# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 00:25:23 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: ~{N}'-[7-(4-methylphenyl)pyrido[3,4-b]pyrazin-5-yl]butane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2cc3nccnc3c(NCCCCN)n2
#
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
 6ZG  6ZG  ~{N}'-[7-(4-methylphenyl)pyrido[3,4-b]pyrazin-5-yl]butane-1,4-diamine  ligand  44  23  .  2022-07-23  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_6ZG
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
 6ZG  C10  C  CR66  0   0.362  -1.1024   2.7078   0.0496
 6ZG  C13  C  CR16  0  -0.120   0.7764   4.6219   0.0775
 6ZG  C15  C  CR66  0   0.077   0.2742   2.4225   0.0345
 6ZG  C20  C  CH2   0  -0.429   4.6068  -1.9890   0.0517
 6ZG  C21  C  CH2   0  -0.270   6.1130  -1.9919  -0.1575
 6ZG  C02  C  CR6   0   0.086  -4.1231  -3.0880  -0.0422
 6ZG  C03  C  CR16  0  -0.278  -2.7622  -3.2028   0.2360
 6ZG  C04  C  CR16  0  -0.272  -1.9336  -2.0932   0.2443
 6ZG  C05  C  CR6   0   0.049  -2.4368  -0.8176  -0.0201
 6ZG  C06  C  CR16  0  -0.315  -3.7974  -0.7032  -0.3091
 6ZG  C07  C  CR16  0  -0.281  -4.6216  -1.8170  -0.3184
 6ZG  C08  C  CR6   0   0.250  -1.5381   0.3573   0.0018
 6ZG  C09  C  CR16  0  -0.461  -2.0251   1.6426   0.0352
 6ZG  N11  N  N     0  -0.394  -1.5239   3.9930   0.0827
 6ZG  C12  C  CR16  0  -0.107  -0.6021   4.9190   0.0951
 6ZG  N14  N  N     0  -0.375   1.2027   3.3846   0.0488
 6ZG  C16  C  CR6   0   0.477   0.6721   1.0347   0.0151
 6ZG  N17  N  NH1   0  -0.665   1.9766   0.7406   0.0042
 6ZG  C18  C  CH2   0  -0.231   2.4960  -0.6053   0.0896
 6ZG  C19  C  CH2   0  -0.474   4.0036  -0.5995  -0.0993
 6ZG  N22  N  NH2   0  -0.801   6.6598  -3.3300   0.0165
 6ZG  N23  N  N     0  -0.511  -0.2164   0.0688   0.0013
 6ZG  H1   H  HCR6  0   0.281   1.5107   5.4175   0.0890
 6ZG  H2   H  HCH2  0   0.217   4.1406  -2.6702  -0.6688
 6ZG  H3   H  HCH2  0   0.219   4.3830  -2.3866   1.0464
 6ZG  H4   H  HCH2  0   0.189   6.3353  -1.5512  -1.1404
 6ZG  H5   H  HCH2  0   0.213   6.5767  -1.3345   0.5833
 6ZG  H6   H  HCH3  0   0.250  -5.2911  -4.5618   0.9938
 6ZG  H7   H  HCH3  0   0.244  -5.9450  -4.1059  -0.5738
 6ZG  H8   H  HCH3  0   0.245  -4.5325  -5.1581  -0.4718
 6ZG  H9   H  HCR6  0   0.247  -2.3403  -4.1784   0.4486
 6ZG  H10  H  HCR6  0   0.257  -0.8805  -2.2138   0.4582
 6ZG  H11  H  HCR6  0   0.250  -4.2308   0.2585  -0.5510
 6ZG  H12  H  HCR6  0   0.250  -5.6722  -1.6924  -0.5525
 6ZG  H13  H  HCR6  0   0.262  -3.0819   1.8650   0.0680
 6ZG  H14  H  HCR6  0   0.280  -0.9276   5.9528   0.1223
 6ZG  H15  H  HNH1  0   0.400   2.6193   1.5126   0.0878
 6ZG  H16  H  HCH2  0   0.225   2.2387  -1.0522   1.0564
 6ZG  H17  H  HCH2  0   0.233   2.0234  -1.2266  -0.6747
 6ZG  H18  H  HCH2  0   0.228   4.4591   0.0761   0.6328
 6ZG  H19  H  HCH2  0   0.231   4.2409  -0.1958  -1.0885
 6ZG  H20  H  HNH2  0   0.337   6.3224  -3.9266  -0.7293
 6ZG  H21  H  HNH2  0   0.346   7.6652  -3.3007  -0.0953
 6ZG  C01  C  CH3   0  -0.722  -5.0200  -4.2899  -0.0285

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
 6ZG  C13  C12  aromatic  1.410  0.020  1.410
 6ZG  C13  N14  aromatic  1.309  0.020  1.309
 6ZG  C12  N11  aromatic  1.307  0.020  1.307
 6ZG  N14  C15  aromatic  1.337  0.020  1.337
 6ZG  N11  C10  aromatic  1.353  0.020  1.353
 6ZG  C15  C10  aromatic  1.406  0.020  1.406
 6ZG  C15  C16  aromatic  1.444  0.020  1.444
 6ZG  C10  C09  aromatic  1.409  0.020  1.409
 6ZG  N17  C16  single    1.337  0.020  1.337
 6ZG  N17  C18  single    1.445  0.020  1.445
 6ZG  C16  N23  aromatic  1.312  0.020  1.312
 6ZG  C09  C08  aromatic  1.375  0.020  1.375
 6ZG  C18  C19  single    1.519  0.020  1.519
 6ZG  C20  C19  single    1.522  0.020  1.522
 6ZG  C20  C21  single    1.521  0.020  1.521
 6ZG  N23  C08  aromatic  1.353  0.020  1.353
 6ZG  N22  C21  single    1.456  0.020  1.456
 6ZG  C08  C05  single    1.479  0.020  1.479
 6ZG  C05  C04  aromatic  1.397  0.020  1.397
 6ZG  C05  C06  aromatic  1.396  0.020  1.396
 6ZG  C04  C03  aromatic  1.385  0.020  1.385
 6ZG  C06  C07  aromatic  1.386  0.020  1.386
 6ZG  C03  C02  aromatic  1.394  0.020  1.394
 6ZG  C07  C02  aromatic  1.393  0.020  1.393
 6ZG  C02  C01  single    1.500  0.020  1.500
 6ZG  C13  H1   single    0.930  0.020  1.080
 6ZG  C20  H2   single    0.970  0.020  1.090
 6ZG  C20  H3   single    0.970  0.020  1.090
 6ZG  C21  H4   single    0.970  0.020  1.090
 6ZG  C21  H5   single    0.970  0.020  1.090
 6ZG  C01  H6   single    0.970  0.020  1.090
 6ZG  C01  H7   single    0.970  0.020  1.090
 6ZG  C01  H8   single    0.970  0.020  1.090
 6ZG  C03  H9   single    0.930  0.020  1.080
 6ZG  C04  H10  single    0.930  0.020  1.080
 6ZG  C06  H11  single    0.930  0.020  1.080
 6ZG  C07  H12  single    0.930  0.020  1.080
 6ZG  C09  H13  single    0.930  0.020  1.080
 6ZG  C12  H14  single    0.930  0.020  1.080
 6ZG  N17  H15  single    0.860  0.020  1.020
 6ZG  C18  H16  single    0.970  0.020  1.090
 6ZG  C18  H17  single    0.970  0.020  1.090
 6ZG  C19  H18  single    0.970  0.020  1.090
 6ZG  C19  H19  single    0.970  0.020  1.090
 6ZG  N22  H20  single    0.890  0.020  1.040
 6ZG  N22  H21  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
 6ZG  N11  C10  C09  120.95  3.000
 6ZG  C09  C10  C15  119.19  3.000
 6ZG  N11  C10  C15  119.87  3.000
 6ZG  H1   C13  N14  118.29  3.000
 6ZG  H1   C13  C12  120.53  3.000
 6ZG  N14  C13  C12  121.18  3.000
 6ZG  C16  C15  N14  120.03  3.000
 6ZG  C16  C15  C10  117.71  3.000
 6ZG  N14  C15  C10  122.26  3.000
 6ZG  H3   C20  H2   106.54  3.000
 6ZG  H3   C20  C19  109.93  3.000
 6ZG  H2   C20  C19  109.49  3.000
 6ZG  H3   C20  C21  109.08  3.000
 6ZG  H2   C20  C21  109.25  3.000
 6ZG  C19  C20  C21  112.37  3.000
 6ZG  H5   C21  H4   106.18  3.000
 6ZG  H5   C21  N22  108.19  3.000
 6ZG  H4   C21  N22  113.53  3.000
 6ZG  H5   C21  C20  109.00  3.000
 6ZG  H4   C21  C20  108.81  3.000
 6ZG  N22  C21  C20  110.94  3.000
 6ZG  C07  C02  C03  117.66  3.000
 6ZG  C07  C02  C01  121.27  3.000
 6ZG  C03  C02  C01  121.07  3.000
 6ZG  H9   C03  C04  119.15  3.000
 6ZG  H9   C03  C02  119.56  3.000
 6ZG  C04  C03  C02  121.29  3.000
 6ZG  H10  C04  C05  119.36  3.000
 6ZG  H10  C04  C03  119.64  3.000
 6ZG  C05  C04  C03  121.01  3.000
 6ZG  C08  C05  C06  122.02  3.000
 6ZG  C06  C05  C04  117.73  3.000
 6ZG  C08  C05  C04  120.25  3.000
 6ZG  H11  C06  C07  118.33  3.000
 6ZG  H11  C06  C05  120.63  3.000
 6ZG  C07  C06  C05  121.03  3.000
 6ZG  H12  C07  C06  119.06  3.000
 6ZG  H12  C07  C02  119.66  3.000
 6ZG  C06  C07  C02  121.28  3.000
 6ZG  N23  C08  C09  123.06  3.000
 6ZG  N23  C08  C05  115.09  3.000
 6ZG  C09  C08  C05  121.84  3.000
 6ZG  H13  C09  C08  122.66  3.000
 6ZG  H13  C09  C10  118.98  3.000
 6ZG  C08  C09  C10  118.35  3.000
 6ZG  C12  N11  C10  116.98  3.000
 6ZG  H14  C12  N11  117.66  3.000
 6ZG  H14  C12  C13  119.65  3.000
 6ZG  N11  C12  C13  122.69  3.000
 6ZG  C15  N14  C13  117.02  3.000
 6ZG  N23  C16  N17  119.89  3.000
 6ZG  N23  C16  C15  121.40  3.000
 6ZG  N17  C16  C15  118.71  3.000
 6ZG  H15  N17  C18  118.63  3.000
 6ZG  H15  N17  C16  116.93  3.000
 6ZG  C18  N17  C16  123.70  3.000
 6ZG  H17  C18  H16  106.49  3.000
 6ZG  H17  C18  C19  110.15  3.000
 6ZG  H16  C18  C19  110.14  3.000
 6ZG  H17  C18  N17  109.44  3.000
 6ZG  H16  C18  N17  110.34  3.000
 6ZG  C19  C18  N17  110.22  3.000
 6ZG  H19  C19  H18  106.65  3.000
 6ZG  H19  C19  C18  109.20  3.000
 6ZG  H18  C19  C18  109.39  3.000
 6ZG  H19  C19  C20  109.90  3.000
 6ZG  H18  C19  C20  109.38  3.000
 6ZG  C18  C19  C20  112.17  3.000
 6ZG  H21  N22  H20  105.46  3.000
 6ZG  H21  N22  C21  109.47  3.000
 6ZG  H20  N22  C21  109.16  3.000
 6ZG  C16  N23  C08  120.29  3.000
 6ZG  H8   C01  H7   108.10  3.000
 6ZG  H8   C01  H6   107.06  3.000
 6ZG  H7   C01  H6   107.45  3.000
 6ZG  H8   C01  C02  111.54  3.000
 6ZG  H7   C01  C02  111.58  3.000
 6ZG  H6   C01  C02  110.89  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
 6ZG  CONST_01  C13  C12  N11  C10    0.00   0.0  0
 6ZG  CONST_02  C13  N14  C15  C10    0.00   0.0  0
 6ZG  CONST_03  N23  C16  C15  C10    0.00   0.0  0
 6ZG  CONST_04  N23  C08  C09  C10    0.00   0.0  0
 6ZG  CONST_05  C05  C08  C09  C10  180.00   0.0  0
 6ZG  CONST_06  C16  C15  N14  C13  180.00   0.0  0
 6ZG  CONST_07  C12  C13  N14  C15    0.00   0.0  0
 6ZG  CONST_08  C12  N11  C10  C15    0.00   0.0  0
 6ZG  CONST_09  C08  C09  C10  C15    0.00   0.0  0
 6ZG  CONST_10  C08  N23  C16  C15    0.00   0.0  0
 6ZG  CONST_11  C05  C04  C03  C02    0.00   0.0  0
 6ZG  CONST_12  C05  C06  C07  C02    0.00   0.0  0
 6ZG  CONST_13  C08  C05  C04  C03  180.00   0.0  0
 6ZG  CONST_14  C06  C05  C04  C03    0.00   0.0  0
 6ZG  CONST_15  C06  C07  C02  C03    0.00   0.0  0
 6ZG  CONST_16  C09  C08  C05  C04  180.00   0.0  0
 6ZG  CONST_17  N23  C08  C05  C04    0.00   0.0  0
 6ZG  CONST_18  C07  C06  C05  C04    0.00   0.0  0
 6ZG  CONST_19  C07  C02  C03  C04    0.00   0.0  0
 6ZG  CONST_20  C16  N23  C08  C05  180.00   0.0  0
 6ZG  CONST_21  C09  C08  C05  C06    0.00   0.0  0
 6ZG  CONST_22  N23  C08  C05  C06  180.00   0.0  0
 6ZG  CONST_23  C08  C05  C06  C07  180.00   0.0  0
 6ZG  CONST_24  N11  C10  C09  C08  180.00   0.0  0
 6ZG  CONST_25  C12  N11  C10  C09  180.00   0.0  0
 6ZG  CONST_26  N14  C15  C10  C09  180.00   0.0  0
 6ZG  CONST_27  C16  C15  C10  C09    0.00   0.0  0
 6ZG  CONST_28  C16  N23  C08  C09    0.00   0.0  0
 6ZG  CONST_29  N14  C13  C12  N11    0.00   0.0  0
 6ZG  CONST_30  N14  C15  C10  N11    0.00   0.0  0
 6ZG  CONST_31  C16  C15  C10  N11  180.00   0.0  0
 6ZG  CONST_32  N23  C16  C15  N14  180.00   0.0  0
 6ZG  CONST_33  N17  C16  C15  C10  180.00   0.0  0
 6ZG  CONST_34  C04  C03  C02  C01  180.00   0.0  0
 6ZG  CONST_35  C06  C07  C02  C01  180.00   0.0  0
 6ZG  CONST_36  N17  C16  N23  C08  180.00   0.0  0
 6ZG  CONST_37  N17  C16  C15  N14    0.00   0.0  0
 6ZG  CONST_38  H14  C12  N11  C10  180.00   0.0  0
 6ZG  CONST_39  H1   C13  N14  C15  180.00   0.0  0
 6ZG  CONST_40  H13  C09  C10  C15  180.00   0.0  0
 6ZG  CONST_41  H10  C04  C03  C02  180.00   0.0  0
 6ZG  CONST_42  H11  C06  C07  C02  180.00   0.0  0
 6ZG  CONST_43  H12  C07  C02  C03  180.00   0.0  0
 6ZG  CONST_44  H9   C03  C04  C05  180.00   0.0  0
 6ZG  CONST_45  C18  N17  C16  C15  180.00   0.0  0
 6ZG  CONST_46  N23  C16  N17  C18    0.00   0.0  0
 6ZG  CONST_47  H15  N17  C16  C15    0.00   0.0  0
 6ZG  Var_01    H6   C01  C02  C03   79.27  30.0  2
 6ZG  Var_02    C19  C18  N17  C16  173.94  30.0  3
 6ZG  Var_03    N17  C18  C19  C20  177.14  30.0  1
 6ZG  Var_04    C18  C19  C20  C21  179.12  30.0  3
 6ZG  Var_05    N22  C21  C20  C19  179.01  30.0  3
 6ZG  Var_06    H20  N22  C21  C20   67.00  30.0  3

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
 6ZG  plan-1  C02  0.020
 6ZG  plan-1  C03  0.020
 6ZG  plan-1  C04  0.020
 6ZG  plan-1  C05  0.020
 6ZG  plan-1  C06  0.020
 6ZG  plan-1  C07  0.020
 6ZG  plan-1  C08  0.020
 6ZG  plan-1  H9   0.020
 6ZG  plan-1  H10  0.020
 6ZG  plan-1  H11  0.020
 6ZG  plan-1  H12  0.020
 6ZG  plan-1  C01  0.020
 6ZG  plan-2  C10  0.020
 6ZG  plan-2  C13  0.020
 6ZG  plan-2  C15  0.020
 6ZG  plan-2  C05  0.020
 6ZG  plan-2  C08  0.020
 6ZG  plan-2  C09  0.020
 6ZG  plan-2  N11  0.020
 6ZG  plan-2  C12  0.020
 6ZG  plan-2  N14  0.020
 6ZG  plan-2  C16  0.020
 6ZG  plan-2  N17  0.020
 6ZG  plan-2  N23  0.020
 6ZG  plan-2  H1   0.020
 6ZG  plan-2  H13  0.020
 6ZG  plan-2  H14  0.020
 6ZG  plan-3  C16  0.020
 6ZG  plan-3  N17  0.020
 6ZG  plan-3  C18  0.020
 6ZG  plan-3  H15  0.020

