# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 08:06:32 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: N-[(1R,3S,5r,7r)-tricyclo[3.3.1.1~3,7~]decan-2-yl]-N'-(2,3,4-trifluorophenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(NC(=O)NC2C3CC4CC(C3)CC2C4)c(F)c1F
#
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
 9ZF  9ZF  N-[(1R,3S,5r,7r)-tricyclo[3.3.1.1~3,7~]decan-2-yl]-N'-(2,3,4-trifluorophenyl)urea  ligand  42  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9ZF
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
 9ZF  C10  C  CH1   0  -0.020   2.5220   0.6489  -0.3727
 9ZF  C16  C  CR6   0   0.348  -3.2348  -0.9034  -0.1066
 9ZF  C17  C  CR6   0   0.278  -4.5715  -0.6671   0.1459
 9ZF  C15  C  CR6   0   0.213  -2.3458   0.1294  -0.3947
 9ZF  C12  C  C     0   0.739   0.0702   0.5666  -0.3179
 9ZF  C18  C  CR6   0   0.394  -5.0467   0.6305   0.1373
 9ZF  C20  C  CR16  0  -0.295  -2.8569   1.4272  -0.4169
 9ZF  C19  C  CR16  0  -0.422  -4.1930   1.6756  -0.1410
 9ZF  C01  C  CH2   0  -0.422   5.6362  -0.6933   0.6560
 9ZF  C02  C  CH1   0  -0.240   4.3672  -1.5183   0.4247
 9ZF  C03  C  CH2   0  -0.445   3.9179  -1.3563  -1.0295
 9ZF  C04  C  CH1   0  -0.273   3.6116   0.1187  -1.3137
 9ZF  C05  C  CH2   0  -0.425   4.8826   0.9416  -1.0817
 9ZF  C06  C  CH1   0  -0.243   5.3512   0.7823   0.3671
 9ZF  C07  C  CH2   0  -0.429   4.2486   1.2778   1.3051
 9ZF  C08  C  CH1   0  -0.249   2.9755   0.4567   1.0831
 9ZF  C09  C  CH2   0  -0.430   3.2606  -1.0202   1.3578
 9ZF  N11  N  NH1   0  -0.699   1.2508   0.0141  -0.6626
 9ZF  O13  O  O     0  -0.520  -0.0355   1.6459   0.2451
 9ZF  N14  N  NH1   0  -0.786  -1.0242  -0.1961  -0.6766
 9ZF  F21  F  F     0  -0.304  -6.3409   0.8443   0.3914
 9ZF  F23  F  F     0  -0.299  -2.7959  -2.1659  -0.0777
 9ZF  H1   H  HCH1  0   0.245   2.4013   1.7202  -0.5616
 9ZF  H2   H  HCR6  0   0.291  -2.2126   2.2576  -0.6555
 9ZF  H3   H  HCR6  0   0.298  -4.5720   2.6886  -0.1573
 9ZF  H4   H  HCH2  0   0.222   5.9775  -0.8129   1.6895
 9ZF  H5   H  HCH2  0   0.222   6.4447  -1.0569   0.0135
 9ZF  H6   H  HCH1  0   0.226   4.5725  -2.5733   0.6289
 9ZF  H7   H  HCH2  0   0.234   4.7079  -1.6934  -1.7078
 9ZF  H8   H  HCH2  0   0.227   3.0566  -2.0000  -1.2383
 9ZF  H9   H  HCH1  0   0.239   3.2796   0.2411  -2.3495
 9ZF  H10  H  HCH2  0   0.228   5.6648   0.6145  -1.7737
 9ZF  H11  H  HCH2  0   0.228   4.6906   1.9976  -1.2974
 9ZF  H12  H  HCH1  0   0.225   6.2589   1.3725   0.5234
 9ZF  H13  H  HCH2  0   0.226   4.5691   1.1916   2.3482
 9ZF  H14  H  HCH2  0   0.225   4.0493   2.3396   1.1238
 9ZF  H15  H  HCH1  0   0.233   2.1876   0.8161   1.7505
 9ZF  H16  H  HCH2  0   0.225   2.3535  -1.6192   1.2284
 9ZF  H17  H  HCH2  0   0.227   3.5649  -1.1483   2.4015
 9ZF  H18  H  HNH1  0   0.396   1.2601  -0.8890  -1.1079
 9ZF  H19  H  HNH1  0   0.410  -0.8523  -1.1277  -1.0222
 9ZF  F22  F  F     0  -0.297  -5.3854  -1.6880   0.4093

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
 9ZF  C06  C01  single    1.530  0.020  1.530
 9ZF  C06  C05  single    1.531  0.020  1.531
 9ZF  C06  C07  single    1.530  0.020  1.530
 9ZF  C01  C02  single    1.531  0.020  1.531
 9ZF  C05  C04  single    1.532  0.020  1.532
 9ZF  C07  C08  single    1.531  0.020  1.531
 9ZF  C02  C03  single    1.531  0.020  1.531
 9ZF  C02  C09  single    1.531  0.020  1.531
 9ZF  C04  C03  single    1.533  0.020  1.533
 9ZF  C04  C10  single    1.534  0.020  1.534
 9ZF  C09  C08  single    1.529  0.020  1.529
 9ZF  C08  C10  single    1.537  0.020  1.537
 9ZF  C10  N11  single    1.450  0.020  1.450
 9ZF  N11  C12  single    1.348  0.020  1.348
 9ZF  O13  C12  double    1.222  0.020  1.222
 9ZF  C12  N14  single    1.381  0.020  1.381
 9ZF  N14  C15  single    1.390  0.020  1.390
 9ZF  C15  C20  aromatic  1.395  0.020  1.395
 9ZF  C15  C16  aromatic  1.393  0.020  1.393
 9ZF  C20  C19  aromatic  1.387  0.020  1.387
 9ZF  C16  F23  single    1.337  0.020  1.337
 9ZF  C16  C17  aromatic  1.381  0.020  1.381
 9ZF  C19  C18  aromatic  1.378  0.020  1.378
 9ZF  C17  C18  aromatic  1.382  0.020  1.382
 9ZF  C17  F22  single    1.332  0.020  1.332
 9ZF  C18  F21  single    1.336  0.020  1.336
 9ZF  C10  H1   single    0.970  0.020  1.090
 9ZF  C20  H2   single    0.930  0.020  1.080
 9ZF  C19  H3   single    0.930  0.020  1.080
 9ZF  C01  H4   single    0.970  0.020  1.090
 9ZF  C01  H5   single    0.970  0.020  1.090
 9ZF  C02  H6   single    0.970  0.020  1.090
 9ZF  C03  H7   single    0.970  0.020  1.090
 9ZF  C03  H8   single    0.970  0.020  1.090
 9ZF  C04  H9   single    0.970  0.020  1.090
 9ZF  C05  H10  single    0.970  0.020  1.090
 9ZF  C05  H11  single    0.970  0.020  1.090
 9ZF  C06  H12  single    0.970  0.020  1.090
 9ZF  C07  H13  single    0.970  0.020  1.090
 9ZF  C07  H14  single    0.970  0.020  1.090
 9ZF  C08  H15  single    0.970  0.020  1.090
 9ZF  C09  H16  single    0.970  0.020  1.090
 9ZF  C09  H17  single    0.970  0.020  1.090
 9ZF  N11  H18  single    0.860  0.020  1.020
 9ZF  N14  H19  single    0.860  0.020  1.020

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
 9ZF  H1   C10  N11  107.30  3.000
 9ZF  H1   C10  C08  108.56  3.000
 9ZF  N11  C10  C08  113.16  3.000
 9ZF  H1   C10  C04  108.10  3.000
 9ZF  N11  C10  C04  110.41  3.000
 9ZF  C08  C10  C04  109.16  3.000
 9ZF  F23  C16  C15  119.68  3.000
 9ZF  F23  C16  C17  118.39  3.000
 9ZF  C15  C16  C17  121.92  3.000
 9ZF  F22  C17  C18  120.72  3.000
 9ZF  F22  C17  C16  119.77  3.000
 9ZF  C18  C17  C16  119.51  3.000
 9ZF  N14  C15  C20  124.26  3.000
 9ZF  C20  C15  C16  117.34  3.000
 9ZF  N14  C15  C16  118.37  3.000
 9ZF  N14  C12  O13  122.60  3.000
 9ZF  N14  C12  N11  113.65  3.000
 9ZF  O13  C12  N11  123.74  3.000
 9ZF  F21  C18  C19  121.14  3.000
 9ZF  F21  C18  C17  118.83  3.000
 9ZF  C19  C18  C17  120.03  3.000
 9ZF  H2   C20  C19  118.81  3.000
 9ZF  H2   C20  C15  120.09  3.000
 9ZF  C19  C20  C15  121.10  3.000
 9ZF  H3   C19  C20  120.16  3.000
 9ZF  H3   C19  C18  119.75  3.000
 9ZF  C20  C19  C18  120.08  3.000
 9ZF  H5   C01  H4   106.71  3.000
 9ZF  H5   C01  C06  110.30  3.000
 9ZF  H4   C01  C06  109.97  3.000
 9ZF  H5   C01  C02  110.15  3.000
 9ZF  H4   C01  C02  110.00  3.000
 9ZF  C06  C01  C02  109.67  3.000
 9ZF  H6   C02  C09  109.61  3.000
 9ZF  H6   C02  C03  109.54  3.000
 9ZF  C09  C02  C03  109.42  3.000
 9ZF  H6   C02  C01  109.62  3.000
 9ZF  C09  C02  C01  109.37  3.000
 9ZF  C03  C02  C01  109.25  3.000
 9ZF  H8   C03  H7   105.57  3.000
 9ZF  H8   C03  C04  111.90  3.000
 9ZF  H7   C03  C04  109.01  3.000
 9ZF  H8   C03  C02  110.47  3.000
 9ZF  H7   C03  C02  110.14  3.000
 9ZF  C04  C03  C02  109.67  3.000
 9ZF  H9   C04  C05  109.57  3.000
 9ZF  H9   C04  C03  110.10  3.000
 9ZF  C05  C04  C03  108.85  3.000
 9ZF  H9   C04  C10  109.05  3.000
 9ZF  C03  C04  C10  111.14  3.000
 9ZF  C05  C04  C10  108.10  3.000
 9ZF  H11  C05  H10  106.80  3.000
 9ZF  H11  C05  C06  109.91  3.000
 9ZF  H10  C05  C06  110.40  3.000
 9ZF  H11  C05  C04  110.05  3.000
 9ZF  H10  C05  C04  109.68  3.000
 9ZF  C06  C05  C04  109.96  3.000
 9ZF  H12  C06  C07  109.61  3.000
 9ZF  H12  C06  C05  109.45  3.000
 9ZF  C07  C06  C05  109.02  3.000
 9ZF  H12  C06  C01  109.80  3.000
 9ZF  C07  C06  C01  109.32  3.000
 9ZF  C05  C06  C01  109.63  3.000
 9ZF  H14  C07  H13  106.69  3.000
 9ZF  H14  C07  C08  110.15  3.000
 9ZF  H13  C07  C08  109.84  3.000
 9ZF  H14  C07  C06  110.09  3.000
 9ZF  H13  C07  C06  110.35  3.000
 9ZF  C08  C07  C06  109.67  3.000
 9ZF  H15  C08  C09  110.01  3.000
 9ZF  H15  C08  C07  109.54  3.000
 9ZF  C09  C08  C07  109.69  3.000
 9ZF  H15  C08  C10  108.93  3.000
 9ZF  C09  C08  C10  110.24  3.000
 9ZF  C07  C08  C10  108.40  3.000
 9ZF  H17  C09  H16  106.20  3.000
 9ZF  H17  C09  C08  109.64  3.000
 9ZF  H16  C09  C08  110.66  3.000
 9ZF  H17  C09  C02  110.01  3.000
 9ZF  H16  C09  C02  110.42  3.000
 9ZF  C08  C09  C02  109.85  3.000
 9ZF  H18  N11  C12  119.25  3.000
 9ZF  H18  N11  C10  118.23  3.000
 9ZF  C12  N11  C10  122.48  3.000
 9ZF  H19  N14  C12  117.64  3.000
 9ZF  H19  N14  C15  116.61  3.000
 9ZF  C12  N14  C15  124.85  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
 9ZF  CONST_01  C19  C20  C15  C16    0.00  0.0  0
 9ZF  CONST_02  C19  C18  C17  C16    0.00  0.0  0
 9ZF  CONST_03  C20  C15  C16  C17    0.00  0.0  0
 9ZF  CONST_04  C20  C19  C18  C17    0.00  0.0  0
 9ZF  CONST_05  C18  C19  C20  C15    0.00  0.0  0
 9ZF  CONST_06  C18  C17  C16  C15    0.00  0.0  0
 9ZF  CONST_07  F21  C18  C17  C16  180.00  0.0  0
 9ZF  CONST_08  N14  C15  C16  C17  180.00  0.0  0
 9ZF  CONST_09  F22  C17  C16  C15  180.00  0.0  0
 9ZF  CONST_10  F23  C16  C17  C18  180.00  0.0  0
 9ZF  CONST_11  F23  C16  C15  C20  180.00  0.0  0
 9ZF  CONST_12  F21  C18  C19  C20  180.00  0.0  0
 9ZF  CONST_13  N14  C15  C20  C19  180.00  0.0  0
 9ZF  CONST_14  F22  C17  C18  C19  180.00  0.0  0
 9ZF  CONST_15  H2   C20  C15  C16  180.00  0.0  0
 9ZF  CONST_16  H3   C19  C18  C17  180.00  0.0  0
 9ZF  CONST_20  O13  C12  N11  C10    0.00  0.0  0
 9ZF  CONST_21  O13  C12  N14  C15    0.00  0.0  0
 9ZF  CONST_22  N11  C12  N14  C15  180.00  0.0  0
 9ZF  CONST_23  N14  C12  N11  C10  180.00  0.0  0
 9ZF  CONST_24  H18  N11  C12  O13  180.00  0.0  0

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
 9ZF  chir_01  C10  C04  C08  N11  positiv
 9ZF  chir_02  C02  C01  C03  C09  positiv
 9ZF  chir_03  C04  C10  C03  C05  positiv
 9ZF  chir_04  C06  C07  C05  C01  positiv
 9ZF  chir_05  C08  C07  C09  C10  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
 9ZF  plan-1  C16  0.020
 9ZF  plan-1  C17  0.020
 9ZF  plan-1  C15  0.020
 9ZF  plan-1  C18  0.020
 9ZF  plan-1  C20  0.020
 9ZF  plan-1  C19  0.020
 9ZF  plan-1  N14  0.020
 9ZF  plan-1  F21  0.020
 9ZF  plan-1  F23  0.020
 9ZF  plan-1  H2   0.020
 9ZF  plan-1  H3   0.020
 9ZF  plan-1  F22  0.020
 9ZF  plan-2  C10  0.020
 9ZF  plan-2  C15  0.020
 9ZF  plan-2  C12  0.020
 9ZF  plan-2  N11  0.020
 9ZF  plan-2  O13  0.020
 9ZF  plan-2  N14  0.020
 9ZF  plan-2  H18  0.020
 9ZF  plan-2  H19  0.020

