Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 536JZ

Calculation Name: 1Y0K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y0K

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HVP2

Base Structure: X-ray

Registration Date: 2023-06-20

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1987244.387886
FMO2-HF: Nuclear repulsion 1916273.597014
FMO2-HF: Total energy -70970.790872
FMO2-MP2: Total energy -71181.734609


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(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-8.46-3.7267.217-2.444-9.506-0.012
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.001
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].
3A3GLU-1-0.832-0.9382.439-4.948-2.6851.408-1.508-2.163-0.013
4A4ALA0-0.029-0.0114.9630.8261.022-0.001-0.010-0.1850.000
5A5ASP-1-0.809-0.9132.896-0.1750.6900.338-0.252-0.9510.000
6A6TYR00.0120.0092.558-0.6151.7264.814-2.622-4.5340.003
7A7LEU00.0170.0023.5061.629-0.2300.0532.236-0.429-0.001
8A8ARG10.8810.9396.366-0.580-0.5800.0000.0000.0000.000
9A9LEU0-0.034-0.0022.556-1.544-0.6360.606-0.285-1.228-0.001
10A10LEU00.006-0.0076.093-0.810-0.790-0.001-0.003-0.0160.000
11A11THR0-0.031-0.0238.611-0.362-0.3620.0000.0000.0000.000
12A12ARG10.9830.9965.140-1.324-1.3240.0000.0000.0000.000
13A13GLN00.0210.0249.674-0.152-0.1520.0000.0000.0000.000
14A14ALA00.0130.00511.375-0.108-0.1080.0000.0000.0000.000
15A15GLU-1-0.883-0.96514.0100.3160.3160.0000.0000.0000.000
16A16GLN00.0200.01311.593-0.011-0.0110.0000.0000.0000.000
17A17ALA0-0.0080.00415.609-0.043-0.0430.0000.0000.0000.000
18A18ASN00.0260.00017.669-0.041-0.0410.0000.0000.0000.000
19A19ASP-1-0.892-0.93918.2910.1710.1710.0000.0000.0000.000
20A20PHE0-0.045-0.02519.788-0.021-0.0210.0000.0000.0000.000
21A21LEU0-0.035-0.02521.575-0.019-0.0190.0000.0000.0000.000
22A22SER0-0.086-0.03823.408-0.016-0.0160.0000.0000.0000.000
23A23ASN00.0130.00923.780-0.016-0.0160.0000.0000.0000.000
24A24ALA0-0.0290.01825.720-0.008-0.0080.0000.0000.0000.000
25A25ARG10.9670.96627.546-0.051-0.0510.0000.0000.0000.000
26A26LYS10.9020.94130.231-0.037-0.0370.0000.0000.0000.000
27A27TRP00.0410.01331.3490.0030.0030.0000.0000.0000.000
28A28ASP-1-0.866-0.92828.0560.0570.0570.0000.0000.0000.000
29A29ARG10.9420.98326.067-0.069-0.0690.0000.0000.0000.000
30A30GLU-1-0.827-0.92326.9420.0480.0480.0000.0000.0000.000
31A31ARG10.8410.91127.731-0.046-0.0460.0000.0000.0000.000
32A32TRP0-0.014-0.00719.413-0.002-0.0020.0000.0000.0000.000
33A33VAL00.0080.00424.1230.0040.0040.0000.0000.0000.000
34A34CYS0-0.023-0.00524.988-0.003-0.0030.0000.0000.0000.000
35A35GLN00.0230.01325.260-0.002-0.0020.0000.0000.0000.000
36A36ARG10.8410.91919.688-0.077-0.0770.0000.0000.0000.000
37A37PHE0-0.009-0.00622.045-0.003-0.0030.0000.0000.0000.000
38A38LEU00.001-0.00624.232-0.007-0.0070.0000.0000.0000.000
39A39GLU-1-0.779-0.85221.4370.0440.0440.0000.0000.0000.000
40A40ALA0-0.014-0.00820.707-0.006-0.0060.0000.0000.0000.000
41A41LEU0-0.107-0.04221.658-0.012-0.0120.0000.0000.0000.000
42A42ASN0-0.045-0.00924.167-0.004-0.0040.0000.0000.0000.000
43A43VAL0-0.017-0.00325.484-0.005-0.0050.0000.0000.0000.000
44A44PRO00.000-0.00628.3710.0040.0040.0000.0000.0000.000
45A45TYR0-0.077-0.06424.9450.0010.0010.0000.0000.0000.000
46A46ARG10.8670.90830.906-0.009-0.0090.0000.0000.0000.000
47A47GLN0-0.015-0.01429.6330.0010.0010.0000.0000.0000.000
48A48GLU-1-0.826-0.90932.8950.0150.0150.0000.0000.0000.000
49A49ASP-1-0.867-0.92634.0310.0100.0100.0000.0000.0000.000
50A50PHE0-0.084-0.03129.5320.0010.0010.0000.0000.0000.000
51A51ALA00.0220.01234.9520.0000.0000.0000.0000.0000.000
52A52ALA00.0020.00337.2630.0010.0010.0000.0000.0000.000
53A53PRO0-0.0140.00438.669-0.002-0.0020.0000.0000.0000.000
54A54GLY0-0.019-0.01241.6610.0010.0010.0000.0000.0000.000
55A55GLU-1-0.939-0.96644.3310.0160.0160.0000.0000.0000.000
56A56GLN0-0.0410.01138.5780.0020.0020.0000.0000.0000.000
57A57PRO0-0.042-0.00939.092-0.001-0.0010.0000.0000.0000.000
58A58PRO00.003-0.00536.826-0.002-0.0020.0000.0000.0000.000
59A59ASP-1-0.827-0.92533.8780.0340.0340.0000.0000.0000.000
60A60VAL0-0.054-0.03531.8190.0000.0000.0000.0000.0000.000
61A61LEU0-0.0100.00134.952-0.001-0.0010.0000.0000.0000.000
62A62PHE00.028-0.00332.3920.0010.0010.0000.0000.0000.000
63A63LYS10.9090.96734.577-0.007-0.0070.0000.0000.0000.000
64A64GLY00.0190.01637.701-0.002-0.0020.0000.0000.0000.000
65A65ALA0-0.019-0.01434.677-0.001-0.0010.0000.0000.0000.000
66A66GLY00.0450.01336.6830.0010.0010.0000.0000.0000.000
67A67PHE0-0.015-0.02231.0430.0000.0000.0000.0000.0000.000
68A68GLU-1-0.695-0.78133.9540.0280.0280.0000.0000.0000.000
69A69VAL0-0.045-0.03028.3770.0010.0010.0000.0000.0000.000
70A70PHE0-0.037-0.03329.0410.0000.0000.0000.0000.0000.000
71A71PHE00.0270.00524.6160.0040.0040.0000.0000.0000.000
72A72VAL0-0.034-0.01223.972-0.007-0.0070.0000.0000.0000.000
73A73LEU00.0210.00521.7360.0130.0130.0000.0000.0000.000
74A74ASP-1-0.818-0.91719.9030.1490.1490.0000.0000.0000.000
75A75GLU-1-0.858-0.93019.5380.1900.1900.0000.0000.0000.000
76A105ARG10.9240.9309.933-0.005-0.0050.0000.0000.0000.000
77A106PRO00.0020.03610.888-0.063-0.0630.0000.0000.0000.000
78A107GLN00.0280.02012.920-0.035-0.0350.0000.0000.0000.000
79A108ARG10.9060.9369.4260.0800.0800.0000.0000.0000.000
80A109ILE0-0.050-0.00915.277-0.018-0.0180.0000.0000.0000.000
81A110ALA00.0980.04318.780-0.001-0.0010.0000.0000.0000.000
82A111ALA00.0280.01120.9890.0200.0200.0000.0000.0000.000
83A112ALA00.005-0.00622.2920.0120.0120.0000.0000.0000.000
84A113GLU-1-0.872-0.95023.100-0.022-0.0220.0000.0000.0000.000
85A114LEU0-0.035-0.01619.5960.0120.0120.0000.0000.0000.000
86A115GLN00.012-0.00522.9670.0090.0090.0000.0000.0000.000
87A116ALA00.0090.02026.0240.0030.0030.0000.0000.0000.000
88A117ARG10.9190.96222.140-0.055-0.0550.0000.0000.0000.000
89A118LEU00.0110.00325.4350.0050.0050.0000.0000.0000.000
90A119ALA0-0.0020.01428.631-0.001-0.0010.0000.0000.0000.000
91A120PRO0-0.022-0.01330.214-0.002-0.0020.0000.0000.0000.000
92A121THR00.0250.00030.479-0.002-0.0020.0000.0000.0000.000
93A122LEU00.0310.02531.213-0.001-0.0010.0000.0000.0000.000
94A123ARG10.8190.87934.222-0.012-0.0120.0000.0000.0000.000
95A124LYS10.9410.97635.496-0.028-0.0280.0000.0000.0000.000
96A125LYS10.8650.93233.642-0.032-0.0320.0000.0000.0000.000
97A126ALA00.0480.02938.176-0.001-0.0010.0000.0000.0000.000
98A127HIS00.0050.00840.129-0.002-0.0020.0000.0000.0000.000
99A128ASN00.014-0.01040.026-0.002-0.0020.0000.0000.0000.000
100A129TYR0-0.084-0.11937.7920.0000.0000.0000.0000.0000.000
101A130SER00.0080.00643.483-0.001-0.0010.0000.0000.0000.000
102A131GLU-1-0.968-0.98145.9350.0080.0080.0000.0000.0000.000
103A132ARG10.8400.93042.610-0.017-0.0170.0000.0000.0000.000
104A133GLY0-0.0040.01848.1590.0000.0000.0000.0000.0000.000
105A134ILE0-0.064-0.03442.7550.0000.0000.0000.0000.0000.000
106A135ASP-1-0.844-0.91745.3410.0040.0040.0000.0000.0000.000
107A136HIS0-0.035-0.03840.5750.0000.0000.0000.0000.0000.000
108A137GLY00.0220.01340.4010.0010.0010.0000.0000.0000.000
109A138GLU-1-0.948-0.96741.8930.0040.0040.0000.0000.0000.000
110A139LEU0-0.081-0.03037.5490.0020.0020.0000.0000.0000.000
111A140ASP-1-0.762-0.84533.8920.0070.0070.0000.0000.0000.000
112A141LEU0-0.025-0.01031.9860.0040.0040.0000.0000.0000.000
113A142LEU00.005-0.00126.181-0.002-0.0020.0000.0000.0000.000
114A143ALA0-0.0170.00325.9320.0040.0040.0000.0000.0000.000
115A144PHE00.0500.00418.9580.0050.0050.0000.0000.0000.000
116A145VAL0-0.039-0.03520.324-0.001-0.0010.0000.0000.0000.000
117A146ASN0-0.061-0.05316.6240.0500.0500.0000.0000.0000.000
118A147LEU0-0.040-0.00917.482-0.020-0.0200.0000.0000.0000.000
119A148LYS10.9190.98115.255-0.247-0.2470.0000.0000.0000.000
120A149ARG10.7960.88915.161-0.122-0.1220.0000.0000.0000.000
121A150ALA0-0.016-0.01015.966-0.034-0.0340.0000.0000.0000.000
122A151VAL00.0150.01511.0090.0530.0530.0000.0000.0000.000
123A152PRO00.0280.01814.318-0.053-0.0530.0000.0000.0000.000
124A153ASP-1-0.862-0.93014.671-0.183-0.1830.0000.0000.0000.000
125A154PHE0-0.022-0.01813.2420.0100.0100.0000.0000.0000.000
126A155ASN0-0.0010.01414.1680.0020.0020.0000.0000.0000.000
127A156THR0-0.044-0.01417.7580.0140.0140.0000.0000.0000.000
128A157PRO00.0270.01420.9370.0090.0090.0000.0000.0000.000
129A158PHE00.015-0.01621.1250.0060.0060.0000.0000.0000.000
130A159PRO0-0.0090.01725.614-0.002-0.0020.0000.0000.0000.000
131A160PRO00.0680.01329.1190.0050.0050.0000.0000.0000.000
132A161PRO00.0400.04130.9120.0010.0010.0000.0000.0000.000
133A162THR00.001-0.02132.5440.0020.0020.0000.0000.0000.000
134A163GLU-1-0.857-0.89434.8860.0060.0060.0000.0000.0000.000
135A164TYR0-0.024-0.04129.5470.0010.0010.0000.0000.0000.000
136A165LEU00.0010.00535.3120.0010.0010.0000.0000.0000.000
137A166ARG10.9260.95437.4820.0080.0080.0000.0000.0000.000
138A167GLN0-0.0020.00535.9320.0020.0020.0000.0000.0000.000
139A168GLY00.0290.02639.8620.0010.0010.0000.0000.0000.000
140A169TRP0-0.038-0.01135.6210.0010.0010.0000.0000.0000.000
141A170ARG10.8810.93238.068-0.009-0.0090.0000.0000.0000.000
142A171SER0-0.068-0.06633.510-0.002-0.0020.0000.0000.0000.000
143A172LEU0-0.0080.01929.6980.0030.0030.0000.0000.0000.000
144A173SER0-0.0010.00327.190-0.007-0.0070.0000.0000.0000.000
145A174MET0-0.035-0.00623.1840.0060.0060.0000.0000.0000.000
146A175VAL00.0250.00720.702-0.007-0.0070.0000.0000.0000.000
147A176GLY00.0490.03618.5140.0000.0000.0000.0000.0000.000
148A177PRO0-0.014-0.01213.970-0.007-0.0070.0000.0000.0000.000
149A178THR0-0.002-0.01011.8000.0050.0050.0000.0000.0000.000
150A179PHE00.0110.00314.158-0.041-0.0410.0000.0000.0000.000
151A180ALA00.0640.04017.4610.0110.0110.0000.0000.0000.000
152A181ARG10.8960.94921.2050.0100.0100.0000.0000.0000.000
153A182VAL00.0410.04024.1110.0070.0070.0000.0000.0000.000
154A183LEU0-0.093-0.05625.864-0.007-0.0070.0000.0000.0000.000
155A184PHE0-0.018-0.02429.152-0.006-0.0060.0000.0000.0000.000
156A185ALA00.034-0.00132.7740.0040.0040.0000.0000.0000.000
157A186HIS00.0120.02135.157-0.004-0.0040.0000.0000.0000.000
158A187SER0-0.020-0.02138.8570.0010.0010.0000.0000.0000.000
159A188GLY00.0300.01741.1250.0000.0000.0000.0000.0000.000
160A189ALA0-0.0020.01036.2770.0010.0010.0000.0000.0000.000
161A190PRO00.0430.01635.250-0.002-0.0020.0000.0000.0000.000
162A191GLU-1-0.929-0.97035.795-0.012-0.0120.0000.0000.0000.000
163A192PHE00.0340.01430.545-0.002-0.0020.0000.0000.0000.000
164A193LEU00.0020.01530.459-0.001-0.0010.0000.0000.0000.000
165A194ARG10.9160.95531.6760.0070.0070.0000.0000.0000.000
166A195ALA0-0.018-0.00432.091-0.003-0.0030.0000.0000.0000.000
167A196ASN0-0.065-0.05227.255-0.008-0.0080.0000.0000.0000.000
168A197LEU0-0.0070.01127.7840.0000.0000.0000.0000.0000.000
169A198GLY0-0.023-0.00928.227-0.004-0.0040.0000.0000.0000.000
170A199ARG10.9370.97223.9620.0220.0220.0000.0000.0000.000
171A200SER0-0.021-0.01920.0940.0110.0110.0000.0000.0000.000
172A201ILE0-0.0130.01518.869-0.018-0.0180.0000.0000.0000.000
173A202LEU00.005-0.00613.5920.0220.0220.0000.0000.0000.000
174A203PHE0-0.043-0.00513.763-0.031-0.0310.0000.0000.0000.000
175A204ASP-1-0.867-0.9289.877-0.025-0.0250.0000.0000.0000.000
176A205ALA0-0.043-0.0426.5490.0630.0630.0000.0000.0000.000
177A206GLY0-0.022-0.0148.537-0.145-0.1450.0000.0000.0000.000
178A207VAL0-0.029-0.00910.654-0.053-0.0530.0000.0000.0000.000
179A208GLY00.0010.01413.597-0.023-0.0230.0000.0000.0000.000
180A209LEU0-0.032-0.01713.713-0.026-0.0260.0000.0000.0000.000