Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: QYZRY

Calculation Name: 2Y4P-B-Xray372

Preferred Name: Death-associated protein kinase 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y4P

Chain ID: B

ChEMBL ID: CHEMBL2558

UniProt ID: P53355

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2096733.787444
FMO2-HF: Nuclear repulsion 2021245.990803
FMO2-HF: Total energy -75487.796642
FMO2-MP2: Total energy -75711.330333


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:57:SER)


Summations of interaction energy for fragment #1(B:57:SER)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-37.887-33.4414.677-10.536-8.587-0.055
Interaction energy analysis for fragmet #1(B:57:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.012
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B59GLU-1-0.884-0.9283.302-6.433-1.6400.000-2.522-2.2710.010
4B60ASP-1-0.802-0.8881.735-30.887-32.17114.587-7.703-5.600-0.064
5B61ILE00.002-0.0102.816-0.4520.4860.090-0.311-0.716-0.001
6B62GLU-1-0.849-0.8985.8230.0450.0450.0000.0000.0000.000
7B63ARG10.8430.9185.2423.7793.7790.0000.0000.0000.000
8B64GLU-1-0.840-0.9128.410-1.634-1.6340.0000.0000.0000.000
9B65VAL00.012-0.0159.8920.3460.3460.0000.0000.0000.000
10B66SER0-0.069-0.02611.9040.2100.2100.0000.0000.0000.000
11B67ILE0-0.003-0.01812.9260.1370.1370.0000.0000.0000.000
12B68LEU00.0010.00412.6640.1250.1250.0000.0000.0000.000
13B69LYS10.8800.94215.8640.5650.5650.0000.0000.0000.000
14B70GLH0-0.0480.00217.9500.0740.0740.0000.0000.0000.000
15B71ILE0-0.0300.00217.8750.0490.0490.0000.0000.0000.000
16B72GLN0-0.019-0.02121.263-0.003-0.0030.0000.0000.0000.000
17B73HIS00.0450.02524.3250.0130.0130.0000.0000.0000.000
18B74PRO0-0.015-0.01225.271-0.013-0.0130.0000.0000.0000.000
19B75ASN0-0.041-0.02525.9820.0080.0080.0000.0000.0000.000
20B76VAL00.0330.03619.963-0.014-0.0140.0000.0000.0000.000
21B77ILE00.0050.03517.2800.0390.0390.0000.0000.0000.000
22B78THR00.0190.00220.3750.0120.0120.0000.0000.0000.000
23B79LEU0-0.018-0.00114.4050.0140.0140.0000.0000.0000.000
24B98GLY0-0.029-0.02027.210-0.004-0.0040.0000.0000.0000.000
25B99GLY0-0.012-0.00825.1620.0110.0110.0000.0000.0000.000
26B100GLU-1-0.792-0.92721.861-0.310-0.3100.0000.0000.0000.000
27B101LEU0-0.034-0.02625.2390.0190.0190.0000.0000.0000.000
28B102PHE00.011-0.02026.2940.0120.0120.0000.0000.0000.000
29B103ASP-1-0.859-0.91827.024-0.179-0.1790.0000.0000.0000.000
30B104PHE0-0.107-0.05529.0550.0170.0170.0000.0000.0000.000
31B105LEU00.014-0.01531.3330.0080.0080.0000.0000.0000.000
32B106ALA0-0.0120.02132.1360.0080.0080.0000.0000.0000.000
33B107GLU-1-1.010-0.99234.013-0.103-0.1030.0000.0000.0000.000
34B108LYS10.8470.92835.8850.1300.1300.0000.0000.0000.000
35B109GLU-1-0.948-0.96138.134-0.102-0.1020.0000.0000.0000.000
36B110SER0-0.035-0.02639.372-0.005-0.0050.0000.0000.0000.000
37B111LEU00.0090.00735.2540.0010.0010.0000.0000.0000.000
38B112THR0-0.058-0.02839.4480.0060.0060.0000.0000.0000.000
39B113GLH0-0.052-0.09039.496-0.007-0.0070.0000.0000.0000.000
40B114GLU-1-0.897-0.96939.195-0.125-0.1250.0000.0000.0000.000
41B115GLU-1-0.783-0.87338.490-0.126-0.1260.0000.0000.0000.000
42B116ALA0-0.012-0.01135.429-0.009-0.0090.0000.0000.0000.000
43B117THR00.008-0.01234.450-0.017-0.0170.0000.0000.0000.000
44B118GLU-1-0.912-0.93835.391-0.155-0.1550.0000.0000.0000.000
45B119PHE0-0.012-0.01531.494-0.010-0.0100.0000.0000.0000.000
46B120LEU00.0580.04529.757-0.018-0.0180.0000.0000.0000.000
47B121LYS10.8880.95530.4840.1380.1380.0000.0000.0000.000
48B122GLN0-0.028-0.02929.567-0.017-0.0170.0000.0000.0000.000
49B123ILE00.0250.01425.221-0.018-0.0180.0000.0000.0000.000
50B124LEU0-0.022-0.02126.719-0.018-0.0180.0000.0000.0000.000
51B125ASN0-0.041-0.03028.6120.0000.0000.0000.0000.0000.000
52B126GLY0-0.006-0.00925.487-0.003-0.0030.0000.0000.0000.000
53B127VAL00.0490.01922.868-0.023-0.0230.0000.0000.0000.000
54B128TYR00.0090.02924.726-0.003-0.0030.0000.0000.0000.000
55B129TYR0-0.0050.00922.757-0.007-0.0070.0000.0000.0000.000
56B130LEU00.0510.03719.296-0.002-0.0020.0000.0000.0000.000
57B131HIS00.010-0.01921.6730.0200.0200.0000.0000.0000.000
58B132SER0-0.143-0.07723.6780.0190.0190.0000.0000.0000.000
59B133LEU0-0.041-0.01821.2660.0180.0180.0000.0000.0000.000
60B134GLN0-0.032-0.01620.721-0.020-0.0200.0000.0000.0000.000
61B135ILE0-0.018-0.00916.195-0.040-0.0400.0000.0000.0000.000
62B136ALA00.0110.02416.6330.0510.0510.0000.0000.0000.000
63B137HIS0-0.057-0.05715.896-0.060-0.0600.0000.0000.0000.000
64B138PHE0-0.074-0.05913.479-0.084-0.0840.0000.0000.0000.000
65B139ASP-1-0.824-0.91113.983-0.734-0.7340.0000.0000.0000.000
66B140LEU0-0.0060.01516.1400.0430.0430.0000.0000.0000.000
67B141LYS10.8160.86815.2480.6130.6130.0000.0000.0000.000
68B142PRO00.0280.00421.266-0.022-0.0220.0000.0000.0000.000
69B143GLU-1-0.829-0.87717.539-0.417-0.4170.0000.0000.0000.000
70B144ASN0-0.079-0.03415.5360.0090.0090.0000.0000.0000.000
71B145ILE0-0.048-0.02519.520-0.009-0.0090.0000.0000.0000.000
72B146MET0-0.0140.00420.1520.0260.0260.0000.0000.0000.000
73B147LEU00.0000.02024.1480.0110.0110.0000.0000.0000.000
74B148LEU0-0.053-0.03125.719-0.007-0.0070.0000.0000.0000.000
75B149ASP-1-0.785-0.88027.956-0.176-0.1760.0000.0000.0000.000
76B150ARG10.8760.92831.3670.1350.1350.0000.0000.0000.000
77B151ASN0-0.012-0.01230.3860.0030.0030.0000.0000.0000.000
78B152VAL00.0260.02133.4910.0020.0020.0000.0000.0000.000
79B153PRO0-0.073-0.04036.4110.0040.0040.0000.0000.0000.000
80B154LYN00.0960.02630.938-0.001-0.0010.0000.0000.0000.000
81B155PRO0-0.104-0.06131.570-0.011-0.0110.0000.0000.0000.000
82B156ARG10.9190.98629.7650.1800.1800.0000.0000.0000.000
83B157ILE00.0790.05825.577-0.004-0.0040.0000.0000.0000.000
84B158LYS10.7980.87722.2830.3410.3410.0000.0000.0000.000
85B159ILE00.0210.01919.0300.0010.0010.0000.0000.0000.000
86B160ILE0-0.028-0.02617.016-0.019-0.0190.0000.0000.0000.000
87B161ASP-1-0.878-0.95011.792-1.081-1.0810.0000.0000.0000.000
88B162PHE00.001-0.00112.7930.0520.0520.0000.0000.0000.000
89B163GLY00.0670.0578.833-0.097-0.0970.0000.0000.0000.000
90B164LEU0-0.030-0.0248.047-0.573-0.5730.0000.0000.0000.000
91B165ALA00.0020.02710.3280.1370.1370.0000.0000.0000.000
92B166HIS0-0.088-0.0648.918-0.282-0.2820.0000.0000.0000.000
93B167LYN0-0.040-0.01713.0950.0950.0950.0000.0000.0000.000
94B168ILE0-0.055-0.03115.191-0.029-0.0290.0000.0000.0000.000
95B169ASP-1-0.956-0.97617.775-0.227-0.2270.0000.0000.0000.000
96B181PRO00.012-0.02731.031-0.001-0.0010.0000.0000.0000.000
97B182GLU-1-0.970-0.97632.0790.0000.0000.0000.0000.0000.000
98B183PHE0-0.039-0.01631.5950.0040.0040.0000.0000.0000.000
99B184VAL0-0.043-0.01026.4550.0070.0070.0000.0000.0000.000
100B185ALA00.0360.03225.199-0.001-0.0010.0000.0000.0000.000
101B186PRO00.0460.01426.859-0.010-0.0100.0000.0000.0000.000
102B187GLU-1-0.853-0.93921.921-0.036-0.0360.0000.0000.0000.000
103B188ILE0-0.019-0.01822.153-0.016-0.0160.0000.0000.0000.000
104B189VAL0-0.075-0.02624.185-0.010-0.0100.0000.0000.0000.000
105B190ASN0-0.115-0.08226.521-0.005-0.0050.0000.0000.0000.000
106B191TYR0-0.0010.03116.934-0.016-0.0160.0000.0000.0000.000
107B192GLU-1-0.956-0.98422.336-0.181-0.1810.0000.0000.0000.000
108B193PRO0-0.034-0.00618.970-0.016-0.0160.0000.0000.0000.000
109B194LEU0-0.023-0.01314.8390.0120.0120.0000.0000.0000.000
110B195GLY00.0700.02418.541-0.003-0.0030.0000.0000.0000.000
111B196LEU00.0120.01219.862-0.032-0.0320.0000.0000.0000.000
112B197GLU-1-0.877-0.95621.802-0.306-0.3060.0000.0000.0000.000
113B198ALA0-0.046-0.01719.5100.0200.0200.0000.0000.0000.000
114B199ASP-1-0.698-0.82919.210-0.531-0.5310.0000.0000.0000.000
115B200MET0-0.035-0.00521.7850.0270.0270.0000.0000.0000.000
116B201TRP0-0.0130.00323.4000.0290.0290.0000.0000.0000.000
117B202SER0-0.002-0.01021.4500.0130.0130.0000.0000.0000.000
118B203ILE00.0260.01423.7490.0120.0120.0000.0000.0000.000
119B204GLY00.0000.01126.3390.0170.0170.0000.0000.0000.000
120B205VAL0-0.027-0.01625.2410.0170.0170.0000.0000.0000.000
121B206ILE00.0190.00723.1460.0120.0120.0000.0000.0000.000
122B207THR0-0.028-0.03527.4710.0140.0140.0000.0000.0000.000
123B208TYR0-0.040-0.04230.7980.0110.0110.0000.0000.0000.000
124B209ILE0-0.047-0.04527.0680.0070.0070.0000.0000.0000.000
125B210LEU0-0.0560.01830.9570.0100.0100.0000.0000.0000.000
126B211LEU0-0.069-0.03132.4200.0090.0090.0000.0000.0000.000
127B212SER0-0.032-0.04534.3170.0110.0110.0000.0000.0000.000
128B213GLY00.1100.09032.924-0.011-0.0110.0000.0000.0000.000
129B214ALA00.0010.01632.092-0.002-0.0020.0000.0000.0000.000
130B215SER0-0.005-0.02126.857-0.012-0.0120.0000.0000.0000.000
131B216PRO00.0080.00928.6040.0080.0080.0000.0000.0000.000
132B217PHE00.022-0.00626.9820.0050.0050.0000.0000.0000.000
133B218LEU0-0.054-0.01826.0240.0000.0000.0000.0000.0000.000
134B219GLY00.0480.01927.8510.0080.0080.0000.0000.0000.000
135B220ASP-1-0.901-0.93828.678-0.076-0.0760.0000.0000.0000.000
136B221THR0-0.032-0.01027.1920.0050.0050.0000.0000.0000.000
137B222LYS10.9980.99818.1500.1550.1550.0000.0000.0000.000
138B223GLN0-0.017-0.03023.176-0.022-0.0220.0000.0000.0000.000
139B224GLU-1-0.871-0.93925.545-0.074-0.0740.0000.0000.0000.000
140B225THR00.0220.00724.470-0.007-0.0070.0000.0000.0000.000
141B226LEU0-0.040-0.02020.541-0.011-0.0110.0000.0000.0000.000
142B227ALA0-0.015-0.00524.658-0.007-0.0070.0000.0000.0000.000
143B228ASN00.0480.02928.0330.0060.0060.0000.0000.0000.000
144B229VAL00.0000.00923.649-0.001-0.0010.0000.0000.0000.000
145B230SER0-0.047-0.01825.717-0.007-0.0070.0000.0000.0000.000
146B231ALA0-0.042-0.01827.5110.0050.0050.0000.0000.0000.000
147B232VAL0-0.063-0.03129.5700.0050.0050.0000.0000.0000.000
148B233ASN0-0.064-0.03431.3060.0080.0080.0000.0000.0000.000
149B234TYR00.0270.01632.191-0.005-0.0050.0000.0000.0000.000
150B235GLU-1-0.903-0.94334.223-0.084-0.0840.0000.0000.0000.000
151B236PHE0-0.059-0.03335.995-0.006-0.0060.0000.0000.0000.000
152B237GLU-1-0.776-0.89738.536-0.076-0.0760.0000.0000.0000.000
153B238ASP-1-0.877-0.91240.504-0.081-0.0810.0000.0000.0000.000
154B239GLU-1-0.934-0.93940.532-0.084-0.0840.0000.0000.0000.000
155B240TYR0-0.097-0.09237.024-0.006-0.0060.0000.0000.0000.000
156B241PHE0-0.038-0.02835.236-0.002-0.0020.0000.0000.0000.000
157B242SER0-0.028-0.00941.3950.0010.0010.0000.0000.0000.000
158B243ASN0-0.072-0.04844.6860.0040.0040.0000.0000.0000.000
159B244THR0-0.0080.01139.5980.0000.0000.0000.0000.0000.000
160B245SER-1-0.707-0.79642.340-0.103-0.1030.0000.0000.0000.000
161B246ALA0-0.042-0.04642.333-0.003-0.0030.0000.0000.0000.000
162B247LEU0-0.027-0.02641.786-0.003-0.0030.0000.0000.0000.000
163B248ALA00.0580.03538.476-0.005-0.0050.0000.0000.0000.000
164B249LYS10.8740.93237.2370.0920.0920.0000.0000.0000.000
165B250ASP-1-0.863-0.89437.719-0.126-0.1260.0000.0000.0000.000
166B251PHE00.0080.01231.985-0.003-0.0030.0000.0000.0000.000
167B252ILE00.0310.01932.530-0.009-0.0090.0000.0000.0000.000
168B253ARG10.9290.95733.0400.1050.1050.0000.0000.0000.000
169B254ARG10.7980.86434.4520.1280.1280.0000.0000.0000.000
170B255LEU00.0030.01629.040-0.004-0.0040.0000.0000.0000.000
171B256LEU0-0.0380.00528.541-0.013-0.0130.0000.0000.0000.000
172B257VAL00.004-0.00829.9530.0150.0150.0000.0000.0000.000
173B258LYS10.9240.95827.5580.1290.1290.0000.0000.0000.000
174B259ASP-1-0.855-0.91827.914-0.162-0.1620.0000.0000.0000.000
175B260PRO00.0720.02025.0820.0020.0020.0000.0000.0000.000
176B261LYS10.9490.97027.2400.1610.1610.0000.0000.0000.000
177B262LYS10.8060.89329.7170.1370.1370.0000.0000.0000.000
178B263ARG10.8470.95123.9980.2610.2610.0000.0000.0000.000
179B264MET0-0.060-0.00530.5300.0060.0060.0000.0000.0000.000
180B265THR00.027-0.01028.715-0.018-0.0180.0000.0000.0000.000
181B266ILE00.0940.01427.0940.0110.0110.0000.0000.0000.000
182B267GLN0-0.005-0.00528.8930.0030.0030.0000.0000.0000.000
183B268ASP-1-0.853-0.89732.387-0.161-0.1610.0000.0000.0000.000
184B269SER0-0.027-0.01931.3580.0060.0060.0000.0000.0000.000
185B270LEU00.011-0.00331.3830.0070.0070.0000.0000.0000.000
186B271GLN0-0.065-0.03434.9000.0130.0130.0000.0000.0000.000
187B272HIS0-0.0070.01036.6180.0090.0090.0000.0000.0000.000
188B273PRO00.0350.04338.487-0.001-0.0010.0000.0000.0000.000
189B274TRP0-0.052-0.02434.7490.0010.0010.0000.0000.0000.000
190B275ILE0-0.114-0.08935.195-0.002-0.0020.0000.0000.0000.000