# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 08:50:21 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: pentyl trihydrogen diphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCO[P@](O)(=O)O[P](O)(O)=O
#
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
 P25  P25  'pentyl trihydrogen diphosphate'  ligand  28  14  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P25
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
 P25  C4    C  CH2   0  -0.418   5.6239   0.3554   0.6407
 P25  CM4   C  CH3   0  -0.662   6.9863   0.2634  -0.0319
 P25  C5    C  CH2   0  -0.422   4.4784   0.0100  -0.3026
 P25  C6    C  CH2   0  -0.461   3.1125   0.1059   0.3680
 P25  C7    C  CH2   0  -0.160   2.0081  -0.2531  -0.5989
 P25  O7    O  O2    0  -0.580   0.7390  -0.0979   0.0753
 P25  PA    P  P     0   1.479  -0.5868  -0.5988  -0.6337
 P25  O1A   O  O     0  -0.693  -0.8123  -0.2093  -2.0331
 P25  O2A   O  OH1   0  -0.725  -0.6719  -2.1744  -0.4573
 P25  O3A   O  O2    0  -0.684  -1.6292   0.0227   0.4384
 P25  PB    P  P     0   1.468  -3.2027   0.3030   0.1617
 P25  O1B   O  O     0  -0.691  -3.8665  -0.6836  -0.7019
 P25  O2B   O  OH1   0  -0.721  -3.6319   0.3922   1.6876
 P25  O3B   O  OH1   0  -0.724  -3.2737   1.7588  -0.4651
 P25  H41   H  HCH2  0   0.214   5.5974  -0.3161   1.5043
 P25  H42   H  HCH2  0   0.215   5.4761   1.3652   1.0351
 P25  HM41  H  HCH3  0   0.228   7.7901   0.5108   0.6625
 P25  HM42  H  HCH3  0   0.217   7.1736  -0.7443  -0.4076
 P25  HM43  H  HCH3  0   0.217   7.0582   0.9491  -0.8781
 P25  H51   H  HCH2  0   0.218   4.5077   0.6808  -1.1678
 P25  H52   H  HCH2  0   0.218   4.6264  -1.0020  -0.6941
 P25  H61   H  HCH2  0   0.233   3.0754  -0.5651   1.2308
 P25  H62   H  HCH2  0   0.234   2.9552   1.1221   0.7404
 P25  H71   H  HCH2  0   0.242   2.0276   0.4028  -1.4718
 P25  H72   H  HCH2  0   0.237   2.1250  -1.2845  -0.9425
 P25  H2A   H  HOH1  0   0.504  -0.5158  -2.5173   0.4339
 P25  H2B   H  HOH1  0   0.511  -4.5843   0.4882   1.8277
 P25  H3B   H  HOH1  0   0.504  -2.9201   2.4774   0.0774

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
 P25  C4   CM4   single  1.522  0.020  1.522
 P25  C4   C5    single  1.524  0.020  1.524
 P25  C4   H41   single  0.970  0.020  1.090
 P25  C4   H42   single  0.970  0.020  1.090
 P25  CM4  HM41  single  0.970  0.020  1.090
 P25  CM4  HM42  single  0.970  0.020  1.090
 P25  CM4  HM43  single  0.970  0.020  1.090
 P25  C5   C6    single  1.525  0.020  1.525
 P25  C5   H51   single  0.970  0.020  1.090
 P25  C5   H52   single  0.970  0.020  1.090
 P25  C6   C7    single  1.511  0.020  1.511
 P25  C6   H61   single  0.970  0.020  1.090
 P25  C6   H62   single  0.970  0.020  1.090
 P25  C7   O7    single  1.445  0.020  1.445
 P25  C7   H71   single  0.970  0.020  1.090
 P25  C7   H72   single  0.970  0.020  1.090
 P25  O7   PA    single  1.585  0.020  1.585
 P25  PA   O1A   double  1.470  0.020  1.470
 P25  PA   O2A   single  1.588  0.020  1.588
 P25  PA   O3A   single  1.619  0.020  1.619
 P25  O2A  H2A   single  0.850  0.020  0.980
 P25  O3A  PB    single  1.622  0.020  1.622
 P25  PB   O1B   double  1.470  0.020  1.470
 P25  PB   O2B   single  1.588  0.020  1.588
 P25  PB   O3B   single  1.587  0.020  1.587
 P25  O2B  H2B   single  0.850  0.020  0.980
 P25  O3B  H3B   single  0.850  0.020  0.980

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
 P25  H42   C4   H41   106.18  3.000
 P25  H42   C4   C5    109.32  3.000
 P25  H41   C4   C5    109.34  3.000
 P25  H42   C4   CM4   109.64  3.000
 P25  H41   C4   CM4   109.47  3.000
 P25  C5    C4   CM4   112.68  3.000
 P25  HM43  CM4  HM42  107.57  3.000
 P25  HM43  CM4  HM41  107.61  3.000
 P25  HM42  CM4  HM41  107.58  3.000
 P25  HM43  CM4  C4    111.32  3.000
 P25  HM42  CM4  C4    111.19  3.000
 P25  HM41  CM4  C4    111.38  3.000
 P25  H52   C5   H51   106.25  3.000
 P25  H52   C5   C6    109.66  3.000
 P25  H51   C5   C6    109.45  3.000
 P25  H52   C5   C4    109.23  3.000
 P25  H51   C5   C4    109.28  3.000
 P25  C6    C5   C4    112.77  3.000
 P25  H62   C6   H61   107.26  3.000
 P25  H62   C6   C7    109.48  3.000
 P25  H61   C6   C7    109.53  3.000
 P25  H62   C6   C5    109.70  3.000
 P25  H61   C6   C5    109.80  3.000
 P25  C7    C6   C5    111.00  3.000
 P25  H72   C7   H71   108.26  3.000
 P25  H72   C7   O7    109.99  3.000
 P25  H71   C7   O7    108.91  3.000
 P25  H72   C7   C6    110.31  3.000
 P25  H71   C7   C6    110.84  3.000
 P25  O7    C7   C6    108.53  3.000
 P25  PA    O7   C7    119.47  3.000
 P25  O3A   PA   O2A   105.83  3.000
 P25  O3A   PA   O1A   115.45  3.000
 P25  O2A   PA   O1A   111.13  3.000
 P25  O3A   PA   O7     96.95  3.000
 P25  O2A   PA   O7    107.99  3.000
 P25  O1A   PA   O7    118.07  3.000
 P25  H2A   O2A  PA    116.45  3.000
 P25  PB    O3A  PA    125.30  3.000
 P25  O3B   PB   O2B   108.43  3.000
 P25  O3B   PB   O1B   111.33  3.000
 P25  O2B   PB   O1B   118.71  3.000
 P25  O3B   PB   O3A   105.63  3.000
 P25  O2B   PB   O3A    96.20  3.000
 P25  O1B   PB   O3A   114.99  3.000
 P25  H2B   O2B  PB    114.26  3.000
 P25  H3B   O3B  PB    116.34  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
 P25  Var_01  C7    C6   C5   C4   -179.62  30.0  3
 P25  Var_02  C6    C5   C4   CM4  -179.82  30.0  3
 P25  Var_03  O7    C7   C6   C5   -177.94  30.0  3
 P25  Var_04  O1A   PA   O7   C7    -48.18  30.0  3
 P25  Var_05  O1B   PB   O3A  PA     35.80  30.0  3
 P25  Var_06  HM41  CM4  C4   C5   -179.78  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
 P25  chir_01  PA  O1A  O2A  O3A  both

