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: V5MR1

Calculation Name: 4AB5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AB5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JXG8

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2550087.342572
FMO2-HF: Nuclear repulsion 2464420.611226
FMO2-HF: Total energy -85666.731347
FMO2-MP2: Total energy -85914.49279


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:92:GLY)


Summations of interaction energy for fragment #1(A:92: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.
-11.737-8.5418.995-6.658-5.535-0.062
Interaction energy analysis for fragmet #1(A:92:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / 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].
3A94ALA0-0.058-0.0283.735-0.3950.745-0.004-0.539-0.5980.001
4A95GLY0-0.0190.0003.7411.1411.4440.000-0.137-0.1670.000
5A96GLU-1-0.912-0.9633.482-2.609-2.0840.025-0.208-0.342-0.001
6A97LEU0-0.025-0.0155.8480.2960.2960.0000.0000.0000.000
7A98ARG10.8350.9159.1321.0391.0390.0000.0000.0000.000
8A99ILE00.000-0.01211.1970.0440.0440.0000.0000.0000.000
9A100ALA00.0010.00214.4900.0240.0240.0000.0000.0000.000
10A101VAL0-0.009-0.01817.7270.0220.0220.0000.0000.0000.000
11A102GLU-1-0.764-0.85220.671-0.173-0.1730.0000.0000.0000.000
12A103CYS00.0020.00423.1370.0200.0200.0000.0000.0000.000
13A104HIS0-0.001-0.01624.707-0.003-0.0030.0000.0000.0000.000
14A105THR00.003-0.00125.7660.0000.0000.0000.0000.0000.000
15A107PHE00.015-0.00619.5680.0010.0010.0000.0000.0000.000
16A108ASP-1-0.906-0.95622.331-0.028-0.0280.0000.0000.0000.000
17A109TRP00.0430.01221.3510.0080.0080.0000.0000.0000.000
18A110LEU00.0030.01017.6080.0050.0050.0000.0000.0000.000
19A111MET0-0.0090.00517.2590.0040.0040.0000.0000.0000.000
20A112PRO0-0.013-0.00317.6480.0220.0220.0000.0000.0000.000
21A113ALA00.0320.02518.0950.0210.0210.0000.0000.0000.000
22A114MET0-0.003-0.00712.3990.0090.0090.0000.0000.0000.000
23A115GLY0-0.089-0.04613.2940.0460.0460.0000.0000.0000.000
24A116GLU-1-0.827-0.89114.9410.1030.1030.0000.0000.0000.000
25A117PHE00.0350.0068.9470.0400.0400.0000.0000.0000.000
26A118ARG10.9650.9888.925-0.224-0.2240.0000.0000.0000.000
27A119PRO0-0.044-0.0239.6950.1290.1290.0000.0000.0000.000
28A120MET0-0.0200.00012.1250.0500.0500.0000.0000.0000.000
29A121TRP0-0.027-0.0228.338-0.066-0.0660.0000.0000.0000.000
30A122PRO0-0.013-0.0016.979-0.029-0.0290.0000.0000.0000.000
31A123GLN0-0.068-0.0453.2362.8753.7410.135-0.406-0.596-0.002
32A124VAL0-0.0060.0152.927-2.419-1.8500.501-0.686-0.384-0.007
33A125GLU-1-0.880-0.9352.021-10.409-10.5958.339-4.667-3.485-0.053
34A126LEU0-0.066-0.0474.557-0.126-0.147-0.001-0.0150.0370.000
35A127ASP-1-0.856-0.9328.366-0.460-0.4600.0000.0000.0000.000
36A128ILE0-0.053-0.02811.0470.0280.0280.0000.0000.0000.000
37A129VAL00.0070.01314.0140.0270.0270.0000.0000.0000.000
38A130SER0-0.055-0.04916.5000.0250.0250.0000.0000.0000.000
39A131GLY00.0200.00219.9990.0030.0030.0000.0000.0000.000
40A132PHE0-0.073-0.06119.2910.0050.0050.0000.0000.0000.000
41A133GLN0-0.064-0.04224.5910.0100.0100.0000.0000.0000.000
42A134ALA0-0.005-0.00125.8960.0090.0090.0000.0000.0000.000
43A135ASP-1-0.759-0.88925.493-0.197-0.1970.0000.0000.0000.000
44A136PRO0-0.0170.00220.623-0.014-0.0140.0000.0000.0000.000
45A137VAL00.0280.00020.701-0.034-0.0340.0000.0000.0000.000
46A138GLY00.0160.00021.820-0.022-0.0220.0000.0000.0000.000
47A139LEU0-0.059-0.03718.339-0.015-0.0150.0000.0000.0000.000
48A140LEU0-0.0060.02416.789-0.046-0.0460.0000.0000.0000.000
49A141LEU00.0130.01018.209-0.038-0.0380.0000.0000.0000.000
50A142GLN0-0.067-0.03220.175-0.016-0.0160.0000.0000.0000.000
51A143HIS0-0.017-0.00315.279-0.061-0.0610.0000.0000.0000.000
52A144ARG10.8330.92914.6180.2380.2380.0000.0000.0000.000
53A145ALA00.0060.00913.528-0.019-0.0190.0000.0000.0000.000
54A146ASP-1-0.772-0.85010.513-0.902-0.9020.0000.0000.0000.000
55A147LEU0-0.009-0.00413.5640.0400.0400.0000.0000.0000.000
56A148ALA00.0000.01215.741-0.003-0.0030.0000.0000.0000.000
57A149ILE0-0.022-0.00618.9050.0160.0160.0000.0000.0000.000
58A150VAL0-0.001-0.00121.6210.0040.0040.0000.0000.0000.000
59A151SER00.015-0.00425.1990.0050.0050.0000.0000.0000.000
60A152GLU-1-0.892-0.94128.289-0.093-0.0930.0000.0000.0000.000
61A153ALA0-0.006-0.00227.921-0.010-0.0100.0000.0000.0000.000
62A154GLU-1-0.895-0.92128.950-0.138-0.1380.0000.0000.0000.000
63A155LYS10.9350.94328.9930.0980.0980.0000.0000.0000.000
64A156GLN00.0090.00226.532-0.008-0.0080.0000.0000.0000.000
65A157ASN0-0.046-0.04227.448-0.001-0.0010.0000.0000.0000.000
66A158GLY00.0220.01324.087-0.005-0.0050.0000.0000.0000.000
67A159ILE00.0150.02721.200-0.030-0.0300.0000.0000.0000.000
68A160SER0-0.045-0.01922.1320.0170.0170.0000.0000.0000.000
69A161PHE00.0300.01122.446-0.013-0.0130.0000.0000.0000.000
70A162GLN00.0140.00920.7660.0200.0200.0000.0000.0000.000
71A163PRO00.0120.01924.072-0.003-0.0030.0000.0000.0000.000
72A164LEU0-0.044-0.00921.672-0.002-0.0020.0000.0000.0000.000
73A165PHE00.0510.00625.1880.0090.0090.0000.0000.0000.000
74A166ALA00.0000.00929.217-0.007-0.0070.0000.0000.0000.000
75A167TYR00.0720.03729.0790.0060.0060.0000.0000.0000.000
76A168GLU-1-0.835-0.91134.352-0.040-0.0400.0000.0000.0000.000
77A169MET0-0.053-0.01534.2990.0020.0020.0000.0000.0000.000
78A170VAL00.0120.01737.2910.0010.0010.0000.0000.0000.000
79A171GLY00.0430.02039.798-0.002-0.0020.0000.0000.0000.000
80A172ILE0-0.046-0.03139.1360.0030.0030.0000.0000.0000.000
81A173CYS0-0.024-0.02443.011-0.002-0.0020.0000.0000.0000.000
82A174ALA00.0650.03445.9170.0010.0010.0000.0000.0000.000
83A175PRO00.0290.01047.644-0.001-0.0010.0000.0000.0000.000
84A176ASP-1-0.904-0.94750.245-0.009-0.0090.0000.0000.0000.000
85A177HIS0-0.079-0.03549.2030.0010.0010.0000.0000.0000.000
86A178PRO00.025-0.00352.0190.0000.0000.0000.0000.0000.000
87A179LEU00.0370.01849.0420.0000.0000.0000.0000.0000.000
88A180ALA00.0410.02750.341-0.001-0.0010.0000.0000.0000.000
89A181ALA0-0.051-0.01251.2900.0010.0010.0000.0000.0000.000
90A182LYS10.7920.88751.8320.0250.0250.0000.0000.0000.000
91A183ASN00.014-0.01350.6030.0000.0000.0000.0000.0000.000
92A184VAL00.0120.01447.887-0.001-0.0010.0000.0000.0000.000
93A185TRP0-0.071-0.03544.5330.0000.0000.0000.0000.0000.000
94A186THR00.003-0.02847.544-0.002-0.0020.0000.0000.0000.000
95A187ALA00.0590.01147.0530.0000.0000.0000.0000.0000.000
96A188GLU-1-0.777-0.89848.028-0.037-0.0370.0000.0000.0000.000
97A189ASP-1-0.791-0.84749.729-0.027-0.0270.0000.0000.0000.000
98A190PHE00.0370.00543.6120.0010.0010.0000.0000.0000.000
99A191ILE0-0.049-0.01148.2760.0000.0000.0000.0000.0000.000
100A192GLY0-0.015-0.00650.565-0.001-0.0010.0000.0000.0000.000
101A193GLU-1-0.873-0.93047.609-0.023-0.0230.0000.0000.0000.000
102A194THR0-0.049-0.02744.115-0.002-0.0020.0000.0000.0000.000
103A195LEU00.0170.01640.6610.0020.0020.0000.0000.0000.000
104A196ILE0-0.035-0.03038.144-0.002-0.0020.0000.0000.0000.000
105A197THR0-0.035-0.02235.8280.0010.0010.0000.0000.0000.000
106A198TYR00.048-0.00230.9690.0030.0030.0000.0000.0000.000
107A199PRO0-0.059-0.01131.0110.0010.0010.0000.0000.0000.000
108A200VAL00.0280.02829.109-0.005-0.0050.0000.0000.0000.000
109A201PRO00.0350.01831.2330.0070.0070.0000.0000.0000.000
110A202ASP-1-0.793-0.91333.730-0.066-0.0660.0000.0000.0000.000
111A203GLU-1-0.869-0.91232.263-0.097-0.0970.0000.0000.0000.000
112A204MET0-0.037-0.01326.889-0.004-0.0040.0000.0000.0000.000
113A205LEU0-0.062-0.02531.5740.0040.0040.0000.0000.0000.000
114A206ASP-1-0.742-0.84933.874-0.072-0.0720.0000.0000.0000.000
115A207LEU0-0.0040.01035.4870.0020.0020.0000.0000.0000.000
116A208PRO00.005-0.01737.6570.0020.0020.0000.0000.0000.000
117A209LYS10.8570.92632.5080.1030.1030.0000.0000.0000.000
118A210LYS10.8290.89834.8190.0740.0740.0000.0000.0000.000
119A211ILE0-0.034-0.01940.1150.0030.0030.0000.0000.0000.000
120A212LEU0-0.064-0.01542.4110.0030.0030.0000.0000.0000.000
121A213ILE00.0410.02440.4490.0020.0020.0000.0000.0000.000
122A214PRO0-0.0170.00042.2590.0010.0010.0000.0000.0000.000
123A215LYS10.8110.89045.1430.0420.0420.0000.0000.0000.000
124A216ASN0-0.055-0.03147.1710.0010.0010.0000.0000.0000.000
125A217ILE0-0.043-0.00246.8510.0020.0020.0000.0000.0000.000
126A218ASN00.0320.00844.105-0.004-0.0040.0000.0000.0000.000
127A219PRO00.0150.03344.4620.0010.0010.0000.0000.0000.000
128A220PRO00.006-0.00844.878-0.003-0.0030.0000.0000.0000.000
129A221ARG10.8430.90639.8770.0550.0550.0000.0000.0000.000
130A222ARG10.9310.96740.4730.0310.0310.0000.0000.0000.000
131A223HIS0-0.019-0.01235.670-0.002-0.0020.0000.0000.0000.000
132A224SER0-0.012-0.01534.7670.0050.0050.0000.0000.0000.000
133A225GLU-1-0.780-0.89129.208-0.075-0.0750.0000.0000.0000.000
134A226LEU0-0.032-0.00929.2660.0000.0000.0000.0000.0000.000
135A227THR00.1140.04830.4840.0010.0010.0000.0000.0000.000
136A228ILE00.0340.02432.7310.0010.0010.0000.0000.0000.000
137A229ALA00.0030.00134.9810.0020.0020.0000.0000.0000.000
138A230ILE00.0090.01634.2790.0010.0010.0000.0000.0000.000
139A231ILE00.0110.01336.3700.0010.0010.0000.0000.0000.000
140A232GLN00.0300.01239.2480.0010.0010.0000.0000.0000.000
141A233LEU0-0.036-0.00639.5390.0010.0010.0000.0000.0000.000
142A234VAL0-0.0120.01341.1860.0010.0010.0000.0000.0000.000
143A235ALA00.0340.02243.3690.0010.0010.0000.0000.0000.000
144A236SER0-0.081-0.04644.8160.0020.0020.0000.0000.0000.000
145A237ARG10.8700.93347.0090.0140.0140.0000.0000.0000.000
146A238ARG10.7950.88844.9820.0160.0160.0000.0000.0000.000
147A239GLY00.0470.01944.650-0.002-0.0020.0000.0000.0000.000
148A240ILE0-0.0220.00944.1420.0020.0020.0000.0000.0000.000
149A241ALA00.0110.00238.698-0.002-0.0020.0000.0000.0000.000
150A242ALA00.007-0.00238.7010.0020.0020.0000.0000.0000.000
151A243LEU0-0.027-0.00833.539-0.003-0.0030.0000.0000.0000.000
152A244PRO00.0650.03631.3170.0020.0020.0000.0000.0000.000
153A245TYR0-0.031-0.01634.4730.0040.0040.0000.0000.0000.000
154A246TRP00.0320.01128.1320.0060.0060.0000.0000.0000.000
155A247THR00.000-0.00631.0860.0030.0030.0000.0000.0000.000
156A248VAL0-0.020-0.01833.3460.0040.0040.0000.0000.0000.000
157A249MET00.0040.01736.4320.0020.0020.0000.0000.0000.000
158A250PRO00.0440.01933.9520.0020.0020.0000.0000.0000.000
159A251TYR0-0.016-0.02633.5240.0050.0050.0000.0000.0000.000
160A252LEU0-0.0260.00339.7900.0010.0010.0000.0000.0000.000
161A253GLU-1-0.923-0.96738.5260.0050.0050.0000.0000.0000.000
162A254LYS10.8140.91838.231-0.003-0.0030.0000.0000.0000.000
163A255GLY0-0.0100.00543.6700.0000.0000.0000.0000.0000.000
164A256TYR0-0.031-0.01939.916-0.001-0.0010.0000.0000.0000.000
165A257VAL00.001-0.00541.211-0.001-0.0010.0000.0000.0000.000
166A258VAL0-0.028-0.00744.5960.0020.0020.0000.0000.0000.000
167A259HIS00.0440.01042.347-0.003-0.0030.0000.0000.0000.000
168A260ARG10.8140.90744.2120.0200.0200.0000.0000.0000.000
169A261GLN0-0.0100.00243.6350.0000.0000.0000.0000.0000.000
170A262ILE0-0.018-0.01541.0860.0010.0010.0000.0000.0000.000
171A263THR00.011-0.01144.190-0.001-0.0010.0000.0000.0000.000
172A264ALA0-0.032-0.01846.6860.0010.0010.0000.0000.0000.000
173A265ASP-1-0.915-0.95545.206-0.039-0.0390.0000.0000.0000.000
174A266GLY00.0040.01843.087-0.001-0.0010.0000.0000.0000.000
175A267LEU0-0.052-0.02837.562-0.002-0.0020.0000.0000.0000.000
176A268GLN00.0300.02535.526-0.004-0.0040.0000.0000.0000.000
177A269SER0-0.020-0.03032.050-0.003-0.0030.0000.0000.0000.000
178A270LYS10.8830.92431.4710.0740.0740.0000.0000.0000.000
179A271LEU00.0130.01425.808-0.006-0.0060.0000.0000.0000.000
180A272TYR00.024-0.00625.2350.0080.0080.0000.0000.0000.000
181A273ALA00.0410.02719.602-0.005-0.0050.0000.0000.0000.000
182A274ALA0-0.020-0.01120.4590.0110.0110.0000.0000.0000.000
183A275ILE00.0330.01016.626-0.026-0.0260.0000.0000.0000.000
184A276ARG10.8350.89213.2120.6100.6100.0000.0000.0000.000
185A277THR0-0.047-0.03119.016-0.001-0.0010.0000.0000.0000.000
186A278GLU-1-0.852-0.94516.785-0.398-0.3980.0000.0000.0000.000
187A279ASP-1-0.806-0.88413.969-0.668-0.6680.0000.0000.0000.000
188A280THR0-0.015-0.00916.2370.0050.0050.0000.0000.0000.000
189A281ASP-1-0.905-0.94317.948-0.232-0.2320.0000.0000.0000.000
190A282LYS10.8300.90610.7180.7990.7990.0000.0000.0000.000
191A283SER00.007-0.00214.1720.0220.0220.0000.0000.0000.000
192A284TYR00.005-0.0148.4570.0870.0870.0000.0000.0000.000
193A285LEU00.0310.02811.8430.0420.0420.0000.0000.0000.000
194A286ASN0-0.010-0.00714.3190.0700.0700.0000.0000.0000.000
195A287ASN0-0.005-0.00114.8300.0390.0390.0000.0000.0000.000
196A288PHE00.0450.01513.9120.0300.0300.0000.0000.0000.000
197A289CYS0-0.036-0.02215.9110.0210.0210.0000.0000.0000.000
198A290GLN0-0.096-0.05019.1210.0050.0050.0000.0000.0000.000
199A291ILE00.0270.02615.6920.0130.0130.0000.0000.0000.000
200A292ILE0-0.012-0.00318.3250.0140.0140.0000.0000.0000.000
201A293ARG10.8150.90121.3560.1210.1210.0000.0000.0000.000
202A294GLU-1-0.882-0.93722.767-0.022-0.0220.0000.0000.0000.000
203A295ARG10.8380.89720.515-0.023-0.0230.0000.0000.0000.000
204A296GLY00.0540.02324.5300.0040.0040.0000.0000.0000.000
205A297PHE0-0.037-0.04226.7910.0040.0040.0000.0000.0000.000
206A298ALA0-0.058-0.01727.6200.0040.0040.0000.0000.0000.000
207A299ASP-1-0.986-0.97427.3130.0110.0110.0000.0000.0000.000
208A300LEU0-0.033-0.00827.022-0.001-0.0010.0000.0000.0000.000
209A301PRO0-0.016-0.01031.042-0.003-0.0030.0000.0000.0000.000
210A302GLY00.006-0.01934.829-0.002-0.0020.0000.0000.0000.000
211A303LEU0-0.051-0.00528.772-0.004-0.0040.0000.0000.0000.000
212A304SER0-0.065-0.03733.0320.0030.0030.0000.0000.0000.000
213A305GLU-1-0.896-0.95431.824-0.051-0.0510.0000.0000.0000.000
214A306LEU0-0.095-0.04529.3090.0000.0000.0000.0000.0000.000
215A307GLU-1-0.960-0.96830.883-0.074-0.0740.0000.0000.0000.000