Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: VRG81

Calculation Name: 3MSQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MSQ

Chain ID: A

ChEMBL ID:

UniProt ID: B2J5W7

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2630512.082146
FMO2-HF: Nuclear repulsion 2544858.484835
FMO2-HF: Total energy -85653.597311
FMO2-MP2: Total energy -85904.63555


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:6:THR)


Summations of interaction energy for fragment #1(A:6:THR)
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.
-0.810.868-0.01-0.871-0.7960.002
Interaction energy analysis for fragmet #1(A:6:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.016
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].
3A8ASN0-0.017-0.0183.702-0.0081.670-0.010-0.871-0.7960.002
4A9ASN00.0840.0256.443-0.157-0.1570.0000.0000.0000.000
5A10ASP-1-0.893-0.9338.515-0.389-0.3890.0000.0000.0000.000
6A11LYS10.9530.97310.2470.8670.8670.0000.0000.0000.000
7A12GLY00.0460.04011.4720.0500.0500.0000.0000.0000.000
8A13LEU0-0.0040.00013.1820.0720.0720.0000.0000.0000.000
9A14LEU0-0.011-0.01714.0770.0360.0360.0000.0000.0000.000
10A15ALA00.0280.02015.9650.0380.0380.0000.0000.0000.000
11A16TYR00.0270.00617.4070.0380.0380.0000.0000.0000.000
12A17ILE0-0.009-0.00718.5200.0300.0300.0000.0000.0000.000
13A18GLN00.0080.01020.4420.0010.0010.0000.0000.0000.000
14A19PHE0-0.0020.01921.7230.0210.0210.0000.0000.0000.000
15A20LEU00.0050.00822.6270.0210.0210.0000.0000.0000.000
16A21ALA00.0180.01124.9620.0120.0120.0000.0000.0000.000
17A22SER0-0.053-0.04425.6130.0120.0120.0000.0000.0000.000
18A23SER0-0.021-0.02727.3150.0060.0060.0000.0000.0000.000
19A24ALA0-0.0380.00129.7770.0090.0090.0000.0000.0000.000
20A25GLN0-0.032-0.01230.5180.0100.0100.0000.0000.0000.000
21A26LYS10.8320.90933.9970.0990.0990.0000.0000.0000.000
22A27ILE0-0.015-0.00131.502-0.007-0.0070.0000.0000.0000.000
23A28GLY00.0140.00533.3120.0080.0080.0000.0000.0000.000
24A29ASP-1-0.870-0.92634.247-0.102-0.1020.0000.0000.0000.000
25A30GLY00.0280.02631.1190.0010.0010.0000.0000.0000.000
26A31ASN0-0.069-0.05529.6990.0020.0020.0000.0000.0000.000
27A32THR00.001-0.00927.9960.0040.0040.0000.0000.0000.000
28A33ASP-1-0.750-0.86525.902-0.177-0.1770.0000.0000.0000.000
29A34ARG10.8960.92524.3540.1380.1380.0000.0000.0000.000
30A35VAL0-0.019-0.00522.894-0.017-0.0170.0000.0000.0000.000
31A36PHE00.005-0.00721.405-0.022-0.0220.0000.0000.0000.000
32A37ASP-1-0.844-0.91520.000-0.311-0.3110.0000.0000.0000.000
33A38PHE0-0.033-0.01617.399-0.049-0.0490.0000.0000.0000.000
34A39GLU-1-0.777-0.89617.026-0.309-0.3090.0000.0000.0000.000
35A40ASP-1-0.776-0.87715.481-0.449-0.4490.0000.0000.0000.000
36A41ALA0-0.0390.00114.090-0.111-0.1110.0000.0000.0000.000
37A42LEU00.0160.00512.538-0.108-0.1080.0000.0000.0000.000
38A43ASP-1-0.781-0.85510.653-0.786-0.7860.0000.0000.0000.000
39A44GLN0-0.062-0.0407.422-0.344-0.3440.0000.0000.0000.000
40A45THR0-0.060-0.0466.803-0.517-0.5170.0000.0000.0000.000
41A46GLN00.0480.0085.4290.0210.0210.0000.0000.0000.000
42A47MET0-0.018-0.0136.4250.0820.0820.0000.0000.0000.000
43A48ALA00.0000.0128.8400.0980.0980.0000.0000.0000.000
44A49GLN0-0.030-0.0286.152-0.131-0.1310.0000.0000.0000.000
45A50LEU00.0180.0108.2420.1550.1550.0000.0000.0000.000
46A51ALA00.0120.00210.1190.0580.0580.0000.0000.0000.000
47A52VAL00.0010.00211.2180.0490.0490.0000.0000.0000.000
48A53ASP-1-0.853-0.9199.268-0.064-0.0640.0000.0000.0000.000
49A54GLU-1-0.867-0.91912.6920.0870.0870.0000.0000.0000.000
50A55LEU0-0.021-0.01615.7590.0150.0150.0000.0000.0000.000
51A56LYS10.8500.91714.7100.0960.0960.0000.0000.0000.000
52A57LYS10.7690.87514.792-0.038-0.0380.0000.0000.0000.000
53A58ILE0-0.0240.01019.4020.0090.0090.0000.0000.0000.000
54A59PRO00.005-0.00922.563-0.010-0.0100.0000.0000.0000.000
55A60GLU-1-0.854-0.93624.375-0.027-0.0270.0000.0000.0000.000
56A61VAL00.0120.00120.182-0.008-0.0080.0000.0000.0000.000
57A62ASN00.0200.00219.230-0.022-0.0220.0000.0000.0000.000
58A63ALA0-0.0010.02321.164-0.001-0.0010.0000.0000.0000.000
59A64LEU0-0.0040.01023.086-0.002-0.0020.0000.0000.0000.000
60A65PHE00.004-0.02015.381-0.011-0.0110.0000.0000.0000.000
61A66SER0-0.092-0.04920.063-0.001-0.0010.0000.0000.0000.000
62A67GLU-1-0.871-0.91921.824-0.046-0.0460.0000.0000.0000.000
63A68ARG10.7900.89815.6470.1690.1690.0000.0000.0000.000
64A69TRP0-0.0070.01822.205-0.009-0.0090.0000.0000.0000.000
65A70LEU0-0.0040.00122.588-0.016-0.0160.0000.0000.0000.000
66A71PRO0-0.048-0.01026.3580.0080.0080.0000.0000.0000.000
67A72ALA00.008-0.00329.895-0.004-0.0040.0000.0000.0000.000
68A73PRO0-0.034-0.01632.912-0.001-0.0010.0000.0000.0000.000
69A74PHE00.000-0.00433.0560.0060.0060.0000.0000.0000.000
70A75ASN00.013-0.01037.734-0.006-0.0060.0000.0000.0000.000
71A76LEU00.0630.02837.6630.0030.0030.0000.0000.0000.000
72A77ASP-1-0.837-0.90741.140-0.049-0.0490.0000.0000.0000.000
73A78ASP-1-0.869-0.91943.405-0.042-0.0420.0000.0000.0000.000
74A79LEU0-0.0050.00437.7490.0020.0020.0000.0000.0000.000
75A80ALA00.005-0.00642.4630.0020.0020.0000.0000.0000.000
76A81LYS10.7870.89745.2340.0430.0430.0000.0000.0000.000
77A82LEU0-0.0210.01742.2740.0020.0020.0000.0000.0000.000
78A83PRO00.019-0.00346.4020.0000.0000.0000.0000.0000.000
79A84GLU-1-0.788-0.85446.375-0.037-0.0370.0000.0000.0000.000
80A85GLY00.0160.01745.343-0.002-0.0020.0000.0000.0000.000
81A86THR0-0.065-0.03542.572-0.001-0.0010.0000.0000.0000.000
82A87LEU00.0080.00134.895-0.002-0.0020.0000.0000.0000.000
83A88GLY00.012-0.00539.251-0.003-0.0030.0000.0000.0000.000
84A89HIS00.0030.01640.442-0.002-0.0020.0000.0000.0000.000
85A90VAL0-0.012-0.01740.166-0.001-0.0010.0000.0000.0000.000
86A91TYR0-0.055-0.05133.464-0.001-0.0010.0000.0000.0000.000
87A92ALA00.013-0.00339.033-0.003-0.0030.0000.0000.0000.000
88A93ARG10.7790.85741.1200.0400.0400.0000.0000.0000.000
89A94GLU-1-0.770-0.86937.461-0.069-0.0690.0000.0000.0000.000
90A95MET0-0.047-0.01935.093-0.002-0.0020.0000.0000.0000.000
91A96LYS10.8330.89739.8050.0530.0530.0000.0000.0000.000
92A97ALA0-0.050-0.01742.5500.0020.0020.0000.0000.0000.000
93A98ARG10.7250.84833.4470.0850.0850.0000.0000.0000.000
94A99GLY00.0260.00637.2060.0020.0020.0000.0000.0000.000
95A100PHE0-0.048-0.03131.962-0.002-0.0020.0000.0000.0000.000
96A101ASP-1-0.809-0.88634.298-0.105-0.1050.0000.0000.0000.000
97A102PRO00.0240.02029.5740.0020.0020.0000.0000.0000.000
98A103TYR0-0.114-0.06730.632-0.004-0.0040.0000.0000.0000.000
99A104PHE0-0.029-0.02730.8680.0010.0010.0000.0000.0000.000
100A105TYR0-0.043-0.04124.822-0.002-0.0020.0000.0000.0000.000
101A106LYS10.8410.91320.3710.3140.3140.0000.0000.0000.000
102A107LYS10.9470.96523.0540.1190.1190.0000.0000.0000.000
103A108VAL00.002-0.01117.455-0.011-0.0110.0000.0000.0000.000
104A109PRO0-0.017-0.00618.4580.0190.0190.0000.0000.0000.000
105A110VAL00.0140.00618.022-0.036-0.0360.0000.0000.0000.000
106A111VAL0-0.0080.00413.9730.0320.0320.0000.0000.0000.000
107A112ASP-1-0.777-0.86011.280-0.553-0.5530.0000.0000.0000.000
108A113ASP-1-0.744-0.86512.702-0.137-0.1370.0000.0000.0000.000
109A114ILE0-0.0020.0028.3120.0460.0460.0000.0000.0000.000
110A115SER0-0.020-0.05712.9130.0820.0820.0000.0000.0000.000
111A116TYR0-0.061-0.03915.4600.0390.0390.0000.0000.0000.000
112A117LEU00.0300.02414.5770.0260.0260.0000.0000.0000.000
113A118LYS10.7670.86415.0510.5650.5650.0000.0000.0000.000
114A119MET00.0090.03018.2180.0280.0280.0000.0000.0000.000
115A120LEU00.0240.03420.6780.0220.0220.0000.0000.0000.000
116A121TRP0-0.023-0.00620.4610.0260.0260.0000.0000.0000.000
117A122ARG10.7290.83919.3300.3190.3190.0000.0000.0000.000
118A123SER0-0.042-0.01624.1400.0150.0150.0000.0000.0000.000
119A124THR0-0.006-0.01325.2890.0150.0150.0000.0000.0000.000
120A125HIS10.8950.96124.4350.1560.1560.0000.0000.0000.000
121A126ASP-1-0.769-0.83627.094-0.090-0.0900.0000.0000.0000.000
122A127ILE00.0410.02830.3820.0080.0080.0000.0000.0000.000
123A128TYR0-0.014-0.01524.9760.0050.0050.0000.0000.0000.000
124A129HIS10.7920.88331.0090.0830.0830.0000.0000.0000.000
125A130VAL00.0350.02933.2260.0050.0050.0000.0000.0000.000
126A131VAL0-0.0010.01333.5660.0050.0050.0000.0000.0000.000
127A132ALA00.0280.01731.9390.0050.0050.0000.0000.0000.000
128A133GLY0-0.0290.00734.0910.0040.0040.0000.0000.0000.000
129A134PHE0-0.050-0.01933.5100.0020.0020.0000.0000.0000.000
130A135ASP-1-0.818-0.91235.594-0.058-0.0580.0000.0000.0000.000
131A136THR0-0.026-0.01234.728-0.004-0.0040.0000.0000.0000.000
132A137ASN0-0.031-0.01135.264-0.006-0.0060.0000.0000.0000.000
133A138VAL00.0450.00731.826-0.002-0.0020.0000.0000.0000.000
134A139PHE00.010-0.00632.140-0.003-0.0030.0000.0000.0000.000
135A140GLY00.0440.04033.1950.0010.0010.0000.0000.0000.000
136A141GLU-1-0.792-0.90527.765-0.122-0.1220.0000.0000.0000.000
137A142ILE0-0.021-0.01127.257-0.004-0.0040.0000.0000.0000.000
138A143GLY00.0260.01128.6820.0010.0010.0000.0000.0000.000
139A144LEU0-0.001-0.00128.2990.0040.0040.0000.0000.0000.000
140A145GLN0-0.027-0.02323.612-0.010-0.0100.0000.0000.0000.000
141A146ALA0-0.0030.00024.863-0.001-0.0010.0000.0000.0000.000
142A147PHE0-0.0010.00226.6230.0050.0050.0000.0000.0000.000
143A148PHE00.035-0.00620.5610.0060.0060.0000.0000.0000.000
144A149LEU0-0.045-0.02220.034-0.001-0.0010.0000.0000.0000.000
145A150ALA0-0.0020.00122.5360.0060.0060.0000.0000.0000.000
146A151GLN0-0.082-0.02925.1730.0010.0010.0000.0000.0000.000
147A152THR00.006-0.01220.6480.0130.0130.0000.0000.0000.000
148A153PRO00.0110.02417.961-0.019-0.0190.0000.0000.0000.000
149A154ILE00.0310.02115.969-0.018-0.0180.0000.0000.0000.000
150A155PRO00.016-0.00212.6230.0280.0280.0000.0000.0000.000
151A156ILE00.0300.01415.5030.0220.0220.0000.0000.0000.000
152A157SER00.0520.01618.3710.0170.0170.0000.0000.0000.000
153A158VAL00.0010.00717.5660.0200.0200.0000.0000.0000.000
154A159MET0-0.0340.00117.1160.0110.0110.0000.0000.0000.000
155A160LEU00.0200.00920.2240.0140.0140.0000.0000.0000.000
156A161LEU00.0180.00723.4130.0130.0130.0000.0000.0000.000
157A162SER0-0.065-0.03521.8760.0150.0150.0000.0000.0000.000
158A163PHE00.0210.00123.9480.0080.0080.0000.0000.0000.000
159A164GLY00.0140.01525.5820.0070.0070.0000.0000.0000.000
160A165MET0-0.009-0.02026.3580.0110.0110.0000.0000.0000.000
161A166VAL00.0140.03125.9980.0070.0070.0000.0000.0000.000
162A167MET0-0.0050.00428.1600.0040.0040.0000.0000.0000.000
163A168ILE0-0.030-0.00731.0840.0060.0060.0000.0000.0000.000
164A169SER0-0.070-0.05731.8080.0050.0050.0000.0000.0000.000
165A170LEU0-0.015-0.00729.9870.0040.0040.0000.0000.0000.000
166A171TYR0-0.004-0.01431.5300.0010.0010.0000.0000.0000.000
167A172GLN00.0020.01236.4970.0040.0040.0000.0000.0000.000
168A173PRO00.0700.03937.7160.0010.0010.0000.0000.0000.000
169A174THR0-0.047-0.03138.6820.0020.0020.0000.0000.0000.000
170A175ASN0-0.018-0.00738.4810.0060.0060.0000.0000.0000.000
171A176PHE00.0300.01532.089-0.001-0.0010.0000.0000.0000.000
172A177LYS10.9900.99236.2920.0300.0300.0000.0000.0000.000
173A178ALA00.0130.02338.2790.0010.0010.0000.0000.0000.000
174A179LEU00.0260.02030.8900.0000.0000.0000.0000.0000.000
175A180MET00.0260.01030.805-0.002-0.0020.0000.0000.0000.000
176A181THR0-0.058-0.02534.4900.0040.0040.0000.0000.0000.000
177A182GLU-1-0.739-0.84134.041-0.050-0.0500.0000.0000.0000.000
178A183ILE0-0.013-0.00429.119-0.001-0.0010.0000.0000.0000.000
179A184SER0-0.052-0.03531.2920.0020.0020.0000.0000.0000.000
180A185ARG10.7190.80933.6330.0530.0530.0000.0000.0000.000
181A186GLY00.0530.01231.0400.0020.0020.0000.0000.0000.000
182A187TYR00.0110.00924.4520.0000.0000.0000.0000.0000.000
183A188ARG10.9100.97029.4480.0320.0320.0000.0000.0000.000
184A189VAL00.015-0.00132.5440.0030.0030.0000.0000.0000.000
185A190GLY00.0090.02629.0460.0010.0010.0000.0000.0000.000
186A191SER0-0.046-0.04828.6650.0020.0020.0000.0000.0000.000
187A192HIS0-0.040-0.01629.6460.0030.0030.0000.0000.0000.000
188A193THR0-0.0140.00430.9240.0010.0010.0000.0000.0000.000
189A194PRO0-0.0170.00330.005-0.003-0.0030.0000.0000.0000.000
190A195GLY00.0440.01229.211-0.001-0.0010.0000.0000.0000.000
191A196LYS10.8660.93924.8930.0320.0320.0000.0000.0000.000
192A197LEU00.0350.00626.835-0.001-0.0010.0000.0000.0000.000
193A198ILE0-0.020-0.01321.005-0.001-0.0010.0000.0000.0000.000
194A199ALA0-0.004-0.00324.231-0.004-0.0040.0000.0000.0000.000
195A200GLN0-0.040-0.01826.0030.0100.0100.0000.0000.0000.000
196A201LYS10.8480.91328.4010.0430.0430.0000.0000.0000.000
197A202TRP00.008-0.01928.0940.0080.0080.0000.0000.0000.000
198A203ASP-1-0.777-0.88931.963-0.065-0.0650.0000.0000.0000.000
199A204GLN0-0.061-0.03133.5220.0030.0030.0000.0000.0000.000
200A205LEU00.015-0.00333.2510.0040.0040.0000.0000.0000.000
201A206TRP00.0310.01434.1730.0010.0010.0000.0000.0000.000
202A207ASP-1-0.875-0.93838.659-0.037-0.0370.0000.0000.0000.000
203A208VAL0-0.0220.00239.1280.0030.0030.0000.0000.0000.000
204A209GLN00.006-0.00340.919-0.003-0.0030.0000.0000.0000.000
205A210VAL00.0510.01338.4080.0000.0000.0000.0000.0000.000
206A211SER0-0.029-0.01739.707-0.001-0.0010.0000.0000.0000.000
207A212GLU-1-0.755-0.85440.918-0.024-0.0240.0000.0000.0000.000
208A213ILE0-0.011-0.00335.3450.0000.0000.0000.0000.0000.000
209A214ARG10.8180.88836.6260.0420.0420.0000.0000.0000.000
210A215GLU-1-0.920-0.95237.581-0.021-0.0210.0000.0000.0000.000
211A216ARG10.8140.88336.3810.0310.0310.0000.0000.0000.000
212A217LEU0-0.055-0.01731.4190.0010.0010.0000.0000.0000.000
213A218GLY00.0660.04133.7510.0010.0010.0000.0000.0000.000
214A219VAL0-0.020-0.01734.4070.0020.0020.0000.0000.0000.000
215A220ASN0-0.0170.00335.997-0.001-0.0010.0000.0000.0000.000
216A221SER0-0.112-0.06135.4490.0050.0050.0000.0000.0000.000