# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:24:40 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 7-[(3S)-3-(aminomethyl)pyrrolidin-1-yl]-6-(2,6-dichlorophenyl)pyrido[2,3-d]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1CCN(C1)c2nc3nc(N)ncc3cc2c4c(Cl)cccc4Cl
#
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
 MQM  MQM  7-[(3S)-3-(aminomethyl)pyrrolidin-1-yl]-6-(2,6-dichlorophenyl)pyrido[2,3-d]pyrimidin-2-amine  ligand  44  26  .  2021-08-14  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MQM
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
 MQM  C4   C   CR66  0   0.379   2.6295   0.4084   0.0384
 MQM  C5   C   CR66  0  -0.126   2.5889  -1.0035   0.0926
 MQM  C6   C   CR16  0  -0.040   3.8226  -1.6639   0.1566
 MQM  N1   N   N     0  -0.461   4.9657  -1.0350   0.1634
 MQM  N3   N   N     0  -0.485   3.8040   1.0576   0.0390
 MQM  CAT  C   CR6   0  -0.119  -1.6628  -1.5974  -1.5698
 MQM  CAU  C   CR16  0  -0.191  -2.8234  -2.2970  -1.8555
 MQM  CAV  C   CR16  0  -0.281  -3.4288  -3.0342  -0.8509
 MQM  CAW  C   CR16  0  -0.192  -2.8836  -3.0677   0.4224
 MQM  CAX  C   CR6   0  -0.108  -1.7241  -2.3542   0.6778
 MQM  CLZ  CL  CL    0  -0.106  -1.0876  -2.3653   2.2868
 MQM  CAS  C   CR6   0   0.184  -1.0820  -1.5967  -0.3013
 MQM  CAH  C   CR6   0  -0.072   0.1907  -0.8876  -0.0509
 MQM  CAG  C   CR16  0  -0.188   1.3326  -1.6289   0.0259
 MQM  C2   C   CR6   0   0.546   4.9014   0.3231   0.0991
 MQM  NAK  N   NH2   0  -0.815   6.0855   0.9522   0.0804
 MQM  NAJ  N   N     0  -0.505   1.5148   1.1418  -0.0018
 MQM  CAI  C   CR6   0   0.512   0.3262   0.5507  -0.0064
 MQM  NAL  N   NR5   0  -0.497  -0.7319   1.3789   0.0128
 MQM  CAM  C   CH2   0  -0.232  -0.5391   2.8223  -0.0797
 MQM  CAP  C   CH2   0  -0.282  -2.1120   1.0433   0.3582
 MQM  CAO  C   CH2   0  -0.465  -2.7037   2.3806   0.7831
 MQM  CAN  C   CR15  0  -0.288  -1.9554   3.3837  -0.0884
 MQM  CAQ  C   CH2   0  -0.276  -2.0233   4.8238   0.3862
 MQM  NAR  N   NH2   0  -0.804  -3.3792   5.3420   0.2922
 MQM  H1   H   HCR6  0   0.273   3.8528  -2.7495   0.2007
 MQM  H2   H   HCR6  0   0.287  -3.2455  -2.2718  -2.8504
 MQM  H3   H   HCR6  0   0.281  -4.3351  -3.5855  -1.0608
 MQM  H4   H   HCR6  0   0.288  -3.3563  -3.6402   1.2080
 MQM  H5   H   HCR6  0   0.272   1.2773  -2.7111  -0.0091
 MQM  H6   H   HNH2  0   0.399   6.1247   1.9548   0.1278
 MQM  H7   H   HNH2  0   0.400   6.9322   0.4331   0.2301
 MQM  H8   H   HCH2  0   0.226   0.0255   3.1961   0.7820
 MQM  H9   H   HCH2  0   0.248   0.0233   3.0864  -0.9759
 MQM  H10  H   HCH2  0   0.245  -2.6570   0.6454  -0.5011
 MQM  H11  H   HCH2  0   0.253  -2.1563   0.3098   1.1624
 MQM  H12  H   HCH2  0   0.255  -3.7849   2.4024   0.6480
 MQM  H13  H   HCH2  0   0.236  -2.4911   2.5680   1.8401
 MQM  H14  H   HCR5  0   0.240  -2.3523   3.3332  -1.1082
 MQM  H15  H   HCH2  0   0.190  -1.5972   4.8782   1.3999
 MQM  H16  H   HCH2  0   0.228  -1.3808   5.4378  -0.2505
 MQM  H17  H   HNH2  0   0.345  -3.9614   4.9033   0.9952
 MQM  H18  H   HNH2  0   0.350  -3.3788   6.3276   0.5205
 MQM  CLY  CL  CL    0  -0.103  -0.9169  -0.6793  -2.8313

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
 MQM  CAO  CAN  single    1.525  0.020  1.525
 MQM  CAO  CAP  single    1.523  0.020  1.523
 MQM  CAN  CAM  single    1.524  0.020  1.524
 MQM  CAN  CAQ  single    1.518  0.020  1.518
 MQM  CAM  NAL  single    1.459  0.020  1.459
 MQM  NAR  CAQ  single    1.455  0.020  1.455
 MQM  CAP  NAL  single    1.462  0.020  1.462
 MQM  NAL  CAI  single    1.344  0.020  1.344
 MQM  CLZ  CAX  single    1.730  0.020  1.730
 MQM  NAJ  CAI  aromatic  1.328  0.020  1.328
 MQM  NAJ  C4   aromatic  1.335  0.020  1.335
 MQM  CAI  CAH  aromatic  1.445  0.020  1.445
 MQM  N3   C4   aromatic  1.342  0.020  1.342
 MQM  N3   C2   aromatic  1.322  0.020  1.322
 MQM  CAX  CAW  aromatic  1.385  0.020  1.385
 MQM  CAX  CAS  aromatic  1.395  0.020  1.395
 MQM  C4   C5   aromatic  1.414  0.020  1.414
 MQM  CAW  CAV  aromatic  1.386  0.020  1.386
 MQM  CAH  CAS  single    1.478  0.020  1.478
 MQM  CAH  CAG  aromatic  1.364  0.020  1.364
 MQM  NAK  C2   single    1.341  0.020  1.341
 MQM  CAS  CAT  aromatic  1.395  0.020  1.395
 MQM  C2   N1   aromatic  1.361  0.020  1.361
 MQM  C5   CAG  aromatic  1.405  0.020  1.405
 MQM  C5   C6   aromatic  1.401  0.020  1.401
 MQM  CAV  CAU  aromatic  1.385  0.020  1.385
 MQM  CAT  CAU  aromatic  1.385  0.020  1.385
 MQM  CAT  CLY  single    1.729  0.020  1.729
 MQM  N1   C6   aromatic  1.305  0.020  1.305
 MQM  C6   H1   single    0.930  0.020  1.080
 MQM  CAU  H2   single    0.930  0.020  1.080
 MQM  CAV  H3   single    0.930  0.020  1.080
 MQM  CAW  H4   single    0.930  0.020  1.080
 MQM  CAG  H5   single    0.930  0.020  1.080
 MQM  NAK  H6   single    0.860  0.020  1.020
 MQM  NAK  H7   single    0.860  0.020  1.020
 MQM  CAM  H8   single    0.970  0.020  1.090
 MQM  CAM  H9   single    0.970  0.020  1.090
 MQM  CAP  H10  single    0.970  0.020  1.090
 MQM  CAP  H11  single    0.970  0.020  1.090
 MQM  CAO  H12  single    0.970  0.020  1.090
 MQM  CAO  H13  single    0.970  0.020  1.090
 MQM  CAN  H14  single    0.970  0.020  1.090
 MQM  CAQ  H15  single    0.970  0.020  1.090
 MQM  CAQ  H16  single    0.970  0.020  1.090
 MQM  NAR  H17  single    0.890  0.020  1.040
 MQM  NAR  H18  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
 MQM  NAJ  C4   N3   117.71  3.000
 MQM  N3   C4   C5   120.56  3.000
 MQM  NAJ  C4   C5   121.73  3.000
 MQM  CAG  C5   C6   125.44  3.000
 MQM  C6   C5   C4   116.57  3.000
 MQM  CAG  C5   C4   117.94  3.000
 MQM  H1   C6   N1   117.19  3.000
 MQM  H1   C6   C5   119.81  3.000
 MQM  N1   C6   C5   123.00  3.000
 MQM  C2   N1   C6   116.06  3.000
 MQM  C2   N3   C4   117.24  3.000
 MQM  CAS  CAT  CAU  122.46  3.000
 MQM  CAU  CAT  CLY  118.63  3.000
 MQM  CAS  CAT  CLY  118.91  3.000
 MQM  H2   CAU  CAV  120.61  3.000
 MQM  H2   CAU  CAT  120.35  3.000
 MQM  CAV  CAU  CAT  119.04  3.000
 MQM  H3   CAV  CAW  119.73  3.000
 MQM  H3   CAV  CAU  119.78  3.000
 MQM  CAW  CAV  CAU  120.49  3.000
 MQM  H4   CAW  CAX  120.32  3.000
 MQM  H4   CAW  CAV  120.57  3.000
 MQM  CAX  CAW  CAV  119.11  3.000
 MQM  CAS  CAX  CLZ  119.14  3.000
 MQM  CAS  CAX  CAW  122.39  3.000
 MQM  CLZ  CAX  CAW  118.43  3.000
 MQM  CAH  CAS  CAX  122.55  3.000
 MQM  CAH  CAS  CAT  120.85  3.000
 MQM  CAX  CAS  CAT  116.51  3.000
 MQM  CAI  CAH  CAG  117.43  3.000
 MQM  CAG  CAH  CAS  118.02  3.000
 MQM  CAI  CAH  CAS  124.28  3.000
 MQM  H5   CAG  CAH  119.87  3.000
 MQM  H5   CAG  C5   119.44  3.000
 MQM  CAH  CAG  C5   120.63  3.000
 MQM  NAK  C2   N3   118.15  3.000
 MQM  NAK  C2   N1   115.27  3.000
 MQM  N3   C2   N1   126.57  3.000
 MQM  H7   NAK  H6   118.42  3.000
 MQM  H7   NAK  C2   119.99  3.000
 MQM  H6   NAK  C2   120.13  3.000
 MQM  CAI  NAJ  C4   120.21  3.000
 MQM  NAL  CAI  NAJ  115.50  3.000
 MQM  NAJ  CAI  CAH  121.81  3.000
 MQM  NAL  CAI  CAH  122.68  3.000
 MQM  CAP  NAL  CAM  111.52  3.000
 MQM  CAP  NAL  CAI  127.25  3.000
 MQM  CAM  NAL  CAI  120.31  3.000
 MQM  H9   CAM  H8   107.33  3.000
 MQM  H9   CAM  CAN  112.67  3.000
 MQM  H8   CAM  CAN  110.96  3.000
 MQM  H9   CAM  NAL  111.09  3.000
 MQM  H8   CAM  NAL  110.83  3.000
 MQM  CAN  CAM  NAL  104.01  3.000
 MQM  H11  CAP  H10  108.36  3.000
 MQM  H11  CAP  CAO  111.69  3.000
 MQM  H10  CAP  CAO  110.21  3.000
 MQM  H11  CAP  NAL  111.56  3.000
 MQM  H10  CAP  NAL  111.64  3.000
 MQM  CAO  CAP  NAL  103.37  3.000
 MQM  H13  CAO  H12  108.00  3.000
 MQM  H13  CAO  CAN  110.12  3.000
 MQM  H12  CAO  CAN  113.76  3.000
 MQM  H13  CAO  CAP  110.14  3.000
 MQM  H12  CAO  CAP  111.62  3.000
 MQM  CAN  CAO  CAP  103.15  3.000
 MQM  H14  CAN  CAQ  108.58  3.000
 MQM  H14  CAN  CAO  108.89  3.000
 MQM  CAQ  CAN  CAO  115.05  3.000
 MQM  H14  CAN  CAM  108.98  3.000
 MQM  CAQ  CAN  CAM  112.92  3.000
 MQM  CAO  CAN  CAM  102.15  3.000
 MQM  H16  CAQ  H15  106.32  3.000
 MQM  H16  CAQ  NAR  108.07  3.000
 MQM  H15  CAQ  NAR  113.74  3.000
 MQM  H16  CAQ  CAN  108.94  3.000
 MQM  H15  CAQ  CAN  108.51  3.000
 MQM  NAR  CAQ  CAN  111.07  3.000
 MQM  H18  NAR  H17  105.40  3.000
 MQM  H18  NAR  CAQ  109.40  3.000
 MQM  H17  NAR  CAQ  109.68  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
 MQM  CONST_01  CAH  CAI  NAJ  C4      0.00   0.0  0
 MQM  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 MQM  CONST_03  CAH  CAG  C5   C4      0.00   0.0  0
 MQM  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 MQM  CONST_05  CAI  NAJ  C4   C5      0.00   0.0  0
 MQM  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 MQM  CONST_07  CAI  CAH  CAG  C5      0.00   0.0  0
 MQM  CONST_08  CAS  CAH  CAG  C5    180.00   0.0  0
 MQM  CONST_09  C2   N1   C6   C5      0.00   0.0  0
 MQM  CONST_10  NAJ  C4   C5   C6    180.00   0.0  0
 MQM  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 MQM  CONST_12  CAH  CAG  C5   C6    180.00   0.0  0
 MQM  CONST_13  N3   C2   N1   C6      0.00   0.0  0
 MQM  CONST_14  CAG  C5   C6   N1    180.00   0.0  0
 MQM  CONST_15  CAI  NAJ  C4   N3    180.00   0.0  0
 MQM  CONST_16  CAG  C5   C4   N3    180.00   0.0  0
 MQM  CONST_17  CAW  CAX  CAS  CAT     0.00   0.0  0
 MQM  CONST_20  CAW  CAV  CAU  CAT     0.00   0.0  0
 MQM  CONST_21  CAX  CAW  CAV  CAU     0.00   0.0  0
 MQM  CONST_22  CAX  CAS  CAT  CAU     0.00   0.0  0
 MQM  CONST_23  CAH  CAS  CAT  CAU   180.00   0.0  0
 MQM  CONST_24  CAS  CAX  CAW  CAV     0.00   0.0  0
 MQM  CONST_25  CAS  CAT  CAU  CAV     0.00   0.0  0
 MQM  CONST_26  CAH  CAS  CAX  CAW   180.00   0.0  0
 MQM  CONST_29  NAJ  CAI  CAH  CAS   180.00   0.0  0
 MQM  CONST_30  NAJ  CAI  CAH  CAG     0.00   0.0  0
 MQM  CONST_31  NAJ  C4   C5   CAG     0.00   0.0  0
 MQM  CONST_32  NAJ  C4   N3   C2    180.00   0.0  0
 MQM  CONST_33  NAL  CAI  NAJ  C4    180.00   0.0  0
 MQM  CONST_34  NAL  CAI  CAH  CAS     0.00   0.0  0
 MQM  CONST_35  NAL  CAI  CAH  CAG   180.00   0.0  0
 MQM  CONST_36  NAK  C2   N3   C4    180.00   0.0  0
 MQM  CONST_37  NAK  C2   N1   C6    180.00   0.0  0
 MQM  CONST_38  CAX  CAS  CAT  CLY   180.00   0.0  0
 MQM  CONST_39  CAH  CAS  CAT  CLY     0.00   0.0  0
 MQM  CONST_40  CAV  CAU  CAT  CLY   180.00   0.0  0
 MQM  CONST_41  CLZ  CAX  CAS  CAT   180.00   0.0  0
 MQM  CONST_42  CLZ  CAX  CAW  CAV   180.00   0.0  0
 MQM  CONST_43  CAH  CAS  CAX  CLZ     0.00   0.0  0
 MQM  CONST_44  H5   CAG  C5   C4    180.00   0.0  0
 MQM  CONST_45  H1   C6   C5   C4    180.00   0.0  0
 MQM  CONST_46  H3   CAV  CAU  CAT   180.00   0.0  0
 MQM  CONST_47  H4   CAW  CAV  CAU   180.00   0.0  0
 MQM  CONST_48  H2   CAU  CAV  CAW   180.00   0.0  0
 MQM  CONST_49  H6   NAK  C2   N1    180.00   0.0  0
 MQM  CONST_50  H7   NAK  C2   N1      0.00   0.0  0
 MQM  Var_01    CAM  NAL  CAI  CAH  -173.74  30.0  1
 MQM  Var_02    CAN  CAM  NAL  CAI   177.49  30.0  1
 MQM  Var_03    CAO  CAP  NAL  CAI   156.69  30.0  1
 MQM  Var_04    CAN  CAO  CAP  NAL    32.17  30.0  1
 MQM  Var_05    H17  NAR  CAQ  CAN    70.78  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
 MQM  chir_01  CAN  CAO  CAM  CAQ  positiv

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
 MQM  plan-1  CAT  0.020
 MQM  plan-1  CAU  0.020
 MQM  plan-1  CAV  0.020
 MQM  plan-1  CAW  0.020
 MQM  plan-1  CAX  0.020
 MQM  plan-1  CLZ  0.020
 MQM  plan-1  CAS  0.020
 MQM  plan-1  CAH  0.020
 MQM  plan-1  H2   0.020
 MQM  plan-1  H3   0.020
 MQM  plan-1  H4   0.020
 MQM  plan-1  CLY  0.020
 MQM  plan-2  C4   0.020
 MQM  plan-2  C5   0.020
 MQM  plan-2  C6   0.020
 MQM  plan-2  N1   0.020
 MQM  plan-2  N3   0.020
 MQM  plan-2  CAS  0.020
 MQM  plan-2  CAH  0.020
 MQM  plan-2  CAG  0.020
 MQM  plan-2  C2   0.020
 MQM  plan-2  NAK  0.020
 MQM  plan-2  NAJ  0.020
 MQM  plan-2  CAI  0.020
 MQM  plan-2  NAL  0.020
 MQM  plan-2  H1   0.020
 MQM  plan-2  H5   0.020
 MQM  plan-3  C2   0.020
 MQM  plan-3  NAK  0.020
 MQM  plan-3  H6   0.020
 MQM  plan-3  H7   0.020

