# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 14:17:02 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 6-[(2S)-3-amino-2-{5-[2-(6-amino-4-methylpyridin-2-yl)ethyl]pyridin-3-yl}propyl]-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cncc(c2)[C@@H](CN)Cc3cc(C)cc(N)n3)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
 71S  71S  6-[(2S)-3-amino-2-{5-[2-(6-amino-4-methylpyridin-2-yl)ethyl]pyridin-3-yl}propyl]-4-methylpyridin-2-amine  ligand  56  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_71S
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
 71S  N22   N  NH2   0  -0.841   5.1526   3.2344  -1.0634
 71S  C22   C  CR6   0   0.436   5.4087   1.9428  -0.6924
 71S  C23   C  CR16  0  -0.457   6.7092   1.5392  -0.3513
 71S  C24   C  CR6   0   0.202   6.9361   0.2120  -0.0405
 71S  C27   C  CH3   0  -0.728   8.3006  -0.2762   0.3413
 71S  C25   C  CR16  0  -0.429   5.8521  -0.6673  -0.0752
 71S  N21   N  N     0  -0.496   4.3861   1.0946  -0.7227
 71S  C26   C  CR6   0   0.337   4.6001  -0.1830  -0.4115
 71S  C28   C  CH2   0  -0.505   3.4201  -1.1108  -0.5181
 71S  C29   C  CH1   0  -0.340   2.1263  -0.5806   0.1083
 71S  C15   C  CR6   0   0.075   0.8902  -1.2592  -0.4259
 71S  C14   C  CR16  0  -0.122   0.8773  -2.5884  -0.8382
 71S  C12   C  CR16  0  -0.118  -1.3515  -2.5440  -1.3025
 71S  C16   C  CR16  0  -0.249  -0.3218  -0.5790  -0.4715
 71S  C11   C  CR6   0   0.050  -1.4751  -1.2141  -0.9126
 71S  C09   C  CH2   0  -0.514  -2.8078  -0.5263  -0.9139
 71S  C08   C  CH2   0  -0.489  -3.5141  -0.6845   0.4395
 71S  C06   C  CR6   0   0.277  -4.8415   0.0181   0.4649
 71S  N01   N  N     0  -0.485  -4.8002   1.3524   0.4338
 71S  C02   C  CR6   0   0.440  -5.9452   2.0249   0.4300
 71S  N02   N  NH2   0  -0.838  -5.8678   3.3860   0.3500
 71S  C03   C  CR16  0  -0.447  -7.1954   1.3810   0.4644
 71S  C04   C  CR6   0   0.205  -7.2395   0.0033   0.5001
 71S  C05   C  CR16  0  -0.434  -6.0255  -0.6947   0.4963
 71S  C07   C  CH3   0  -0.726  -8.5420  -0.7350   0.5471
 71S  C18   C  CH2   0  -0.246   2.1154  -0.7052   1.6369
 71S  N11   N  N     0  -0.399  -0.2100  -3.2169  -1.2702
 71S  H221  H  HNH2  0   0.385   5.7971   3.9407  -0.7495
 71S  H222  H  HNH2  0   0.377   4.1874   3.5190  -1.0245
 71S  H23   H  HCR6  0   0.252   7.5175   2.2604  -0.3375
 71S  H271  H  HCH3  0   0.251   8.3080  -0.6316   1.3729
 71S  H272  H  HCH3  0   0.249   8.6060  -1.1151  -0.2854
 71S  H273  H  HCH3  0   0.245   9.0520   0.5063   0.2499
 71S  H25   H  HCR6  0   0.235   5.9835  -1.7139   0.1701
 71S  H281  H  HCH2  0   0.253   3.2434  -1.2853  -1.5853
 71S  H282  H  HCH2  0   0.243   3.6846  -2.0807  -0.0906
 71S  H29   H  HCH1  0   0.251   2.0476   0.4819  -0.1458
 71S  H181  H  HCH2  0   0.203   1.1552  -0.3094   2.0012
 71S  H182  H  HCH2  0   0.213   2.1249  -1.7686   1.8981
 71S  H14   H  HCR6  0   0.256   1.7885  -3.1776  -0.8275
 71S  H16   H  HCR6  0   0.254  -0.3645   0.4618  -0.1648
 71S  HA1   H  HNH2  0   0.338   3.2726   0.9135   2.0361
 71S  HB2   H  HNH2  0   0.347   3.2087  -0.1561   3.2491
 71S  H12   H  HCR6  0   0.251  -2.2238  -3.0845  -1.6601
 71S  H091  H  HCH2  0   0.254  -2.6833   0.5361  -1.1320
 71S  H092  H  HCH2  0   0.252  -3.4403  -0.9441  -1.7008
 71S  H081  H  HCH2  0   0.249  -3.6511  -1.7462   0.6552
 71S  H082  H  HCH2  0   0.249  -2.8738  -0.2754   1.2259
 71S  H05   H  HCR6  0   0.243  -6.0095  -1.7772   0.5218
 71S  H021  H  HNH2  0   0.379  -4.9838   3.7952   0.6050
 71S  H022  H  HNH2  0   0.388  -6.6671   3.9151   0.6561
 71S  H03   H  HCR6  0   0.255  -8.1069   1.9669   0.4646
 71S  H071  H  HCH3  0   0.251  -8.6324  -1.4175  -0.2992
 71S  H072  H  HCH3  0   0.252  -8.6105  -1.3404   1.4523
 71S  H073  H  HCH3  0   0.247  -9.3933  -0.0564   0.5283
 71S  N18   N  NH2   0  -0.782   3.2729  -0.0775   2.2422

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
 71S  N22  C22   single    1.368  0.020  1.368
 71S  C22  C23   aromatic  1.404  0.020  1.404
 71S  C22  N21   aromatic  1.329  0.020  1.329
 71S  C23  C24   aromatic  1.382  0.020  1.382
 71S  C24  C27   single    1.499  0.020  1.499
 71S  C24  C25   aromatic  1.396  0.020  1.396
 71S  C25  C26   aromatic  1.384  0.020  1.384
 71S  N21  C26   aromatic  1.332  0.020  1.332
 71S  C26  C28   single    1.505  0.020  1.505
 71S  C28  C29   single    1.532  0.020  1.532
 71S  C29  C15   single    1.508  0.020  1.508
 71S  C29  C18   single    1.534  0.020  1.534
 71S  C15  C14   aromatic  1.392  0.020  1.392
 71S  C15  C16   aromatic  1.391  0.020  1.391
 71S  C14  N11   aromatic  1.328  0.020  1.328
 71S  N18  C18   single    1.449  0.020  1.449
 71S  C12  C11   aromatic  1.391  0.020  1.391
 71S  C12  N11   aromatic  1.325  0.020  1.325
 71S  C16  C11   aromatic  1.389  0.020  1.389
 71S  C11  C09   single    1.500  0.020  1.500
 71S  C09  C08   single    1.535  0.020  1.535
 71S  C08  C06   single    1.502  0.020  1.502
 71S  C06  N01   aromatic  1.335  0.020  1.335
 71S  C06  C05   aromatic  1.382  0.020  1.382
 71S  N01  C02   aromatic  1.328  0.020  1.328
 71S  C02  N02   single    1.366  0.020  1.366
 71S  C02  C03   aromatic  1.407  0.020  1.407
 71S  C03  C04   aromatic  1.379  0.020  1.379
 71S  C04  C05   aromatic  1.400  0.020  1.400
 71S  C04  C07   single    1.498  0.020  1.498
 71S  N22  H221  single    0.890  0.020  1.040
 71S  N22  H222  single    0.890  0.020  1.040
 71S  C23  H23   single    0.930  0.020  1.080
 71S  C27  H271  single    0.970  0.020  1.090
 71S  C27  H272  single    0.970  0.020  1.090
 71S  C27  H273  single    0.970  0.020  1.090
 71S  C25  H25   single    0.930  0.020  1.080
 71S  C28  H281  single    0.970  0.020  1.090
 71S  C28  H282  single    0.970  0.020  1.090
 71S  C29  H29   single    0.970  0.020  1.090
 71S  C18  H181  single    0.970  0.020  1.090
 71S  C18  H182  single    0.970  0.020  1.090
 71S  C14  H14   single    0.930  0.020  1.080
 71S  C16  H16   single    0.930  0.020  1.080
 71S  N18  HA1   single    0.890  0.020  1.040
 71S  N18  HB2   single    0.890  0.020  1.040
 71S  C12  H12   single    0.930  0.020  1.080
 71S  C09  H091  single    0.970  0.020  1.090
 71S  C09  H092  single    0.970  0.020  1.090
 71S  C08  H081  single    0.970  0.020  1.090
 71S  C08  H082  single    0.970  0.020  1.090
 71S  C05  H05   single    0.930  0.020  1.080
 71S  N02  H021  single    0.890  0.020  1.040
 71S  N02  H022  single    0.890  0.020  1.040
 71S  C03  H03   single    0.930  0.020  1.080
 71S  C07  H071  single    0.970  0.020  1.090
 71S  C07  H072  single    0.970  0.020  1.090
 71S  C07  H073  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
 71S  H222  N22  H221  113.80  3.000
 71S  H222  N22  C22   115.83  3.000
 71S  H221  N22  C22   117.27  3.000
 71S  N21   C22  C23   122.34  3.000
 71S  N21   C22  N22   116.90  3.000
 71S  C23   C22  N22   120.72  3.000
 71S  H23   C23  C24   120.93  3.000
 71S  H23   C23  C22   120.19  3.000
 71S  C24   C23  C22   118.88  3.000
 71S  C25   C24  C27   120.53  3.000
 71S  C25   C24  C23   118.15  3.000
 71S  C27   C24  C23   121.31  3.000
 71S  H273  C27  H272  108.14  3.000
 71S  H273  C27  H271  107.98  3.000
 71S  H272  C27  H271  106.91  3.000
 71S  H273  C27  C24   111.89  3.000
 71S  H272  C27  C24   111.05  3.000
 71S  H271  C27  C24   110.68  3.000
 71S  H25   C25  C26   120.20  3.000
 71S  H25   C25  C24   120.59  3.000
 71S  C26   C25  C24   119.21  3.000
 71S  C26   N21  C22   118.89  3.000
 71S  C28   C26  N21   116.66  3.000
 71S  C28   C26  C25   120.72  3.000
 71S  N21   C26  C25   122.53  3.000
 71S  H282  C28  H281  106.19  3.000
 71S  H282  C28  C29   110.59  3.000
 71S  H281  C28  C29   108.49  3.000
 71S  H282  C28  C26   109.25  3.000
 71S  H281  C28  C26   107.08  3.000
 71S  C29   C28  C26   114.82  3.000
 71S  H29   C29  C18   108.03  3.000
 71S  H29   C29  C15   107.18  3.000
 71S  C18   C29  C15   108.10  3.000
 71S  H29   C29  C28   107.55  3.000
 71S  C18   C29  C28   112.67  3.000
 71S  C15   C29  C28   113.06  3.000
 71S  C16   C15  C14   116.71  3.000
 71S  C16   C15  C29   120.39  3.000
 71S  C14   C15  C29   122.84  3.000
 71S  H14   C14  N11   115.70  3.000
 71S  H14   C14  C15   120.52  3.000
 71S  N11   C14  C15   123.77  3.000
 71S  H12   C12  N11   116.54  3.000
 71S  H12   C12  C11   119.75  3.000
 71S  N11   C12  C11   123.71  3.000
 71S  H16   C16  C11   119.70  3.000
 71S  H16   C16  C15   119.60  3.000
 71S  C11   C16  C15   120.70  3.000
 71S  C09   C11  C16   121.91  3.000
 71S  C09   C11  C12   121.14  3.000
 71S  C16   C11  C12   116.90  3.000
 71S  H092  C09  H091  107.11  3.000
 71S  H092  C09  C08   109.22  3.000
 71S  H091  C09  C08   109.20  3.000
 71S  H092  C09  C11   109.86  3.000
 71S  H091  C09  C11   110.19  3.000
 71S  C08   C09  C11   111.16  3.000
 71S  H082  C08  H081  107.17  3.000
 71S  H082  C08  C06   109.29  3.000
 71S  H081  C08  C06   109.91  3.000
 71S  H082  C08  C09   109.03  3.000
 71S  H081  C08  C09   109.39  3.000
 71S  C06   C08  C09   111.92  3.000
 71S  C05   C06  N01   122.84  3.000
 71S  C05   C06  C08   121.07  3.000
 71S  N01   C06  C08   116.08  3.000
 71S  C02   N01  C06   118.65  3.000
 71S  C03   C02  N02   120.54  3.000
 71S  C03   C02  N01   122.31  3.000
 71S  N02   C02  N01   117.13  3.000
 71S  H022  N02  H021  113.99  3.000
 71S  H022  N02  C02   117.46  3.000
 71S  H021  N02  C02   116.11  3.000
 71S  H03   C03  C04   120.88  3.000
 71S  H03   C03  C02   120.01  3.000
 71S  C04   C03  C02   119.11  3.000
 71S  C07   C04  C05   120.55  3.000
 71S  C07   C04  C03   121.41  3.000
 71S  C05   C04  C03   118.04  3.000
 71S  H05   C05  C04   120.73  3.000
 71S  H05   C05  C06   120.22  3.000
 71S  C04   C05  C06   119.05  3.000
 71S  H073  C07  H072  108.12  3.000
 71S  H073  C07  H071  108.16  3.000
 71S  H072  C07  H071  106.94  3.000
 71S  H073  C07  C04   111.84  3.000
 71S  H072  C07  C04   110.74  3.000
 71S  H071  C07  C04   110.85  3.000
 71S  H182  C18  H181  106.12  3.000
 71S  H182  C18  N18   108.30  3.000
 71S  H181  C18  N18   113.76  3.000
 71S  H182  C18  C29   108.45  3.000
 71S  H181  C18  C29   107.87  3.000
 71S  N18   C18  C29   112.05  3.000
 71S  C12   N11  C14   118.21  3.000
 71S  HB2   N18  HA1   106.18  3.000
 71S  HB2   N18  C18   109.35  3.000
 71S  HA1   N18  C18   109.80  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
 71S  CONST_01  C25   C24  C23  C22    0.00   0.0  0
 71S  CONST_02  C25   C26  N21  C22    0.00   0.0  0
 71S  CONST_03  C26   N21  C22  C23    0.00   0.0  0
 71S  CONST_04  C26   C25  C24  C23    0.00   0.0  0
 71S  CONST_05  N21   C22  C23  C24    0.00   0.0  0
 71S  CONST_06  N21   C26  C25  C24    0.00   0.0  0
 71S  CONST_07  C12   N11  C14  C15    0.00   0.0  0
 71S  CONST_08  C12   C11  C16  C15    0.00   0.0  0
 71S  CONST_09  C11   C16  C15  C14    0.00   0.0  0
 71S  CONST_10  C11   C12  N11  C14    0.00   0.0  0
 71S  CONST_11  N11   C14  C15  C16    0.00   0.0  0
 71S  CONST_12  N11   C12  C11  C16    0.00   0.0  0
 71S  CONST_13  C03   C02  N01  C06    0.00   0.0  0
 71S  CONST_14  C03   C04  C05  C06    0.00   0.0  0
 71S  CONST_15  C04   C05  C06  N01    0.00   0.0  0
 71S  CONST_16  C04   C03  C02  N01    0.00   0.0  0
 71S  CONST_17  C05   C06  N01  C02    0.00   0.0  0
 71S  CONST_18  C05   C04  C03  C02    0.00   0.0  0
 71S  CONST_19  C24   C23  C22  N22  180.00   0.0  0
 71S  CONST_20  C26   N21  C22  N22  180.00   0.0  0
 71S  CONST_21  C27   C24  C23  C22  180.00   0.0  0
 71S  CONST_22  C28   C26  N21  C22  180.00   0.0  0
 71S  CONST_23  C28   C26  C25  C24  180.00   0.0  0
 71S  CONST_24  C26   C25  C24  C27  180.00   0.0  0
 71S  CONST_25  N11   C14  C15  C29  180.00   0.0  0
 71S  CONST_26  C11   C16  C15  C29  180.00   0.0  0
 71S  CONST_27  C09   C11  C16  C15  180.00   0.0  0
 71S  CONST_28  N11   C12  C11  C09  180.00   0.0  0
 71S  CONST_29  C02   N01  C06  C08  180.00   0.0  0
 71S  CONST_30  C04   C05  C06  C08  180.00   0.0  0
 71S  CONST_31  N02   C02  N01  C06  180.00   0.0  0
 71S  CONST_32  C07   C04  C05  C06  180.00   0.0  0
 71S  CONST_33  C07   C04  C03  C02  180.00   0.0  0
 71S  CONST_34  C04   C03  C02  N02  180.00   0.0  0
 71S  CONST_35  H25   C25  C24  C23  180.00   0.0  0
 71S  CONST_36  H23   C23  C24  C25  180.00   0.0  0
 71S  CONST_37  H16   C16  C15  C14  180.00   0.0  0
 71S  CONST_38  H12   C12  N11  C14  180.00   0.0  0
 71S  CONST_39  H14   C14  N11  C12  180.00   0.0  0
 71S  CONST_40  H05   C05  C06  N01  180.00   0.0  0
 71S  CONST_41  H03   C03  C02  N01  180.00   0.0  0
 71S  Var_01    C29   C28  C26  C25  137.07  30.0  2
 71S  Var_02    C08   C09  C11  C12   90.21  30.0  2
 71S  Var_03    C06   C08  C09  C11  179.04  30.0  3
 71S  Var_04    N01   C06  C08  C09  -68.76  30.0  2
 71S  Var_05    H271  C27  C24  C23  115.41  30.0  2
 71S  Var_06    H071  C07  C04  C03  121.95  30.0  2
 71S  Var_07    HA1   N18  C18  C29   61.98  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
 71S  chir_01  C29  C28  C15  C18  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
 71S  plan-1  N22   0.020
 71S  plan-1  C22   0.020
 71S  plan-1  C23   0.020
 71S  plan-1  C24   0.020
 71S  plan-1  C27   0.020
 71S  plan-1  C25   0.020
 71S  plan-1  N21   0.020
 71S  plan-1  C26   0.020
 71S  plan-1  C28   0.020
 71S  plan-1  H23   0.020
 71S  plan-1  H25   0.020
 71S  plan-2  C29   0.020
 71S  plan-2  C15   0.020
 71S  plan-2  C14   0.020
 71S  plan-2  C12   0.020
 71S  plan-2  C16   0.020
 71S  plan-2  C11   0.020
 71S  plan-2  C09   0.020
 71S  plan-2  N11   0.020
 71S  plan-2  H14   0.020
 71S  plan-2  H16   0.020
 71S  plan-2  H12   0.020
 71S  plan-3  C08   0.020
 71S  plan-3  C06   0.020
 71S  plan-3  N01   0.020
 71S  plan-3  C02   0.020
 71S  plan-3  N02   0.020
 71S  plan-3  C03   0.020
 71S  plan-3  C04   0.020
 71S  plan-3  C05   0.020
 71S  plan-3  C07   0.020
 71S  plan-3  H05   0.020
 71S  plan-3  H03   0.020
 71S  plan-4  N22   0.020
 71S  plan-4  C22   0.020
 71S  plan-4  H221  0.020
 71S  plan-4  H222  0.020
 71S  plan-5  C02   0.020
 71S  plan-5  N02   0.020
 71S  plan-5  H021  0.020
 71S  plan-5  H022  0.020

