# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 21:37:59 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 1-(4-carbamimidamidobenzyl)-3-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)Nc1ccc(CNC(=O)NC23CC4CC(CC(C4)C2)C3)cc1
#
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
 AGB  AGB  1-(4-carbamimidamidobenzyl)-3-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]urea  ligand  52  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 PERFECT
;

data_comp_AGB
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
 AGB  C1    C  CH1   0  -0.249  -0.6616   1.1665  -5.3997
 AGB  C2    C  CH2   0  -0.417  -1.9909   0.4930  -5.0537
 AGB  C3    C  CH2   0  -0.465   0.0181   1.6324  -4.1120
 AGB  C4    C  CH2   0  -0.417   0.2451   0.1699  -6.1235
 AGB  C5    C  CH2   0  -0.417  -0.8192  -1.7051  -4.8589
 AGB  C6    C  CH1   0  -0.254  -1.7284  -0.7058  -4.1403
 AGB  C7    C  CH1   0  -0.254   0.5075  -1.0279  -5.2102
 AGB  C8    C  CH2   0  -0.418  -1.0510  -0.2284  -2.8527
 AGB  C9    C  CH2   0  -0.422   1.1942  -0.5505  -3.9270
 AGB  C10   C  CT    0   0.184   0.2904   0.4417  -3.1811
 AGB  N1    N  NH1   0  -0.686   2.0768   1.0510  -0.0181
 AGB  N2    N  NH1   0  -0.733   0.9346   0.9930  -1.9955
 AGB  O1    O  O     0  -0.541   1.2872  -0.9225  -0.8047
 AGB  C11   C  CH2   0  -0.325   2.5398   0.5097   1.2273
 AGB  C13   C  CR16  0  -0.284   1.9003   0.0133   3.5993
 AGB  C14   C  CR6   0   0.069   1.5098   0.4448   2.3338
 AGB  C15   C  CR16  0  -0.294   0.1811   0.8031   2.1534
 AGB  C16   C  CR16  0  -0.310  -0.7318   0.7101   3.1946
 AGB  C17   C  CR6   0   0.313  -0.3359   0.2752   4.4572
 AGB  C18   C  CR16  0  -0.289   1.0061  -0.0593   4.6535
 AGB  N3    N  NH1   0  -0.742  -1.2757   0.2617   5.4934
 AGB  C19   C  C     0   0.522  -1.4528  -0.6803   6.4860
 AGB  N5    N  NH2   0  -0.812  -0.6599  -1.7947   6.4076
 AGB  H1    H  HCH1  0   0.228  -0.8420   2.0349  -6.0397
 AGB  H21   H  HCH2  0   0.222  -2.6549   1.2075  -4.5558
 AGB  H22   H  HCH2  0   0.223  -2.5014   0.1700  -5.9670
 AGB  H31   H  HCH2  0   0.235  -0.6172   2.3616  -3.5962
 AGB  H32   H  HCH2  0   0.235   0.9636   2.1342  -4.3486
 AGB  H41   H  HCH2  0   0.223  -0.2239  -0.1563  -7.0571
 AGB  H42   H  HCH2  0   0.222   1.1911   0.6489  -6.3954
 AGB  H51   H  HCH2  0   0.222  -0.6403  -2.5791  -4.2247
 AGB  H52   H  HCH2  0   0.223  -1.3085  -2.0684  -5.7682
 AGB  H6    H  HCH1  0   0.224  -2.6764  -1.1889  -3.8848
 AGB  H7    H  HCH1  0   0.224   1.1612  -1.7418  -5.7203
 AGB  H81   H  HCH2  0   0.235  -0.8948  -1.0678  -2.1727
 AGB  H82   H  HCH2  0   0.219  -1.6933   0.4901  -2.3323
 AGB  H91   H  HCH2  0   0.220   2.1418  -0.0563  -4.1677
 AGB  H92   H  HCH2  0   0.236   1.4280  -1.4042  -3.2882
 AGB  HN1   H  HNH1  0   0.392   2.0745   2.0536  -0.1107
 AGB  HN2   H  HNH1  0   0.386   1.1252   1.9822  -2.0206
 AGB  H111  H  HCH2  0   0.263   3.3815   1.1202   1.5607
 AGB  H112  H  HCH2  0   0.257   2.9453  -0.4883   1.0538
 AGB  H15   H  HCR6  0   0.246  -0.1640   1.1601   1.1915
 AGB  H16   H  HCR6  0   0.262  -1.7671   0.9784   3.0213
 AGB  H18   H  HCR6  0   0.269   1.3575  -0.3659   5.6288
 AGB  HN3   H  HNH1  0   0.400  -2.0332   0.9191   5.3983
 AGB  HN4   H  H     0   0.318  -2.7106   0.3702   7.4464
 AGB  HN51  H  HNH2  0   0.387  -0.9392  -2.5239   7.0442
 AGB  HN52  H  HNH2  0   0.391  -0.4395  -2.1451   5.4882
 AGB  C12   C  C     0   0.740   1.4130   0.2907  -0.9396
 AGB  H13   H  HCR6  0   0.249   2.9362  -0.2535   3.7773
 AGB  N4    N  N     0  -0.708  -2.2759  -0.5451   7.4581

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
 AGB  C1   C2    single    1.530  0.020  1.530
 AGB  C1   C3    single    1.529  0.020  1.529
 AGB  C1   C4    single    1.529  0.020  1.529
 AGB  C1   H1    single    0.970  0.020  1.090
 AGB  C2   C6    single    1.530  0.020  1.530
 AGB  C2   H21   single    0.970  0.020  1.090
 AGB  C2   H22   single    0.970  0.020  1.090
 AGB  C3   C10   single    1.536  0.020  1.536
 AGB  C3   H31   single    0.970  0.020  1.090
 AGB  C3   H32   single    0.970  0.020  1.090
 AGB  C4   C7    single    1.529  0.020  1.529
 AGB  C4   H41   single    0.970  0.020  1.090
 AGB  C4   H42   single    0.970  0.020  1.090
 AGB  C5   C6    single    1.530  0.020  1.530
 AGB  C5   C7    single    1.530  0.020  1.530
 AGB  C5   H51   single    0.970  0.020  1.090
 AGB  C5   H52   single    0.970  0.020  1.090
 AGB  C6   C8    single    1.531  0.020  1.531
 AGB  C6   H6    single    0.970  0.020  1.090
 AGB  C7   C9    single    1.532  0.020  1.532
 AGB  C7   H7    single    0.970  0.020  1.090
 AGB  C8   C10   single    1.535  0.020  1.535
 AGB  C8   H81   single    0.970  0.020  1.090
 AGB  C8   H82   single    0.970  0.020  1.090
 AGB  C9   C10   single    1.536  0.020  1.536
 AGB  C9   H91   single    0.970  0.020  1.090
 AGB  C9   H92   single    0.970  0.020  1.090
 AGB  C10  N2    single    1.458  0.020  1.458
 AGB  N1   C12   single    1.367  0.020  1.367
 AGB  N1   C11   single    1.435  0.020  1.435
 AGB  N1   HN1   single    0.860  0.020  1.020
 AGB  C12  N2    single    1.355  0.020  1.355
 AGB  C12  O1    double    1.227  0.020  1.227
 AGB  N2   HN2   single    0.860  0.020  1.020
 AGB  C11  C14   single    1.513  0.020  1.513
 AGB  C11  H111  single    0.970  0.020  1.090
 AGB  C11  H112  single    0.970  0.020  1.090
 AGB  C13  C14   aromatic  1.393  0.020  1.393
 AGB  C13  C18   aromatic  1.384  0.020  1.384
 AGB  C13  H13   single    0.930  0.020  1.080
 AGB  C14  C15   aromatic  1.388  0.020  1.388
 AGB  C15  C16   aromatic  1.388  0.020  1.388
 AGB  C15  H15   single    0.930  0.020  1.080
 AGB  C16  C17   aromatic  1.393  0.020  1.393
 AGB  C16  H16   single    0.930  0.020  1.080
 AGB  C17  C18   aromatic  1.397  0.020  1.397
 AGB  C17  N3    single    1.399  0.020  1.399
 AGB  C18  H18   single    0.930  0.020  1.080
 AGB  N3   C19   single    1.380  0.020  1.380
 AGB  N3   HN3   single    0.860  0.020  1.020
 AGB  N4   C19   double    1.281  0.020  1.281
 AGB  N4   HN4   single    0.890  0.020  1.040
 AGB  C19  N5    single    1.370  0.020  1.370
 AGB  N5   HN51  single    0.890  0.020  1.040
 AGB  N5   HN52  single    0.890  0.020  1.040

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
 AGB  H1    C1   C4    109.77  3.000
 AGB  H1    C1   C3    108.92  3.000
 AGB  C4    C1   C3    109.48  3.000
 AGB  H1    C1   C2    109.80  3.000
 AGB  C4    C1   C2    109.59  3.000
 AGB  C3    C1   C2    109.27  3.000
 AGB  H22   C2   H21   106.79  3.000
 AGB  H22   C2   C6    110.29  3.000
 AGB  H21   C2   C6    110.11  3.000
 AGB  H22   C2   C1    110.26  3.000
 AGB  H21   C2   C1    110.03  3.000
 AGB  C6    C2   C1    109.33  3.000
 AGB  H32   C3   H31   107.28  3.000
 AGB  H32   C3   C10   109.44  3.000
 AGB  H31   C3   C10   109.47  3.000
 AGB  H32   C3   C1    109.95  3.000
 AGB  H31   C3   C1    109.96  3.000
 AGB  C10   C3   C1    110.68  3.000
 AGB  H42   C4   H41   106.79  3.000
 AGB  H42   C4   C7    110.05  3.000
 AGB  H41   C4   C7    110.46  3.000
 AGB  H42   C4   C1    110.16  3.000
 AGB  H41   C4   C1    110.11  3.000
 AGB  C7    C4   C1    109.24  3.000
 AGB  H52   C5   H51   106.82  3.000
 AGB  H52   C5   C7    110.10  3.000
 AGB  H51   C5   C7    110.16  3.000
 AGB  H52   C5   C6    109.95  3.000
 AGB  H51   C5   C6    110.27  3.000
 AGB  C7    C5   C6    109.51  3.000
 AGB  H6    C6   C8    108.94  3.000
 AGB  H6    C6   C5    109.64  3.000
 AGB  C8    C6   C5    109.61  3.000
 AGB  H6    C6   C2    109.68  3.000
 AGB  C8    C6   C2    109.49  3.000
 AGB  C5    C6   C2    109.47  3.000
 AGB  H7    C7   C9    109.03  3.000
 AGB  H7    C7   C5    109.65  3.000
 AGB  C9    C7   C5    109.53  3.000
 AGB  H7    C7   C4    109.59  3.000
 AGB  C9    C7   C4    109.46  3.000
 AGB  C5    C7   C4    109.57  3.000
 AGB  H82   C8   H81   107.00  3.000
 AGB  H82   C8   C10   109.13  3.000
 AGB  H81   C8   C10   110.12  3.000
 AGB  H82   C8   C6    110.16  3.000
 AGB  H81   C8   C6    110.33  3.000
 AGB  C10   C8   C6    110.05  3.000
 AGB  H92   C9   H91   107.23  3.000
 AGB  H92   C9   C10   110.31  3.000
 AGB  H91   C9   C10   108.93  3.000
 AGB  H92   C9   C7    110.03  3.000
 AGB  H91   C9   C7    110.14  3.000
 AGB  C10   C9   C7    110.15  3.000
 AGB  N2    C10  C9    112.29  3.000
 AGB  N2    C10  C8    112.17  3.000
 AGB  C9    C10  C8    109.64  3.000
 AGB  N2    C10  C3    106.15  3.000
 AGB  C9    C10  C3    108.12  3.000
 AGB  C8    C10  C3    108.26  3.000
 AGB  HN1   N1   C11   117.15  3.000
 AGB  HN1   N1   C12   119.40  3.000
 AGB  C11   N1   C12   122.15  3.000
 AGB  HN2   N2   C12   117.47  3.000
 AGB  HN2   N2   C10   115.76  3.000
 AGB  C12   N2   C10   126.42  3.000
 AGB  H112  C11  H111  105.87  3.000
 AGB  H112  C11  C14   109.27  3.000
 AGB  H111  C11  C14   109.00  3.000
 AGB  H112  C11  N1    109.08  3.000
 AGB  H111  C11  N1    107.63  3.000
 AGB  C14   C11  N1    115.55  3.000
 AGB  H13   C13  C18   118.63  3.000
 AGB  H13   C13  C14   119.55  3.000
 AGB  C18   C13  C14   121.81  3.000
 AGB  C15   C14  C13   117.80  3.000
 AGB  C15   C14  C11   123.06  3.000
 AGB  C13   C14  C11   119.13  3.000
 AGB  H15   C15  C16   118.62  3.000
 AGB  H15   C15  C14   120.38  3.000
 AGB  C16   C15  C14   120.99  3.000
 AGB  H16   C16  C17   119.60  3.000
 AGB  H16   C16  C15   119.47  3.000
 AGB  C17   C16  C15   120.93  3.000
 AGB  N3    C17  C18   122.61  3.000
 AGB  N3    C17  C16   118.91  3.000
 AGB  C18   C17  C16   118.37  3.000
 AGB  H18   C18  C17   120.47  3.000
 AGB  H18   C18  C13   119.46  3.000
 AGB  C17   C18  C13   120.07  3.000
 AGB  HN3   N3   C19   114.64  3.000
 AGB  HN3   N3   C17   115.40  3.000
 AGB  C19   N3   C17   128.72  3.000
 AGB  N5    C19  N4    120.08  3.000
 AGB  N5    C19  N3    116.10  3.000
 AGB  N4    C19  N3    123.80  3.000
 AGB  HN52  N5   HN51  112.66  3.000
 AGB  HN52  N5   C19   117.48  3.000
 AGB  HN51  N5   C19   113.09  3.000
 AGB  O1    C12  N2    124.18  3.000
 AGB  O1    C12  N1    121.72  3.000
 AGB  N2    C12  N1    114.10  3.000
 AGB  HN4   N4   C19   111.24  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
 AGB  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 AGB  CONST_02  C16   C17  C18  C13     0.00   0.0  0
 AGB  CONST_03  C17   C18  C13  C14     0.00   0.0  0
 AGB  CONST_04  C17   C16  C15  C14     0.00   0.0  0
 AGB  CONST_05  C18   C13  C14  C15     0.00   0.0  0
 AGB  CONST_06  C18   C17  C16  C15     0.00   0.0  0
 AGB  CONST_07  C18   C13  C14  C11   180.00   0.0  0
 AGB  CONST_08  C16   C15  C14  C11   180.00   0.0  0
 AGB  CONST_09  N3    C17  C18  C13   180.00   0.0  0
 AGB  CONST_10  N3    C17  C16  C15   180.00   0.0  0
 AGB  CONST_11  H15   C15  C14  C13   180.00   0.0  0
 AGB  CONST_12  H18   C18  C13  C14   180.00   0.0  0
 AGB  CONST_13  H16   C16  C15  C14   180.00   0.0  0
 AGB  CONST_14  H13   C13  C14  C15   180.00   0.0  0
 AGB  CONST_18  O1    C12  N2   C10     0.00   0.0  0
 AGB  CONST_19  N4    C19  N3   C17   180.00   0.0  0
 AGB  CONST_20  N5    C19  N3   C17     0.00   0.0  0
 AGB  CONST_21  N1    C12  N2   C10   180.00   0.0  0
 AGB  CONST_22  C11   N1   C12  O1      0.00   0.0  0
 AGB  CONST_23  C11   N1   C12  N2    180.00   0.0  0
 AGB  CONST_24  HN1   N1   C12  O1    180.00   0.0  0
 AGB  CONST_25  HN2   N2   C12  O1    180.00   0.0  0
 AGB  CONST_26  HN4   N4   C19  N3      0.00   0.0  0
 AGB  CONST_27  HN51  N5   C19  N3    180.00   0.0  0
 AGB  Var_01    C13   C14  C11  N1   -175.87  30.0  2
 AGB  Var_02    C14   C11  N1   C12   -83.16  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
 AGB  chir_01  C1   C2  C3  C4  negativ
 AGB  chir_02  C6   C2  C5  C8  negativ
 AGB  chir_03  C7   C4  C5  C9  positiv
 AGB  chir_04  C10  C9  C8  C3  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
 AGB  plan-1  C11   0.020
 AGB  plan-1  C13   0.020
 AGB  plan-1  C14   0.020
 AGB  plan-1  C15   0.020
 AGB  plan-1  C16   0.020
 AGB  plan-1  C17   0.020
 AGB  plan-1  C18   0.020
 AGB  plan-1  N3    0.020
 AGB  plan-1  H15   0.020
 AGB  plan-1  H16   0.020
 AGB  plan-1  H18   0.020
 AGB  plan-1  H13   0.020
 AGB  plan-2  C10   0.020
 AGB  plan-2  N1    0.020
 AGB  plan-2  N2    0.020
 AGB  plan-2  O1    0.020
 AGB  plan-2  C11   0.020
 AGB  plan-2  HN1   0.020
 AGB  plan-2  HN2   0.020
 AGB  plan-2  C12   0.020
 AGB  plan-3  C17   0.020
 AGB  plan-3  N3    0.020
 AGB  plan-3  C19   0.020
 AGB  plan-3  N5    0.020
 AGB  plan-3  HN3   0.020
 AGB  plan-3  HN4   0.020
 AGB  plan-3  HN51  0.020
 AGB  plan-3  HN52  0.020
 AGB  plan-3  N4    0.020

