# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:42:12 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-{[(S)-{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)CCO[P@@](O)(=O)OC[C@H](O)CO
#
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
 CH5  CH5  2-{[(S)-{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium  ligand  36  16  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CH5
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
 CH5  C1   C  CH2    0  -0.158   2.4826  -0.4283  -0.3719
 CH5  C2   C  CH1    0  -0.046   3.4162   0.4257   0.4701
 CH5  C3   C  CH2    0  -0.164   4.8552   0.1812   0.0437
 CH5  C4   C  CH2    0  -0.186  -2.3996  -1.4152   0.3127
 CH5  C5   C  CH2    0  -0.339  -3.5030  -0.5018   0.7950
 CH5  C6   C  CH3    0  -0.565  -3.9667   0.4434  -1.4437
 CH5  C7   C  CH3    0  -0.554  -2.6861   1.7605   0.1464
 CH5  C8   C  CH3    0  -0.546  -5.0337   1.3391   0.5420
 CH5  N    N  NT     1  -0.378  -3.7752   0.7504   0.0005
 CH5  O2   O  OH1    0  -0.658   3.0675   1.7890   0.4376
 CH5  O3   O  OH1    0  -0.668   5.7120   0.9123   0.8865
 CH5  O1P  O  O      0  -0.776  -0.4821  -0.0442  -1.8340
 CH5  O2P  O  OP    -1  -0.787   0.2479  -2.4026  -1.0462
 CH5  O3P  O  O2     0  -0.610   1.1675  -0.3015   0.1320
 CH5  O4P  O  O2     0  -0.609  -1.1204  -0.8612   0.5118
 CH5  P    P  P      0   1.354  -0.0468  -0.9692  -0.7338
 CH5  H11  H  HCH2   0   0.216   2.8124  -1.4718  -0.3361
 CH5  H12  H  HCH2   0   0.208   2.5402  -0.1073  -1.4209
 CH5  H2   H  HCH1   0   0.232   3.3116   0.1183   1.5165
 CH5  H31  H  HCH2   0   0.200   5.0569  -0.8966   0.0959
 CH5  H32  H  HCH2   0   0.194   4.9765   0.4738  -1.0098
 CH5  H41  H  HCH2   0   0.263  -2.5038  -2.3239   0.9135
 CH5  H42  H  HCH2   0   0.237  -2.5796  -1.7194  -0.7225
 CH5  H51  H  HCH2   0   0.304  -3.3228  -0.1845   1.8221
 CH5  H52  H  HCH2   0   0.302  -4.4294  -1.0762   0.7777
 CH5  H61  H  HCH3   0   0.295  -3.0225   0.1296  -1.8795
 CH5  H62  H  HCH3   0   0.292  -4.7150  -0.3380  -1.5518
 CH5  H63  H  HCH3   0   0.295  -4.3071   1.3450  -1.9464
 CH5  H71  H  HCH3   0   0.283  -3.0238   2.6888  -0.3068
 CH5  H72  H  HCH3   0   0.286  -2.4865   1.9208   1.2021
 CH5  H73  H  HCH3   0   0.302  -1.7921   1.4181  -0.3607
 CH5  H81  H  HCH3   0   0.294  -5.8474   0.6303   0.4155
 CH5  H82  H  HCH3   0   0.295  -4.8992   1.5599   1.5976
 CH5  H83  H  HCH3   0   0.294  -5.2610   2.2554   0.0043
 CH5  HO2  H  HOH1   0   0.442   3.1645   2.1089  -0.4661
 CH5  HO3  H  HOH1   0   0.455   6.6161   0.7494   0.6042

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
 CH5  C1   C2   single  1.520  0.020  1.520
 CH5  C1   O3P  single  1.414  0.020  1.414
 CH5  C1   H11  single  0.970  0.020  1.090
 CH5  C1   H12  single  0.970  0.020  1.090
 CH5  C2   C3   single  1.521  0.020  1.521
 CH5  C2   O2   single  1.408  0.020  1.408
 CH5  C2   H2   single  0.970  0.020  1.090
 CH5  C3   O3   single  1.407  0.020  1.407
 CH5  C3   H31  single  0.970  0.020  1.090
 CH5  C3   H32  single  0.970  0.020  1.090
 CH5  C4   C5   single  1.511  0.020  1.511
 CH5  C4   O4P  single  1.408  0.020  1.408
 CH5  C4   H41  single  0.970  0.020  1.090
 CH5  C4   H42  single  0.970  0.020  1.090
 CH5  C5   N    single  1.508  0.020  1.508
 CH5  C5   H51  single  0.970  0.020  1.090
 CH5  C5   H52  single  0.970  0.020  1.090
 CH5  C6   N    single  1.489  0.020  1.489
 CH5  C6   H61  single  0.970  0.020  1.090
 CH5  C6   H62  single  0.970  0.020  1.090
 CH5  C6   H63  single  0.970  0.020  1.090
 CH5  C7   N    single  1.493  0.020  1.493
 CH5  C7   H71  single  0.970  0.020  1.090
 CH5  C7   H72  single  0.970  0.020  1.090
 CH5  C7   H73  single  0.970  0.020  1.090
 CH5  C8   N    single  1.491  0.020  1.491
 CH5  C8   H81  single  0.970  0.020  1.090
 CH5  C8   H82  single  0.970  0.020  1.090
 CH5  C8   H83  single  0.970  0.020  1.090
 CH5  O2   HO2  single  0.850  0.020  0.980
 CH5  O3   HO3  single  0.850  0.020  0.980
 CH5  O1P  P    deloc   1.502  0.020  1.502
 CH5  O2P  P    deloc   1.496  0.020  1.496
 CH5  O3P  P    single  1.634  0.020  1.634
 CH5  O4P  P    single  1.648  0.020  1.648

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
 CH5  H12  C1   H11  107.09  3.000
 CH5  H12  C1   O3P  111.28  3.000
 CH5  H11  C1   O3P  110.73  3.000
 CH5  H12  C1   C2   109.42  3.000
 CH5  H11  C1   C2   109.41  3.000
 CH5  O3P  C1   C2   108.88  3.000
 CH5  H2   C2   O2   105.67  3.000
 CH5  H2   C2   C3   108.24  3.000
 CH5  O2   C2   C3   112.56  3.000
 CH5  H2   C2   C1   108.23  3.000
 CH5  O2   C2   C1   112.29  3.000
 CH5  C3   C2   C1   109.61  3.000
 CH5  H32  C3   H31  106.64  3.000
 CH5  H32  C3   O3   111.61  3.000
 CH5  H31  C3   O3   111.71  3.000
 CH5  H32  C3   C2   109.27  3.000
 CH5  H31  C3   C2   108.57  3.000
 CH5  O3   C3   C2   108.96  3.000
 CH5  H42  C4   H41  105.84  3.000
 CH5  H42  C4   O4P  113.12  3.000
 CH5  H41  C4   O4P  109.61  3.000
 CH5  H42  C4   C5   110.48  3.000
 CH5  H41  C4   C5   104.90  3.000
 CH5  O4P  C4   C5   112.35  3.000
 CH5  H52  C5   H51  107.98  3.000
 CH5  H52  C5   N    106.01  3.000
 CH5  H51  C5   N    106.54  3.000
 CH5  H52  C5   C4   107.27  3.000
 CH5  H51  C5   C4   110.85  3.000
 CH5  N    C5   C4   117.75  3.000
 CH5  H63  C6   H62  109.54  3.000
 CH5  H63  C6   H61  109.04  3.000
 CH5  H62  C6   H61  110.54  3.000
 CH5  H63  C6   N    108.53  3.000
 CH5  H62  C6   N    109.46  3.000
 CH5  H61  C6   N    109.69  3.000
 CH5  H73  C7   H72  110.48  3.000
 CH5  H73  C7   H71  109.34  3.000
 CH5  H72  C7   H71  109.65  3.000
 CH5  H73  C7   N    110.03  3.000
 CH5  H72  C7   N    109.20  3.000
 CH5  H71  C7   N    108.09  3.000
 CH5  H83  C8   H82  109.59  3.000
 CH5  H83  C8   H81  109.62  3.000
 CH5  H82  C8   H81  109.78  3.000
 CH5  H83  C8   N    109.26  3.000
 CH5  H82  C8   N    109.18  3.000
 CH5  H81  C8   N    109.40  3.000
 CH5  C8   N    C7   108.25  3.000
 CH5  C8   N    C6   108.98  3.000
 CH5  C7   N    C6   109.16  3.000
 CH5  C8   N    C5   106.79  3.000
 CH5  C7   N    C5   112.26  3.000
 CH5  C6   N    C5   111.29  3.000
 CH5  HO2  O2   C2   108.56  3.000
 CH5  HO3  O3   C3   107.99  3.000
 CH5  P    O3P  C1   117.76  3.000
 CH5  P    O4P  C4   117.34  3.000
 CH5  O4P  P    O3P   93.26  3.000
 CH5  O4P  P    O2P  110.42  3.000
 CH5  O3P  P    O2P  110.84  3.000
 CH5  O4P  P    O1P  108.94  3.000
 CH5  O3P  P    O1P  110.61  3.000
 CH5  O2P  P    O1P  119.61  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
 CH5  Var_01  O1P  P   O3P  C1   -83.06  30.0  3
 CH5  Var_02  C6   N   C5   C4    51.86  30.0  3
 CH5  Var_03  O4P  C4  C5   N     71.09  30.0  1
 CH5  Var_04  H61  C6  N    C5   -69.46  30.0  3
 CH5  Var_05  H71  C7  N    C5  -170.47  30.0  3
 CH5  Var_06  H81  C8  N    C5   -60.76  30.0  3
 CH5  Var_07  H11  C1  O3P  P    -67.77  30.0  1

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
 CH5  chir_01  C2  C1  C3  O2  negativ

