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: 94452

Calculation Name: 5MJW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MJW

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DJT8

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptHSide
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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2118224.182428
FMO2-HF: Nuclear repulsion 2040417.320199
FMO2-HF: Total energy -77806.86223
FMO2-MP2: Total energy -78036.68451


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:PRO)


Summations of interaction energy for fragment #1(A:4: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.
-0.3781.459-0.016-0.831-0.990.005
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.017
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].
3A6THR00.0470.0043.854-0.6411.196-0.016-0.831-0.9900.005
4A7VAL00.0530.0036.0480.4450.4450.0000.0000.0000.000
5A8SER00.008-0.0059.5530.1940.1940.0000.0000.0000.000
6A9ASP-1-0.750-0.8426.437-1.950-1.9500.0000.0000.0000.000
7A10THR0-0.043-0.0139.0950.2680.2680.0000.0000.0000.000
8A11LYS10.9800.99811.2680.5090.5090.0000.0000.0000.000
9A12ARG10.8940.9319.8080.9570.9570.0000.0000.0000.000
10A13ALA0-0.0100.00112.0410.0530.0530.0000.0000.0000.000
11A14PHE0-0.0060.00414.0640.0520.0520.0000.0000.0000.000
12A15TYR00.016-0.00917.0750.0180.0180.0000.0000.0000.000
13A16ALA0-0.025-0.00316.7260.0170.0170.0000.0000.0000.000
14A17ALA0-0.026-0.00418.1920.0250.0250.0000.0000.0000.000
15A18HIS0-0.045-0.01619.9000.0290.0290.0000.0000.0000.000
16A19THR00.0230.00822.541-0.013-0.0130.0000.0000.0000.000
17A20ARG10.9300.97424.2730.0370.0370.0000.0000.0000.000
18A21PRO00.0460.01926.489-0.009-0.0090.0000.0000.0000.000
19A22ILE0-0.020-0.00624.1090.0090.0090.0000.0000.0000.000
20A23HIS00.0450.01427.952-0.005-0.0050.0000.0000.0000.000
21A24SER00.0290.00630.447-0.004-0.0040.0000.0000.0000.000
22A25ILE00.0320.01932.5020.0040.0040.0000.0000.0000.000
23A26TYR00.0710.03132.3520.0030.0030.0000.0000.0000.000
24A27ARG10.8620.94329.2070.1000.1000.0000.0000.0000.000
25A28ARG10.8740.93034.8550.0530.0530.0000.0000.0000.000
26A29PHE00.0280.00838.0910.0030.0030.0000.0000.0000.000
27A30ILE00.0210.01335.0810.0020.0020.0000.0000.0000.000
28A31GLU-1-0.915-0.96835.209-0.073-0.0730.0000.0000.0000.000
29A32GLU-1-0.874-0.92839.707-0.048-0.0480.0000.0000.0000.000
30A33LEU0-0.0090.00042.4300.0030.0030.0000.0000.0000.000
31A34LEU0-0.009-0.00738.8780.0010.0010.0000.0000.0000.000
32A35VAL00.0040.01142.8100.0030.0030.0000.0000.0000.000
33A36GLU-1-0.820-0.87345.190-0.044-0.0440.0000.0000.0000.000
34A37ILE0-0.037-0.02645.6120.0030.0030.0000.0000.0000.000
35A38HIS00.0750.04946.2950.0010.0010.0000.0000.0000.000
36A39LEU0-0.069-0.04848.3060.0030.0030.0000.0000.0000.000
37A40LEU0-0.076-0.03350.9290.0020.0020.0000.0000.0000.000
38A41ARG10.8450.91949.3100.0510.0510.0000.0000.0000.000
39A42VAL0-0.0130.00551.0740.0010.0010.0000.0000.0000.000
40A43ASN0-0.035-0.00753.8410.0030.0030.0000.0000.0000.000
41A44VAL00.0540.01557.088-0.001-0.0010.0000.0000.0000.000
42A45ASP-1-0.869-0.92160.108-0.028-0.0280.0000.0000.0000.000
43A46PHE0-0.054-0.01453.6010.0000.0000.0000.0000.0000.000
44A47ARG10.9420.96658.3200.0320.0320.0000.0000.0000.000
45A48TYR0-0.043-0.04051.645-0.001-0.0010.0000.0000.0000.000
46A49SER00.009-0.00655.9110.0010.0010.0000.0000.0000.000
47A50PRO00.1010.03055.173-0.001-0.0010.0000.0000.0000.000
48A51LEU0-0.0010.03254.791-0.001-0.0010.0000.0000.0000.000
49A52PHE00.005-0.00950.026-0.001-0.0010.0000.0000.0000.000
50A53ALA00.0020.01050.768-0.002-0.0020.0000.0000.0000.000
51A54LEU00.0050.00949.979-0.002-0.0020.0000.0000.0000.000
52A55GLY00.0160.01850.324-0.001-0.0010.0000.0000.0000.000
53A56VAL0-0.018-0.01246.046-0.002-0.0020.0000.0000.0000.000
54A57VAL0-0.011-0.00345.661-0.003-0.0030.0000.0000.0000.000
55A58THR00.0090.00545.424-0.002-0.0020.0000.0000.0000.000
56A59ALA0-0.038-0.02345.917-0.001-0.0010.0000.0000.0000.000
57A60PHE0-0.039-0.01737.794-0.003-0.0030.0000.0000.0000.000
58A61ASP-1-0.880-0.95241.333-0.077-0.0770.0000.0000.0000.000
59A62GLN00.0260.02741.555-0.001-0.0010.0000.0000.0000.000
60A63PHE0-0.048-0.02739.079-0.001-0.0010.0000.0000.0000.000
61A64MET0-0.039-0.02234.777-0.004-0.0040.0000.0000.0000.000
62A65GLU-1-0.850-0.90336.816-0.076-0.0760.0000.0000.0000.000
63A66GLY0-0.023-0.01135.503-0.002-0.0020.0000.0000.0000.000
64A67TYR0-0.095-0.03429.695-0.004-0.0040.0000.0000.0000.000
65A68GLN00.0350.02728.174-0.002-0.0020.0000.0000.0000.000
66A69PRO0-0.041-0.02826.807-0.004-0.0040.0000.0000.0000.000
67A70GLU-1-0.813-0.93129.032-0.113-0.1130.0000.0000.0000.000
68A71GLY0-0.029-0.01031.3710.0060.0060.0000.0000.0000.000
69A72ASP-1-0.871-0.94428.596-0.163-0.1630.0000.0000.0000.000
70A73ARG10.9060.96932.0580.1120.1120.0000.0000.0000.000
71A74ASP-1-0.762-0.88035.543-0.088-0.0880.0000.0000.0000.000
72A75ARG10.8450.91529.1710.1600.1600.0000.0000.0000.000
73A76ILE00.0000.00432.2810.0030.0030.0000.0000.0000.000
74A77PHE00.0180.01935.8800.0050.0050.0000.0000.0000.000
75A78HIS0-0.010-0.01137.8480.0040.0040.0000.0000.0000.000
76A79ALA00.001-0.01535.9270.0040.0040.0000.0000.0000.000
77A80LEU0-0.012-0.00638.0670.0040.0040.0000.0000.0000.000
78A81CYS0-0.0180.00140.6400.0050.0050.0000.0000.0000.000
79A82VAL0-0.025-0.01139.2140.0030.0030.0000.0000.0000.000
80A83ALA0-0.042-0.01039.9640.0030.0030.0000.0000.0000.000
81A84GLU-1-0.866-0.94441.914-0.053-0.0530.0000.0000.0000.000
82A85GLU-1-0.932-0.95145.010-0.047-0.0470.0000.0000.0000.000
83A86MET0-0.051-0.02046.1060.0030.0030.0000.0000.0000.000
84A87ASN00.0380.01045.934-0.006-0.0060.0000.0000.0000.000
85A88PRO00.0500.00842.5250.0020.0020.0000.0000.0000.000
86A89GLN0-0.085-0.05545.337-0.002-0.0020.0000.0000.0000.000
87A90GLN00.0050.00446.9210.0000.0000.0000.0000.0000.000
88A91LEU00.0240.01247.0550.0020.0020.0000.0000.0000.000
89A92LYS10.8820.93141.6210.0840.0840.0000.0000.0000.000
90A93GLU-1-0.873-0.92048.100-0.057-0.0570.0000.0000.0000.000
91A94ASP-1-0.821-0.88851.270-0.047-0.0470.0000.0000.0000.000
92A95ALA0-0.038-0.01449.6290.0020.0020.0000.0000.0000.000
93A96ALA00.0430.01150.0470.0010.0010.0000.0000.0000.000
94A97SER0-0.069-0.04451.9530.0020.0020.0000.0000.0000.000
95A98TRP0-0.011-0.03054.5900.0030.0030.0000.0000.0000.000
96A99GLN0-0.025-0.00551.3030.0000.0000.0000.0000.0000.000
97A100GLN0-0.074-0.02955.6410.0020.0020.0000.0000.0000.000
98A101TYR0-0.053-0.04358.9790.0010.0010.0000.0000.0000.000
99A102GLN0-0.010-0.01453.2900.0000.0000.0000.0000.0000.000
100A103GLY0-0.028-0.00958.5490.0010.0010.0000.0000.0000.000
101A104ARG10.8370.92360.9250.0360.0360.0000.0000.0000.000
102A105PRO00.0010.00363.5660.0000.0000.0000.0000.0000.000
103A106LEU00.1000.03164.6670.0000.0000.0000.0000.0000.000
104A107SER00.002-0.00466.6210.0000.0000.0000.0000.0000.000
105A108GLN00.0380.00068.0670.0000.0000.0000.0000.0000.000
106A109ILE0-0.0040.02063.8240.0000.0000.0000.0000.0000.000
107A110LEU00.017-0.00467.2290.0000.0000.0000.0000.0000.000
108A111ASP-1-0.938-0.95569.804-0.025-0.0250.0000.0000.0000.000
109A112GLU-1-0.738-0.82867.028-0.033-0.0330.0000.0000.0000.000
110A113LEU0-0.036-0.01465.9350.0000.0000.0000.0000.0000.000
111A114ASN0-0.054-0.03069.9760.0010.0010.0000.0000.0000.000
112A115SER0-0.038-0.02072.0550.0010.0010.0000.0000.0000.000
113A116GLY0-0.016-0.00573.5750.0010.0010.0000.0000.0000.000
114A117GLN0-0.105-0.05771.7200.0010.0010.0000.0000.0000.000
115A118PRO0-0.0020.01467.154-0.001-0.0010.0000.0000.0000.000
116A119SER0-0.019-0.02465.169-0.001-0.0010.0000.0000.0000.000
117A120ALA0-0.0100.01961.7980.0000.0000.0000.0000.0000.000
118A121PRO00.0480.01857.7340.0000.0000.0000.0000.0000.000
119A122LEU00.0430.03560.6200.0000.0000.0000.0000.0000.000
120A123ASN00.009-0.02162.8690.0000.0000.0000.0000.0000.000
121A124SER0-0.061-0.05360.0970.0010.0010.0000.0000.0000.000
122A125LEU00.0020.00060.8020.0000.0000.0000.0000.0000.000
123A126ASN00.009-0.00363.2920.0010.0010.0000.0000.0000.000
124A127HIS0-0.076-0.02963.6820.0010.0010.0000.0000.0000.000
125A128THR00.0110.00960.095-0.001-0.0010.0000.0000.0000.000
126A129GLY0-0.0320.00159.965-0.001-0.0010.0000.0000.0000.000
127A130LYS10.8050.88258.2490.0300.0300.0000.0000.0000.000
128A131TYR0-0.048-0.05157.675-0.001-0.0010.0000.0000.0000.000
129A132SER00.0220.01153.1850.0000.0000.0000.0000.0000.000
130A133ARG10.8420.88446.7120.0480.0480.0000.0000.0000.000
131A134LEU00.011-0.00448.5140.0000.0000.0000.0000.0000.000
132A135HIS00.0570.02052.5200.0000.0000.0000.0000.0000.000
133A136ALA00.0090.01455.5370.0000.0000.0000.0000.0000.000
134A137VAL00.0040.00549.4880.0000.0000.0000.0000.0000.000
135A138GLY00.0360.02752.978-0.001-0.0010.0000.0000.0000.000
136A139LEU0-0.019-0.01654.1330.0000.0000.0000.0000.0000.000
137A140TYR00.001-0.01451.7740.0010.0010.0000.0000.0000.000
138A141ALA00.0240.00951.9250.0000.0000.0000.0000.0000.000
139A142PHE00.026-0.00453.6280.0000.0000.0000.0000.0000.000
140A143LEU0-0.006-0.00856.8160.0010.0010.0000.0000.0000.000
141A144GLN0-0.059-0.03651.2720.0000.0000.0000.0000.0000.000
142A145GLU-1-0.866-0.90552.839-0.049-0.0490.0000.0000.0000.000
143A146LEU0-0.056-0.00356.5950.0010.0010.0000.0000.0000.000
144A147ALA0-0.020-0.01359.8340.0000.0000.0000.0000.0000.000
145A148GLY0-0.033-0.03762.1260.0010.0010.0000.0000.0000.000
146A149GLU-1-0.950-0.96558.619-0.035-0.0350.0000.0000.0000.000
147A150VAL00.0460.02160.4520.0010.0010.0000.0000.0000.000
148A151THR0-0.003-0.00556.2910.0010.0010.0000.0000.0000.000
149A152ILE00.0020.01758.9290.0000.0000.0000.0000.0000.000
150A153HIS00.0170.00960.2150.0000.0000.0000.0000.0000.000
151A154LEU0-0.0040.00057.6060.0000.0000.0000.0000.0000.000
152A155ASN0-0.024-0.05061.538-0.001-0.0010.0000.0000.0000.000
153A156GLU-1-0.881-0.91763.891-0.025-0.0250.0000.0000.0000.000
154A157THR00.0320.00762.9760.0010.0010.0000.0000.0000.000
155A158LEU0-0.058-0.03760.5690.0000.0000.0000.0000.0000.000
156A159ASP-1-0.824-0.89664.903-0.024-0.0240.0000.0000.0000.000
157A160GLN0-0.082-0.05668.3440.0000.0000.0000.0000.0000.000
158A161LEU00.001-0.00863.6510.0000.0000.0000.0000.0000.000
159A162ALA0-0.032-0.00767.7620.0000.0000.0000.0000.0000.000
160A163PRO0-0.046-0.01269.1230.0000.0000.0000.0000.0000.000
161A164VAL0-0.029-0.00169.3790.0000.0000.0000.0000.0000.000
162A165ILE0-0.007-0.00463.8580.0000.0000.0000.0000.0000.000
163A166PRO00.0000.00766.3820.0010.0010.0000.0000.0000.000
164A167LEU0-0.011-0.00560.6630.0000.0000.0000.0000.0000.000
165A168PRO0-0.026-0.01462.2390.0010.0010.0000.0000.0000.000
166A169ILE00.0830.02963.254-0.001-0.0010.0000.0000.0000.000
167A170GLU-1-0.815-0.89763.592-0.024-0.0240.0000.0000.0000.000
168A171LYS10.8970.95160.1080.0270.0270.0000.0000.0000.000
169A172VAL00.0110.01859.003-0.001-0.0010.0000.0000.0000.000
170A173LYS10.8260.88658.6620.0230.0230.0000.0000.0000.000
171A174ARG10.8410.91457.2020.0290.0290.0000.0000.0000.000
172A175ASP-1-0.811-0.89055.038-0.034-0.0340.0000.0000.0000.000
173A176LEU0-0.010-0.00954.054-0.002-0.0020.0000.0000.0000.000
174A177GLU-1-0.876-0.91954.598-0.029-0.0290.0000.0000.0000.000
175A178LEU0-0.056-0.02150.798-0.001-0.0010.0000.0000.0000.000
176A179TYR0-0.043-0.05347.262-0.001-0.0010.0000.0000.0000.000
177A180ARG10.9530.98049.1990.0340.0340.0000.0000.0000.000
178A181SER00.0730.05949.767-0.001-0.0010.0000.0000.0000.000
179A182ASN0-0.036-0.04546.3370.0010.0010.0000.0000.0000.000
180A183LEU00.0280.02744.108-0.002-0.0020.0000.0000.0000.000
181A184ASP-1-0.882-0.93444.954-0.045-0.0450.0000.0000.0000.000
182A185LYS10.8330.90744.5040.0370.0370.0000.0000.0000.000
183A186ILE0-0.037-0.01639.873-0.002-0.0020.0000.0000.0000.000
184A187ASN00.0440.01840.261-0.007-0.0070.0000.0000.0000.000
185A188GLN0-0.0050.00440.933-0.001-0.0010.0000.0000.0000.000
186A189ALA0-0.011-0.00538.299-0.002-0.0020.0000.0000.0000.000
187A190ARG10.8600.91136.2730.0690.0690.0000.0000.0000.000
188A191SER0-0.0030.00836.085-0.004-0.0040.0000.0000.0000.000
189A192LEU00.0140.01936.885-0.001-0.0010.0000.0000.0000.000
190A193MET0-0.051-0.03330.8290.0000.0000.0000.0000.0000.000
191A194LYS10.8120.90331.9340.0760.0760.0000.0000.0000.000
192A195GLU-1-0.950-0.99632.958-0.062-0.0620.0000.0000.0000.000
193A196LEU0-0.048-0.01028.885-0.002-0.0020.0000.0000.0000.000
194A197VAL0-0.084-0.03426.555-0.005-0.0050.0000.0000.0000.000
195A198GLU-1-0.880-0.91527.989-0.090-0.0900.0000.0000.0000.000