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: K9JY3

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 OptAll
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 -2098201.742891
FMO2-HF: Nuclear repulsion 2022712.516307
FMO2-HF: Total energy -75489.226584
FMO2-MP2: Total energy -75713.383435


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.
-33.164-34.55720.18-11.318-7.468-0.058
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 : 0.017 / 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-1-0.861-0.9273.153-5.352-1.2950.085-2.251-1.8900.007
4B60ASP-1-0.800-0.8671.627-27.585-33.85420.033-8.831-4.933-0.063
5B61ILE00.0000.0073.130-0.3170.5020.062-0.236-0.645-0.002
6B62GLU-1-0.800-0.8715.816-0.145-0.1450.0000.0000.0000.000
7B63ARG10.8000.8935.1133.3223.3220.0000.0000.0000.000
8B64GLU-1-0.807-0.9097.914-1.271-1.2710.0000.0000.0000.000
9B65VAL0-0.009-0.0199.6060.2990.2990.0000.0000.0000.000
10B66SER0-0.033-0.02611.5490.1930.1930.0000.0000.0000.000
11B67ILE0-0.018-0.00212.5480.1170.1170.0000.0000.0000.000
12B68LEU00.000-0.01112.8810.1150.1150.0000.0000.0000.000
13B69LYS10.8650.93415.4910.5530.5530.0000.0000.0000.000
14B70GLH0-0.043-0.00217.4220.0670.0670.0000.0000.0000.000
15B71ILE0-0.0190.00917.0680.0400.0400.0000.0000.0000.000
16B72GLN0-0.015-0.02220.717-0.004-0.0040.0000.0000.0000.000
17B73HIS00.0540.03224.0450.0150.0150.0000.0000.0000.000
18B74PRO0-0.025-0.01625.259-0.011-0.0110.0000.0000.0000.000
19B75ASN0-0.040-0.02225.9110.0070.0070.0000.0000.0000.000
20B76VAL00.0320.03319.715-0.010-0.0100.0000.0000.0000.000
21B77ILE00.0000.01617.0890.0340.0340.0000.0000.0000.000
22B78THR00.0070.00420.1370.0080.0080.0000.0000.0000.000
23B79LEU0-0.033-0.00914.5990.0120.0120.0000.0000.0000.000
24B98GLY0-0.035-0.02127.545-0.004-0.0040.0000.0000.0000.000
25B99GLY00.0160.01025.2790.0130.0130.0000.0000.0000.000
26B100GLU-1-0.832-0.94322.261-0.261-0.2610.0000.0000.0000.000
27B101LEU0-0.025-0.02325.5460.0180.0180.0000.0000.0000.000
28B102PHE00.005-0.01526.2540.0120.0120.0000.0000.0000.000
29B103ASP-1-0.851-0.92127.382-0.151-0.1510.0000.0000.0000.000
30B104PHE0-0.073-0.05529.2460.0130.0130.0000.0000.0000.000
31B105LEU0-0.005-0.01731.2950.0090.0090.0000.0000.0000.000
32B106ALA0-0.0110.01932.1250.0090.0090.0000.0000.0000.000
33B107GLU-1-0.983-0.98133.946-0.092-0.0920.0000.0000.0000.000
34B108LYS10.7840.88835.9340.1090.1090.0000.0000.0000.000
35B109GLU-1-0.883-0.92437.947-0.089-0.0890.0000.0000.0000.000
36B110SER0-0.029-0.02839.586-0.005-0.0050.0000.0000.0000.000
37B111LEU0-0.023-0.00535.5830.0010.0010.0000.0000.0000.000
38B112THR0-0.038-0.01639.6900.0060.0060.0000.0000.0000.000
39B113GLH0-0.060-0.09339.452-0.005-0.0050.0000.0000.0000.000
40B114GLU-1-0.867-0.94238.928-0.104-0.1040.0000.0000.0000.000
41B115GLU-1-0.821-0.89438.336-0.110-0.1100.0000.0000.0000.000
42B116ALA00.0200.01135.183-0.009-0.0090.0000.0000.0000.000
43B117THR00.014-0.00234.233-0.014-0.0140.0000.0000.0000.000
44B118GLU-1-0.925-0.95434.862-0.137-0.1370.0000.0000.0000.000
45B119PHE0-0.014-0.01831.489-0.011-0.0110.0000.0000.0000.000
46B120LEU00.0330.02329.343-0.017-0.0170.0000.0000.0000.000
47B121LYS10.8810.93229.9830.1160.1160.0000.0000.0000.000
48B122GLN0-0.030-0.01729.250-0.017-0.0170.0000.0000.0000.000
49B123ILE00.0390.02624.560-0.018-0.0180.0000.0000.0000.000
50B124LEU0-0.009-0.00326.010-0.018-0.0180.0000.0000.0000.000
51B125ASN0-0.006-0.01227.746-0.003-0.0030.0000.0000.0000.000
52B126GLY00.000-0.00224.704-0.004-0.0040.0000.0000.0000.000
53B127VAL00.0340.00922.225-0.021-0.0210.0000.0000.0000.000
54B128TYR0-0.0150.00323.919-0.002-0.0020.0000.0000.0000.000
55B129TYR0-0.0020.00622.296-0.003-0.0030.0000.0000.0000.000
56B130LEU00.0470.03718.603-0.001-0.0010.0000.0000.0000.000
57B131HIS00.000-0.02021.2100.0220.0220.0000.0000.0000.000
58B132SER0-0.135-0.07423.2200.0170.0170.0000.0000.0000.000
59B133LEU0-0.030-0.00820.8020.0180.0180.0000.0000.0000.000
60B134GLN0-0.048-0.02520.356-0.012-0.0120.0000.0000.0000.000
61B135ILE0-0.022-0.01115.835-0.032-0.0320.0000.0000.0000.000
62B136ALA00.0160.01316.1360.0470.0470.0000.0000.0000.000
63B137HIS0-0.069-0.06715.476-0.046-0.0460.0000.0000.0000.000
64B138PHE0-0.074-0.05612.893-0.068-0.0680.0000.0000.0000.000
65B139ASP-1-0.811-0.90113.899-0.569-0.5690.0000.0000.0000.000
66B140LEU0-0.002-0.00116.0550.0300.0300.0000.0000.0000.000
67B141LYS10.7950.88215.2270.5220.5220.0000.0000.0000.000
68B142PRO0-0.002-0.01421.050-0.023-0.0230.0000.0000.0000.000
69B143GLU-1-0.801-0.87117.396-0.357-0.3570.0000.0000.0000.000
70B144ASN0-0.062-0.02315.232-0.005-0.0050.0000.0000.0000.000
71B145ILE0-0.053-0.03219.319-0.012-0.0120.0000.0000.0000.000
72B146MET00.0090.02620.1960.0340.0340.0000.0000.0000.000
73B147LEU0-0.0020.01724.0040.0060.0060.0000.0000.0000.000
74B148LEU0-0.041-0.03325.786-0.012-0.0120.0000.0000.0000.000
75B149ASP-1-0.791-0.89328.471-0.158-0.1580.0000.0000.0000.000
76B150ARG10.8640.93032.0150.1210.1210.0000.0000.0000.000
77B151ASN0-0.006-0.02130.7890.0010.0010.0000.0000.0000.000
78B152VAL00.0180.02333.8290.0020.0020.0000.0000.0000.000
79B153PRO0-0.050-0.01437.1230.0040.0040.0000.0000.0000.000
80B154LYN00.0820.02231.312-0.003-0.0030.0000.0000.0000.000
81B155PRO0-0.103-0.03632.239-0.008-0.0080.0000.0000.0000.000
82B156ARG10.8940.96130.1050.1600.1600.0000.0000.0000.000
83B157ILE00.0800.05125.496-0.004-0.0040.0000.0000.0000.000
84B158LYS10.7670.85622.5540.3060.3060.0000.0000.0000.000
85B159ILE00.0270.02618.7370.0010.0010.0000.0000.0000.000
86B160ILE0-0.049-0.03217.146-0.017-0.0170.0000.0000.0000.000
87B161ASP-1-0.868-0.93011.680-0.995-0.9950.0000.0000.0000.000
88B162PHE00.028-0.00412.3930.0880.0880.0000.0000.0000.000
89B163GLY00.0460.0508.175-0.117-0.1170.0000.0000.0000.000
90B164LEU0-0.021-0.0187.715-0.493-0.4930.0000.0000.0000.000
91B165ALA00.0080.03110.1020.1140.1140.0000.0000.0000.000
92B166HIS0-0.091-0.0698.676-0.297-0.2970.0000.0000.0000.000
93B167LYN0-0.050-0.02312.7360.0970.0970.0000.0000.0000.000
94B168ILE0-0.054-0.02214.945-0.021-0.0210.0000.0000.0000.000
95B169ASP-1-0.969-0.97717.767-0.176-0.1760.0000.0000.0000.000
96B181PRO00.040-0.01131.0570.0000.0000.0000.0000.0000.000
97B182GLU-1-0.981-0.98432.0780.0270.0270.0000.0000.0000.000
98B183PHE0-0.043-0.01831.8810.0040.0040.0000.0000.0000.000
99B184VAL0-0.039-0.01026.6690.0080.0080.0000.0000.0000.000
100B185ALA00.0370.03025.210-0.004-0.0040.0000.0000.0000.000
101B186PRO00.0220.00826.747-0.009-0.0090.0000.0000.0000.000
102B187GLU-1-0.839-0.93622.2010.0350.0350.0000.0000.0000.000
103B188ILE0-0.023-0.00922.038-0.014-0.0140.0000.0000.0000.000
104B189VAL0-0.081-0.04324.015-0.013-0.0130.0000.0000.0000.000
105B190ASN0-0.095-0.06426.345-0.009-0.0090.0000.0000.0000.000
106B191TYR00.0050.02716.968-0.013-0.0130.0000.0000.0000.000
107B192GLU-1-0.959-0.98222.062-0.105-0.1050.0000.0000.0000.000
108B193PRO0-0.047-0.00918.748-0.015-0.0150.0000.0000.0000.000
109B194LEU0-0.011-0.01214.9760.0090.0090.0000.0000.0000.000
110B195GLY00.0840.04018.046-0.024-0.0240.0000.0000.0000.000
111B196LEU00.0290.01619.817-0.020-0.0200.0000.0000.0000.000
112B197GLU-1-0.871-0.95521.402-0.236-0.2360.0000.0000.0000.000
113B198ALA0-0.0150.00419.1850.0220.0220.0000.0000.0000.000
114B199ASP-1-0.718-0.83119.060-0.432-0.4320.0000.0000.0000.000
115B200MET0-0.045-0.00821.6970.0220.0220.0000.0000.0000.000
116B201TRP00.0180.00723.0390.0220.0220.0000.0000.0000.000
117B202SER0-0.016-0.01321.2200.0130.0130.0000.0000.0000.000
118B203ILE00.0290.01323.4750.0100.0100.0000.0000.0000.000
119B204GLY00.0130.02126.0840.0150.0150.0000.0000.0000.000
120B205VAL0-0.021-0.01124.8560.0150.0150.0000.0000.0000.000
121B206ILE00.0070.00022.8600.0110.0110.0000.0000.0000.000
122B207THR0-0.028-0.03527.0760.0110.0110.0000.0000.0000.000
123B208TYR0-0.038-0.04430.4190.0090.0090.0000.0000.0000.000
124B209ILE0-0.0070.01226.5360.0070.0070.0000.0000.0000.000
125B210LEU0-0.062-0.02430.6630.0060.0060.0000.0000.0000.000
126B211LEU0-0.075-0.03132.1940.0060.0060.0000.0000.0000.000
127B212SER0-0.024-0.02133.7470.0090.0090.0000.0000.0000.000
128B213GLY00.0520.03533.231-0.003-0.0030.0000.0000.0000.000
129B214ALA0-0.0170.00632.1070.0010.0010.0000.0000.0000.000
130B215SER00.009-0.01526.377-0.011-0.0110.0000.0000.0000.000
131B216PRO0-0.0060.00328.1650.0080.0080.0000.0000.0000.000
132B217PHE00.020-0.00226.7280.0060.0060.0000.0000.0000.000
133B218LEU0-0.043-0.01826.2070.0050.0050.0000.0000.0000.000
134B219GLY00.0460.02128.1260.0050.0050.0000.0000.0000.000
135B220ASP-1-0.903-0.94028.441-0.036-0.0360.0000.0000.0000.000
136B221THR0-0.061-0.03326.8000.0090.0090.0000.0000.0000.000
137B222LYS10.9860.98917.5840.0400.0400.0000.0000.0000.000
138B223GLN00.001-0.01923.457-0.023-0.0230.0000.0000.0000.000
139B224GLU-1-0.831-0.90224.956-0.032-0.0320.0000.0000.0000.000
140B225THR00.0420.02224.377-0.009-0.0090.0000.0000.0000.000
141B226LEU0-0.019-0.01520.121-0.011-0.0110.0000.0000.0000.000
142B227ALA0-0.0200.00624.282-0.006-0.0060.0000.0000.0000.000
143B228ASN00.0270.01827.6760.0030.0030.0000.0000.0000.000
144B229VAL00.0030.00723.344-0.003-0.0030.0000.0000.0000.000
145B230SER0-0.051-0.03225.298-0.005-0.0050.0000.0000.0000.000
146B231ALA0-0.068-0.03427.1360.0030.0030.0000.0000.0000.000
147B232VAL0-0.055-0.02929.0810.0010.0010.0000.0000.0000.000
148B233ASN0-0.064-0.03430.9050.0030.0030.0000.0000.0000.000
149B234TYR00.0070.00631.950-0.004-0.0040.0000.0000.0000.000
150B235GLU-1-0.919-0.95633.982-0.054-0.0540.0000.0000.0000.000
151B236PHE0-0.054-0.03535.679-0.005-0.0050.0000.0000.0000.000
152B237GLU-1-0.772-0.88138.482-0.053-0.0530.0000.0000.0000.000
153B238ASP-1-0.839-0.91640.429-0.061-0.0610.0000.0000.0000.000
154B239GLU-1-0.946-0.95140.502-0.061-0.0610.0000.0000.0000.000
155B240TYR0-0.092-0.07737.031-0.005-0.0050.0000.0000.0000.000
156B241PHE0-0.015-0.00934.872-0.002-0.0020.0000.0000.0000.000
157B242SER0-0.061-0.02141.0420.0000.0000.0000.0000.0000.000
158B243ASN0-0.080-0.06244.9140.0020.0020.0000.0000.0000.000
159B244THR00.0390.03939.1860.0000.0000.0000.0000.0000.000
160B245SER-1-0.714-0.80741.699-0.082-0.0820.0000.0000.0000.000
161B246ALA0-0.044-0.03841.753-0.002-0.0020.0000.0000.0000.000
162B247LEU0-0.024-0.01841.453-0.002-0.0020.0000.0000.0000.000
163B248ALA00.0740.04737.975-0.005-0.0050.0000.0000.0000.000
164B249LYS10.8700.93036.9740.0680.0680.0000.0000.0000.000
165B250ASP-1-0.868-0.88637.772-0.095-0.0950.0000.0000.0000.000
166B251PHE00.0070.00831.637-0.002-0.0020.0000.0000.0000.000
167B252ILE00.0320.01932.167-0.006-0.0060.0000.0000.0000.000
168B253ARG10.8950.93332.6420.0780.0780.0000.0000.0000.000
169B254ARG10.8050.87133.9760.0980.0980.0000.0000.0000.000
170B255LEU00.0010.02328.707-0.004-0.0040.0000.0000.0000.000
171B256LEU0-0.028-0.00828.198-0.010-0.0100.0000.0000.0000.000
172B257VAL00.0030.00129.6810.0140.0140.0000.0000.0000.000
173B258LYS10.9310.95927.5560.0670.0670.0000.0000.0000.000
174B259ASP-1-0.813-0.90227.313-0.117-0.1170.0000.0000.0000.000
175B260PRO00.0740.02624.4760.0000.0000.0000.0000.0000.000
176B261LYS10.9310.97026.7810.1080.1080.0000.0000.0000.000
177B262LYS10.7640.85629.6880.1080.1080.0000.0000.0000.000
178B263ARG10.7990.92723.6140.1890.1890.0000.0000.0000.000
179B264MET0-0.038-0.00530.0440.0020.0020.0000.0000.0000.000
180B265THR00.012-0.02428.664-0.015-0.0150.0000.0000.0000.000
181B266ILE00.0700.02626.7370.0080.0080.0000.0000.0000.000
182B267GLN00.0100.00328.5090.0050.0050.0000.0000.0000.000
183B268ASP-1-0.846-0.88532.119-0.124-0.1240.0000.0000.0000.000
184B269SER0-0.061-0.04431.0340.0040.0040.0000.0000.0000.000
185B270LEU00.026-0.00531.0850.0060.0060.0000.0000.0000.000
186B271GLN0-0.058-0.03134.5910.0100.0100.0000.0000.0000.000
187B272HIS0-0.0210.00336.4240.0070.0070.0000.0000.0000.000
188B273PRO0-0.031-0.02638.274-0.001-0.0010.0000.0000.0000.000
189B274TRP0-0.009-0.01134.3720.0010.0010.0000.0000.0000.000
190B275ILE0-0.072-0.02334.583-0.003-0.0030.0000.0000.0000.000