# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 10:21:47 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N-[(2S)-1-hydroxy-3-phenylpropan-2-yl]-4-(pyridin-4-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](Cc1ccccc1)NC(=O)c2ccc(cc2)c3ccncc3
#
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
 9CY  9CY  N-[(2S)-1-hydroxy-3-phenylpropan-2-yl]-4-(pyridin-4-yl)benzamide  ligand  45  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9CY
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
 9CY  N1   N  N     0  -0.406  -6.9512  -0.9381  -0.4750
 9CY  C4   C  CR16  0  -0.293   4.5436  -1.3156   0.6964
 9CY  C5   C  CR16  0  -0.241   4.2331  -2.5752   1.1881
 9CY  C6   C  CR16  0  -0.274   3.2460  -3.3383   0.5761
 9CY  C7   C  CR16  0  -0.240   2.5778  -2.8325  -0.5304
 9CY  C8   C  CR16  0  -0.313   2.8974  -1.5730  -1.0208
 9CY  C10  C  CR6   0  -0.041  -0.1252   0.6168   0.6107
 9CY  C13  C  CR6   0   0.093  -2.8273  -0.0007   0.1794
 9CY  C15  C  CR16  0  -0.276  -0.5662   0.2066  -0.6448
 9CY  C17  C  CR16  0  -0.377  -5.2653   0.3821   0.5925
 9CY  C20  C  CR16  0  -0.377  -4.6341  -1.3490  -0.9079
 9CY  O1   O  O     0  -0.481   1.7738   0.7360   2.0172
 9CY  N    N  NH1   0  -0.643   2.0149   1.4278  -0.1252
 9CY  C1   C  CH1   0  -0.114   3.4433   1.6580  -0.0942
 9CY  C2   C  CH2   0  -0.511   4.1854   0.5867  -0.9100
 9CY  C3   C  CR6   0   0.144   3.8819  -0.7976  -0.4149
 9CY  C    C  CH2   0  -0.156   3.7637   3.0672  -0.5623
 9CY  O    O  OH1   0  -0.673   3.3039   3.2223  -1.8857
 9CY  C14  C  CR16  0  -0.292  -1.8993  -0.1044  -0.8558
 9CY  C12  C  CR16  0  -0.294  -2.3804   0.4086   1.4366
 9CY  C11  C  CR16  0  -0.255  -1.0453   0.6989   1.6524
 9CY  C16  C  CR6   0   0.174  -4.2479  -0.3240  -0.0464
 9CY  C19  C  CR16  0  -0.059  -5.9828  -1.6129  -1.0840
 9CY  C18  C  CR16  0  -0.059  -6.5849   0.0399   0.3453
 9CY  H2   H  HCR6  0   0.250   4.7619  -2.9628   2.0498
 9CY  H3   H  HCR6  0   0.251   3.0026  -4.3217   0.9573
 9CY  H4   H  HCR6  0   0.250   1.8089  -3.4201  -1.0157
 9CY  H5   H  HCR6  0   0.244   2.3760  -1.1900  -1.8907
 9CY  H6   H  HCR6  0   0.261   0.1273   0.0977  -1.4689
 9CY  H7   H  HCR6  0   0.271  -5.0461   1.2043   1.2607
 9CY  H8   H  HCR6  0   0.271  -3.9024  -1.9546  -1.4261
 9CY  H9   H  HNH1  0   0.397   1.5406   1.6330  -0.9902
 9CY  H10  H  HCH1  0   0.270   3.7630   1.5855   0.9461
 9CY  H11  H  HCH2  0   0.252   3.9130   0.6760  -1.9640
 9CY  H12  H  HCH2  0   0.250   5.2577   0.7881  -0.8391
 9CY  H13  H  HCH2  0   0.218   3.2843   3.7814   0.1179
 9CY  H14  H  HCH2  0   0.207   4.8476   3.2200  -0.4854
 9CY  H15  H  HOH1  0   0.462   3.4381   4.1367  -2.1501
 9CY  H16  H  HCR6  0   0.266  -2.2172  -0.4159  -1.8423
 9CY  H17  H  HCR6  0   0.264  -3.0751   0.4754   2.2638
 9CY  H18  H  HCR6  0   0.264  -0.7168   0.9956   2.6393
 9CY  H19  H  HCR6  0   0.267  -6.2917  -2.4139  -1.7467
 9CY  H20  H  HCR6  0   0.267  -7.3823   0.5900   0.8326
 9CY  C9   C  C     0   0.540   1.3102   0.9238   0.9014
 9CY  H1   H  HCR6  0   0.242   5.3111  -0.7238   1.1823

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
 9CY  C7   C6   aromatic  1.388  0.020  1.388
 9CY  C7   C8   aromatic  1.389  0.020  1.389
 9CY  C6   C5   aromatic  1.390  0.020  1.390
 9CY  O1   C9   double    1.223  0.020  1.223
 9CY  C8   C3   aromatic  1.392  0.020  1.392
 9CY  C5   C4   aromatic  1.387  0.020  1.387
 9CY  C9   C10  single    1.496  0.020  1.496
 9CY  C9   N    single    1.343  0.020  1.343
 9CY  C15  C14  aromatic  1.385  0.020  1.385
 9CY  C15  C10  aromatic  1.392  0.020  1.392
 9CY  C3   C4   aromatic  1.393  0.020  1.393
 9CY  C3   C2   single    1.501  0.020  1.501
 9CY  C1   N    single    1.447  0.020  1.447
 9CY  C1   C2   single    1.537  0.020  1.537
 9CY  C1   C    single    1.519  0.020  1.519
 9CY  C14  C13  aromatic  1.394  0.020  1.394
 9CY  C10  C11  aromatic  1.392  0.020  1.392
 9CY  O    C    single    1.410  0.020  1.410
 9CY  C20  C19  aromatic  1.386  0.020  1.386
 9CY  C20  C16  aromatic  1.394  0.020  1.394
 9CY  C13  C12  aromatic  1.396  0.020  1.396
 9CY  C13  C16  single    1.474  0.020  1.474
 9CY  C11  C12  aromatic  1.383  0.020  1.383
 9CY  C19  N1   aromatic  1.328  0.020  1.328
 9CY  C16  C17  aromatic  1.393  0.020  1.393
 9CY  N1   C18  aromatic  1.328  0.020  1.328
 9CY  C17  C18  aromatic  1.385  0.020  1.385
 9CY  C4   H1   single    0.930  0.020  1.080
 9CY  C5   H2   single    0.930  0.020  1.080
 9CY  C6   H3   single    0.930  0.020  1.080
 9CY  C7   H4   single    0.930  0.020  1.080
 9CY  C8   H5   single    0.930  0.020  1.080
 9CY  C15  H6   single    0.930  0.020  1.080
 9CY  C17  H7   single    0.930  0.020  1.080
 9CY  C20  H8   single    0.930  0.020  1.080
 9CY  N    H9   single    0.860  0.020  1.020
 9CY  C1   H10  single    0.970  0.020  1.090
 9CY  C2   H11  single    0.970  0.020  1.090
 9CY  C2   H12  single    0.970  0.020  1.090
 9CY  C    H13  single    0.970  0.020  1.090
 9CY  C    H14  single    0.970  0.020  1.090
 9CY  O    H15  single    0.850  0.020  0.980
 9CY  C14  H16  single    0.930  0.020  1.080
 9CY  C12  H17  single    0.930  0.020  1.080
 9CY  C11  H18  single    0.930  0.020  1.080
 9CY  C19  H19  single    0.930  0.020  1.080
 9CY  C18  H20  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
 9CY  C18  N1   C19  117.15  3.000
 9CY  H1   C4   C3   119.39  3.000
 9CY  H1   C4   C5   119.68  3.000
 9CY  C3   C4   C5   120.93  3.000
 9CY  H2   C5   C6   120.05  3.000
 9CY  H2   C5   C4   119.85  3.000
 9CY  C6   C5   C4   120.09  3.000
 9CY  H3   C6   C7   120.24  3.000
 9CY  H3   C6   C5   120.23  3.000
 9CY  C7   C6   C5   119.53  3.000
 9CY  H4   C7   C8   119.82  3.000
 9CY  H4   C7   C6   120.10  3.000
 9CY  C8   C7   C6   120.08  3.000
 9CY  H5   C8   C3   119.51  3.000
 9CY  H5   C8   C7   119.54  3.000
 9CY  C3   C8   C7   120.95  3.000
 9CY  C11  C10  C9   118.45  3.000
 9CY  C11  C10  C15  118.86  3.000
 9CY  C9   C10  C15  122.65  3.000
 9CY  C16  C13  C12  120.72  3.000
 9CY  C16  C13  C14  120.76  3.000
 9CY  C12  C13  C14  118.52  3.000
 9CY  H6   C15  C14  118.56  3.000
 9CY  H6   C15  C10  120.87  3.000
 9CY  C14  C15  C10  120.55  3.000
 9CY  H7   C17  C18  119.40  3.000
 9CY  H7   C17  C16  121.36  3.000
 9CY  C18  C17  C16  119.23  3.000
 9CY  H8   C20  C19  119.40  3.000
 9CY  H8   C20  C16  121.36  3.000
 9CY  C19  C20  C16  119.24  3.000
 9CY  H9   N    C1   116.78  3.000
 9CY  H9   N    C9   119.05  3.000
 9CY  C1   N    C9   124.13  3.000
 9CY  H10  C1   C    107.08  3.000
 9CY  H10  C1   C2   108.56  3.000
 9CY  C    C1   C2   112.40  3.000
 9CY  H10  C1   N    107.40  3.000
 9CY  C    C1   N    110.44  3.000
 9CY  C2   C1   N    110.74  3.000
 9CY  H12  C2   H11  106.99  3.000
 9CY  H12  C2   C3   110.28  3.000
 9CY  H11  C2   C3   110.07  3.000
 9CY  H12  C2   C1   108.10  3.000
 9CY  H11  C2   C1   109.55  3.000
 9CY  C3   C2   C1   111.72  3.000
 9CY  C2   C3   C8   120.87  3.000
 9CY  C2   C3   C4   120.66  3.000
 9CY  C8   C3   C4   118.42  3.000
 9CY  H14  C    H13  107.31  3.000
 9CY  H14  C    O    111.88  3.000
 9CY  H13  C    O    111.60  3.000
 9CY  H14  C    C1   108.41  3.000
 9CY  H13  C    C1   108.72  3.000
 9CY  O    C    C1   108.82  3.000
 9CY  H15  O    C    108.51  3.000
 9CY  H16  C14  C15  119.09  3.000
 9CY  H16  C14  C13  120.18  3.000
 9CY  C15  C14  C13  120.72  3.000
 9CY  H17  C12  C11  119.16  3.000
 9CY  H17  C12  C13  120.07  3.000
 9CY  C11  C12  C13  120.75  3.000
 9CY  H18  C11  C12  119.54  3.000
 9CY  H18  C11  C10  119.88  3.000
 9CY  C12  C11  C10  120.58  3.000
 9CY  C20  C16  C17  116.99  3.000
 9CY  C17  C16  C13  121.48  3.000
 9CY  C20  C16  C13  121.53  3.000
 9CY  H19  C19  C20  119.71  3.000
 9CY  H19  C19  N1   116.60  3.000
 9CY  C20  C19  N1   123.69  3.000
 9CY  H20  C18  C17  119.67  3.000
 9CY  H20  C18  N1   116.63  3.000
 9CY  C17  C18  N1   123.70  3.000
 9CY  N    C9   O1   123.79  3.000
 9CY  N    C9   C10  115.57  3.000
 9CY  O1   C9   C10  120.63  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
 9CY  CONST_01  C16  C20  C19  N1      0.00   0.0  0
 9CY  CONST_02  C16  C17  C18  N1      0.00   0.0  0
 9CY  CONST_03  C7   C6   C5   C4      0.00   0.0  0
 9CY  CONST_04  C7   C8   C3   C4      0.00   0.0  0
 9CY  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 9CY  CONST_06  C8   C3   C4   C5      0.00   0.0  0
 9CY  CONST_07  C3   C8   C7   C6      0.00   0.0  0
 9CY  CONST_08  C3   C4   C5   C6      0.00   0.0  0
 9CY  CONST_09  C13  C14  C15  C10     0.00   0.0  0
 9CY  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 9CY  CONST_11  C19  C20  C16  C13   180.00   0.0  0
 9CY  CONST_12  C18  C17  C16  C13   180.00   0.0  0
 9CY  CONST_13  C12  C13  C14  C15     0.00   0.0  0
 9CY  CONST_14  C16  C13  C14  C15   180.00   0.0  0
 9CY  CONST_15  C12  C11  C10  C15     0.00   0.0  0
 9CY  CONST_16  C19  C20  C16  C17     0.00   0.0  0
 9CY  CONST_19  C19  N1   C18  C17     0.00   0.0  0
 9CY  CONST_20  C18  N1   C19  C20     0.00   0.0  0
 9CY  CONST_23  C18  C17  C16  C20     0.00   0.0  0
 9CY  CONST_24  C11  C10  C15  C14     0.00   0.0  0
 9CY  CONST_25  C11  C12  C13  C14     0.00   0.0  0
 9CY  CONST_26  C16  C13  C12  C11   180.00   0.0  0
 9CY  CONST_27  C2   C3   C4   C5    180.00   0.0  0
 9CY  CONST_28  C2   C3   C8   C7    180.00   0.0  0
 9CY  CONST_29  C14  C15  C10  C9    180.00   0.0  0
 9CY  CONST_30  C12  C11  C10  C9    180.00   0.0  0
 9CY  CONST_31  H8   C20  C19  N1    180.00   0.0  0
 9CY  CONST_32  H7   C17  C18  N1    180.00   0.0  0
 9CY  CONST_33  H3   C6   C5   C4    180.00   0.0  0
 9CY  CONST_34  H5   C8   C3   C4    180.00   0.0  0
 9CY  CONST_35  H4   C7   C6   C5    180.00   0.0  0
 9CY  CONST_36  H1   C4   C5   C6    180.00   0.0  0
 9CY  CONST_37  H2   C5   C6   C7    180.00   0.0  0
 9CY  CONST_38  H16  C14  C15  C10   180.00   0.0  0
 9CY  CONST_39  H17  C12  C11  C10   180.00   0.0  0
 9CY  CONST_40  H6   C15  C14  C13   180.00   0.0  0
 9CY  CONST_41  H18  C11  C12  C13   180.00   0.0  0
 9CY  CONST_42  H19  C19  C20  C16   180.00   0.0  0
 9CY  CONST_43  H20  C18  C17  C16   180.00   0.0  0
 9CY  CONST_44  C1   N    C9   C10   180.00   0.0  0
 9CY  CONST_45  H9   N    C9   C10     0.00   0.0  0
 9CY  CONST_46  C1   N    C9   O1      0.00   0.0  0
 9CY  Var_01    C1   C2   C3   C4    -81.10  30.0  2
 9CY  Var_02    O1   C9   C10  C15  -149.26  30.0  2

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
 9CY  chir_01  C1  N  C2  C  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
 9CY  plan-1  C4   0.020
 9CY  plan-1  C5   0.020
 9CY  plan-1  C6   0.020
 9CY  plan-1  C7   0.020
 9CY  plan-1  C8   0.020
 9CY  plan-1  C2   0.020
 9CY  plan-1  C3   0.020
 9CY  plan-1  H2   0.020
 9CY  plan-1  H3   0.020
 9CY  plan-1  H4   0.020
 9CY  plan-1  H5   0.020
 9CY  plan-1  H1   0.020
 9CY  plan-2  C10  0.020
 9CY  plan-2  C13  0.020
 9CY  plan-2  C15  0.020
 9CY  plan-2  C14  0.020
 9CY  plan-2  C12  0.020
 9CY  plan-2  C11  0.020
 9CY  plan-2  C16  0.020
 9CY  plan-2  H6   0.020
 9CY  plan-2  H16  0.020
 9CY  plan-2  H17  0.020
 9CY  plan-2  H18  0.020
 9CY  plan-2  C9   0.020
 9CY  plan-3  N1   0.020
 9CY  plan-3  C13  0.020
 9CY  plan-3  C17  0.020
 9CY  plan-3  C20  0.020
 9CY  plan-3  C16  0.020
 9CY  plan-3  C19  0.020
 9CY  plan-3  C18  0.020
 9CY  plan-3  H7   0.020
 9CY  plan-3  H8   0.020
 9CY  plan-3  H19  0.020
 9CY  plan-3  H20  0.020
 9CY  plan-4  C10  0.020
 9CY  plan-4  O1   0.020
 9CY  plan-4  N    0.020
 9CY  plan-4  C1   0.020
 9CY  plan-4  H9   0.020
 9CY  plan-4  C9   0.020

