# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 21:03:19 2020
#   Inital geometry file: a 170 line input string
#   Ligand name: (4S,7R)-7-(heptanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphahexadecan-1-aminium 4-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC(=O)OC[C@H](CO[P@](O)(=O)OCC[N+](C)(C)C)OC(=O)CCCCCC
#
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
 XP5  XP5  '(4S,7R)-7-(heptanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphahexadecan-1-aminium 4-oxide'  ligand  76  32  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XP5
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
 XP5  O1    O  O      0  -0.781  -1.6905  -1.0228  -1.6923
 XP5  O2    O  OP    -1  -0.776   0.9066  -1.0939  -1.8215
 XP5  P1    P  P      0   1.400  -0.3608  -0.3485  -1.5366
 XP5  O3    O  O2     0  -0.598  -0.2910   0.3089  -0.0214
 XP5  C1    C  CH2    0  -0.187  -0.5126  -0.5521   1.0678
 XP5  C2    C  CH2    0  -0.355  -1.9897  -0.4569   1.4359
 XP5  N1    N  NT     1  -0.382  -2.4119  -1.2397   2.6453
 XP5  C3    C  CH3    0  -0.557  -1.6340  -0.8333   3.8493
 XP5  C4    C  CH3    0  -0.553  -3.8532  -0.9522   2.8900
 XP5  C5    C  CH3    0  -0.552  -2.2482  -2.7017   2.4144
 XP5  O4    O  O2     0  -0.605  -0.4185   1.0485  -2.3788
 XP5  C6    C  CH2    0  -0.211   0.6802   1.5576  -3.1021
 XP5  C8    C  CH2    0  -0.234   0.9421   3.7651  -1.8100
 XP5  O5    O  O2     0  -0.452  -0.1328   3.5418  -0.9027
 XP5  C9    C  C      0   0.625  -1.3837   3.5595  -1.3536
 XP5  O6    O  O      0  -0.464  -1.6873   3.8511  -2.4838
 XP5  C10   C  CH2    0  -0.567  -2.3777   3.2288  -0.2733
 XP5  C11   C  CH2    0  -0.446  -3.4607   2.2676  -0.7512
 XP5  C12   C  CH2    0  -0.423  -4.5648   2.0732   0.2816
 XP5  C13   C  CH2    0  -0.417  -5.5057   0.9333  -0.0843
 XP5  C14   C  CH2    0  -0.428  -6.6465   0.7419   0.9078
 XP5  C15   C  CH3    0  -0.662  -7.5236  -0.4560   0.5733
 XP5  O7    O  O      0  -0.461   3.7327   0.8363  -2.3198
 XP5  O8    O  O2     0  -0.463   2.0981   1.8071  -1.1433
 XP5  C18   C  CH2    0  -0.584   3.4335   0.2559  -0.0034
 XP5  C19   C  CH2    0  -0.417   4.8099  -0.3895   0.0206
 XP5  C20   C  CH2    0  -0.414   5.0645  -1.1435   1.3198
 XP5  C21   C  CH2    0  -0.406   6.4410  -1.7944   1.3667
 XP5  C22   C  CH2    0  -0.418   6.7041  -2.5543   2.6611
 XP5  C23   C  CH3    0  -0.662   8.0818  -3.2012   2.7003
 XP5  CAM   C  CH1    0  -0.004   1.5803   2.4783  -2.2922
 XP5  H11C  H  HCH2   0   0.229  -0.2262  -1.5853   0.8456
 XP5  H12C  H  HCH2   0   0.251   0.1230  -0.2137   1.8878
 XP5  H21C  H  HCH2   0   0.292  -2.2476   0.5837   1.6337
 XP5  H22C  H  HCH2   0   0.305  -2.5894  -0.8112   0.5980
 XP5  H31C  H  HCH3   0   0.298  -1.6925   0.2463   3.9621
 XP5  H32C  H  HCH3   0   0.303  -2.0634  -1.3174   4.7221
 XP5  H33C  H  HCH3   0   0.298  -0.5991  -1.1423   3.7434
 XP5  H41C  H  HCH3   0   0.289  -4.4237  -1.1983   1.9977
 XP5  H42C  H  HCH3   0   0.306  -4.2002  -1.5557   3.7240
 XP5  H43C  H  HCH3   0   0.294  -3.9712   0.1019   3.1272
 XP5  H51C  H  HCH3   0   0.296  -1.2004  -2.9355   2.2567
 XP5  H52C  H  HCH3   0   0.300  -2.6080  -3.2373   3.2888
 XP5  H53C  H  HCH3   0   0.296  -2.8281  -2.9913   1.5421
 XP5  H61C  H  HCH2   0   0.241   1.2806   0.7494  -3.5236
 XP5  H62C  H  HCH2   0   0.241   0.2823   2.1344  -3.9402
 XP5  HAM   H  HCH1   0   0.258   2.3972   2.7843  -2.9551
 XP5  H81C  H  HCH2   0   0.249   0.6226   4.3480  -2.6744
 XP5  H82C  H  HCH2   0   0.265   1.6809   4.3530  -1.2644
 XP5  H101  H  HCH2   0   0.252  -1.8613   2.8213   0.5960
 XP5  H102  H  HCH2   0   0.267  -2.8351   4.1728   0.0434
 XP5  H111  H  HCH2   0   0.229  -3.9017   2.6392  -1.6793
 XP5  H112  H  HCH2   0   0.243  -3.0061   1.3030  -0.9912
 XP5  H121  H  HCH2   0   0.202  -4.1265   1.8731   1.2663
 XP5  H122  H  HCH2   0   0.223  -5.1308   3.0037   0.3944
 XP5  H131  H  HCH2   0   0.219  -5.9193   1.1055  -1.0837
 XP5  H132  H  HCH2   0   0.203  -4.9285   0.0036  -0.1600
 XP5  H141  H  HCH2   0   0.208  -6.2368   0.6230   1.9164
 XP5  H142  H  HCH2   0   0.221  -7.2553   1.6502   0.9381
 XP5  H151  H  HCH3   0   0.215  -6.9417  -1.3803   0.5650
 XP5  H152  H  HCH3   0   0.228  -8.3286  -0.5796   1.2985
 XP5  H153  H  HCH3   0   0.219  -7.9794  -0.3494  -0.4127
 XP5  H181  H  HCH2   0   0.255   3.3081   0.9434   0.8369
 XP5  H182  H  HCH2   0   0.281   2.6547  -0.5049   0.1076
 XP5  H191  H  HCH2   0   0.222   4.9093  -1.0787  -0.8218
 XP5  H192  H  HCH2   0   0.221   5.5806   0.3757  -0.1116
 XP5  H201  H  HCH2   0   0.210   4.9579  -0.4576   2.1672
 XP5  H202  H  HCH2   0   0.210   4.2943  -1.9116   1.4502
 XP5  H211  H  HCH2   0   0.207   6.5485  -2.4792   0.5181
 XP5  H212  H  HCH2   0   0.207   7.2106  -1.0254   1.2363
 XP5  H221  H  HCH2   0   0.210   6.5979  -1.8708   3.5092
 XP5  H222  H  HCH2   0   0.210   5.9356  -3.3225   2.7918
 XP5  H231  H  HCH3   0   0.216   8.2052  -3.9211   1.8889
 XP5  H232  H  HCH3   0   0.216   8.8718  -2.4546   2.5993
 XP5  H233  H  HCH3   0   0.225   8.2474  -3.7318   3.6388
 XP5  C17   C  C      0   0.622   3.1276   0.9762  -1.2857

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
 XP5  O1   P1    deloc   1.499  0.020  1.499
 XP5  O2   P1    deloc   1.498  0.020  1.498
 XP5  P1   O3    single  1.653  0.020  1.653
 XP5  P1   O4    single  1.632  0.020  1.632
 XP5  O3   C1    single  1.406  0.020  1.406
 XP5  C1   C2    single  1.525  0.020  1.525
 XP5  C2   N1    single  1.501  0.020  1.501
 XP5  N1   C3    single  1.490  0.020  1.490
 XP5  N1   C4    single  1.490  0.020  1.490
 XP5  N1   C5    single  1.489  0.020  1.489
 XP5  O4   C6    single  1.411  0.020  1.411
 XP5  C6   CAM   single  1.521  0.020  1.521
 XP5  C8   O5    single  1.424  0.020  1.424
 XP5  C8   CAM   single  1.515  0.020  1.515
 XP5  O5   C9    single  1.330  0.020  1.330
 XP5  C9   O6    double  1.206  0.020  1.206
 XP5  C9   C10   single  1.505  0.020  1.505
 XP5  C10  C11   single  1.525  0.020  1.525
 XP5  C11  C12   single  1.524  0.020  1.524
 XP5  C12  C13   single  1.523  0.020  1.523
 XP5  C13  C14   single  1.524  0.020  1.524
 XP5  C14  C15   single  1.522  0.020  1.522
 XP5  O7   C17   double  1.206  0.020  1.206
 XP5  C17  O8    single  1.331  0.020  1.331
 XP5  C17  C18   single  1.502  0.020  1.502
 XP5  O8   CAM   single  1.428  0.020  1.428
 XP5  C18  C19   single  1.520  0.020  1.520
 XP5  C19  C20   single  1.524  0.020  1.524
 XP5  C20  C21   single  1.523  0.020  1.523
 XP5  C21  C22   single  1.524  0.020  1.524
 XP5  C22  C23   single  1.523  0.020  1.523
 XP5  C1   H11C  single  0.970  0.020  1.090
 XP5  C1   H12C  single  0.970  0.020  1.090
 XP5  C2   H21C  single  0.970  0.020  1.090
 XP5  C2   H22C  single  0.970  0.020  1.090
 XP5  C3   H31C  single  0.970  0.020  1.090
 XP5  C3   H32C  single  0.970  0.020  1.090
 XP5  C3   H33C  single  0.970  0.020  1.090
 XP5  C4   H41C  single  0.970  0.020  1.090
 XP5  C4   H42C  single  0.970  0.020  1.090
 XP5  C4   H43C  single  0.970  0.020  1.090
 XP5  C5   H51C  single  0.970  0.020  1.090
 XP5  C5   H52C  single  0.970  0.020  1.090
 XP5  C5   H53C  single  0.970  0.020  1.090
 XP5  C6   H61C  single  0.970  0.020  1.090
 XP5  C6   H62C  single  0.970  0.020  1.090
 XP5  CAM  HAM   single  0.970  0.020  1.090
 XP5  C8   H81C  single  0.970  0.020  1.090
 XP5  C8   H82C  single  0.970  0.020  1.090
 XP5  C10  H101  single  0.970  0.020  1.090
 XP5  C10  H102  single  0.970  0.020  1.090
 XP5  C11  H111  single  0.970  0.020  1.090
 XP5  C11  H112  single  0.970  0.020  1.090
 XP5  C12  H121  single  0.970  0.020  1.090
 XP5  C12  H122  single  0.970  0.020  1.090
 XP5  C13  H131  single  0.970  0.020  1.090
 XP5  C13  H132  single  0.970  0.020  1.090
 XP5  C14  H141  single  0.970  0.020  1.090
 XP5  C14  H142  single  0.970  0.020  1.090
 XP5  C15  H151  single  0.970  0.020  1.090
 XP5  C15  H152  single  0.970  0.020  1.090
 XP5  C15  H153  single  0.970  0.020  1.090
 XP5  C18  H181  single  0.970  0.020  1.090
 XP5  C18  H182  single  0.970  0.020  1.090
 XP5  C19  H191  single  0.970  0.020  1.090
 XP5  C19  H192  single  0.970  0.020  1.090
 XP5  C20  H201  single  0.970  0.020  1.090
 XP5  C20  H202  single  0.970  0.020  1.090
 XP5  C21  H211  single  0.970  0.020  1.090
 XP5  C21  H212  single  0.970  0.020  1.090
 XP5  C22  H221  single  0.970  0.020  1.090
 XP5  C22  H222  single  0.970  0.020  1.090
 XP5  C23  H231  single  0.970  0.020  1.090
 XP5  C23  H232  single  0.970  0.020  1.090
 XP5  C23  H233  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
 XP5  O4    P1   O3     97.70  3.000
 XP5  O4    P1   O2    110.97  3.000
 XP5  O3    P1   O2    109.67  3.000
 XP5  O4    P1   O1    107.46  3.000
 XP5  O3    P1   O1    108.15  3.000
 XP5  O2    P1   O1    120.46  3.000
 XP5  C1    O3   P1    117.38  3.000
 XP5  H12C  C1   H11C  107.02  3.000
 XP5  H12C  C1   C2    111.31  3.000
 XP5  H11C  C1   C2    111.17  3.000
 XP5  H12C  C1   O3    107.48  3.000
 XP5  H11C  C1   O3    112.30  3.000
 XP5  C2    C1   O3    107.54  3.000
 XP5  H22C  C2   H21C  108.65  3.000
 XP5  H22C  C2   N1    107.17  3.000
 XP5  H21C  C2   N1    106.56  3.000
 XP5  H22C  C2   C1    109.09  3.000
 XP5  H21C  C2   C1    109.42  3.000
 XP5  N1    C2   C1    115.74  3.000
 XP5  C5    N1   C4    108.74  3.000
 XP5  C5    N1   C3    109.62  3.000
 XP5  C4    N1   C3    108.64  3.000
 XP5  C5    N1   C2    110.86  3.000
 XP5  C4    N1   C2    107.69  3.000
 XP5  C3    N1   C2    111.22  3.000
 XP5  H33C  C3   H32C  109.17  3.000
 XP5  H33C  C3   H31C  110.14  3.000
 XP5  H32C  C3   H31C  109.75  3.000
 XP5  H33C  C3   N1    109.96  3.000
 XP5  H32C  C3   N1    108.74  3.000
 XP5  H31C  C3   N1    109.06  3.000
 XP5  H43C  C4   H42C  109.67  3.000
 XP5  H43C  C4   H41C  109.98  3.000
 XP5  H42C  C4   H41C  109.67  3.000
 XP5  H43C  C4   N1    109.15  3.000
 XP5  H42C  C4   N1    109.14  3.000
 XP5  H41C  C4   N1    109.21  3.000
 XP5  H53C  C5   H52C  109.74  3.000
 XP5  H53C  C5   H51C  109.95  3.000
 XP5  H52C  C5   H51C  109.29  3.000
 XP5  H53C  C5   N1    109.12  3.000
 XP5  H52C  C5   N1    108.83  3.000
 XP5  H51C  C5   N1    109.89  3.000
 XP5  C6    O4   P1    123.09  3.000
 XP5  H62C  C6   H61C  107.16  3.000
 XP5  H62C  C6   CAM   107.72  3.000
 XP5  H61C  C6   CAM   109.17  3.000
 XP5  H62C  C6   O4    107.47  3.000
 XP5  H61C  C6   O4    111.05  3.000
 XP5  CAM   C6   O4    113.98  3.000
 XP5  H82C  C8   H81C  107.87  3.000
 XP5  H82C  C8   CAM   109.37  3.000
 XP5  H81C  C8   CAM   108.97  3.000
 XP5  H82C  C8   O5    106.09  3.000
 XP5  H81C  C8   O5    111.57  3.000
 XP5  CAM   C8   O5    112.80  3.000
 XP5  C9    O5   C8    119.46  3.000
 XP5  C10   C9   O6    124.03  3.000
 XP5  C10   C9   O5    112.03  3.000
 XP5  O6    C9   O5    123.90  3.000
 XP5  H102  C10  H101  106.81  3.000
 XP5  H102  C10  C11   109.70  3.000
 XP5  H101  C10  C11   110.53  3.000
 XP5  H102  C10  C9    107.09  3.000
 XP5  H101  C10  C9    109.98  3.000
 XP5  C11   C10  C9    112.50  3.000
 XP5  H112  C11  H111  106.35  3.000
 XP5  H112  C11  C12   109.72  3.000
 XP5  H111  C11  C12   109.06  3.000
 XP5  H112  C11  C10   109.25  3.000
 XP5  H111  C11  C10   109.79  3.000
 XP5  C12   C11  C10   112.49  3.000
 XP5  H122  C12  H121  105.62  3.000
 XP5  H122  C12  C13   109.97  3.000
 XP5  H121  C12  C13   109.04  3.000
 XP5  H122  C12  C11   109.63  3.000
 XP5  H121  C12  C11   110.02  3.000
 XP5  C13   C12  C11   112.35  3.000
 XP5  H132  C13  H131  105.60  3.000
 XP5  H132  C13  C14   109.41  3.000
 XP5  H131  C13  C14   109.34  3.000
 XP5  H132  C13  C12   109.02  3.000
 XP5  H131  C13  C12   109.56  3.000
 XP5  C14   C13  C12   113.59  3.000
 XP5  H142  C14  H141  105.84  3.000
 XP5  H142  C14  C15   109.81  3.000
 XP5  H141  C14  C15   109.42  3.000
 XP5  H142  C14  C13   109.29  3.000
 XP5  H141  C14  C13   109.46  3.000
 XP5  C15   C14  C13   112.78  3.000
 XP5  H153  C15  H152  107.67  3.000
 XP5  H153  C15  H151  107.35  3.000
 XP5  H152  C15  H151  107.60  3.000
 XP5  H153  C15  C14   111.24  3.000
 XP5  H152  C15  C14   111.62  3.000
 XP5  H151  C15  C14   111.14  3.000
 XP5  CAM   O8   C17   119.21  3.000
 XP5  H182  C18  H181  106.12  3.000
 XP5  H182  C18  C19   110.34  3.000
 XP5  H181  C18  C19   111.02  3.000
 XP5  H182  C18  C17   105.96  3.000
 XP5  H181  C18  C17   109.35  3.000
 XP5  C19   C18  C17   113.66  3.000
 XP5  H192  C19  H191  106.49  3.000
 XP5  H192  C19  C20   109.36  3.000
 XP5  H191  C19  C20   109.27  3.000
 XP5  H192  C19  C18   109.81  3.000
 XP5  H191  C19  C18   109.74  3.000
 XP5  C20   C19  C18   112.01  3.000
 XP5  H202  C20  H201  106.17  3.000
 XP5  H202  C20  C21   109.39  3.000
 XP5  H201  C20  C21   109.37  3.000
 XP5  H202  C20  C19   109.33  3.000
 XP5  H201  C20  C19   109.48  3.000
 XP5  C21   C20  C19   112.88  3.000
 XP5  H212  C21  H211  106.12  3.000
 XP5  H212  C21  C22   109.26  3.000
 XP5  H211  C21  C22   109.22  3.000
 XP5  H212  C21  C20   109.34  3.000
 XP5  H211  C21  C20   109.38  3.000
 XP5  C22   C21  C20   113.28  3.000
 XP5  H222  C22  H221  106.12  3.000
 XP5  H222  C22  C23   109.52  3.000
 XP5  H221  C22  C23   109.46  3.000
 XP5  H222  C22  C21   109.29  3.000
 XP5  H221  C22  C21   109.27  3.000
 XP5  C23   C22  C21   112.95  3.000
 XP5  H233  C23  H232  107.61  3.000
 XP5  H233  C23  H231  107.55  3.000
 XP5  H232  C23  H231  107.49  3.000
 XP5  H233  C23  C22   111.48  3.000
 XP5  H232  C23  C22   111.21  3.000
 XP5  H231  C23  C22   111.30  3.000
 XP5  HAM   CAM  O8    110.35  3.000
 XP5  HAM   CAM  C8    105.63  3.000
 XP5  O8    CAM  C8    107.21  3.000
 XP5  HAM   CAM  C6    106.74  3.000
 XP5  O8    CAM  C6    111.01  3.000
 XP5  C8    CAM  C6    115.74  3.000
 XP5  C18   C17  O8    111.45  3.000
 XP5  C18   C17  O7    125.03  3.000
 XP5  O8    C17  O7    123.52  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
 XP5  Var_01  C2    C1   O3   P1    -94.51  30.0  3
 XP5  Var_02  CAM   C6   O4   P1    -90.04  30.0  3
 XP5  Var_03  N1    C2   C1   O3   -176.05  30.0  3
 XP5  Var_04  O4    P1   O3   C1    166.77  30.0  1
 XP5  Var_05  C3    N1   C2   C1     57.54  30.0  3
 XP5  Var_06  O6    C9   O5   C8     -5.59  30.0  3
 XP5  Var_07  C11   C10  C9   O5   -136.62  30.0  3
 XP5  Var_08  CAM   C8   O5   C9    -97.80  30.0  1
 XP5  Var_09  C12   C11  C10  C9   -172.61  30.0  3
 XP5  Var_10  C13   C12  C11  C10  -169.64  30.0  3
 XP5  Var_11  C14   C13  C12  C11  -178.21  30.0  3
 XP5  Var_12  C15   C14  C13  C12  -176.35  30.0  3
 XP5  Var_13  C19   C18  C17  O7     16.21  30.0  3
 XP5  Var_14  C20   C19  C18  C17  -178.31  30.0  3
 XP5  Var_15  C21   C20  C19  C18  -179.81  30.0  3
 XP5  Var_16  C22   C21  C20  C19  -179.85  30.0  3
 XP5  Var_17  C23   C22  C21  C20  -179.97  30.0  3
 XP5  Var_18  H31C  C3   N1   C2     52.42  30.0  3
 XP5  Var_19  H41C  C4   N1   C2     56.58  30.0  3
 XP5  Var_20  H51C  C5   N1   C2     63.11  30.0  3
 XP5  Var_21  H151  C15  C14  C13    59.44  30.0  3
 XP5  Var_22  H231  C23  C22  C21   -60.34  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
 XP5  chir_02  CAM  C6  C8  O8  negativ

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
 XP5  plan-1  O5   0.020
 XP5  plan-1  C9   0.020
 XP5  plan-1  O6   0.020
 XP5  plan-1  C10  0.020
 XP5  plan-2  O7   0.020
 XP5  plan-2  O8   0.020
 XP5  plan-2  C18  0.020
 XP5  plan-2  C17  0.020

