524  0.020  1.524
 LUH  C    O    double    1.219  0.020  1.219
 LUH  NAB  OAR  single    1.409  0.020  1.409
 LUH  OAR  CB   single    1.405  0.020  1.405
 LUH  OAG  H1   single    0.850  0.020  0.980
 LUH  OAH  H2   single    0.850  0.020  0.980
 LUH  CAK  H3   single    0.970  0.020  1.090
 LUH  CAK  H4   single    0.970  0.020  1.090
 LUH  CAJ  H5   single    0.930  0.020  1.080
 LUH  CAA  H6   single    0.970  0.020  1.090
 LUH  CAA  H7   single    0.970  0.020  1.090
 LUH  CAA  H8   single    0.970  0.020  1.090
 LUH  OAF  H9   single    0.850  0.020  0.980
 LUH  CAI  H10  single    0.930  0.020  1.080
 LUH  CAM  H11  single    0.970  0.020  1.090
 LUH  CAM  H12  single    0.970  0.020  1.090
 LUH  CBB  H13  single    0.970  0.020  1.090
 LUH  N    H14  single    0.860  0.020  1.020
 LUH  NAQ  H15  single    0.860  0.020  1.020
 LUH  CA   H16  single    0.970  0.020  1.090
 LUH  CB   H17  single    0.970  0.020  1.090
 LUH  CB   H18  single    0.970  0.020  1.090
 LUH  NAB  H19  single    0.890  0.020  1.040
 LUH  NAB  H20  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
 LUH  H1   OAG  PBC  114.09  3.000
 LUH  OAT  PBC  OAE  116.33  3.000
 LUH  OAT  PBC  OAH  106.75  3.000
 LUH  OAE  PBC  OAH  109.53  3.000
 LUH  OAT  PBC  OAG   96.52  3.000
 LUH  OAH  PBC  OAG  108.27  3.000
 LUH  OAE  PBC  OAG  118.31  3.000
 LUH  H2   OAH  PBC  116.37  3.000
 LUH  CAK  OAT  PBC  119.53  3.000
 LUH  H4   CAK  H3   107.39  3.000
 LUH  H4   CAK  CAX  109.95  3.000
 LUH  H3   CAK  CAX  109.87  3.000
 LUH  H4   CAK  OAT  109.82  3.000
 LUH  H3   CAK  OAT  110.25  3.000
 LUH  CAX  CAK  OAT  109.53  3.000
 LUH  CAZ  CAX  CAJ  118.07  3.000
 LUH  CAJ  CAX  CAK  122.63  3.000
 LUH  CAZ  CAX  CAK  119.30  3.000
 LUH  H5   CAJ  NAO  115.89  3.000
 LUH  H5   CAJ  CAX  120.93  3.000
 LUH  NAO  CAJ  CAX  123.17  3.000
 LUH  CAW  NAO  CAJ  119.96  3.000
 LUH  CAY  CAW  CAA  119.99  3.000
 LUH  CAA  CAW  NAO  118.71  3.000
 LUH  CAY  CAW  NAO  121.29  3.000
 LUH  H8   CAA  H7   108.28  3.000
 LUH  H8   CAA  H6   108.74  3.000
 LUH  H7   CAA  H6   106.80  3.000
 LUH  H8   CAA  CAW  109.91  3.000
 LUH  H7   CAA  CAW  111.59  3.000
 LUH  H6   CAA  CAW  111.40  3.000
 LUH  CAZ  CAY  OAF  123.85  3.000
 LUH  CAZ  CAY  CAW  119.23  3.000
 LUH  OAF  CAY  CAW  116.86  3.000
 LUH  H9   OAF  CAY  109.97  3.000
 LUH  CAI  CAZ  CAY  123.06  3.000
 LUH  CAY  CAZ  CAX  118.28  3.000
 LUH  CAI  CAZ  CAX  118.55  3.000
 LUH  H10  CAI  NAN  112.71  3.000
 LUH  H10  CAI  CAZ  117.59  3.000
 LUH  NAN  CAI  CAZ  129.70  3.000
 LUH  OAS  NAN  CAI  113.02  3.000
 LUH  CAM  OAS  NAN  111.02  3.000
 LUH  H12  CAM  H11  108.86  3.000
 LUH  H12  CAM  CBB  111.49  3.000
 LUH  H11  CAM  CBB  109.30  3.000
 LUH  H12  CAM  OAS  109.83  3.000
 LUH  H11  CAM  OAS  110.27  3.000
 LUH  CBB  CAM  OAS  107.08  3.000
 LUH  H13  CBB  NAQ  107.00  3.000
 LUH  H13  CBB  CAV  107.01  3.000
 LUH  NAQ  CBB  CAV  113.20  3.000
 LUH  H13  CBB  CAM  108.46  3.000
 LUH  NAQ  CBB  CAM  114.09  3.000
 LUH  CAV  CBB  CAM  106.79  3.000
 LUH  N    CAV  OAD  123.74  3.000
 LUH  N    CAV  CBB  116.55  3.000
 LUH  OAD  CAV  CBB  119.69  3.000
 LUH  H14  N    CA   116.23  3.000
 LUH  H14  N    CAV  116.35  3.000
 LUH  CA   N    CAV  127.12  3.000
 LUH  H15  NAQ  C    116.20  3.000
 LUH  H15  NAQ  CBB  116.66  3.000
 LUH  C    NAQ  CBB  127.14  3.000
 LUH  CA   C    O    120.14  3.000
 LUH  O    C    NAQ  123.34  3.000
 LUH  CA   C    NAQ  116.52  3.000
 LUH  H16  CA   CB   106.96  3.000
 LUH  H16  CA   C    106.61  3.000
 LUH  CB   CA   C    109.39  3.000
 LUH  H16  CA   N    107.57  3.000
 LUH  CB   CA   N    113.08  3.000
 LUH  C    CA   N    112.83  3.000
 LUH  H18  CB   H17  107.81  3.000
 LUH  H18  CB   OAR  111.72  3.000
 LUH  H17  CB   OAR  111.62  3.000
 LUH  H18  CB   CA   109.59  3.000
 LUH  H17  CB   CA   108.72  3.000
 LUH  OAR  CB   CA   107.35  3.000
 LUH  NAB  OAR  CB   109.98  3.000
 LUH  H20  NAB  H19  105.84  3.000
 LUH  H20  NAB  OAR  105.00  3.000
 LUH  H19  NAB  OAR  104.45  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
 LUH  CONST_01  CAW  CAY  CAZ  CAX     0.00   0.0  0
 LUH  CONST_02  CAW  NAO  CAJ  CAX     0.00   0.0  0
 LUH  CONST_03  CAY  CAZ  CAX  CAJ     0.00   0.0  0
 LUH  CONST_04  CAY  CAW  NAO  CAJ     0.00   0.0  0
 LUH  CONST_05  CAZ  CAY  CAW  NAO     0.00   0.0  0
 LUH  CONST_06  CAZ  CAX  CAJ  NAO     0.00   0.0  0
 LUH  CONST_07  CA   N    CAV  CBB     0.00   0.0  0
 LUH  CONST_08  CA   C    NAQ  CBB     0.00   0.0  0
 LUH  CONST_09  CAY  CAZ  CAX  CAK   180.00   0.0  0
 LUH  CONST_10  NAO  CAJ  CAX  CAK   180.00   0.0  0
 LUH  CONST_11  OAF  CAY  CAZ  CAX   180.00   0.0  0
 LUH  CONST_12  CAI  CAZ  CAX  CAJ   180.00   0.0  0
 LUH  CONST_13  CAA  CAW  NAO  CAJ   180.00   0.0  0
 LUH  CONST_14  OAF  CAY  CAW  NAO   180.00   0.0  0
 LUH  CONST_15  CAI  CAZ  CAY  CAW   180.00   0.0  0
 LUH  CONST_16  CAZ  CAY  CAW  CAA   180.00   0.0  0
 LUH  CONST_17  O    C    NAQ  CBB   180.00   0.0  0
 LUH  CONST_18  CA   N    CAV  OAD   180.00   0.0  0
 LUH  CONST_19  H5   CAJ  NAO  CAW   180.00   0.0  0
 LUH  CONST_20  H14  N    CAV  CBB   180.00   0.0  0
 LUH  CONST_21  H15  NAQ  C    CA    180.00   0.0  0
 LUH  CONST_22  OAS  NAN  CAI  CAZ     0.00   0.0  0
 LUH  CONST_23  H10  CAI  NAN  OAS   180.00   0.0  0
 LUH  Var_01    CAZ  CAX  CAK  OAT   175.82  30.0  2
 LUH  Var_02    NAN  CAI  CAZ  CAX  -135.96  30.0  1
 LUH  Var_03    H6   CAA  CAW  NAO   125.10  30.0  2
 LUH  Var_04    CAX  CAK  OAT  PBC   178.34  30.0  3
 LUH  Var_05    CBB  CAM  OAS  NAN  -168.30  30.0  1
 LUH  Var_06    H19  NAB  OAR  CB    132.68  30.0  3
 LUH  Var_07    H17  CB   OAR  NAB    60.65  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
 LUH  chir_01  CBB  CAV  CAM  NAQ  positiv
 LUH  chir_02  CA   N    C    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
 LUH  plan-1  CAK  0.020
 LUH  plan-1  CAX  0.020
 LUH  plan-1  CAJ  0.020
 LUH  plan-1  NAO  0.020
 LUH  plan-1  CAW  0.020
 LUH  plan-1  CAA  0.020
 LUH  plan-1  CAY  0.020
 LUH  plan-1  OAF  0.020
 LUH  plan-1  CAZ  0.020
 LUH  plan-1  CAI  0.020
 LUH  plan-1  H5   0.020
 LUH  plan-2  CBB  0.020
 LUH  plan-2  CAV  0.020
 LUH  plan-2  OAD  0.020
 LUH  plan-2  N    0.020
 LUH  plan-2  CA   0.020
 LUH  plan-2  H14  0.020
 LUH  plan-3  CBB  0.020
 LUH  plan-3  NAQ  0.020
 LUH  plan-3  C    0.020
 LUH  plan-3  O    0.020
 LUH  plan-3  CA   0.020
 LUH  plan-3  H15  0.020
 LUH  plan-4  CAZ  0.020
 LUH  plan-4  CAI  0.020
 LUH  plan-4  NAN  0.020
 LUH  plan-4  OAS  0.020
 LUH  plan-4  H10  0.020

