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: YV442

Calculation Name: 1J2W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1J2W

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SJ28

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptH
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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2370815.704805
FMO2-HF: Nuclear repulsion 2292304.393095
FMO2-HF: Total energy -78511.311709
FMO2-MP2: Total energy -78742.828429


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-6.208-0.512.866-3.932-4.631-0.011
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.062 / 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].
3A3LEU0-0.026-0.0223.267-1.5470.4660.005-0.846-1.1720.002
4A4ALA00.0540.0393.3410.4501.0510.027-0.171-0.4560.000
5A5ALA00.0340.0134.8770.6320.740-0.001-0.008-0.0990.000
6A6HIS10.8400.9157.7151.3251.3250.0000.0000.0000.000
7A7ILE00.0060.0066.0690.2300.2300.0000.0000.0000.000
8A8ASP-1-0.719-0.8239.744-0.587-0.5870.0000.0000.0000.000
9A9HIS0-0.065-0.05510.676-0.016-0.0160.0000.0000.0000.000
10A10THR0-0.062-0.05212.2750.0820.0820.0000.0000.0000.000
11A11LEU00.0100.01215.7270.0070.0070.0000.0000.0000.000
12A12LEU00.005-0.02118.5120.0130.0130.0000.0000.0000.000
13A13LYS10.8270.92121.7530.2090.2090.0000.0000.0000.000
14A14PRO00.0500.00523.768-0.002-0.0020.0000.0000.0000.000
15A15THR0-0.029-0.01726.9330.0000.0000.0000.0000.0000.000
16A16ALA0-0.0120.01122.8500.0030.0030.0000.0000.0000.000
17A17THR00.0420.02724.5400.0050.0050.0000.0000.0000.000
18A18LEU00.0480.00623.910-0.015-0.0150.0000.0000.0000.000
19A19GLU-1-0.936-0.95723.213-0.144-0.1440.0000.0000.0000.000
20A20GLU-1-0.770-0.87720.705-0.200-0.2000.0000.0000.0000.000
21A21VAL0-0.014-0.00919.214-0.032-0.0320.0000.0000.0000.000
22A22ALA0-0.026-0.01518.920-0.031-0.0310.0000.0000.0000.000
23A23LYS10.9791.00614.8240.2350.2350.0000.0000.0000.000
24A24ALA00.0080.00114.873-0.034-0.0340.0000.0000.0000.000
25A25ALA0-0.012-0.02214.001-0.069-0.0690.0000.0000.0000.000
26A26GLU-1-0.944-0.97414.371-0.264-0.2640.0000.0000.0000.000
27A27GLU-1-0.828-0.91110.892-0.461-0.4610.0000.0000.0000.000
28A28ALA0-0.029-0.0209.811-0.123-0.1230.0000.0000.0000.000
29A29LEU0-0.066-0.0349.853-0.144-0.1440.0000.0000.0000.000
30A30GLU-1-0.977-0.9758.770-0.275-0.2750.0000.0000.0000.000
31A31TYR0-0.038-0.0405.0240.0250.0250.0000.0000.0000.000
32A32GLY0-0.0050.0134.935-0.777-0.696-0.001-0.002-0.0780.000
33A33PHE0-0.068-0.0285.489-0.288-0.2880.0000.0000.0000.000
34A34TYR0-0.038-0.0098.3240.2030.2030.0000.0000.0000.000
35A35GLY00.0190.00910.8750.1380.1380.0000.0000.0000.000
36A36LEU0-0.0100.01812.537-0.064-0.0640.0000.0000.0000.000
37A37CYS0-0.065-0.02815.0670.0550.0550.0000.0000.0000.000
38A38ILE00.0090.01017.7280.0050.0050.0000.0000.0000.000
39A39PRO00.0530.01720.4720.0090.0090.0000.0000.0000.000
40A40PRO00.0940.05024.233-0.004-0.0040.0000.0000.0000.000
41A41SER0-0.043-0.02326.5140.0020.0020.0000.0000.0000.000
42A42TYR0-0.041-0.04023.8620.0120.0120.0000.0000.0000.000
43A43VAL0-0.0110.00723.605-0.010-0.0100.0000.0000.0000.000
44A44ALA00.0370.01324.788-0.005-0.0050.0000.0000.0000.000
45A45TRP00.0070.01021.279-0.003-0.0030.0000.0000.0000.000
46A46VAL00.0280.00919.5450.0000.0000.0000.0000.0000.000
47A47ARG10.8570.94520.1700.2920.2920.0000.0000.0000.000
48A48ALA0-0.010-0.00823.6560.0040.0040.0000.0000.0000.000
49A49ARG10.8840.96420.8900.2070.2070.0000.0000.0000.000
50A50TYR0-0.032-0.03218.3890.0050.0050.0000.0000.0000.000
51A51PRO00.0270.01420.644-0.023-0.0230.0000.0000.0000.000
52A52HIS0-0.013-0.01619.506-0.009-0.0090.0000.0000.0000.000
53A53ALA0-0.027-0.00616.506-0.019-0.0190.0000.0000.0000.000
54A54PRO0-0.0020.00811.7340.0040.0040.0000.0000.0000.000
55A55PHE0-0.0150.00412.530-0.042-0.0420.0000.0000.0000.000
56A56ARG10.9450.96913.9090.6310.6310.0000.0000.0000.000
57A57LEU0-0.043-0.01816.428-0.028-0.0280.0000.0000.0000.000
58A58VAL0-0.017-0.01017.1280.0270.0270.0000.0000.0000.000
59A59THR00.025-0.00319.7530.0130.0130.0000.0000.0000.000
60A60VAL0-0.072-0.03322.333-0.006-0.0060.0000.0000.0000.000
61A61VAL00.0280.01524.7460.0100.0100.0000.0000.0000.000
62A62GLY00.004-0.00328.376-0.001-0.0010.0000.0000.0000.000
63A63PHE0-0.0310.00923.4610.0000.0000.0000.0000.0000.000
64A64PRO0-0.014-0.02626.9910.0060.0060.0000.0000.0000.000
65A65LEU00.030-0.01628.5960.0000.0000.0000.0000.0000.000
66A66GLY00.0510.05031.7650.0050.0050.0000.0000.0000.000
67A67TYR0-0.033-0.01632.7870.0030.0030.0000.0000.0000.000
68A68GLN0-0.012-0.00533.7410.0010.0010.0000.0000.0000.000
69A69GLU-1-0.858-0.93336.932-0.092-0.0920.0000.0000.0000.000
70A70LYS10.9630.98036.7690.0890.0890.0000.0000.0000.000
71A71GLU-1-0.842-0.93736.923-0.101-0.1010.0000.0000.0000.000
72A72VAL0-0.023-0.00535.434-0.002-0.0020.0000.0000.0000.000
73A73LYS10.7580.85732.4840.1310.1310.0000.0000.0000.000
74A74ALA00.0190.01532.711-0.009-0.0090.0000.0000.0000.000
75A75LEU00.0200.00033.948-0.005-0.0050.0000.0000.0000.000
76A76GLU-1-0.883-0.93730.387-0.166-0.1660.0000.0000.0000.000
77A77ALA00.013-0.00229.370-0.010-0.0100.0000.0000.0000.000
78A78ALA00.0440.01929.782-0.009-0.0090.0000.0000.0000.000
79A79LEU0-0.047-0.01931.788-0.002-0.0020.0000.0000.0000.000
80A80ALA0-0.008-0.00626.729-0.004-0.0040.0000.0000.0000.000
81A81CYS00.0160.00627.052-0.014-0.0140.0000.0000.0000.000
82A82ALA0-0.0150.01228.120-0.002-0.0020.0000.0000.0000.000
83A83ARG10.8810.92728.8520.1460.1460.0000.0000.0000.000
84A84GLY00.0240.00625.419-0.002-0.0020.0000.0000.0000.000
85A85ALA0-0.047-0.01923.035-0.022-0.0220.0000.0000.0000.000
86A86ASP-1-0.794-0.88819.947-0.342-0.3420.0000.0000.0000.000
87A87GLU-1-0.795-0.90718.517-0.450-0.4500.0000.0000.0000.000
88A88VAL0-0.0040.00622.1850.0020.0020.0000.0000.0000.000
89A89ASP-1-0.711-0.86820.194-0.353-0.3530.0000.0000.0000.000
90A90MET00.0120.01523.6910.0070.0070.0000.0000.0000.000
91A91VAL0-0.0200.00726.990-0.007-0.0070.0000.0000.0000.000
92A92LEU00.0190.02628.8310.0080.0080.0000.0000.0000.000
93A93HIS00.0430.02431.825-0.001-0.0010.0000.0000.0000.000
94A94LEU00.036-0.00730.8240.0050.0050.0000.0000.0000.000
95A95GLY0-0.0070.00634.9380.0050.0050.0000.0000.0000.000
96A96ARG10.8880.94038.3680.0880.0880.0000.0000.0000.000
97A97ALA00.0330.02235.0960.0030.0030.0000.0000.0000.000
98A98LYS10.9120.96737.0740.0880.0880.0000.0000.0000.000
99A99ALA0-0.046-0.02538.6610.0040.0040.0000.0000.0000.000
100A100GLY00.0000.00840.1150.0040.0040.0000.0000.0000.000
101A101ASP-1-0.864-0.93940.803-0.081-0.0810.0000.0000.0000.000
102A102LEU00.004-0.03237.200-0.005-0.0050.0000.0000.0000.000
103A103ASP-1-0.848-0.91138.729-0.086-0.0860.0000.0000.0000.000
104A104TYR0-0.054-0.02337.873-0.002-0.0020.0000.0000.0000.000
105A105LEU0-0.054-0.03034.741-0.005-0.0050.0000.0000.0000.000
106A106GLU-1-0.896-0.94635.393-0.109-0.1090.0000.0000.0000.000
107A107ALA00.0070.00236.385-0.005-0.0050.0000.0000.0000.000
108A108GLU-1-0.797-0.89734.259-0.130-0.1300.0000.0000.0000.000
109A109VAL0-0.052-0.01930.816-0.007-0.0070.0000.0000.0000.000
110A110ARG10.9160.96632.9680.1170.1170.0000.0000.0000.000
111A111ALA0-0.001-0.00135.399-0.001-0.0010.0000.0000.0000.000
112A112VAL00.001-0.01129.989-0.002-0.0020.0000.0000.0000.000
113A113ARG10.7500.85727.4720.1880.1880.0000.0000.0000.000
114A114GLU-1-0.948-0.98832.075-0.115-0.1150.0000.0000.0000.000
115A115ALA0-0.0380.00433.4630.0030.0030.0000.0000.0000.000
116A116VAL0-0.062-0.02828.546-0.001-0.0010.0000.0000.0000.000
117A117PRO00.0150.01029.617-0.014-0.0140.0000.0000.0000.000
118A118GLN0-0.039-0.02528.2030.0020.0020.0000.0000.0000.000
119A119ALA00.0060.02325.261-0.015-0.0150.0000.0000.0000.000
120A120VAL0-0.0170.01120.5340.0080.0080.0000.0000.0000.000
121A121LEU0-0.005-0.01423.602-0.006-0.0060.0000.0000.0000.000
122A122LYS10.7710.88217.9060.4040.4040.0000.0000.0000.000
123A123VAL00.0260.01023.8000.0090.0090.0000.0000.0000.000
124A124ILE0-0.060-0.04523.460-0.009-0.0090.0000.0000.0000.000
125A125LEU00.018-0.00925.8870.0130.0130.0000.0000.0000.000
126A126GLU-1-0.800-0.87026.531-0.171-0.1710.0000.0000.0000.000
127A127THR0-0.019-0.04225.5070.0110.0110.0000.0000.0000.000
128A128GLY0-0.042-0.00627.8850.0100.0100.0000.0000.0000.000
129A129TYR0-0.037-0.02129.2030.0070.0070.0000.0000.0000.000
130A130PHE0-0.065-0.03031.2600.0080.0080.0000.0000.0000.000
131A131SER00.0190.01932.114-0.002-0.0020.0000.0000.0000.000
132A132PRO00.0460.00131.204-0.006-0.0060.0000.0000.0000.000
133A133GLU-1-0.877-0.95032.513-0.083-0.0830.0000.0000.0000.000
134A134GLU-1-0.913-0.95935.040-0.091-0.0910.0000.0000.0000.000
135A135ILE00.0030.00528.512-0.005-0.0050.0000.0000.0000.000
136A136ALA0-0.008-0.00231.468-0.007-0.0070.0000.0000.0000.000
137A137ARG10.9630.97932.6620.0820.0820.0000.0000.0000.000
138A138LEU00.0020.00731.786-0.002-0.0020.0000.0000.0000.000
139A139ALA0-0.003-0.00329.286-0.006-0.0060.0000.0000.0000.000
140A140GLU-1-0.798-0.87230.575-0.117-0.1170.0000.0000.0000.000
141A141ALA00.0230.00933.346-0.001-0.0010.0000.0000.0000.000
142A142ALA00.0310.00729.561-0.001-0.0010.0000.0000.0000.000
143A143ILE0-0.014-0.00728.613-0.005-0.0050.0000.0000.0000.000
144A144ARG10.8710.94431.0120.0960.0960.0000.0000.0000.000
145A145GLY00.0510.03033.6850.0040.0040.0000.0000.0000.000
146A146GLY0-0.036-0.02831.4800.0000.0000.0000.0000.0000.000
147A147ALA0-0.040-0.01227.001-0.010-0.0100.0000.0000.0000.000
148A148ASP-1-0.772-0.86223.720-0.227-0.2270.0000.0000.0000.000
149A149PHE0-0.079-0.05617.622-0.022-0.0220.0000.0000.0000.000
150A150LEU00.0260.03022.9440.0150.0150.0000.0000.0000.000
151A151LYS10.8290.91119.5240.2970.2970.0000.0000.0000.000
152A152THR00.0170.01721.0210.0100.0100.0000.0000.0000.000
153A153SER00.029-0.00621.8830.0290.0290.0000.0000.0000.000
154A154THR0-0.026-0.03622.235-0.027-0.0270.0000.0000.0000.000
155A155GLY0-0.059-0.03621.980-0.019-0.0190.0000.0000.0000.000
156A156PHE0-0.077-0.04522.7670.0050.0050.0000.0000.0000.000
157A157GLY00.0540.04926.1350.0130.0130.0000.0000.0000.000
158A158PRO0-0.052-0.02727.751-0.001-0.0010.0000.0000.0000.000
159A159ARG10.8430.90324.7940.1570.1570.0000.0000.0000.000
160A160GLY0-0.0160.00121.456-0.008-0.0080.0000.0000.0000.000
161A161ALA0-0.021-0.01218.8610.0160.0160.0000.0000.0000.000
162A162SER00.0380.04620.576-0.001-0.0010.0000.0000.0000.000
163A163LEU00.039-0.00517.434-0.014-0.0140.0000.0000.0000.000
164A164GLU-1-0.887-0.95521.019-0.118-0.1180.0000.0000.0000.000
165A165ASP-1-0.780-0.85422.980-0.164-0.1640.0000.0000.0000.000
166A166VAL0-0.035-0.01918.675-0.003-0.0030.0000.0000.0000.000
167A167ALA00.0440.02221.8680.0030.0030.0000.0000.0000.000
168A168LEU0-0.080-0.03323.6950.0090.0090.0000.0000.0000.000
169A169LEU00.0330.00623.5390.0050.0050.0000.0000.0000.000
170A170VAL00.0020.02121.4180.0010.0010.0000.0000.0000.000
171A171ARG10.9070.96624.5750.1120.1120.0000.0000.0000.000
172A172VAL00.0180.01727.8660.0080.0080.0000.0000.0000.000
173A173ALA00.0370.01726.1010.0060.0060.0000.0000.0000.000
174A174GLN0-0.100-0.05628.0800.0070.0070.0000.0000.0000.000
175A175GLY0-0.002-0.00425.5470.0050.0050.0000.0000.0000.000
176A176ARG10.7520.85126.6330.1180.1180.0000.0000.0000.000
177A177ALA00.0350.02425.082-0.004-0.0040.0000.0000.0000.000
178A178GLN00.0000.02818.380-0.034-0.0340.0000.0000.0000.000
179A179VAL00.0490.02819.9310.0110.0110.0000.0000.0000.000
180A180LYS10.7460.86216.0010.4050.4050.0000.0000.0000.000
181A181ALA00.0210.01616.1590.0410.0410.0000.0000.0000.000
182A182ALA00.002-0.01316.229-0.060-0.0600.0000.0000.0000.000
183A183GLY00.0520.02817.6350.0360.0360.0000.0000.0000.000
184A184GLY00.017-0.01018.3980.0070.0070.0000.0000.0000.000
185A185ILE0-0.0050.01512.0020.0160.0160.0000.0000.0000.000
186A186ARG10.8940.92813.4890.3120.3120.0000.0000.0000.000
187A187ASP-1-0.788-0.85210.674-0.294-0.2940.0000.0000.0000.000
188A188ARG10.9840.9824.390-0.406-0.343-0.001-0.003-0.0580.000
189A189GLU-1-0.832-0.9238.228-0.070-0.0700.0000.0000.0000.000
190A190THR0-0.049-0.05811.2330.0180.0180.0000.0000.0000.000
191A191ALA0-0.004-0.0108.9320.0160.0160.0000.0000.0000.000
192A192LEU00.0130.0007.4060.0030.0030.0000.0000.0000.000
193A193ARG10.8470.93810.7480.2000.2000.0000.0000.0000.000
194A194MET0-0.017-0.00913.7910.0270.0270.0000.0000.0000.000
195A195LEU0-0.021-0.0089.640-0.003-0.0030.0000.0000.0000.000
196A196LYS10.9350.98113.8680.0660.0660.0000.0000.0000.000
197A197ALA0-0.054-0.02415.7750.0260.0260.0000.0000.0000.000
198A198GLY00.0250.00217.3380.0190.0190.0000.0000.0000.000
199A199ALA0-0.052-0.00715.761-0.009-0.0090.0000.0000.0000.000
200A200SER0-0.017-0.02814.777-0.026-0.0260.0000.0000.0000.000
201A201ARG10.7790.87213.0330.4780.4780.0000.0000.0000.000
202A202LEU00.0180.0009.8190.0840.0840.0000.0000.0000.000
203A203GLY0-0.002-0.00212.840-0.053-0.0530.0000.0000.0000.000
204A204THR0-0.031-0.04810.9920.0560.0560.0000.0000.0000.000
205A205SER00.0580.03913.277-0.040-0.0400.0000.0000.0000.000
206A206SER0-0.0270.00011.9930.0430.0430.0000.0000.0000.000
207A207GLY00.0670.0408.305-0.048-0.0480.0000.0000.0000.000
208A208VAL00.0710.0336.728-0.250-0.2500.0000.0000.0000.000
209A209ALA0-0.014-0.0067.282-0.098-0.0980.0000.0000.0000.000
210A210LEU0-0.081-0.0326.5670.0070.0070.0000.0000.0000.000
211A211VAL0-0.039-0.0132.148-1.989-0.8672.685-2.026-1.781-0.003
212A212ALA0-0.0220.0092.925-3.381-1.6710.152-0.876-0.987-0.010