# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 15:23:40 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)O[C@@H](COC(=O)CCCC)CO[P](O)(=O)OCC[N+](C)(C)C
#
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
 6O8  6O8  (4R,7S)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(pentanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphatetradecan-1-aminium  ligand  68  29  .  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_6O8
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
 6O8  C01   C  CH3   0  -0.635   3.8278   4.7116   1.6306
 6O8  C02   C  CH2   0  -0.418   2.9840   3.4638   1.4196
 6O8  C03   C  CH2   0  -0.438   2.1557   3.5161   0.1412
 6O8  C04   C  CH2   0  -0.598   1.3350   2.2516  -0.0397
 6O8  C05   C  C     0   0.617   0.5046   2.2189  -1.2923
 6O8  O06   O  O     0  -0.465   0.5649   3.0113  -2.1972
 6O8  O07   O  O2    0  -0.463  -0.3189   1.1761  -1.2869
 6O8  C08   C  CH2   0  -0.181  -1.0987   0.9366  -2.4514
 6O8  C09   C  CH1   0  -0.041  -1.7325  -0.4362  -2.3322
 6O8  C10   C  CH2   0  -0.178  -0.7777  -1.6010  -2.4755
 6O8  O11   O  O2    0  -0.625   0.2069  -1.6342  -1.4359
 6O8  P12   P  P     0   1.470   1.7405  -1.4098  -1.7864
 6O8  O13   O  OH1   0  -0.703   2.2726  -2.7345  -2.5003
 6O8  O14   O  O     0  -0.698   2.0994  -0.2348  -2.6004
 6O8  O15   O  O2    0  -0.542   2.2987  -1.4295  -0.2845
 6O8  C16   C  CH2   0  -0.267   3.7057  -1.5242  -0.0627
 6O8  C17   C  CH2   0  -0.318   4.1616  -0.6250   1.0586
 6O8  N18   N  NT    1  -0.380   3.7171  -0.9607   2.4567
 6O8  C19   C  CH3   0  -0.553   3.9972  -2.3862   2.7829
 6O8  C20   C  CH3   0  -0.565   4.5020  -0.0944   3.3850
 6O8  C21   C  CH3   0  -0.546   2.2675  -0.6763   2.6691
 6O8  O22   O  O2    0  -0.336  -2.4075  -0.5923  -1.0836
 6O8  C23   C  C     0   0.578  -3.6393  -0.0949  -0.9522
 6O8  O24   O  O     0  -0.650  -4.2125   0.4904  -1.8348
 6O8  C25   C  CH2   0  -0.584  -4.1899  -0.3563   0.4214
 6O8  C26   C  CH2   0  -0.427  -5.6601   0.0046   0.5669
 6O8  C27   C  CH2   0  -0.399  -6.1894  -0.3216   1.9573
 6O8  C28   C  CH2   0  -0.471  -7.6677   0.0104   2.1222
 6O8  C29   C  CH3   0  -0.697  -8.2003  -0.3430   3.5037
 6O8  H011  H  HCH3  0   0.225   3.2030   5.6050   1.6805
 6O8  H012  H  HCH3  0   0.213   4.3968   4.6543   2.5588
 6O8  H1    H  HCH3  0   0.235   4.5387   4.8505   0.8144
 6O8  H022  H  HCH2  0   0.140   3.6412   2.5876   1.3877
 6O8  H021  H  HCH2  0   0.229   2.3219   3.3184   2.2788
 6O8  H031  H  HCH2  0   0.256   1.4963   4.3873   0.1737
 6O8  H032  H  HCH2  0   0.256   2.8186   3.6577  -0.7161
 6O8  H041  H  HCH2  0   0.283   1.9929   1.3778  -0.0810
 6O8  H042  H  HCH2  0   0.275   0.6771   2.0890   0.8189
 6O8  H081  H  HCH2  0   0.276  -1.8696   1.7032  -2.5515
 6O8  H082  H  HCH2  0   0.245  -0.4837   0.9637  -3.3542
 6O8  H091  H  HCH1  0   0.288  -2.4379  -0.5315  -3.1640
 6O8  H102  H  HCH2  0   0.299  -1.3322  -2.5381  -2.4211
 6O8  H101  H  HCH2  0   0.214  -0.3245  -1.5477  -3.4686
 6O8  H2    H  HOH1  0   0.522   2.0533  -3.5716  -2.0677
 6O8  H162  H  HCH2  0   0.305   3.9729  -2.5663   0.1138
 6O8  H161  H  HCH2  0   0.305   4.2763  -1.1920  -0.9340
 6O8  H171  H  HCH2  0   0.340   5.2511  -0.6625   1.0639
 6O8  H172  H  HCH2  0   0.320   3.8719   0.4088   0.8720
 6O8  H193  H  HCH3  0   0.290   5.0449  -2.5993   2.5880
 6O8  H191  H  HCH3  0   0.337   3.7788  -2.5484   3.8344
 6O8  H192  H  HCH3  0   0.259   3.3659  -3.0354   2.1845
 6O8  H202  H  HCH3  0   0.299   4.3091   0.9498   3.1520
 6O8  H203  H  HCH3  0   0.295   4.1969  -0.3013   4.4067
 6O8  H201  H  HCH3  0   0.284   5.5607  -0.3063   3.2650
 6O8  H213  H  HCH3  0   0.316   1.6609  -1.3247   2.0483
 6O8  H212  H  HCH3  0   0.329   2.0334  -0.8504   3.7156
 6O8  H211  H  HCH3  0   0.248   2.0694   0.3647   2.4254
 6O8  H252  H  HCH2  0   0.311  -4.0248  -1.4090   0.6683
 6O8  H251  H  HCH2  0   0.266  -3.5836   0.2102   1.1365
 6O8  H262  H  HCH2  0   0.208  -5.8040   1.0683   0.3606
 6O8  H261  H  HCH2  0   0.243  -6.2467  -0.5392  -0.1786
 6O8  H272  H  HCH2  0   0.221  -6.0334  -1.3855   2.1667
 6O8  H271  H  HCH2  0   0.252  -5.6096   0.2241   2.7096
 6O8  H281  H  HCH2  0   0.180  -7.8235   1.0760   1.9284
 6O8  H282  H  HCH2  0   0.249  -8.2440  -0.5236   1.3604
 6O8  H291  H  HCH3  0   0.236  -8.0822  -1.4085   3.7101
 6O8  H292  H  HCH3  0   0.205  -7.6700   0.2041   4.2854
 6O8  H3    H  HCH3  0   0.261  -9.2607  -0.1061   3.5976

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
 6O8  C21  N18   single  1.492  0.020  1.492
 6O8  C20  N18   single  1.493  0.020  1.493
 6O8  O14  P12   double  1.474  0.020  1.474
 6O8  N18  C17   single  1.505  0.020  1.505
 6O8  N18  C19   single  1.489  0.020  1.489
 6O8  C17  C16   single  1.508  0.020  1.508
 6O8  O13  P12   single  1.596  0.020  1.596
 6O8  P12  O11   single  1.589  0.020  1.589
 6O8  P12  O15   single  1.602  0.020  1.602
 6O8  O06  C05   double  1.204  0.020  1.204
 6O8  C16  O15   single  1.427  0.020  1.427
 6O8  O11  C10   single  1.432  0.020  1.432
 6O8  C05  O07   single  1.329  0.020  1.329
 6O8  C05  C04   single  1.503  0.020  1.503
 6O8  C10  C09   single  1.513  0.020  1.513
 6O8  O07  C08   single  1.422  0.020  1.422
 6O8  C04  C03   single  1.518  0.020  1.518
 6O8  C09  C08   single  1.517  0.020  1.517
 6O8  C09  O22   single  1.428  0.020  1.428
 6O8  C03  C02   single  1.524  0.020  1.524
 6O8  C02  C01   single  1.521  0.020  1.521
 6O8  O22  C23   single  1.335  0.020  1.335
 6O8  C23  O24   double  1.204  0.020  1.204
 6O8  C23  C25   single  1.503  0.020  1.503
 6O8  C25  C26   single  1.521  0.020  1.521
 6O8  C26  C27   single  1.523  0.020  1.523
 6O8  C27  C28   single  1.524  0.020  1.524
 6O8  C28  C29   single  1.522  0.020  1.522
 6O8  C01  H011  single  0.970  0.020  1.090
 6O8  C01  H012  single  0.970  0.020  1.090
 6O8  C01  H1    single  0.970  0.020  1.090
 6O8  C02  H022  single  0.970  0.020  1.090
 6O8  C02  H021  single  0.970  0.020  1.090
 6O8  C03  H031  single  0.970  0.020  1.090
 6O8  C03  H032  single  0.970  0.020  1.090
 6O8  C04  H041  single  0.970  0.020  1.090
 6O8  C04  H042  single  0.970  0.020  1.090
 6O8  C08  H081  single  0.970  0.020  1.090
 6O8  C08  H082  single  0.970  0.020  1.090
 6O8  C09  H091  single  0.970  0.020  1.090
 6O8  C10  H102  single  0.970  0.020  1.090
 6O8  C10  H101  single  0.970  0.020  1.090
 6O8  O13  H2    single  0.850  0.020  0.980
 6O8  C16  H162  single  0.970  0.020  1.090
 6O8  C16  H161  single  0.970  0.020  1.090
 6O8  C17  H171  single  0.970  0.020  1.090
 6O8  C17  H172  single  0.970  0.020  1.090
 6O8  C19  H193  single  0.970  0.020  1.090
 6O8  C19  H191  single  0.970  0.020  1.090
 6O8  C19  H192  single  0.970  0.020  1.090
 6O8  C20  H202  single  0.970  0.020  1.090
 6O8  C20  H203  single  0.970  0.020  1.090
 6O8  C20  H201  single  0.970  0.020  1.090
 6O8  C21  H213  single  0.970  0.020  1.090
 6O8  C21  H212  single  0.970  0.020  1.090
 6O8  C21  H211  single  0.970  0.020  1.090
 6O8  C25  H252  single  0.970  0.020  1.090
 6O8  C25  H251  single  0.970  0.020  1.090
 6O8  C26  H262  single  0.970  0.020  1.090
 6O8  C26  H261  single  0.970  0.020  1.090
 6O8  C27  H272  single  0.970  0.020  1.090
 6O8  C27  H271  single  0.970  0.020  1.090
 6O8  C28  H281  single  0.970  0.020  1.090
 6O8  C28  H282  single  0.970  0.020  1.090
 6O8  C29  H291  single  0.970  0.020  1.090
 6O8  C29  H292  single  0.970  0.020  1.090
 6O8  C29  H3    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
 6O8  H1    C01  H012  107.66  3.000
 6O8  H1    C01  H011  107.63  3.000
 6O8  H012  C01  H011  107.63  3.000
 6O8  H1    C01  C02   111.23  3.000
 6O8  H012  C01  C02   111.38  3.000
 6O8  H011  C01  C02   111.13  3.000
 6O8  H021  C02  H022  106.23  3.000
 6O8  H021  C02  C03   109.53  3.000
 6O8  H022  C02  C03   109.20  3.000
 6O8  H021  C02  C01   109.62  3.000
 6O8  H022  C02  C01   109.11  3.000
 6O8  C03   C02  C01   112.93  3.000
 6O8  H032  C03  H031  106.61  3.000
 6O8  H032  C03  C04   110.02  3.000
 6O8  H031  C03  C04   109.95  3.000
 6O8  H032  C03  C02   109.44  3.000
 6O8  H031  C03  C02   109.28  3.000
 6O8  C04   C03  C02   111.41  3.000
 6O8  H042  C04  H041  105.81  3.000
 6O8  H042  C04  C05   108.58  3.000
 6O8  H041  C04  C05   106.45  3.000
 6O8  H042  C04  C03   110.82  3.000
 6O8  H041  C04  C03   110.15  3.000
 6O8  C05   C04  C03   114.58  3.000
 6O8  O07   C05  O06   123.40  3.000
 6O8  O07   C05  C04   110.86  3.000
 6O8  O06   C05  C04   125.74  3.000
 6O8  C08   O07  C05   117.96  3.000
 6O8  H082  C08  H081  107.71  3.000
 6O8  H082  C08  C09   108.82  3.000
 6O8  H081  C08  C09   110.34  3.000
 6O8  H082  C08  O07   111.34  3.000
 6O8  H081  C08  O07   110.12  3.000
 6O8  C09   C08  O07   108.50  3.000
 6O8  H091  C09  O22   110.50  3.000
 6O8  H091  C09  C10   105.52  3.000
 6O8  O22   C09  C10   107.28  3.000
 6O8  H091  C09  C08   106.76  3.000
 6O8  O22   C09  C08   111.42  3.000
 6O8  C10   C09  C08   115.19  3.000
 6O8  H101  C10  H102  107.34  3.000
 6O8  H101  C10  O11   112.07  3.000
 6O8  H102  C10  O11   107.07  3.000
 6O8  H101  C10  C09   108.08  3.000
 6O8  H102  C10  C09   109.63  3.000
 6O8  O11   C10  C09   112.52  3.000
 6O8  P12   O11  C10   120.00  3.000
 6O8  O15   P12  O14   116.27  3.000
 6O8  O15   P12  O13   107.03  3.000
 6O8  O14   P12  O13   109.48  3.000
 6O8  O15   P12  O11    97.34  3.000
 6O8  O13   P12  O11   107.65  3.000
 6O8  O14   P12  O11   118.00  3.000
 6O8  H2    O13  P12   116.26  3.000
 6O8  C16   O15  P12   119.33  3.000
 6O8  H161  C16  H162  106.95  3.000
 6O8  H161  C16  C17   104.69  3.000
 6O8  H162  C16  C17   112.06  3.000
 6O8  H161  C16  O15   111.74  3.000
 6O8  H162  C16  O15   109.28  3.000
 6O8  C17   C16  O15   111.96  3.000
 6O8  H172  C17  H171  107.41  3.000
 6O8  H172  C17  N18   106.99  3.000
 6O8  H171  C17  N18   106.44  3.000
 6O8  H172  C17  C16   110.98  3.000
 6O8  H171  C17  C16   106.57  3.000
 6O8  N18   C17  C16   117.94  3.000
 6O8  C21   N18  C20   108.16  3.000
 6O8  C20   N18  C19   108.69  3.000
 6O8  C21   N18  C19   109.51  3.000
 6O8  C19   N18  C17   111.19  3.000
 6O8  C20   N18  C17   107.04  3.000
 6O8  C21   N18  C17   112.12  3.000
 6O8  H192  C19  H191  109.11  3.000
 6O8  H192  C19  H193  110.16  3.000
 6O8  H191  C19  H193  109.77  3.000
 6O8  H192  C19  N18   110.02  3.000
 6O8  H191  C19  N18   108.50  3.000
 6O8  H193  C19  N18   109.26  3.000
 6O8  H201  C20  H203  109.91  3.000
 6O8  H201  C20  H202  109.67  3.000
 6O8  H203  C20  H202  109.56  3.000
 6O8  H201  C20  N18   109.30  3.000
 6O8  H203  C20  N18   109.07  3.000
 6O8  H202  C20  N18   109.32  3.000
 6O8  H211  C21  H212  109.27  3.000
 6O8  H211  C21  H213  110.03  3.000
 6O8  H212  C21  H213  109.60  3.000
 6O8  H211  C21  N18   109.11  3.000
 6O8  H212  C21  N18   108.41  3.000
 6O8  H213  C21  N18   110.38  3.000
 6O8  C23   O22  C09   118.79  3.000
 6O8  C25   C23  O24   125.45  3.000
 6O8  C25   C23  O22   111.30  3.000
 6O8  O24   C23  O22   123.24  3.000
 6O8  H251  C25  H252  105.47  3.000
 6O8  H251  C25  C26   110.48  3.000
 6O8  H252  C25  C26   110.66  3.000
 6O8  H251  C25  C23   107.69  3.000
 6O8  H252  C25  C23   108.57  3.000
 6O8  C26   C25  C23   113.61  3.000
 6O8  H261  C26  H262  106.54  3.000
 6O8  H261  C26  C27   109.24  3.000
 6O8  H262  C26  C27   109.57  3.000
 6O8  H261  C26  C25   109.59  3.000
 6O8  H262  C26  C25   109.88  3.000
 6O8  C27   C26  C25   111.87  3.000
 6O8  H271  C27  H272  106.10  3.000
 6O8  H271  C27  C28   109.31  3.000
 6O8  H272  C27  C28   109.21  3.000
 6O8  H271  C27  C26   109.65  3.000
 6O8  H272  C27  C26   109.45  3.000
 6O8  C28   C27  C26   112.90  3.000
 6O8  H282  C28  H281  106.08  3.000
 6O8  H282  C28  C29   109.53  3.000
 6O8  H281  C28  C29   109.70  3.000
 6O8  H282  C28  C27   109.22  3.000
 6O8  H281  C28  C27   109.33  3.000
 6O8  C29   C28  C27   112.77  3.000
 6O8  H3    C29  H292  107.57  3.000
 6O8  H3    C29  H291  107.51  3.000
 6O8  H292  C29  H291  107.53  3.000
 6O8  H3    C29  C28   111.59  3.000
 6O8  H292  C29  C28   111.32  3.000
 6O8  H291  C29  C28   111.12  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
 6O8  Var_01  C04   C03  C02  C01   179.63  30.0  1
 6O8  Var_02  C05   C04  C03  C02  -179.13  30.0  2
 6O8  Var_03  O06   C05  C04  C03     9.23  30.0  1
 6O8  Var_04  C09   C08  O07  C05   168.50  30.0  3
 6O8  Var_05  O24   C23  O22  C09    -0.49  30.0  3
 6O8  Var_06  O14   P12  O11  C10    50.46  30.0  1
 6O8  Var_07  C17   C16  O15  P12   139.17  30.0  1
 6O8  Var_08  N18   C17  C16  O15    67.99  30.0  1
 6O8  Var_09  C21   N18  C17  C16   -72.17  30.0  3
 6O8  Var_10  C26   C25  C23  O22  -171.53  30.0  3
 6O8  Var_11  C27   C26  C25  C23   177.98  30.0  3
 6O8  Var_12  C28   C27  C26  C25  -179.08  30.0  3
 6O8  Var_13  C29   C28  C27  C26   178.83  30.0  3
 6O8  Var_14  H011  C01  C02  C03    59.09  30.0  3
 6O8  Var_15  H102  C10  O11  P12   125.14  30.0  3
 6O8  Var_16  H213  C21  N18  C17    65.18  30.0  3
 6O8  Var_17  H202  C20  N18  C17    59.51  30.0  3
 6O8  Var_18  H193  C19  N18  C17    53.24  30.0  3
 6O8  Var_19  H291  C29  C28  C27   -59.50  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
 6O8  chir_01  C09  C10  C08  O22  positiv
 6O8  chir_02  P12  O13  O11  O15  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
 6O8  plan-1  C04  0.020
 6O8  plan-1  C05  0.020
 6O8  plan-1  O06  0.020
 6O8  plan-1  O07  0.020
 6O8  plan-2  O22  0.020
 6O8  plan-2  C23  0.020
 6O8  plan-2  O24  0.020
 6O8  plan-2  C25  0.020

