# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 15:40:35 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (4S,7R)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-(propanoyloxy)-3,5,9-trioxa-4-phosphadodecan-1-aminium 4-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)OC[C@H](CO[P](O)(=O)OCC[N+](C)(C)C)OC(=O)CC
#
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
 43Y  43Y  '(4S,7R)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-(propanoyloxy)-3,5,9-trioxa-4-phosphadodecan-1-aminium 4-oxide'  ligand  53  24  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_43Y
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
 43Y  C11  C  C     0   0.604   5.2751  -0.6231   0.2676
 43Y  O11  O  O     0  -0.448   5.7513  -1.6888  -0.0292
 43Y  O3   O  O2    0  -0.459   3.9632  -0.4218   0.3825
 43Y  C3   C  CH2   0  -0.169   3.1014  -1.5285   0.1407
 43Y  C2   C  CH1   0  -0.063   1.6855  -1.0236   0.3217
 43Y  C1   C  CH2   0  -0.189   0.6961  -2.1590   0.1557
 43Y  O3P  O  O2    0  -0.572  -0.6074  -1.7334   0.5594
 43Y  P    P  P     0   1.476  -1.7882  -1.4982  -0.4777
 43Y  O1P  O  O     0  -0.688  -1.6039  -0.4783  -1.5293
 43Y  O2P  O  OH1   0  -0.726  -2.1418  -2.9002  -1.1451
 43Y  O4P  O  O2    0  -0.573  -2.9134  -1.1679   0.6084
 43Y  C4   C  CH2   0  -0.215  -4.2480  -0.8853   0.1881
 43Y  C5   C  CH2   0  -0.345  -4.8180   0.3079   0.9126
 43Y  N    N  NT    1  -0.382  -4.3482   1.6760   0.4945
 43Y  C7   C  CH3   0  -0.561  -4.5453   1.8963  -0.9657
 43Y  C8   C  CH3   0  -0.550  -5.1763   2.6641   1.2461
 43Y  C6   C  CH3   0  -0.561  -2.9146   1.9086   0.8366
 43Y  O2   O  O2    0  -0.467   1.4518  -0.0367  -0.6801
 43Y  C31  C  C     0   0.614   0.8635   1.1210  -0.3703
 43Y  O31  O  O     0  -0.446   0.4739   1.4008   0.7338
 43Y  C32  C  CH2   0  -0.578   0.7716   2.0138  -1.5760
 43Y  C33  C  CH3   0  -0.664   0.2139   3.3901  -1.2640
 43Y  H2   H  HCH2  0   0.253   3.2533  -1.9248  -0.8665
 43Y  H3   H  HCH2  0   0.255   3.2947  -2.3307   0.8563
 43Y  H4   H  HCH1  0   0.276   1.5777  -0.5963   1.3220
 43Y  H5   H  HCH2  0   0.259   0.7045  -2.5312  -0.8721
 43Y  H6   H  HCH2  0   0.274   0.9732  -2.9860   0.8097
 43Y  H7   H  HOH1  0   0.503  -2.2771  -3.6419  -0.5385
 43Y  H8   H  HCH2  0   0.267  -4.3282  -0.7754  -0.8951
 43Y  H9   H  HCH2  0   0.299  -4.8772  -1.7322   0.4644
 43Y  H10  H  HCH2  0   0.318  -5.8960   0.2934   0.7512
 43Y  H11  H  HCH2  0   0.320  -4.6420   0.2263   1.9850
 43Y  H12  H  HCH3  0   0.302  -5.5778   1.6820  -1.2286
 43Y  H13  H  HCH3  0   0.303  -4.3194   2.9346  -1.1920
 43Y  H14  H  HCH3  0   0.290  -3.8751   1.2577  -1.5338
 43Y  H15  H  HCH3  0   0.298  -6.2237   2.5178   0.9977
 43Y  H16  H  HCH3  0   0.299  -5.0275   2.5161   2.3124
 43Y  H17  H  HCH3  0   0.299  -4.8694   3.6681   0.9683
 43Y  H18  H  HCH3  0   0.294  -2.6935   2.9611   0.6813
 43Y  H19  H  HCH3  0   0.300  -2.7464   1.6495   1.8778
 43Y  H20  H  HCH3  0   0.286  -2.2782   1.3152   0.1930
 43Y  H21  H  HCH2  0   0.271   1.7662   2.0906  -2.0229
 43Y  H22  H  HCH2  0   0.279   0.1519   1.5037  -2.3174
 43Y  H23  H  HCH3  0   0.241   0.1902   3.9956  -2.1688
 43Y  H24  H  HCH3  0   0.225  -0.8035   3.3349  -0.8792
 43Y  H25  H  HCH3  0   0.233   0.8227   3.9152  -0.5288
 43Y  C9   C  CH2   0  -0.573   6.0526   0.6300   0.5616
 43Y  C10  C  CH3   0  -0.663   7.5499   0.4632   0.3782
 43Y  H1   H  HCH2  0   0.275   5.6680   1.4307  -0.0758
 43Y  H26  H  HCH2  0   0.278   5.8207   0.9368   1.5857
 43Y  H27  H  HCH3  0   0.240   8.0587   1.3962   0.6165
 43Y  H28  H  HCH3  0   0.232   7.9511  -0.3091   1.0332
 43Y  H29  H  HCH3  0   0.232   7.8025   0.1995  -0.6480

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
 43Y  C6   N    single  1.492  0.020  1.492
 43Y  C8   N    single  1.492  0.020  1.492
 43Y  O1P  P    double  1.476  0.020  1.476
 43Y  N    C7   single  1.490  0.020  1.490
 43Y  N    C5   single  1.506  0.020  1.506
 43Y  O2P  P    single  1.593  0.020  1.593
 43Y  O4P  P    single  1.598  0.020  1.598
 43Y  O4P  C4   single  1.427  0.020  1.427
 43Y  P    O3P  single  1.589  0.020  1.589
 43Y  C4   C5   single  1.508  0.020  1.508
 43Y  O3P  C1   single  1.429  0.020  1.429
 43Y  C1   C2   single  1.515  0.020  1.515
 43Y  O2   C2   single  1.426  0.020  1.426
 43Y  O2   C31  single  1.335  0.020  1.335
 43Y  C2   C3   single  1.514  0.020  1.514
 43Y  C3   O3   single  1.423  0.020  1.423
 43Y  C32  C31  single  1.503  0.020  1.503
 43Y  C32  C33  single  1.517  0.020  1.517
 43Y  C31  O31  double  1.204  0.020  1.204
 43Y  O3   C11  single  1.332  0.020  1.332
 43Y  C11  O11  double  1.204  0.020  1.204
 43Y  C3   H2   single  0.970  0.020  1.090
 43Y  C3   H3   single  0.970  0.020  1.090
 43Y  C2   H4   single  0.970  0.020  1.090
 43Y  C1   H5   single  0.970  0.020  1.090
 43Y  C1   H6   single  0.970  0.020  1.090
 43Y  O2P  H7   single  0.850  0.020  0.980
 43Y  C4   H8   single  0.970  0.020  1.090
 43Y  C4   H9   single  0.970  0.020  1.090
 43Y  C5   H10  single  0.970  0.020  1.090
 43Y  C5   H11  single  0.970  0.020  1.090
 43Y  C7   H12  single  0.970  0.020  1.090
 43Y  C7   H13  single  0.970  0.020  1.090
 43Y  C7   H14  single  0.970  0.020  1.090
 43Y  C8   H15  single  0.970  0.020  1.090
 43Y  C8   H16  single  0.970  0.020  1.090
 43Y  C8   H17  single  0.970  0.020  1.090
 43Y  C6   H18  single  0.970  0.020  1.090
 43Y  C6   H19  single  0.970  0.020  1.090
 43Y  C6   H20  single  0.970  0.020  1.090
 43Y  C32  H21  single  0.970  0.020  1.090
 43Y  C32  H22  single  0.970  0.020  1.090
 43Y  C33  H23  single  0.970  0.020  1.090
 43Y  C33  H24  single  0.970  0.020  1.090
 43Y  C33  H25  single  0.970  0.020  1.090
 43Y  C11  C9   single  1.504  0.020  1.504
 43Y  C9   C10  single  1.518  0.020  1.518
 43Y  C9   H1   single  0.970  0.020  1.090
 43Y  C9   H26  single  0.970  0.020  1.090
 43Y  C10  H27  single  0.970  0.020  1.090
 43Y  C10  H28  single  0.970  0.020  1.090
 43Y  C10  H29  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
 43Y  C9   C11  O3   111.49  3.000
 43Y  C9   C11  O11  125.53  3.000
 43Y  O3   C11  O11  122.98  3.000
 43Y  C3   O3   C11  117.65  3.000
 43Y  H3   C3   H2   108.23  3.000
 43Y  H3   C3   C2   109.39  3.000
 43Y  H2   C3   C2   111.16  3.000
 43Y  H3   C3   O3   110.65  3.000
 43Y  H2   C3   O3   110.75  3.000
 43Y  C2   C3   O3   106.66  3.000
 43Y  H4   C2   O2   110.87  3.000
 43Y  H4   C2   C1   109.20  3.000
 43Y  O2   C2   C1   109.56  3.000
 43Y  H4   C2   C3   109.39  3.000
 43Y  O2   C2   C3   107.47  3.000
 43Y  C1   C2   C3   110.35  3.000
 43Y  H6   C1   H5   107.69  3.000
 43Y  H6   C1   O3P  106.75  3.000
 43Y  H5   C1   O3P  111.96  3.000
 43Y  H6   C1   C2   109.68  3.000
 43Y  H5   C1   C2   110.68  3.000
 43Y  O3P  C1   C2   109.96  3.000
 43Y  P    O3P  C1   122.50  3.000
 43Y  O4P  P    O2P  108.08  3.000
 43Y  O4P  P    O1P  115.41  3.000
 43Y  O2P  P    O1P  109.72  3.000
 43Y  O4P  P    O3P   96.33  3.000
 43Y  O2P  P    O3P  107.95  3.000
 43Y  O1P  P    O3P  118.32  3.000
 43Y  H7   O2P  P    116.31  3.000
 43Y  C4   O4P  P    119.93  3.000
 43Y  H9   C4   H8   106.69  3.000
 43Y  H9   C4   C5   105.94  3.000
 43Y  H8   C4   C5   111.68  3.000
 43Y  H9   C4   O4P  108.12  3.000
 43Y  H8   C4   O4P  112.38  3.000
 43Y  C5   C4   O4P  111.63  3.000
 43Y  H11  C5   H10  107.72  3.000
 43Y  H11  C5   N    106.91  3.000
 43Y  H10  C5   N    106.24  3.000
 43Y  H11  C5   C4   110.64  3.000
 43Y  H10  C5   C4   106.98  3.000
 43Y  N    C5   C4   117.88  3.000
 43Y  C6   N    C8   108.33  3.000
 43Y  C8   N    C7   108.80  3.000
 43Y  C6   N    C7   109.19  3.000
 43Y  C7   N    C5   111.42  3.000
 43Y  C8   N    C5   106.78  3.000
 43Y  C6   N    C5   112.20  3.000
 43Y  H14  C7   H13  108.95  3.000
 43Y  H14  C7   H12  110.11  3.000
 43Y  H13  C7   H12  109.61  3.000
 43Y  H14  C7   N    110.13  3.000
 43Y  H13  C7   N    108.54  3.000
 43Y  H12  C7   N    109.48  3.000
 43Y  H17  C8   H16  109.77  3.000
 43Y  H17  C8   H15  109.79  3.000
 43Y  H16  C8   H15  109.76  3.000
 43Y  H17  C8   N    109.06  3.000
 43Y  H16  C8   N    109.14  3.000
 43Y  H15  C8   N    109.31  3.000
 43Y  H20  C6   H19  110.38  3.000
 43Y  H20  C6   H18  109.05  3.000
 43Y  H19  C6   H18  109.66  3.000
 43Y  H20  C6   N    110.07  3.000
 43Y  H19  C6   N    109.35  3.000
 43Y  H18  C6   N    108.28  3.000
 43Y  C31  O2   C2   120.63  3.000
 43Y  C32  C31  O31  125.30  3.000
 43Y  O31  C31  O2   123.85  3.000
 43Y  C32  C31  O2   110.85  3.000
 43Y  H22  C32  H21  105.75  3.000
 43Y  H22  C32  C33  110.77  3.000
 43Y  H21  C32  C33  110.78  3.000
 43Y  H22  C32  C31  107.56  3.000
 43Y  H21  C32  C31  108.30  3.000
 43Y  C33  C32  C31  113.34  3.000
 43Y  H25  C33  H24  107.94  3.000
 43Y  H25  C33  H23  107.75  3.000
 43Y  H24  C33  H23  107.54  3.000
 43Y  H25  C33  C32  111.75  3.000
 43Y  H24  C33  C32  111.72  3.000
 43Y  H23  C33  C32  109.97  3.000
 43Y  H26  C9   H1   105.42  3.000
 43Y  H26  C9   C10  110.68  3.000
 43Y  H1   C9   C10  110.92  3.000
 43Y  H26  C9   C11  107.88  3.000
 43Y  H1   C9   C11  108.33  3.000
 43Y  C10  C9   C11  113.26  3.000
 43Y  H29  C10  H28  108.03  3.000
 43Y  H29  C10  H27  107.77  3.000
 43Y  H28  C10  H27  107.68  3.000
 43Y  H29  C10  C9   111.67  3.000
 43Y  H28  C10  C9   111.63  3.000
 43Y  H27  C10  C9   109.89  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
 43Y  Var_01  C2   C3   O3   C11  -179.36  30.0  1
 43Y  Var_02  C10  C9   C11  O11     3.12  30.0  3
 43Y  Var_03  C32  C31  O2   C2    177.95  30.0  3
 43Y  Var_04  O1P  P    O3P  C1    -60.62  30.0  1
 43Y  Var_05  C5   C4   O4P  P    -135.26  30.0  3
 43Y  Var_06  N    C5   C4   O4P    75.74  30.0  3
 43Y  Var_07  C6   N    C5   C4    -68.02  30.0  3
 43Y  Var_08  C33  C32  C31  O2   -175.32  30.0  1
 43Y  Var_09  H27  C10  C9   C11  -179.30  30.0  3
 43Y  Var_10  H5   C1   O3P  P     -14.15  30.0  3
 43Y  Var_11  H18  C6   N    C5   -169.60  30.0  3
 43Y  Var_12  H15  C8   N    C5    -59.75  30.0  3
 43Y  Var_13  H12  C7   N    C5     52.83  30.0  3
 43Y  Var_14  H23  C33  C32  C31   178.87  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
 43Y  chir_01  C2  C1   O2   C3   positiv
 43Y  chir_02  P   O2P  O4P  O3P  both

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
 43Y  plan-1  O2   0.020
 43Y  plan-1  C31  0.020
 43Y  plan-1  O31  0.020
 43Y  plan-1  C32  0.020
 43Y  plan-2  C11  0.020
 43Y  plan-2  O11  0.020
 43Y  plan-2  O3   0.020
 43Y  plan-2  C9   0.020

