# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 22:01:05 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 6,6'-{[(2R)-3-aminopropane-1,2-diyl]bis(oxymethanediyl)}bis(4-methylpyridin-2-amine)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(COC[C@@H](CN)OCc2cc(C)cc(N)n2)c1
#
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
 1Q7  1Q7  6,6'-{[(2R)-3-aminopropane-1,2-diyl]bis(oxymethanediyl)}bis(4-methylpyridin-2-amine)  ligand  49  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1Q7
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
 1Q7  N22  N  NH2   0  -0.839   4.6967  -1.8698  -2.0541
 1Q7  C22  C  CR6   0   0.444   3.6635  -1.4307  -1.2771
 1Q7  C23  C  CR16  0  -0.450   2.6458  -2.3119  -0.8721
 1Q7  C24  C  CR6   0   0.206   1.6433  -1.8457  -0.0468
 1Q7  C27  C  CH3   0  -0.731   0.5390  -2.7500   0.4088
 1Q7  C25  C  CR16  0  -0.402   1.6828  -0.5042   0.3573
 1Q7  N21  N  N     0  -0.493   3.6921  -0.1610  -0.8915
 1Q7  C26  C  CR6   0   0.198   2.7217   0.2862  -0.0916
 1Q7  C15  C  CH2   0  -0.212   2.9011   1.7250   0.3328
 1Q7  O14  O  O2    0  -0.490   1.7980   2.2857   0.9906
 1Q7  C11  C  CH1   0   0.007   0.9915   3.1576   0.2193
 1Q7  C12  C  CH2   0  -0.303   0.1356   3.9521   1.1918
 1Q7  N13  N  NH2   0  -0.802   0.9662   4.7965   2.0378
 1Q7  C10  C  CH2   0  -0.161   0.1732   2.4315  -0.8324
 1Q7  O09  O  O2    0  -0.480  -0.7733   1.6030  -0.2139
 1Q7  C08  C  CH2   0  -0.153  -1.3984   0.7084  -1.0828
 1Q7  C06  C  CR6   0   0.178  -2.1770  -0.3195  -0.3100
 1Q7  N01  N  N     0  -0.490  -2.8309  -1.1939  -1.0773
 1Q7  C02  C  CR6   0   0.440  -3.5139  -2.1683  -0.4893
 1Q7  N02  N  NH2   0  -0.839  -4.1348  -3.0726  -1.3027
 1Q7  C03  C  CR16  0  -0.434  -3.5669  -2.3064   0.9095
 1Q7  C05  C  CR16  0  -0.401  -2.1847  -0.3656   1.0691
 1Q7  C04  C  CR6   0   0.203  -2.8982  -1.3942   1.6974
 1Q7  C07  C  CH3   0  -0.727  -2.9050  -1.5052   3.1911
 1Q7  H1   H  HNH2  0   0.387   4.5517  -2.7046  -2.5966
 1Q7  H2   H  HNH2  0   0.379   5.2347  -1.1604  -2.5237
 1Q7  H3   H  HCR6  0   0.253   2.6563  -3.3429  -1.2052
 1Q7  H4   H  HCH3  0   0.246   0.4238  -2.7118   1.4925
 1Q7  H5   H  HCH3  0   0.261  -0.4169  -2.4405  -0.0151
 1Q7  H6   H  HCH3  0   0.245   0.7189  -3.7840   0.1188
 1Q7  H7   H  HCR6  0   0.252   0.9121  -0.0951   0.9947
 1Q7  H8   H  HCH2  0   0.253   3.7536   1.7633   1.0209
 1Q7  H9   H  HCH2  0   0.226   3.1947   2.3147  -0.5453
 1Q7  H10  H  HCH1  0   0.216   1.6327   3.8690  -0.3230
 1Q7  H11  H  HCH2  0   0.223  -0.5256   4.5947   0.6055
 1Q7  H12  H  HCH2  0   0.209  -0.5102   3.2652   1.7528
 1Q7  H13  H  HNH2  0   0.348   0.3687   5.3529   2.6352
 1Q7  H14  H  HNH2  0   0.340   1.5043   4.2117   2.6643
 1Q7  H16  H  HCH2  0   0.216  -0.3117   3.1786  -1.4774
 1Q7  H17  H  HCH2  0   0.219   0.8418   1.8459  -1.4802
 1Q7  H18  H  HCH2  0   0.226  -2.0749   1.2259  -1.7794
 1Q7  H19  H  HCH2  0   0.219  -0.6595   0.1812  -1.7051
 1Q7  H20  H  HNH2  0   0.379  -4.2887  -2.7784  -2.2533
 1Q7  H21  H  HNH2  0   0.388  -4.8951  -3.6036  -0.9118
 1Q7  H22  H  HCR6  0   0.254  -4.1246  -3.1219   1.3540
 1Q7  H23  H  HCR6  0   0.247  -1.6416   0.3627   1.6546
 1Q7  H24  H  HCH3  0   0.252  -1.9084  -1.7553   3.5593
 1Q7  H25  H  HCH3  0   0.250  -3.1880  -0.5598   3.6551
 1Q7  H26  H  HCH3  0   0.246  -3.5924  -2.2753   3.5372

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
 1Q7  C07  C04  single    1.498  0.020  1.498
 1Q7  C04  C03  aromatic  1.378  0.020  1.378
 1Q7  C04  C05  aromatic  1.401  0.020  1.401
 1Q7  C03  C02  aromatic  1.407  0.020  1.407
 1Q7  C05  C06  aromatic  1.380  0.020  1.380
 1Q7  C10  O09  single    1.402  0.020  1.402
 1Q7  C10  C11  single    1.518  0.020  1.518
 1Q7  C02  N02  single    1.366  0.020  1.366
 1Q7  C02  N01  aromatic  1.327  0.020  1.327
 1Q7  C06  N01  aromatic  1.335  0.020  1.335
 1Q7  C06  C08  single    1.503  0.020  1.503
 1Q7  O09  C08  single    1.395  0.020  1.395
 1Q7  O14  C11  single    1.416  0.020  1.416
 1Q7  O14  C15  single    1.401  0.020  1.401
 1Q7  C11  C12  single    1.520  0.020  1.520
 1Q7  C12  N13  single    1.456  0.020  1.456
 1Q7  C15  C26  single    1.511  0.020  1.511
 1Q7  C25  C26  aromatic  1.380  0.020  1.380
 1Q7  C25  C24  aromatic  1.402  0.020  1.402
 1Q7  C26  N21  aromatic  1.335  0.020  1.335
 1Q7  C27  C24  single    1.498  0.020  1.498
 1Q7  C24  C23  aromatic  1.380  0.020  1.380
 1Q7  N21  C22  aromatic  1.327  0.020  1.327
 1Q7  C22  C23  aromatic  1.406  0.020  1.406
 1Q7  C22  N22  single    1.365  0.020  1.365
 1Q7  N22  H1   single    0.890  0.020  1.040
 1Q7  N22  H2   single    0.890  0.020  1.040
 1Q7  C23  H3   single    0.930  0.020  1.080
 1Q7  C27  H4   single    0.970  0.020  1.090
 1Q7  C27  H5   single    0.970  0.020  1.090
 1Q7  C27  H6   single    0.970  0.020  1.090
 1Q7  C25  H7   single    0.930  0.020  1.080
 1Q7  C15  H8   single    0.970  0.020  1.090
 1Q7  C15  H9   single    0.970  0.020  1.090
 1Q7  C11  H10  single    0.970  0.020  1.090
 1Q7  C12  H11  single    0.970  0.020  1.090
 1Q7  C12  H12  single    0.970  0.020  1.090
 1Q7  N13  H13  single    0.890  0.020  1.040
 1Q7  N13  H14  single    0.890  0.020  1.040
 1Q7  C10  H16  single    0.970  0.020  1.090
 1Q7  C10  H17  single    0.970  0.020  1.090
 1Q7  C08  H18  single    0.970  0.020  1.090
 1Q7  C08  H19  single    0.970  0.020  1.090
 1Q7  N02  H20  single    0.890  0.020  1.040
 1Q7  N02  H21  single    0.890  0.020  1.040
 1Q7  C03  H22  single    0.930  0.020  1.080
 1Q7  C05  H23  single    0.930  0.020  1.080
 1Q7  C07  H24  single    0.970  0.020  1.090
 1Q7  C07  H25  single    0.970  0.020  1.090
 1Q7  C07  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
 1Q7  H2   N22  H1   114.22  3.000
 1Q7  H2   N22  C22  116.31  3.000
 1Q7  H1   N22  C22  117.69  3.000
 1Q7  N21  C22  C23  122.11  3.000
 1Q7  C23  C22  N22  120.68  3.000
 1Q7  N21  C22  N22  117.17  3.000
 1Q7  H3   C23  C24  120.83  3.000
 1Q7  H3   C23  C22  120.05  3.000
 1Q7  C24  C23  C22  119.11  3.000
 1Q7  C25  C24  C27  120.72  3.000
 1Q7  C27  C24  C23  120.90  3.000
 1Q7  C25  C24  C23  118.39  3.000
 1Q7  H6   C27  H5   108.11  3.000
 1Q7  H6   C27  H4   108.38  3.000
 1Q7  H5   C27  H4   106.48  3.000
 1Q7  H6   C27  C24  111.74  3.000
 1Q7  H5   C27  C24  110.90  3.000
 1Q7  H4   C27  C24  111.03  3.000
 1Q7  H7   C25  C26  120.79  3.000
 1Q7  H7   C25  C24  120.82  3.000
 1Q7  C26  C25  C24  118.39  3.000
 1Q7  C26  N21  C22  118.62  3.000
 1Q7  C15  C26  N21  113.65  3.000
 1Q7  N21  C26  C25  123.38  3.000
 1Q7  C15  C26  C25  122.91  3.000
 1Q7  H9   C15  H8   105.98  3.000
 1Q7  H9   C15  O14  111.78  3.000
 1Q7  H8   C15  O14  107.67  3.000
 1Q7  H9   C15  C26  108.58  3.000
 1Q7  H8   C15  C26  107.57  3.000
 1Q7  O14  C15  C26  114.80  3.000
 1Q7  C11  O14  C15  116.04  3.000
 1Q7  H10  C11  C10  106.38  3.000
 1Q7  H10  C11  C12  107.79  3.000
 1Q7  C10  C11  C12  112.95  3.000
 1Q7  H10  C11  O14  109.55  3.000
 1Q7  C12  C11  O14  107.10  3.000
 1Q7  C10  C11  O14  112.95  3.000
 1Q7  H12  C12  H11  106.64  3.000
 1Q7  H12  C12  N13  113.70  3.000
 1Q7  H11  C12  N13  108.42  3.000
 1Q7  H12  C12  C11  109.35  3.000
 1Q7  H11  C12  C11  107.75  3.000
 1Q7  N13  C12  C11  110.72  3.000
 1Q7  H14  N13  H13  105.45  3.000
 1Q7  H14  N13  C12  109.14  3.000
 1Q7  H13  N13  C12  108.98  3.000
 1Q7  H17  C10  H16  106.52  3.000
 1Q7  H17  C10  O09  110.83  3.000
 1Q7  H16  C10  O09  111.26  3.000
 1Q7  H17  C10  C11  109.58  3.000
 1Q7  H16  C10  C11  108.61  3.000
 1Q7  O09  C10  C11  109.95  3.000
 1Q7  C08  O09  C10  114.00  3.000
 1Q7  H19  C08  H18  106.27  3.000
 1Q7  H19  C08  C06  108.11  3.000
 1Q7  H18  C08  C06  109.19  3.000
 1Q7  H19  C08  O09  111.01  3.000
 1Q7  H18  C08  O09  111.61  3.000
 1Q7  C06  C08  O09  110.51  3.000
 1Q7  C05  C06  N01  123.37  3.000
 1Q7  N01  C06  C08  113.96  3.000
 1Q7  C05  C06  C08  122.65  3.000
 1Q7  C02  N01  C06  118.58  3.000
 1Q7  C03  C02  N02  120.67  3.000
 1Q7  N02  C02  N01  117.14  3.000
 1Q7  C03  C02  N01  122.14  3.000
 1Q7  H21  N02  H20  113.91  3.000
 1Q7  H21  N02  C02  117.49  3.000
 1Q7  H20  N02  C02  115.99  3.000
 1Q7  H22  C03  C04  120.88  3.000
 1Q7  H22  C03  C02  120.09  3.000
 1Q7  C04  C03  C02  119.03  3.000
 1Q7  H23  C05  C04  120.52  3.000
 1Q7  H23  C05  C06  121.06  3.000
 1Q7  C04  C05  C06  118.41  3.000
 1Q7  C07  C04  C05  120.27  3.000
 1Q7  C05  C04  C03  118.47  3.000
 1Q7  C07  C04  C03  121.26  3.000
 1Q7  H26  C07  H25  108.31  3.000
 1Q7  H26  C07  H24  107.89  3.000
 1Q7  H25  C07  H24  106.98  3.000
 1Q7  H26  C07  C04  111.85  3.000
 1Q7  H25  C07  C04  111.18  3.000
 1Q7  H24  C07  C04  110.45  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
 1Q7  CONST_01  C25  C26  N21  C22    0.00   0.0  0
 1Q7  CONST_02  C25  C24  C23  C22    0.00   0.0  0
 1Q7  CONST_03  C26  C25  C24  C23    0.00   0.0  0
 1Q7  CONST_04  C26  N21  C22  C23    0.00   0.0  0
 1Q7  CONST_05  N21  C26  C25  C24    0.00   0.0  0
 1Q7  CONST_06  N21  C22  C23  C24    0.00   0.0  0
 1Q7  CONST_07  C03  C04  C05  C06    0.00   0.0  0
 1Q7  CONST_08  C03  C02  N01  C06    0.00   0.0  0
 1Q7  CONST_09  C04  C03  C02  N01    0.00   0.0  0
 1Q7  CONST_10  C04  C05  C06  N01    0.00   0.0  0
 1Q7  CONST_11  C05  C04  C03  C02    0.00   0.0  0
 1Q7  CONST_12  C05  C06  N01  C02    0.00   0.0  0
 1Q7  CONST_13  C26  N21  C22  N22  180.00   0.0  0
 1Q7  CONST_14  C24  C23  C22  N22  180.00   0.0  0
 1Q7  CONST_15  C15  C26  N21  C22  180.00   0.0  0
 1Q7  CONST_16  C27  C24  C23  C22  180.00   0.0  0
 1Q7  CONST_17  C15  C26  C25  C24  180.00   0.0  0
 1Q7  CONST_18  C26  C25  C24  C27  180.00   0.0  0
 1Q7  CONST_19  C04  C05  C06  C08  180.00   0.0  0
 1Q7  CONST_20  C02  N01  C06  C08  180.00   0.0  0
 1Q7  CONST_21  C07  C04  C05  C06  180.00   0.0  0
 1Q7  CONST_22  N02  C02  N01  C06  180.00   0.0  0
 1Q7  CONST_23  C07  C04  C03  C02  180.00   0.0  0
 1Q7  CONST_24  C04  C03  C02  N02  180.00   0.0  0
 1Q7  CONST_25  H7   C25  C24  C23  180.00   0.0  0
 1Q7  CONST_26  H3   C23  C24  C25  180.00   0.0  0
 1Q7  CONST_27  H22  C03  C02  N01  180.00   0.0  0
 1Q7  CONST_28  H23  C05  C06  N01  180.00   0.0  0
 1Q7  Var_01    O14  C15  C26  C25  -12.57  30.0  3
 1Q7  Var_02    C05  C06  C08  O09   -2.90  30.0  3
 1Q7  Var_03    H4   C27  C24  C23  128.52  30.0  2
 1Q7  Var_04    H24  C07  C04  C03  112.22  30.0  2
 1Q7  Var_05    C06  C08  O09  C10  168.40  30.0  3
 1Q7  Var_06    H13  N13  C12  C11  176.66  30.0  3
 1Q7  Var_07    H16  C10  O09  C08   71.17  30.0  1

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
 1Q7  chir_01  C11  C10  O14  C12  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
 1Q7  plan-1  N22  0.020
 1Q7  plan-1  C22  0.020
 1Q7  plan-1  C23  0.020
 1Q7  plan-1  C24  0.020
 1Q7  plan-1  C27  0.020
 1Q7  plan-1  C25  0.020
 1Q7  plan-1  N21  0.020
 1Q7  plan-1  C26  0.020
 1Q7  plan-1  C15  0.020
 1Q7  plan-1  H3   0.020
 1Q7  plan-1  H7   0.020
 1Q7  plan-2  C08  0.020
 1Q7  plan-2  C06  0.020
 1Q7  plan-2  N01  0.020
 1Q7  plan-2  C02  0.020
 1Q7  plan-2  N02  0.020
 1Q7  plan-2  C03  0.020
 1Q7  plan-2  C05  0.020
 1Q7  plan-2  C04  0.020
 1Q7  plan-2  C07  0.020
 1Q7  plan-2  H22  0.020
 1Q7  plan-2  H23  0.020
 1Q7  plan-3  N22  0.020
 1Q7  plan-3  C22  0.020
 1Q7  plan-3  H1   0.020
 1Q7  plan-3  H2   0.020
 1Q7  plan-4  C02  0.020
 1Q7  plan-4  N02  0.020
 1Q7  plan-4  H20  0.020
 1Q7  plan-4  H21  0.020

