# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  1 08:06:38 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(naphthalen-1-yl)pentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)C[C@@H](CCCc1cccc2ccccc12)C[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
 LC5  LC5  '[(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(naphthalen-1-yl)pentyl]phosphonic acid'  ligand  47  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LC5
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
 LC5  O12  O  O      0  -0.502  -2.1451   2.2709  -1.0260
 LC5  C4   C  C      0   0.544  -2.9897   1.9563  -0.1972
 LC5  N9   N  NT     0  -0.207  -4.0000   2.8118   0.1006
 LC5  O10  O  OH1    0  -0.549  -4.8792   2.4911   1.1013
 LC5  C11  C  CH3    0  -0.514  -4.1386   4.1516  -0.4105
 LC5  C3   C  CH2    0  -0.594  -3.0203   0.6162   0.4973
 LC5  C2   C  CH1    0  -0.203  -1.7660  -0.2281   0.2851
 LC5  C1   C  CH2    0  -0.713  -2.0504  -1.6863   0.6516
 LC5  P5   P  P      0   1.166  -3.1794  -2.6299  -0.4935
 LC5  O6   O  OP    -1  -0.914  -3.1495  -4.0669   0.0509
 LC5  O7   O  OP    -1  -0.895  -4.5733  -1.9811  -0.3889
 LC5  O8   O  O      0  -0.911  -2.5481  -2.4855  -1.8864
 LC5  C13  C  CH2    0  -0.402  -0.5961   0.3477   1.0910
 LC5  C14  C  CH2    0  -0.418   0.7741  -0.1832   0.6895
 LC5  C15  C  CH2    0  -0.536   1.8823   0.3356   1.6104
 LC5  C16  C  CR6    0   0.130   3.2524  -0.1250   1.1974
 LC5  C17  C  CR6    0   0.078   3.9692   0.5242   0.1480
 LC5  C23  C  C1     0  -0.337   3.4564   1.6525  -0.5387
 LC5  C25  C  C1     0  -0.252   4.1705   2.2626  -1.5347
 LC5  C24  C  C1     0  -0.262   5.4407   1.7762  -1.9035
 LC5  C22  C  C1     0  -0.312   5.9653   0.6875  -1.2636
 LC5  C19  C  CR6    0   0.117   5.2499   0.0354  -0.2308
 LC5  C21  C  CR16   0  -0.340   5.7906  -1.0916   0.4312
 LC5  C20  C  CR16   0  -0.240   5.0883  -1.7031   1.4308
 LC5  C18  C  CR16   0  -0.343   3.8225  -1.2137   1.8100
 LC5  H1   H  HOH1   0   0.474  -5.6458   2.0844   0.6742
 LC5  H2   H  HCH3   0   0.241  -5.1272   4.2912  -0.8503
 LC5  H3   H  HCH3   0   0.242  -3.9985   4.8891   0.3818
 LC5  H4   H  HCH3   0   0.253  -3.3928   4.3208  -1.1801
 LC5  H5   H  HCH2   0   0.238  -3.1939   0.7503   1.5688
 LC5  H6   H  HCH2   0   0.290  -3.8856   0.0535   0.1265
 LC5  H7   H  HCH1   0   0.196  -1.5031  -0.1997  -0.7767
 LC5  H8   H  HCH2   0   0.195  -1.1049  -2.2384   0.6806
 LC5  H9   H  HCH2   0   0.177  -2.4402  -1.7280   1.6778
 LC5  H12  H  HCH2   0   0.215  -0.5751   1.4375   0.9911
 LC5  H13  H  HCH2   0   0.196  -0.7656   0.1441   2.1559
 LC5  H14  H  HCH2   0   0.223   0.7897  -1.2768   0.7131
 LC5  H15  H  HCH2   0   0.219   0.9809   0.1029  -0.3464
 LC5  H16  H  HCH2   0   0.235   1.8373   1.4272   1.6585
 LC5  H17  H  HCH2   0   0.248   1.6840  -0.0144   2.6266
 LC5  H18  H  H      0   0.248   2.4840   2.0468  -0.2753
 LC5  H19  H  H      0   0.257   3.7581   3.1245  -2.0431
 LC5  H20  H  H      0   0.256   5.9985   2.2673  -2.6902
 LC5  H21  H  H      0   0.253   6.9419   0.3086  -1.5396
 LC5  H22  H  HCR6   0   0.252   6.7662  -1.4591   0.1365
 LC5  H23  H  HCR6   0   0.254   5.5002  -2.5650   1.9400
 LC5  H24  H  HCR6   0   0.247   3.2849  -1.7127   2.6081

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
 LC5  C20  C21  aromatic  1.366  0.020  1.366
 LC5  C20  C18  aromatic  1.409  0.020  1.409
 LC5  C21  C19  aromatic  1.414  0.020  1.414
 LC5  C18  C16  aromatic  1.373  0.020  1.373
 LC5  C19  C22  aromatic  1.416  0.020  1.416
 LC5  C19  C17  aromatic  1.422  0.020  1.422
 LC5  C22  C24  aromatic  1.367  0.020  1.367
 LC5  C16  C17  aromatic  1.427  0.020  1.427
 LC5  C16  C15  single    1.503  0.020  1.503
 LC5  C17  C23  aromatic  1.417  0.020  1.417
 LC5  C15  C14  single    1.531  0.020  1.531
 LC5  C24  C25  aromatic  1.409  0.020  1.409
 LC5  O10  N9   single    1.370  0.020  1.370
 LC5  C23  C25  aromatic  1.369  0.020  1.369
 LC5  C11  N9   single    1.441  0.020  1.441
 LC5  C13  C14  single    1.523  0.020  1.523
 LC5  C13  C2   single    1.533  0.020  1.533
 LC5  N9   C4   single    1.357  0.020  1.357
 LC5  O8   P5   deloc     1.536  0.020  1.536
 LC5  C4   O12  double    1.224  0.020  1.224
 LC5  C4   C3   single    1.510  0.020  1.510
 LC5  C2   C3   single    1.527  0.020  1.527
 LC5  C2   C1   single    1.530  0.020  1.530
 LC5  C1   P5   single    1.864  0.020  1.864
 LC5  P5   O6   deloc     1.537  0.020  1.537
 LC5  P5   O7   deloc     1.541  0.020  1.541
 LC5  O10  H1   single    0.850  0.020  0.980
 LC5  C11  H2   single    0.970  0.020  1.090
 LC5  C11  H3   single    0.970  0.020  1.090
 LC5  C11  H4   single    0.970  0.020  1.090
 LC5  C3   H5   single    0.970  0.020  1.090
 LC5  C3   H6   single    0.970  0.020  1.090
 LC5  C2   H7   single    0.970  0.020  1.090
 LC5  C1   H8   single    0.970  0.020  1.090
 LC5  C1   H9   single    0.970  0.020  1.090
 LC5  C13  H12  single    0.970  0.020  1.090
 LC5  C13  H13  single    0.970  0.020  1.090
 LC5  C14  H14  single    0.970  0.020  1.090
 LC5  C14  H15  single    0.970  0.020  1.090
 LC5  C15  H16  single    0.970  0.020  1.090
 LC5  C15  H17  single    0.970  0.020  1.090
 LC5  C23  H18  single    0.930  0.020  1.080
 LC5  C25  H19  single    0.930  0.020  1.080
 LC5  C24  H20  single    0.930  0.020  1.080
 LC5  C22  H21  single    0.930  0.020  1.080
 LC5  C21  H22  single    0.930  0.020  1.080
 LC5  C20  H23  single    0.930  0.020  1.080
 LC5  C18  H24  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
 LC5  C3   C4   N9   116.34  3.000
 LC5  C3   C4   O12  123.60  3.000
 LC5  N9   C4   O12  120.01  3.000
 LC5  C11  N9   O10  114.52  3.000
 LC5  C11  N9   C4   125.46  3.000
 LC5  O10  N9   C4   119.37  3.000
 LC5  H1   O10  N9   106.53  3.000
 LC5  H4   C11  H3   108.74  3.000
 LC5  H4   C11  H2   108.49  3.000
 LC5  H3   C11  H2   108.81  3.000
 LC5  H4   C11  N9   109.30  3.000
 LC5  H3   C11  N9   111.01  3.000
 LC5  H2   C11  N9   110.44  3.000
 LC5  H6   C3   H5   105.60  3.000
 LC5  H6   C3   C2   108.51  3.000
 LC5  H5   C3   C2   109.54  3.000
 LC5  H6   C3   C4   108.41  3.000
 LC5  H5   C3   C4   110.19  3.000
 LC5  C2   C3   C4   114.22  3.000
 LC5  H7   C2   C13  108.49  3.000
 LC5  H7   C2   C1   107.57  3.000
 LC5  C13  C2   C1   111.95  3.000
 LC5  H7   C2   C3   108.54  3.000
 LC5  C1   C2   C3   109.93  3.000
 LC5  C13  C2   C3   110.25  3.000
 LC5  H9   C1   H8   105.22  3.000
 LC5  H9   C1   P5   109.85  3.000
 LC5  H8   C1   P5   106.49  3.000
 LC5  H9   C1   C2   109.02  3.000
 LC5  H8   C1   C2   109.04  3.000
 LC5  P5   C1   C2   116.60  3.000
 LC5  O8   P5   O7   113.19  3.000
 LC5  O7   P5   O6   112.78  3.000
 LC5  O8   P5   O6   113.64  3.000
 LC5  O7   P5   C1   107.04  3.000
 LC5  O6   P5   C1   104.12  3.000
 LC5  O8   P5   C1   105.10  3.000
 LC5  H13  C13  H12  106.04  3.000
 LC5  H13  C13  C14  109.27  3.000
 LC5  H12  C13  C14  107.79  3.000
 LC5  H13  C13  C2   108.83  3.000
 LC5  H12  C13  C2   109.91  3.000
 LC5  C14  C13  C2   114.65  3.000
 LC5  H15  C14  H14  106.20  3.000
 LC5  H15  C14  C15  110.12  3.000
 LC5  H14  C14  C15  108.38  3.000
 LC5  H15  C14  C13  109.17  3.000
 LC5  H14  C14  C13  110.82  3.000
 LC5  C15  C14  C13  111.98  3.000
 LC5  H17  C15  H16  105.74  3.000
 LC5  H17  C15  C16  108.83  3.000
 LC5  H16  C15  C16  110.81  3.000
 LC5  H17  C15  C14  108.63  3.000
 LC5  H16  C15  C14  109.56  3.000
 LC5  C16  C15  C14  112.99  3.000
 LC5  C18  C16  C17  118.70  3.000
 LC5  C17  C16  C15  121.36  3.000
 LC5  C18  C16  C15  119.91  3.000
 LC5  C19  C17  C23  118.07  3.000
 LC5  C23  C17  C16  122.47  3.000
 LC5  C19  C17  C16  119.46  3.000
 LC5  H18  C23  C25  118.92  3.000
 LC5  H18  C23  C17  119.83  3.000
 LC5  C25  C23  C17  121.25  3.000
 LC5  H19  C25  C24  119.69  3.000
 LC5  H19  C25  C23  119.86  3.000
 LC5  C24  C25  C23  120.44  3.000
 LC5  H20  C24  C22  120.25  3.000
 LC5  H20  C24  C25  119.87  3.000
 LC5  C22  C24  C25  119.88  3.000
 LC5  H21  C22  C19  118.71  3.000
 LC5  H21  C22  C24  120.34  3.000
 LC5  C19  C22  C24  120.95  3.000
 LC5  C21  C19  C22  121.02  3.000
 LC5  C22  C19  C17  119.41  3.000
 LC5  C21  C19  C17  119.57  3.000
 LC5  H22  C21  C20  120.67  3.000
 LC5  H22  C21  C19  119.16  3.000
 LC5  C20  C21  C19  120.17  3.000
 LC5  H23  C20  C18  119.46  3.000
 LC5  H23  C20  C21  120.33  3.000
 LC5  C18  C20  C21  120.21  3.000
 LC5  H24  C18  C20  118.93  3.000
 LC5  H24  C18  C16  119.18  3.000
 LC5  C20  C18  C16  121.89  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
 LC5  CONST_01  C21  C20  C18  C16     0.00   0.0  0
 LC5  CONST_02  C21  C19  C17  C16     0.00   0.0  0
 LC5  CONST_03  C22  C19  C17  C16   180.00   0.0  0
 LC5  CONST_04  C25  C23  C17  C16   180.00   0.0  0
 LC5  CONST_05  C20  C21  C19  C17     0.00   0.0  0
 LC5  CONST_06  C24  C22  C19  C17     0.00   0.0  0
 LC5  CONST_07  C20  C18  C16  C17     0.00   0.0  0
 LC5  CONST_08  C24  C25  C23  C17     0.00   0.0  0
 LC5  CONST_09  C21  C19  C17  C23   180.00   0.0  0
 LC5  CONST_10  C22  C19  C17  C23     0.00   0.0  0
 LC5  CONST_11  C18  C16  C17  C23   180.00   0.0  0
 LC5  CONST_12  C22  C24  C25  C23     0.00   0.0  0
 LC5  CONST_13  C19  C22  C24  C25     0.00   0.0  0
 LC5  CONST_14  C19  C17  C23  C25     0.00   0.0  0
 LC5  CONST_15  C21  C19  C22  C24   180.00   0.0  0
 LC5  CONST_16  C20  C21  C19  C22   180.00   0.0  0
 LC5  CONST_17  C18  C20  C21  C19     0.00   0.0  0
 LC5  CONST_18  C18  C16  C17  C19     0.00   0.0  0
 LC5  CONST_19  C20  C18  C16  C15   180.00   0.0  0
 LC5  CONST_20  C19  C17  C16  C15   180.00   0.0  0
 LC5  CONST_21  C23  C17  C16  C15     0.00   0.0  0
 LC5  CONST_22  H23  C20  C18  C16   180.00   0.0  0
 LC5  CONST_23  H18  C23  C17  C16     0.00   0.0  0
 LC5  CONST_24  H22  C21  C19  C17   180.00   0.0  0
 LC5  CONST_25  H21  C22  C19  C17   180.00   0.0  0
 LC5  CONST_26  H24  C18  C16  C17   180.00   0.0  0
 LC5  CONST_27  H19  C25  C23  C17   180.00   0.0  0
 LC5  CONST_28  H20  C24  C25  C23   180.00   0.0  0
 LC5  CONST_29  O10  N9   C4   O12   180.00   0.0  0
 LC5  CONST_30  C11  N9   C4   O12     0.00   0.0  0
 LC5  CONST_31  C3   C4   N9   O10     0.00   0.0  0
 LC5  CONST_32  C3   C4   N9   C11   180.00   0.0  0
 LC5  Var_01    C18  C16  C15  C14   -97.59  30.0  2
 LC5  Var_02    C16  C15  C14  C13  -177.42  30.0  1
 LC5  Var_03    C2   C3   C4   O12    10.95  30.0  3
 LC5  Var_04    C15  C14  C13  C2   -174.98  30.0  3
 LC5  Var_05    O8   P5   C1   C2     54.63  30.0  3
 LC5  Var_06    H2   C11  N9   C4    127.47  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
 LC5  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
 LC5  plan-1  C15  0.020
 LC5  plan-1  C16  0.020
 LC5  plan-1  C17  0.020
 LC5  plan-1  C23  0.020
 LC5  plan-1  C25  0.020
 LC5  plan-1  C24  0.020
 LC5  plan-1  C22  0.020
 LC5  plan-1  C19  0.020
 LC5  plan-1  C21  0.020
 LC5  plan-1  C20  0.020
 LC5  plan-1  C18  0.020
 LC5  plan-1  H18  0.020
 LC5  plan-1  H19  0.020
 LC5  plan-1  H20  0.020
 LC5  plan-1  H21  0.020
 LC5  plan-1  H22  0.020
 LC5  plan-1  H23  0.020
 LC5  plan-1  H24  0.020
 LC5  plan-2  O12  0.020
 LC5  plan-2  C4   0.020
 LC5  plan-2  N9   0.020
 LC5  plan-2  O10  0.020
 LC5  plan-2  C11  0.020
 LC5  plan-2  C3   0.020

