# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:07:50 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (8R)-8-[(dimethylamino)methyl]-1-[3-(dimethylamino)propyl]-1,7,8,9-tetrahydrochromeno[5,6-d]imidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCn1c(N)nc2ccc3OC[C@@H](CN(C)C)Cc3c12
#
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
 SS0  SS0  (8R)-8-[(dimethylamino)methyl]-1-[3-(dimethylamino)propyl]-1,7,8,9-tetrahydrochromeno[5,6-d]imidazol-2-amine  ligand  53  24  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SS0
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
 SS0  C     C  CH3   0  -0.518   4.8728  -2.4005  -0.0180
 SS0  N     N  NT    0  -0.405   3.5726  -2.3877  -0.6529
 SS0  O     O  O2    0  -0.492  -2.3096   3.0204  -0.1984
 SS0  C01   C  CR6   0   0.320  -2.5276   1.6780  -0.1839
 SS0  N01   N  N     0  -0.523  -3.2769  -2.3788  -0.2104
 SS0  C02   C  CR16  0  -0.376  -3.8142   1.2707  -0.5596
 SS0  N02   N  NR5   0  -0.570  -1.2293  -1.7463   0.4367
 SS0  C03   C  CR16  0  -0.345  -4.1524  -0.0689  -0.6076
 SS0  C04   C  CR56  0   0.125  -3.1894  -1.0057  -0.2520
 SS0  N04   N  NT    0  -0.395   2.5066   2.4436   0.4786
 SS0  C05   C  CR56  0   0.310  -1.9109  -0.5768   0.1373
 SS0  C06   C  CR6   0  -0.032  -1.5265   0.7667   0.1605
 SS0  C07   C  CR5   0   0.603  -2.0997  -2.7740   0.1909
 SS0  C08   C  CH2   0  -0.481  -0.1354   1.2431   0.4865
 SS0  C09   C  CH1   0  -0.334   0.0751   2.6871   0.0545
 SS0  C10   C  CH2   0  -0.157  -1.1470   3.4864   0.4626
 SS0  C11   C  CH2   0  -0.255   1.3370   3.2768   0.6727
 SS0  C12   C  CH2   0  -0.352   0.1392  -1.8931   0.8855
 SS0  C13   C  CH3   0  -0.528   2.9031   2.3526  -0.9084
 SS0  C14   C  CH3   0  -0.513   3.6088   2.8796   1.3059
 SS0  C15   C  CH2   0  -0.467   1.1367  -2.0659  -0.2544
 SS0  C16   C  CH2   0  -0.263   2.5595  -1.9131   0.2682
 SS0  C17   C  CH3   0  -0.535   3.6107  -1.6250  -1.8814
 SS0  H     H  HCH3  0   0.232   4.8506  -3.0341   0.8704
 SS0  HA    H  HCH3  0   0.232   5.6187  -2.8101  -0.7006
 SS0  HB    H  HCH3  0   0.188   5.2167  -1.4009   0.2929
 SS0  H02   H  HCR6  0   0.250  -4.5441   2.0271  -0.8210
 SS0  H03   H  HCR6  0   0.246  -5.1445  -0.3793  -0.9093
 SS0  HN03  H  HNH2  0   0.396  -2.4862  -4.7256   0.3139
 SS0  HN0A  H  HNH2  0   0.397  -1.0111  -4.3042   0.9792
 SS0  H08   H  HCH2  0   0.247   0.0568   1.1652   1.5624
 SS0  H08A  H  HCH2  0   0.267   0.6097   0.6130   0.0009
 SS0  H09   H  HCH1  0   0.252   0.1425   2.7333  -1.0382
 SS0  H10   H  HCH2  0   0.244  -1.0482   4.5391   0.1950
 SS0  H10A  H  HCH2  0   0.213  -1.2856   3.4266   1.5506
 SS0  H11   H  HCH2  0   0.227   1.1773   3.3770   1.7517
 SS0  H11A  H  HCH2  0   0.206   1.4906   4.2999   0.2839
 SS0  H12   H  HCH2  0   0.281   0.3891  -1.0265   1.4940
 SS0  H12A  H  HCH2  0   0.272   0.1989  -2.7414   1.5694
 SS0  H13   H  HCH3  0   0.195   3.1714   3.3266  -1.3483
 SS0  H13A  H  HCH3  0   0.234   3.7678   1.6940  -1.0011
 SS0  H13B  H  HCH3  0   0.234   2.1072   1.9193  -1.5151
 SS0  H14   H  HCH3  0   0.230   3.3058   2.8993   2.3540
 SS0  H14A  H  HCH3  0   0.230   4.4420   2.1810   1.2145
 SS0  H14B  H  HCH3  0   0.188   3.9845   3.8828   1.0472
 SS0  H15   H  HCH2  0   0.245   1.0121  -3.0521  -0.7079
 SS0  H15A  H  HCH2  0   0.238   0.9244  -1.3276  -1.0311
 SS0  H16   H  HCH2  0   0.231   2.6573  -2.4953   1.1901
 SS0  H16A  H  HCH2  0   0.195   2.7262  -0.8552   0.5486
 SS0  H17   H  HCH3  0   0.235   4.3934  -2.0161  -2.5328
 SS0  H17A  H  HCH3  0   0.237   2.6692  -1.7038  -2.4255
 SS0  H17B  H  HCH3  0   0.196   3.8166  -0.5544  -1.7193
 SS0  N03   N  NH2   0  -0.857  -1.7163  -4.0759   0.2967

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
 SS0  C    N     single    1.447  0.020  1.447
 SS0  N    C16   single    1.449  0.020  1.449
 SS0  N    C17   single    1.446  0.020  1.446
 SS0  O    C01   single    1.360  0.020  1.360
 SS0  O    C10   single    1.416  0.020  1.416
 SS0  C01  C02   aromatic  1.401  0.020  1.401
 SS0  C01  C06   aromatic  1.397  0.020  1.397
 SS0  N01  C04   aromatic  1.376  0.020  1.376
 SS0  N01  C07   aromatic  1.305  0.020  1.305
 SS0  C02  C03   aromatic  1.382  0.020  1.382
 SS0  N02  C05   aromatic  1.386  0.020  1.386
 SS0  N02  C07   aromatic  1.369  0.020  1.369
 SS0  N02  C12   single    1.448  0.020  1.448
 SS0  C03  C04   aromatic  1.390  0.020  1.390
 SS0  N03  C07   single    1.361  0.020  1.361
 SS0  C04  C05   aromatic  1.404  0.020  1.404
 SS0  N04  C11   single    1.449  0.020  1.449
 SS0  N04  C13   single    1.445  0.020  1.445
 SS0  N04  C14   single    1.445  0.020  1.445
 SS0  C05  C06   aromatic  1.398  0.020  1.398
 SS0  C06  C08   single    1.506  0.020  1.506
 SS0  C08  C09   single    1.522  0.020  1.522
 SS0  C09  C10   single    1.516  0.020  1.516
 SS0  C09  C11   single    1.524  0.020  1.524
 SS0  C12  C15   single    1.525  0.020  1.525
 SS0  C15  C16   single    1.523  0.020  1.523
 SS0  C    H     single    0.970  0.020  1.090
 SS0  C    HA    single    0.970  0.020  1.090
 SS0  C    HB    single    0.970  0.020  1.090
 SS0  C02  H02   single    0.930  0.020  1.080
 SS0  C03  H03   single    0.930  0.020  1.080
 SS0  N03  HN03  single    0.890  0.020  1.040
 SS0  N03  HN0A  single    0.890  0.020  1.040
 SS0  C08  H08   single    0.970  0.020  1.090
 SS0  C08  H08A  single    0.970  0.020  1.090
 SS0  C09  H09   single    0.970  0.020  1.090
 SS0  C10  H10   single    0.970  0.020  1.090
 SS0  C10  H10A  single    0.970  0.020  1.090
 SS0  C11  H11   single    0.970  0.020  1.090
 SS0  C11  H11A  single    0.970  0.020  1.090
 SS0  C12  H12   single    0.970  0.020  1.090
 SS0  C12  H12A  single    0.970  0.020  1.090
 SS0  C13  H13   single    0.970  0.020  1.090
 SS0  C13  H13A  single    0.970  0.020  1.090
 SS0  C13  H13B  single    0.970  0.020  1.090
 SS0  C14  H14   single    0.970  0.020  1.090
 SS0  C14  H14A  single    0.970  0.020  1.090
 SS0  C14  H14B  single    0.970  0.020  1.090
 SS0  C15  H15   single    0.970  0.020  1.090
 SS0  C15  H15A  single    0.970  0.020  1.090
 SS0  C16  H16   single    0.970  0.020  1.090
 SS0  C16  H16A  single    0.970  0.020  1.090
 SS0  C17  H17   single    0.970  0.020  1.090
 SS0  C17  H17A  single    0.970  0.020  1.090
 SS0  C17  H17B  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
 SS0  HB    C    HA    107.68  3.000
 SS0  HB    C    H     107.66  3.000
 SS0  HA    C    H     107.77  3.000
 SS0  HB    C    N     113.34  3.000
 SS0  HA    C    N     110.07  3.000
 SS0  H     C    N     110.13  3.000
 SS0  C17   N    C16   112.68  3.000
 SS0  C17   N    C     110.71  3.000
 SS0  C16   N    C     110.62  3.000
 SS0  C10   O    C01   116.83  3.000
 SS0  C06   C01  C02   122.32  3.000
 SS0  C06   C01  O     122.12  3.000
 SS0  C02   C01  O     115.55  3.000
 SS0  C07   N01  C04   104.72  3.000
 SS0  H02   C02  C03   120.22  3.000
 SS0  H02   C02  C01   118.73  3.000
 SS0  C03   C02  C01   121.05  3.000
 SS0  C12   N02  C07   125.49  3.000
 SS0  C12   N02  C05   128.11  3.000
 SS0  C07   N02  C05   106.38  3.000
 SS0  H03   C03  C04   120.87  3.000
 SS0  H03   C03  C02   120.79  3.000
 SS0  C04   C03  C02   118.34  3.000
 SS0  C05   C04  C03   119.74  3.000
 SS0  C05   C04  N01   110.75  3.000
 SS0  C03   C04  N01   129.51  3.000
 SS0  C14   N04  C13   111.04  3.000
 SS0  C14   N04  C11   111.43  3.000
 SS0  C13   N04  C11   112.71  3.000
 SS0  C06   C05  C04   123.29  3.000
 SS0  C06   C05  N02   132.23  3.000
 SS0  C04   C05  N02   104.47  3.000
 SS0  C08   C06  C05   124.18  3.000
 SS0  C08   C06  C01   120.59  3.000
 SS0  C05   C06  C01   115.21  3.000
 SS0  N03   C07  N02   121.66  3.000
 SS0  N03   C07  N01   124.58  3.000
 SS0  N02   C07  N01   113.67  3.000
 SS0  H08A  C08  H08   106.05  3.000
 SS0  H08A  C08  C09   109.11  3.000
 SS0  H08   C08  C09   108.78  3.000
 SS0  H08A  C08  C06   110.62  3.000
 SS0  H08   C08  C06   110.61  3.000
 SS0  C09   C08  C06   111.50  3.000
 SS0  H09   C09  C11   109.71  3.000
 SS0  H09   C09  C10   107.20  3.000
 SS0  C11   C09  C10   110.75  3.000
 SS0  H09   C09  C08   109.36  3.000
 SS0  C11   C09  C08   111.50  3.000
 SS0  C10   C09  C08   108.20  3.000
 SS0  H10A  C10  H10   107.88  3.000
 SS0  H10A  C10  C09   109.85  3.000
 SS0  H10   C10  C09   111.70  3.000
 SS0  H10A  C10  O     109.93  3.000
 SS0  H10   C10  O     106.11  3.000
 SS0  C09   C10  O     111.26  3.000
 SS0  H11A  C11  H11   106.39  3.000
 SS0  H11A  C11  C09   109.30  3.000
 SS0  H11   C11  C09   108.32  3.000
 SS0  H11A  C11  N04   111.90  3.000
 SS0  H11   C11  N04   107.59  3.000
 SS0  C09   C11  N04   113.05  3.000
 SS0  H12A  C12  H12   104.83  3.000
 SS0  H12A  C12  C15   110.16  3.000
 SS0  H12   C12  C15   110.99  3.000
 SS0  H12A  C12  N02   108.95  3.000
 SS0  H12   C12  N02   108.05  3.000
 SS0  C15   C12  N02   113.47  3.000
 SS0  H13B  C13  H13A  106.94  3.000
 SS0  H13B  C13  H13   107.88  3.000
 SS0  H13A  C13  H13   107.86  3.000
 SS0  H13B  C13  N04   111.01  3.000
 SS0  H13A  C13  N04   109.69  3.000
 SS0  H13   C13  N04   113.22  3.000
 SS0  H14B  C14  H14A  107.63  3.000
 SS0  H14B  C14  H14   107.68  3.000
 SS0  H14A  C14  H14   107.70  3.000
 SS0  H14B  C14  N04   113.59  3.000
 SS0  H14A  C14  N04   109.94  3.000
 SS0  H14   C14  N04   110.09  3.000
 SS0  H15A  C15  H15   107.02  3.000
 SS0  H15A  C15  C16   110.95  3.000
 SS0  H15   C15  C16   109.84  3.000
 SS0  H15A  C15  C12   109.14  3.000
 SS0  H15   C15  C12   109.76  3.000
 SS0  C16   C15  C12   110.08  3.000
 SS0  H16A  C16  H16   106.34  3.000
 SS0  H16A  C16  C15   108.87  3.000
 SS0  H16   C16  C15   108.60  3.000
 SS0  H16A  C16  N     111.63  3.000
 SS0  H16   C16  N     107.38  3.000
 SS0  C15   C16  N     113.71  3.000
 SS0  H17B  C17  H17A  107.76  3.000
 SS0  H17B  C17  H17   107.57  3.000
 SS0  H17A  C17  H17   107.20  3.000
 SS0  H17B  C17  N     113.09  3.000
 SS0  H17A  C17  N     111.29  3.000
 SS0  H17   C17  N     109.70  3.000
 SS0  HN0A  N03  HN03  112.15  3.000
 SS0  HN0A  N03  C07   117.80  3.000
 SS0  HN03  N03  C07   113.75  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
 SS0  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 SS0  CONST_02  N02  C05  C06  C01   180.00   0.0  0
 SS0  CONST_03  C04  C05  C06  C01     0.00   0.0  0
 SS0  CONST_04  C02  C03  C04  N01   180.00   0.0  0
 SS0  CONST_05  N02  C05  C04  N01     0.00   0.0  0
 SS0  CONST_06  C06  C05  C04  N01   180.00   0.0  0
 SS0  CONST_07  C05  N02  C07  N01     0.00   0.0  0
 SS0  CONST_08  C05  C06  C01  C02     0.00   0.0  0
 SS0  CONST_09  C05  C04  C03  C02     0.00   0.0  0
 SS0  CONST_10  C03  C04  C05  N02   180.00   0.0  0
 SS0  CONST_11  C04  N01  C07  N02     0.00   0.0  0
 SS0  CONST_12  C06  C01  C02  C03     0.00   0.0  0
 SS0  CONST_13  C07  N01  C04  C03   180.00   0.0  0
 SS0  CONST_14  C06  C05  C04  C03     0.00   0.0  0
 SS0  CONST_15  C07  N02  C05  C04     0.00   0.0  0
 SS0  CONST_16  C07  N01  C04  C05     0.00   0.0  0
 SS0  CONST_17  C07  N02  C05  C06   180.00   0.0  0
 SS0  CONST_18  C12  N02  C07  N01   180.00   0.0  0
 SS0  CONST_19  C04  N01  C07  N03   180.00   0.0  0
 SS0  CONST_20  C05  N02  C07  N03   180.00   0.0  0
 SS0  CONST_21  C12  N02  C05  C04   180.00   0.0  0
 SS0  CONST_22  C12  N02  C05  C06     0.00   0.0  0
 SS0  CONST_23  H02  C02  C01  O       0.00   0.0  0
 SS0  CONST_24  H03  C03  C02  C01   180.00   0.0  0
 SS0  Var_01    C09  C10  O    C01    48.42  30.0  1
 SS0  Var_02    C09  C08  C06  C01   -14.22  30.0  1
 SS0  Var_03    C15  C12  N02  C05   -90.80  30.0  2
 SS0  Var_04    C16  C15  C12  N02   167.88  30.0  3
 SS0  Var_05    C13  N04  C11  C09    66.56  30.0  2
 SS0  Var_06    C15  C16  N    C    -171.36  30.0  3
 SS0  Var_07    C12  C15  C16  N     165.29  30.0  2
 SS0  Var_08    H17  C17  N    C      55.00  30.0  3
 SS0  Var_09    H13  C13  N04  C11    61.04  30.0  3
 SS0  Var_10    H14  C14  N04  C11    56.02  30.0  3
 SS0  Var_11    H    C    N    C16    58.24  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
 SS0  chir_01  C09  C08  C10  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
 SS0  plan-1  C07   0.020
 SS0  plan-1  HN03  0.020
 SS0  plan-1  HN0A  0.020
 SS0  plan-1  N03   0.020
 SS0  plan-2  O     0.020
 SS0  plan-2  C01   0.020
 SS0  plan-2  N01   0.020
 SS0  plan-2  C02   0.020
 SS0  plan-2  N02   0.020
 SS0  plan-2  C03   0.020
 SS0  plan-2  C04   0.020
 SS0  plan-2  C05   0.020
 SS0  plan-2  C06   0.020
 SS0  plan-2  C07   0.020
 SS0  plan-2  C08   0.020
 SS0  plan-2  C12   0.020
 SS0  plan-2  H02   0.020
 SS0  plan-2  H03   0.020
 SS0  plan-2  N03   0.020

