# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 06:57:20 2021
#   Inital geometry file: a 113 line input string
#   Ligand name: [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(3-methoxyphenyl)pentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CCC[C@H](CC(=O)N(C)O)C[P](O)(O)=O)c1
#
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
 6JB  6JB  '[(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(3-methoxyphenyl)pentyl]phosphonic acid'  ligand  47  23  .  2021-08-05  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6JB
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
 6JB  C1   C  CH2   0  -0.768   0.1024  14.4044  21.5024
 6JB  C2   C  CH1   0  -0.250   1.1561  14.4002  20.3892
 6JB  C3   C  CH2   0  -0.556   2.4047  13.6641  20.9050
 6JB  C4   C  C     0   0.522   3.6159  14.0002  20.0745
 6JB  O7   O  OH1   0  -0.748  -0.8070  16.7999  20.8421
 6JB  O8   O  O     0  -0.714  -2.3532  14.8316  20.1411
 6JB  C11  C  CH3   0  -0.519   3.7970  11.7192  18.9881
 6JB  C15  C  CH2   0  -0.517  -0.4544  11.9186  17.7810
 6JB  C17  C  CR16  0  -0.436   1.1479  10.0928  17.1875
 6JB  C18  C  CR16  0  -0.341   1.3351  12.1827  16.0163
 6JB  C19  C  CR6   0   0.394   2.2243   9.5820  16.4698
 6JB  C20  C  CR16  0  -0.227   2.4147  11.6720  15.3017
 6JB  C21  C  CR16  0  -0.361   2.8635  10.3826  15.5194
 6JB  P5   P  P     0   1.373  -1.4016  15.3379  21.1650
 6JB  O6   O  OH1   0  -0.745  -2.0390  15.4347  22.6429
 6JB  N9   N  NT    0  -0.171   4.1999  13.0555  19.3307
 6JB  O10  O  OH1   0  -0.562   5.2948  13.4535  18.5990
 6JB  O12  O  O     0  -0.532   4.0920  15.1400  20.0764
 6JB  C13  C  CH2   0  -0.443   0.6586  13.8218  19.0587
 6JB  C16  C  CR6   0   0.152   0.6965  11.3958  16.9666
 6JB  C23  C  CH3   0  -0.436   2.1186   7.4869  17.5829
 6JB  H1   H  HCH2  0   0.291  -0.2046  13.3875  21.7610
 6JB  H2   H  HCH2  0   0.300   0.5409  14.8279  22.4102
 6JB  H3   H  HCH1  0   0.262   1.4512  15.4369  20.2093
 6JB  H4   H  HCH2  0   0.263   2.2149  12.5951  20.9853
 6JB  H5   H  HCH2  0   0.284   2.6350  14.0082  21.9162
 6JB  H6   H  HOH1  0   0.490  -1.4369  17.3874  20.4031
 6JB  H7   H  HCH3  0   0.255   2.9375  11.4203  19.5760
 6JB  H8   H  HCH3  0   0.263   3.5237  11.6640  17.9343
 6JB  H9   H  HCH3  0   0.261   4.6088  11.0196  19.1872
 6JB  H10  H  HCH2  0   0.238  -0.9495  12.5770  19.7470
 6JB  H11  H  HCH2  0   0.221   0.5783  11.7346  19.6698
 6JB  H12  H  HCH2  0   0.240  -0.9797  12.7006  17.2256
 6JB  H13  H  HCH2  0   0.248  -1.1774  11.1143  17.9354
 6JB  H14  H  HCR6  0   0.270   0.6365   9.4875  17.9255
 6JB  H15  H  HCR6  0   0.244   0.9905  13.1918  15.8274
 6JB  H16  H  HCR6  0   0.254   2.9113  12.2883  14.5631
 6JB  H17  H  HCR6  0   0.259   3.7024   9.9857  14.9610
 6JB  H18  H  HOH1  0   0.490  -2.9992  15.5437  22.6399
 6JB  H19  H  HOH1  0   0.468   5.3581  14.4060  18.7982
 6JB  H20  H  HCH2  0   0.241   1.5064  13.7597  18.3681
 6JB  H21  H  HCH2  0   0.239  -0.0328  14.5315  18.5960
 6JB  H22  H  HCH3  0   0.259   2.6593   6.5444  17.5417
 6JB  H23  H  HCH3  0   0.225   2.1996   7.8937  18.5948
 6JB  H24  H  HCH3  0   0.227   1.0642   7.2967  17.3648
 6JB  C14  C  CH2   0  -0.434  -0.0419  12.4726  19.1506
 6JB  O22  O  O2    0  -0.473   2.7135   8.3347  16.6219

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
 6JB  C20  C21  aromatic  1.382  0.020  1.382
 6JB  C20  C18  aromatic  1.392  0.020  1.392
 6JB  C21  C19  aromatic  1.397  0.020  1.397
 6JB  C18  C16  aromatic  1.389  0.020  1.389
 6JB  C19  O22  single    1.348  0.020  1.348
 6JB  C19  C17  aromatic  1.391  0.020  1.391
 6JB  O22  C23  single    1.413  0.020  1.413
 6JB  C16  C17  aromatic  1.397  0.020  1.397
 6JB  C16  C15  single    1.504  0.020  1.504
 6JB  C15  C14  single    1.534  0.020  1.534
 6JB  C11  N9   single    1.437  0.020  1.437
 6JB  O10  N9   single    1.376  0.020  1.376
 6JB  C13  C14  single    1.523  0.020  1.523
 6JB  C13  C2   single    1.534  0.020  1.534
 6JB  N9   C4   single    1.337  0.020  1.337
 6JB  O8   P5   double    1.487  0.020  1.487
 6JB  C4   O12  double    1.235  0.020  1.235
 6JB  C4   C3   single    1.507  0.020  1.507
 6JB  C2   C3   single    1.538  0.020  1.538
 6JB  C2   C1   single    1.533  0.020  1.533
 6JB  C1   P5   single    1.802  0.020  1.802
 6JB  P5   O6   single    1.612  0.020  1.612
 6JB  P5   O7   single    1.611  0.020  1.611
 6JB  C1   H1   single    0.970  0.020  1.090
 6JB  C1   H2   single    0.970  0.020  1.090
 6JB  C2   H3   single    0.970  0.020  1.090
 6JB  C3   H4   single    0.970  0.020  1.090
 6JB  C3   H5   single    0.970  0.020  1.090
 6JB  O7   H6   single    0.850  0.020  0.980
 6JB  C11  H7   single    0.970  0.020  1.090
 6JB  C11  H8   single    0.970  0.020  1.090
 6JB  C11  H9   single    0.970  0.020  1.090
 6JB  C14  H10  single    0.970  0.020  1.090
 6JB  C14  H11  single    0.970  0.020  1.090
 6JB  C15  H12  single    0.970  0.020  1.090
 6JB  C15  H13  single    0.970  0.020  1.090
 6JB  C17  H14  single    0.930  0.020  1.080
 6JB  C18  H15  single    0.930  0.020  1.080
 6JB  C20  H16  single    0.930  0.020  1.080
 6JB  C21  H17  single    0.930  0.020  1.080
 6JB  O6   H18  single    0.850  0.020  0.980
 6JB  O10  H19  single    0.850  0.020  0.980
 6JB  C13  H20  single    0.970  0.020  1.090
 6JB  C13  H21  single    0.970  0.020  1.090
 6JB  C23  H22  single    0.970  0.020  1.090
 6JB  C23  H23  single    0.970  0.020  1.090
 6JB  C23  H24  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
 6JB  H2   C1   H1   106.05  3.000
 6JB  H2   C1   P5   106.83  3.000
 6JB  H1   C1   P5   106.96  3.000
 6JB  H2   C1   C2   109.17  3.000
 6JB  H1   C1   C2   111.24  3.000
 6JB  P5   C1   C2   116.05  3.000
 6JB  H3   C2   C13  107.61  3.000
 6JB  H3   C2   C3   106.85  3.000
 6JB  C13  C2   C3   111.94  3.000
 6JB  H3   C2   C1   107.61  3.000
 6JB  C3   C2   C1   108.40  3.000
 6JB  C13  C2   C1   114.09  3.000
 6JB  H5   C3   H4   106.12  3.000
 6JB  H5   C3   C4   105.69  3.000
 6JB  H4   C3   C4   113.57  3.000
 6JB  H5   C3   C2   109.31  3.000
 6JB  H4   C3   C2   110.67  3.000
 6JB  C4   C3   C2   111.16  3.000
 6JB  O12  C4   N9   118.99  3.000
 6JB  O12  C4   C3   120.99  3.000
 6JB  N9   C4   C3   120.02  3.000
 6JB  H6   O7   P5   113.71  3.000
 6JB  H9   C11  H8   109.31  3.000
 6JB  H9   C11  H7   108.34  3.000
 6JB  H8   C11  H7   108.16  3.000
 6JB  H9   C11  N9   110.15  3.000
 6JB  H8   C11  N9   110.36  3.000
 6JB  H7   C11  N9   110.46  3.000
 6JB  H13  C15  H12  106.28  3.000
 6JB  H13  C15  C16  109.09  3.000
 6JB  H12  C15  C16  109.95  3.000
 6JB  H13  C15  C14  108.52  3.000
 6JB  H12  C15  C14  108.93  3.000
 6JB  C16  C15  C14  113.79  3.000
 6JB  H14  C17  C16  118.47  3.000
 6JB  H14  C17  C19  120.79  3.000
 6JB  C16  C17  C19  120.74  3.000
 6JB  H15  C18  C16  120.05  3.000
 6JB  H15  C18  C20  119.95  3.000
 6JB  C16  C18  C20  120.00  3.000
 6JB  O22  C19  C21  116.15  3.000
 6JB  O22  C19  C17  124.21  3.000
 6JB  C21  C19  C17  119.64  3.000
 6JB  H16  C20  C21  119.31  3.000
 6JB  H16  C20  C18  119.82  3.000
 6JB  C21  C20  C18  120.87  3.000
 6JB  H17  C21  C20  120.80  3.000
 6JB  H17  C21  C19  119.67  3.000
 6JB  C20  C21  C19  119.53  3.000
 6JB  O6   P5   O8   113.49  3.000
 6JB  O6   P5   O7   105.97  3.000
 6JB  O8   P5   O7   114.03  3.000
 6JB  O7   P5   C1   101.52  3.000
 6JB  O6   P5   C1   100.92  3.000
 6JB  O8   P5   C1   119.13  3.000
 6JB  H18  O6   P5   113.37  3.000
 6JB  O10  N9   C11  111.43  3.000
 6JB  O10  N9   C4   116.05  3.000
 6JB  C11  N9   C4   131.86  3.000
 6JB  H19  O10  N9   103.04  3.000
 6JB  H21  C13  H20  105.04  3.000
 6JB  H21  C13  C14  108.04  3.000
 6JB  H20  C13  C14  110.11  3.000
 6JB  H21  C13  C2   109.11  3.000
 6JB  H20  C13  C2   108.50  3.000
 6JB  C14  C13  C2   115.52  3.000
 6JB  C18  C16  C17  119.21  3.000
 6JB  C17  C16  C15  119.08  3.000
 6JB  C18  C16  C15  121.70  3.000
 6JB  H24  C23  H23  108.70  3.000
 6JB  H24  C23  H22  108.73  3.000
 6JB  H23  C23  H22  108.70  3.000
 6JB  H24  C23  O22  112.01  3.000
 6JB  H23  C23  O22  112.02  3.000
 6JB  H22  C23  O22  106.56  3.000
 6JB  H11  C14  H10  106.05  3.000
 6JB  H11  C14  C13  111.42  3.000
 6JB  H10  C14  C13  109.32  3.000
 6JB  H11  C14  C15  109.41  3.000
 6JB  H10  C14  C15  107.40  3.000
 6JB  C13  C14  C15  112.94  3.000
 6JB  C23  O22  C19  118.62  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
 6JB  CONST_01  C20  C21  C19  C17     0.00   0.0  0
 6JB  CONST_02  C20  C18  C16  C17     0.00   0.0  0
 6JB  CONST_03  C19  C21  C20  C18     0.00   0.0  0
 6JB  CONST_04  C19  C17  C16  C18     0.00   0.0  0
 6JB  CONST_05  C16  C18  C20  C21     0.00   0.0  0
 6JB  CONST_06  C16  C17  C19  C21     0.00   0.0  0
 6JB  CONST_07  C20  C18  C16  C15   180.00   0.0  0
 6JB  CONST_08  C19  C17  C16  C15   180.00   0.0  0
 6JB  CONST_09  O22  C19  C21  C20   180.00   0.0  0
 6JB  CONST_10  O22  C19  C17  C16   180.00   0.0  0
 6JB  CONST_11  H17  C21  C19  C17   180.00   0.0  0
 6JB  CONST_12  H15  C18  C16  C17   180.00   0.0  0
 6JB  CONST_13  H14  C17  C16  C18   180.00   0.0  0
 6JB  CONST_14  H16  C20  C21  C19   180.00   0.0  0
 6JB  CONST_15  C11  N9   C4   C3      0.00   0.0  0
 6JB  CONST_16  O10  N9   C4   C3    180.00   0.0  0
 6JB  CONST_17  O12  C4   N9   C11   180.00   0.0  0
 6JB  CONST_18  O12  C4   N9   O10     0.00   0.0  0
 6JB  Var_01    C18  C16  C15  C14   -95.21  30.0  2
 6JB  Var_02    C16  C15  C14  C13    73.88  30.0  2
 6JB  Var_03    H22  C23  O22  C19  -179.92  30.0  3
 6JB  Var_04    C15  C14  C13  C2   -177.23  30.0  3
 6JB  Var_05    N9   C4   C3   C2   -113.78  30.0  1
 6JB  Var_06    O8   P5   C1   C2     69.50  30.0  3
 6JB  Var_07    H7   C11  N9   C4    -10.14  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
 6JB  chir_01  C2  C13  C3  C1  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
 6JB  plan-1  C15  0.020
 6JB  plan-1  C17  0.020
 6JB  plan-1  C18  0.020
 6JB  plan-1  C19  0.020
 6JB  plan-1  C20  0.020
 6JB  plan-1  C21  0.020
 6JB  plan-1  C16  0.020
 6JB  plan-1  H14  0.020
 6JB  plan-1  H15  0.020
 6JB  plan-1  H16  0.020
 6JB  plan-1  H17  0.020
 6JB  plan-1  O22  0.020
 6JB  plan-2  C3   0.020
 6JB  plan-2  C4   0.020
 6JB  plan-2  C11  0.020
 6JB  plan-2  N9   0.020
 6JB  plan-2  O10  0.020
 6JB  plan-2  O12  0.020

