# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 16:08:55 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (4-amino-1-hydroxybutane-1,1-diyl)bis(phosphonate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC(O)([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
 AHD  AHD  (4-amino-1-hydroxybutane-1,1-diyl)bis(phosphonate)  ligand  23  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AHD
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
 AHD  C2    C  CH2    0  -0.424   2.3986  -0.5129  -0.1953
 AHD  C3    C  CH2    0  -0.269   3.4715  -1.3188   0.5191
 AHD  C7    C  CH2    0  -0.416   1.0066  -0.7940   0.3587
 AHD  C8    C  CT     0  -0.289  -0.1722  -0.1016  -0.3472
 AHD  O12   O  OP    -1  -0.927  -1.6957  -2.1182  -1.0314
 AHD  P9    P  P      0   1.158  -1.7406  -1.0522   0.1163
 AHD  O10   O  OP    -1  -0.893  -2.9839  -0.1687   0.0116
 AHD  O11   O  O      0  -0.909  -1.5619  -1.6842   1.5026
 AHD  P14   P  P      0   1.160  -0.2404   1.7269   0.0130
 AHD  O15   O  OP    -1  -0.930  -0.5608   1.8211   1.5153
 AHD  O16   O  OP    -1  -0.925  -1.3110   2.3408  -0.9005
 AHD  O17   O  O      0  -0.919   1.1560   2.3086  -0.3149
 AHD  O13   O  OH1    0  -0.763  -0.0507  -0.3057  -1.7653
 AHD  N4    N  NH2    0  -0.802   4.7967  -1.0376  -0.0244
 AHD  H21   H  HCH2   0   0.212   2.6065   0.5549  -0.1121
 AHD  H22   H  HCH2   0   0.176   2.4280  -0.7568  -1.2611
 AHD  H31   H  HCH2   0   0.192   3.2739  -2.3881   0.3877
 AHD  H32   H  HCH2   0   0.170   3.3995  -1.1309   1.6019
 AHD  H71   H  HCH2   0   0.160   0.8567  -1.8818   0.3270
 AHD  H72   H  HCH2   0   0.174   0.9734  -0.5300   1.4190
 AHD  H13   H  HOH1   0   0.398  -0.5871  -1.1306  -1.8624
 AHD  HN41  H  HNH2   0   0.330   5.0245  -0.0673   0.1563
 AHD  HN42  H  HNH2   0   0.337   5.4921  -1.5760   0.4770

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
 AHD  C2   C3    single  1.520  0.020  1.520
 AHD  C2   C7    single  1.524  0.020  1.524
 AHD  C2   H21   single  0.970  0.020  1.090
 AHD  C2   H22   single  0.970  0.020  1.090
 AHD  C3   N4    single  1.460  0.020  1.460
 AHD  C3   H31   single  0.970  0.020  1.090
 AHD  C3   H32   single  0.970  0.020  1.090
 AHD  C7   C8    single  1.539  0.020  1.539
 AHD  C7   H71   single  0.970  0.020  1.090
 AHD  C7   H72   single  0.970  0.020  1.090
 AHD  C8   P9    single  1.892  0.020  1.892
 AHD  C8   P14   single  1.865  0.020  1.865
 AHD  C8   O13   single  1.438  0.020  1.438
 AHD  O12  P9    deloc   1.567  0.020  1.567
 AHD  P9   O10   deloc   1.529  0.020  1.529
 AHD  P9   O11   deloc   1.534  0.020  1.534
 AHD  P14  O15   deloc   1.539  0.020  1.539
 AHD  P14  O16   deloc   1.535  0.020  1.535
 AHD  P14  O17   deloc   1.548  0.020  1.548
 AHD  O13  H13   single  0.850  0.020  0.980
 AHD  N4   HN41  single  0.890  0.020  1.040
 AHD  N4   HN42  single  0.890  0.020  1.040

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
 AHD  H22   C2   H21   106.71  3.000
 AHD  H22   C2   C7    109.73  3.000
 AHD  H21   C2   C7    109.07  3.000
 AHD  H22   C2   C3    108.71  3.000
 AHD  H21   C2   C3    110.40  3.000
 AHD  C7    C2   C3    112.08  3.000
 AHD  H32   C3   H31   105.83  3.000
 AHD  H32   C3   N4    113.11  3.000
 AHD  H31   C3   N4    107.89  3.000
 AHD  H32   C3   C2    108.99  3.000
 AHD  H31   C3   C2    109.50  3.000
 AHD  N4    C3   C2    111.32  3.000
 AHD  H72   C7   H71   105.25  3.000
 AHD  H72   C7   C8    108.24  3.000
 AHD  H71   C7   C8    109.14  3.000
 AHD  H72   C7   C2    109.61  3.000
 AHD  H71   C7   C2    107.26  3.000
 AHD  C8    C7   C2    116.74  3.000
 AHD  O13   C8   P14   109.44  3.000
 AHD  O13   C8   P9    103.91  3.000
 AHD  P14   C8   P9    114.53  3.000
 AHD  O13   C8   C7    108.90  3.000
 AHD  P14   C8   C7    112.37  3.000
 AHD  P9    C8   C7    107.26  3.000
 AHD  O11   P9   O10   113.25  3.000
 AHD  O11   P9   O12   112.23  3.000
 AHD  O10   P9   O12   111.49  3.000
 AHD  O11   P9   C8    109.38  3.000
 AHD  O10   P9   C8    111.54  3.000
 AHD  O12   P9   C8     97.97  3.000
 AHD  O17   P14  O16   110.65  3.000
 AHD  O17   P14  O15   111.82  3.000
 AHD  O16   P14  O15   114.27  3.000
 AHD  O17   P14  C8    107.14  3.000
 AHD  O16   P14  C8    107.61  3.000
 AHD  O15   P14  C8    104.84  3.000
 AHD  H13   O13  C8     99.75  3.000
 AHD  HN42  N4   HN41  105.46  3.000
 AHD  HN42  N4   C3    109.68  3.000
 AHD  HN41  N4   C3    108.80  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
 AHD  Var_01  P9    C8   C7  C2   160.79  30.0  3
 AHD  Var_02  C8    C7   C2  C3  -176.23  30.0  3
 AHD  Var_03  N4    C3   C2  C7   179.97  30.0  3
 AHD  Var_04  O12   P9   C8  C7   -87.99  30.0  3
 AHD  Var_05  O15   P14  C8  C7   -66.37  30.0  3
 AHD  Var_06  HN41  N4   C3  C2    64.30  30.0  3

