# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:49:06 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: N-[2-(pyridin-2-yl)-6-(1,2,4,5-tetrahydro-3H-3-benzazepin-3-yl)pyrimidin-4-yl]-beta-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCNc1cc(nc(n1)c2ccccn2)N3CCc4ccccc4CC3
#
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
 K0I  K0I  N-[2-(pyridin-2-yl)-6-(1,2,4,5-tetrahydro-3H-3-benzazepin-3-yl)pyrimidin-4-yl]-beta-alanine  ligand  51  29  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K0I
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
 K0I  O2    O  O      0  -0.606   4.2638   4.4362  -0.1768
 K0I  C1    C  C      0   0.423   5.1627   3.6543   0.1883
 K0I  O1    O  OC    -1  -0.624   6.3430   3.9501   0.4615
 K0I  C2    C  CH2    0  -0.632   4.7976   2.1653   0.3290
 K0I  C3    C  CH2    0  -0.245   3.3739   1.8238  -0.0677
 K0I  N1    N  NH1    0  -0.667   3.1434   0.4041   0.0884
 K0I  C4    C  C      0   0.543   1.9796  -0.2179  -0.1542
 K0I  N3    N  N      0  -0.512   1.9596  -1.5429   0.0730
 K0I  C7    C  C      0   0.356   0.8146  -2.1602  -0.1491
 K0I  C8    C  CR6    0   0.140   0.8048  -3.6302   0.1118
 K0I  N4    N  N      0  -0.402  -0.3357  -4.2817  -0.0949
 K0I  C12   C  CR16   0  -0.087  -0.3678  -5.5873   0.1264
 K0I  C11   C  CR16   0  -0.315   0.7278  -6.3192   0.5632
 K0I  C10   C  CR16   0  -0.154   1.9169  -5.6409   0.7794
 K0I  C9    C  CR16   0  -0.298   1.9589  -4.2751   0.5521
 K0I  N2    N  N      0  -0.492  -0.3108  -1.6213  -0.5745
 K0I  C6    C  C      0   0.562  -0.3071  -0.3011  -0.8213
 K0I  C5    C  C1     0  -0.539   0.8457   0.4623  -0.6079
 K0I  N5    N  NT     0  -0.479  -1.4671   0.2264  -1.3025
 K0I  C22   C  CH2    0  -0.327  -2.7045  -0.5154  -1.1563
 K0I  C21   C  CH2    0  -0.532  -3.3894  -0.2847   0.1949
 K0I  C20   C  CR6    0   0.103  -4.1237   1.0250   0.3275
 K0I  C15   C  CR6    0   0.101  -3.4896   2.2656   0.1588
 K0I  C14   C  CH2    0  -0.528  -2.0250   2.3814  -0.1761
 K0I  C13   C  CH2    0  -0.349  -1.6184   1.6549  -1.4632
 K0I  C19   C  CR16   0  -0.318  -5.4846   1.0037   0.6260
 K0I  C18   C  CR16   0  -0.257  -6.2226   2.1716   0.7626
 K0I  C17   C  CR16   0  -0.259  -5.5954   3.3957   0.5973
 K0I  C16   C  CR16   0  -0.316  -4.2407   3.4307   0.2961
 K0I  H21C  H  HCH2   0   0.236   5.4992   1.5752  -0.2702
 K0I  H22C  H  HCH2   0   0.238   4.9707   1.8633   1.3681
 K0I  H31C  H  HCH2   0   0.222   2.6692   2.3914   0.5480
 K0I  H32C  H  HCH2   0   0.223   3.1935   2.1212  -1.1053
 K0I  HA    H  HNH1   0   0.384   3.8902  -0.1716   0.4425
 K0I  H5    H  H      0   0.275   0.8766   1.5290  -0.7625
 K0I  H9    H  HCR6   0   0.269   2.8667  -3.7115   0.7105
 K0I  H12   H  HCR6   0   0.260  -1.3158  -6.0831  -0.0538
 K0I  H11   H  HCR6   0   0.272   0.6448  -7.3849   0.7256
 K0I  H10   H  HCR6   0   0.273   2.8002  -6.1652   1.1195
 K0I  H221  H  HCH2   0   0.246  -3.3737  -0.2278  -1.9707
 K0I  H222  H  HCH2   0   0.273  -2.4884  -1.5739  -1.2673
 K0I  H131  H  HCH2   0   0.266  -0.6935   2.0785  -1.8517
 K0I  H132  H  HCH2   0   0.263  -2.3726   1.8269  -2.2345
 K0I  H211  H  HCH2   0   0.255  -4.1030  -1.0966   0.3516
 K0I  H212  H  HCH2   0   0.251  -2.6387  -0.3857   0.9866
 K0I  H19   H  HCR6   0   0.246  -5.9784   0.0475   0.7566
 K0I  H141  H  HCH2   0   0.259  -1.7749   3.4382  -0.2877
 K0I  H142  H  HCH2   0   0.254  -1.4131   2.0099   0.6536
 K0I  H16   H  HCR6   0   0.246  -3.7521   4.3889   0.1609
 K0I  H18   H  HCR6   0   0.251  -7.2790   2.1209   0.9929
 K0I  H17   H  HCR6   0   0.251  -6.1526   4.3181   0.6997

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
 K0I  O2   C1    deloc     1.246  0.020  1.246
 K0I  C1   O1    deloc     1.247  0.020  1.247
 K0I  C1   C2    single    1.540  0.020  1.540
 K0I  C2   C3    single    1.517  0.020  1.517
 K0I  C3   N1    single    1.447  0.020  1.447
 K0I  N1   C4    single    1.342  0.020  1.342
 K0I  C4   N3    aromatic  1.344  0.020  1.344
 K0I  C4   C5    aromatic  1.398  0.020  1.398
 K0I  N3   C7    aromatic  1.320  0.020  1.320
 K0I  C7   C8    single    1.493  0.020  1.493
 K0I  C7   N2    aromatic  1.318  0.020  1.318
 K0I  C8   N4    aromatic  1.330  0.020  1.330
 K0I  C8   C9    aromatic  1.393  0.020  1.393
 K0I  N4   C12   aromatic  1.325  0.020  1.325
 K0I  C12  C11   aromatic  1.388  0.020  1.388
 K0I  C11  C10   aromatic  1.386  0.020  1.386
 K0I  C10  C9    aromatic  1.385  0.020  1.385
 K0I  N2   C6    aromatic  1.343  0.020  1.343
 K0I  C6   C5    aromatic  1.399  0.020  1.399
 K0I  C6   N5    single    1.362  0.020  1.362
 K0I  N5   C22   single    1.450  0.020  1.450
 K0I  N5   C13   single    1.445  0.020  1.445
 K0I  C22  C21   single    1.532  0.020  1.532
 K0I  C21  C20   single    1.507  0.020  1.507
 K0I  C20  C15   aromatic  1.403  0.020  1.403
 K0I  C20  C19   aromatic  1.393  0.020  1.393
 K0I  C15  C14   single    1.507  0.020  1.507
 K0I  C15  C16   aromatic  1.393  0.020  1.393
 K0I  C14  C13   single    1.533  0.020  1.533
 K0I  C19  C18   aromatic  1.388  0.020  1.388
 K0I  C18  C17   aromatic  1.385  0.020  1.385
 K0I  C17  C16   aromatic  1.388  0.020  1.388
 K0I  C2   H21C  single    0.970  0.020  1.090
 K0I  C2   H22C  single    0.970  0.020  1.090
 K0I  C3   H31C  single    0.970  0.020  1.090
 K0I  C3   H32C  single    0.970  0.020  1.090
 K0I  N1   HA    single    0.860  0.020  1.020
 K0I  C5   H5    single    0.930  0.020  1.080
 K0I  C9   H9    single    0.930  0.020  1.080
 K0I  C12  H12   single    0.930  0.020  1.080
 K0I  C11  H11   single    0.930  0.020  1.080
 K0I  C10  H10   single    0.930  0.020  1.080
 K0I  C22  H221  single    0.970  0.020  1.090
 K0I  C22  H222  single    0.970  0.020  1.090
 K0I  C13  H131  single    0.970  0.020  1.090
 K0I  C13  H132  single    0.970  0.020  1.090
 K0I  C21  H211  single    0.970  0.020  1.090
 K0I  C21  H212  single    0.970  0.020  1.090
 K0I  C19  H19   single    0.930  0.020  1.080
 K0I  C14  H141  single    0.970  0.020  1.090
 K0I  C14  H142  single    0.970  0.020  1.090
 K0I  C16  H16   single    0.930  0.020  1.080
 K0I  C18  H18   single    0.930  0.020  1.080
 K0I  C17  H17   single    0.930  0.020  1.080

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
 K0I  C2    C1   O1    115.72  3.000
 K0I  C2    C1   O2    117.55  3.000
 K0I  O1    C1   O2    126.73  3.000
 K0I  H22C  C2   H21C  105.61  3.000
 K0I  H22C  C2   C3    109.53  3.000
 K0I  H21C  C2   C3    109.69  3.000
 K0I  H22C  C2   C1    108.40  3.000
 K0I  H21C  C2   C1    108.61  3.000
 K0I  C3    C2   C1    114.61  3.000
 K0I  H32C  C3   H31C  106.64  3.000
 K0I  H32C  C3   N1    110.05  3.000
 K0I  H31C  C3   N1    110.23  3.000
 K0I  H32C  C3   C2    109.96  3.000
 K0I  H31C  C3   C2    109.90  3.000
 K0I  N1    C3   C2    110.01  3.000
 K0I  HA    N1   C4    116.21  3.000
 K0I  HA    N1   C3    118.73  3.000
 K0I  C4    N1   C3    125.01  3.000
 K0I  C5    C4   N3    121.49  3.000
 K0I  C5    C4   N1    122.45  3.000
 K0I  N3    C4   N1    116.06  3.000
 K0I  C7    N3   C4    116.45  3.000
 K0I  N2    C7   C8    116.96  3.000
 K0I  N2    C7   N3    127.14  3.000
 K0I  C8    C7   N3    115.90  3.000
 K0I  C9    C8   N4    122.19  3.000
 K0I  C9    C8   C7    120.36  3.000
 K0I  N4    C8   C7    117.44  3.000
 K0I  C12   N4   C8    118.54  3.000
 K0I  H12   C12  C11   120.07  3.000
 K0I  H12   C12  N4    116.35  3.000
 K0I  C11   C12  N4    123.58  3.000
 K0I  H11   C11  C10   121.66  3.000
 K0I  H11   C11  C12   120.42  3.000
 K0I  C10   C11  C12   117.92  3.000
 K0I  H10   C10  C9    120.31  3.000
 K0I  H10   C10  C11   120.81  3.000
 K0I  C9    C10  C11   118.88  3.000
 K0I  H9    C9   C10   121.05  3.000
 K0I  H9    C9   C8    120.06  3.000
 K0I  C10   C9   C8    118.88  3.000
 K0I  C6    N2   C7    117.31  3.000
 K0I  N5    C6   C5    122.98  3.000
 K0I  N5    C6   N2    116.31  3.000
 K0I  C5    C6   N2    120.70  3.000
 K0I  H5    C5   C6    122.79  3.000
 K0I  H5    C5   C4    120.31  3.000
 K0I  C6    C5   C4    116.89  3.000
 K0I  C13   N5   C22   115.31  3.000
 K0I  C13   N5   C6    120.74  3.000
 K0I  C22   N5   C6    119.54  3.000
 K0I  H222  C22  H221  107.59  3.000
 K0I  H222  C22  C21   109.01  3.000
 K0I  H221  C22  C21   110.11  3.000
 K0I  H222  C22  N5    108.57  3.000
 K0I  H221  C22  N5    108.23  3.000
 K0I  C21   C22  N5    113.16  3.000
 K0I  H212  C21  H211  105.99  3.000
 K0I  H212  C21  C20   110.51  3.000
 K0I  H211  C21  C20   108.36  3.000
 K0I  H212  C21  C22   108.48  3.000
 K0I  H211  C21  C22   107.85  3.000
 K0I  C20   C21  C22   115.22  3.000
 K0I  C19   C20  C15   118.72  3.000
 K0I  C19   C20  C21   118.78  3.000
 K0I  C15   C20  C21   122.51  3.000
 K0I  C16   C15  C14   118.79  3.000
 K0I  C16   C15  C20   118.94  3.000
 K0I  C14   C15  C20   122.26  3.000
 K0I  H142  C14  H141  106.12  3.000
 K0I  H142  C14  C13   109.08  3.000
 K0I  H141  C14  C13   108.19  3.000
 K0I  H142  C14  C15   110.39  3.000
 K0I  H141  C14  C15   108.65  3.000
 K0I  C13   C14  C15   114.08  3.000
 K0I  H132  C13  H131  105.86  3.000
 K0I  H132  C13  C14   109.58  3.000
 K0I  H131  C13  C14   109.91  3.000
 K0I  H132  C13  N5    107.84  3.000
 K0I  H131  C13  N5    109.59  3.000
 K0I  C14   C13  N5    113.75  3.000
 K0I  H19   C19  C18   119.21  3.000
 K0I  H19   C19  C20   118.96  3.000
 K0I  C18   C19  C20   121.83  3.000
 K0I  H18   C18  C17   120.57  3.000
 K0I  H18   C18  C19   120.03  3.000
 K0I  C17   C18  C19   119.40  3.000
 K0I  H17   C17  C16   120.09  3.000
 K0I  H17   C17  C18   120.57  3.000
 K0I  C16   C17  C18   119.34  3.000
 K0I  H16   C16  C17   119.29  3.000
 K0I  H16   C16  C15   118.95  3.000
 K0I  C17   C16  C15   121.76  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
 K0I  CONST_01  C8   C7   N3   C4   180.00   0.0  0
 K0I  CONST_02  N2   C7   N3   C4     0.00   0.0  0
 K0I  CONST_03  N2   C6   C5   C4     0.00   0.0  0
 K0I  CONST_04  C6   C5   C4   N3     0.00   0.0  0
 K0I  CONST_05  N4   C8   C7   N3   180.00   0.0  0
 K0I  CONST_06  C9   C8   C7   N3     0.00   0.0  0
 K0I  CONST_07  C6   N2   C7   N3     0.00   0.0  0
 K0I  CONST_08  C5   C4   N3   C7     0.00   0.0  0
 K0I  CONST_09  C12  N4   C8   C7   180.00   0.0  0
 K0I  CONST_10  C10  C9   C8   C7   180.00   0.0  0
 K0I  CONST_11  C5   C6   N2   C7     0.00   0.0  0
 K0I  CONST_12  C6   N2   C7   C8   180.00   0.0  0
 K0I  CONST_13  C11  C12  N4   C8     0.00   0.0  0
 K0I  CONST_14  C11  C10  C9   C8     0.00   0.0  0
 K0I  CONST_15  N2   C7   C8   N4     0.00   0.0  0
 K0I  CONST_16  C10  C9   C8   N4     0.00   0.0  0
 K0I  CONST_17  C10  C11  C12  N4     0.00   0.0  0
 K0I  CONST_18  C9   C8   N4   C12    0.00   0.0  0
 K0I  CONST_19  C9   C10  C11  C12    0.00   0.0  0
 K0I  CONST_20  N2   C7   C8   C9   180.00   0.0  0
 K0I  CONST_21  C17  C18  C19  C20    0.00   0.0  0
 K0I  CONST_22  C18  C17  C16  C15    0.00   0.0  0
 K0I  CONST_23  C16  C17  C18  C19    0.00   0.0  0
 K0I  CONST_24  N5   C6   C5   C4   180.00   0.0  0
 K0I  CONST_25  N5   C6   N2   C7   180.00   0.0  0
 K0I  CONST_26  C7   N3   C4   N1   180.00   0.0  0
 K0I  CONST_27  C6   C5   C4   N1   180.00   0.0  0
 K0I  CONST_28  H5   C5   C4   N3   180.00   0.0  0
 K0I  CONST_29  H9   C9   C8   C7     0.00   0.0  0
 K0I  CONST_30  H12  C12  N4   C8   180.00   0.0  0
 K0I  CONST_31  H10  C10  C9   C8   180.00   0.0  0
 K0I  CONST_32  H11  C11  C12  N4   180.00   0.0  0
 K0I  CONST_33  H18  C18  C19  C20  180.00   0.0  0
 K0I  CONST_34  H17  C17  C16  C15  180.00   0.0  0
 K0I  CONST_35  H16  C16  C17  C18  180.00   0.0  0
 K0I  CONST_36  H19  C19  C18  C17  180.00   0.0  0
 K0I  CONST_37  N3   C4   N1   C3   180.00   0.0  0
 K0I  CONST_38  C5   C4   N1   C3     0.00   0.0  0
 K0I  CONST_39  HA   N1   C4   N3     0.00   0.0  0
 K0I  Var_01    C4   N1   C3   C2   178.71  30.0  3
 K0I  Var_02    C3   C2   C1   O2     2.82  30.0  3
 K0I  Var_03    N1   C3   C2   C1   179.38  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
 K0I  plan-1  N1   0.020
 K0I  plan-1  C4   0.020
 K0I  plan-1  N3   0.020
 K0I  plan-1  C7   0.020
 K0I  plan-1  C8   0.020
 K0I  plan-1  N2   0.020
 K0I  plan-1  C6   0.020
 K0I  plan-1  C5   0.020
 K0I  plan-1  N5   0.020
 K0I  plan-1  H5   0.020
 K0I  plan-2  C7   0.020
 K0I  plan-2  C8   0.020
 K0I  plan-2  N4   0.020
 K0I  plan-2  C12  0.020
 K0I  plan-2  C11  0.020
 K0I  plan-2  C10  0.020
 K0I  plan-2  C9   0.020
 K0I  plan-2  H9   0.020
 K0I  plan-2  H12  0.020
 K0I  plan-2  H11  0.020
 K0I  plan-2  H10  0.020
 K0I  plan-3  C21  0.020
 K0I  plan-3  C20  0.020
 K0I  plan-3  C15  0.020
 K0I  plan-3  C14  0.020
 K0I  plan-3  C19  0.020
 K0I  plan-3  C18  0.020
 K0I  plan-3  C17  0.020
 K0I  plan-3  C16  0.020
 K0I  plan-3  H19  0.020
 K0I  plan-3  H16  0.020
 K0I  plan-3  H18  0.020
 K0I  plan-3  H17  0.020
 K0I  plan-4  C3   0.020
 K0I  plan-4  N1   0.020
 K0I  plan-4  C4   0.020
 K0I  plan-4  HA   0.020
 K0I  plan-5  O2   0.020
 K0I  plan-5  C1   0.020
 K0I  plan-5  O1   0.020
 K0I  plan-5  C2   0.020

