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: 4J66N

Calculation Name: 1CQ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CQ3

Chain ID: A

ChEMBL ID:

UniProt ID: Q85307

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2564376.69017
FMO2-HF: Nuclear repulsion 2476554.395361
FMO2-HF: Total energy -87822.294809
FMO2-MP2: Total energy -88069.854675


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:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-9.6-4.199-0.038-2.723-2.641-0.005
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.031
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].
3A3SER00.0030.0353.631-5.838-0.855-0.045-2.644-2.294-0.005
4A4SER00.0710.0105.754-0.345-0.335-0.001-0.001-0.0080.000
5A5SER00.033-0.0108.5960.0820.0820.0000.0000.0000.000
6A6SER0-0.118-0.0583.913-0.399-0.2440.001-0.029-0.1280.000
7A7SER0-0.030-0.0153.5640.1300.3830.007-0.049-0.2110.000
8A8CYS00.0000.0105.6240.2420.2420.0000.0000.0000.000
9A9THR0-0.002-0.0137.314-0.696-0.6960.0000.0000.0000.000
10A10GLU-1-0.952-0.9755.896-2.852-2.8520.0000.0000.0000.000
11A11GLU-1-0.943-0.9539.497-0.396-0.3960.0000.0000.0000.000
12A12GLU-1-0.917-0.96612.204-0.339-0.3390.0000.0000.0000.000
13A13ASN0-0.077-0.06015.5810.0320.0320.0000.0000.0000.000
14A14LYS10.8440.91814.2060.4550.4550.0000.0000.0000.000
15A15HIS0-0.048-0.04715.135-0.060-0.0600.0000.0000.0000.000
16A16HIS00.0180.02110.079-0.173-0.1730.0000.0000.0000.000
17A17MET0-0.0310.00815.1910.0140.0140.0000.0000.0000.000
18A18GLY00.012-0.00518.5030.0280.0280.0000.0000.0000.000
19A19ILE00.0420.01620.058-0.016-0.0160.0000.0000.0000.000
20A20ASP-1-0.795-0.83822.7380.0780.0780.0000.0000.0000.000
21A21VAL00.0470.02724.708-0.010-0.0100.0000.0000.0000.000
22A22ILE0-0.039-0.01627.8090.0100.0100.0000.0000.0000.000
23A23ILE00.0430.01330.350-0.006-0.0060.0000.0000.0000.000
24A24LYS10.8430.91833.640-0.027-0.0270.0000.0000.0000.000
25A25VAL00.0460.02736.498-0.004-0.0040.0000.0000.0000.000
26A26THR0-0.057-0.02339.6340.0020.0020.0000.0000.0000.000
27A27LYS10.9100.95041.716-0.047-0.0470.0000.0000.0000.000
28A28GLN0-0.015-0.00645.065-0.001-0.0010.0000.0000.0000.000
29A29ASP-1-0.871-0.91848.8550.0250.0250.0000.0000.0000.000
30A30GLN0-0.077-0.04351.1830.0010.0010.0000.0000.0000.000
31A31THR0-0.004-0.00146.3120.0000.0000.0000.0000.0000.000
32A32PRO0-0.030-0.02148.7130.0000.0000.0000.0000.0000.000
33A33THR0-0.009-0.01345.6420.0010.0010.0000.0000.0000.000
34A34ASN00.0220.00041.9310.0030.0030.0000.0000.0000.000
35A35ASP-1-0.936-0.96140.0610.0560.0560.0000.0000.0000.000
36A36LYS10.8080.90938.326-0.051-0.0510.0000.0000.0000.000
37A37ILE00.0110.02032.697-0.001-0.0010.0000.0000.0000.000
38A38CYS00.0200.03626.0410.0020.0020.0000.0000.0000.000
39A39GLN0-0.045-0.02832.9550.0040.0040.0000.0000.0000.000
40A40SER0-0.032-0.02433.2740.0020.0020.0000.0000.0000.000
41A41VAL00.0280.01528.198-0.003-0.0030.0000.0000.0000.000
42A42THR0-0.040-0.01031.1080.0050.0050.0000.0000.0000.000
43A43GLU-1-0.769-0.85325.6140.1180.1180.0000.0000.0000.000
44A44VAL0-0.0030.00230.0610.0020.0020.0000.0000.0000.000
45A45THR0-0.0260.00827.859-0.003-0.0030.0000.0000.0000.000
46A46GLU-1-0.793-0.86730.5810.0280.0280.0000.0000.0000.000
47A47SER0-0.059-0.05931.612-0.002-0.0020.0000.0000.0000.000
48A48GLU-1-0.926-0.94629.4650.0780.0780.0000.0000.0000.000
49A49ASP-1-0.956-0.98630.8520.0530.0530.0000.0000.0000.000
50A50GLU-1-0.955-0.96933.8630.0410.0410.0000.0000.0000.000
51A51SER0-0.098-0.06434.702-0.005-0.0050.0000.0000.0000.000
52A52GLU-1-0.933-0.94735.7960.0330.0330.0000.0000.0000.000
53A53GLU-1-0.905-0.95435.4090.0170.0170.0000.0000.0000.000
54A54VAL00.0040.01334.015-0.003-0.0030.0000.0000.0000.000
55A55VAL0-0.040-0.01435.943-0.003-0.0030.0000.0000.0000.000
56A56LYS10.8840.92138.2090.0030.0030.0000.0000.0000.000
57A57GLY00.0000.01036.5540.0020.0020.0000.0000.0000.000
58A58ASP-1-0.859-0.94231.075-0.007-0.0070.0000.0000.0000.000
59A59PRO00.0050.00329.0410.0010.0010.0000.0000.0000.000
60A60THR0-0.012-0.00130.286-0.001-0.0010.0000.0000.0000.000
61A61THR0-0.047-0.02927.0130.0030.0030.0000.0000.0000.000
62A62TYR0-0.091-0.08030.008-0.003-0.0030.0000.0000.0000.000
63A63TYR0-0.089-0.07825.5920.0080.0080.0000.0000.0000.000
64A64THR0-0.018-0.01531.491-0.005-0.0050.0000.0000.0000.000
65A65VAL0-0.044-0.04130.9560.0070.0070.0000.0000.0000.000
66A66VAL0-0.0240.00633.819-0.005-0.0050.0000.0000.0000.000
67A67GLY00.0490.00835.7640.0060.0060.0000.0000.0000.000
68A68GLY00.0080.00537.315-0.003-0.0030.0000.0000.0000.000
69A69GLY00.0220.00939.658-0.003-0.0030.0000.0000.0000.000
70A70LEU0-0.036-0.01538.989-0.004-0.0040.0000.0000.0000.000
71A71THR00.0400.01738.3910.0050.0050.0000.0000.0000.000
72A72MET0-0.065-0.02433.940-0.006-0.0060.0000.0000.0000.000
73A73ASP-1-0.786-0.87035.2200.0500.0500.0000.0000.0000.000
74A74PHE0-0.010-0.03031.613-0.004-0.0040.0000.0000.0000.000
75A75GLY00.0490.02432.8620.0040.0040.0000.0000.0000.000
76A76PHE0-0.032-0.01527.993-0.003-0.0030.0000.0000.0000.000
77A77THR00.0740.03430.0370.0050.0050.0000.0000.0000.000
78A78LYS10.8140.91127.7920.0110.0110.0000.0000.0000.000
79A79CYS0-0.117-0.02825.996-0.001-0.0010.0000.0000.0000.000
80A80PRO0-0.016-0.00120.4690.0100.0100.0000.0000.0000.000
81A81LYS10.8630.91919.580-0.130-0.1300.0000.0000.0000.000
82A82ILE00.0400.05020.7400.0060.0060.0000.0000.0000.000
83A83SER0-0.090-0.06318.4690.0240.0240.0000.0000.0000.000
84A84SER0-0.094-0.05520.2020.0250.0250.0000.0000.0000.000
85A85ILE00.0750.04922.048-0.016-0.0160.0000.0000.0000.000
86A86SER0-0.050-0.02925.7830.0080.0080.0000.0000.0000.000
87A87GLU-1-0.732-0.89427.5790.0630.0630.0000.0000.0000.000
88A88TYR0-0.001-0.00131.0990.0050.0050.0000.0000.0000.000
89A89SER00.0580.03433.460-0.005-0.0050.0000.0000.0000.000
90A90ASP-1-0.835-0.92137.2000.0550.0550.0000.0000.0000.000
91A91GLY00.0020.02739.098-0.003-0.0030.0000.0000.0000.000
92A92ASN0-0.028-0.01542.8140.0020.0020.0000.0000.0000.000
93A93THR0-0.038-0.03239.217-0.001-0.0010.0000.0000.0000.000
94A94VAL00.0140.01236.1410.0030.0030.0000.0000.0000.000
95A95ASN0-0.066-0.03633.384-0.006-0.0060.0000.0000.0000.000
96A96ALA00.0440.01830.9220.0060.0060.0000.0000.0000.000
97A97ARG10.8380.88823.718-0.070-0.0700.0000.0000.0000.000
98A98LEU00.0000.01625.7440.0130.0130.0000.0000.0000.000
99A99SER00.003-0.00420.762-0.010-0.0100.0000.0000.0000.000
100A100SER00.0580.03118.4730.0110.0110.0000.0000.0000.000
101A101VAL0-0.070-0.03614.3600.0000.0000.0000.0000.0000.000
102A102SER00.0350.02613.8630.0240.0240.0000.0000.0000.000
103A103PRO0-0.021-0.0238.6660.0790.0790.0000.0000.0000.000
104A104GLY0-0.024-0.0027.701-0.047-0.0470.0000.0000.0000.000
105A105GLN0-0.043-0.0378.6520.0130.0130.0000.0000.0000.000
106A106GLY0-0.026-0.00710.148-0.053-0.0530.0000.0000.0000.000
107A107LYS10.9150.96511.532-0.373-0.3730.0000.0000.0000.000
108A108ASP-1-0.850-0.89711.1570.7880.7880.0000.0000.0000.000
109A109SER00.0150.00011.808-0.105-0.1050.0000.0000.0000.000
110A110PRO00.0300.00412.433-0.054-0.0540.0000.0000.0000.000
111A111ALA0-0.0060.00712.759-0.028-0.0280.0000.0000.0000.000
112A112ILE00.0110.01014.702-0.003-0.0030.0000.0000.0000.000
113A113THR0-0.012-0.03618.108-0.035-0.0350.0000.0000.0000.000
114A114ARG10.9620.98320.0410.1920.1920.0000.0000.0000.000
115A115GLU-1-0.858-0.90922.150-0.171-0.1710.0000.0000.0000.000
116A116GLU-1-0.877-0.94321.600-0.064-0.0640.0000.0000.0000.000
117A117ALA00.0150.01121.6810.0180.0180.0000.0000.0000.000
118A118LEU0-0.027-0.02123.6310.0160.0160.0000.0000.0000.000
119A119SER0-0.064-0.03027.0600.0110.0110.0000.0000.0000.000
120A120MET00.0040.01922.5800.0110.0110.0000.0000.0000.000
121A121ILE0-0.052-0.03224.7880.0070.0070.0000.0000.0000.000
122A122LYS10.8830.94327.9050.0670.0670.0000.0000.0000.000
123A123ASP-1-0.878-0.92329.854-0.026-0.0260.0000.0000.0000.000
124A125GLU-1-0.825-0.91629.7320.0050.0050.0000.0000.0000.000
125A126MET0-0.039-0.02430.8600.0080.0080.0000.0000.0000.000
126A127SER0-0.0100.01732.753-0.002-0.0020.0000.0000.0000.000
127A128ILE00.005-0.01934.4470.0050.0050.0000.0000.0000.000
128A129ASN0-0.013-0.01137.006-0.003-0.0030.0000.0000.0000.000
129A130ILE00.0100.01637.7420.0040.0040.0000.0000.0000.000
130A131LYS10.8830.92640.645-0.039-0.0390.0000.0000.0000.000
131A132CYS0-0.066-0.04842.4670.0020.0020.0000.0000.0000.000
132A133SER0-0.027-0.00241.7720.0010.0010.0000.0000.0000.000
133A134GLU-1-0.954-0.98843.8380.0400.0400.0000.0000.0000.000
134A135GLU-1-0.854-0.92840.1070.0570.0570.0000.0000.0000.000
135A136GLU-1-0.840-0.90842.9670.0490.0490.0000.0000.0000.000
136A137LYS10.7600.88335.749-0.078-0.0780.0000.0000.0000.000
137A138ASP-1-0.884-0.93338.2660.0680.0680.0000.0000.0000.000
138A139SER0-0.031-0.03934.1540.0000.0000.0000.0000.0000.000
139A140ASN0-0.068-0.03231.7240.0050.0050.0000.0000.0000.000
140A141ILE00.007-0.00329.2370.0030.0030.0000.0000.0000.000
141A142LYS10.8610.92422.536-0.173-0.1730.0000.0000.0000.000
142A143THR0-0.030-0.01925.923-0.002-0.0020.0000.0000.0000.000
143A144HIS0-0.014-0.01420.229-0.010-0.0100.0000.0000.0000.000
144A145PRO00.0250.01419.978-0.012-0.0120.0000.0000.0000.000
145A146VAL0-0.0010.00020.6820.0170.0170.0000.0000.0000.000
146A147LEU0-0.0270.00116.0720.0040.0040.0000.0000.0000.000
147A148GLY00.0470.03117.692-0.022-0.0220.0000.0000.0000.000
148A149SER00.054-0.00917.0840.0200.0200.0000.0000.0000.000
149A150ASN0-0.090-0.05816.1080.0020.0020.0000.0000.0000.000
150A151ILE00.0440.03818.566-0.023-0.0230.0000.0000.0000.000
151A152SER0-0.025-0.00721.5990.0150.0150.0000.0000.0000.000
152A153HIS00.0150.01624.719-0.015-0.0150.0000.0000.0000.000
153A154LYS10.8740.93925.1040.0470.0470.0000.0000.0000.000
154A155LYS10.8370.90529.7740.0080.0080.0000.0000.0000.000
155A156VAL0-0.037-0.01827.286-0.005-0.0050.0000.0000.0000.000
156A157SER0-0.032-0.01630.0490.0050.0050.0000.0000.0000.000
157A158TYR0-0.062-0.04631.641-0.002-0.0020.0000.0000.0000.000
158A159GLU-1-0.912-0.97331.323-0.041-0.0410.0000.0000.0000.000
159A160ASP-1-0.992-0.95933.814-0.004-0.0040.0000.0000.0000.000
160A161ILE0-0.005-0.02529.4530.0000.0000.0000.0000.0000.000
161A162ILE0-0.095-0.06033.2670.0050.0050.0000.0000.0000.000
162A163GLY00.1120.07235.260-0.003-0.0030.0000.0000.0000.000
163A164SER0-0.099-0.06437.6890.0010.0010.0000.0000.0000.000
164A165THR00.0570.02638.9490.0040.0040.0000.0000.0000.000
165A166ILE0-0.089-0.04140.738-0.002-0.0020.0000.0000.0000.000
166A167VAL00.0320.01241.8990.0030.0030.0000.0000.0000.000
167A168ASP-1-0.787-0.86844.2340.0250.0250.0000.0000.0000.000
168A169THR00.022-0.00946.7870.0010.0010.0000.0000.0000.000
169A170LYS10.9240.97048.969-0.028-0.0280.0000.0000.0000.000
170A171CYS0-0.037-0.02445.2220.0010.0010.0000.0000.0000.000
171A172VAL00.0110.01242.8470.0010.0010.0000.0000.0000.000
172A173LYS10.8020.91345.269-0.024-0.0240.0000.0000.0000.000
173A174ASN0-0.008-0.03043.260-0.003-0.0030.0000.0000.0000.000
174A175LEU00.0020.00637.7790.0030.0030.0000.0000.0000.000
175A176GLU-1-0.874-0.93137.6870.0210.0210.0000.0000.0000.000
176A177ILE0-0.0080.00632.4310.0050.0050.0000.0000.0000.000
177A178SER0-0.002-0.00730.500-0.007-0.0070.0000.0000.0000.000
178A179VAL00.0240.01228.5550.0080.0080.0000.0000.0000.000
179A180ARG10.7580.86424.1930.0220.0220.0000.0000.0000.000
180A181ILE00.0510.01423.9830.0090.0090.0000.0000.0000.000
181A182GLY00.0390.00722.342-0.007-0.0070.0000.0000.0000.000
182A183ASP-1-0.787-0.88216.438-0.247-0.2470.0000.0000.0000.000
183A184MET0-0.047-0.00515.4500.0250.0250.0000.0000.0000.000
184A185CYS0-0.085-0.02912.2140.0030.0030.0000.0000.0000.000
185A186LYS10.8320.90114.4750.3490.3490.0000.0000.0000.000
186A187GLU-1-0.810-0.88316.953-0.062-0.0620.0000.0000.0000.000
187A188SER0-0.034-0.00919.362-0.029-0.0290.0000.0000.0000.000
188A189SER0-0.006-0.00921.7710.0110.0110.0000.0000.0000.000
189A190GLU-1-0.891-0.95024.346-0.142-0.1420.0000.0000.0000.000
190A191LEU0-0.051-0.03520.8720.0040.0040.0000.0000.0000.000
191A192GLU-1-0.782-0.86622.125-0.071-0.0710.0000.0000.0000.000
192A193VAL00.0210.00625.8030.0010.0010.0000.0000.0000.000
193A194LYS10.7680.85428.0740.0020.0020.0000.0000.0000.000
194A195ASP-1-0.666-0.79930.693-0.005-0.0050.0000.0000.0000.000
195A196GLY0-0.064-0.05733.0250.0040.0040.0000.0000.0000.000
196A197PHE00.0100.01835.610-0.002-0.0020.0000.0000.0000.000
197A198LYS10.8880.94738.704-0.007-0.0070.0000.0000.0000.000
198A199TYR00.0220.02141.305-0.003-0.0030.0000.0000.0000.000
199A200VAL0-0.039-0.04143.9720.0020.0020.0000.0000.0000.000
200A201ASP-1-0.870-0.95346.4710.0170.0170.0000.0000.0000.000
201A202GLY0-0.021-0.00748.167-0.001-0.0010.0000.0000.0000.000
202A203SER0-0.082-0.03248.985-0.002-0.0020.0000.0000.0000.000
203A204ALA00.0360.01344.3510.0020.0020.0000.0000.0000.000
204A205SER0-0.113-0.07943.976-0.001-0.0010.0000.0000.0000.000
205A206GLU-1-0.792-0.89639.653-0.002-0.0020.0000.0000.0000.000
206A207ASP-1-0.933-0.92240.351-0.002-0.0020.0000.0000.0000.000
207A208ALA00.0620.03636.5230.0010.0010.0000.0000.0000.000
208A209ALA0-0.025-0.02636.082-0.001-0.0010.0000.0000.0000.000
209A210ASP-1-0.848-0.91132.0840.0010.0010.0000.0000.0000.000
210A211ASP-1-0.793-0.89332.0270.0150.0150.0000.0000.0000.000
211A212THR0-0.075-0.06127.8410.0050.0050.0000.0000.0000.000
212A213SER0-0.092-0.06029.8410.0060.0060.0000.0000.0000.000
213A214LEU0-0.0170.02832.5510.0020.0020.0000.0000.0000.000
214A215ILE00.0160.00729.4230.0010.0010.0000.0000.0000.000
215A216ASN0-0.016-0.02431.1730.0030.0030.0000.0000.0000.000
216A217SER00.0790.00826.0350.0050.0050.0000.0000.0000.000
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