# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:15:12 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  45  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 OK
;

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  -0.338   0.4767  -1.8878  -1.0289
 GG3  C6    C  CH2    0  -0.274   2.5617  -2.8315  -1.7905
 GG3  C7    C  CH2    0  -0.472  -0.2065  -0.7286  -0.3127
 GG3  C8    C  CT     0  -0.254  -1.3890  -1.0834   0.6056
 GG3  O16   O  OP    -1  -0.985   0.4788  -1.7031   2.4625
 GG3  P14   P  P      0   1.171  -0.8732  -2.2694   1.9630
 GG3  O17   O  O      0  -0.846  -0.7558  -3.6682   1.3290
 GG3  O15   O  OP    -1  -1.011  -1.9416  -2.2006   3.0650
 GG3  P9    P  P      0   1.137  -2.9140  -1.5516  -0.3951
 GG3  O11   O  OP    -1  -0.894  -3.8515  -2.4314   0.4344
 GG3  O10   O  O      0  -0.819  -2.4943  -2.2011  -1.7207
 GG3  O12   O  OP    -1  -1.054  -3.5041  -0.1162  -0.6061
 GG3  O13   O  OH1    0  -0.685  -1.7722   0.1511   1.2474
 GG3  N13   N  NT     0  -0.340   1.8900  -1.6434  -1.3003
 GG3  C21   C  CH3    0  -0.511   2.0824  -0.5518  -2.2231
 GG3  C22   C  CH2    0  -0.478   2.4647  -4.0339  -0.8580
 GG3  C26   C  CH2    0  -0.405   2.8607  -3.7495   0.5849
 GG3  C27   C  CH2    0  -0.523   2.5574  -4.9470   1.4860
 GG3  C28   C  C      0   0.111   3.0548  -4.7735   2.8931
 GG3  C33   C  C1     0  -0.234   4.0732  -5.5767   3.4007
 GG3  C32   C  C1     0  -0.315   4.5393  -5.4087   4.7003
 GG3  C31   C  C1     0  -0.259   3.9881  -4.4271   5.5120
 GG3  C30   C  C1     0  -0.288   2.9743  -3.6164   5.0108
 GG3  C29   C  C1     0  -0.217   2.5076  -3.7830   3.7134
 GG3  H21   H  HCH2   0   0.262   0.3997  -2.7565  -0.3800
 GG3  H22   H  HCH2   0   0.250  -0.0672  -2.1312  -1.9538
 GG3  H61   H  HCH2   0   0.184   2.1790  -3.1315  -2.7856
 GG3  H62   H  HCH2   0   0.158   3.6183  -2.5807  -1.9399
 GG3  H71   H  HCH2   0   0.170  -0.5360   0.0294  -1.0356
 GG3  H72   H  HCH2   0   0.206   0.5459  -0.2523   0.3241
 GG3  HO13  H  HOH1   0   0.373  -2.5014   0.4389   0.6453
 GG3  H211  H  HCH3   0   0.241   1.6399   0.3654  -1.8340
 GG3  H212  H  HCH3   0   0.168   1.6376  -0.7386  -3.2172
 GG3  H213  H  HCH3   0   0.145   3.1483  -0.3631  -2.3736
 GG3  H221  H  HCH2   0   0.247   3.0987  -4.8273  -1.2682
 GG3  H222  H  HCH2   0   0.258   1.4474  -4.4334  -0.8669
 GG3  H261  H  HCH2   0   0.261   3.9254  -3.4939   0.6362
 GG3  H262  H  HCH2   0   0.209   2.2959  -2.8937   0.9609
 GG3  H271  H  HCH2   0   0.180   1.4695  -5.0615   1.4927
 GG3  H272  H  HCH2   0   0.228   2.9871  -5.8598   1.0605
 GG3  H33   H  H      0   0.257   4.5078  -6.3440   2.7690
 GG3  H32   H  H      0   0.221   5.3315  -6.0443   5.0769
 GG3  H31   H  H      0   0.268   4.3449  -4.2930   6.5255
 GG3  H30   H  H      0   0.240   2.5415  -2.8478   5.6405
 GG3  H29   H  H      0   0.256   1.7251  -3.1336   3.3131

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    1.460  0.020  1.460
 GG3  C2   C7    single    1.524  0.020  1.524
 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    1.450  0.020  1.450
 GG3  C6   H61   single    0.970  0.020  1.090
 GG3  C6   H62   single    0.970  0.020  1.090
 GG3  C7   C8    single    1.539  0.020  1.539
 GG3  C7   H71   single    0.970  0.020  1.090
 GG3  C7   H72   single    0.970  0.020  1.090
 GG3  C8   O13   single    1.443  0.020  1.443
 GG3  C8   P9    single    1.883  0.020  1.883
 GG3  C8   P14   single    1.875  0.020  1.875
 GG3  O16  P14   deloc     1.549  0.020  1.549
 GG3  P14  O17   deloc     1.540  0.020  1.540
 GG3  P14  O15   deloc     1.536  0.020  1.536
 GG3  P9   O10   deloc     1.535  0.020  1.535
 GG3  P9   O12   deloc     1.566  0.020  1.566
 GG3  P9   O11   deloc     1.530  0.020  1.530
 GG3  O13  HO13  single    0.850  0.020  0.980
 GG3  N13  C21   single    1.442  0.020  1.442
 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    1.523  0.020  1.523
 GG3  C22  H221  single    0.970  0.020  1.090
 GG3  C22  H222  single    0.970  0.020  1.090
 GG3  C26  C27   single    1.529  0.020  1.529
 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  1.393  0.020  1.393
 GG3  C28  C29   aromatic  1.398  0.020  1.398
 GG3  C33  C32   aromatic  1.391  0.020  1.391
 GG3  C33  H33   single    0.930  0.020  1.080
 GG3  C32  C31   aromatic  1.388  0.020  1.388
 GG3  C32  H32   single    0.930  0.020  1.080
 GG3  C31  C30   aromatic  1.391  0.020  1.391
 GG3  C31  H31   single    0.930  0.020  1.080
 GG3  C30  C29   aromatic  1.389  0.020  1.389
 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   106.86  3.000
 GG3  H22   C2   N13   111.06  3.000
 GG3  H21   C2   N13   108.26  3.000
 GG3  H22   C2   C7    109.98  3.000
 GG3  H21   C2   C7    107.19  3.000
 GG3  N13   C2   C7    113.20  3.000
 GG3  H62   C6   H61   105.82  3.000
 GG3  H62   C6   C22   108.97  3.000
 GG3  H61   C6   C22   108.29  3.000
 GG3  H62   C6   N13   107.76  3.000
 GG3  H61   C6   N13   111.44  3.000
 GG3  C22   C6   N13   114.20  3.000
 GG3  H72   C7   H71   106.78  3.000
 GG3  H72   C7   C8    106.34  3.000
 GG3  H71   C7   C8    108.75  3.000
 GG3  H72   C7   C2    107.23  3.000
 GG3  H71   C7   C2    110.50  3.000
 GG3  C8    C7   C2    116.72  3.000
 GG3  O13   C8   P9    103.53  3.000
 GG3  P9    C8   P14   116.76  3.000
 GG3  O13   C8   P14   106.99  3.000
 GG3  P14   C8   C7    111.50  3.000
 GG3  P9    C8   C7    111.26  3.000
 GG3  O13   C8   C7    105.80  3.000
 GG3  O15   P14  O17   112.88  3.000
 GG3  O15   P14  O16   111.06  3.000
 GG3  O17   P14  O16   113.48  3.000
 GG3  O15   P14  C8    107.43  3.000
 GG3  O17   P14  C8    107.30  3.000
 GG3  O16   P14  C8    104.03  3.000
 GG3  O12   P9   O10   111.99  3.000
 GG3  O12   P9   O11   111.67  3.000
 GG3  O10   P9   O11   113.11  3.000
 GG3  O11   P9   C8    110.55  3.000
 GG3  O12   P9   C8     98.56  3.000
 GG3  O10   P9   C8    110.04  3.000
 GG3  HO13  O13  C8    100.02  3.000
 GG3  C21   N13  C6    110.00  3.000
 GG3  C21   N13  C2    112.01  3.000
 GG3  C6    N13  C2    111.97  3.000
 GG3  H213  C21  H212  107.34  3.000
 GG3  H213  C21  H211  107.44  3.000
 GG3  H212  C21  H211  107.45  3.000
 GG3  H213  C21  N13   110.42  3.000
 GG3  H212  C21  N13   113.20  3.000
 GG3  H211  C21  N13   110.75  3.000
 GG3  H222  C22  H221  105.72  3.000
 GG3  H222  C22  C26   108.54  3.000
 GG3  H221  C22  C26   109.85  3.000
 GG3  H222  C22  C6    110.03  3.000
 GG3  H221  C22  C6    107.78  3.000
 GG3  C26   C22  C6    114.56  3.000
 GG3  H262  C26  H261  107.67  3.000
 GG3  H262  C26  C27   107.95  3.000
 GG3  H261  C26  C27   110.35  3.000
 GG3  H262  C26  C22   109.76  3.000
 GG3  H261  C26  C22   109.91  3.000
 GG3  C27   C26  C22   111.13  3.000
 GG3  H272  C27  H271  107.78  3.000
 GG3  H272  C27  C28   109.28  3.000
 GG3  H271  C27  C28   109.61  3.000
 GG3  H272  C27  C26   110.24  3.000
 GG3  H271  C27  C26   106.43  3.000
 GG3  C28   C27  C26   113.32  3.000
 GG3  C29   C28  C33   118.75  3.000
 GG3  C29   C28  C27   120.12  3.000
 GG3  C33   C28  C27   121.12  3.000
 GG3  H33   C33  C32   119.69  3.000
 GG3  H33   C33  C28   119.25  3.000
 GG3  C32   C33  C28   121.06  3.000
 GG3  H32   C32  C31   120.14  3.000
 GG3  H32   C32  C33   119.94  3.000
 GG3  C31   C32  C33   119.92  3.000
 GG3  H31   C31  C30   120.34  3.000
 GG3  H31   C31  C32   120.27  3.000
 GG3  C30   C31  C32   119.39  3.000
 GG3  H30   C30  C29   119.59  3.000
 GG3  H30   C30  C31   119.65  3.000
 GG3  C29   C30  C31   120.76  3.000
 GG3  H29   C29  C30   120.76  3.000
 GG3  H29   C29  C28   119.11  3.000
 GG3  C30   C29  C28   120.12  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
 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  -113.76  30.0  2
 GG3  Var_02    C28   C27  C26  C22   174.19  30.0  3
 GG3  Var_03    C22   C6   N13  C2    -57.00  30.0  1
 GG3  Var_04    O13   C8   C7   C2    174.89  30.0  3
 GG3  Var_05    C27   C26  C22  C6    172.35  30.0  3
 GG3  Var_06    C7    C2   N13  C6    171.08  30.0  1
 GG3  Var_07    O10   P9   C8   C7     30.75  30.0  3
 GG3  Var_08    O16   P14  C8   C7     43.79  30.0  3
 GG3  Var_09    N13   C2   C7   C8   -150.78  30.0  2
 GG3  Var_10    C26   C22  C6   N13   -50.91  30.0  3
 GG3  Var_11    H211  C21  N13  C2     58.63  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

