# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:52:49 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2S)-2-(4-chlorophenyl)-2-hydroxy-2-[4-(1H-pyrazol-4-yl)phenyl]ethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]C[C@@](O)(c1ccc(Cl)cc1)c2ccc(cc2)c3c[nH]nc3
#
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
 RKD  RKD  (2S)-2-(4-chlorophenyl)-2-hydroxy-2-[4-(1H-pyrazol-4-yl)phenyl]ethanaminium  ligand  39  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RKD
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
 RKD  N1    N   NT3   1  -0.787  -0.0371  -3.8246   0.4558
 RKD  C2    C   CH2   0  -0.320  -1.0810  -2.8222   0.7700
 RKD  C4    C   CR6   0   0.174  -2.1527  -0.6682   0.0172
 RKD  C5    C   CR16  0  -0.300  -2.2726   0.4116  -0.8571
 RKD  C6    C   CR16  0  -0.196  -3.2523   1.3724  -0.6840
 RKD  C7    C   CR6   0  -0.054  -4.1256   1.2587   0.3886
 RKD  O7    O   OH1   0  -0.647  -1.3115  -2.3506  -1.4899
 RKD  CL8   CL  CL    0  -0.121  -5.3541   2.4565   0.6182
 RKD  C9    C   CR16  0  -0.185  -4.0256   0.2031   1.2759
 RKD  C10   C   CR16  0  -0.341  -3.0402  -0.7573   1.0818
 RKD  C11   C   CR6   0  -0.001   0.3052  -1.0231  -0.2399
 RKD  C12   C   CR16  0  -0.294   1.2532  -1.2412  -1.2327
 RKD  C13   C   CR16  0  -0.320   2.5030  -0.6401  -1.1621
 RKD  C14   C   CR6   0   0.104   2.8472   0.1880  -0.0962
 RKD  C15   C   CR16  0  -0.321   1.8925   0.3935   0.9054
 RKD  C16   C   CR16  0  -0.241   0.6483  -0.2022   0.8346
 RKD  C17   C   CR5   0  -0.111   4.1606   0.8205  -0.0314
 RKD  C18   C   CR15  0  -0.112   5.0826   1.0340  -1.0798
 RKD  N19   N   N     0  -0.261   6.1753   1.6348  -0.6532
 RKD  N20   N   NR15  0  -0.424   5.9814   1.8104   0.6483
 RKD  C21   C   CR15  0  -0.004   4.8003   1.3473   1.0756
 RKD  C60   C   CT    0   0.102  -1.0643  -1.6974  -0.2676
 RKD  HN1   H   HNT3  0   0.471   0.9034  -3.4264   0.4804
 RKD  HN1A  H   HNT3  0   0.487  -0.0522  -4.5892   1.1303
 RKD  HN1B  H   HNT3  0   0.471  -0.1725  -4.2364  -0.4684
 RKD  HN20  H   HNR5  0   0.425   6.6951   2.2495   1.2079
 RKD  H2    H   HCH2  0   0.322  -2.0311  -3.3535   0.7703
 RKD  H2A   H   HCH2  0   0.315  -0.8784  -2.4518   1.7715
 RKD  HO7   H   HOH1  0   0.468  -1.2365  -1.7286  -2.2226
 RKD  H5    H   HCR6  0   0.268  -1.5828   0.5299  -1.6846
 RKD  H6    H   HCR6  0   0.286  -3.3286   2.2029  -1.3722
 RKD  H9    H   HCR6  0   0.286  -4.7045   0.1191   2.1132
 RKD  H10   H   HCR6  0   0.274  -2.9911  -1.5705   1.7927
 RKD  H16   H   HCR6  0   0.260  -0.0692  -0.0144   1.6247
 RKD  H15   H   HCR6  0   0.254   2.1168   1.0410   1.7437
 RKD  H13   H   HCR6  0   0.255   3.2204  -0.8347  -1.9492
 RKD  H12   H   HCR6  0   0.265   1.0378  -1.8865  -2.0745
 RKD  H18   H   HCR5  0   0.260   4.9757   0.7825  -2.1247
 RKD  H21   H   HCR5  0   0.292   4.5106   1.4099   2.1117

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
 RKD  N1   C2    single    1.481  0.020  1.481
 RKD  N1   HN1   single    0.890  0.020  1.040
 RKD  N1   HN1A  single    0.890  0.020  1.040
 RKD  N1   HN1B  single    0.890  0.020  1.040
 RKD  C2   C60   single    1.530  0.020  1.530
 RKD  C2   H2    single    0.970  0.020  1.090
 RKD  C2   H2A   single    0.970  0.020  1.090
 RKD  C4   C5    aromatic  1.395  0.020  1.395
 RKD  C4   C10   aromatic  1.389  0.020  1.389
 RKD  C4   C60   single    1.525  0.020  1.525
 RKD  C5   C6    aromatic  1.383  0.020  1.383
 RKD  C5   H5    single    0.930  0.020  1.080
 RKD  C6   C7    aromatic  1.388  0.020  1.388
 RKD  C6   H6    single    0.930  0.020  1.080
 RKD  C7   CL8   single    1.731  0.020  1.731
 RKD  C7   C9    aromatic  1.383  0.020  1.383
 RKD  O7   C60   single    1.408  0.020  1.408
 RKD  O7   HO7   single    0.850  0.020  0.980
 RKD  C9   C10   aromatic  1.390  0.020  1.390
 RKD  C9   H9    single    0.930  0.020  1.080
 RKD  C10  H10   single    0.930  0.020  1.080
 RKD  C11  C12   aromatic  1.390  0.020  1.390
 RKD  C11  C16   aromatic  1.395  0.020  1.395
 RKD  C11  C60   single    1.527  0.020  1.527
 RKD  C12  C13   aromatic  1.389  0.020  1.389
 RKD  C12  H12   single    0.930  0.020  1.080
 RKD  C13  C14   aromatic  1.393  0.020  1.393
 RKD  C13  H13   single    0.930  0.020  1.080
 RKD  C14  C15   aromatic  1.399  0.020  1.399
 RKD  C14  C17   single    1.459  0.020  1.459
 RKD  C15  C16   aromatic  1.381  0.020  1.381
 RKD  C15  H15   single    0.930  0.020  1.080
 RKD  C16  H16   single    0.930  0.020  1.080
 RKD  C17  C18   aromatic  1.412  0.020  1.412
 RKD  C17  C21   aromatic  1.383  0.020  1.383
 RKD  C18  N19   aromatic  1.318  0.020  1.318
 RKD  C18  H18   single    0.930  0.020  1.080
 RKD  N19  N20   aromatic  1.328  0.020  1.328
 RKD  N20  C21   aromatic  1.339  0.020  1.339
 RKD  N20  HN20  single    0.860  0.020  1.020
 RKD  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
 RKD  HN1B  N1   HN1A  107.13  3.000
 RKD  HN1B  N1   HN1   107.53  3.000
 RKD  HN1A  N1   HN1   106.86  3.000
 RKD  HN1B  N1   C2    111.81  3.000
 RKD  HN1A  N1   C2    110.90  3.000
 RKD  HN1   N1   C2    112.33  3.000
 RKD  H2A   C2   H2    109.19  3.000
 RKD  H2A   C2   C60   111.86  3.000
 RKD  H2    C2   C60   111.62  3.000
 RKD  H2A   C2   N1    107.14  3.000
 RKD  H2    C2   N1    106.56  3.000
 RKD  C60   C2   N1    110.24  3.000
 RKD  C60   C4   C10   123.78  3.000
 RKD  C60   C4   C5    117.83  3.000
 RKD  C10   C4   C5    118.38  3.000
 RKD  H5    C5   C6    118.07  3.000
 RKD  H5    C5   C4    120.56  3.000
 RKD  C6    C5   C4    121.36  3.000
 RKD  H6    C6   C7    120.69  3.000
 RKD  H6    C6   C5    120.26  3.000
 RKD  C7    C6   C5    119.04  3.000
 RKD  C9    C7   CL8   119.64  3.000
 RKD  C9    C7   C6    120.87  3.000
 RKD  CL8   C7   C6    119.49  3.000
 RKD  HO7   O7   C60   110.29  3.000
 RKD  H9    C9   C10   119.98  3.000
 RKD  H9    C9   C7    120.73  3.000
 RKD  C10   C9   C7    119.30  3.000
 RKD  H10   C10  C9    117.40  3.000
 RKD  H10   C10  C4    121.55  3.000
 RKD  C9    C10  C4    121.05  3.000
 RKD  C60   C11  C16   119.64  3.000
 RKD  C60   C11  C12   121.97  3.000
 RKD  C16   C11  C12   118.34  3.000
 RKD  H12   C12  C13   118.47  3.000
 RKD  H12   C12  C11   120.89  3.000
 RKD  C13   C12  C11   120.64  3.000
 RKD  H13   C13  C14   119.96  3.000
 RKD  H13   C13  C12   118.80  3.000
 RKD  C14   C13  C12   121.24  3.000
 RKD  C17   C14  C15   121.25  3.000
 RKD  C17   C14  C13   120.94  3.000
 RKD  C15   C14  C13   117.81  3.000
 RKD  H15   C15  C16   118.96  3.000
 RKD  H15   C15  C14   120.06  3.000
 RKD  C16   C15  C14   120.98  3.000
 RKD  H16   C16  C15   118.97  3.000
 RKD  H16   C16  C11   120.04  3.000
 RKD  C15   C16  C11   120.98  3.000
 RKD  C21   C17  C18   103.57  3.000
 RKD  C21   C17  C14   128.10  3.000
 RKD  C18   C17  C14   128.32  3.000
 RKD  H18   C18  N19   120.09  3.000
 RKD  H18   C18  C17   128.20  3.000
 RKD  N19   C18  C17   111.71  3.000
 RKD  N20   N19  C18   104.87  3.000
 RKD  HN20  N20  C21   126.76  3.000
 RKD  HN20  N20  N19   119.91  3.000
 RKD  C21   N20  N19   113.33  3.000
 RKD  H21   C21  N20   121.60  3.000
 RKD  H21   C21  C17   131.87  3.000
 RKD  N20   C21  C17   106.52  3.000
 RKD  C11   C60  O7    112.23  3.000
 RKD  C11   C60  C4    109.80  3.000
 RKD  O7    C60  C4    110.49  3.000
 RKD  C11   C60  C2    108.79  3.000
 RKD  O7    C60  C2    104.23  3.000
 RKD  C4    C60  C2    111.20  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
 RKD  CONST_01  C7    C6   C5   C4     0.00   0.0  0
 RKD  CONST_02  C7    C9   C10  C4     0.00   0.0  0
 RKD  CONST_03  C9    C10  C4   C5     0.00   0.0  0
 RKD  CONST_04  C9    C7   C6   C5     0.00   0.0  0
 RKD  CONST_05  C10   C4   C5   C6     0.00   0.0  0
 RKD  CONST_06  C10   C9   C7   C6     0.00   0.0  0
 RKD  CONST_07  C14   C13  C12  C11    0.00   0.0  0
 RKD  CONST_08  C14   C15  C16  C11    0.00   0.0  0
 RKD  CONST_09  C15   C16  C11  C12    0.00   0.0  0
 RKD  CONST_10  C15   C14  C13  C12    0.00   0.0  0
 RKD  CONST_11  C17   C14  C13  C12  180.00   0.0  0
 RKD  CONST_12  C16   C11  C12  C13    0.00   0.0  0
 RKD  CONST_13  C16   C15  C14  C13    0.00   0.0  0
 RKD  CONST_16  N19   C18  C17  C14  180.00   0.0  0
 RKD  CONST_17  N20   C21  C17  C14  180.00   0.0  0
 RKD  CONST_20  C17   C14  C15  C16  180.00   0.0  0
 RKD  CONST_21  N20   N19  C18  C17    0.00   0.0  0
 RKD  CONST_22  N19   N20  C21  C17    0.00   0.0  0
 RKD  CONST_23  N20   C21  C17  C18    0.00   0.0  0
 RKD  CONST_24  C21   N20  N19  C18    0.00   0.0  0
 RKD  CONST_25  C21   C17  C18  N19    0.00   0.0  0
 RKD  CONST_26  CL8   C7   C6   C5   180.00   0.0  0
 RKD  CONST_27  C60   C4   C5   C6   180.00   0.0  0
 RKD  CONST_28  C10   C9   C7   CL8  180.00   0.0  0
 RKD  CONST_29  C60   C4   C10  C9   180.00   0.0  0
 RKD  CONST_30  C60   C11  C12  C13  180.00   0.0  0
 RKD  CONST_31  C60   C11  C16  C15  180.00   0.0  0
 RKD  CONST_32  H6    C6   C5   C4   180.00   0.0  0
 RKD  CONST_33  H9    C9   C10  C4   180.00   0.0  0
 RKD  CONST_34  H10   C10  C4   C5   180.00   0.0  0
 RKD  CONST_35  H5    C5   C6   C7   180.00   0.0  0
 RKD  CONST_36  H13   C13  C12  C11  180.00   0.0  0
 RKD  CONST_37  H15   C15  C16  C11  180.00   0.0  0
 RKD  CONST_38  H16   C16  C11  C12  180.00   0.0  0
 RKD  CONST_39  H12   C12  C13  C14  180.00   0.0  0
 RKD  CONST_40  H18   C18  C17  C14    0.00   0.0  0
 RKD  CONST_41  H21   C21  C17  C14    0.00   0.0  0
 RKD  CONST_42  HN20  N20  C21  C17  180.00   0.0  0
 RKD  Var_01    HN1   N1   C2   C60   61.69  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
 RKD  chir_01  C60  C4  O7  C11  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
 RKD  plan-1  C14   0.020
 RKD  plan-1  C17   0.020
 RKD  plan-1  C18   0.020
 RKD  plan-1  N19   0.020
 RKD  plan-1  N20   0.020
 RKD  plan-1  C21   0.020
 RKD  plan-1  HN20  0.020
 RKD  plan-1  H18   0.020
 RKD  plan-1  H21   0.020
 RKD  plan-2  C4    0.020
 RKD  plan-2  C5    0.020
 RKD  plan-2  C6    0.020
 RKD  plan-2  C7    0.020
 RKD  plan-2  CL8   0.020
 RKD  plan-2  C9    0.020
 RKD  plan-2  C10   0.020
 RKD  plan-2  C60   0.020
 RKD  plan-2  H5    0.020
 RKD  plan-2  H6    0.020
 RKD  plan-2  H9    0.020
 RKD  plan-2  H10   0.020
 RKD  plan-3  C11   0.020
 RKD  plan-3  C12   0.020
 RKD  plan-3  C13   0.020
 RKD  plan-3  C14   0.020
 RKD  plan-3  C15   0.020
 RKD  plan-3  C16   0.020
 RKD  plan-3  C17   0.020
 RKD  plan-3  C60   0.020
 RKD  plan-3  H16   0.020
 RKD  plan-3  H15   0.020
 RKD  plan-3  H13   0.020
 RKD  plan-3  H12   0.020

