# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 11:16:20 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (4aS)-5-[(2,4-diaminopteridin-6-yl)methyl]-4a,5-dihydro-2H-dibenzo[b,f]azepin-8-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2nc(CN3[C@H]4C=CCC=C4C=Cc5cc(O)ccc35)cnc2n1
#
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
 Q22  Q22  (4aS)-5-[(2,4-diaminopteridin-6-yl)methyl]-4a,5-dihydro-2H-dibenzo[b,f]azepin-8-ol  ligand  48  29  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q22
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
 Q22  C7'   C  CR16  0  -0.109  -1.9989   0.6045  -2.2735
 Q22  N8'   N  N     0  -0.392  -3.2865   0.7530  -2.0797
 Q22  C8    C  CR66  0   0.390  -3.7874   0.3052  -0.9114
 Q22  N1'   N  N     0  -0.511  -5.0999   0.4425  -0.6781
 Q22  C2'   C  CR6   0   0.547  -5.5266  -0.0090   0.4921
 Q22  N2'   N  NH2   0  -0.814  -6.8326   0.1197   0.7672
 Q22  N3'   N  N     0  -0.502  -4.7892  -0.5828   1.4719
 Q22  C4'   C  CR6   0   0.480  -3.5018  -0.7266   1.2599
 Q22  N4'   N  NH2   0  -0.806  -2.7188  -1.2751   2.1812
 Q22  C4    C  CR66  0   0.007  -2.9125  -0.2830   0.0183
 Q22  N5'   N  N     0  -0.370  -1.6109  -0.4344  -0.1993
 Q22  C6'   C  CR6   0   0.165  -1.1297   0.0019  -1.3409
 Q22  C9'   C  CH2   0  -0.352   0.3391  -0.1679  -1.6381
 Q22  N'0   N  NT    0  -0.519   1.1554   0.0514  -0.4701
 Q22  C'0   C  CH1   0  -0.160   1.2112   1.4064   0.0456
 Q22  C'1   C  C1    0  -0.193   0.8325   1.4504   1.5011
 Q22  C'2   C  C1    0  -0.246   1.4042   2.2546   2.3891
 Q22  C'3   C  CH2   0  -0.503   2.5110   3.1931   2.0366
 Q22  C'4   C  C1    0  -0.284   3.0760   2.9294   0.6799
 Q22  C'5   C  C     0   0.047   2.5316   2.1006  -0.2120
 Q22  C'6   C  C1    0  -0.262   3.2225   1.8300  -1.4884
 Q22  C6    C  C1    0  -0.263   3.6430   0.6168  -1.8574
 Q22  C'7   C  CR6   0   0.131   3.4597  -0.5877  -1.0414
 Q22  C'8   C  CR16  0  -0.466   4.4846  -1.5304  -0.9707
 Q22  C7    C  CR6   0   0.207   2.2778  -0.7921  -0.3159
 Q22  C9    C  CR16  0  -0.264   2.1749  -1.9188   0.4924
 Q22  C11   C  CR16  0  -0.357   3.2006  -2.8454   0.5833
 Q22  C'9   C  CR6   0   0.373   4.3622  -2.6552  -0.1621
 Q22  O1    O  OH1   0  -0.635   5.3316  -3.5879  -0.0670
 Q22  H7'   H  HCR6  0   0.273  -1.5969   0.9771  -3.2108
 Q22  HN2'  H  HNH2  0   0.398  -7.4658   0.4407   0.0566
 Q22  HN2A  H  HNH2  0   0.399  -7.2162  -0.3005   1.5945
 Q22  HN4'  H  HNH2  0   0.408  -3.1019  -1.6221   3.0437
 Q22  HN4A  H  HNH2  0   0.416  -1.7410  -1.4145   1.9902
 Q22  H9'   H  HCH2  0   0.270   0.5028  -1.1928  -1.9807
 Q22  H9'A  H  HCH2  0   0.233   0.6064   0.4780  -2.4870
 Q22  H'0   H  HCH1  0   0.260   0.4435   1.9665  -0.5081
 Q22  H'1   H  H     0   0.240   0.0250   0.7882   1.7926
 Q22  H'2   H  H     0   0.242   1.0665   2.2484   3.4195
 Q22  H'3   H  HCH2  0   0.256   2.1571   4.2299   2.1017
 Q22  H'3A  H  HCH2  0   0.249   3.3097   3.1305   2.7832
 Q22  H'4   H  H     0   0.243   4.0091   3.4279   0.4365
 Q22  H6    H  H     0   0.256   4.2278   0.5164  -2.7657
 Q22  H'8   H  HCR6  0   0.266   5.3891  -1.3771  -1.5516
 Q22  H9    H  HCR6  0   0.253   1.2547  -2.0748   1.0418
 Q22  H11   H  HCR6  0   0.261   3.1007  -3.7194   1.2148
 Q22  HO1   H  HOH1  0   0.474   6.0789  -3.3551  -0.6291
 Q22  H19   H  H     0   0.260   3.4711   2.6790  -2.1170

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
 Q22  C7'  N8'   aromatic  1.311  0.020  1.311
 Q22  C7'  C6'   aromatic  1.410  0.020  1.410
 Q22  C7'  H7'   single    0.930  0.020  1.080
 Q22  N8'  C8    aromatic  1.348  0.020  1.348
 Q22  C8   N1'   aromatic  1.340  0.020  1.340
 Q22  C8   C4    aromatic  1.406  0.020  1.406
 Q22  N1'  C2'   aromatic  1.325  0.020  1.325
 Q22  C2'  N2'   single    1.341  0.020  1.341
 Q22  C2'  N3'   aromatic  1.354  0.020  1.354
 Q22  N2'  HN2'  single    0.860  0.020  1.020
 Q22  N2'  HN2A  single    0.860  0.020  1.020
 Q22  N3'  C4'   aromatic  1.313  0.020  1.313
 Q22  C4'  N4'   single    1.328  0.020  1.328
 Q22  C4'  C4    aromatic  1.444  0.020  1.444
 Q22  N4'  HN4'  single    0.860  0.020  1.020
 Q22  N4'  HN4A  single    0.860  0.020  1.020
 Q22  C4   N5'   aromatic  1.328  0.020  1.328
 Q22  N5'  C6'   aromatic  1.313  0.020  1.313
 Q22  C6'  C9'   single    1.508  0.020  1.508
 Q22  C9'  N'0   single    1.442  0.020  1.442
 Q22  C9'  H9'   single    0.970  0.020  1.090
 Q22  C9'  H9'A  single    0.970  0.020  1.090
 Q22  N'0  C'0   single    1.451  0.020  1.451
 Q22  N'0  C7    single    1.412  0.020  1.412
 Q22  C'0  C'1   single    1.505  0.020  1.505
 Q22  C'0  C'5   single    1.514  0.020  1.514
 Q22  C'0  H'0   single    0.970  0.020  1.090
 Q22  C'1  C'2   double    1.327  0.020  1.327
 Q22  C'1  H'1   single    0.930  0.020  1.080
 Q22  C'2  C'3   single    1.493  0.020  1.493
 Q22  C'2  H'2   single    0.930  0.020  1.080
 Q22  C'3  C'4   single    1.493  0.020  1.493
 Q22  C'3  H'3   single    0.970  0.020  1.090
 Q22  C'3  H'3A  single    0.970  0.020  1.090
 Q22  C'4  C'5   double    1.334  0.020  1.334
 Q22  C'4  H'4   single    0.930  0.020  1.080
 Q22  C'5  C'6   single    1.476  0.020  1.476
 Q22  C'6  C6    double    1.336  0.020  1.336
 Q22  C6   C'7   single    1.466  0.020  1.466
 Q22  C6   H6    single    0.930  0.020  1.080
 Q22  C'7  C'8   aromatic  1.394  0.020  1.394
 Q22  C'7  C7    aromatic  1.402  0.020  1.402
 Q22  C'8  C'9   aromatic  1.391  0.020  1.391
 Q22  C'8  H'8   single    0.930  0.020  1.080
 Q22  C7   C9    aromatic  1.390  0.020  1.390
 Q22  C9   C11   aromatic  1.385  0.020  1.385
 Q22  C9   H9    single    0.930  0.020  1.080
 Q22  C11  C'9   aromatic  1.393  0.020  1.393
 Q22  C11  H11   single    0.930  0.020  1.080
 Q22  C'9  O1    single    1.349  0.020  1.349
 Q22  O1   HO1   single    0.850  0.020  0.980
 Q22  C'6  H19   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
 Q22  H7'   C7'  C6'   119.30  3.000
 Q22  H7'   C7'  N8'   116.91  3.000
 Q22  C6'   C7'  N8'   123.79  3.000
 Q22  C8    N8'  C7'   117.11  3.000
 Q22  C4    C8   N1'   122.50  3.000
 Q22  C4    C8   N8'   118.75  3.000
 Q22  N1'   C8   N8'   118.74  3.000
 Q22  C2'   N1'  C8    115.74  3.000
 Q22  N3'   C2'  N2'   115.01  3.000
 Q22  N3'   C2'  N1'   127.46  3.000
 Q22  N2'   C2'  N1'   117.53  3.000
 Q22  HN2A  N2'  HN2'  118.41  3.000
 Q22  HN2A  N2'  C2'   120.06  3.000
 Q22  HN2'  N2'  C2'   119.97  3.000
 Q22  C4'   N3'  C2'   117.63  3.000
 Q22  C4    C4'  N4'   118.87  3.000
 Q22  C4    C4'  N3'   120.36  3.000
 Q22  N4'   C4'  N3'   120.77  3.000
 Q22  HN4A  N4'  HN4'  119.03  3.000
 Q22  HN4A  N4'  C4'   119.92  3.000
 Q22  HN4'  N4'  C4'   120.87  3.000
 Q22  N5'   C4   C4'   120.38  3.000
 Q22  N5'   C4   C8    123.32  3.000
 Q22  C4'   C4   C8    116.31  3.000
 Q22  C6'   N5'  C4    117.62  3.000
 Q22  C9'   C6'  N5'   119.39  3.000
 Q22  C9'   C6'  C7'   121.21  3.000
 Q22  N5'   C6'  C7'   119.40  3.000
 Q22  H9'A  C9'  H9'   105.81  3.000
 Q22  H9'A  C9'  N'0   113.48  3.000
 Q22  H9'   C9'  N'0   108.16  3.000
 Q22  H9'A  C9'  C6'   108.83  3.000
 Q22  H9'   C9'  C6'   108.25  3.000
 Q22  N'0   C9'  C6'   112.00  3.000
 Q22  C7    N'0  C'0   119.23  3.000
 Q22  C7    N'0  C9'   116.59  3.000
 Q22  C'0   N'0  C9'   116.85  3.000
 Q22  H'0   C'0  C'5   106.84  3.000
 Q22  H'0   C'0  C'1   107.25  3.000
 Q22  C'5   C'0  C'1   111.76  3.000
 Q22  H'0   C'0  N'0   105.65  3.000
 Q22  C'5   C'0  N'0   113.66  3.000
 Q22  C'1   C'0  N'0   111.19  3.000
 Q22  H'1   C'1  C'2   120.72  3.000
 Q22  H'1   C'1  C'0   115.45  3.000
 Q22  C'2   C'1  C'0   123.81  3.000
 Q22  H'2   C'2  C'3   117.30  3.000
 Q22  H'2   C'2  C'1   119.88  3.000
 Q22  C'3   C'2  C'1   122.82  3.000
 Q22  H'3A  C'3  H'3   104.40  3.000
 Q22  H'3A  C'3  C'4   109.48  3.000
 Q22  H'3   C'3  C'4   110.04  3.000
 Q22  H'3A  C'3  C'2   110.11  3.000
 Q22  H'3   C'3  C'2   109.92  3.000
 Q22  C'4   C'3  C'2   112.58  3.000
 Q22  H'4   C'4  C'5   119.09  3.000
 Q22  H'4   C'4  C'3   116.61  3.000
 Q22  C'5   C'4  C'3   124.26  3.000
 Q22  C'6   C'5  C'4   120.07  3.000
 Q22  C'6   C'5  C'0   118.11  3.000
 Q22  C'4   C'5  C'0   121.82  3.000
 Q22  H19   C'6  C6    118.58  3.000
 Q22  H19   C'6  C'5   117.68  3.000
 Q22  C6    C'6  C'5   123.54  3.000
 Q22  H6    C6   C'7   117.21  3.000
 Q22  H6    C6   C'6   119.00  3.000
 Q22  C'7   C6   C'6   123.57  3.000
 Q22  C7    C'7  C'8   119.66  3.000
 Q22  C7    C'7  C6    120.87  3.000
 Q22  C'8   C'7  C6    119.45  3.000
 Q22  H'8   C'8  C'9   119.90  3.000
 Q22  H'8   C'8  C'7   119.32  3.000
 Q22  C'9   C'8  C'7   120.77  3.000
 Q22  C9    C7   C'7   118.78  3.000
 Q22  C9    C7   N'0   119.24  3.000
 Q22  C'7   C7   N'0   121.76  3.000
 Q22  H9    C9   C11   119.97  3.000
 Q22  H9    C9   C7    118.33  3.000
 Q22  C11   C9   C7    121.69  3.000
 Q22  H11   C11  C'9   119.94  3.000
 Q22  H11   C11  C9    120.65  3.000
 Q22  C'9   C11  C9    119.40  3.000
 Q22  O1    C'9  C11   117.85  3.000
 Q22  O1    C'9  C'8   122.49  3.000
 Q22  C11   C'9  C'8   119.66  3.000
 Q22  HO1   O1   C'9   110.44  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
 Q22  CONST_01  N1'   C8   N8'  C7'  180.00   0.0  0
 Q22  CONST_02  C4    C8   N8'  C7'    0.00   0.0  0
 Q22  CONST_03  C4    N5'  C6'  C7'    0.00   0.0  0
 Q22  CONST_04  N5'   C6'  C7'  N8'    0.00   0.0  0
 Q22  CONST_05  C2'   N1'  C8   N8'  180.00   0.0  0
 Q22  CONST_06  C4'   C4   C8   N8'  180.00   0.0  0
 Q22  CONST_07  N5'   C4   C8   N8'    0.00   0.0  0
 Q22  CONST_08  C6'   C7'  N8'  C8     0.00   0.0  0
 Q22  CONST_09  N3'   C2'  N1'  C8     0.00   0.0  0
 Q22  CONST_10  N3'   C4'  C4   C8     0.00   0.0  0
 Q22  CONST_11  C6'   N5'  C4   C8     0.00   0.0  0
 Q22  CONST_12  C4'   C4   C8   N1'    0.00   0.0  0
 Q22  CONST_13  N5'   C4   C8   N1'  180.00   0.0  0
 Q22  CONST_14  C4'   N3'  C2'  N1'    0.00   0.0  0
 Q22  CONST_15  C4    C8   N1'  C2'    0.00   0.0  0
 Q22  CONST_16  C4    C4'  N3'  C2'    0.00   0.0  0
 Q22  CONST_17  N5'   C4   C4'  N3'  180.00   0.0  0
 Q22  CONST_18  C6'   N5'  C4   C4'  180.00   0.0  0
 Q22  CONST_19  C11   C'9  C'8  C'7    0.00   0.0  0
 Q22  CONST_20  C9    C11  C'9  C'8    0.00   0.0  0
 Q22  CONST_21  C'9   C11  C9   C7     0.00   0.0  0
 Q22  CONST_22  C9'   C6'  C7'  N8'  180.00   0.0  0
 Q22  CONST_23  N2'   C2'  N1'  C8   180.00   0.0  0
 Q22  CONST_24  N4'   C4'  C4   C8   180.00   0.0  0
 Q22  CONST_25  N4'   C4'  N3'  C2'  180.00   0.0  0
 Q22  CONST_26  C4'   N3'  C2'  N2'  180.00   0.0  0
 Q22  CONST_27  N5'   C4   C4'  N4'    0.00   0.0  0
 Q22  CONST_28  C9'   C6'  N5'  C4   180.00   0.0  0
 Q22  CONST_29  O1    C'9  C'8  C'7  180.00   0.0  0
 Q22  CONST_30  O1    C'9  C11  C9   180.00   0.0  0
 Q22  CONST_31  H7'   C7'  N8'  C8   180.00   0.0  0
 Q22  CONST_32  H11   C11  C'9  C'8  180.00   0.0  0
 Q22  CONST_33  H'8   C'8  C'9  C11  180.00   0.0  0
 Q22  CONST_34  H9    C9   C11  C'9  180.00   0.0  0
 Q22  CONST_35  HN2'  N2'  C2'  N1'    0.00   0.0  0
 Q22  CONST_36  HN2A  N2'  C2'  N1'  180.00   0.0  0
 Q22  CONST_37  HN4'  N4'  C4'  N3'    0.00   0.0  0
 Q22  CONST_38  HN4A  N4'  C4'  N3'  180.00   0.0  0
 Q22  Var_01    C'3   C'2  C'1  C'0   -1.09  30.0  1
 Q22  Var_02    C'4   C'3  C'2  C'1  -11.64  30.0  1
 Q22  Var_03    C'5   C'4  C'3  C'2   10.08  30.0  1
 Q22  Var_04    N'0   C9'  C6'  C7'  142.10  30.0  2

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
 Q22  chir_01  C'0  N'0  C'1  C'5  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
 Q22  plan-1  C7'   0.020
 Q22  plan-1  N8'   0.020
 Q22  plan-1  C8    0.020
 Q22  plan-1  N1'   0.020
 Q22  plan-1  C2'   0.020
 Q22  plan-1  N2'   0.020
 Q22  plan-1  N3'   0.020
 Q22  plan-1  C4'   0.020
 Q22  plan-1  N4'   0.020
 Q22  plan-1  C4    0.020
 Q22  plan-1  N5'   0.020
 Q22  plan-1  C6'   0.020
 Q22  plan-1  C9'   0.020
 Q22  plan-1  H7'   0.020
 Q22  plan-2  N'0   0.020
 Q22  plan-2  C6    0.020
 Q22  plan-2  C'7   0.020
 Q22  plan-2  C'8   0.020
 Q22  plan-2  C7    0.020
 Q22  plan-2  C9    0.020
 Q22  plan-2  C11   0.020
 Q22  plan-2  C'9   0.020
 Q22  plan-2  O1    0.020
 Q22  plan-2  H'8   0.020
 Q22  plan-2  H9    0.020
 Q22  plan-2  H11   0.020
 Q22  plan-3  C2'   0.020
 Q22  plan-3  N2'   0.020
 Q22  plan-3  HN2'  0.020
 Q22  plan-3  HN2A  0.020
 Q22  plan-4  C4'   0.020
 Q22  plan-4  N4'   0.020
 Q22  plan-4  HN4'  0.020
 Q22  plan-4  HN4A  0.020

