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: R5668

Calculation Name: 3IF8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IF8

Chain ID: A

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 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 265
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2969732.56341
FMO2-HF: Nuclear repulsion 2866076.557501
FMO2-HF: Total energy -103656.005909
FMO2-MP2: Total energy -103960.491281


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:-4:GLY)


Summations of interaction energy for fragment #1(A:-4:GLY)
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.
-5.752-2.9950.3-1.385-1.6740.006
Interaction energy analysis for fragmet #1(A:-4:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.006
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].
3A-2LEU0-0.006-0.0022.865-3.110-0.7380.283-1.217-1.4390.007
4A-1GLY0-0.0030.0034.250-1.789-1.751-0.001-0.031-0.0060.000
5A0SER0-0.043-0.0326.395-0.099-0.0990.0000.0000.0000.000
6A1MET00.0260.0038.3690.2680.2680.0000.0000.0000.000
7A2TRP00.0370.0077.2550.0920.0920.0000.0000.0000.000
8A3GLU-1-0.874-0.8997.1280.6970.6970.0000.0000.0000.000
9A4ARG10.8930.9178.0910.0550.0550.0000.0000.0000.000
10A5LEU00.0130.01811.2250.0650.0650.0000.0000.0000.000
11A6ASN00.0330.0106.804-0.076-0.0760.0000.0000.0000.000
12A7CYS0-0.024-0.0039.0730.2260.2260.0000.0000.0000.000
13A8ALA00.0340.0146.2220.1170.1170.0000.0000.0000.000
14A9ALA00.000-0.0077.8700.0300.0300.0000.0000.0000.000
15A10GLU-1-0.680-0.82710.9020.4070.4070.0000.0000.0000.000
16A11ASP-1-0.774-0.8849.1790.9840.9840.0000.0000.0000.000
17A12PHE0-0.029-0.0129.177-0.092-0.0920.0000.0000.0000.000
18A13TYR00.0530.02510.763-0.180-0.1800.0000.0000.0000.000
19A14SER00.0170.01413.765-0.114-0.1140.0000.0000.0000.000
20A15ARG10.8490.9228.036-1.132-1.1320.0000.0000.0000.000
21A16LEU00.0080.01213.611-0.096-0.0960.0000.0000.0000.000
22A17LEU00.0130.00815.883-0.073-0.0730.0000.0000.0000.000
23A18GLN0-0.041-0.01816.592-0.089-0.0890.0000.0000.0000.000
24A19LYS10.8130.90016.845-0.388-0.3880.0000.0000.0000.000
25A20PHE00.0680.02519.543-0.039-0.0390.0000.0000.0000.000
26A21ASN00.0150.00121.928-0.042-0.0420.0000.0000.0000.000
27A22GLU-1-0.793-0.88121.1300.2510.2510.0000.0000.0000.000
28A23GLU-1-0.761-0.85522.9480.1450.1450.0000.0000.0000.000
29A24LYS10.7940.92425.131-0.216-0.2160.0000.0000.0000.000
30A25LYS10.8350.90127.595-0.143-0.1430.0000.0000.0000.000
31A26GLY00.0640.05126.489-0.010-0.0100.0000.0000.0000.000
32A27ILE0-0.022-0.03125.7420.0010.0010.0000.0000.0000.000
33A28ARG10.8370.91117.343-0.276-0.2760.0000.0000.0000.000
34A29LYS10.9130.97521.705-0.115-0.1150.0000.0000.0000.000
35A30ASP-1-0.777-0.88417.1700.2380.2380.0000.0000.0000.000
36A31PRO0-0.053-0.00816.7050.0260.0260.0000.0000.0000.000
37A32PHE00.0380.01011.3510.0040.0040.0000.0000.0000.000
38A33LEU00.0620.02710.2390.0400.0400.0000.0000.0000.000
39A34TYR0-0.051-0.0206.1990.1880.1880.0000.0000.0000.000
40A35GLU-1-0.813-0.9183.203-0.495-0.1480.018-0.137-0.229-0.001
41A36ALA0-0.0060.0095.709-0.406-0.4060.0000.0000.0000.000
42A37ASP-1-0.790-0.8837.937-0.145-0.1450.0000.0000.0000.000
43A38VAL0-0.0260.0018.1620.0240.0240.0000.0000.0000.000
44A39GLN0-0.009-0.0149.9200.1030.1030.0000.0000.0000.000
45A40VAL00.006-0.00611.756-0.010-0.0100.0000.0000.0000.000
46A41GLN00.0190.01314.5130.0070.0070.0000.0000.0000.000
47A42LEU0-0.034-0.00918.2680.0050.0050.0000.0000.0000.000
48A43ILE0-0.051-0.02121.069-0.018-0.0180.0000.0000.0000.000
49A44SER00.017-0.03524.489-0.001-0.0010.0000.0000.0000.000
50A45LYS10.8290.88427.336-0.154-0.1540.0000.0000.0000.000
51A46GLY00.0590.03430.919-0.005-0.0050.0000.0000.0000.000
52A47GLN0-0.042-0.00124.605-0.011-0.0110.0000.0000.0000.000
53A48PRO0-0.002-0.02128.5570.0010.0010.0000.0000.0000.000
54A49ASN00.0650.03426.5000.0100.0100.0000.0000.0000.000
55A50PRO0-0.026-0.02223.611-0.007-0.0070.0000.0000.0000.000
56A51LEU00.0380.02523.256-0.007-0.0070.0000.0000.0000.000
57A52LYS10.8780.94627.041-0.065-0.0650.0000.0000.0000.000
58A53ASN0-0.071-0.03229.308-0.002-0.0020.0000.0000.0000.000
59A54ILE0-0.061-0.02926.220-0.007-0.0070.0000.0000.0000.000
60A55LEU0-0.0120.01427.6740.0000.0000.0000.0000.0000.000
61A56ASN0-0.031-0.02531.777-0.004-0.0040.0000.0000.0000.000
62A57GLU-1-0.833-0.91630.7190.0690.0690.0000.0000.0000.000
63A58ASN0-0.036-0.03330.109-0.001-0.0010.0000.0000.0000.000
64A59ASP-1-0.880-0.92928.3330.1070.1070.0000.0000.0000.000
65A60ILE0-0.058-0.03124.5430.0040.0040.0000.0000.0000.000
66A61VAL00.0140.01322.3310.0070.0070.0000.0000.0000.000
67A62PHE0-0.010-0.02317.4580.0140.0140.0000.0000.0000.000
68A63ILE0-0.010-0.00318.705-0.016-0.0160.0000.0000.0000.000
69A64VAL0-0.009-0.01012.2950.0340.0340.0000.0000.0000.000
70A65GLU-1-0.810-0.90914.3670.0570.0570.0000.0000.0000.000
71A66LYS10.8830.92612.9960.1530.1530.0000.0000.0000.000
72A67VAL0-0.019-0.01112.2910.0250.0250.0000.0000.0000.000
73A68PRO0-0.0130.00314.759-0.035-0.0350.0000.0000.0000.000
74A97GLY00.0330.01724.9220.0000.0000.0000.0000.0000.000
75A98PRO0-0.062-0.03521.083-0.003-0.0030.0000.0000.0000.000
76A99LEU0-0.0090.00517.643-0.014-0.0140.0000.0000.0000.000
77A100ALA00.0000.00217.2550.0170.0170.0000.0000.0000.000
78A101LEU0-0.016-0.01111.406-0.022-0.0220.0000.0000.0000.000
79A102PRO00.0470.01612.8190.0140.0140.0000.0000.0000.000
80A103VAL00.0170.02613.9230.0130.0130.0000.0000.0000.000
81A104GLY0-0.003-0.00513.9870.0290.0290.0000.0000.0000.000
82A105LYS10.8300.8985.1680.3390.3390.0000.0000.0000.000
83A106ALA00.0280.00710.6860.1090.1090.0000.0000.0000.000
84A107ARG10.9860.97713.1740.0630.0630.0000.0000.0000.000
85A108GLN00.0260.0197.0620.0680.0680.0000.0000.0000.000
86A109LEU0-0.0140.0067.8550.1410.1410.0000.0000.0000.000
87A110ILE00.0280.02911.0850.0510.0510.0000.0000.0000.000
88A111GLY00.0290.02613.333-0.005-0.0050.0000.0000.0000.000
89A112LEU0-0.008-0.0157.3390.0030.0030.0000.0000.0000.000
90A113TYR0-0.017-0.03111.894-0.001-0.0010.0000.0000.0000.000
91A114THR0-0.0020.00014.850-0.046-0.0460.0000.0000.0000.000
92A115MET0-0.072-0.04111.535-0.049-0.0490.0000.0000.0000.000
93A116ALA00.0190.00613.930-0.032-0.0320.0000.0000.0000.000
94A117HIS10.8200.90515.936-0.359-0.3590.0000.0000.0000.000
95A118ASN0-0.0010.01618.975-0.044-0.0440.0000.0000.0000.000
96A119PRO00.0340.01320.8280.0150.0150.0000.0000.0000.000
97A120ASN0-0.032-0.02122.902-0.010-0.0100.0000.0000.0000.000
98A121MET0-0.052-0.00913.491-0.001-0.0010.0000.0000.0000.000
99A122THR0-0.017-0.01418.791-0.005-0.0050.0000.0000.0000.000
100A123HIS0-0.0200.00117.1810.0710.0710.0000.0000.0000.000
101A124LEU0-0.045-0.04214.580-0.049-0.0490.0000.0000.0000.000
102A125LYS10.7550.86710.044-0.892-0.8920.0000.0000.0000.000
103A126ILE0-0.071-0.02716.065-0.021-0.0210.0000.0000.0000.000
104A127ASN00.0090.00318.998-0.009-0.0090.0000.0000.0000.000
105A128LEU0-0.0030.00022.624-0.026-0.0260.0000.0000.0000.000
106A129PRO00.0040.00323.1590.0170.0170.0000.0000.0000.000
107A130VAL00.0110.00819.5310.0050.0050.0000.0000.0000.000
108A131THR0-0.009-0.00522.230-0.026-0.0260.0000.0000.0000.000
109A132ALA00.0300.00222.1360.0260.0260.0000.0000.0000.000
110A133LEU0-0.054-0.02717.9790.0010.0010.0000.0000.0000.000
111A134PRO00.0220.01021.283-0.013-0.0130.0000.0000.0000.000
112A135PRO00.0540.05120.8750.0320.0320.0000.0000.0000.000
113A136LEU0-0.049-0.00714.5070.0130.0130.0000.0000.0000.000
114A137TRP00.0300.00818.863-0.017-0.0170.0000.0000.0000.000
115A138VAL0-0.020-0.01713.9630.0210.0210.0000.0000.0000.000
116A139ARG10.8930.94817.102-0.110-0.1100.0000.0000.0000.000
117A140CYS0-0.057-0.02417.185-0.006-0.0060.0000.0000.0000.000
118A141ASP-1-0.795-0.89818.214-0.091-0.0910.0000.0000.0000.000
119A142SER0-0.031-0.00920.020-0.006-0.0060.0000.0000.0000.000
120A143SER0-0.047-0.03818.900-0.008-0.0080.0000.0000.0000.000
121A144ASP-1-0.822-0.89120.539-0.043-0.0430.0000.0000.0000.000
122A145PRO00.008-0.01122.2790.0080.0080.0000.0000.0000.000
123A146GLU-1-0.929-0.95624.797-0.001-0.0010.0000.0000.0000.000
124A147GLY0-0.039-0.01324.5110.0080.0080.0000.0000.0000.000
125A148THR0-0.056-0.06520.7240.0130.0130.0000.0000.0000.000
126A149CYS0-0.066-0.03421.658-0.004-0.0040.0000.0000.0000.000
127A150TRP00.0280.00020.3800.0120.0120.0000.0000.0000.000
128A151LEU0-0.0020.00416.589-0.011-0.0110.0000.0000.0000.000
129A152GLY00.0270.00319.4840.0160.0160.0000.0000.0000.000
130A153ALA0-0.038-0.01118.622-0.012-0.0120.0000.0000.0000.000
131A154GLU-1-0.828-0.89820.5500.1400.1400.0000.0000.0000.000
132A155LEU0-0.021-0.00521.172-0.002-0.0020.0000.0000.0000.000
133A156ILE00.0120.01724.693-0.010-0.0100.0000.0000.0000.000
134A157THR00.006-0.02127.5220.0100.0100.0000.0000.0000.000
135A158THR00.0200.01429.813-0.011-0.0110.0000.0000.0000.000
136A159ASN0-0.020-0.02533.0730.0000.0000.0000.0000.0000.000
137A160ASN0-0.021-0.01829.8170.0050.0050.0000.0000.0000.000
138A161SER0-0.0110.01229.3670.0120.0120.0000.0000.0000.000
139A162ILE00.0180.00323.048-0.005-0.0050.0000.0000.0000.000
140A163THR0-0.055-0.01527.150-0.011-0.0110.0000.0000.0000.000
141A164GLY00.0340.02125.323-0.008-0.0080.0000.0000.0000.000
142A165ILE0-0.028-0.01320.7250.0150.0150.0000.0000.0000.000
143A166VAL00.0120.02224.076-0.017-0.0170.0000.0000.0000.000
144A167LEU0-0.027-0.02719.5340.0170.0170.0000.0000.0000.000
145A168TYR0-0.041-0.03322.767-0.023-0.0230.0000.0000.0000.000
146A169VAL0-0.004-0.01622.0520.0060.0060.0000.0000.0000.000
147A170VAL00.0240.01923.717-0.003-0.0030.0000.0000.0000.000
148A171SER00.0160.03524.644-0.001-0.0010.0000.0000.0000.000
149A172CYS0-0.012-0.00726.6880.0040.0040.0000.0000.0000.000
150A173LYS10.8420.89928.0100.0040.0040.0000.0000.0000.000
151A174ALA00.0220.01031.8670.0040.0040.0000.0000.0000.000
152A175ASP-1-0.798-0.88434.638-0.015-0.0150.0000.0000.0000.000
153A176LYS10.9220.96737.9870.0110.0110.0000.0000.0000.000
154A177ASN0-0.092-0.05740.9500.0020.0020.0000.0000.0000.000
155A178TYR00.0370.02039.7940.0000.0000.0000.0000.0000.000
156A179SER0-0.021-0.02240.328-0.001-0.0010.0000.0000.0000.000
157A180VAL00.0020.00539.3040.0000.0000.0000.0000.0000.000
158A181ASN00.0330.01341.5630.0010.0010.0000.0000.0000.000
159A182LEU00.0860.05042.2360.0010.0010.0000.0000.0000.000
160A183GLU-1-0.746-0.87742.6970.0210.0210.0000.0000.0000.000
161A184ASN0-0.035-0.01740.9690.0010.0010.0000.0000.0000.000
162A185LEU00.0220.01736.8270.0000.0000.0000.0000.0000.000
163A186LYS10.9550.99338.586-0.023-0.0230.0000.0000.0000.000
164A187ASN0-0.028-0.02140.5080.0020.0020.0000.0000.0000.000
165A188LEU0-0.040-0.00733.5060.0000.0000.0000.0000.0000.000
166A189HIS00.0260.00534.3230.0000.0000.0000.0000.0000.000
167A190LYS10.8360.90036.698-0.019-0.0190.0000.0000.0000.000
168A191LYS10.9470.97337.986-0.010-0.0100.0000.0000.0000.000
169A192ARG10.9090.96827.409-0.038-0.0380.0000.0000.0000.000
170A193HIS0-0.003-0.01030.5930.0040.0040.0000.0000.0000.000
171A194HIS0-0.0170.00734.7900.0010.0010.0000.0000.0000.000
172A195LEU0-0.0040.00836.8290.0010.0010.0000.0000.0000.000
173A196SER00.010-0.00240.325-0.002-0.0020.0000.0000.0000.000
174A197THR0-0.027-0.01743.239-0.001-0.0010.0000.0000.0000.000
175A198VAL00.0160.00140.0610.0020.0020.0000.0000.0000.000
176A199THR00.0110.01241.860-0.003-0.0030.0000.0000.0000.000
177A200SER00.016-0.00440.7840.0000.0000.0000.0000.0000.000
178A201LYS10.9200.97438.447-0.048-0.0480.0000.0000.0000.000
179A202GLY00.0150.01640.1450.0000.0000.0000.0000.0000.000
180A203PHE0-0.052-0.04537.0170.0030.0030.0000.0000.0000.000
181A204ALA00.0220.02040.612-0.002-0.0020.0000.0000.0000.000
182A205GLN0-0.059-0.04036.2520.0010.0010.0000.0000.0000.000
183A206TYR00.0080.00940.971-0.002-0.0020.0000.0000.0000.000
184A207GLU-1-0.796-0.89139.3210.0260.0260.0000.0000.0000.000
185A208LEU0-0.034-0.02042.717-0.002-0.0020.0000.0000.0000.000
186A209PHE0-0.016-0.00743.900-0.001-0.0010.0000.0000.0000.000
187A210LYS10.8150.88937.915-0.021-0.0210.0000.0000.0000.000
188A211SER0-0.010-0.00540.374-0.003-0.0030.0000.0000.0000.000
189A222GLN00.0580.03637.3280.0010.0010.0000.0000.0000.000
190A223THR0-0.067-0.03838.609-0.003-0.0030.0000.0000.0000.000
191A224ALA00.0240.01438.310-0.002-0.0020.0000.0000.0000.000
192A225ILE0-0.018-0.00940.3140.0030.0030.0000.0000.0000.000
193A226ALA00.0220.02139.812-0.003-0.0030.0000.0000.0000.000
194A227LEU0-0.001-0.00141.8930.0020.0020.0000.0000.0000.000
195A228ASP-1-0.740-0.85937.8470.0460.0460.0000.0000.0000.000
196A229ILE0-0.011-0.01541.3540.0000.0000.0000.0000.0000.000
197A230SER0-0.026-0.00741.0700.0010.0010.0000.0000.0000.000
198A231TRP00.0120.00143.0420.0010.0010.0000.0000.0000.000
199A232SER0-0.038-0.02843.6960.0020.0020.0000.0000.0000.000
200A233PRO0-0.0210.00345.4420.0000.0000.0000.0000.0000.000
201A234VAL0-0.013-0.01142.8030.0000.0000.0000.0000.0000.000
202A235ASP-1-0.910-0.93845.9300.0210.0210.0000.0000.0000.000
203A236GLU-1-0.860-0.94147.7840.0140.0140.0000.0000.0000.000
204A237ILE0-0.069-0.04343.1690.0020.0020.0000.0000.0000.000
205A238LEU0-0.019-0.03143.317-0.001-0.0010.0000.0000.0000.000
206A239GLN0-0.0070.00645.5010.0010.0010.0000.0000.0000.000
207A240ILE00.0130.00847.0670.0010.0010.0000.0000.0000.000
208A241PRO0-0.019-0.00345.9740.0000.0000.0000.0000.0000.000
209A242PRO00.0280.03248.308-0.001-0.0010.0000.0000.0000.000
210A243LEU00.0330.00150.4590.0020.0020.0000.0000.0000.000
211A244SER0-0.0210.00151.0000.0000.0000.0000.0000.0000.000
212A245SER0-0.047-0.03746.5310.0020.0020.0000.0000.0000.000
213A246THR0-0.029-0.00543.5030.0010.0010.0000.0000.0000.000
214A247ALA00.010-0.01344.0050.0000.0000.0000.0000.0000.000
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