# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 01:42:34 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: {5-[(3-aminopropyl)amino]pentyl}boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNCCCCCB(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
 OKP  OKP  '{5-[(3-aminopropyl)amino]pentyl}boronic acid'  ligand  34  13  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OKP
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
 OKP  C10  C  CH2   0  -0.667  -3.9309  -0.6733  -0.0397
 OKP  B11  B  B     0   0.528  -5.3258   0.0657   0.0206
 OKP  C02  C  CH2   0  -0.274   6.0804  -0.3530   0.0408
 OKP  C03  C  CH2   0  -0.453   4.7745   0.4268   0.0538
 OKP  C04  C  CH2   0  -0.253   3.5572  -0.4833   0.0168
 OKP  C06  C  CH2   0  -0.248   1.1408  -0.5628  -0.0134
 OKP  C07  C  CH2   0  -0.441  -0.1374   0.2609   0.0166
 OKP  C08  C  CH2   0  -0.406  -1.3915  -0.6023  -0.0418
 OKP  C09  C  CH2   0  -0.421  -2.6834   0.2054   0.0088
 OKP  N01  N  NH2   0  -0.800   7.2241   0.5484   0.0679
 OKP  N05  N  NH1   0  -0.600   2.3222   0.2766   0.0554
 OKP  O12  O  OH1   0  -0.635  -6.4420  -0.7140   0.1555
 OKP  O13  O  OH1   0  -0.631  -5.3635   1.4263  -0.0732
 OKP  H1   H  HCH2  0   0.228  -3.8892  -1.4073   0.7742
 OKP  H2   H  HCH2  0   0.232  -3.9097  -1.2814  -0.9537
 OKP  H3   H  HCH2  0   0.213   6.1243  -0.9877   0.9304
 OKP  H4   H  HCH2  0   0.189   6.0820  -1.0346  -0.8223
 OKP  H5   H  HCH2  0   0.218   4.7347   1.0572   0.9466
 OKP  H6   H  HCH2  0   0.214   4.7490   1.1008  -0.8108
 OKP  H7   H  HCH2  0   0.183   3.6186  -1.1409  -0.8666
 OKP  H8   H  HCH2  0   0.211   3.5773  -1.1469   0.8881
 OKP  H9   H  HCH2  0   0.210   1.1517  -1.2387   0.8486
 OKP  H10  H  HCH2  0   0.181   1.1362  -1.2098  -0.9068
 OKP  H11  H  HCH2  0   0.212  -0.1486   0.8708   0.9255
 OKP  H12  H  HCH2  0   0.211  -0.1398   0.9610  -0.8268
 OKP  H13  H  HCH2  0   0.206  -1.3780  -1.2055  -0.9569
 OKP  H14  H  HCH2  0   0.206  -1.3795  -1.3157   0.7900
 OKP  H15  H  HCH2  0   0.208  -2.6917   0.9165  -0.8231
 OKP  H16  H  HCH2  0   0.207  -2.6887   0.8111   0.9211
 OKP  H17  H  HNH2  0   0.345   8.0785   0.0065   0.0935
 OKP  H18  H  HNH2  0   0.337   7.2585   1.0632  -0.8036
 OKP  H20  H  HNH1  0   0.333   2.3108   0.9145  -0.7335
 OKP  H22  H  HOH1  0   0.477  -7.2817  -0.2440   0.1741
 OKP  H19  H  HOH1  0   0.479  -6.2395   1.8226  -0.0350

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
 OKP  C07  C08  single  1.524  0.020  1.524
 OKP  C07  C06  single  1.521  0.020  1.521
 OKP  C08  C09  single  1.525  0.020  1.525
 OKP  N05  C06  single  1.451  0.020  1.451
 OKP  N05  C04  single  1.451  0.020  1.451
 OKP  C02  N01  single  1.457  0.020  1.457
 OKP  C02  C03  single  1.521  0.020  1.521
 OKP  C04  C03  single  1.520  0.020  1.520
 OKP  C09  C10  single  1.527  0.020  1.527
 OKP  C10  B11  single  1.580  0.020  1.580
 OKP  O12  B11  single  1.368  0.020  1.368
 OKP  B11  O13  single  1.364  0.020  1.364
 OKP  C10  H1   single  0.970  0.020  1.090
 OKP  C10  H2   single  0.970  0.020  1.090
 OKP  C02  H3   single  0.970  0.020  1.090
 OKP  C02  H4   single  0.970  0.020  1.090
 OKP  C03  H5   single  0.970  0.020  1.090
 OKP  C03  H6   single  0.970  0.020  1.090
 OKP  C04  H7   single  0.970  0.020  1.090
 OKP  C04  H8   single  0.970  0.020  1.090
 OKP  C06  H9   single  0.970  0.020  1.090
 OKP  C06  H10  single  0.970  0.020  1.090
 OKP  C07  H11  single  0.970  0.020  1.090
 OKP  C07  H12  single  0.970  0.020  1.090
 OKP  C08  H13  single  0.970  0.020  1.090
 OKP  C08  H14  single  0.970  0.020  1.090
 OKP  C09  H15  single  0.970  0.020  1.090
 OKP  C09  H16  single  0.970  0.020  1.090
 OKP  N01  H17  single  0.890  0.020  1.040
 OKP  N01  H18  single  0.890  0.020  1.040
 OKP  N05  H20  single  0.890  0.020  1.040
 OKP  O12  H22  single  0.850  0.020  0.980
 OKP  O13  H19  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
 OKP  H2   C10  H1   104.26  3.000
 OKP  H2   C10  C09  109.24  3.000
 OKP  H1   C10  C09  109.30  3.000
 OKP  H2   C10  B11  107.93  3.000
 OKP  H1   C10  B11  108.56  3.000
 OKP  C09  C10  B11  116.81  3.000
 OKP  O13  B11  O12  123.55  3.000
 OKP  O13  B11  C10  119.23  3.000
 OKP  O12  B11  C10  117.23  3.000
 OKP  H4   C02  H3   106.18  3.000
 OKP  H4   C02  N01  113.39  3.000
 OKP  H3   C02  N01  108.21  3.000
 OKP  H4   C02  C03  109.01  3.000
 OKP  H3   C02  C03  108.97  3.000
 OKP  N01  C02  C03  110.90  3.000
 OKP  H6   C03  H5   106.77  3.000
 OKP  H6   C03  C04  109.27  3.000
 OKP  H5   C03  C04  109.62  3.000
 OKP  H6   C03  C02  109.17  3.000
 OKP  H5   C03  C02  109.50  3.000
 OKP  C04  C03  C02  112.35  3.000
 OKP  H8   C04  H7   105.96  3.000
 OKP  H8   C04  N05  108.17  3.000
 OKP  H7   C04  N05  112.40  3.000
 OKP  H8   C04  C03  109.18  3.000
 OKP  H7   C04  C03  109.37  3.000
 OKP  N05  C04  C03  111.56  3.000
 OKP  H10  C06  H9   105.99  3.000
 OKP  H10  C06  N05  112.40  3.000
 OKP  H9   C06  N05  108.16  3.000
 OKP  H10  C06  C07  109.28  3.000
 OKP  H9   C06  C07  109.09  3.000
 OKP  N05  C06  C07  111.72  3.000
 OKP  H12  C07  H11  106.44  3.000
 OKP  H12  C07  C08  109.31  3.000
 OKP  H11  C07  C08  109.82  3.000
 OKP  H12  C07  C06  109.42  3.000
 OKP  H11  C07  C06  109.07  3.000
 OKP  C08  C07  C06  112.59  3.000
 OKP  H14  C08  H13  105.98  3.000
 OKP  H14  C08  C09  109.21  3.000
 OKP  H13  C08  C09  109.25  3.000
 OKP  H14  C08  C07  109.32  3.000
 OKP  H13  C08  C07  109.49  3.000
 OKP  C09  C08  C07  113.33  3.000
 OKP  H16  C09  H15  105.89  3.000
 OKP  H16  C09  C08  108.95  3.000
 OKP  H15  C09  C08  108.99  3.000
 OKP  H16  C09  C10  109.93  3.000
 OKP  H15  C09  C10  110.10  3.000
 OKP  C08  C09  C10  112.74  3.000
 OKP  H18  N01  H17  105.39  3.000
 OKP  H18  N01  C02  108.98  3.000
 OKP  H17  N01  C02  109.39  3.000
 OKP  H20  N05  C06  108.52  3.000
 OKP  H20  N05  C04  108.56  3.000
 OKP  C06  N05  C04  112.89  3.000
 OKP  H22  O12  B11  115.81  3.000
 OKP  H19  O13  B11  115.66  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
 OKP  Var_01  C07  C08  C09  C10  -179.56  30.0  1
 OKP  Var_02  C08  C09  C10  B11   179.46  30.0  1
 OKP  Var_03  N05  C04  C03  C02   178.91  30.0  1
 OKP  Var_04  C06  N05  C04  C03   178.51  30.0  1
 OKP  Var_05  C07  C06  N05  C04  -179.49  30.0  3
 OKP  Var_06  N01  C02  C03  C04   179.62  30.0  1
 OKP  Var_07  C09  C08  C07  C06   179.12  30.0  3
 OKP  Var_08  N05  C06  C07  C08  -179.47  30.0  3
 OKP  Var_09  O12  B11  C10  C09  -171.61  30.0  3
 OKP  Var_10  H17  N01  C02  C03   177.91  30.0  3

