# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 12:44:35 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: {1-hydroxy-3-[methyl(4-phenylbutyl)amino]propane-1,1-diyl}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCCCc1ccccc1)CCC(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
 GG3  GG3  '{1-hydroxy-3-[methyl(4-phenylbutyl)amino]propane-1,1-diyl}bis(phosphonic acid)'  ligand  49  24  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GG3
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
 GG3  C2    C  CH2   0  -0.300   0.5118  -1.8857  -1.1223
 GG3  C6    C  CH2   0  -0.261   2.4801  -3.0138  -1.9683
 GG3  C7    C  CH2   0  -0.528   0.0595  -0.7295  -0.2236
 GG3  C8    C  CT    0  -0.287  -1.1668  -0.9518   0.6771
 GG3  O16   O  OH1   0  -0.744   0.4836  -1.8303   2.6315
 GG3  P14   P  P     0   1.379  -0.8905  -2.2737   1.9436
 GG3  O17   O  O     0  -0.682  -0.9394  -3.6473   1.3880
 GG3  O15   O  OH1   0  -0.731  -1.9095  -1.9599   3.1355
 GG3  P9    P  P     0   1.383  -2.6644  -1.3625  -0.3264
 GG3  O11   O  OH1   0  -0.754  -3.7300  -1.5629   0.8573
 GG3  O10   O  O     0  -0.683  -2.5674  -2.4614  -1.3128
 GG3  O12   O  OH1   0  -0.741  -3.0600   0.0659  -0.9467
 GG3  O13   O  OH1   0  -0.653  -1.4406   0.2085   1.4289
 GG3  N13   N  NT    0  -0.415   1.9294  -1.7886  -1.4143
 GG3  C21   C  CH3   0  -0.526   2.2314  -0.6607  -2.2681
 GG3  C22   C  CH2   0  -0.483   2.3612  -4.2190  -1.0412
 GG3  C26   C  CH2   0  -0.409   2.7979  -3.9346   0.3889
 GG3  C27   C  CH2   0  -0.497   2.6049  -5.1440   1.3064
 GG3  C28   C  CR6   0   0.132   2.7688  -4.7814   2.7552
 GG3  C33   C  CR16  0  -0.299   4.0239  -4.4792   3.2829
 GG3  C32   C  CR16  0  -0.235   4.1649  -4.0894   4.6070
 GG3  C31   C  CR16  0  -0.268   3.0510  -3.9905   5.4329
 GG3  C30   C  CR16  0  -0.230   1.7965  -4.2937   4.9243
 GG3  C29   C  CR16  0  -0.412   1.6590  -4.6877   3.5962
 GG3  H21   H  HCH2  0   0.257   0.3246  -2.8321  -0.6186
 GG3  H22   H  HCH2  0   0.215  -0.0932  -1.9052  -2.0408
 GG3  H61   H  HCH2  0   0.198   2.0253  -3.2648  -2.9422
 GG3  H62   H  HCH2  0   0.224   3.5396  -2.8272  -2.1662
 GG3  H71   H  HCH2  0   0.266  -0.1537   0.1538  -0.8357
 GG3  H72   H  HCH2  0   0.277   0.8917  -0.4530   0.4277
 GG3  HO16  H  HOH1  0   0.501   1.0560  -2.5723   2.8878
 GG3  HO15  H  HOH1  0   0.494  -2.8423  -2.0377   2.8891
 GG3  HO11  H  HOH1  0   0.505  -4.5700  -1.9580   0.5812
 GG3  HO12  H  HOH1  0   0.499  -2.9964   0.1036  -1.9102
 GG3  HO13  H  HOH1  0   0.466  -1.2999   0.9841   0.8719
 GG3  H211  H  HCH3  0   0.239   1.8859   0.2708  -1.8193
 GG3  H212  H  HCH3  0   0.190   1.7735  -0.7390  -3.2673
 GG3  H213  H  HCH3  0   0.234   3.3106  -0.5740  -2.4029
 GG3  H221  H  HCH2  0   0.240   2.9663  -5.0265  -1.4638
 GG3  H222  H  HCH2  0   0.224   1.3349  -4.5978  -1.0333
 GG3  H261  H  HCH2  0   0.223   3.8438  -3.6142   0.4065
 GG3  H262  H  HCH2  0   0.218   2.2234  -3.0920   0.7797
 GG3  H271  H  HCH2  0   0.238   1.6012  -5.5472   1.1501
 GG3  H272  H  HCH2  0   0.241   3.3090  -5.9340   1.0302
 GG3  H33   H  HCR6  0   0.250   4.9010  -4.5520   2.6500
 GG3  H32   H  HCR6  0   0.257   5.1484  -3.8616   4.9976
 GG3  H31   H  HCR6  0   0.257   3.1627  -3.6854   6.4652
 GG3  H30   H  HCR6  0   0.261   0.9222  -4.2301   5.5595
 GG3  H29   H  HCR6  0   0.273   0.6777  -4.9445   3.2117

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
 GG3  C2   N13   single    1.451  0.020  1.451
 GG3  C2   C7    single    1.533  0.020  1.533
 GG3  C2   H21   single    0.970  0.020  1.090
 GG3  C2   H22   single    0.970  0.020  1.090
 GG3  C6   C22   single    1.525  0.020  1.525
 GG3  C6   N13   single    1.453  0.020  1.453
 GG3  C6   H61   single    0.970  0.020  1.090
 GG3  C6   H62   single    0.970  0.020  1.090
 GG3  C7   C8    single    1.538  0.020  1.538
 GG3  C7   H71   single    0.970  0.020  1.090
 GG3  C7   H72   single    0.970  0.020  1.090
 GG3  C8   O13   single    1.409  0.020  1.409
 GG3  C8   P9    single    1.849  0.020  1.849
 GG3  C8   P14   single    1.851  0.020  1.851
 GG3  O16  P14   single    1.599  0.020  1.599
 GG3  O16  HO16  single    0.850  0.020  0.980
 GG3  P14  O17   double    1.483  0.020  1.483
 GG3  P14  O15   single    1.599  0.020  1.599
 GG3  O15  HO15  single    0.850  0.020  0.980
 GG3  P9   O10   double    1.480  0.020  1.480
 GG3  P9   O12   single    1.607  0.020  1.607
 GG3  P9   O11   single    1.605  0.020  1.605
 GG3  O11  HO11  single    0.850  0.020  0.980
 GG3  O12  HO12  single    0.850  0.020  0.980
 GG3  O13  HO13  single    0.850  0.020  0.980
 GG3  N13  C21   single    1.446  0.020  1.446
 GG3  C21  H211  single    0.970  0.020  1.090
 GG3  C21  H212  single    0.970  0.020  1.090
 GG3  C21  H213  single    0.970  0.020  1.090
 GG3  C22  C26   single    1.522  0.020  1.522
 GG3  C22  H221  single    0.970  0.020  1.090
 GG3  C22  H222  single    0.970  0.020  1.090
 GG3  C26  C27   single    1.530  0.020  1.530
 GG3  C26  H261  single    0.970  0.020  1.090
 GG3  C26  H262  single    0.970  0.020  1.090
 GG3  C27  C28   single    1.502  0.020  1.502
 GG3  C27  H271  single    0.970  0.020  1.090
 GG3  C27  H272  single    0.970  0.020  1.090
 GG3  C28  C33   aromatic  1.395  0.020  1.395
 GG3  C28  C29   aromatic  1.396  0.020  1.396
 GG3  C33  C32   aromatic  1.387  0.020  1.387
 GG3  C33  H33   single    0.930  0.020  1.080
 GG3  C32  C31   aromatic  1.390  0.020  1.390
 GG3  C32  H32   single    0.930  0.020  1.080
 GG3  C31  C30   aromatic  1.387  0.020  1.387
 GG3  C31  H31   single    0.930  0.020  1.080
 GG3  C30  C29   aromatic  1.392  0.020  1.392
 GG3  C30  H30   single    0.930  0.020  1.080
 GG3  C29  H29   single    0.930  0.020  1.080

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
 GG3  H22   C2   H21   106.05  3.000
 GG3  H22   C2   N13   111.75  3.000
 GG3  H21   C2   N13   108.63  3.000
 GG3  H22   C2   C7    109.92  3.000
 GG3  H21   C2   C7    109.51  3.000
 GG3  N13   C2   C7    110.85  3.000
 GG3  H62   C6   H61   106.15  3.000
 GG3  H62   C6   C22   108.68  3.000
 GG3  H61   C6   C22   108.94  3.000
 GG3  H62   C6   N13   106.99  3.000
 GG3  H61   C6   N13   111.84  3.000
 GG3  C22   C6   N13   113.90  3.000
 GG3  H72   C7   H71   106.10  3.000
 GG3  H72   C7   C8    107.15  3.000
 GG3  H71   C7   C8    106.77  3.000
 GG3  H72   C7   C2    108.41  3.000
 GG3  H71   C7   C2    109.76  3.000
 GG3  C8    C7   C2    118.02  3.000
 GG3  O13   C8   P9    108.36  3.000
 GG3  P9    C8   P14   109.49  3.000
 GG3  O13   C8   P14   104.59  3.000
 GG3  P14   C8   C7    112.64  3.000
 GG3  P9    C8   C7    111.11  3.000
 GG3  O13   C8   C7    110.39  3.000
 GG3  HO16  O16  P14   114.08  3.000
 GG3  O15   P14  O17   116.11  3.000
 GG3  O15   P14  O16    99.93  3.000
 GG3  O17   P14  O16   116.51  3.000
 GG3  O15   P14  C8    105.94  3.000
 GG3  O17   P14  C8    113.59  3.000
 GG3  O16   P14  C8    102.97  3.000
 GG3  HO15  O15  P14   114.11  3.000
 GG3  O12   P9   O10   114.77  3.000
 GG3  O12   P9   O11   103.43  3.000
 GG3  O10   P9   O11   116.25  3.000
 GG3  O11   P9   C8     99.51  3.000
 GG3  O12   P9   C8    102.21  3.000
 GG3  O10   P9   C8    118.27  3.000
 GG3  HO11  O11  P9    114.62  3.000
 GG3  HO12  O12  P9    113.79  3.000
 GG3  HO13  O13  C8    108.98  3.000
 GG3  C21   N13  C6    110.69  3.000
 GG3  C21   N13  C2    112.03  3.000
 GG3  C6    N13  C2    112.99  3.000
 GG3  H213  C21  H212  107.74  3.000
 GG3  H213  C21  H211  107.24  3.000
 GG3  H212  C21  H211  107.60  3.000
 GG3  H213  C21  N13   109.96  3.000
 GG3  H212  C21  N13   113.15  3.000
 GG3  H211  C21  N13   110.92  3.000
 GG3  H222  C22  H221  105.43  3.000
 GG3  H222  C22  C26   109.08  3.000
 GG3  H221  C22  C26   110.01  3.000
 GG3  H222  C22  C6    110.56  3.000
 GG3  H221  C22  C6    107.79  3.000
 GG3  C26   C22  C6    113.65  3.000
 GG3  H262  C26  H261  105.73  3.000
 GG3  H262  C26  C27   109.20  3.000
 GG3  H261  C26  C27   110.02  3.000
 GG3  H262  C26  C22   109.24  3.000
 GG3  H261  C26  C22   110.12  3.000
 GG3  C27   C26  C22   112.30  3.000
 GG3  H272  C27  H271  106.78  3.000
 GG3  H272  C27  C28   110.34  3.000
 GG3  H271  C27  C28   109.10  3.000
 GG3  H272  C27  C26   109.77  3.000
 GG3  H271  C27  C26   108.76  3.000
 GG3  C28   C27  C26   111.94  3.000
 GG3  C29   C28  C33   118.23  3.000
 GG3  C29   C28  C27   120.70  3.000
 GG3  C33   C28  C27   121.02  3.000
 GG3  H33   C33  C32   119.59  3.000
 GG3  H33   C33  C28   119.52  3.000
 GG3  C32   C33  C28   120.89  3.000
 GG3  H32   C32  C31   119.91  3.000
 GG3  H32   C32  C33   119.72  3.000
 GG3  C31   C32  C33   120.37  3.000
 GG3  H31   C31  C30   120.31  3.000
 GG3  H31   C31  C32   120.27  3.000
 GG3  C30   C31  C32   119.42  3.000
 GG3  H30   C30  C29   119.78  3.000
 GG3  H30   C30  C31   120.16  3.000
 GG3  C29   C30  C31   120.06  3.000
 GG3  H29   C29  C30   119.64  3.000
 GG3  H29   C29  C28   119.33  3.000
 GG3  C30   C29  C28   121.02  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
 GG3  CONST_01  C31   C32  C33  C28     0.00   0.0  0
 GG3  CONST_02  C31   C30  C29  C28     0.00   0.0  0
 GG3  CONST_03  C30   C29  C28  C33     0.00   0.0  0
 GG3  CONST_04  C30   C31  C32  C33     0.00   0.0  0
 GG3  CONST_05  C29   C28  C33  C32     0.00   0.0  0
 GG3  CONST_06  C29   C30  C31  C32     0.00   0.0  0
 GG3  CONST_07  C32   C33  C28  C27   180.00   0.0  0
 GG3  CONST_08  C30   C29  C28  C27   180.00   0.0  0
 GG3  CONST_09  H32   C32  C33  C28   180.00   0.0  0
 GG3  CONST_10  H30   C30  C29  C28   180.00   0.0  0
 GG3  CONST_11  H29   C29  C28  C33   180.00   0.0  0
 GG3  CONST_12  H31   C31  C32  C33   180.00   0.0  0
 GG3  CONST_13  H33   C33  C32  C31   180.00   0.0  0
 GG3  Var_01    C33   C28  C27  C26   -71.64  30.0  2
 GG3  Var_02    C28   C27  C26  C22  -168.39  30.0  3
 GG3  Var_03    C22   C6   N13  C2    -60.87  30.0  1
 GG3  Var_04    O13   C8   C7   C2   -179.91  30.0  3
 GG3  Var_05    C27   C26  C22  C6    177.33  30.0  3
 GG3  Var_06    C7    C2   N13  C6    165.39  30.0  2
 GG3  Var_07    O10   P9   C8   C7     51.99  30.0  3
 GG3  Var_08    O16   P14  C8   C7     51.51  30.0  3
 GG3  Var_09    N13   C2   C7   C8   -153.73  30.0  3
 GG3  Var_10    C26   C22  C6   N13   -47.15  30.0  3
 GG3  Var_11    H211  C21  N13  C2     57.18  30.0  3

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
 GG3  plan-1  C27  0.020
 GG3  plan-1  C28  0.020
 GG3  plan-1  C33  0.020
 GG3  plan-1  C32  0.020
 GG3  plan-1  C31  0.020
 GG3  plan-1  C30  0.020
 GG3  plan-1  C29  0.020
 GG3  plan-1  H33  0.020
 GG3  plan-1  H32  0.020
 GG3  plan-1  H31  0.020
 GG3  plan-1  H30  0.020
 GG3  plan-1  H29  0.020

