# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 06:40:58 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: [(2R)-5-(3-fluorophenyl)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}pentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)C[C@@H](CCCc1cccc(F)c1)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
 LC7  LC7  '[(2R)-5-(3-fluorophenyl)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}pentyl]phosphonic acid'  ligand  43  22  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LC7
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
 LC7  O12  O  O     0  -0.489  -2.0014   2.2509  -1.1979
 LC7  C4   C  C     0   0.555  -2.8191   1.9096  -0.3560
 LC7  N9   N  NT    0  -0.210  -3.8782   2.7013  -0.0598
 LC7  O10  O  OH1   0  -0.546  -4.8964   2.1649   0.6872
 LC7  C11  C  CH3   0  -0.516  -4.2455   3.8775  -0.8101
 LC7  C3   C  CH2   0  -0.567  -2.7186   0.6118   0.4158
 LC7  C2   C  CH1   0  -0.247  -1.3822  -0.1029   0.2266
 LC7  C1   C  CH2   0  -0.763  -1.4970  -1.5500   0.7364
 LC7  P5   P  P     0   1.373  -2.2984  -2.6689  -0.4268
 LC7  O7   O  OH1   0  -0.750  -1.3063  -2.8025  -1.6903
 LC7  O6   O  OH1   0  -0.745  -2.2189  -4.0612   0.3748
 LC7  O8   O  O     0  -0.714  -3.6465  -2.2893  -0.9187
 LC7  C13  C  CH2   0  -0.417  -0.2547   0.6267   0.9635
 LC7  C14  C  CH2   0  -0.422   1.1421   0.2004   0.5295
 LC7  C15  C  CH2   0  -0.507   2.2357   0.9672   1.2752
 LC7  C16  C  CR6   0   0.152   3.6116   0.5607   0.8304
 LC7  C17  C  CR16  0  -0.469   4.2051   1.1812  -0.2668
 LC7  C18  C  CR16  0  -0.325   4.2973  -0.4688   1.4720
 LC7  C20  C  CR16  0  -0.224   5.5509  -0.8688   1.0302
 LC7  C21  C  CR16  0  -0.428   6.1478  -0.2518  -0.0610
 LC7  C19  C  CR6   0   0.540   5.4532   0.7652  -0.6866
 LC7  F22  F  F     0  -0.319   6.0153   1.3788  -1.7433
 LC7  H1   H  HOH1  0   0.477  -4.8205   2.5565   1.5680
 LC7  H2   H  HCH3  0   0.243  -4.9794   3.6493  -1.5859
 LC7  H3   H  HCH3  0   0.248  -4.6658   4.6216  -0.1346
 LC7  H4   H  HCH3  0   0.255  -3.3619   4.3005  -1.2766
 LC7  H5   H  HCH2  0   0.261  -2.8877   0.7889   1.4816
 LC7  H6   H  HCH2  0   0.288  -3.5394  -0.0327   0.0907
 LC7  H7   H  HCH1  0   0.242  -1.1329  -0.1110  -0.8389
 LC7  H8   H  HCH2  0   0.294  -0.5108  -1.9653   0.9604
 LC7  H9   H  HCH2  0   0.288  -2.0564  -1.5738   1.6759
 LC7  H10  H  HOH1  0   0.488  -0.4136  -3.1087  -1.4847
 LC7  H11  H  HOH1  0   0.493  -2.7429  -4.7715  -0.0209
 LC7  H12  H  HCH2  0   0.239  -0.3503   1.7019   0.7944
 LC7  H13  H  HCH2  0   0.220  -0.3719   0.4746   2.0424
 LC7  H14  H  HCH2  0   0.227   1.2901  -0.8715   0.6919
 LC7  H15  H  HCH2  0   0.229   1.2516   0.3675  -0.5466
 LC7  H16  H  HCH2  0   0.243   2.0969   2.0397   1.1146
 LC7  H17  H  HCH2  0   0.244   2.1293   0.7931   2.3491
 LC7  H18  H  HCR6  0   0.268   3.6990   1.9855  -0.7880
 LC7  H19  H  HCR6  0   0.251   3.8478  -0.9597   2.3267
 LC7  H20  H  HCR6  0   0.265   6.0751  -1.6660   1.5407
 LC7  H21  H  HCR6  0   0.276   7.1270  -0.5497  -0.4117

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
 LC7  C20  C21  aromatic  1.388  0.020  1.388
 LC7  C20  C18  aromatic  1.388  0.020  1.388
 LC7  C21  C19  aromatic  1.381  0.020  1.381
 LC7  C18  C16  aromatic  1.393  0.020  1.393
 LC7  C19  F22  single    1.345  0.020  1.345
 LC7  C19  C17  aromatic  1.381  0.020  1.381
 LC7  C16  C17  aromatic  1.393  0.020  1.393
 LC7  C16  C15  single    1.502  0.020  1.502
 LC7  C15  C14  single    1.530  0.020  1.530
 LC7  C11  N9   single    1.443  0.020  1.443
 LC7  O10  N9   single    1.372  0.020  1.372
 LC7  C13  C14  single    1.523  0.020  1.523
 LC7  C13  C2   single    1.532  0.020  1.532
 LC7  N9   C4   single    1.355  0.020  1.355
 LC7  O8   P5   double    1.484  0.020  1.484
 LC7  C4   O12  double    1.222  0.020  1.222
 LC7  C4   C3   single    1.513  0.020  1.513
 LC7  C2   C3   single    1.527  0.020  1.527
 LC7  C2   C1   single    1.539  0.020  1.539
 LC7  C1   P5   single    1.802  0.020  1.802
 LC7  P5   O6   single    1.609  0.020  1.609
 LC7  P5   O7   single    1.612  0.020  1.612
 LC7  O10  H1   single    0.850  0.020  0.980
 LC7  C11  H2   single    0.970  0.020  1.090
 LC7  C11  H3   single    0.970  0.020  1.090
 LC7  C11  H4   single    0.970  0.020  1.090
 LC7  C3   H5   single    0.970  0.020  1.090
 LC7  C3   H6   single    0.970  0.020  1.090
 LC7  C2   H7   single    0.970  0.020  1.090
 LC7  C1   H8   single    0.970  0.020  1.090
 LC7  C1   H9   single    0.970  0.020  1.090
 LC7  O7   H10  single    0.850  0.020  0.980
 LC7  O6   H11  single    0.850  0.020  0.980
 LC7  C13  H12  single    0.970  0.020  1.090
 LC7  C13  H13  single    0.970  0.020  1.090
 LC7  C14  H14  single    0.970  0.020  1.090
 LC7  C14  H15  single    0.970  0.020  1.090
 LC7  C15  H16  single    0.970  0.020  1.090
 LC7  C15  H17  single    0.970  0.020  1.090
 LC7  C17  H18  single    0.930  0.020  1.080
 LC7  C18  H19  single    0.930  0.020  1.080
 LC7  C20  H20  single    0.930  0.020  1.080
 LC7  C21  H21  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
 LC7  C3   C4   N9   116.20  3.000
 LC7  C3   C4   O12  123.12  3.000
 LC7  N9   C4   O12  120.68  3.000
 LC7  C11  N9   O10  114.39  3.000
 LC7  O10  N9   C4   118.07  3.000
 LC7  C11  N9   C4   124.17  3.000
 LC7  H1   O10  N9   106.22  3.000
 LC7  H4   C11  H3   108.34  3.000
 LC7  H4   C11  H2   108.86  3.000
 LC7  H3   C11  H2   108.91  3.000
 LC7  H4   C11  N9   109.51  3.000
 LC7  H3   C11  N9   109.43  3.000
 LC7  H2   C11  N9   111.73  3.000
 LC7  H6   C3   H5   105.62  3.000
 LC7  H6   C3   C2   110.14  3.000
 LC7  H5   C3   C2   109.38  3.000
 LC7  H6   C3   C4   107.70  3.000
 LC7  H5   C3   C4   110.36  3.000
 LC7  C2   C3   C4   113.34  3.000
 LC7  H7   C2   C13  107.72  3.000
 LC7  H7   C2   C1   109.43  3.000
 LC7  C13  C2   C1   110.09  3.000
 LC7  H7   C2   C3   108.87  3.000
 LC7  C1   C2   C3   109.49  3.000
 LC7  C13  C2   C3   111.20  3.000
 LC7  H9   C1   H8   106.09  3.000
 LC7  H9   C1   P5   108.28  3.000
 LC7  H8   C1   P5   107.31  3.000
 LC7  H9   C1   C2   110.07  3.000
 LC7  H8   C1   C2   110.97  3.000
 LC7  P5   C1   C2   113.78  3.000
 LC7  O8   P5   O6   115.56  3.000
 LC7  O6   P5   O7   106.77  3.000
 LC7  O8   P5   O7   108.69  3.000
 LC7  O7   P5   C1   106.48  3.000
 LC7  O6   P5   C1   101.17  3.000
 LC7  O8   P5   C1   117.32  3.000
 LC7  H10  O7   P5   115.36  3.000
 LC7  H11  O6   P5   113.88  3.000
 LC7  H13  C13  H12  106.24  3.000
 LC7  H13  C13  C14  109.86  3.000
 LC7  H12  C13  C14  108.15  3.000
 LC7  H13  C13  C2   109.20  3.000
 LC7  H12  C13  C2   109.26  3.000
 LC7  C14  C13  C2   113.86  3.000
 LC7  H15  C14  H14  106.38  3.000
 LC7  H15  C14  C15  109.35  3.000
 LC7  H14  C14  C15  108.78  3.000
 LC7  H15  C14  C13  109.22  3.000
 LC7  H14  C14  C13  110.85  3.000
 LC7  C15  C14  C13  112.10  3.000
 LC7  H17  C15  H16  106.75  3.000
 LC7  H17  C15  C16  109.69  3.000
 LC7  H16  C15  C16  109.77  3.000
 LC7  H17  C15  C14  109.24  3.000
 LC7  H16  C15  C14  109.23  3.000
 LC7  C16  C15  C14  112.02  3.000
 LC7  C18  C16  C17  118.82  3.000
 LC7  C17  C16  C15  120.19  3.000
 LC7  C18  C16  C15  120.96  3.000
 LC7  H18  C17  C19  119.96  3.000
 LC7  H18  C17  C16  120.68  3.000
 LC7  C19  C17  C16  119.36  3.000
 LC7  H19  C18  C20  119.69  3.000
 LC7  H19  C18  C16  119.59  3.000
 LC7  C20  C18  C16  120.72  3.000
 LC7  H20  C20  C21  119.33  3.000
 LC7  H20  C20  C18  119.98  3.000
 LC7  C21  C20  C18  120.69  3.000
 LC7  H21  C21  C19  120.73  3.000
 LC7  H21  C21  C20  121.43  3.000
 LC7  C19  C21  C20  117.84  3.000
 LC7  F22  C19  C21  118.78  3.000
 LC7  F22  C19  C17  118.63  3.000
 LC7  C21  C19  C17  122.59  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
 LC7  CONST_01  C21  C20  C18  C16     0.00   0.0  0
 LC7  CONST_02  C21  C19  C17  C16     0.00   0.0  0
 LC7  CONST_03  C20  C21  C19  C17     0.00   0.0  0
 LC7  CONST_04  C20  C18  C16  C17     0.00   0.0  0
 LC7  CONST_05  C19  C21  C20  C18     0.00   0.0  0
 LC7  CONST_06  C19  C17  C16  C18     0.00   0.0  0
 LC7  CONST_07  C20  C18  C16  C15   180.00   0.0  0
 LC7  CONST_08  C19  C17  C16  C15   180.00   0.0  0
 LC7  CONST_09  F22  C19  C17  C16   180.00   0.0  0
 LC7  CONST_10  F22  C19  C21  C20   180.00   0.0  0
 LC7  CONST_11  H20  C20  C18  C16   180.00   0.0  0
 LC7  CONST_12  H21  C21  C19  C17   180.00   0.0  0
 LC7  CONST_13  H19  C18  C16  C17   180.00   0.0  0
 LC7  CONST_14  H18  C17  C16  C18   180.00   0.0  0
 LC7  CONST_15  C11  N9   C4   O12     0.00   0.0  0
 LC7  CONST_16  O10  N9   C4   O12   180.00   0.0  0
 LC7  CONST_17  C3   C4   N9   O10     0.00   0.0  0
 LC7  CONST_18  C3   C4   N9   C11   180.00   0.0  0
 LC7  Var_01    C18  C16  C15  C14   -90.94  30.0  3
 LC7  Var_02    C16  C15  C14  C13  -179.11  30.0  1
 LC7  Var_03    C2   C3   C4   O12    10.33  30.0  3
 LC7  Var_04    C15  C14  C13  C2    179.18  30.0  3
 LC7  Var_05    O8   P5   C1   C2    -54.89  30.0  3
 LC7  Var_06    H2   C11  N9   C4     92.98  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
 LC7  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
 LC7  plan-1  C15  0.020
 LC7  plan-1  C16  0.020
 LC7  plan-1  C17  0.020
 LC7  plan-1  C18  0.020
 LC7  plan-1  C20  0.020
 LC7  plan-1  C21  0.020
 LC7  plan-1  C19  0.020
 LC7  plan-1  F22  0.020
 LC7  plan-1  H18  0.020
 LC7  plan-1  H19  0.020
 LC7  plan-1  H20  0.020
 LC7  plan-1  H21  0.020
 LC7  plan-2  O12  0.020
 LC7  plan-2  C4   0.020
 LC7  plan-2  N9   0.020
 LC7  plan-2  O10  0.020
 LC7  plan-2  C11  0.020
 LC7  plan-2  C3   0.020

