# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 23:29:36 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 1-(1-adamantyl)-3-(3-imidazol-1-ylpropyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCCCn1ccnc1)NC23CC4CC(CC(C4)C2)C3
#
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
 6XD  6XD  1-(1-adamantyl)-3-(3-imidazol-1-ylpropyl)urea  ligand  48  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6XD
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
 6XD  C4   C  CH2   0  -0.417  -5.1125  -1.4611   0.2530
 6XD  C5   C  CH1   0  -0.254  -4.7768  -0.8403  -1.1053
 6XD  C6   C  CH2   0  -0.415  -5.4457   0.5308  -1.2167
 6XD  C7   C  CH1   0  -0.250  -4.9276   1.4382  -0.0991
 6XD  C8   C  CH2   0  -0.461  -3.4105   1.5829  -0.2224
 6XD  C10  C  CH2   0  -0.416  -5.2715   0.8208   1.2578
 6XD  N02  N  NH1   0  -0.734  -1.2935   0.4617  -0.2449
 6XD  C03  C  C     0   0.745  -0.3083  -0.4685  -0.1716
 6XD  N04  N  NH1   0  -0.692   0.9557   0.0479  -0.2032
 6XD  C05  C  CH2   0  -0.236   2.1126  -0.8072  -0.3353
 6XD  C06  C  CH2   0  -0.476   3.3820  -0.0069  -0.0876
 6XD  C07  C  CH2   0  -0.295   4.6141  -0.8916  -0.2094
 6XD  N08  N  NR5   0  -0.399   5.8403  -0.1648   0.0475
 6XD  C09  C  CR15  0   0.094   6.5691  -0.2061   1.1823
 6XD  N10  N  N     0  -0.457   7.6004   0.5981   1.1349
 6XD  C11  C  CR15  0  -0.218   7.5332   1.1955  -0.0917
 6XD  C12  C  CR15  0  -0.108   6.4467   0.7378  -0.7814
 6XD  O13  O  O     0  -0.549  -0.5083  -1.6758  -0.0711
 6XD  C1   C  CT    0   0.182  -2.7239   0.2145  -0.1112
 6XD  C2   C  CH2   0  -0.419  -3.0856  -0.3944   1.2515
 6XD  C3   C  CH1   0  -0.254  -4.6036  -0.5499   1.3724
 6XD  C9   C  CH2   0  -0.419  -3.2593  -0.6840  -1.2353
 6XD  H1   H  HCH2  0   0.222  -6.1948  -1.6002   0.3452
 6XD  H2   H  HCH2  0   0.222  -4.6596  -2.4539   0.3391
 6XD  H3   H  HCH1  0   0.224  -5.1385  -1.4918  -1.9063
 6XD  H4   H  HCH2  0   0.221  -5.2353   0.9754  -2.1947
 6XD  H5   H  HCH2  0   0.223  -6.5332   0.4283  -1.1429
 6XD  H6   H  HCH1  0   0.227  -5.3848   2.4281  -0.1838
 6XD  H7   H  HCH2  0   0.235  -3.1495   2.0426  -1.1821
 6XD  H8   H  HCH2  0   0.234  -3.0312   2.2460   0.5634
 6XD  H9   H  HCH2  0   0.222  -4.9349   1.4754   2.0681
 6XD  H10  H  HCH2  0   0.223  -6.3569   0.7228   1.3615
 6XD  H11  H  HNH1  0   0.385  -1.0142   1.4303  -0.2503
 6XD  H12  H  HNH1  0   0.386   1.0731   1.0045  -0.4981
 6XD  H13  H  HCH2  0   0.236   2.0451  -1.6165   0.3934
 6XD  H14  H  HCH2  0   0.222   2.1590  -1.2756  -1.3262
 6XD  H15  H  HCH2  0   0.244   3.4501   0.8134  -0.8086
 6XD  H16  H  HCH2  0   0.247   3.3496   0.4393   0.9094
 6XD  H17  H  HCH2  0   0.266   4.5655  -1.7124   0.5070
 6XD  H18  H  HCH2  0   0.266   4.6737  -1.3359  -1.2040
 6XD  H19  H  HCR5  0   0.278   6.3008  -0.8484   2.0085
 6XD  H20  H  HCR5  0   0.249   8.2683   1.9152  -0.4185
 6XD  H21  H  HCR5  0   0.288   6.0659   0.9653  -1.7633
 6XD  H22  H  HCH2  0   0.235  -2.5997  -1.3645   1.3729
 6XD  H23  H  HCH2  0   0.219  -2.7052   0.2546   2.0477
 6XD  H24  H  HCH1  0   0.224  -4.8417  -0.9926   2.3441
 6XD  H25  H  HCH2  0   0.236  -2.7756  -1.6610  -1.1970
 6XD  H26  H  HCH2  0   0.219  -3.0063  -0.2378  -2.2027

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
 6XD  C6   C7   single    1.530  0.020  1.530
 6XD  C6   C5   single    1.530  0.020  1.530
 6XD  C10  C7   single    1.530  0.020  1.530
 6XD  C10  C3   single    1.529  0.020  1.529
 6XD  C7   C8   single    1.529  0.020  1.529
 6XD  C4   C5   single    1.531  0.020  1.531
 6XD  C4   C3   single    1.530  0.020  1.530
 6XD  C5   C9   single    1.531  0.020  1.531
 6XD  C3   C2   single    1.531  0.020  1.531
 6XD  C8   C1   single    1.535  0.020  1.535
 6XD  C9   C1   single    1.535  0.020  1.535
 6XD  C2   C1   single    1.536  0.020  1.536
 6XD  C1   N02  single    1.458  0.020  1.458
 6XD  N02  C03  single    1.357  0.020  1.357
 6XD  O13  C03  double    1.228  0.020  1.228
 6XD  C03  N04  single    1.366  0.020  1.366
 6XD  N04  C05  single    1.445  0.020  1.445
 6XD  C05  C06  single    1.521  0.020  1.521
 6XD  C12  C11  aromatic  1.366  0.020  1.366
 6XD  C12  N08  aromatic  1.367  0.020  1.367
 6XD  C11  N10  aromatic  1.366  0.020  1.366
 6XD  C06  C07  single    1.522  0.020  1.522
 6XD  C07  N08  single    1.448  0.020  1.448
 6XD  N08  C09  aromatic  1.349  0.020  1.349
 6XD  N10  C09  aromatic  1.309  0.020  1.309
 6XD  C4   H1   single    0.970  0.020  1.090
 6XD  C4   H2   single    0.970  0.020  1.090
 6XD  C5   H3   single    0.970  0.020  1.090
 6XD  C6   H4   single    0.970  0.020  1.090
 6XD  C6   H5   single    0.970  0.020  1.090
 6XD  C7   H6   single    0.970  0.020  1.090
 6XD  C8   H7   single    0.970  0.020  1.090
 6XD  C8   H8   single    0.970  0.020  1.090
 6XD  C10  H9   single    0.970  0.020  1.090
 6XD  C10  H10  single    0.970  0.020  1.090
 6XD  N02  H11  single    0.860  0.020  1.020
 6XD  N04  H12  single    0.890  0.020  1.040
 6XD  C05  H13  single    0.970  0.020  1.090
 6XD  C05  H14  single    0.970  0.020  1.090
 6XD  C06  H15  single    0.970  0.020  1.090
 6XD  C06  H16  single    0.970  0.020  1.090
 6XD  C07  H17  single    0.970  0.020  1.090
 6XD  C07  H18  single    0.970  0.020  1.090
 6XD  C09  H19  single    0.930  0.020  1.080
 6XD  C11  H20  single    0.930  0.020  1.080
 6XD  C12  H21  single    0.930  0.020  1.080
 6XD  C2   H22  single    0.970  0.020  1.090
 6XD  C2   H23  single    0.970  0.020  1.090
 6XD  C3   H24  single    0.970  0.020  1.090
 6XD  C9   H25  single    0.970  0.020  1.090
 6XD  C9   H26  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
 6XD  H2   C4   H1   106.69  3.000
 6XD  H2   C4   C3   110.17  3.000
 6XD  H1   C4   C3   110.04  3.000
 6XD  H2   C4   C5   110.30  3.000
 6XD  H1   C4   C5   110.06  3.000
 6XD  C3   C4   C5   109.55  3.000
 6XD  H3   C5   C9   109.05  3.000
 6XD  H3   C5   C6   109.63  3.000
 6XD  C9   C5   C6   109.62  3.000
 6XD  H3   C5   C4   109.61  3.000
 6XD  C9   C5   C4   109.52  3.000
 6XD  C6   C5   C4   109.41  3.000
 6XD  H5   C6   H4   106.81  3.000
 6XD  H5   C6   C7   110.04  3.000
 6XD  H4   C6   C7   110.28  3.000
 6XD  H5   C6   C5   110.21  3.000
 6XD  H4   C6   C5   110.18  3.000
 6XD  C7   C6   C5   109.29  3.000
 6XD  H6   C7   C10  109.87  3.000
 6XD  H6   C7   C8   108.84  3.000
 6XD  C10  C7   C8   109.43  3.000
 6XD  H6   C7   C6   109.80  3.000
 6XD  C8   C7   C6   109.47  3.000
 6XD  C10  C7   C6   109.41  3.000
 6XD  H8   C8   H7   106.97  3.000
 6XD  H8   C8   C1   109.43  3.000
 6XD  H7   C8   C1   109.33  3.000
 6XD  H8   C8   C7   110.05  3.000
 6XD  H7   C8   C7   110.28  3.000
 6XD  C1   C8   C7   110.71  3.000
 6XD  H10  C10  H9   106.75  3.000
 6XD  H10  C10  C3   110.23  3.000
 6XD  H9   C10  C3   110.26  3.000
 6XD  H10  C10  C7   110.06  3.000
 6XD  H9   C10  C7   110.25  3.000
 6XD  C3   C10  C7   109.27  3.000
 6XD  H11  N02  C1   115.80  3.000
 6XD  H11  N02  C03  117.25  3.000
 6XD  C1   N02  C03  126.24  3.000
 6XD  O13  C03  N04  121.63  3.000
 6XD  N04  C03  N02  114.30  3.000
 6XD  O13  C03  N02  124.07  3.000
 6XD  H12  N04  C05  116.21  3.000
 6XD  H12  N04  C03  118.26  3.000
 6XD  C05  N04  C03  121.29  3.000
 6XD  H14  C05  H13  106.81  3.000
 6XD  H14  C05  C06  109.66  3.000
 6XD  H13  C05  C06  109.46  3.000
 6XD  H14  C05  N04  111.67  3.000
 6XD  H13  C05  N04  109.18  3.000
 6XD  C06  C05  N04  110.00  3.000
 6XD  H16  C06  H15  107.27  3.000
 6XD  H16  C06  C07  109.53  3.000
 6XD  H15  C06  C07  109.43  3.000
 6XD  H16  C06  C05  109.80  3.000
 6XD  H15  C06  C05  109.82  3.000
 6XD  C07  C06  C05  110.91  3.000
 6XD  H18  C07  H17  107.15  3.000
 6XD  H18  C07  N08  108.65  3.000
 6XD  H17  C07  N08  107.40  3.000
 6XD  H18  C07  C06  110.73  3.000
 6XD  H17  C07  C06  110.42  3.000
 6XD  N08  C07  C06  112.30  3.000
 6XD  C12  N08  C09  106.90  3.000
 6XD  C09  N08  C07  126.23  3.000
 6XD  C12  N08  C07  126.81  3.000
 6XD  H19  C09  N10  126.07  3.000
 6XD  H19  C09  N08  121.82  3.000
 6XD  N10  C09  N08  112.11  3.000
 6XD  C11  N10  C09  105.22  3.000
 6XD  H20  C11  C12  127.75  3.000
 6XD  H20  C11  N10  122.01  3.000
 6XD  C12  C11  N10  110.25  3.000
 6XD  H21  C12  C11  132.11  3.000
 6XD  H21  C12  N08  122.36  3.000
 6XD  C11  C12  N08  105.53  3.000
 6XD  C9   C1   C2   109.60  3.000
 6XD  C2   C1   N02  112.31  3.000
 6XD  C9   C1   N02  111.98  3.000
 6XD  N02  C1   C8   106.33  3.000
 6XD  C2   C1   C8   108.21  3.000
 6XD  C9   C1   C8   108.22  3.000
 6XD  H23  C2   H22  106.92  3.000
 6XD  H23  C2   C3   110.31  3.000
 6XD  H22  C2   C3   110.02  3.000
 6XD  H23  C2   C1   109.16  3.000
 6XD  H22  C2   C1   110.26  3.000
 6XD  C3   C2   C1   110.11  3.000
 6XD  H24  C3   C2   109.09  3.000
 6XD  H24  C3   C10  109.53  3.000
 6XD  C2   C3   C10  109.65  3.000
 6XD  H24  C3   C4   109.65  3.000
 6XD  C2   C3   C4   109.42  3.000
 6XD  C10  C3   C4   109.49  3.000
 6XD  H26  C9   H25  107.07  3.000
 6XD  H26  C9   C1   109.13  3.000
 6XD  H25  C9   C1   110.11  3.000
 6XD  H26  C9   C5   110.22  3.000
 6XD  H25  C9   C5   110.19  3.000
 6XD  C1   C9   C5   110.07  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
 6XD  CONST_01  N10  C11  C12  N08     0.00   0.0  0
 6XD  CONST_02  C11  N10  C09  N08     0.00   0.0  0
 6XD  CONST_03  C11  C12  N08  C09     0.00   0.0  0
 6XD  CONST_04  C12  C11  N10  C09     0.00   0.0  0
 6XD  CONST_05  C12  N08  C09  N10     0.00   0.0  0
 6XD  CONST_06  C11  C12  N08  C07   180.00   0.0  0
 6XD  CONST_07  N10  C09  N08  C07   180.00   0.0  0
 6XD  CONST_08  H20  C11  C12  N08   180.00   0.0  0
 6XD  CONST_09  H21  C12  N08  C09   180.00   0.0  0
 6XD  CONST_10  H19  C09  N10  C11   180.00   0.0  0
 6XD  CONST_11  C1   N02  C03  O13     0.00   0.0  0
 6XD  CONST_12  C1   N02  C03  N04   180.00   0.0  0
 6XD  CONST_13  O13  C03  N04  C05     0.00   0.0  0
 6XD  CONST_14  C05  N04  C03  N02   180.00   0.0  0
 6XD  CONST_15  H11  N02  C03  O13   180.00   0.0  0
 6XD  CONST_16  H12  N04  C03  O13   180.00   0.0  0
 6XD  Var_01    C12  N08  C07  C06   -74.05  30.0  2
 6XD  Var_02    N08  C07  C06  C05  -178.84  30.0  3
 6XD  Var_03    C06  C05  N04  C03  -169.66  30.0  3
 6XD  Var_04    C07  C06  C05  N04   179.49  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
 6XD  chir_01  C5  C6  C4   C9   positiv
 6XD  chir_02  C7  C8  C10  C6   positiv
 6XD  chir_03  C1  C2  C9   C8   negativ
 6XD  chir_04  C3  C2  C4   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
 6XD  plan-1  C07  0.020
 6XD  plan-1  N08  0.020
 6XD  plan-1  C09  0.020
 6XD  plan-1  N10  0.020
 6XD  plan-1  C11  0.020
 6XD  plan-1  C12  0.020
 6XD  plan-1  H19  0.020
 6XD  plan-1  H20  0.020
 6XD  plan-1  H21  0.020
 6XD  plan-2  N02  0.020
 6XD  plan-2  C03  0.020
 6XD  plan-2  N04  0.020
 6XD  plan-2  C05  0.020
 6XD  plan-2  O13  0.020
 6XD  plan-2  C1   0.020
 6XD  plan-2  H11  0.020
 6XD  plan-2  H12  0.020

