FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: M344Z

Calculation Name: 3IF8-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IF8

Chain ID: B

ChEMBL ID:

UniProt ID: Q9H900

Base Structure: X-ray

Registration Date: 2023-06-19

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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2664846.928019
FMO2-HF: Nuclear repulsion 2567806.238932
FMO2-HF: Total energy -97040.689087
FMO2-MP2: Total energy -97323.029887


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:339:LEU)


Summations of interaction energy for fragment #1(B:339:LEU)
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.
-3.559-1.5431.727-1.521-2.221-0.01
Interaction energy analysis for fragmet #1(B:339:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.026
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].
3B341LYS10.9840.9922.443-2.329-0.5001.728-1.505-2.051-0.010
4B342VAL00.0310.0184.0720.3640.551-0.001-0.016-0.1700.000
5B343ARG10.7750.8656.2490.2300.2300.0000.0000.0000.000
6B344SER00.010-0.0119.4030.0510.0510.0000.0000.0000.000
7B345ASP-1-0.902-0.93011.203-0.262-0.2620.0000.0000.0000.000
8B346LEU0-0.040-0.03013.4600.0450.0450.0000.0000.0000.000
9B347ASP-1-0.737-0.86916.482-0.141-0.1410.0000.0000.0000.000
10B348PHE00.0490.00820.2420.0040.0040.0000.0000.0000.000
11B349ALA00.0370.01522.7810.0080.0080.0000.0000.0000.000
12B350GLU-1-0.730-0.85717.712-0.182-0.1820.0000.0000.0000.000
13B351GLN0-0.077-0.04717.8330.0100.0100.0000.0000.0000.000
14B352LEU0-0.019-0.00719.3920.0090.0090.0000.0000.0000.000
15B353TRP00.0530.04217.9740.0110.0110.0000.0000.0000.000
16B354CYS0-0.049-0.02116.2740.0060.0060.0000.0000.0000.000
17B355LYS10.9510.97818.6330.1410.1410.0000.0000.0000.000
18B356MET0-0.0160.00321.1240.0120.0120.0000.0000.0000.000
19B357SER0-0.051-0.02019.6890.0120.0120.0000.0000.0000.000
20B358SER0-0.015-0.01319.3870.0080.0080.0000.0000.0000.000
21B359SER0-0.090-0.04221.3980.0050.0050.0000.0000.0000.000
22B360VAL0-0.031-0.00224.9670.0040.0040.0000.0000.0000.000
23B361ILE00.0230.01227.5430.0060.0060.0000.0000.0000.000
24B362SER0-0.036-0.02430.0760.0040.0040.0000.0000.0000.000
25B363TYR00.011-0.02232.510-0.004-0.0040.0000.0000.0000.000
26B364GLN00.0520.00634.624-0.005-0.0050.0000.0000.0000.000
27B365ASP-1-0.844-0.90330.618-0.024-0.0240.0000.0000.0000.000
28B366LEU0-0.0010.00629.127-0.005-0.0050.0000.0000.0000.000
29B367VAL00.0170.02032.121-0.004-0.0040.0000.0000.0000.000
30B368LYS10.9620.98834.1340.0200.0200.0000.0000.0000.000
31B369CYS0-0.009-0.00829.384-0.004-0.0040.0000.0000.0000.000
32B370PHE00.015-0.01128.533-0.005-0.0050.0000.0000.0000.000
33B371THR0-0.030-0.03332.628-0.001-0.0010.0000.0000.0000.000
34B372LEU0-0.019-0.00732.291-0.002-0.0020.0000.0000.0000.000
35B373ILE00.000-0.00128.398-0.003-0.0030.0000.0000.0000.000
36B374ILE00.0290.01132.204-0.002-0.0020.0000.0000.0000.000
37B375GLN00.0180.00835.274-0.002-0.0020.0000.0000.0000.000
38B376SER0-0.036-0.01232.2080.0000.0000.0000.0000.0000.000
39B377LEU0-0.038-0.02031.709-0.003-0.0030.0000.0000.0000.000
40B378GLN00.004-0.01235.2910.0000.0000.0000.0000.0000.000
41B379ARG10.7960.91836.4060.0540.0540.0000.0000.0000.000
42B380GLY00.0200.01236.8340.0000.0000.0000.0000.0000.000
43B381ASP-1-0.861-0.92534.931-0.064-0.0640.0000.0000.0000.000
44B382ILE0-0.085-0.03929.830-0.007-0.0070.0000.0000.0000.000
45B383GLN00.0120.00430.5610.0030.0030.0000.0000.0000.000
46B384PRO0-0.034-0.00426.961-0.009-0.0090.0000.0000.0000.000
47B385TRP00.0130.01118.7100.0120.0120.0000.0000.0000.000
48B386LEU00.002-0.01023.862-0.002-0.0020.0000.0000.0000.000
49B387HIS10.7580.89017.8730.2130.2130.0000.0000.0000.000
50B388SER00.008-0.00422.7280.0100.0100.0000.0000.0000.000
51B389GLY0-0.011-0.00224.320-0.003-0.0030.0000.0000.0000.000
52B390SER00.0180.00424.760-0.003-0.0030.0000.0000.0000.000
53B391ASN0-0.022-0.01326.7170.0000.0000.0000.0000.0000.000
54B392SER00.0350.03827.0590.0060.0060.0000.0000.0000.000
55B393LEU00.043-0.00229.225-0.004-0.0040.0000.0000.0000.000
56B394LEU00.0120.00326.804-0.002-0.0020.0000.0000.0000.000
57B395SER0-0.002-0.01827.743-0.003-0.0030.0000.0000.0000.000
58B396LYS10.9370.98529.5550.0310.0310.0000.0000.0000.000
59B397LEU0-0.030-0.02933.161-0.001-0.0010.0000.0000.0000.000
60B398ILE00.0370.02628.179-0.001-0.0010.0000.0000.0000.000
61B399HIS0-0.018-0.01329.219-0.003-0.0030.0000.0000.0000.000
62B400GLN0-0.011-0.02033.6920.0010.0010.0000.0000.0000.000
63B401SER0-0.0120.00134.5310.0030.0030.0000.0000.0000.000
64B402TYR0-0.0180.00131.4620.0000.0000.0000.0000.0000.000
65B403HIS0-0.034-0.01933.9070.0040.0040.0000.0000.0000.000
66B404GLY0-0.015-0.00438.0700.0030.0030.0000.0000.0000.000
67B405THR0-0.007-0.01040.6060.0000.0000.0000.0000.0000.000
68B406MET0-0.041-0.01135.8250.0010.0010.0000.0000.0000.000
69B407ASP-1-0.859-0.91739.459-0.031-0.0310.0000.0000.0000.000
70B408THR0-0.066-0.03940.481-0.001-0.0010.0000.0000.0000.000
71B409VAL0-0.026-0.01236.5940.0020.0020.0000.0000.0000.000
72B410SER00.0210.01439.8790.0030.0030.0000.0000.0000.000
73B411LEU0-0.0040.00335.1680.0010.0010.0000.0000.0000.000
74B412SER00.0150.01138.5990.0020.0020.0000.0000.0000.000
75B413GLY00.0570.01739.3800.0000.0000.0000.0000.0000.000
76B414THR00.0380.01235.923-0.002-0.0020.0000.0000.0000.000
77B415ILE00.0330.02834.8740.0000.0000.0000.0000.0000.000
78B416PRO00.0320.01833.370-0.003-0.0030.0000.0000.0000.000
79B417VAL00.0210.00430.917-0.002-0.0020.0000.0000.0000.000
80B418GLN0-0.0170.00230.0220.0020.0020.0000.0000.0000.000
81B419MET0-0.009-0.00529.719-0.001-0.0010.0000.0000.0000.000
82B420LEU00.0140.01124.640-0.006-0.0060.0000.0000.0000.000
83B421LEU00.004-0.01125.367-0.003-0.0030.0000.0000.0000.000
84B422GLU-1-0.853-0.91625.351-0.029-0.0290.0000.0000.0000.000
85B423ILE0-0.0030.00022.723-0.004-0.0040.0000.0000.0000.000
86B424GLY00.031-0.00621.127-0.012-0.0120.0000.0000.0000.000
87B425LEU0-0.022-0.00620.437-0.001-0.0010.0000.0000.0000.000
88B426ASP-1-0.904-0.94721.036-0.061-0.0610.0000.0000.0000.000
89B427LYS10.8830.94413.5290.1580.1580.0000.0000.0000.000
90B428LEU00.003-0.00515.797-0.020-0.0200.0000.0000.0000.000
91B429LYS10.9240.97816.5370.0230.0230.0000.0000.0000.000
92B430LYS10.9180.95716.6400.1200.1200.0000.0000.0000.000
93B431ASP-1-0.828-0.90512.536-0.223-0.2230.0000.0000.0000.000
94B432TYR00.007-0.00712.550-0.037-0.0370.0000.0000.0000.000
95B433ILE00.0060.00714.5390.0180.0180.0000.0000.0000.000
96B434SER0-0.090-0.04311.583-0.033-0.0330.0000.0000.0000.000
97B435PHE00.0230.0158.293-0.047-0.0470.0000.0000.0000.000
98B436PHE00.022-0.01111.3150.0410.0410.0000.0000.0000.000
99B437ILE0-0.016-0.01014.4760.0200.0200.0000.0000.0000.000
100B438GLY0-0.0150.00911.6730.0080.0080.0000.0000.0000.000
101B439GLN0-0.032-0.0157.146-0.288-0.2880.0000.0000.0000.000
102B440GLU-1-0.943-0.96011.0930.0460.0460.0000.0000.0000.000
103B441LEU0-0.050-0.03011.9460.0490.0490.0000.0000.0000.000
104B442ALA0-0.016-0.02415.7450.0040.0040.0000.0000.0000.000
105B443SER0-0.0020.01218.295-0.034-0.0340.0000.0000.0000.000
106B444LEU00.1080.01320.6550.0110.0110.0000.0000.0000.000
107B445ASN00.0160.01922.0440.0070.0070.0000.0000.0000.000
108B446HIS0-0.025-0.01422.3190.0090.0090.0000.0000.0000.000
109B447LEU00.0110.00118.3540.0110.0110.0000.0000.0000.000
110B448GLU-1-0.867-0.92222.946-0.014-0.0140.0000.0000.0000.000
111B449TYR0-0.016-0.00425.945-0.002-0.0020.0000.0000.0000.000
112B450PHE0-0.031-0.01322.5870.0010.0010.0000.0000.0000.000
113B451ILE00.0030.00920.430-0.004-0.0040.0000.0000.0000.000
114B452ALA0-0.041-0.01924.237-0.009-0.0090.0000.0000.0000.000
115B453PRO00.0210.00628.0220.0020.0020.0000.0000.0000.000
116B454SER0-0.029-0.01529.5630.0010.0010.0000.0000.0000.000
117B455VAL0-0.0180.00329.9910.0010.0010.0000.0000.0000.000
118B456ASP-1-0.794-0.90132.0390.0190.0190.0000.0000.0000.000
119B457ILE00.0410.00229.1370.0030.0030.0000.0000.0000.000
120B458GLN00.007-0.00429.2220.0050.0050.0000.0000.0000.000
121B459GLU-1-0.800-0.85829.6590.0560.0560.0000.0000.0000.000
122B460GLN0-0.037-0.02926.5890.0020.0020.0000.0000.0000.000
123B461VAL0-0.0070.00025.0390.0040.0040.0000.0000.0000.000
124B462TYR00.0460.03924.6500.0130.0130.0000.0000.0000.000
125B463ARG10.7760.84225.215-0.026-0.0260.0000.0000.0000.000
126B464VAL00.0180.01219.5170.0110.0110.0000.0000.0000.000
127B465GLN0-0.002-0.00820.4900.0090.0090.0000.0000.0000.000
128B466LYS10.8640.93721.607-0.065-0.0650.0000.0000.0000.000
129B467LEU0-0.030-0.00918.2230.0230.0230.0000.0000.0000.000
130B468HIS00.0140.00914.4310.0180.0180.0000.0000.0000.000
131B469HIS00.0140.01217.0520.0420.0420.0000.0000.0000.000
132B470ILE00.0140.00516.9150.0340.0340.0000.0000.0000.000
133B471LEU0-0.024-0.00810.6120.0580.0580.0000.0000.0000.000
134B472GLU-1-0.876-0.94513.7170.4070.4070.0000.0000.0000.000
135B473ILE0-0.0110.02015.7660.0600.0600.0000.0000.0000.000
136B474LEU0-0.017-0.02212.8240.0580.0580.0000.0000.0000.000
137B475VAL0-0.018-0.0209.8980.1390.1390.0000.0000.0000.000
138B476SER0-0.026-0.02812.2470.0720.0720.0000.0000.0000.000
139B477CYS0-0.023-0.00915.184-0.036-0.0360.0000.0000.0000.000
140B478MET0-0.0170.0078.7920.2100.2100.0000.0000.0000.000
141B479PRO0-0.089-0.04312.0180.0860.0860.0000.0000.0000.000
142B480PHE0-0.012-0.00912.990-0.066-0.0660.0000.0000.0000.000
143B481ILE0-0.0180.00014.027-0.083-0.0830.0000.0000.0000.000
144B482LYS10.9680.9867.932-1.805-1.8050.0000.0000.0000.000
145B483SER0-0.025-0.02910.515-0.036-0.0360.0000.0000.0000.000
146B484GLN00.0170.02511.386-0.187-0.1870.0000.0000.0000.000
147B485HIS00.0190.00711.7560.0430.0430.0000.0000.0000.000
148B486GLU-1-0.814-0.91713.9500.2610.2610.0000.0000.0000.000
149B487LEU0-0.0330.01616.755-0.022-0.0220.0000.0000.0000.000
150B488LEU00.0320.01210.752-0.008-0.0080.0000.0000.0000.000
151B489PHE00.0050.02615.292-0.037-0.0370.0000.0000.0000.000
152B490SER0-0.034-0.06017.275-0.037-0.0370.0000.0000.0000.000
153B491LEU0-0.0070.00916.937-0.030-0.0300.0000.0000.0000.000
154B492THR00.0640.00816.523-0.010-0.0100.0000.0000.0000.000
155B493GLN0-0.060-0.02618.797-0.046-0.0460.0000.0000.0000.000
156B494ILE0-0.079-0.04322.157-0.023-0.0230.0000.0000.0000.000
157B495CYS0-0.027-0.00320.572-0.009-0.0090.0000.0000.0000.000
158B496ILE00.0140.01320.038-0.021-0.0210.0000.0000.0000.000
159B497LYS10.8920.93523.491-0.116-0.1160.0000.0000.0000.000
160B498TYR00.016-0.00125.894-0.009-0.0090.0000.0000.0000.000
161B499TYR00.0840.03222.845-0.014-0.0140.0000.0000.0000.000
162B500LYS10.8740.95426.581-0.081-0.0810.0000.0000.0000.000
163B501GLN0-0.060-0.02328.689-0.016-0.0160.0000.0000.0000.000
164B502ASN0-0.0260.00229.661-0.006-0.0060.0000.0000.0000.000
165B503PRO00.0080.00729.4160.0020.0020.0000.0000.0000.000
166B504LEU0-0.046-0.05523.7640.0070.0070.0000.0000.0000.000
167B505ASP-1-0.934-0.96127.3280.1080.1080.0000.0000.0000.000
168B506GLU-1-0.907-0.94329.8920.1000.1000.0000.0000.0000.000
169B507GLN0-0.043-0.01329.0010.0190.0190.0000.0000.0000.000
170B508HIS00.0160.00327.060-0.019-0.0190.0000.0000.0000.000
171B509ILE0-0.026-0.00727.2300.0160.0160.0000.0000.0000.000
172B510PHE00.0050.01123.743-0.008-0.0080.0000.0000.0000.000
173B511GLN0-0.022-0.02525.6180.0120.0120.0000.0000.0000.000
174B512LEU00.0210.00719.405-0.010-0.0100.0000.0000.0000.000
175B513PRO0-0.041-0.01823.8170.0070.0070.0000.0000.0000.000
176B514VAL00.0670.03821.3260.0120.0120.0000.0000.0000.000
177B515ARG10.9550.97323.248-0.166-0.1660.0000.0000.0000.000
178B516PRO00.0760.01823.6010.0190.0190.0000.0000.0000.000
179B517THR00.013-0.00223.8310.0120.0120.0000.0000.0000.000
180B518ALA0-0.0110.00019.5030.0080.0080.0000.0000.0000.000
181B519VAL00.0440.02119.3220.0390.0390.0000.0000.0000.000
182B520LYS10.9210.97921.457-0.185-0.1850.0000.0000.0000.000
183B521ASN0-0.020-0.03119.094-0.040-0.0400.0000.0000.0000.000
184B522LEU00.0070.01518.174-0.003-0.0030.0000.0000.0000.000
185B523TYR00.0180.00122.220-0.014-0.0140.0000.0000.0000.000
186B524GLN0-0.018-0.00826.004-0.012-0.0120.0000.0000.0000.000
187B525SER0-0.0260.00426.921-0.018-0.0180.0000.0000.0000.000
188B526GLU-1-0.937-0.95825.1520.2220.2220.0000.0000.0000.000
189B527LYS10.8350.90628.356-0.155-0.1550.0000.0000.0000.000
190B528PRO0-0.0110.00330.5180.0080.0080.0000.0000.0000.000
191B529GLN00.021-0.00328.8880.0030.0030.0000.0000.0000.000
192B530LYS10.9210.94532.310-0.153-0.1530.0000.0000.0000.000
193B531TRP00.0010.01734.2050.0040.0040.0000.0000.0000.000
194B532ARG10.8910.91936.551-0.119-0.1190.0000.0000.0000.000
195B533VAL00.0110.02239.1960.0020.0020.0000.0000.0000.000
196B534GLU-1-0.894-0.96041.9740.0810.0810.0000.0000.0000.000
197B535ILE00.0020.00043.8460.0000.0000.0000.0000.0000.000
198B536TYR00.0440.00443.393-0.002-0.0020.0000.0000.0000.000
199B537SER00.0540.01748.7600.0000.0000.0000.0000.0000.000
200B538GLY00.0320.04149.793-0.002-0.0020.0000.0000.0000.000
201B539GLN00.024-0.01850.1640.0010.0010.0000.0000.0000.000
202B540LYS10.8510.94642.570-0.076-0.0760.0000.0000.0000.000
203B541LYS10.9440.95346.996-0.053-0.0530.0000.0000.0000.000
204B542ILE0-0.0200.00049.0260.0010.0010.0000.0000.0000.000
205B543LYS10.9030.94844.619-0.073-0.0730.0000.0000.0000.000
206B544THR00.0120.01148.486-0.002-0.0020.0000.0000.0000.000
207B545VAL0-0.040-0.02242.7930.0020.0020.0000.0000.0000.000
208B546TRP00.0590.03641.8010.0000.0000.0000.0000.0000.000
209B547GLN00.0400.03338.3760.0050.0050.0000.0000.0000.000
210B548LEU0-0.0090.01038.883-0.003-0.0030.0000.0000.0000.000
211B549SER00.012-0.00736.7380.0080.0080.0000.0000.0000.000
212B550ASP-1-0.855-0.91733.3020.1480.1480.0000.0000.0000.000
213B551SER00.0000.00134.5960.0010.0010.0000.0000.0000.000
214B552SER00.026-0.00237.141-0.003-0.0030.0000.0000.0000.000
215B553PRO0-0.047-0.01337.9310.0040.0040.0000.0000.0000.000
216B554ILE0-0.049-0.02039.011-0.001-0.0010.0000.0000.0000.000
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