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: LN8M9

Calculation Name: 3M4X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M4X

Chain ID: A

ChEMBL ID:

UniProt ID: Q3Y1J9

Base Structure: X-ray

Registration Date: 2023-09-24

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 440
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8107320.01804
FMO2-HF: Nuclear repulsion 7935146.259223
FMO2-HF: Total energy -172173.758818
FMO2-MP2: Total energy -172680.394364


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:7:THR)


Summations of interaction energy for fragment #1(A:7: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.
-1.4760.7080.008-0.769-1.4220.003
Interaction energy analysis for fragmet #1(A:7:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.024
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].
3A9PRO00.0450.0293.852-1.579-0.252-0.007-0.561-0.7590.003
4A10GLN00.0590.0176.5320.3180.3180.0000.0000.0000.000
5A11GLN0-0.047-0.0118.2520.1140.1140.0000.0000.0000.000
6A12PHE00.0750.0448.2880.0560.0560.0000.0000.0000.000
7A13ILE00.0030.0025.1670.0260.0260.0000.0000.0000.000
8A14LYS10.8020.8759.6560.0600.0600.0000.0000.0000.000
9A15LYS10.8370.90713.134-0.083-0.0830.0000.0000.0000.000
10A16TYR00.029-0.02911.920-0.014-0.0140.0000.0000.0000.000
11A17ARG10.9610.97910.506-0.336-0.3360.0000.0000.0000.000
12A18LEU0-0.047-0.01915.172-0.019-0.0190.0000.0000.0000.000
13A19LEU0-0.023-0.00217.304-0.010-0.0100.0000.0000.0000.000
14A20LEU0-0.032-0.01114.266-0.008-0.0080.0000.0000.0000.000
15A21GLY00.0200.01818.130-0.010-0.0100.0000.0000.0000.000
16A22GLU-1-0.936-0.97516.9730.1370.1370.0000.0000.0000.000
17A23GLU-1-0.719-0.82216.6540.1750.1750.0000.0000.0000.000
18A24ALA0-0.031-0.02013.0250.0300.0300.0000.0000.0000.000
19A25SER0-0.059-0.02811.8630.1190.1190.0000.0000.0000.000
20A26ASP-1-0.880-0.94611.7630.2770.2770.0000.0000.0000.000
21A27PHE0-0.028-0.01011.4370.0330.0330.0000.0000.0000.000
22A28PHE0-0.009-0.0197.4660.0360.0360.0000.0000.0000.000
23A29SER00.0280.0287.4150.1500.1500.0000.0000.0000.000
24A30ALA00.0150.0058.976-0.110-0.1100.0000.0000.0000.000
25A31LEU0-0.044-0.0296.200-0.124-0.1240.0000.0000.0000.000
26A32GLU-1-0.962-0.9603.6660.9151.2920.012-0.092-0.2970.000
27A33GLN0-0.051-0.0325.048-0.805-0.739-0.0010.000-0.0650.000
28A34GLY0-0.0180.0138.5360.0070.0070.0000.0000.0000.000
29A35SER0-0.019-0.01510.011-0.028-0.0280.0000.0000.0000.000
30A36VAL00.0030.00210.9900.0290.0290.0000.0000.0000.000
31A37LYS10.8380.92613.307-0.096-0.0960.0000.0000.0000.000
32A38LYS10.8830.93216.850-0.028-0.0280.0000.0000.0000.000
33A39GLY00.0780.03419.641-0.006-0.0060.0000.0000.0000.000
34A40PHE0-0.058-0.02223.2010.0060.0060.0000.0000.0000.000
35A41ARG10.8180.90726.396-0.054-0.0540.0000.0000.0000.000
36A42TRP00.0740.04729.815-0.001-0.0010.0000.0000.0000.000
37A43ASN0-0.013-0.02333.3970.0010.0010.0000.0000.0000.000
38A44PRO0-0.014-0.02235.683-0.002-0.0020.0000.0000.0000.000
39A45LEU0-0.088-0.02738.267-0.002-0.0020.0000.0000.0000.000
40A46LYS10.7510.87637.780-0.031-0.0310.0000.0000.0000.000
41A47PRO00.0350.02041.5430.0000.0000.0000.0000.0000.000
42A48ALA00.0350.03343.1300.0000.0000.0000.0000.0000.000
43A49GLY00.0000.00539.4460.0000.0000.0000.0000.0000.000
44A50LEU0-0.007-0.00236.0920.0010.0010.0000.0000.0000.000
45A51ASP-1-0.750-0.85938.1310.0180.0180.0000.0000.0000.000
46A52MET0-0.0230.01739.627-0.001-0.0010.0000.0000.0000.000
47A53VAL0-0.013-0.01633.1700.0000.0000.0000.0000.0000.000
48A54GLN0-0.069-0.05435.6150.0010.0010.0000.0000.0000.000
49A55THR0-0.029-0.01937.439-0.001-0.0010.0000.0000.0000.000
50A56TYR0-0.129-0.10437.225-0.001-0.0010.0000.0000.0000.000
51A57HIS0-0.161-0.07428.4320.0000.0000.0000.0000.0000.000
52A58SER0-0.040-0.05532.118-0.001-0.0010.0000.0000.0000.000
53A59GLU-1-0.839-0.90934.2420.0180.0180.0000.0000.0000.000
54A60GLU-1-0.891-0.92332.5100.0150.0150.0000.0000.0000.000
55A61LEU0-0.084-0.02729.6250.0010.0010.0000.0000.0000.000
56A62GLN00.0380.01726.2340.0030.0030.0000.0000.0000.000
57A63PRO00.0280.01527.9960.0030.0030.0000.0000.0000.000
58A64ALA0-0.038-0.02325.3370.0020.0020.0000.0000.0000.000
59A65PRO0-0.009-0.01823.620-0.001-0.0010.0000.0000.0000.000
60A66TYR0-0.024-0.02721.062-0.002-0.0020.0000.0000.0000.000
61A67SER00.004-0.00727.0930.0000.0000.0000.0000.0000.000
62A68ASN00.0080.01630.0060.0000.0000.0000.0000.0000.000
63A69GLU-1-0.830-0.90831.7250.0400.0400.0000.0000.0000.000
64A70GLY0-0.014-0.00828.6070.0000.0000.0000.0000.0000.000
65A71PHE00.0340.02627.878-0.002-0.0020.0000.0000.0000.000
66A72LEU0-0.003-0.00722.1620.0070.0070.0000.0000.0000.000
67A73GLY00.0320.00823.233-0.006-0.0060.0000.0000.0000.000
68A74THR0-0.057-0.04121.1740.0070.0070.0000.0000.0000.000
69A75VAL00.0420.03324.117-0.004-0.0040.0000.0000.0000.000
70A76ASN00.0590.03026.1830.0040.0040.0000.0000.0000.000
71A77GLY00.026-0.00527.164-0.001-0.0010.0000.0000.0000.000
72A78LYS10.8850.94728.461-0.037-0.0370.0000.0000.0000.000
73A79SER00.0370.02431.415-0.003-0.0030.0000.0000.0000.000
74A80PHE00.0650.02033.7220.0020.0020.0000.0000.0000.000
75A81LEU00.0320.03933.6980.0010.0010.0000.0000.0000.000
76A82HIS0-0.0080.00429.3930.0040.0040.0000.0000.0000.000
77A83GLN0-0.029-0.02532.4600.0010.0010.0000.0000.0000.000
78A84ALA00.0340.01135.0830.0010.0010.0000.0000.0000.000
79A85GLY00.000-0.00634.0510.0000.0000.0000.0000.0000.000
80A86TYR0-0.014-0.02035.1230.0010.0010.0000.0000.0000.000
81A87GLU-1-0.791-0.88830.2310.0350.0350.0000.0000.0000.000
82A88TYR0-0.056-0.03725.9200.0020.0020.0000.0000.0000.000
83A89SER0-0.0020.00823.416-0.001-0.0010.0000.0000.0000.000
84A90GLN0-0.042-0.03522.9130.0000.0000.0000.0000.0000.000
85A91GLU-1-0.793-0.86617.3810.1180.1180.0000.0000.0000.000
86A92PRO00.0820.01719.1760.0000.0000.0000.0000.0000.000
87A93SER0-0.020-0.02118.3450.0000.0000.0000.0000.0000.000
88A94ALA00.0080.00220.459-0.005-0.0050.0000.0000.0000.000
89A95MET0-0.089-0.02822.077-0.008-0.0080.0000.0000.0000.000
90A96ILE00.0570.03823.526-0.006-0.0060.0000.0000.0000.000
91A97VAL00.0060.01724.169-0.004-0.0040.0000.0000.0000.000
92A98GLY00.0430.01926.956-0.004-0.0040.0000.0000.0000.000
93A99THR0-0.060-0.04429.243-0.005-0.0050.0000.0000.0000.000
94A100ALA00.0100.00629.168-0.003-0.0030.0000.0000.0000.000
95A101ALA00.0010.00331.046-0.003-0.0030.0000.0000.0000.000
96A102ALA0-0.0180.00733.067-0.003-0.0030.0000.0000.0000.000
97A103ALA00.0100.00635.936-0.002-0.0020.0000.0000.0000.000
98A104LYS10.8820.91738.055-0.030-0.0300.0000.0000.0000.000
99A105PRO0-0.036-0.02041.6540.0000.0000.0000.0000.0000.000
100A106GLY0-0.032-0.01644.033-0.001-0.0010.0000.0000.0000.000
101A107GLU-1-0.805-0.87640.5450.0310.0310.0000.0000.0000.000
102A108LYS10.8530.92742.939-0.024-0.0240.0000.0000.0000.000
103A109VAL00.011-0.01236.4860.0010.0010.0000.0000.0000.000
104A110LEU00.0110.01334.958-0.001-0.0010.0000.0000.0000.000
105A111ASP-1-0.799-0.88230.1410.0590.0590.0000.0000.0000.000
106A112LEU00.0080.00431.130-0.001-0.0010.0000.0000.0000.000
107A113CYS0-0.073-0.04826.637-0.002-0.0020.0000.0000.0000.000
108A114ALA00.0780.05726.8900.0050.0050.0000.0000.0000.000
109A115ALA0-0.039-0.00326.2160.0010.0010.0000.0000.0000.000
110A116PRO0-0.008-0.01923.1520.0050.0050.0000.0000.0000.000
111A117GLY00.0480.00726.134-0.005-0.0050.0000.0000.0000.000
112A118GLY0-0.047-0.00726.146-0.003-0.0030.0000.0000.0000.000
113A119LYS10.8340.90922.386-0.096-0.0960.0000.0000.0000.000
114A120SER00.024-0.04028.465-0.004-0.0040.0000.0000.0000.000
115A121THR0-0.033-0.01930.427-0.004-0.0040.0000.0000.0000.000
116A122GLN0-0.0120.00028.1610.0010.0010.0000.0000.0000.000
117A123LEU0-0.0210.00232.488-0.003-0.0030.0000.0000.0000.000
118A124ALA00.0260.00134.871-0.003-0.0030.0000.0000.0000.000
119A125ALA00.0080.01135.334-0.002-0.0020.0000.0000.0000.000
120A126GLN0-0.017-0.02533.137-0.003-0.0030.0000.0000.0000.000
121A127MET0-0.045-0.01538.072-0.001-0.0010.0000.0000.0000.000
122A128LYS10.9150.95540.458-0.028-0.0280.0000.0000.0000.000
123A129GLY00.0300.02841.877-0.001-0.0010.0000.0000.0000.000
124A130LYS10.9340.96843.650-0.022-0.0220.0000.0000.0000.000
125A131GLY00.0520.03243.8560.0010.0010.0000.0000.0000.000
126A132LEU0-0.072-0.02342.706-0.001-0.0010.0000.0000.0000.000
127A133LEU00.0240.03035.4730.0010.0010.0000.0000.0000.000
128A134VAL0-0.029-0.00537.606-0.001-0.0010.0000.0000.0000.000
129A135THR00.011-0.00632.7750.0010.0010.0000.0000.0000.000
130A136ASN0-0.004-0.02332.242-0.003-0.0030.0000.0000.0000.000
131A137GLU-1-0.769-0.89526.5170.0720.0720.0000.0000.0000.000
132A138ILE0-0.0110.00727.653-0.003-0.0030.0000.0000.0000.000
133A139PHE0-0.027-0.00924.687-0.002-0.0020.0000.0000.0000.000
134A140PRO00.0670.02729.2140.0020.0020.0000.0000.0000.000
135A141LYS10.9370.96324.328-0.069-0.0690.0000.0000.0000.000
136A142ARG10.8830.94621.335-0.088-0.0880.0000.0000.0000.000
137A143ALA00.0700.02828.2580.0000.0000.0000.0000.0000.000
138A144LYS10.8170.90531.690-0.037-0.0370.0000.0000.0000.000
139A145ILE00.0530.02127.210-0.001-0.0010.0000.0000.0000.000
140A146LEU00.0150.02829.749-0.001-0.0010.0000.0000.0000.000
141A147SER00.0030.00231.192-0.002-0.0020.0000.0000.0000.000
142A148GLU-1-0.823-0.90033.0550.0370.0370.0000.0000.0000.000
143A149ASN0-0.022-0.02029.156-0.002-0.0020.0000.0000.0000.000
144A150ILE00.0180.01332.713-0.001-0.0010.0000.0000.0000.000
145A151GLU-1-0.829-0.90935.4580.0280.0280.0000.0000.0000.000
146A152ARG10.7950.89529.999-0.046-0.0460.0000.0000.0000.000
147A153TRP00.0410.01632.268-0.001-0.0010.0000.0000.0000.000
148A154GLY00.0450.03436.017-0.001-0.0010.0000.0000.0000.000
149A155VAL0-0.058-0.03736.674-0.001-0.0010.0000.0000.0000.000
150A156SER00.0360.01839.8420.0000.0000.0000.0000.0000.000
151A157ASN0-0.056-0.03542.1730.0000.0000.0000.0000.0000.000
152A158ALA00.0340.01138.3180.0000.0000.0000.0000.0000.000
153A159ILE0-0.021-0.00639.974-0.001-0.0010.0000.0000.0000.000
154A160VAL00.0020.01234.4790.0020.0020.0000.0000.0000.000
155A161THR0-0.033-0.02235.647-0.003-0.0030.0000.0000.0000.000
156A162ASN0-0.006-0.01133.3690.0050.0050.0000.0000.0000.000
157A163HIS00.020-0.00134.392-0.003-0.0030.0000.0000.0000.000
158A164ALA00.0270.02432.6300.0030.0030.0000.0000.0000.000
159A165PRO00.040-0.00231.268-0.003-0.0030.0000.0000.0000.000
160A166ALA00.0570.03034.427-0.001-0.0010.0000.0000.0000.000
161A167GLU-1-0.802-0.87936.7140.0280.0280.0000.0000.0000.000
162A168LEU0-0.0010.00735.587-0.001-0.0010.0000.0000.0000.000
163A169VAL00.0400.01738.916-0.001-0.0010.0000.0000.0000.000
164A170PRO0-0.029-0.02641.428-0.001-0.0010.0000.0000.0000.000
165A171HIS10.8350.93242.889-0.024-0.0240.0000.0000.0000.000
166A172PHE00.0150.00041.0740.0000.0000.0000.0000.0000.000
167A173SER0-0.008-0.01443.2750.0010.0010.0000.0000.0000.000
168A174GLY0-0.010-0.01743.950-0.001-0.0010.0000.0000.0000.000
169A175PHE0-0.0340.00043.0420.0000.0000.0000.0000.0000.000
170A176PHE00.008-0.00639.948-0.001-0.0010.0000.0000.0000.000
171A177ASP-1-0.820-0.90242.2010.0260.0260.0000.0000.0000.000
172A178ARG10.8030.89436.312-0.037-0.0370.0000.0000.0000.000
173A179ILE0-0.0090.00033.8700.0000.0000.0000.0000.0000.000
174A180VAL00.0000.00829.3290.0010.0010.0000.0000.0000.000
175A181VAL0-0.011-0.02528.166-0.001-0.0010.0000.0000.0000.000
176A182ASP-1-0.728-0.81923.5750.0930.0930.0000.0000.0000.000
177A183ALA00.0130.00524.100-0.002-0.0020.0000.0000.0000.000
178A184PRO0-0.043-0.03221.6300.0080.0080.0000.0000.0000.000
179A185CYS0-0.0070.01218.981-0.002-0.0020.0000.0000.0000.000
180A186SER0-0.057-0.05715.0870.0160.0160.0000.0000.0000.000
181A187GLY00.0520.02814.0410.0080.0080.0000.0000.0000.000
182A188GLU-1-0.724-0.84811.0840.1890.1890.0000.0000.0000.000
183A189GLY00.0050.00510.7490.0490.0490.0000.0000.0000.000
184A190MET0-0.070-0.05312.288-0.015-0.0150.0000.0000.0000.000
185A191PHE00.0070.0086.7150.0210.0210.0000.0000.0000.000
186A192ARG10.8040.8797.2860.0250.0250.0000.0000.0000.000
187A193LYS10.8610.9378.273-0.204-0.2040.0000.0000.0000.000
188A194ASP-1-0.826-0.91410.1380.3870.3870.0000.0000.0000.000
189A195PRO00.0330.0125.9990.0140.0140.0000.0000.0000.000
190A196ASN0-0.091-0.0527.3100.0030.0030.0000.0000.0000.000
191A197ALA00.0440.02710.207-0.074-0.0740.0000.0000.0000.000
192A198ILE0-0.034-0.0093.882-0.536-0.1220.004-0.116-0.3010.000
193A199LYS10.7710.8757.192-0.648-0.6480.0000.0000.0000.000
194A200GLU-1-0.872-0.9308.3990.1070.1070.0000.0000.0000.000
195A201TRP0-0.036-0.0069.967-0.061-0.0610.0000.0000.0000.000
196A202THR00.0140.00311.139-0.061-0.0610.0000.0000.0000.000
197A203GLU-1-0.829-0.92013.513-0.019-0.0190.0000.0000.0000.000
198A204GLU-1-0.928-0.96015.339-0.004-0.0040.0000.0000.0000.000
199A205SER0-0.041-0.02515.5520.0160.0160.0000.0000.0000.000
200A206PRO00.0150.00616.2670.0070.0070.0000.0000.0000.000
201A207LEU00.0350.02319.2200.0010.0010.0000.0000.0000.000
202A208TYR0-0.067-0.03020.5600.0000.0000.0000.0000.0000.000
203A209CYS0-0.055-0.03518.959-0.001-0.0010.0000.0000.0000.000
204A210GLN0-0.041-0.01022.299-0.004-0.0040.0000.0000.0000.000
205A211LYS10.9810.99524.777-0.024-0.0240.0000.0000.0000.000
206A212ARG11.0071.01024.265-0.051-0.0510.0000.0000.0000.000
207A213GLN0-0.021-0.04621.574-0.003-0.0030.0000.0000.0000.000
208A214GLN00.0280.01927.168-0.004-0.0040.0000.0000.0000.000
209A215GLU-1-0.931-0.97129.2260.0340.0340.0000.0000.0000.000
210A216ILE0-0.042-0.01927.203-0.002-0.0020.0000.0000.0000.000
211A217LEU00.0290.01028.941-0.002-0.0020.0000.0000.0000.000
212A218SER0-0.0050.00432.450-0.003-0.0030.0000.0000.0000.000
213A219SER0-0.093-0.03834.698-0.003-0.0030.0000.0000.0000.000
214A220ALA00.006-0.01033.611-0.001-0.0010.0000.0000.0000.000
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