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: R96Z8

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 OptH
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 -2099487.705317
FMO2-HF: Nuclear repulsion 2024005.523552
FMO2-HF: Total energy -75482.181765
FMO2-MP2: Total energy -75705.931777


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.
-24.161-13.8972.796-6.059-7.0030.004
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 : 0.051 / q_NPA : 0.030
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-1-0.887-0.9292.964-7.317-2.3160.145-2.489-2.6580.014
4B60ASP-1-0.840-0.9392.101-13.595-10.1092.411-2.757-3.141-0.006
5B61ILE0-0.010-0.0092.808-2.330-0.5530.240-0.813-1.204-0.004
6B62GLU-1-0.890-0.9325.9100.4130.4130.0000.0000.0000.000
7B63ARG10.8680.9465.7442.6492.6490.0000.0000.0000.000
8B64GLU-1-0.865-0.9188.199-1.611-1.6110.0000.0000.0000.000
9B65VAL0-0.005-0.0219.9020.2540.2540.0000.0000.0000.000
10B66SER0-0.107-0.03811.8720.1320.1320.0000.0000.0000.000
11B67ILE00.0770.00512.6180.0920.0920.0000.0000.0000.000
12B68LEU00.0000.01112.8010.0930.0930.0000.0000.0000.000
13B69LYS10.8700.93215.7450.3840.3840.0000.0000.0000.000
14B70GLH00.000-0.07317.8790.0540.0540.0000.0000.0000.000
15B71ILE0-0.034-0.01717.7290.0320.0320.0000.0000.0000.000
16B72GLN0-0.052-0.02021.244-0.010-0.0100.0000.0000.0000.000
17B73HIS00.0560.01724.3860.0100.0100.0000.0000.0000.000
18B74PRO0-0.035-0.02325.323-0.009-0.0090.0000.0000.0000.000
19B75ASN0-0.031-0.03226.0150.0070.0070.0000.0000.0000.000
20B76VAL00.0210.03220.083-0.013-0.0130.0000.0000.0000.000
21B77ILE0-0.0230.01117.3640.0340.0340.0000.0000.0000.000
22B78THR00.001-0.00920.4760.0110.0110.0000.0000.0000.000
23B79LEU0-0.0190.00014.6810.0160.0160.0000.0000.0000.000
24B98GLY0-0.030-0.02027.250-0.003-0.0030.0000.0000.0000.000
25B99GLY0-0.011-0.01025.1820.0080.0080.0000.0000.0000.000
26B100GLU-1-0.779-0.91522.008-0.261-0.2610.0000.0000.0000.000
27B101LEU00.0320.03225.2430.0200.0200.0000.0000.0000.000
28B102PHE00.009-0.03026.8470.0110.0110.0000.0000.0000.000
29B103ASP-1-0.837-0.90526.370-0.154-0.1540.0000.0000.0000.000
30B104PHE00.008-0.00629.0460.0150.0150.0000.0000.0000.000
31B105LEU0-0.117-0.06331.3260.0060.0060.0000.0000.0000.000
32B106ALA00.0080.02732.1840.0060.0060.0000.0000.0000.000
33B107GLU-1-1.020-0.99633.997-0.083-0.0830.0000.0000.0000.000
34B108LYS10.8800.94436.0820.1080.1080.0000.0000.0000.000
35B109GLU-1-0.951-0.95738.129-0.085-0.0850.0000.0000.0000.000
36B110SER0-0.044-0.03439.346-0.005-0.0050.0000.0000.0000.000
37B111LEU0-0.024-0.01235.1510.0010.0010.0000.0000.0000.000
38B112THR0-0.0970.00239.4310.0060.0060.0000.0000.0000.000
39B113GLH0-0.184-0.18439.478-0.004-0.0040.0000.0000.0000.000
40B114GLU-1-0.938-0.98839.178-0.104-0.1040.0000.0000.0000.000
41B115GLU-1-0.608-0.83238.843-0.105-0.1050.0000.0000.0000.000
42B116ALA0-0.025-0.00535.417-0.008-0.0080.0000.0000.0000.000
43B117THR00.004-0.01834.437-0.014-0.0140.0000.0000.0000.000
44B118GLU-1-0.995-1.00135.384-0.122-0.1220.0000.0000.0000.000
45B119PHE00.5460.37131.484-0.009-0.0090.0000.0000.0000.000
46B120LEU00.0380.03229.730-0.015-0.0150.0000.0000.0000.000
47B121LYS10.9711.00730.5170.1170.1170.0000.0000.0000.000
48B122GLN0-0.016-0.01129.502-0.014-0.0140.0000.0000.0000.000
49B123ILE00.0440.02525.439-0.014-0.0140.0000.0000.0000.000
50B124LEU0-0.041-0.03326.739-0.015-0.0150.0000.0000.0000.000
51B125ASN0-0.031-0.01928.6150.0000.0000.0000.0000.0000.000
52B126GLY0-0.012-0.01125.496-0.002-0.0020.0000.0000.0000.000
53B127VAL00.0600.02222.921-0.018-0.0180.0000.0000.0000.000
54B128TYR0-0.0100.02424.725-0.003-0.0030.0000.0000.0000.000
55B129TYR00.0400.04222.522-0.006-0.0060.0000.0000.0000.000
56B130LEU00.0510.08519.320-0.001-0.0010.0000.0000.0000.000
57B131HIS00.0230.00121.9380.0120.0120.0000.0000.0000.000
58B132SER0-0.204-0.15223.8770.0090.0090.0000.0000.0000.000
59B133LEU0-0.026-0.02021.3760.0180.0180.0000.0000.0000.000
60B134GLN0-0.041-0.01620.892-0.025-0.0250.0000.0000.0000.000
61B135ILE0-0.019-0.01016.412-0.035-0.0350.0000.0000.0000.000
62B136ALA00.0100.01616.9900.0410.0410.0000.0000.0000.000
63B137HIS0-0.060-0.05415.951-0.070-0.0700.0000.0000.0000.000
64B138PHE0-0.057-0.05913.796-0.069-0.0690.0000.0000.0000.000
65B139ASP-1-0.864-0.92913.853-0.681-0.6810.0000.0000.0000.000
66B140LEU0-0.0440.00016.2000.0400.0400.0000.0000.0000.000
67B141LYS10.9310.94116.0850.4780.4780.0000.0000.0000.000
68B142PRO00.010-0.00921.241-0.017-0.0170.0000.0000.0000.000
69B143GLU-1-0.880-0.91517.805-0.337-0.3370.0000.0000.0000.000
70B144ASN0-0.050-0.01515.5100.0200.0200.0000.0000.0000.000
71B145ILE0-0.069-0.03219.512-0.004-0.0040.0000.0000.0000.000
72B146MET0-0.012-0.00419.9290.0210.0210.0000.0000.0000.000
73B147LEU0-0.0260.02924.1640.0090.0090.0000.0000.0000.000
74B148LEU0-0.053-0.02525.951-0.005-0.0050.0000.0000.0000.000
75B149ASP-1-0.784-0.87728.001-0.140-0.1400.0000.0000.0000.000
76B150ARG10.8920.92831.4410.1070.1070.0000.0000.0000.000
77B151ASN0-0.013-0.00630.1880.0030.0030.0000.0000.0000.000
78B152VAL00.0520.01833.3410.0000.0000.0000.0000.0000.000
79B153PRO0-0.114-0.06335.7720.0020.0020.0000.0000.0000.000
80B154LYN0-0.513-0.40330.7560.0010.0010.0000.0000.0000.000
81B155PRO0-0.125-0.08631.803-0.005-0.0050.0000.0000.0000.000
82B156ARG10.8690.96729.6980.1440.1440.0000.0000.0000.000
83B157ILE00.0890.05425.793-0.003-0.0030.0000.0000.0000.000
84B158LYS10.8890.93822.3000.2750.2750.0000.0000.0000.000
85B159ILE00.0080.01019.1220.0000.0000.0000.0000.0000.000
86B160ILE0-0.023-0.02416.584-0.012-0.0120.0000.0000.0000.000
87B161ASP-1-0.864-0.93811.994-0.897-0.8970.0000.0000.0000.000
88B162PHE00.0120.00012.8920.0250.0250.0000.0000.0000.000
89B163GLY00.0700.0508.845-0.061-0.0610.0000.0000.0000.000
90B164LEU0-0.033-0.0248.072-0.474-0.4740.0000.0000.0000.000
91B165ALA0-0.0040.02010.3510.1020.1020.0000.0000.0000.000
92B166HIS0-0.091-0.0549.671-0.211-0.2110.0000.0000.0000.000
93B167LYN0-0.0450.07413.4140.0960.0960.0000.0000.0000.000
94B168ILE0-0.033-0.01515.421-0.034-0.0340.0000.0000.0000.000
95B169ASP-1-0.968-0.98118.020-0.222-0.2220.0000.0000.0000.000
96B181PRO0-0.001-0.03931.155-0.001-0.0010.0000.0000.0000.000
97B182GLU-1-0.958-0.96732.180-0.030-0.0300.0000.0000.0000.000
98B183PHE0-0.035-0.01131.6200.0030.0030.0000.0000.0000.000
99B184VAL0-0.026-0.00426.5930.0030.0030.0000.0000.0000.000
100B185ALA00.0260.02025.4210.0020.0020.0000.0000.0000.000
101B186PRO00.0370.00227.020-0.008-0.0080.0000.0000.0000.000
102B187GLU-1-0.885-0.94622.195-0.101-0.1010.0000.0000.0000.000
103B188ILE0-0.014-0.01822.277-0.016-0.0160.0000.0000.0000.000
104B189VAL0-0.101-0.03624.356-0.006-0.0060.0000.0000.0000.000
105B190ASN0-0.057-0.04926.6460.0020.0020.0000.0000.0000.000
106B191TYR0-0.0080.02617.195-0.016-0.0160.0000.0000.0000.000
107B192GLU-1-0.951-0.97522.579-0.201-0.2010.0000.0000.0000.000
108B193PRO0-0.037-0.01719.217-0.018-0.0180.0000.0000.0000.000
109B194LEU0-0.017-0.00515.5830.0150.0150.0000.0000.0000.000
110B195GLY00.0800.03018.925-0.002-0.0020.0000.0000.0000.000
111B196LEU00.0240.00920.279-0.025-0.0250.0000.0000.0000.000
112B197GLU-1-0.926-0.97122.175-0.269-0.2690.0000.0000.0000.000
113B198ALA0-0.033-0.02019.6990.0170.0170.0000.0000.0000.000
114B199ASP-1-0.703-0.84119.377-0.459-0.4590.0000.0000.0000.000
115B200MET0-0.038-0.01421.8060.0250.0250.0000.0000.0000.000
116B201TRP0-0.0140.00423.7540.0230.0230.0000.0000.0000.000
117B202SER0-0.005-0.01121.5020.0120.0120.0000.0000.0000.000
118B203ILE00.0290.02023.8020.0110.0110.0000.0000.0000.000
119B204GLY00.0080.03226.3860.0160.0160.0000.0000.0000.000
120B205VAL0-0.021-0.01425.4750.0150.0150.0000.0000.0000.000
121B206ILE00.0280.01023.3150.0110.0110.0000.0000.0000.000
122B207THR0-0.034-0.05727.5440.0120.0120.0000.0000.0000.000
123B208TYR0-0.045-0.03430.8630.0100.0100.0000.0000.0000.000
124B209ILE0-0.054-0.05527.1370.0060.0060.0000.0000.0000.000
125B210LEU0-0.0460.02230.9870.0090.0090.0000.0000.0000.000
126B211LEU0-0.077-0.03032.3850.0080.0080.0000.0000.0000.000
127B212SER0-0.028-0.04334.2950.0090.0090.0000.0000.0000.000
128B213GLY00.1050.09232.880-0.009-0.0090.0000.0000.0000.000
129B214ALA00.0070.01232.039-0.002-0.0020.0000.0000.0000.000
130B215SER0-0.005-0.02126.842-0.011-0.0110.0000.0000.0000.000
131B216PRO0-0.0020.00928.7230.0070.0070.0000.0000.0000.000
132B217PHE00.024-0.00427.1090.0040.0040.0000.0000.0000.000
133B218LEU0-0.055-0.01926.079-0.002-0.0020.0000.0000.0000.000
134B219GLY00.0510.02027.9700.0070.0070.0000.0000.0000.000
135B220ASP-1-0.897-0.93728.710-0.075-0.0750.0000.0000.0000.000
136B221THR0-0.040-0.02427.3220.0010.0010.0000.0000.0000.000
137B222LYS10.9930.97918.6330.1530.1530.0000.0000.0000.000
138B223GLN0-0.046-0.04222.861-0.013-0.0130.0000.0000.0000.000
139B224GLU-1-0.825-0.88225.686-0.080-0.0800.0000.0000.0000.000
140B225THR00.018-0.00224.326-0.006-0.0060.0000.0000.0000.000
141B226LEU0-0.046-0.02820.880-0.010-0.0100.0000.0000.0000.000
142B227ALA0-0.009-0.00324.752-0.007-0.0070.0000.0000.0000.000
143B228ASN00.0510.03628.1220.0040.0040.0000.0000.0000.000
144B229VAL0-0.0010.01023.900-0.001-0.0010.0000.0000.0000.000
145B230SER0-0.049-0.03126.327-0.006-0.0060.0000.0000.0000.000
146B231ALA0-0.041-0.01827.5880.0040.0040.0000.0000.0000.000
147B232VAL0-0.068-0.03029.7820.0050.0050.0000.0000.0000.000
148B233ASN0-0.053-0.03231.3710.0090.0090.0000.0000.0000.000
149B234TYR00.0030.01232.293-0.005-0.0050.0000.0000.0000.000
150B235GLU-1-0.880-0.93134.307-0.081-0.0810.0000.0000.0000.000
151B236PHE0-0.099-0.05636.181-0.005-0.0050.0000.0000.0000.000
152B237GLU-1-0.807-0.92938.628-0.069-0.0690.0000.0000.0000.000
153B238ASP-1-0.906-0.93440.600-0.073-0.0730.0000.0000.0000.000
154B239GLU-1-1.003-0.99340.843-0.074-0.0740.0000.0000.0000.000
155B240TYR0-0.043-0.03737.271-0.004-0.0040.0000.0000.0000.000
156B241PHE0-0.053-0.04335.537-0.001-0.0010.0000.0000.0000.000
157B242SER0-0.0330.00541.4830.0020.0020.0000.0000.0000.000
158B243ASN0-0.037-0.03244.6940.0040.0040.0000.0000.0000.000
159B244THR0-0.0170.00439.8140.0000.0000.0000.0000.0000.000
160B245SER-1-0.637-0.73842.723-0.095-0.0950.0000.0000.0000.000
161B246ALA0-0.035-0.03742.394-0.003-0.0030.0000.0000.0000.000
162B247LEU0-0.027-0.02541.688-0.003-0.0030.0000.0000.0000.000
163B248ALA00.0950.03838.441-0.005-0.0050.0000.0000.0000.000
164B249LYS10.9720.98437.2910.0840.0840.0000.0000.0000.000
165B250ASP-1-0.953-0.97437.772-0.113-0.1130.0000.0000.0000.000
166B251PHE00.000-0.00132.331-0.004-0.0040.0000.0000.0000.000
167B252ILE00.0290.02132.597-0.008-0.0080.0000.0000.0000.000
168B253ARG10.9390.95833.0880.0960.0960.0000.0000.0000.000
169B254ARG10.9040.95134.5640.1160.1160.0000.0000.0000.000
170B255LEU00.0080.01929.006-0.004-0.0040.0000.0000.0000.000
171B256LEU0-0.0400.00328.706-0.013-0.0130.0000.0000.0000.000
172B257VAL00.0070.00330.0100.0120.0120.0000.0000.0000.000
173B258LYS10.9280.96127.6960.1430.1430.0000.0000.0000.000
174B259ASP-1-0.927-0.97428.314-0.162-0.1620.0000.0000.0000.000
175B260PRO00.0570.01825.5650.0030.0030.0000.0000.0000.000
176B261LYS10.9760.98327.6760.1670.1670.0000.0000.0000.000
177B262LYS10.8820.94130.1170.1300.1300.0000.0000.0000.000
178B263ARG10.8430.95324.4580.2400.2400.0000.0000.0000.000
179B264MET0-0.052-0.00230.7940.0050.0050.0000.0000.0000.000
180B265THR00.026-0.00228.940-0.015-0.0150.0000.0000.0000.000
181B266ILE00.0860.00526.9720.0100.0100.0000.0000.0000.000
182B267GLN0-0.021-0.01429.4740.0020.0020.0000.0000.0000.000
183B268ASP-1-0.855-0.90832.520-0.144-0.1440.0000.0000.0000.000
184B269SER0-0.043-0.02231.3420.0060.0060.0000.0000.0000.000
185B270LEU00.002-0.00631.2930.0060.0060.0000.0000.0000.000
186B271GLN0-0.022-0.00934.9050.0080.0080.0000.0000.0000.000
187B272HIS0-0.065-0.01836.6710.0070.0070.0000.0000.0000.000
188B273PRO00.0550.02038.5010.0000.0000.0000.0000.0000.000
189B274TRP0-0.087-0.04234.8570.0010.0010.0000.0000.0000.000
190B275ILE0-0.090-0.03234.790-0.001-0.0010.0000.0000.0000.000