# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 23:37:36 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: N-{6-[4-(hydroxyacetyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC(=O)N1CCCN(CC1)c2cc(NCCC(O)=O)nc(n2)c3ccccn3
#
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
 H6M  H6M  N-{6-[4-(hydroxyacetyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine  ligand  52  29  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H6M
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
 H6M  C02  C  C      0   0.423   5.1558   3.6697  -0.4691
 H6M  C04  C  CH2    0  -0.632   4.8835   2.1709  -0.2439
 H6M  C05  C  CH2    0  -0.245   3.4225   1.7759  -0.3366
 H6M  C07  C  CR6    0   0.545   2.1122  -0.3126  -0.1637
 H6M  C08  C  CR16   0  -0.548   0.8931   0.3284  -0.4017
 H6M  C09  C  CR6    0   0.567  -0.2503  -0.4763  -0.4364
 H6M  C11  C  CH2    0  -0.326  -2.6576  -0.8100  -0.3694
 H6M  C12  C  CH2    0  -0.489  -3.0417  -0.6915   1.1085
 H6M  C13  C  CH2    0  -0.284  -3.9666   0.4779   1.4488
 H6M  C15  C  C      0   0.522  -4.7150   2.4665   0.2831
 H6M  C16  C  CH2    0  -0.281  -4.3610   3.7298  -0.4935
 H6M  C19  C  CH2    0  -0.353  -2.2978   2.0556   0.4525
 H6M  C20  C  CH2    0  -0.326  -1.7579   1.4166  -0.8309
 H6M  C22  C  CR6    0   0.354   1.0380  -2.2997  -0.0073
 H6M  C23  C  CR6    0   0.141   1.1253  -3.7737   0.2141
 H6M  C24  C  CR16   0  -0.298   2.3498  -4.3702   0.5078
 H6M  C25  C  CR16   0  -0.154   2.3956  -5.7405   0.7053
 H6M  C26  C  CR16   0  -0.314   1.2226  -6.4712   0.6023
 H6M  C27  C  CR16   0  -0.087   0.0530  -5.7853   0.3050
 H6M  N06  N  NH1    0  -0.668   3.2753   0.3543  -0.1115
 H6M  N10  N  NT     0  -0.487  -1.4981   0.0032  -0.7040
 H6M  N14  N  NT     0  -0.462  -3.6830   1.7051   0.7138
 H6M  N21  N  N      0  -0.491  -0.1622  -1.7988  -0.2232
 H6M  N28  N  N      0  -0.402   0.0001  -4.4753   0.1159
 H6M  N29  N  N      0  -0.512   2.1806  -1.6411   0.0330
 H6M  O01  O  OC    -1  -0.624   6.3523   4.0173  -0.4171
 H6M  O03  O  O      0  -0.606   4.1738   4.4072  -0.6804
 H6M  O17  O  OH1    0  -0.657  -5.5475   4.3001  -0.9587
 H6M  O18  O  O      0  -0.496  -5.8832   2.1894   0.5012
 H6M  H1   H  HCH2   0   0.236   5.4677   1.5972  -0.9717
 H6M  H2   H  HCH2   0   0.237   5.2794   1.8907   0.7384
 H6M  H3   H  HCH2   0   0.222   2.8369   2.3362   0.3988
 H6M  H4   H  HCH2   0   0.222   3.0244   2.0411  -1.3211
 H6M  H5   H  HCR6   0   0.277   0.8598   1.3976  -0.5330
 H6M  H6   H  HCH2   0   0.274  -2.4350  -1.8455  -0.6068
 H6M  H7   H  HCH2   0   0.248  -3.4854  -0.4984  -1.0119
 H6M  H8   H  HCH2   0   0.256  -3.5608  -1.6006   1.4199
 H6M  H9   H  HCH2   0   0.243  -2.1297  -0.6564   1.7086
 H6M  H10  H  HCH2   0   0.254  -4.9910   0.1939   1.2208
 H6M  H11  H  HCH2   0   0.245  -3.9228   0.6705   2.5252
 H6M  H12  H  HCH2   0   0.238  -3.8122   4.4095   0.1742
 H6M  H13  H  HCH2   0   0.233  -3.6738   3.4839  -1.3136
 H6M  H14  H  HCH2   0   0.279  -1.6909   1.7546   1.3087
 H6M  H15  H  HCH2   0   0.276  -2.1889   3.1373   0.3891
 H6M  H16  H  HCH2   0   0.259  -2.4873   1.5590  -1.6333
 H6M  H17  H  HCH2   0   0.269  -0.8599   1.9405  -1.1481
 H6M  H18  H  HCR6   0   0.269   3.2422  -3.7659   0.5786
 H6M  H19  H  HCR6   0   0.273   3.3333  -6.2285   0.9367
 H6M  H20  H  HCR6   0   0.272   1.2074  -7.5428   0.7454
 H6M  H21  H  HCR6   0   0.260  -0.8847  -6.3235   0.2151
 H6M  H22  H  HNH1   0   0.384   4.0992  -0.1987   0.0615
 H6M  H24  H  HOH1   0   0.460  -5.3148   5.1157  -1.4118

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
 H6M  C26  C27  aromatic  1.388  0.020  1.388
 H6M  C26  C25  aromatic  1.386  0.020  1.386
 H6M  C27  N28  aromatic  1.325  0.020  1.325
 H6M  C25  C24  aromatic  1.385  0.020  1.385
 H6M  N28  C23  aromatic  1.330  0.020  1.330
 H6M  C24  C23  aromatic  1.393  0.020  1.393
 H6M  C23  C22  single    1.493  0.020  1.493
 H6M  C22  N29  aromatic  1.319  0.020  1.319
 H6M  C22  N21  aromatic  1.318  0.020  1.318
 H6M  O17  C16  single    1.396  0.020  1.396
 H6M  C16  C15  single    1.525  0.020  1.525
 H6M  N29  C07  aromatic  1.345  0.020  1.345
 H6M  N21  C09  aromatic  1.342  0.020  1.342
 H6M  C19  C20  single    1.532  0.020  1.532
 H6M  C19  N14  single    1.453  0.020  1.453
 H6M  C07  N06  single    1.342  0.020  1.342
 H6M  C07  C08  aromatic  1.398  0.020  1.398
 H6M  C15  N14  single    1.353  0.020  1.353
 H6M  C15  O18  double    1.220  0.020  1.220
 H6M  C09  C08  aromatic  1.399  0.020  1.399
 H6M  C09  N10  single    1.363  0.020  1.363
 H6M  C20  N10  single    1.443  0.020  1.443
 H6M  N06  C05  single    1.447  0.020  1.447
 H6M  N14  C13  single    1.458  0.020  1.458
 H6M  N10  C11  single    1.455  0.020  1.455
 H6M  C05  C04  single    1.516  0.020  1.516
 H6M  C13  C12  single    1.529  0.020  1.529
 H6M  C11  C12  single    1.532  0.020  1.532
 H6M  C04  C02  single    1.540  0.020  1.540
 H6M  C02  O03  deloc     1.246  0.020  1.246
 H6M  C02  O01  deloc     1.247  0.020  1.247
 H6M  C04  H1   single    0.970  0.020  1.090
 H6M  C04  H2   single    0.970  0.020  1.090
 H6M  C05  H3   single    0.970  0.020  1.090
 H6M  C05  H4   single    0.970  0.020  1.090
 H6M  C08  H5   single    0.930  0.020  1.080
 H6M  C11  H6   single    0.970  0.020  1.090
 H6M  C11  H7   single    0.970  0.020  1.090
 H6M  C12  H8   single    0.970  0.020  1.090
 H6M  C12  H9   single    0.970  0.020  1.090
 H6M  C13  H10  single    0.970  0.020  1.090
 H6M  C13  H11  single    0.970  0.020  1.090
 H6M  C16  H12  single    0.970  0.020  1.090
 H6M  C16  H13  single    0.970  0.020  1.090
 H6M  C19  H14  single    0.970  0.020  1.090
 H6M  C19  H15  single    0.970  0.020  1.090
 H6M  C20  H16  single    0.970  0.020  1.090
 H6M  C20  H17  single    0.970  0.020  1.090
 H6M  C24  H18  single    0.930  0.020  1.080
 H6M  C25  H19  single    0.930  0.020  1.080
 H6M  C26  H20  single    0.930  0.020  1.080
 H6M  C27  H21  single    0.930  0.020  1.080
 H6M  N06  H22  single    0.860  0.020  1.020
 H6M  O17  H24  single    0.850  0.020  0.980

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
 H6M  O03  C02  O01  126.74  3.000
 H6M  O01  C02  C04  115.78  3.000
 H6M  O03  C02  C04  117.48  3.000
 H6M  H2   C04  H1   105.61  3.000
 H6M  H2   C04  C05  109.65  3.000
 H6M  H1   C04  C05  109.69  3.000
 H6M  H2   C04  C02  108.43  3.000
 H6M  H1   C04  C02  108.56  3.000
 H6M  C05  C04  C02  114.52  3.000
 H6M  H4   C05  H3   106.60  3.000
 H6M  H4   C05  N06  109.94  3.000
 H6M  H3   C05  N06  110.13  3.000
 H6M  H4   C05  C04  110.02  3.000
 H6M  H3   C05  C04  109.95  3.000
 H6M  N06  C05  C04  110.15  3.000
 H6M  N29  C07  N06  116.18  3.000
 H6M  N06  C07  C08  122.33  3.000
 H6M  N29  C07  C08  121.49  3.000
 H6M  H5   C08  C09  122.85  3.000
 H6M  H5   C08  C07  120.18  3.000
 H6M  C09  C08  C07  116.96  3.000
 H6M  N21  C09  N10  115.96  3.000
 H6M  N10  C09  C08  123.42  3.000
 H6M  N21  C09  C08  120.61  3.000
 H6M  H7   C11  H6   107.38  3.000
 H6M  H7   C11  N10  107.99  3.000
 H6M  H6   C11  N10  108.62  3.000
 H6M  H7   C11  C12  110.81  3.000
 H6M  H6   C11  C12  109.65  3.000
 H6M  N10  C11  C12  112.24  3.000
 H6M  H9   C12  H8   105.48  3.000
 H6M  H9   C12  C13  110.99  3.000
 H6M  H8   C12  C13  106.59  3.000
 H6M  H9   C12  C11  108.86  3.000
 H6M  H8   C12  C11  109.26  3.000
 H6M  C13  C12  C11  115.19  3.000
 H6M  H11  C13  H10  106.85  3.000
 H6M  H11  C13  N14  109.87  3.000
 H6M  H10  C13  N14  107.30  3.000
 H6M  H11  C13  C12  109.22  3.000
 H6M  H10  C13  C12  108.87  3.000
 H6M  N14  C13  C12  114.44  3.000
 H6M  O18  C15  N14  123.06  3.000
 H6M  O18  C15  C16  120.10  3.000
 H6M  N14  C15  C16  116.84  3.000
 H6M  H13  C16  H12  106.24  3.000
 H6M  H13  C16  O17  112.00  3.000
 H6M  H12  C16  O17  111.96  3.000
 H6M  H13  C16  C15  109.89  3.000
 H6M  H12  C16  C15  108.59  3.000
 H6M  O17  C16  C15  108.11  3.000
 H6M  H15  C19  H14  105.30  3.000
 H6M  H15  C19  N14  110.22  3.000
 H6M  H14  C19  N14  108.81  3.000
 H6M  H15  C19  C20  109.29  3.000
 H6M  H14  C19  C20  110.25  3.000
 H6M  N14  C19  C20  112.71  3.000
 H6M  H17  C20  H16  105.91  3.000
 H6M  H17  C20  N10  110.43  3.000
 H6M  H16  C20  N10  108.19  3.000
 H6M  H17  C20  C19  109.55  3.000
 H6M  H16  C20  C19  108.99  3.000
 H6M  N10  C20  C19  113.48  3.000
 H6M  N29  C22  N21  127.14  3.000
 H6M  N21  C22  C23  116.91  3.000
 H6M  N29  C22  C23  115.95  3.000
 H6M  N28  C23  C24  122.23  3.000
 H6M  C24  C23  C22  120.35  3.000
 H6M  N28  C23  C22  117.42  3.000
 H6M  H18  C24  C25  121.12  3.000
 H6M  H18  C24  C23  120.02  3.000
 H6M  C25  C24  C23  118.86  3.000
 H6M  H19  C25  C26  120.77  3.000
 H6M  H19  C25  C24  120.35  3.000
 H6M  C26  C25  C24  118.88  3.000
 H6M  H20  C26  C27  120.41  3.000
 H6M  H20  C26  C25  121.64  3.000
 H6M  C27  C26  C25  117.94  3.000
 H6M  H21  C27  N28  116.38  3.000
 H6M  H21  C27  C26  120.05  3.000
 H6M  N28  C27  C26  123.57  3.000
 H6M  H22  N06  C07  116.29  3.000
 H6M  H22  N06  C05  118.88  3.000
 H6M  C07  N06  C05  124.78  3.000
 H6M  C20  N10  C11  115.10  3.000
 H6M  C11  N10  C09  119.18  3.000
 H6M  C20  N10  C09  121.79  3.000
 H6M  C19  N14  C15  122.30  3.000
 H6M  C15  N14  C13  119.06  3.000
 H6M  C19  N14  C13  118.64  3.000
 H6M  C22  N21  C09  117.39  3.000
 H6M  C27  N28  C23  118.52  3.000
 H6M  C22  N29  C07  116.40  3.000
 H6M  H24  O17  C16  107.32  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
 H6M  CONST_01  C23  C22  N29  C07   180.00   0.0  0
 H6M  CONST_02  N21  C22  N29  C07     0.00   0.0  0
 H6M  CONST_03  N21  C09  C08  C07     0.00   0.0  0
 H6M  CONST_04  C22  N29  C07  C08     0.00   0.0  0
 H6M  CONST_05  C22  N21  C09  C08     0.00   0.0  0
 H6M  CONST_06  C23  C22  N21  C09   180.00   0.0  0
 H6M  CONST_07  N29  C22  N21  C09     0.00   0.0  0
 H6M  CONST_08  N29  C07  C08  C09     0.00   0.0  0
 H6M  CONST_09  C27  N28  C23  C22   180.00   0.0  0
 H6M  CONST_10  C25  C24  C23  C22   180.00   0.0  0
 H6M  CONST_11  C26  C27  N28  C23     0.00   0.0  0
 H6M  CONST_12  C26  C25  C24  C23     0.00   0.0  0
 H6M  CONST_13  C27  C26  C25  C24     0.00   0.0  0
 H6M  CONST_14  C27  N28  C23  C24     0.00   0.0  0
 H6M  CONST_15  N29  C22  C23  C24     0.00   0.0  0
 H6M  CONST_16  N21  C22  C23  C24   180.00   0.0  0
 H6M  CONST_17  N28  C27  C26  C25     0.00   0.0  0
 H6M  CONST_18  N28  C23  C24  C25     0.00   0.0  0
 H6M  CONST_19  N28  C23  C22  N21     0.00   0.0  0
 H6M  CONST_20  N29  C22  C23  N28   180.00   0.0  0
 H6M  CONST_21  N10  C09  C08  C07   180.00   0.0  0
 H6M  CONST_22  N10  C09  N21  C22   180.00   0.0  0
 H6M  CONST_23  N06  C07  C08  C09   180.00   0.0  0
 H6M  CONST_24  N06  C07  N29  C22   180.00   0.0  0
 H6M  CONST_25  H18  C24  C23  C22     0.00   0.0  0
 H6M  CONST_26  H21  C27  N28  C23   180.00   0.0  0
 H6M  CONST_27  H19  C25  C24  C23   180.00   0.0  0
 H6M  CONST_28  H20  C26  C25  C24   180.00   0.0  0
 H6M  CONST_29  H5   C08  C09  N10     0.00   0.0  0
 H6M  CONST_30  N29  C07  N06  C05   180.00   0.0  0
 H6M  CONST_31  C08  C07  N06  C05     0.00   0.0  0
 H6M  CONST_32  H22  N06  C07  C08   180.00   0.0  0
 H6M  Var_01    C07  N06  C05  C04  -178.05  30.0  2
 H6M  Var_02    O17  C16  C15  N14   174.27  30.0  2
 H6M  Var_03    N06  C05  C04  C02   179.97  30.0  1
 H6M  Var_04    O03  C02  C04  C05     1.09  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
 H6M  plan-1  C07  0.020
 H6M  plan-1  C08  0.020
 H6M  plan-1  C09  0.020
 H6M  plan-1  C22  0.020
 H6M  plan-1  C23  0.020
 H6M  plan-1  N06  0.020
 H6M  plan-1  N10  0.020
 H6M  plan-1  N21  0.020
 H6M  plan-1  N29  0.020
 H6M  plan-1  H5   0.020
 H6M  plan-2  C22  0.020
 H6M  plan-2  C23  0.020
 H6M  plan-2  C24  0.020
 H6M  plan-2  C25  0.020
 H6M  plan-2  C26  0.020
 H6M  plan-2  C27  0.020
 H6M  plan-2  N28  0.020
 H6M  plan-2  H18  0.020
 H6M  plan-2  H19  0.020
 H6M  plan-2  H20  0.020
 H6M  plan-2  H21  0.020
 H6M  plan-3  C13  0.020
 H6M  plan-3  C15  0.020
 H6M  plan-3  C16  0.020
 H6M  plan-3  C19  0.020
 H6M  plan-3  N14  0.020
 H6M  plan-3  O18  0.020
 H6M  plan-4  C05  0.020
 H6M  plan-4  C07  0.020
 H6M  plan-4  N06  0.020
 H6M  plan-4  H22  0.020
 H6M  plan-5  C02  0.020
 H6M  plan-5  C04  0.020
 H6M  plan-5  O01  0.020
 H6M  plan-5  O03  0.020

