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: MVZ6Z

Calculation Name: 1IAR-B-Xray372

Preferred Name: Interleukin-4 receptor subunit alpha

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1IAR

Chain ID: B

ChEMBL ID: CHEMBL3580490

UniProt ID: P24394

Base Structure: X-ray

Registration Date: 2023-06-26

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2069912.734669
FMO2-HF: Nuclear repulsion 1990468.767831
FMO2-HF: Total energy -79443.966838
FMO2-MP2: Total energy -79673.418963


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:1:PHE)


Summations of interaction energy for fragment #1(B:1:PHE)
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.
-18.461-7.2748.04-6.158-13.067-0.023
Interaction energy analysis for fragmet #1(B:1:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.009
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].
3B3VAL00.0320.0243.707-0.9601.131-0.008-0.960-1.1230.002
4B4LEU0-0.043-0.0385.749-0.159-0.1590.0000.0000.0000.000
5B5GLN0-0.058-0.0238.575-0.068-0.0680.0000.0000.0000.000
6B6GLU-1-0.825-0.91010.0420.3860.3860.0000.0000.0000.000
7B7PRO0-0.011-0.00910.403-0.043-0.0430.0000.0000.0000.000
8B8THR0-0.0160.01712.891-0.038-0.0380.0000.0000.0000.000
9B9CYS0-0.078-0.04414.9260.0130.0130.0000.0000.0000.000
10B10VAL00.0190.01218.896-0.018-0.0180.0000.0000.0000.000
11B11SER00.025-0.00522.3860.0060.0060.0000.0000.0000.000
12B12ASP-1-0.726-0.84425.0540.0750.0750.0000.0000.0000.000
13B13TYR00.0100.00027.852-0.008-0.0080.0000.0000.0000.000
14B14MET0-0.0070.00629.155-0.008-0.0080.0000.0000.0000.000
15B15SER00.0390.01627.836-0.003-0.0030.0000.0000.0000.000
16B16ILE0-0.048-0.01322.7800.0050.0050.0000.0000.0000.000
17B17SER00.012-0.01421.518-0.009-0.0090.0000.0000.0000.000
18B18THR0-0.040-0.00818.5640.0080.0080.0000.0000.0000.000
19B20GLU-1-0.850-0.93113.4990.1600.1600.0000.0000.0000.000
20B21TRP00.0180.0046.879-0.099-0.0990.0000.0000.0000.000
21B22LYS10.8350.9098.725-0.194-0.1940.0000.0000.0000.000
22B23MET00.0450.0542.163-1.208-0.7393.026-0.886-2.6100.000
23B24ASN0-0.038-0.0274.129-0.620-0.3080.000-0.051-0.2610.000
24B25GLY00.0150.0163.646-0.776-0.2420.007-0.149-0.392-0.001
25B26PRO0-0.042-0.0324.9420.0270.170-0.001-0.012-0.1300.000
26B27THR00.0120.0033.623-1.838-0.3860.097-0.351-1.1970.002
27B28ASN00.0060.0224.7190.5250.600-0.001-0.011-0.0630.000
28B29CYS00.0170.0076.1630.0750.0750.0000.0000.0000.000
29B30SER00.0410.0317.8200.0500.0500.0000.0000.0000.000
30B31THR0-0.031-0.0166.2160.0810.0810.0000.0000.0000.000
31B32GLU-1-0.900-0.9452.441-11.008-7.6073.147-2.596-3.952-0.029
32B33LEU0-0.027-0.0013.371-0.4730.4740.090-0.277-0.7600.002
33B34ARG10.8500.9005.838-0.590-0.5900.0000.0000.0000.000
34B35LEU00.0020.0209.1880.1490.1490.0000.0000.0000.000
35B36LEU0-0.003-0.00111.631-0.100-0.1000.0000.0000.0000.000
36B37TYR0-0.018-0.02714.3210.0270.0270.0000.0000.0000.000
37B38GLN0-0.028-0.02817.591-0.006-0.0060.0000.0000.0000.000
38B39LEU00.0150.02220.9140.0060.0060.0000.0000.0000.000
39B40VAL0-0.030-0.02122.9710.0020.0020.0000.0000.0000.000
40B41PHE00.022-0.00125.307-0.013-0.0130.0000.0000.0000.000
41B42LEU0-0.023-0.00127.9610.0060.0060.0000.0000.0000.000
42B43LEU0-0.026-0.00529.4050.0020.0020.0000.0000.0000.000
43B44SER00.0070.00325.2070.0050.0050.0000.0000.0000.000
44B45GLU-1-0.893-0.96122.9540.1280.1280.0000.0000.0000.000
45B46ALA0-0.0120.01318.5100.0070.0070.0000.0000.0000.000
46B47HIS10.8850.95618.934-0.179-0.1790.0000.0000.0000.000
47B48THR00.0250.00013.0370.0540.0540.0000.0000.0000.000
48B49CYS0-0.076-0.01613.461-0.045-0.0450.0000.0000.0000.000
49B50ILE0-0.038-0.02211.6820.0750.0750.0000.0000.0000.000
50B51PRO00.000-0.0169.215-0.035-0.0350.0000.0000.0000.000
51B52GLU-1-0.870-0.92212.029-0.012-0.0120.0000.0000.0000.000
52B53ASN0-0.041-0.0578.7690.0710.0710.0000.0000.0000.000
53B54ASN0-0.0090.00112.6470.0020.0020.0000.0000.0000.000
54B55GLY00.0410.02613.6660.0090.0090.0000.0000.0000.000
55B56GLY0-0.006-0.01510.5720.0180.0180.0000.0000.0000.000
56B57ALA00.0090.0027.633-0.129-0.1290.0000.0000.0000.000
57B58GLY0-0.0100.0118.1460.1770.1770.0000.0000.0000.000
58B60VAL00.0610.02410.786-0.005-0.0050.0000.0000.0000.000
59B62HIS00.0290.02015.2680.0030.0030.0000.0000.0000.000
60B63LEU0-0.022-0.01816.2210.0020.0020.0000.0000.0000.000
61B64LEU00.0120.00519.703-0.019-0.0190.0000.0000.0000.000
62B65MET0-0.0180.01022.6930.0170.0170.0000.0000.0000.000
63B66ASP-1-0.951-0.97825.6600.0740.0740.0000.0000.0000.000
64B67ASP-1-0.852-0.92128.9450.0690.0690.0000.0000.0000.000
65B68VAL0-0.113-0.04927.5340.0110.0110.0000.0000.0000.000
66B69VAL0-0.0070.00330.247-0.009-0.0090.0000.0000.0000.000
67B70SER0-0.010-0.01730.6520.0090.0090.0000.0000.0000.000
68B71ALA00.007-0.01030.8100.0050.0050.0000.0000.0000.000
69B72ASP-1-0.804-0.87427.3130.1180.1180.0000.0000.0000.000
70B73ASN0-0.036-0.04024.5010.0090.0090.0000.0000.0000.000
71B74TYR00.0310.01620.4010.0010.0010.0000.0000.0000.000
72B75THR0-0.0170.00417.3540.0050.0050.0000.0000.0000.000
73B76LEU0-0.014-0.02114.435-0.005-0.0050.0000.0000.0000.000
74B77ASP-1-0.765-0.86912.3460.4720.4720.0000.0000.0000.000
75B78LEU00.0190.0126.487-0.047-0.0470.0000.0000.0000.000
76B79TRP00.006-0.0027.5430.2580.2580.0000.0000.0000.000
77B80ALA00.0620.0312.294-0.629-0.1970.940-0.461-0.9100.000
78B81GLY0-0.014-0.0144.268-0.0440.056-0.001-0.008-0.0900.000
79B82GLN0-0.031-0.0216.743-0.071-0.0710.0000.0000.0000.000
80B83GLN0-0.026-0.0074.638-0.679-0.548-0.001-0.002-0.1280.000
81B84LEU0-0.021-0.0046.7010.4060.4060.0000.0000.0000.000
82B85LEU0-0.027-0.0242.329-1.0780.0220.745-0.394-1.4510.001
83B86TRP0-0.027-0.0326.738-0.300-0.3000.0000.0000.0000.000
84B87LYS10.8150.8869.967-0.355-0.3550.0000.0000.0000.000
85B88GLY00.0200.02113.397-0.046-0.0460.0000.0000.0000.000
86B89SER0-0.021-0.01516.257-0.001-0.0010.0000.0000.0000.000
87B90PHE0-0.016-0.00919.087-0.003-0.0030.0000.0000.0000.000
88B91LYS10.9040.95520.944-0.112-0.1120.0000.0000.0000.000
89B92PRO00.0240.00624.173-0.006-0.0060.0000.0000.0000.000
90B93SER0-0.017-0.02225.655-0.004-0.0040.0000.0000.0000.000
91B94GLU-1-0.885-0.91726.6560.1020.1020.0000.0000.0000.000
92B95HIS0-0.071-0.03222.9770.0020.0020.0000.0000.0000.000
93B96VAL00.0250.01925.2990.0040.0040.0000.0000.0000.000
94B97LYS10.8570.91925.145-0.074-0.0740.0000.0000.0000.000
95B98PRO0-0.021-0.00327.9990.0020.0020.0000.0000.0000.000
96B99ARG10.8680.91229.441-0.065-0.0650.0000.0000.0000.000
97B100ALA0-0.013-0.00831.260-0.003-0.0030.0000.0000.0000.000
98B101PRO0-0.0050.00533.251-0.001-0.0010.0000.0000.0000.000
99B102GLY00.0300.00536.439-0.002-0.0020.0000.0000.0000.000
100B103ASN0-0.045-0.03638.081-0.001-0.0010.0000.0000.0000.000
101B104LEU0-0.0230.00740.696-0.001-0.0010.0000.0000.0000.000
102B105THR0-0.048-0.01742.528-0.002-0.0020.0000.0000.0000.000
103B106VAL00.010-0.00545.9250.0010.0010.0000.0000.0000.000
104B107HIS00.0100.01149.017-0.001-0.0010.0000.0000.0000.000
105B108THR0-0.036-0.03252.5750.0000.0000.0000.0000.0000.000
106B109ASN0-0.0050.01555.4230.0000.0000.0000.0000.0000.000
107B110VAL0-0.059-0.02557.428-0.001-0.0010.0000.0000.0000.000
108B111SER0-0.046-0.04860.6660.0000.0000.0000.0000.0000.000
109B112ASP-1-0.807-0.88359.9420.0040.0040.0000.0000.0000.000
110B113THR0-0.054-0.02556.5040.0000.0000.0000.0000.0000.000
111B114LEU00.0520.04350.685-0.001-0.0010.0000.0000.0000.000
112B115LEU0-0.026-0.00951.4250.0010.0010.0000.0000.0000.000
113B116LEU0-0.0050.00245.578-0.001-0.0010.0000.0000.0000.000
114B117THR00.007-0.00646.8630.0010.0010.0000.0000.0000.000
115B118TRP0-0.019-0.00541.059-0.002-0.0020.0000.0000.0000.000
116B119SER00.0220.01240.3110.0000.0000.0000.0000.0000.000
117B120ASN00.0460.02339.1000.0030.0030.0000.0000.0000.000
118B121PRO0-0.048-0.03334.691-0.001-0.0010.0000.0000.0000.000
119B122TYR0-0.027-0.01631.3690.0000.0000.0000.0000.0000.000
120B123PRO00.0160.01036.255-0.004-0.0040.0000.0000.0000.000
121B124PRO00.000-0.04039.2460.0020.0020.0000.0000.0000.000
122B125ASP-1-0.910-0.94739.2120.0480.0480.0000.0000.0000.000
123B126ASN00.0170.02533.5300.0020.0020.0000.0000.0000.000
124B127TYR00.0360.00835.296-0.004-0.0040.0000.0000.0000.000
125B128LEU0-0.0060.00132.377-0.002-0.0020.0000.0000.0000.000
126B129TYR0-0.0100.02437.006-0.004-0.0040.0000.0000.0000.000
127B130ASN0-0.013-0.02739.837-0.001-0.0010.0000.0000.0000.000
128B131HIS0-0.065-0.05038.469-0.003-0.0030.0000.0000.0000.000
129B132LEU0-0.0360.00136.1620.0000.0000.0000.0000.0000.000
130B133THR0-0.058-0.02238.969-0.003-0.0030.0000.0000.0000.000
131B134TYR00.0230.00039.0310.0020.0020.0000.0000.0000.000
132B135ALA00.0160.01338.779-0.001-0.0010.0000.0000.0000.000
133B136VAL00.0100.00039.8960.0000.0000.0000.0000.0000.000
134B137ASN0-0.059-0.02240.079-0.001-0.0010.0000.0000.0000.000
135B138ILE00.0110.00342.099-0.001-0.0010.0000.0000.0000.000
136B139TRP00.010-0.01539.6020.0010.0010.0000.0000.0000.000
137B140SER00.0650.04445.4200.0000.0000.0000.0000.0000.000
138B141GLU-1-0.801-0.89344.625-0.007-0.0070.0000.0000.0000.000
139B142ASN0-0.077-0.04245.392-0.001-0.0010.0000.0000.0000.000
140B143ASP-1-0.851-0.91945.502-0.009-0.0090.0000.0000.0000.000
141B144PRO00.0420.02141.5620.0010.0010.0000.0000.0000.000
142B145ALA0-0.0290.00843.1800.0000.0000.0000.0000.0000.000
143B146ASP-1-0.957-0.97844.5770.0040.0040.0000.0000.0000.000
144B147PHE0-0.076-0.05542.2340.0000.0000.0000.0000.0000.000
145B148ARG10.9550.97945.470-0.006-0.0060.0000.0000.0000.000
146B149ILE00.003-0.01040.1470.0000.0000.0000.0000.0000.000
147B150TYR00.0070.00744.139-0.001-0.0010.0000.0000.0000.000
148B151ASN00.001-0.00542.5060.0010.0010.0000.0000.0000.000
149B152VAL00.0000.00243.905-0.001-0.0010.0000.0000.0000.000
150B153THR0-0.004-0.00343.7980.0020.0020.0000.0000.0000.000
151B154TYR00.0590.02042.846-0.001-0.0010.0000.0000.0000.000
152B155LEU0-0.057-0.02043.9860.0000.0000.0000.0000.0000.000
153B156GLU-1-0.764-0.85847.3740.0180.0180.0000.0000.0000.000
154B157PRO0-0.0150.01243.8180.0000.0000.0000.0000.0000.000
155B158SER0-0.079-0.08945.633-0.002-0.0020.0000.0000.0000.000
156B159LEU0-0.001-0.00546.7470.0010.0010.0000.0000.0000.000
157B160ARG10.9150.97449.476-0.014-0.0140.0000.0000.0000.000
158B161ILE0-0.005-0.00348.7950.0000.0000.0000.0000.0000.000
159B162ALA00.0560.02353.449-0.001-0.0010.0000.0000.0000.000
160B163ALA00.009-0.01554.285-0.001-0.0010.0000.0000.0000.000
161B164SER0-0.008-0.01255.505-0.001-0.0010.0000.0000.0000.000
162B165THR00.0710.00657.5560.0000.0000.0000.0000.0000.000
163B166LEU0-0.0140.00459.462-0.001-0.0010.0000.0000.0000.000
164B167LYS10.8260.92757.951-0.003-0.0030.0000.0000.0000.000
165B168SER0-0.035-0.01355.9510.0000.0000.0000.0000.0000.000
166B169GLY00.0560.02056.6200.0000.0000.0000.0000.0000.000
167B170ILE0-0.0020.03050.811-0.001-0.0010.0000.0000.0000.000
168B171SER00.0020.03048.7390.0000.0000.0000.0000.0000.000
169B172TYR0-0.002-0.00747.6470.0000.0000.0000.0000.0000.000
170B173ARG10.8720.92840.0700.0050.0050.0000.0000.0000.000
171B174ALA00.014-0.00643.1460.0010.0010.0000.0000.0000.000
172B175ARG10.8960.94234.786-0.012-0.0120.0000.0000.0000.000
173B176VAL0-0.0100.00938.5820.0000.0000.0000.0000.0000.000
174B177ARG10.9260.98933.345-0.030-0.0300.0000.0000.0000.000
175B178ALA00.018-0.01034.996-0.002-0.0020.0000.0000.0000.000
176B179TRP00.0210.01134.2380.0030.0030.0000.0000.0000.000
177B180ALA00.0540.01734.591-0.003-0.0030.0000.0000.0000.000
178B181GLN00.009-0.00135.4560.0040.0040.0000.0000.0000.000
179B182ALA00.0110.00936.8550.0020.0020.0000.0000.0000.000
180B183TYR00.0000.00032.6460.0020.0020.0000.0000.0000.000
181B184ASN0-0.071-0.02732.3090.0020.0020.0000.0000.0000.000
182B185THR00.0110.02130.5360.0020.0020.0000.0000.0000.000
183B186THR0-0.0010.00426.977-0.006-0.0060.0000.0000.0000.000
184B187TRP0-0.018-0.02630.148-0.002-0.0020.0000.0000.0000.000
185B188SER00.0490.03529.8670.0030.0030.0000.0000.0000.000
186B189GLU-1-0.870-0.92527.0310.0410.0410.0000.0000.0000.000
187B190TRP0-0.033-0.03730.541-0.001-0.0010.0000.0000.0000.000
188B191SER00.0360.04133.2340.0000.0000.0000.0000.0000.000
189B192PRO00.003-0.00935.058-0.002-0.0020.0000.0000.0000.000
190B193SER0-0.032-0.01636.6170.0010.0010.0000.0000.0000.000
191B194THR0-0.0020.00239.544-0.003-0.0030.0000.0000.0000.000
192B195LYS10.8410.89343.0970.0060.0060.0000.0000.0000.000
193B196TRP00.0340.02546.2480.0000.0000.0000.0000.0000.000
194B197HIS0-0.015-0.01950.0660.0000.0000.0000.0000.0000.000