# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:39:40 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5-[(2R)-2-amino-2-carboxyethyl]-1-[4-(3-fluoropropyl)phenyl]-1H-pyrazole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1cc(nn1c2ccc(CCCF)cc2)C(O)=O)C(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
 5DY  5DY  '5-[(2R)-2-amino-2-carboxyethyl]-1-[4-(3-fluoropropyl)phenyl]-1H-pyrazole-3-carboxylic acid'  ligand  42  24  .  2022-07-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5DY
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
 5DY  N01  N  NH2   0  -0.769  -1.4043  -1.9268  -1.5837
 5DY  C02  C  CH1   0  -0.193  -2.2683  -2.3730  -0.5245
 5DY  C03  C  CH2   0  -0.569  -1.9864  -1.5808   0.7668
 5DY  C04  C  CR5   0   0.465  -2.1291  -0.1166   0.5469
 5DY  C05  C  CR15  0  -0.531  -3.2632   0.6578   0.5450
 5DY  C06  C  CR5   0   0.141  -2.8162   1.9449   0.2084
 5DY  N07  N  N     0  -0.275  -1.5070   1.9688   0.0220
 5DY  N08  N  NR5   0  -0.436  -1.1073   0.7254   0.2318
 5DY  C09  C  CR6   0   0.299   0.2695   0.4123   0.0953
 5DY  C10  C  CR16  0  -0.234   0.8926   0.6025  -1.1286
 5DY  C11  C  CR16  0  -0.318   2.2425   0.3183  -1.2572
 5DY  C12  C  CR6   0   0.146   2.9815  -0.1721  -0.1827
 5DY  C13  C  CH2   0  -0.528   4.4534  -0.4368  -0.3196
 5DY  C14  C  CH2   0  -0.489   5.2843   0.7407   0.1964
 5DY  C15  C  CH2   0   0.000   6.7605   0.4834   0.0110
 5DY  F16  F  F     0  -0.383   7.5022   1.5507   0.5192
 5DY  C17  C  CR16  0  -0.311   2.3336  -0.3606   1.0352
 5DY  C18  C  CR16  0  -0.259   0.9874  -0.0624   1.1829
 5DY  C19  C  C     0   0.502  -3.6471   3.1486   0.0821
 5DY  O20  O  OH1   0  -0.591  -2.9489   4.2302  -0.2264
 5DY  O21  O  O     0  -0.439  -4.8435   3.1385   0.2478
 5DY  C22  C  C     0   0.519  -2.1693  -3.8645  -0.2249
 5DY  O23  O  O     0  -0.432  -1.3270  -4.5969  -0.6778
 5DY  O24  O  OH1   0  -0.592  -3.1219  -4.2674   0.6067
 5DY  H1   H  HNH2  0   0.345  -0.4408  -2.1705  -1.3919
 5DY  H2   H  HNH2  0   0.360  -1.6485  -2.3783  -2.4553
 5DY  H4   H  HCH1  0   0.288  -3.3028  -2.1706  -0.8191
 5DY  H5   H  HCH2  0   0.293  -2.6836  -1.8804   1.5487
 5DY  H6   H  HCH2  0   0.279  -0.9869  -1.8265   1.1313
 5DY  H7   H  HCR5  0   0.278  -4.2701   0.3345   0.7508
 5DY  H8   H  HCR6  0   0.269   0.3265   0.9659  -1.9756
 5DY  H9   H  HCR6  0   0.257   2.7263   0.4709  -2.2144
 5DY  H10  H  HCH2  0   0.253   4.7226  -1.3404   0.2339
 5DY  H11  H  HCH2  0   0.252   4.6960  -0.6276  -1.3681
 5DY  H12  H  HCH2  0   0.243   4.9978   1.6524  -0.3348
 5DY  H13  H  HCH2  0   0.242   5.0699   0.9019   1.2561
 5DY  H14  H  HCH2  0   0.203   7.0718  -0.4216   0.5371
 5DY  H15  H  HCH2  0   0.204   7.0105   0.3732  -1.0464
 5DY  H16  H  HCR6  0   0.258   2.8862  -0.7360   1.8881
 5DY  H17  H  HCR6  0   0.280   0.5066  -0.1880   2.1448
 5DY  H18  H  HOH1  0   0.487  -3.5401   4.9946  -0.2951
 5DY  H19  H  HOH1  0   0.484  -3.0217  -5.2117   0.8010

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
 5DY  C13  C12  single    1.502  0.020  1.502
 5DY  C13  C14  single    1.531  0.020  1.531
 5DY  C11  C12  aromatic  1.393  0.020  1.393
 5DY  C11  C10  aromatic  1.385  0.020  1.385
 5DY  C12  C17  aromatic  1.392  0.020  1.392
 5DY  C14  C15  single    1.510  0.020  1.510
 5DY  F16  C15  single    1.396  0.020  1.396
 5DY  C10  C09  aromatic  1.387  0.020  1.387
 5DY  C17  C18  aromatic  1.387  0.020  1.387
 5DY  C09  C18  aromatic  1.387  0.020  1.387
 5DY  C09  N08  single    1.419  0.020  1.419
 5DY  N01  C02  single    1.438  0.020  1.438
 5DY  C03  C04  single    1.488  0.020  1.488
 5DY  C03  C02  single    1.541  0.020  1.541
 5DY  N08  C04  aromatic  1.361  0.020  1.361
 5DY  N08  N07  aromatic  1.323  0.020  1.323
 5DY  C04  C05  aromatic  1.373  0.020  1.373
 5DY  C02  C22  single    1.525  0.020  1.525
 5DY  N07  C06  aromatic  1.323  0.020  1.323
 5DY  O23  C22  double    1.205  0.020  1.205
 5DY  C22  O24  single    1.327  0.020  1.327
 5DY  C05  C06  aromatic  1.403  0.020  1.403
 5DY  C06  C19  single    1.468  0.020  1.468
 5DY  C19  O21  double    1.208  0.020  1.208
 5DY  C19  O20  single    1.324  0.020  1.324
 5DY  N01  H1   single    0.890  0.020  1.040
 5DY  N01  H2   single    0.890  0.020  1.040
 5DY  C02  H4   single    0.970  0.020  1.090
 5DY  C03  H5   single    0.970  0.020  1.090
 5DY  C03  H6   single    0.970  0.020  1.090
 5DY  C05  H7   single    0.930  0.020  1.080
 5DY  C10  H8   single    0.930  0.020  1.080
 5DY  C11  H9   single    0.930  0.020  1.080
 5DY  C13  H10  single    0.970  0.020  1.090
 5DY  C13  H11  single    0.970  0.020  1.090
 5DY  C14  H12  single    0.970  0.020  1.090
 5DY  C14  H13  single    0.970  0.020  1.090
 5DY  C15  H14  single    0.970  0.020  1.090
 5DY  C15  H15  single    0.970  0.020  1.090
 5DY  C17  H16  single    0.930  0.020  1.080
 5DY  C18  H17  single    0.930  0.020  1.080
 5DY  O20  H18  single    0.850  0.020  0.980
 5DY  O24  H19  single    0.850  0.020  0.980

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
 5DY  H2   N01  H1   106.60  3.000
 5DY  H2   N01  C02  110.56  3.000
 5DY  H1   N01  C02  110.95  3.000
 5DY  H4   C02  C22  107.17  3.000
 5DY  H4   C02  C03  107.66  3.000
 5DY  C22  C02  C03  109.05  3.000
 5DY  H4   C02  N01  108.20  3.000
 5DY  C22  C02  N01  114.16  3.000
 5DY  C03  C02  N01  110.36  3.000
 5DY  H6   C03  H5   106.52  3.000
 5DY  H6   C03  C04  111.02  3.000
 5DY  H5   C03  C04  108.38  3.000
 5DY  H6   C03  C02  109.36  3.000
 5DY  H5   C03  C02  110.05  3.000
 5DY  C04  C03  C02  111.38  3.000
 5DY  N08  C04  C05  105.71  3.000
 5DY  C05  C04  C03  129.39  3.000
 5DY  N08  C04  C03  124.83  3.000
 5DY  H7   C05  C06  128.22  3.000
 5DY  H7   C05  C04  127.04  3.000
 5DY  C06  C05  C04  104.74  3.000
 5DY  C19  C06  N07  122.23  3.000
 5DY  C19  C06  C05  126.32  3.000
 5DY  N07  C06  C05  111.44  3.000
 5DY  N08  N07  C06  105.06  3.000
 5DY  C09  N08  N07  119.04  3.000
 5DY  N07  N08  C04  113.04  3.000
 5DY  C09  N08  C04  127.91  3.000
 5DY  C18  C09  C10  120.43  3.000
 5DY  C18  C09  N08  120.16  3.000
 5DY  C10  C09  N08  119.40  3.000
 5DY  H8   C10  C11  120.42  3.000
 5DY  H8   C10  C09  120.14  3.000
 5DY  C11  C10  C09  119.45  3.000
 5DY  H9   C11  C12  119.61  3.000
 5DY  H9   C11  C10  119.22  3.000
 5DY  C12  C11  C10  121.16  3.000
 5DY  C17  C12  C13  120.79  3.000
 5DY  C17  C12  C11  118.39  3.000
 5DY  C13  C12  C11  120.77  3.000
 5DY  H11  C13  H10  106.66  3.000
 5DY  H11  C13  C14  109.70  3.000
 5DY  H10  C13  C14  109.36  3.000
 5DY  H11  C13  C12  109.62  3.000
 5DY  H10  C13  C12  109.93  3.000
 5DY  C14  C13  C12  111.45  3.000
 5DY  H13  C14  H12  107.25  3.000
 5DY  H13  C14  C15  109.63  3.000
 5DY  H12  C14  C15  109.80  3.000
 5DY  H13  C14  C13  109.50  3.000
 5DY  H12  C14  C13  109.60  3.000
 5DY  C15  C14  C13  110.99  3.000
 5DY  H15  C15  H14  108.52  3.000
 5DY  H15  C15  F16  107.94  3.000
 5DY  H14  C15  F16  107.87  3.000
 5DY  H15  C15  C14  111.09  3.000
 5DY  H14  C15  C14  111.15  3.000
 5DY  F16  C15  C14  110.16  3.000
 5DY  H16  C17  C18  119.07  3.000
 5DY  H16  C17  C12  119.88  3.000
 5DY  C18  C17  C12  121.05  3.000
 5DY  H17  C18  C17  120.05  3.000
 5DY  H17  C18  C09  120.43  3.000
 5DY  C17  C18  C09  119.51  3.000
 5DY  O21  C19  O20  124.14  3.000
 5DY  O20  C19  C06  113.04  3.000
 5DY  O21  C19  C06  122.82  3.000
 5DY  H18  O20  C19  109.83  3.000
 5DY  O24  C22  O23  123.57  3.000
 5DY  O24  C22  C02  111.94  3.000
 5DY  O23  C22  C02  124.49  3.000
 5DY  H19  O24  C22  110.32  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
 5DY  CONST_03  C06  N07  N08  C04     0.00   0.0  0
 5DY  CONST_04  N07  C06  C05  C04     0.00   0.0  0
 5DY  CONST_05  C09  N08  C04  C05   180.00   0.0  0
 5DY  CONST_06  N07  N08  C04  C05     0.00   0.0  0
 5DY  CONST_07  N08  N07  C06  C05     0.00   0.0  0
 5DY  CONST_08  C09  N08  N07  C06   180.00   0.0  0
 5DY  CONST_09  N08  C04  C05  C06     0.00   0.0  0
 5DY  CONST_12  C11  C10  C09  N08   180.00   0.0  0
 5DY  CONST_13  C17  C18  C09  N08   180.00   0.0  0
 5DY  CONST_14  C12  C11  C10  C09     0.00   0.0  0
 5DY  CONST_15  C12  C17  C18  C09     0.00   0.0  0
 5DY  CONST_16  C17  C12  C11  C10     0.00   0.0  0
 5DY  CONST_17  C17  C18  C09  C10     0.00   0.0  0
 5DY  CONST_18  C18  C17  C12  C11     0.00   0.0  0
 5DY  CONST_19  C18  C09  C10  C11     0.00   0.0  0
 5DY  CONST_20  C09  N08  C04  C03     0.00   0.0  0
 5DY  CONST_21  N07  N08  C04  C03   180.00   0.0  0
 5DY  CONST_22  C06  C05  C04  C03   180.00   0.0  0
 5DY  CONST_23  C19  C06  C05  C04   180.00   0.0  0
 5DY  CONST_24  C19  C06  N07  N08   180.00   0.0  0
 5DY  CONST_25  C13  C12  C11  C10   180.00   0.0  0
 5DY  CONST_26  C18  C17  C12  C13   180.00   0.0  0
 5DY  CONST_27  H7   C05  C06  N07   180.00   0.0  0
 5DY  CONST_28  H8   C10  C09  N08     0.00   0.0  0
 5DY  CONST_29  H17  C18  C09  N08     0.00   0.0  0
 5DY  CONST_30  H9   C11  C10  C09   180.00   0.0  0
 5DY  CONST_31  H16  C17  C18  C09   180.00   0.0  0
 5DY  CONST_32  H18  O20  C19  C06   180.00   0.0  0
 5DY  CONST_33  H19  O24  C22  C02   180.00   0.0  0
 5DY  Var_01    N08  C04  C03  C02   -93.99  30.0  2
 5DY  Var_02    O21  C19  C06  C05    -0.93  30.0  2
 5DY  Var_03    C14  C13  C12  C11    96.46  30.0  2
 5DY  Var_04    C15  C14  C13  C12  -178.08  30.0  3
 5DY  Var_05    F16  C15  C14  C13  -178.42  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
 5DY  chir_01  C02  N01  C03  C22  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
 5DY  plan-1  C03  0.020
 5DY  plan-1  C04  0.020
 5DY  plan-1  C05  0.020
 5DY  plan-1  C06  0.020
 5DY  plan-1  N07  0.020
 5DY  plan-1  N08  0.020
 5DY  plan-1  C09  0.020
 5DY  plan-1  C19  0.020
 5DY  plan-1  H7   0.020
 5DY  plan-2  N08  0.020
 5DY  plan-2  C09  0.020
 5DY  plan-2  C10  0.020
 5DY  plan-2  C11  0.020
 5DY  plan-2  C12  0.020
 5DY  plan-2  C13  0.020
 5DY  plan-2  C17  0.020
 5DY  plan-2  C18  0.020
 5DY  plan-2  H8   0.020
 5DY  plan-2  H9   0.020
 5DY  plan-2  H16  0.020
 5DY  plan-2  H17  0.020
 5DY  plan-3  C06  0.020
 5DY  plan-3  C19  0.020
 5DY  plan-3  O20  0.020
 5DY  plan-3  O21  0.020
 5DY  plan-3  H18  0.020
 5DY  plan-4  C02  0.020
 5DY  plan-4  C22  0.020
 5DY  plan-4  O23  0.020
 5DY  plan-4  O24  0.020
 5DY  plan-4  H19  0.020

