# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:36:08 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: [(R)-(benzylamino)(phenyl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)[C@@H](NCc1ccccc1)c2ccccc2
#
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
 2BF  2BF  '[(R)-(benzylamino)(phenyl)methyl]phosphonic acid'  ligand  35  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2BF
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
 2BF  C1    C  CR16  0  -0.241   2.3986   1.1877   2.8526
 2BF  C2    C  CR16  0  -0.265   2.7334   0.1897   3.7585
 2BF  C3    C  CR16  0  -0.240   2.0829  -1.0351   3.6999
 2BF  C4    C  CR16  0  -0.301   1.1048  -1.2573   2.7405
 2BF  C5    C  CR6   0   0.118   0.7682  -0.2653   1.8235
 2BF  C6    C  CR16  0  -0.288   1.4193   0.9643   1.8946
 2BF  C7    C  CH1   0  -0.427  -0.3129  -0.5219   0.7985
 2BF  C8    C  CR6   0   0.093   0.0427  -0.2929  -2.9360
 2BF  C9    C  CR16  0  -0.286   1.4266  -0.4088  -3.0569
 2BF  C10   C  CR16  0  -0.242   2.0566  -0.1254  -4.2597
 2BF  C11   C  CR16  0  -0.270   1.3124   0.2829  -5.3612
 2BF  C12   C  CR16  0  -0.241  -0.0650   0.4052  -5.2491
 2BF  C13   C  CR16  0  -0.315  -0.6928   0.1211  -4.0417
 2BF  P     P  P     0   1.353  -1.8656   0.2263   1.4330
 2BF  O1P   O  O     0  -0.709  -1.8961   1.7062   1.3078
 2BF  O2P   O  OH1   0  -0.742  -2.0726  -0.3376   2.9287
 2BF  O3P   O  OH1   0  -0.740  -3.0108  -0.5746   0.6473
 2BF  N     N  NH1   0  -0.590   0.0508  -0.0358  -0.5147
 2BF  C19   C  CH2   0  -0.330  -0.6485  -0.6289  -1.6396
 2BF  H1    H  HCR6  0   0.258   2.9002   2.1460   2.8921
 2BF  H2    H  HCR6  0   0.258   3.4982   0.3640   4.5042
 2BF  H3    H  HCR6  0   0.258   2.3390  -1.8216   4.3980
 2BF  H4    H  HCR6  0   0.256   0.6070  -2.2187   2.6970
 2BF  H6    H  HCR6  0   0.250   1.1762   1.7593   1.2013
 2BF  H7    H  HCH1  0   0.304  -0.4705  -1.6028   0.7325
 2BF  H9    H  HCR6  0   0.247   2.0106  -0.7167  -2.1986
 2BF  H10   H  HCR6  0   0.252   3.1321  -0.2211  -4.3396
 2BF  H11   H  HCR6  0   0.254   1.8048   0.5080  -6.2985
 2BF  H12   H  HCR6  0   0.253  -0.6526   0.7285  -6.0989
 2BF  H13   H  HCR6  0   0.249  -1.7686   0.2257  -3.9598
 2BF  HOP2  H  HOH1  0   0.492  -1.5810   0.1475   3.6039
 2BF  HOP3  H  HOH1  0   0.496  -3.8529  -0.1013   0.5927
 2BF  HN    H  HNH1  0   0.359  -0.0002   0.9738  -0.5660
 2BF  H191  H  HCH2  0   0.248  -0.6375  -1.7143  -1.4992
 2BF  H192  H  HCH2  0   0.227  -1.7045  -0.3419  -1.7161

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
 2BF  C1   C2    aromatic  1.389  0.020  1.389
 2BF  C1   C6    aromatic  1.388  0.020  1.388
 2BF  C1   H1    single    0.930  0.020  1.080
 2BF  C2   C3    aromatic  1.388  0.020  1.388
 2BF  C2   H2    single    0.930  0.020  1.080
 2BF  C3   C4    aromatic  1.388  0.020  1.388
 2BF  C3   H3    single    0.930  0.020  1.080
 2BF  C4   C5    aromatic  1.392  0.020  1.392
 2BF  C4   H4    single    0.930  0.020  1.080
 2BF  C5   C6    aromatic  1.393  0.020  1.393
 2BF  C5   C7    single    1.512  0.020  1.512
 2BF  C6   H6    single    0.930  0.020  1.080
 2BF  C7   P     single    1.837  0.020  1.837
 2BF  C7   N     single    1.447  0.020  1.447
 2BF  C7   H7    single    0.970  0.020  1.090
 2BF  C8   C9    aromatic  1.394  0.020  1.394
 2BF  C8   C13   aromatic  1.391  0.020  1.391
 2BF  C8   C19   single    1.507  0.020  1.507
 2BF  C9   C10   aromatic  1.387  0.020  1.387
 2BF  C9   H9    single    0.930  0.020  1.080
 2BF  C10  C11   aromatic  1.391  0.020  1.391
 2BF  C10  H10   single    0.930  0.020  1.080
 2BF  C11  C12   aromatic  1.387  0.020  1.387
 2BF  C11  H11   single    0.930  0.020  1.080
 2BF  C12  C13   aromatic  1.390  0.020  1.390
 2BF  C12  H12   single    0.930  0.020  1.080
 2BF  C13  H13   single    0.930  0.020  1.080
 2BF  P    O1P   double    1.485  0.020  1.485
 2BF  P    O2P   single    1.612  0.020  1.612
 2BF  P    O3P   single    1.603  0.020  1.603
 2BF  O2P  HOP2  single    0.850  0.020  0.980
 2BF  O3P  HOP3  single    0.850  0.020  0.980
 2BF  N    C19   single    1.451  0.020  1.451
 2BF  N    HN    single    0.890  0.020  1.040
 2BF  C19  H191  single    0.970  0.020  1.090
 2BF  C19  H192  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
 2BF  H1    C1   C6    119.64  3.000
 2BF  H1    C1   C2    120.05  3.000
 2BF  C6    C1   C2    120.31  3.000
 2BF  H2    C2   C3    120.16  3.000
 2BF  H2    C2   C1    120.27  3.000
 2BF  C3    C2   C1    119.57  3.000
 2BF  H3    C3   C4    119.75  3.000
 2BF  H3    C3   C2    120.20  3.000
 2BF  C4    C3   C2    120.05  3.000
 2BF  H4    C4   C5    119.66  3.000
 2BF  H4    C4   C3    119.57  3.000
 2BF  C5    C4   C3    120.77  3.000
 2BF  C7    C5   C6    121.25  3.000
 2BF  C7    C5   C4    119.90  3.000
 2BF  C6    C5   C4    118.84  3.000
 2BF  H6    C6   C5    120.70  3.000
 2BF  H6    C6   C1    118.83  3.000
 2BF  C5    C6   C1    120.46  3.000
 2BF  H7    C7   N     108.26  3.000
 2BF  H7    C7   P     107.54  3.000
 2BF  N     C7   P     112.90  3.000
 2BF  H7    C7   C5    108.16  3.000
 2BF  N     C7   C5    112.25  3.000
 2BF  P     C7   C5    107.53  3.000
 2BF  C19   C8   C13   120.51  3.000
 2BF  C19   C8   C9    120.75  3.000
 2BF  C13   C8   C9    118.73  3.000
 2BF  H9    C9   C10   120.03  3.000
 2BF  H9    C9   C8    119.36  3.000
 2BF  C10   C9   C8    120.60  3.000
 2BF  H10   C10  C11   119.95  3.000
 2BF  H10   C10  C9    119.80  3.000
 2BF  C11   C10  C9    120.25  3.000
 2BF  H11   C11  C12   120.22  3.000
 2BF  H11   C11  C10   120.23  3.000
 2BF  C12   C11  C10   119.55  3.000
 2BF  H12   C12  C13   119.85  3.000
 2BF  H12   C12  C11   120.11  3.000
 2BF  C13   C12  C11   120.03  3.000
 2BF  H13   C13  C12   119.60  3.000
 2BF  H13   C13  C8    119.57  3.000
 2BF  C12   C13  C8    120.83  3.000
 2BF  O3P   P    O2P   100.85  3.000
 2BF  O3P   P    O1P   116.21  3.000
 2BF  O2P   P    O1P   115.09  3.000
 2BF  O3P   P    C7    103.36  3.000
 2BF  O2P   P    C7    106.66  3.000
 2BF  O1P   P    C7    113.21  3.000
 2BF  HOP2  O2P  P     114.06  3.000
 2BF  HOP3  O3P  P     113.89  3.000
 2BF  HN    N    C19   110.13  3.000
 2BF  HN    N    C7    111.62  3.000
 2BF  C19   N    C7    116.43  3.000
 2BF  H192  C19  H191  106.14  3.000
 2BF  H192  C19  N     114.27  3.000
 2BF  H191  C19  N     107.52  3.000
 2BF  H192  C19  C8    108.85  3.000
 2BF  H191  C19  C8    109.08  3.000
 2BF  N     C19  C8    110.77  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
 2BF  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 2BF  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 2BF  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 2BF  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 2BF  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 2BF  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 2BF  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 2BF  CONST_08  C11  C12  C13  C8      0.00   0.0  0
 2BF  CONST_09  C12  C13  C8   C9      0.00   0.0  0
 2BF  CONST_10  C12  C11  C10  C9      0.00   0.0  0
 2BF  CONST_11  C13  C8   C9   C10     0.00   0.0  0
 2BF  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 2BF  CONST_13  C7   C5   C6   C1    180.00   0.0  0
 2BF  CONST_14  C7   C5   C4   C3    180.00   0.0  0
 2BF  CONST_15  C19  C8   C9   C10   180.00   0.0  0
 2BF  CONST_16  C19  C8   C13  C12   180.00   0.0  0
 2BF  CONST_17  H3   C3   C2   C1    180.00   0.0  0
 2BF  CONST_18  H6   C6   C1   C2    180.00   0.0  0
 2BF  CONST_19  H4   C4   C3   C2    180.00   0.0  0
 2BF  CONST_20  H1   C1   C2   C3    180.00   0.0  0
 2BF  CONST_21  H2   C2   C3   C4    180.00   0.0  0
 2BF  CONST_22  H10  C10  C9   C8    180.00   0.0  0
 2BF  CONST_23  H12  C12  C13  C8    180.00   0.0  0
 2BF  CONST_24  H13  C13  C8   C9    180.00   0.0  0
 2BF  CONST_25  H11  C11  C10  C9    180.00   0.0  0
 2BF  CONST_26  H9   C9   C10  C11   180.00   0.0  0
 2BF  Var_01    N    C19  C8   C9     45.97  30.0  2
 2BF  Var_02    C8   C19  N    C7   -166.22  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
 2BF  chir_01  C7  C5  P  N  negativ

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
 2BF  plan-1  C1   0.020
 2BF  plan-1  C2   0.020
 2BF  plan-1  C3   0.020
 2BF  plan-1  C4   0.020
 2BF  plan-1  C5   0.020
 2BF  plan-1  C6   0.020
 2BF  plan-1  C7   0.020
 2BF  plan-1  H1   0.020
 2BF  plan-1  H2   0.020
 2BF  plan-1  H3   0.020
 2BF  plan-1  H4   0.020
 2BF  plan-1  H6   0.020
 2BF  plan-2  C8   0.020
 2BF  plan-2  C9   0.020
 2BF  plan-2  C10  0.020
 2BF  plan-2  C11  0.020
 2BF  plan-2  C12  0.020
 2BF  plan-2  C13  0.020
 2BF  plan-2  C19  0.020
 2BF  plan-2  H9   0.020
 2BF  plan-2  H10  0.020
 2BF  plan-2  H11  0.020
 2BF  plan-2  H12  0.020
 2BF  plan-2  H13  0.020

