# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 02:59:45 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: [(1S)-4-[hydroxy(methyl)amino]-1-(4-methylphenyl)-4-oxobutyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)CC[C@@H](c1ccc(C)cc1)[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
 IB3  IB3  '[(1S)-4-[hydroxy(methyl)amino]-1-(4-methylphenyl)-4-oxobutyl]phosphonic acid'  ligand  35  19  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IB3
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
 IB3  C1   C  CR16   0  -0.295   3.9867  -0.4799   1.1817
 IB3  C2   C  CR16   0  -0.293   2.6931   0.0072   1.2815
 IB3  C3   C  CR6    0   0.171   1.7271  -0.2680   0.3113
 IB3  C4   C  CR16   0  -0.302   2.1314  -1.0369  -0.7791
 IB3  C5   C  CR16   0  -0.297   3.4283  -1.5270  -0.8811
 IB3  C6   C  CR6    0   0.069   4.3840  -1.2565   0.0931
 IB3  P8   P  P      0   1.185   0.3344   2.0087  -0.3750
 IB3  O11  O  O      0  -0.884  -1.0829   2.5621  -0.1430
 IB3  O10  O  OP    -1  -0.895   0.6526   1.7429  -1.8506
 IB3  C7   C  CH1    0  -0.570   0.3477   0.2958   0.4293
 IB3  C12  C  CH2    0  -0.413  -0.7300  -0.6329  -0.1410
 IB3  C13  C  CH2    0  -0.591  -2.1127  -0.3003   0.3992
 IB3  C14  C  C      0   0.546  -3.2019  -1.1636  -0.1874
 IB3  N16  N  NT     0  -0.208  -4.4727  -0.8634   0.1817
 IB3  C17  C  CH3    0  -0.514  -5.6358  -1.6549  -0.1296
 IB3  O18  O  OH1    0  -0.549  -4.6661   0.0499   1.1863
 IB3  O15  O  O      0  -0.503  -2.9858  -2.0775  -0.9722
 IB3  C19  C  CH3    0  -0.723   5.7944  -1.7597  -0.0286
 IB3  H1   H  HCR6   0   0.229   4.7044  -0.2513   1.9628
 IB3  H2   H  HCR6   0   0.219   2.4166   0.6090   2.1386
 IB3  H3   H  HCR6   0   0.227   1.4237  -1.2712  -1.5634
 IB3  H4   H  HCR6   0   0.229   3.7011  -2.1296  -1.7411
 IB3  H7   H  HCH1   0   0.193   0.1444   0.4491   1.4973
 IB3  H8   H  HCH2   0   0.206  -0.7319  -0.5558  -1.2308
 IB3  H9   H  HCH2   0   0.204  -0.4898  -1.6757   0.0910
 IB3  H10  H  HCH2   0   0.246  -2.1229  -0.4179   1.4880
 IB3  H11  H  HCH2   0   0.280  -2.3053   0.7598   0.2164
 IB3  H12  H  HCH3   0   0.242  -6.4424  -1.0156  -0.4902
 IB3  H13  H  HCH3   0   0.253  -5.3887  -2.3677  -0.9094
 IB3  H14  H  HCH3   0   0.241  -5.9865  -2.2027   0.7474
 IB3  H15  H  HOH1   0   0.475  -4.9132   0.8793   0.7552
 IB3  H16  H  HCH3   0   0.239   6.4653  -0.9782  -0.3933
 IB3  H17  H  HCH3   0   0.236   6.1878  -2.0924   0.9326
 IB3  H18  H  HCH3   0   0.236   5.8633  -2.5957  -0.7246
 IB3  O9   O  OP    -1  -0.890   1.4150   2.7962   0.3724

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
 IB3  C19  C6   single    1.502  0.020  1.502
 IB3  C6   C5   aromatic  1.391  0.020  1.391
 IB3  C6   C1   aromatic  1.395  0.020  1.395
 IB3  C5   C4   aromatic  1.390  0.020  1.390
 IB3  C1   C2   aromatic  1.386  0.020  1.386
 IB3  C17  N16  single    1.441  0.020  1.441
 IB3  C4   C3   aromatic  1.394  0.020  1.394
 IB3  C2   C3   aromatic  1.397  0.020  1.397
 IB3  C3   C7   single    1.495  0.020  1.495
 IB3  N16  O18  single    1.371  0.020  1.371
 IB3  N16  C14  single    1.357  0.020  1.357
 IB3  C13  C14  single    1.509  0.020  1.509
 IB3  C13  C12  single    1.521  0.020  1.521
 IB3  C7   C12  single    1.533  0.020  1.533
 IB3  C7   P8   single    1.892  0.020  1.892
 IB3  C14  O15  double    1.224  0.020  1.224
 IB3  O11  P8   deloc     1.539  0.020  1.539
 IB3  O9   P8   deloc     1.532  0.020  1.532
 IB3  P8   O10  deloc     1.533  0.020  1.533
 IB3  C1   H1   single    0.930  0.020  1.080
 IB3  C2   H2   single    0.930  0.020  1.080
 IB3  C4   H3   single    0.930  0.020  1.080
 IB3  C5   H4   single    0.930  0.020  1.080
 IB3  C7   H7   single    0.970  0.020  1.090
 IB3  C12  H8   single    0.970  0.020  1.090
 IB3  C12  H9   single    0.970  0.020  1.090
 IB3  C13  H10  single    0.970  0.020  1.090
 IB3  C13  H11  single    0.970  0.020  1.090
 IB3  C17  H12  single    0.970  0.020  1.090
 IB3  C17  H13  single    0.970  0.020  1.090
 IB3  C17  H14  single    0.970  0.020  1.090
 IB3  O18  H15  single    0.850  0.020  0.980
 IB3  C19  H16  single    0.970  0.020  1.090
 IB3  C19  H17  single    0.970  0.020  1.090
 IB3  C19  H18  single    0.970  0.020  1.090

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
 IB3  H1   C1   C6   119.39  3.000
 IB3  H1   C1   C2   119.44  3.000
 IB3  C6   C1   C2   121.18  3.000
 IB3  H2   C2   C3   118.86  3.000
 IB3  H2   C2   C1   119.37  3.000
 IB3  C3   C2   C1   121.76  3.000
 IB3  C7   C3   C4   122.51  3.000
 IB3  C7   C3   C2   120.60  3.000
 IB3  C4   C3   C2   116.84  3.000
 IB3  H3   C4   C5   118.73  3.000
 IB3  H3   C4   C3   119.78  3.000
 IB3  C5   C4   C3   121.49  3.000
 IB3  H4   C5   C6   119.36  3.000
 IB3  H4   C5   C4   119.24  3.000
 IB3  C6   C5   C4   121.40  3.000
 IB3  C19  C6   C5   121.54  3.000
 IB3  C5   C6   C1   117.33  3.000
 IB3  C19  C6   C1   121.13  3.000
 IB3  C7   P8   O10  104.52  3.000
 IB3  O10  P8   O11  113.49  3.000
 IB3  C7   P8   O11  105.54  3.000
 IB3  O10  P8   O9   114.35  3.000
 IB3  O11  P8   O9   113.03  3.000
 IB3  C7   P8   O9   104.65  3.000
 IB3  H7   C7   C12  108.44  3.000
 IB3  H7   C7   P8   106.60  3.000
 IB3  C12  C7   P8   112.66  3.000
 IB3  H7   C7   C3   107.48  3.000
 IB3  P8   C7   C3   108.32  3.000
 IB3  C12  C7   C3   113.01  3.000
 IB3  H9   C12  H8   106.20  3.000
 IB3  H9   C12  C13  109.42  3.000
 IB3  H8   C12  C13  109.70  3.000
 IB3  H9   C12  C7   110.12  3.000
 IB3  H8   C12  C7   109.25  3.000
 IB3  C13  C12  C7   111.99  3.000
 IB3  H11  C13  H10  105.60  3.000
 IB3  H11  C13  C14  111.28  3.000
 IB3  H10  C13  C14  108.56  3.000
 IB3  H11  C13  C12  108.23  3.000
 IB3  H10  C13  C12  109.75  3.000
 IB3  C14  C13  C12  113.14  3.000
 IB3  O15  C14  N16  120.33  3.000
 IB3  O15  C14  C13  123.31  3.000
 IB3  N16  C14  C13  116.35  3.000
 IB3  O18  N16  C17  114.22  3.000
 IB3  O18  N16  C14  118.60  3.000
 IB3  C17  N16  C14  125.15  3.000
 IB3  H14  C17  H13  108.71  3.000
 IB3  H14  C17  H12  108.80  3.000
 IB3  H13  C17  H12  108.41  3.000
 IB3  H14  C17  N16  111.18  3.000
 IB3  H13  C17  N16  109.41  3.000
 IB3  H12  C17  N16  110.27  3.000
 IB3  H15  O18  N16  106.30  3.000
 IB3  H18  C19  H17  107.82  3.000
 IB3  H18  C19  H16  107.26  3.000
 IB3  H17  C19  H16  106.91  3.000
 IB3  H18  C19  C6   111.59  3.000
 IB3  H17  C19  C6   111.68  3.000
 IB3  H16  C19  C6   111.34  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
 IB3  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 IB3  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 IB3  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 IB3  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 IB3  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 IB3  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 IB3  CONST_07  C7   C3   C2   C1    180.00   0.0  0
 IB3  CONST_08  C19  C6   C1   C2    180.00   0.0  0
 IB3  CONST_09  C19  C6   C5   C4    180.00   0.0  0
 IB3  CONST_10  C7   C3   C4   C5    180.00   0.0  0
 IB3  CONST_11  H4   C5   C6   C1    180.00   0.0  0
 IB3  CONST_12  H3   C4   C3   C2    180.00   0.0  0
 IB3  CONST_13  H1   C1   C2   C3    180.00   0.0  0
 IB3  CONST_14  H2   C2   C3   C4    180.00   0.0  0
 IB3  CONST_15  C17  N16  C14  C13   180.00   0.0  0
 IB3  CONST_16  O18  N16  C14  C13     0.00   0.0  0
 IB3  CONST_17  O15  C14  N16  C17     0.00   0.0  0
 IB3  CONST_18  O15  C14  N16  O18   180.00   0.0  0
 IB3  Var_01    H16  C19  C6   C1    -79.09  30.0  2
 IB3  Var_02    C14  C13  C12  C7    177.71  30.0  1
 IB3  Var_03    N16  C14  C13  C12  -175.75  30.0  3
 IB3  Var_04    H12  C17  N16  C14  -134.01  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
 IB3  chir_01  C7  C3  C12  P8  positiv

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
 IB3  plan-1  C1   0.020
 IB3  plan-1  C2   0.020
 IB3  plan-1  C3   0.020
 IB3  plan-1  C4   0.020
 IB3  plan-1  C5   0.020
 IB3  plan-1  C6   0.020
 IB3  plan-1  C7   0.020
 IB3  plan-1  C19  0.020
 IB3  plan-1  H1   0.020
 IB3  plan-1  H2   0.020
 IB3  plan-1  H3   0.020
 IB3  plan-1  H4   0.020
 IB3  plan-2  C13  0.020
 IB3  plan-2  C14  0.020
 IB3  plan-2  N16  0.020
 IB3  plan-2  C17  0.020
 IB3  plan-2  O18  0.020
 IB3  plan-2  O15  0.020

