# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:24:41 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 7-[(3R)-3-aminopyrrolidin-1-yl]-6-(naphthalen-1-yl)pyrido[2,3-d]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCN(C1)c2nc3nc(N)ncc3cc2c4cccc5ccccc45
#
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
 MV4  MV4  7-[(3R)-3-aminopyrrolidin-1-yl]-6-(naphthalen-1-yl)pyrido[2,3-d]pyrimidin-2-amine  ligand  47  27  .  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_MV4
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
 MV4  C4   C  CR66  0   0.374  -2.8146   0.0050   0.3060
 MV4  C5   C  CR66  0  -0.123  -2.3235   1.3017   0.5766
 MV4  C6   C  CR16  0  -0.043  -3.2544   2.2376   1.0449
 MV4  N1   N  N     0  -0.461  -4.5158   1.9550   1.2306
 MV4  N3   N  N     0  -0.484  -4.1117  -0.2872   0.4908
 MV4  CAZ  C  CH2   0  -0.286   1.4657  -1.9489  -0.5543
 MV4  CAY  C  CH2   0  -0.478   1.6641  -3.4526  -0.4382
 MV4  CAX  C  CR15  0  -0.126   0.5212  -4.0199  -1.2806
 MV4  NBA  N  NH2   0  -0.795   0.1605  -5.4085  -1.0970
 MV4  CAW  C  CH2   0  -0.247  -0.6318  -3.0921  -0.9132
 MV4  NAV  N  NR5   0  -0.498   0.0126  -1.8066  -0.6836
 MV4  CAC  C  CR6   0   0.497  -0.7222  -0.7373  -0.3222
 MV4  NAD  N  N     0  -0.505  -2.0136  -0.9728  -0.1240
 MV4  C2   C  CR6   0   0.543  -4.8922   0.6813   0.9368
 MV4  NAK  N  NH2   0  -0.816  -6.1977   0.4142   1.1061
 MV4  CAA  C  CR16  0  -0.203  -0.9692   1.5640   0.3010
 MV4  CAB  C  CR6   0  -0.097  -0.1496   0.5835  -0.1773
 MV4  CAL  C  CR6   0   0.027   1.2047   0.9585  -0.6531
 MV4  CAM  C  CR66  0   0.107   2.2390   1.3231   0.2558
 MV4  CAR  C  CR16  0  -0.331   2.0733   1.2623   1.6606
 MV4  CAS  C  CR16  0  -0.255   3.0912   1.6142   2.5054
 MV4  CAT  C  CR16  0  -0.258   4.3305   2.0459   1.9906
 MV4  CAU  C  CR16  0  -0.313   4.5262   2.1033   0.6384
 MV4  CAN  C  CR66  0   0.113   3.4959   1.7389  -0.2607
 MV4  CAO  C  CR16  0  -0.328   3.6976   1.7740  -1.6597
 MV4  CAP  C  CR16  0  -0.245   2.6932   1.4109  -2.5125
 MV4  CAQ  C  CR16  0  -0.297   1.4434   1.0083  -2.0039
 MV4  H1   H  HCR6  0   0.272  -2.9347   3.2518   1.2690
 MV4  H2   H  HCH2  0   0.258   1.8381  -1.4166   0.3202
 MV4  H3   H  HCH2  0   0.246   1.9833  -1.5566  -1.4321
 MV4  H4   H  HCH2  0   0.252   2.6509  -3.7639  -0.7806
 MV4  H5   H  HCH2  0   0.233   1.5475  -3.7765   0.6004
 MV4  H6   H  HCR5  0   0.242   0.7641  -3.8779  -2.3389
 MV4  H7   H  HNH2  0   0.350   0.9283  -6.0014  -1.3858
 MV4  H8   H  HNH2  0   0.339   0.0175  -5.5959  -0.1111
 MV4  H10  H  HCH2  0   0.248  -1.3881  -3.0214  -1.6953
 MV4  H11  H  HCH2  0   0.226  -1.1317  -3.4500  -0.0052
 MV4  H12  H  HNH2  0   0.398  -6.7865   1.0874   1.5636
 MV4  H13  H  HNH2  0   0.397  -6.5234  -0.5346   1.0468
 MV4  H14  H  HCR6  0   0.268  -0.5857   2.5708   0.4281
 MV4  H15  H  HCR6  0   0.253   1.1303   0.9249   2.0700
 MV4  H16  H  HCR6  0   0.260   2.9463   1.5580   3.5764
 MV4  H17  H  HCR6  0   0.259   5.1266   2.3251   2.6685
 MV4  H18  H  HCR6  0   0.257   5.4784   2.4280   0.2366
 MV4  H19  H  HCR6  0   0.257   4.6582   2.0947  -2.0443
 MV4  H20  H  HCR6  0   0.260   2.8478   1.4390  -3.5831
 MV4  H21  H  HCR6  0   0.254   0.6544   0.7368  -2.6946

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
 MV4  CAP  CAO  aromatic  1.367  0.020  1.367
 MV4  CAP  CAQ  aromatic  1.408  0.020  1.408
 MV4  CAO  CAN  aromatic  1.414  0.020  1.414
 MV4  CAY  CAZ  single    1.521  0.020  1.521
 MV4  CAY  CAX  single    1.529  0.020  1.529
 MV4  CAQ  CAL  aromatic  1.373  0.020  1.373
 MV4  CAN  CAU  aromatic  1.415  0.020  1.415
 MV4  CAN  CAM  aromatic  1.421  0.020  1.421
 MV4  CAU  CAT  aromatic  1.368  0.020  1.368
 MV4  CAZ  NAV  single    1.466  0.020  1.466
 MV4  CAX  NBA  single    1.446  0.020  1.446
 MV4  CAX  CAW  single    1.525  0.020  1.525
 MV4  CAT  CAS  aromatic  1.410  0.020  1.410
 MV4  CAL  CAM  aromatic  1.424  0.020  1.424
 MV4  CAL  CAB  single    1.484  0.020  1.484
 MV4  CAM  CAR  aromatic  1.416  0.020  1.416
 MV4  NAV  CAW  single    1.456  0.020  1.456
 MV4  NAV  CAC  single    1.347  0.020  1.347
 MV4  CAS  CAR  aromatic  1.369  0.020  1.369
 MV4  CAB  CAC  aromatic  1.447  0.020  1.447
 MV4  CAB  CAA  aromatic  1.365  0.020  1.365
 MV4  CAC  NAD  aromatic  1.328  0.020  1.328
 MV4  CAA  C5   aromatic  1.407  0.020  1.407
 MV4  NAD  C4   aromatic  1.335  0.020  1.335
 MV4  C5   C4   aromatic  1.413  0.020  1.413
 MV4  C5   C6   aromatic  1.401  0.020  1.401
 MV4  C4   N3   aromatic  1.342  0.020  1.342
 MV4  C6   N1   aromatic  1.306  0.020  1.306
 MV4  N3   C2   aromatic  1.321  0.020  1.321
 MV4  N1   C2   aromatic  1.360  0.020  1.360
 MV4  C2   NAK  single    1.343  0.020  1.343
 MV4  C6   H1   single    0.930  0.020  1.080
 MV4  CAZ  H2   single    0.970  0.020  1.090
 MV4  CAZ  H3   single    0.970  0.020  1.090
 MV4  CAY  H4   single    0.970  0.020  1.090
 MV4  CAY  H5   single    0.970  0.020  1.090
 MV4  CAX  H6   single    0.970  0.020  1.090
 MV4  NBA  H7   single    0.890  0.020  1.040
 MV4  NBA  H8   single    0.890  0.020  1.040
 MV4  CAW  H10  single    0.970  0.020  1.090
 MV4  CAW  H11  single    0.970  0.020  1.090
 MV4  NAK  H12  single    0.860  0.020  1.020
 MV4  NAK  H13  single    0.860  0.020  1.020
 MV4  CAA  H14  single    0.930  0.020  1.080
 MV4  CAR  H15  single    0.930  0.020  1.080
 MV4  CAS  H16  single    0.930  0.020  1.080
 MV4  CAT  H17  single    0.930  0.020  1.080
 MV4  CAU  H18  single    0.930  0.020  1.080
 MV4  CAO  H19  single    0.930  0.020  1.080
 MV4  CAP  H20  single    0.930  0.020  1.080
 MV4  CAQ  H21  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
 MV4  NAD  C4   N3   117.69  3.000
 MV4  N3   C4   C5   120.62  3.000
 MV4  NAD  C4   C5   121.69  3.000
 MV4  CAA  C5   C6   125.51  3.000
 MV4  C6   C5   C4   116.51  3.000
 MV4  CAA  C5   C4   117.92  3.000
 MV4  H1   C6   N1   117.18  3.000
 MV4  H1   C6   C5   119.80  3.000
 MV4  N1   C6   C5   123.02  3.000
 MV4  C2   N1   C6   116.05  3.000
 MV4  C2   N3   C4   117.24  3.000
 MV4  H3   CAZ  H2   107.92  3.000
 MV4  H3   CAZ  NAV  111.35  3.000
 MV4  H2   CAZ  NAV  111.24  3.000
 MV4  H3   CAZ  CAY  110.78  3.000
 MV4  H2   CAZ  CAY  112.16  3.000
 MV4  NAV  CAZ  CAY  103.42  3.000
 MV4  H5   CAY  H4   108.07  3.000
 MV4  H5   CAY  CAX  109.48  3.000
 MV4  H4   CAY  CAX  113.44  3.000
 MV4  H5   CAY  CAZ  110.56  3.000
 MV4  H4   CAY  CAZ  112.11  3.000
 MV4  CAX  CAY  CAZ  103.13  3.000
 MV4  H6   CAX  CAW  108.76  3.000
 MV4  H6   CAX  NBA  107.61  3.000
 MV4  CAW  CAX  NBA  111.41  3.000
 MV4  H6   CAX  CAY  108.57  3.000
 MV4  CAW  CAX  CAY  101.93  3.000
 MV4  NBA  CAX  CAY  118.21  3.000
 MV4  H8   NBA  H7   106.03  3.000
 MV4  H8   NBA  CAX  109.64  3.000
 MV4  H7   NBA  CAX  109.70  3.000
 MV4  H11  CAW  H10  107.39  3.000
 MV4  H11  CAW  NAV  111.06  3.000
 MV4  H10  CAW  NAV  111.27  3.000
 MV4  H11  CAW  CAX  110.22  3.000
 MV4  H10  CAW  CAX  113.03  3.000
 MV4  NAV  CAW  CAX  103.92  3.000
 MV4  CAC  NAV  CAW  120.11  3.000
 MV4  CAC  NAV  CAZ  126.47  3.000
 MV4  CAW  NAV  CAZ  111.52  3.000
 MV4  CAB  CAC  NAD  122.14  3.000
 MV4  NAD  CAC  NAV  115.46  3.000
 MV4  CAB  CAC  NAV  122.39  3.000
 MV4  CAC  NAD  C4   120.11  3.000
 MV4  NAK  C2   N3   118.09  3.000
 MV4  NAK  C2   N1   115.33  3.000
 MV4  N3   C2   N1   126.57  3.000
 MV4  H13  NAK  H12  118.01  3.000
 MV4  H13  NAK  C2   119.69  3.000
 MV4  H12  NAK  C2   119.60  3.000
 MV4  H14  CAA  CAB  119.71  3.000
 MV4  H14  CAA  C5   119.37  3.000
 MV4  CAB  CAA  C5   120.86  3.000
 MV4  CAL  CAB  CAA  118.63  3.000
 MV4  CAA  CAB  CAC  116.96  3.000
 MV4  CAL  CAB  CAC  124.05  3.000
 MV4  CAQ  CAL  CAM  119.49  3.000
 MV4  CAM  CAL  CAB  121.53  3.000
 MV4  CAQ  CAL  CAB  118.92  3.000
 MV4  CAN  CAM  CAR  118.47  3.000
 MV4  CAR  CAM  CAL  122.49  3.000
 MV4  CAN  CAM  CAL  119.03  3.000
 MV4  H15  CAR  CAS  119.65  3.000
 MV4  H15  CAR  CAM  119.40  3.000
 MV4  CAS  CAR  CAM  120.94  3.000
 MV4  H16  CAS  CAT  119.67  3.000
 MV4  H16  CAS  CAR  119.85  3.000
 MV4  CAT  CAS  CAR  120.47  3.000
 MV4  H17  CAT  CAU  120.22  3.000
 MV4  H17  CAT  CAS  119.80  3.000
 MV4  CAU  CAT  CAS  119.98  3.000
 MV4  H18  CAU  CAN  118.78  3.000
 MV4  H18  CAU  CAT  120.34  3.000
 MV4  CAN  CAU  CAT  120.88  3.000
 MV4  CAO  CAN  CAU  121.23  3.000
 MV4  CAU  CAN  CAM  119.23  3.000
 MV4  CAO  CAN  CAM  119.54  3.000
 MV4  H19  CAO  CAP  120.59  3.000
 MV4  H19  CAO  CAN  119.01  3.000
 MV4  CAP  CAO  CAN  120.40  3.000
 MV4  H20  CAP  CAQ  119.45  3.000
 MV4  H20  CAP  CAO  120.36  3.000
 MV4  CAQ  CAP  CAO  120.19  3.000
 MV4  H21  CAQ  CAP  119.20  3.000
 MV4  H21  CAQ  CAL  119.45  3.000
 MV4  CAP  CAQ  CAL  121.35  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
 MV4  CONST_01  CAB  CAC  NAD  C4     0.00   0.0  0
 MV4  CONST_02  CAB  CAA  C5   C4     0.00   0.0  0
 MV4  CONST_03  N1   C6   C5   C4     0.00   0.0  0
 MV4  CONST_04  N1   C2   N3   C4     0.00   0.0  0
 MV4  CONST_05  CAL  CAB  CAA  C5   180.00   0.0  0
 MV4  CONST_06  CAC  CAB  CAA  C5     0.00   0.0  0
 MV4  CONST_07  CAC  NAD  C4   C5     0.00   0.0  0
 MV4  CONST_08  C2   N3   C4   C5     0.00   0.0  0
 MV4  CONST_09  C2   N1   C6   C5     0.00   0.0  0
 MV4  CONST_10  CAB  CAA  C5   C6   180.00   0.0  0
 MV4  CONST_11  NAD  C4   C5   C6   180.00   0.0  0
 MV4  CONST_12  N3   C4   C5   C6     0.00   0.0  0
 MV4  CONST_13  N3   C2   N1   C6     0.00   0.0  0
 MV4  CONST_14  CAA  C5   C6   N1   180.00   0.0  0
 MV4  CONST_15  CAC  NAD  C4   N3   180.00   0.0  0
 MV4  CONST_16  CAA  C5   C4   N3   180.00   0.0  0
 MV4  CONST_19  CAL  CAB  CAC  NAD  180.00   0.0  0
 MV4  CONST_20  CAA  CAB  CAC  NAD    0.00   0.0  0
 MV4  CONST_21  CAA  C5   C4   NAD    0.00   0.0  0
 MV4  CONST_22  C2   N3   C4   NAD  180.00   0.0  0
 MV4  CONST_25  CAP  CAQ  CAL  CAB  180.00   0.0  0
 MV4  CONST_26  CAN  CAM  CAL  CAB  180.00   0.0  0
 MV4  CONST_27  CAR  CAM  CAL  CAB    0.00   0.0  0
 MV4  CONST_28  CAO  CAP  CAQ  CAL    0.00   0.0  0
 MV4  CONST_29  CAO  CAN  CAM  CAL    0.00   0.0  0
 MV4  CONST_30  CAU  CAN  CAM  CAL  180.00   0.0  0
 MV4  CONST_31  CAS  CAR  CAM  CAL  180.00   0.0  0
 MV4  CONST_32  CAP  CAO  CAN  CAM    0.00   0.0  0
 MV4  CONST_33  CAT  CAU  CAN  CAM    0.00   0.0  0
 MV4  CONST_34  CAP  CAQ  CAL  CAM    0.00   0.0  0
 MV4  CONST_35  CAT  CAS  CAR  CAM    0.00   0.0  0
 MV4  CONST_36  CAO  CAN  CAM  CAR  180.00   0.0  0
 MV4  CONST_37  CAU  CAN  CAM  CAR    0.00   0.0  0
 MV4  CONST_38  CAQ  CAL  CAM  CAR  180.00   0.0  0
 MV4  CONST_39  CAU  CAT  CAS  CAR    0.00   0.0  0
 MV4  CONST_40  CAN  CAU  CAT  CAS    0.00   0.0  0
 MV4  CONST_41  CAN  CAM  CAR  CAS    0.00   0.0  0
 MV4  CONST_42  CAO  CAN  CAU  CAT  180.00   0.0  0
 MV4  CONST_43  CAP  CAO  CAN  CAU  180.00   0.0  0
 MV4  CONST_44  CAQ  CAP  CAO  CAN    0.00   0.0  0
 MV4  CONST_45  CAQ  CAL  CAM  CAN    0.00   0.0  0
 MV4  CONST_46  NAV  CAC  NAD  C4   180.00   0.0  0
 MV4  CONST_47  CAL  CAB  CAC  NAV    0.00   0.0  0
 MV4  CONST_48  CAA  CAB  CAC  NAV  180.00   0.0  0
 MV4  CONST_49  NAK  C2   N3   C4   180.00   0.0  0
 MV4  CONST_50  NAK  C2   N1   C6   180.00   0.0  0
 MV4  CONST_51  H14  CAA  C5   C4   180.00   0.0  0
 MV4  CONST_52  H1   C6   C5   C4   180.00   0.0  0
 MV4  CONST_53  H21  CAQ  CAL  CAB    0.00   0.0  0
 MV4  CONST_54  H20  CAP  CAQ  CAL  180.00   0.0  0
 MV4  CONST_55  H15  CAR  CAM  CAL    0.00   0.0  0
 MV4  CONST_56  H19  CAO  CAN  CAM  180.00   0.0  0
 MV4  CONST_57  H18  CAU  CAN  CAM  180.00   0.0  0
 MV4  CONST_58  H16  CAS  CAR  CAM  180.00   0.0  0
 MV4  CONST_59  H17  CAT  CAS  CAR  180.00   0.0  0
 MV4  CONST_60  H12  NAK  C2   N1     0.00   0.0  0
 MV4  CONST_61  H13  NAK  C2   N1   180.00   0.0  0
 MV4  Var_01    CAX  CAW  NAV  CAZ  -14.12  30.0  1
 MV4  Var_02    CAB  CAC  NAV  CAZ   21.72  30.0  2
 MV4  Var_03    CAW  NAV  CAZ  CAY  -11.08  30.0  1
 MV4  Var_04    NAV  CAZ  CAY  CAX   31.66  30.0  1

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
 MV4  chir_01  CAX  CAY  NBA  CAW  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
 MV4  plan-1  C4   0.020
 MV4  plan-1  C5   0.020
 MV4  plan-1  C6   0.020
 MV4  plan-1  N1   0.020
 MV4  plan-1  N3   0.020
 MV4  plan-1  NAV  0.020
 MV4  plan-1  CAC  0.020
 MV4  plan-1  NAD  0.020
 MV4  plan-1  C2   0.020
 MV4  plan-1  NAK  0.020
 MV4  plan-1  CAA  0.020
 MV4  plan-1  CAB  0.020
 MV4  plan-1  CAL  0.020
 MV4  plan-1  H1   0.020
 MV4  plan-1  H14  0.020
 MV4  plan-2  CAB  0.020
 MV4  plan-2  CAL  0.020
 MV4  plan-2  CAM  0.020
 MV4  plan-2  CAR  0.020
 MV4  plan-2  CAS  0.020
 MV4  plan-2  CAT  0.020
 MV4  plan-2  CAU  0.020
 MV4  plan-2  CAN  0.020
 MV4  plan-2  CAO  0.020
 MV4  plan-2  CAP  0.020
 MV4  plan-2  CAQ  0.020
 MV4  plan-2  H15  0.020
 MV4  plan-2  H16  0.020
 MV4  plan-2  H17  0.020
 MV4  plan-2  H18  0.020
 MV4  plan-2  H19  0.020
 MV4  plan-2  H20  0.020
 MV4  plan-2  H21  0.020
 MV4  plan-3  C2   0.020
 MV4  plan-3  NAK  0.020
 MV4  plan-3  H12  0.020
 MV4  plan-3  H13  0.020

