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: 166JZ

Calculation Name: 3IO0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IO0

Chain ID: A

ChEMBL ID:

UniProt ID: A5N734

Base Structure: X-ray

Registration Date: 2023-09-27

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2498231.042851
FMO2-HF: Nuclear repulsion 2414527.797315
FMO2-HF: Total energy -83703.245536
FMO2-MP2: Total energy -83945.199783


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:76:PRO)


Summations of interaction energy for fragment #1(A:76:PRO)
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.
-0.9040.6630.006-0.671-0.9020.001
Interaction energy analysis for fragmet #1(A:76:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.011
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].
3A78MET0-0.0070.0063.660-0.8730.6940.006-0.671-0.9020.001
4A79THR0-0.028-0.0365.4700.6500.6500.0000.0000.0000.000
5A80GLU-1-0.844-0.9117.781-1.204-1.2040.0000.0000.0000.000
6A81PHE0-0.0250.0038.8610.1770.1770.0000.0000.0000.000
7A82VAL0-0.053-0.02110.7310.0290.0290.0000.0000.0000.000
8A83GLY00.0640.02713.2460.0770.0770.0000.0000.0000.000
9A84THR0-0.051-0.01514.469-0.085-0.0850.0000.0000.0000.000
10A85ALA00.011-0.00116.6590.0180.0180.0000.0000.0000.000
11A86GLY00.0220.00420.431-0.006-0.0060.0000.0000.0000.000
12A87GLY0-0.034-0.02623.465-0.015-0.0150.0000.0000.0000.000
13A88ASP-1-0.820-0.91220.216-0.100-0.1000.0000.0000.0000.000
14A89THR0-0.060-0.02419.816-0.037-0.0370.0000.0000.0000.000
15A90VAL00.0130.00014.713-0.006-0.0060.0000.0000.0000.000
16A91GLY00.020-0.00516.2110.0370.0370.0000.0000.0000.000
17A92LEU0-0.039-0.02712.965-0.084-0.0840.0000.0000.0000.000
18A93VAL00.017-0.00413.7510.0960.0960.0000.0000.0000.000
19A94ILE0-0.005-0.00213.819-0.105-0.1050.0000.0000.0000.000
20A95ALA00.0340.00614.2650.0740.0740.0000.0000.0000.000
21A96ASN00.000-0.00416.1330.0920.0920.0000.0000.0000.000
22A97VAL00.0010.01917.980-0.033-0.0330.0000.0000.0000.000
23A98ASP-1-0.806-0.90119.681-0.284-0.2840.0000.0000.0000.000
24A99SER00.014-0.00221.1430.0220.0220.0000.0000.0000.000
25A100LEU0-0.028-0.01723.9060.0210.0210.0000.0000.0000.000
26A101LEU0-0.033-0.03220.4510.0170.0170.0000.0000.0000.000
27A102HIS0-0.056-0.03123.0010.0250.0250.0000.0000.0000.000
28A103LYS10.9500.96626.3320.1970.1970.0000.0000.0000.000
29A104HIS0-0.024-0.00325.9900.0190.0190.0000.0000.0000.000
30A105LEU00.0210.02023.171-0.005-0.0050.0000.0000.0000.000
31A106GLY00.0330.02027.7380.0100.0100.0000.0000.0000.000
32A107LEU0-0.038-0.00723.4610.0020.0020.0000.0000.0000.000
33A108ASP-1-0.740-0.85927.626-0.169-0.1690.0000.0000.0000.000
34A109ASN00.020-0.00627.011-0.027-0.0270.0000.0000.0000.000
35A110THR0-0.068-0.03927.058-0.005-0.0050.0000.0000.0000.000
36A111CYS0-0.0420.00226.015-0.010-0.0100.0000.0000.0000.000
37A112ARG10.8880.91922.0650.2620.2620.0000.0000.0000.000
38A113SER0-0.0370.00019.251-0.035-0.0350.0000.0000.0000.000
39A114ILE00.013-0.01918.6340.0330.0330.0000.0000.0000.000
40A115GLY00.0270.01718.174-0.052-0.0520.0000.0000.0000.000
41A116ILE0-0.047-0.02217.9030.0330.0330.0000.0000.0000.000
42A117ILE00.0260.01319.156-0.020-0.0200.0000.0000.0000.000
43A118SER0-0.0070.00719.3590.0350.0350.0000.0000.0000.000
44A119ALA00.0230.00920.259-0.011-0.0110.0000.0000.0000.000
45A120ARG10.8330.88721.2370.1540.1540.0000.0000.0000.000
46A121VAL00.006-0.00524.0850.0150.0150.0000.0000.0000.000
47A122GLY00.0340.04426.493-0.005-0.0050.0000.0000.0000.000
48A123ALA00.0470.01228.084-0.011-0.0110.0000.0000.0000.000
49A124PRO00.0090.00129.882-0.007-0.0070.0000.0000.0000.000
50A125ALA00.0100.01229.419-0.002-0.0020.0000.0000.0000.000
51A126GLN00.019-0.00224.7470.0060.0060.0000.0000.0000.000
52A127MET0-0.008-0.00127.425-0.010-0.0100.0000.0000.0000.000
53A128MET0-0.027-0.00329.8580.0000.0000.0000.0000.0000.000
54A129ALA0-0.0230.00226.2340.0030.0030.0000.0000.0000.000
55A130ALA00.0430.01726.322-0.006-0.0060.0000.0000.0000.000
56A131ASP-1-0.759-0.86027.301-0.102-0.1020.0000.0000.0000.000
57A132GLU-1-0.864-0.90828.910-0.088-0.0880.0000.0000.0000.000
58A133ALA00.0010.00925.0100.0020.0020.0000.0000.0000.000
59A134VAL0-0.007-0.00227.031-0.003-0.0030.0000.0000.0000.000
60A135LYS10.7590.88328.9170.1000.1000.0000.0000.0000.000
61A136GLY0-0.032-0.00428.8130.0100.0100.0000.0000.0000.000
62A137THR0-0.103-0.05624.126-0.009-0.0090.0000.0000.0000.000
63A138ASN0-0.060-0.03426.6200.0160.0160.0000.0000.0000.000
64A139THR0-0.041-0.02123.749-0.014-0.0140.0000.0000.0000.000
65A140GLU-1-0.867-0.93626.834-0.146-0.1460.0000.0000.0000.000
66A141VAL00.013-0.00227.341-0.018-0.0180.0000.0000.0000.000
67A142ALA0-0.0130.01026.1600.0120.0120.0000.0000.0000.000
68A143THR0-0.078-0.08626.4180.0190.0190.0000.0000.0000.000
69A144ILE00.005-0.00327.717-0.010-0.0100.0000.0000.0000.000
70A145GLU-1-0.882-0.89427.821-0.184-0.1840.0000.0000.0000.000
71A146LEU00.0280.00228.225-0.008-0.0080.0000.0000.0000.000
72A147PRO00.0280.05126.5020.0100.0100.0000.0000.0000.000
73A148ARG10.8690.93129.8400.0890.0890.0000.0000.0000.000
74A149ASP-1-0.817-0.90225.521-0.136-0.1360.0000.0000.0000.000
75A150THR0-0.040-0.00327.8590.0110.0110.0000.0000.0000.000
76A151LYS10.8430.93222.8030.0920.0920.0000.0000.0000.000
77A152GLY0-0.024-0.00327.878-0.001-0.0010.0000.0000.0000.000
78A153GLY0-0.031-0.00131.0850.0060.0060.0000.0000.0000.000
79A154ALA00.0540.00732.7910.0000.0000.0000.0000.0000.000
80A155GLY00.0670.00733.2960.0010.0010.0000.0000.0000.000
81A156HIS00.0000.00130.844-0.005-0.0050.0000.0000.0000.000
82A157GLY0-0.043-0.00727.1200.0080.0080.0000.0000.0000.000
83A158ILE0-0.010-0.02224.9990.0050.0050.0000.0000.0000.000
84A159PHE00.0210.01020.839-0.024-0.0240.0000.0000.0000.000
85A160ILE00.0200.01624.3840.0150.0150.0000.0000.0000.000
86A161VAL0-0.012-0.00522.471-0.029-0.0290.0000.0000.0000.000
87A162LEU0-0.011-0.00723.0370.0250.0250.0000.0000.0000.000
88A163LYS10.8170.91322.7880.1510.1510.0000.0000.0000.000
89A164ALA00.0640.01522.8020.0200.0200.0000.0000.0000.000
90A165ALA00.0310.02623.769-0.017-0.0170.0000.0000.0000.000
91A166ASP-1-0.841-0.89121.156-0.266-0.2660.0000.0000.0000.000
92A167VAL00.0410.01315.324-0.006-0.0060.0000.0000.0000.000
93A168SER0-0.080-0.05518.038-0.016-0.0160.0000.0000.0000.000
94A169ASP-1-0.795-0.89519.003-0.177-0.1770.0000.0000.0000.000
95A170ALA00.0100.00219.3980.0060.0060.0000.0000.0000.000
96A171ARG10.8060.89111.0570.6230.6230.0000.0000.0000.000
97A172ARG10.9450.98117.8560.1800.1800.0000.0000.0000.000
98A173ALA00.0320.01620.6120.0190.0190.0000.0000.0000.000
99A174VAL0-0.0020.01517.1710.0180.0180.0000.0000.0000.000
100A175GLU-1-0.795-0.90515.203-0.330-0.3300.0000.0000.0000.000
101A176ILE0-0.062-0.02619.1510.0310.0310.0000.0000.0000.000
102A177ALA00.0240.00422.5530.0180.0180.0000.0000.0000.000
103A178LEU0-0.0070.01516.8150.0170.0170.0000.0000.0000.000
104A179LYS10.9110.96221.2480.1150.1150.0000.0000.0000.000
105A180GLN0-0.0060.00122.6900.0300.0300.0000.0000.0000.000
106A181THR00.0420.00823.9600.0090.0090.0000.0000.0000.000
107A182ASP-1-0.803-0.91123.531-0.078-0.0780.0000.0000.0000.000
108A183LYS10.7430.86526.5760.0950.0950.0000.0000.0000.000
109A184TYR0-0.011-0.02829.5620.0110.0110.0000.0000.0000.000
110A185LEU00.0370.03525.9730.0050.0050.0000.0000.0000.000
111A186GLY00.0340.02130.3180.0070.0070.0000.0000.0000.000
112A187ASN0-0.080-0.05332.8210.0120.0120.0000.0000.0000.000
113A188VAL00.005-0.00431.490-0.001-0.0010.0000.0000.0000.000
114A189TYR0-0.003-0.01734.0640.0030.0030.0000.0000.0000.000
115A190LEU00.008-0.00731.041-0.004-0.0040.0000.0000.0000.000
116A191CYS0-0.066-0.04135.7490.0050.0050.0000.0000.0000.000
117A192ASP-1-0.825-0.90137.090-0.020-0.0200.0000.0000.0000.000
118A193ALA00.0090.01038.329-0.003-0.0030.0000.0000.0000.000
119A194GLY0-0.030-0.01838.088-0.003-0.0030.0000.0000.0000.000
120A195HIS0-0.050-0.01635.6920.0040.0040.0000.0000.0000.000
121A196LEU0-0.024-0.00837.5440.0010.0010.0000.0000.0000.000
122A197GLU-1-0.744-0.85933.011-0.083-0.0830.0000.0000.0000.000
123A198VAL0-0.033-0.02137.1810.0000.0000.0000.0000.0000.000
124A199GLN0-0.049-0.04433.1950.0050.0050.0000.0000.0000.000
125A200TYR00.039-0.00637.0070.0020.0020.0000.0000.0000.000
126A201THR00.0120.00535.755-0.001-0.0010.0000.0000.0000.000
127A202ALA00.003-0.00337.8380.0030.0030.0000.0000.0000.000
128A203ARG10.8700.94137.6610.0740.0740.0000.0000.0000.000
129A204ALA00.0440.03436.889-0.006-0.0060.0000.0000.0000.000
130A205SER0-0.015-0.03033.6620.0000.0000.0000.0000.0000.000
131A206LEU00.0840.02931.633-0.001-0.0010.0000.0000.0000.000
132A207ILE0-0.0240.00028.231-0.003-0.0030.0000.0000.0000.000
133A208PHE00.0420.00032.4000.0000.0000.0000.0000.0000.000
134A209GLU-1-0.835-0.89935.815-0.092-0.0920.0000.0000.0000.000
135A210LYS10.8390.92831.0530.1580.1580.0000.0000.0000.000
136A211ALA0-0.038-0.01533.7480.0010.0010.0000.0000.0000.000
137A212PHE0-0.025-0.02635.6800.0030.0030.0000.0000.0000.000
138A213GLY00.0320.03339.2930.0050.0050.0000.0000.0000.000
139A214ALA0-0.056-0.02639.2440.0050.0050.0000.0000.0000.000
140A215PRO0-0.002-0.01541.172-0.002-0.0020.0000.0000.0000.000
141A216SER00.003-0.01239.7700.0010.0010.0000.0000.0000.000
142A217GLY0-0.011-0.00439.9020.0050.0050.0000.0000.0000.000
143A218GLN0-0.048-0.02240.9780.0070.0070.0000.0000.0000.000
144A219ALA00.0010.01541.394-0.003-0.0030.0000.0000.0000.000
145A220PHE00.017-0.00537.8210.0010.0010.0000.0000.0000.000
146A221GLY00.0210.00540.2580.0000.0000.0000.0000.0000.000
147A222ILE0-0.0180.01035.731-0.001-0.0010.0000.0000.0000.000
148A223MET0-0.042-0.01239.5240.0040.0040.0000.0000.0000.000
149A224HIS0-0.004-0.00834.7750.0020.0020.0000.0000.0000.000
150A225ALA00.0090.00039.5310.0020.0020.0000.0000.0000.000
151A226ALA0-0.0150.01838.594-0.002-0.0020.0000.0000.0000.000
152A227PRO00.0580.01740.5850.0020.0020.0000.0000.0000.000
153A228ALA00.0160.00242.6000.0010.0010.0000.0000.0000.000
154A229GLY0-0.015-0.00644.1000.0000.0000.0000.0000.0000.000
155A230VAL00.0330.00843.8800.0010.0010.0000.0000.0000.000
156A231GLY00.0370.02143.8710.0000.0000.0000.0000.0000.000
157A232MET00.0140.00244.564-0.002-0.0020.0000.0000.0000.000
158A233ILE00.0130.01848.1510.0010.0010.0000.0000.0000.000
159A234VAL0-0.0220.01143.3400.0010.0010.0000.0000.0000.000
160A235ALA00.0130.00646.4380.0000.0000.0000.0000.0000.000
161A236ASP-1-0.808-0.88847.590-0.032-0.0320.0000.0000.0000.000
162A237THR0-0.028-0.04449.6020.0010.0010.0000.0000.0000.000
163A238ALA00.0090.02447.0440.0010.0010.0000.0000.0000.000
164A239LEU0-0.023-0.01049.0860.0000.0000.0000.0000.0000.000
165A240LYS10.8030.88151.5360.0310.0310.0000.0000.0000.000
166A241THR0-0.073-0.02651.2320.0020.0020.0000.0000.0000.000
167A242ALA0-0.003-0.00551.5520.0010.0010.0000.0000.0000.000
168A243ASP-1-0.828-0.89953.455-0.040-0.0400.0000.0000.0000.000
169A244VAL0-0.064-0.02448.469-0.002-0.0020.0000.0000.0000.000
170A245LYS10.8420.91848.8440.0430.0430.0000.0000.0000.000
171A246LEU00.003-0.00746.693-0.002-0.0020.0000.0000.0000.000
172A247ILE0-0.048-0.01243.1260.0000.0000.0000.0000.0000.000
173A248THR0-0.003-0.01041.134-0.004-0.0040.0000.0000.0000.000
174A249TYR00.0360.01244.1440.0020.0020.0000.0000.0000.000
175A250GLY00.0120.01641.691-0.003-0.0030.0000.0000.0000.000
176A251SER00.0290.00242.7550.0030.0030.0000.0000.0000.000
177A252PRO00.0580.02440.925-0.003-0.0030.0000.0000.0000.000
178A253THR0-0.055-0.04041.417-0.001-0.0010.0000.0000.0000.000
179A254ASN0-0.025-0.00743.118-0.003-0.0030.0000.0000.0000.000
180A255GLY00.0340.02640.8090.0000.0000.0000.0000.0000.000
181A256VAL0-0.028-0.00539.579-0.005-0.0050.0000.0000.0000.000
182A257LEU0-0.042-0.00537.177-0.004-0.0040.0000.0000.0000.000
183A258SER0-0.011-0.01733.1110.0040.0040.0000.0000.0000.000
184A259TYR0-0.047-0.03535.291-0.002-0.0020.0000.0000.0000.000
185A260THR0-0.060-0.02834.6770.0020.0020.0000.0000.0000.000
186A261ASN0-0.005-0.00537.3450.0040.0040.0000.0000.0000.000
187A262GLU-1-0.751-0.88135.795-0.073-0.0730.0000.0000.0000.000
188A263ILE0-0.069-0.03340.5600.0000.0000.0000.0000.0000.000
189A264LEU0-0.024-0.00837.9700.0010.0010.0000.0000.0000.000
190A265ILE00.005-0.00241.8330.0010.0010.0000.0000.0000.000
191A266THR0-0.011-0.00240.218-0.003-0.0030.0000.0000.0000.000
192A267ILE00.0080.00042.4750.0020.0020.0000.0000.0000.000
193A268SER0-0.023-0.02343.423-0.003-0.0030.0000.0000.0000.000
194A269GLY00.0420.02045.5180.0030.0030.0000.0000.0000.000
195A270ASP-1-0.864-0.92846.824-0.042-0.0420.0000.0000.0000.000
196A271SER00.008-0.00745.1320.0010.0010.0000.0000.0000.000
197A272GLY00.0190.01646.3870.0000.0000.0000.0000.0000.000
198A273ALA00.0420.02249.0760.0010.0010.0000.0000.0000.000
199A274VAL00.0230.00843.5610.0000.0000.0000.0000.0000.000
200A275LEU0-0.004-0.00142.2740.0000.0000.0000.0000.0000.000
201A276GLN0-0.047-0.00445.7980.0020.0020.0000.0000.0000.000
202A277SER00.026-0.01748.1010.0020.0020.0000.0000.0000.000
203A278LEU00.009-0.00341.4610.0000.0000.0000.0000.0000.000
204A279THR0-0.067-0.04544.6740.0010.0010.0000.0000.0000.000
205A280ALA0-0.021-0.00546.1060.0020.0020.0000.0000.0000.000
206A281ALA00.0360.02345.0520.0010.0010.0000.0000.0000.000
207A282ARG10.8590.93939.0960.0370.0370.0000.0000.0000.000
208A283LYS10.9590.97644.1590.0210.0210.0000.0000.0000.000
209A284ALA00.0080.00647.2430.0020.0020.0000.0000.0000.000
210A285GLY00.0590.01944.3690.0010.0010.0000.0000.0000.000
211A286LEU0-0.038-0.02141.1500.0010.0010.0000.0000.0000.000
212A287SER0-0.0240.00344.8650.0030.0030.0000.0000.0000.000
213A288ILE00.0100.01147.3140.0020.0020.0000.0000.0000.000
214A289LEU00.0390.00541.4630.0010.0010.0000.0000.0000.000
215A290ARG10.8210.89642.0360.0160.0160.0000.0000.0000.000
216A291SER0-0.063-0.03447.3790.0020.0020.0000.0000.0000.000
217A292MET0-0.098-0.04245.0430.0000.0000.0000.0000.0000.000
218A293GLY00.0010.00747.2840.0000.0000.0000.0000.0000.000
219A294GLN0-0.049-0.03141.4640.0010.0010.0000.0000.0000.000
220A295ASP-1-0.823-0.91641.721-0.007-0.0070.0000.0000.0000.000
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