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: N9YJQ

Calculation Name: 3EVZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EVZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U2I7

Base Structure: X-ray

Registration Date: 2023-09-20

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2339988.165002
FMO2-HF: Nuclear repulsion 2262595.264691
FMO2-HF: Total energy -77392.900311
FMO2-MP2: Total energy -77622.884008


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:34:PHE)


Summations of interaction energy for fragment #1(A:34:PHE)
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.
-20.211-12.1994.395-4.168-8.2410.038
Interaction energy analysis for fragmet #1(A:34:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.101 / q_NPA : 0.027
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].
3A36ASN00.0640.0412.633-6.319-1.9593.993-3.020-5.3330.034
4A37ARG10.8520.9172.861-7.124-4.6230.394-0.908-1.9870.004
5A38GLN00.0370.0143.861-0.762-0.1190.001-0.148-0.4970.000
6A39ALA00.0530.0246.378-0.231-0.2310.0000.0000.0000.000
7A40ARG10.9000.9393.515-2.782-2.3600.008-0.090-0.3410.000
8A41ILE0-0.0080.0027.664-0.235-0.2350.0000.0000.0000.000
9A42LEU00.0160.0209.905-0.188-0.1880.0000.0000.0000.000
10A43TYR00.0090.01111.972-0.105-0.1050.0000.0000.0000.000
11A44ASN0-0.018-0.03611.704-0.184-0.1840.0000.0000.0000.000
12A45LYS10.8620.93213.997-0.442-0.4420.0000.0000.0000.000
13A46ALA00.0150.01415.884-0.064-0.0640.0000.0000.0000.000
14A47ILE00.001-0.00617.488-0.046-0.0460.0000.0000.0000.000
15A48ALA0-0.022-0.01918.360-0.036-0.0360.0000.0000.0000.000
16A49LYS10.8890.94920.080-0.251-0.2510.0000.0000.0000.000
17A50ALA0-0.013-0.01321.804-0.026-0.0260.0000.0000.0000.000
18A51LEU0-0.018-0.00822.430-0.017-0.0170.0000.0000.0000.000
19A52PHE0-0.002-0.00421.757-0.007-0.0070.0000.0000.0000.000
20A53GLY00.0660.04825.064-0.007-0.0070.0000.0000.0000.000
21A54LEU0-0.050-0.02922.131-0.012-0.0120.0000.0000.0000.000
22A55ASP-1-0.816-0.89119.2420.3030.3030.0000.0000.0000.000
23A56ILE00.0190.02316.148-0.002-0.0020.0000.0000.0000.000
24A57GLU-1-0.804-0.85914.3250.4230.4230.0000.0000.0000.000
25A58TYR0-0.048-0.04710.7300.0210.0210.0000.0000.0000.000
26A59HIS00.0680.02110.8030.2830.2830.0000.0000.0000.000
27A60PRO00.0030.0036.8720.3690.3690.0000.0000.0000.000
28A61LYS10.8370.9024.735-1.920-1.834-0.001-0.002-0.0830.000
29A62GLY00.1020.0728.937-0.119-0.1190.0000.0000.0000.000
30A63LEU0-0.0100.0049.4870.3040.3040.0000.0000.0000.000
31A64VAL0-0.001-0.0037.3300.0520.0520.0000.0000.0000.000
32A65THR0-0.013-0.02610.532-0.107-0.1070.0000.0000.0000.000
33A66THR00.0250.01913.202-0.020-0.0200.0000.0000.0000.000
34A67PRO00.0300.04115.517-0.046-0.0460.0000.0000.0000.000
35A68ILE00.0740.03019.089-0.032-0.0320.0000.0000.0000.000
36A69SER0-0.030-0.01318.591-0.025-0.0250.0000.0000.0000.000
37A70ARG10.9540.96015.711-0.468-0.4680.0000.0000.0000.000
38A71TYR00.0930.04521.898-0.025-0.0250.0000.0000.0000.000
39A72ILE0-0.012-0.01224.158-0.019-0.0190.0000.0000.0000.000
40A73PHE0-0.021-0.01223.873-0.013-0.0130.0000.0000.0000.000
41A74LEU00.0120.01625.733-0.014-0.0140.0000.0000.0000.000
42A75LYS10.8840.94828.054-0.167-0.1670.0000.0000.0000.000
43A76THR0-0.0130.01028.455-0.016-0.0160.0000.0000.0000.000
44A77PHE0-0.035-0.01727.685-0.012-0.0120.0000.0000.0000.000
45A78LEU0-0.0180.01530.379-0.007-0.0070.0000.0000.0000.000
46A79ARG10.7160.82333.224-0.122-0.1220.0000.0000.0000.000
47A80GLY00.0480.02235.983-0.002-0.0020.0000.0000.0000.000
48A81GLY0-0.035-0.00736.961-0.006-0.0060.0000.0000.0000.000
49A82GLU-1-0.809-0.89935.8310.1240.1240.0000.0000.0000.000
50A83VAL00.0210.01236.1490.0070.0070.0000.0000.0000.000
51A84ALA0-0.008-0.01432.1380.0000.0000.0000.0000.0000.000
52A85LEU00.0070.01430.4370.0020.0020.0000.0000.0000.000
53A86GLU-1-0.806-0.91823.1050.2890.2890.0000.0000.0000.000
54A87ILE0-0.009-0.00825.823-0.002-0.0020.0000.0000.0000.000
55A88GLY00.0020.01522.3930.0070.0070.0000.0000.0000.000
56A89THR0-0.020-0.00821.1060.0170.0170.0000.0000.0000.000
57A90GLY0-0.0070.00717.6940.0350.0350.0000.0000.0000.000
58A91HIS0-0.023-0.01012.542-0.040-0.0400.0000.0000.0000.000
59A92THR0-0.045-0.00715.115-0.001-0.0010.0000.0000.0000.000
60A93ALA00.0820.04117.490-0.028-0.0280.0000.0000.0000.000
61A94MET0-0.012-0.00318.024-0.035-0.0350.0000.0000.0000.000
62A95MET0-0.050-0.02021.056-0.020-0.0200.0000.0000.0000.000
63A96ALA00.0750.03823.874-0.021-0.0210.0000.0000.0000.000
64A97LEU00.0160.01722.100-0.016-0.0160.0000.0000.0000.000
65A98MET0-0.078-0.03422.491-0.014-0.0140.0000.0000.0000.000
66A99ALA00.0230.00726.704-0.016-0.0160.0000.0000.0000.000
67A100GLU-1-0.748-0.84329.3450.1560.1560.0000.0000.0000.000
68A101LYS10.8480.92626.636-0.210-0.2100.0000.0000.0000.000
69A102PHE0-0.057-0.03726.704-0.005-0.0050.0000.0000.0000.000
70A103PHE0-0.031-0.02128.914-0.004-0.0040.0000.0000.0000.000
71A104ASN00.0420.03233.685-0.007-0.0070.0000.0000.0000.000
72A105CYS0-0.0430.00632.708-0.005-0.0050.0000.0000.0000.000
73A106LYS10.9800.98534.018-0.102-0.1020.0000.0000.0000.000
74A107VAL0-0.021-0.00528.869-0.001-0.0010.0000.0000.0000.000
75A108THR0-0.0080.00131.244-0.005-0.0050.0000.0000.0000.000
76A109ALA00.001-0.00825.8390.0050.0050.0000.0000.0000.000
77A110THR00.0270.01726.6530.0000.0000.0000.0000.0000.000
78A111GLU-1-0.850-0.92120.4280.3820.3820.0000.0000.0000.000
79A112VAL00.019-0.00121.119-0.023-0.0230.0000.0000.0000.000
80A113ASP-1-0.817-0.88217.7460.3850.3850.0000.0000.0000.000
81A114GLU-1-0.778-0.89920.5750.2300.2300.0000.0000.0000.000
82A115GLU-1-0.869-0.90214.4170.4410.4410.0000.0000.0000.000
83A116PHE0-0.088-0.07213.4690.0580.0580.0000.0000.0000.000
84A117PHE00.0590.02917.939-0.002-0.0020.0000.0000.0000.000
85A118GLU-1-0.729-0.83019.3480.2270.2270.0000.0000.0000.000
86A119TYR0-0.017-0.02512.5260.0190.0190.0000.0000.0000.000
87A120ALA0-0.0120.00018.129-0.006-0.0060.0000.0000.0000.000
88A121ARG10.7830.85620.789-0.221-0.2210.0000.0000.0000.000
89A122ARG10.8490.90016.011-0.346-0.3460.0000.0000.0000.000
90A123ASN0-0.050-0.03516.840-0.024-0.0240.0000.0000.0000.000
91A124ILE00.0230.01621.082-0.009-0.0090.0000.0000.0000.000
92A125GLU-1-0.826-0.89524.2160.1720.1720.0000.0000.0000.000
93A126ARG10.7830.85718.368-0.328-0.3280.0000.0000.0000.000
94A127ASN0-0.099-0.07421.836-0.015-0.0150.0000.0000.0000.000
95A128ASN0-0.051-0.02025.816-0.014-0.0140.0000.0000.0000.000
96A129SER0-0.065-0.04327.438-0.004-0.0040.0000.0000.0000.000
97A130ASN0-0.023-0.02929.391-0.010-0.0100.0000.0000.0000.000
98A131VAL0-0.055-0.01126.925-0.004-0.0040.0000.0000.0000.000
99A132ARG10.9730.98929.643-0.126-0.1260.0000.0000.0000.000
100A133LEU00.0010.00023.8220.0030.0030.0000.0000.0000.000
101A134VAL0-0.062-0.02327.826-0.014-0.0140.0000.0000.0000.000
102A135LYS10.8360.90223.810-0.197-0.1970.0000.0000.0000.000
103A136SER0-0.020-0.01926.438-0.018-0.0180.0000.0000.0000.000
104A137ASN00.002-0.01626.8820.0150.0150.0000.0000.0000.000
105A138GLY00.004-0.00127.142-0.005-0.0050.0000.0000.0000.000
106A139GLY0-0.0010.02028.2180.0010.0010.0000.0000.0000.000
107A140ILE0-0.040-0.01527.8220.0150.0150.0000.0000.0000.000
108A141ILE0-0.018-0.03029.4470.0090.0090.0000.0000.0000.000
109A142LYS10.8430.89932.393-0.103-0.1030.0000.0000.0000.000
110A143GLY00.0140.00734.0680.0030.0030.0000.0000.0000.000
111A144VAL0-0.104-0.03429.4320.0050.0050.0000.0000.0000.000
112A145VAL0-0.057-0.04431.9990.0020.0020.0000.0000.0000.000
113A146GLU-1-0.909-0.94834.6800.0910.0910.0000.0000.0000.000
114A147GLY0-0.0070.00138.0560.0030.0030.0000.0000.0000.000
115A148THR0-0.052-0.03839.4860.0010.0010.0000.0000.0000.000
116A149PHE0-0.005-0.00235.0660.0030.0030.0000.0000.0000.000
117A150ASP-1-0.774-0.86837.9320.0970.0970.0000.0000.0000.000
118A151VAL0-0.082-0.04132.1350.0000.0000.0000.0000.0000.000
119A152ILE00.0450.04030.8340.0040.0040.0000.0000.0000.000
120A153PHE0-0.021-0.01825.946-0.002-0.0020.0000.0000.0000.000
121A154SER00.020-0.00424.2670.0090.0090.0000.0000.0000.000
122A155ALA0-0.030-0.02119.643-0.007-0.0070.0000.0000.0000.000
123A156PRO00.0260.03620.1680.0260.0260.0000.0000.0000.000
124A157PRO00.0520.00718.5300.0110.0110.0000.0000.0000.000
125A158TYR0-0.0060.00615.2510.0240.0240.0000.0000.0000.000
126A159TYR00.0000.00113.337-0.046-0.0460.0000.0000.0000.000
127A175GLY00.0850.04824.0890.0050.0050.0000.0000.0000.000
128A176GLY0-0.042-0.03224.9630.0020.0020.0000.0000.0000.000
129A177LYS10.8940.93426.839-0.083-0.0830.0000.0000.0000.000
130A178TYR0-0.084-0.06025.377-0.009-0.0090.0000.0000.0000.000
131A179GLY00.0420.03623.3210.0080.0080.0000.0000.0000.000
132A180GLU-1-0.788-0.90624.1510.1310.1310.0000.0000.0000.000
133A181GLU-1-0.832-0.89927.1220.1430.1430.0000.0000.0000.000
134A182PHE00.0820.03524.831-0.002-0.0020.0000.0000.0000.000
135A183SER00.010-0.00925.4750.0050.0050.0000.0000.0000.000
136A184VAL0-0.022-0.01027.641-0.005-0.0050.0000.0000.0000.000
137A185LYS10.8940.93528.709-0.144-0.1440.0000.0000.0000.000
138A186LEU00.0060.01427.542-0.002-0.0020.0000.0000.0000.000
139A187LEU0-0.036-0.02030.833-0.004-0.0040.0000.0000.0000.000
140A188GLU-1-0.806-0.88033.4760.0920.0920.0000.0000.0000.000
141A189GLU-1-0.822-0.90832.6670.1290.1290.0000.0000.0000.000
142A190ALA00.013-0.00733.498-0.003-0.0030.0000.0000.0000.000
143A191PHE00.0400.03835.492-0.003-0.0030.0000.0000.0000.000
144A192ASP-1-0.834-0.91138.9090.0840.0840.0000.0000.0000.000
145A193HIS0-0.028-0.00737.178-0.003-0.0030.0000.0000.0000.000
146A194LEU0-0.033-0.00435.9220.0040.0040.0000.0000.0000.000
147A195ASN00.0380.01439.584-0.007-0.0070.0000.0000.0000.000
148A196PRO00.0220.00042.2010.0020.0020.0000.0000.0000.000
149A197GLY0-0.014-0.00142.8840.0010.0010.0000.0000.0000.000
150A198GLY0-0.032-0.00139.2630.0040.0040.0000.0000.0000.000
151A199LYS10.8060.87334.278-0.118-0.1180.0000.0000.0000.000
152A200VAL00.0530.02530.8590.0060.0060.0000.0000.0000.000
153A201ALA0-0.0110.00229.265-0.004-0.0040.0000.0000.0000.000
154A202LEU00.011-0.00726.1950.0140.0140.0000.0000.0000.000
155A203TYR0-0.046-0.02818.0160.0090.0090.0000.0000.0000.000
156A204LEU00.0400.00822.0670.0170.0170.0000.0000.0000.000
157A205PRO0-0.056-0.03218.8500.0060.0060.0000.0000.0000.000
158A206ASP-1-0.761-0.87120.1810.1120.1120.0000.0000.0000.000
159A207LYS10.9250.96217.838-0.182-0.1820.0000.0000.0000.000
160A208GLU-1-0.733-0.85123.3470.0790.0790.0000.0000.0000.000
161A209LYS10.9050.93627.068-0.071-0.0710.0000.0000.0000.000
162A210LEU0-0.0120.01423.089-0.001-0.0010.0000.0000.0000.000
163A211LEU0-0.017-0.00624.9730.0000.0000.0000.0000.0000.000
164A212ASN00.007-0.01928.0560.0000.0000.0000.0000.0000.000
165A213VAL00.0180.01630.092-0.003-0.0030.0000.0000.0000.000
166A214ILE0-0.010-0.00426.471-0.001-0.0010.0000.0000.0000.000
167A215LYS10.8270.91331.019-0.104-0.1040.0000.0000.0000.000
168A216GLU-1-0.849-0.91533.6740.0700.0700.0000.0000.0000.000
169A217ARG10.8230.88433.822-0.096-0.0960.0000.0000.0000.000
170A218GLY00.0400.01834.769-0.002-0.0020.0000.0000.0000.000
171A219ILE00.019-0.00236.063-0.003-0.0030.0000.0000.0000.000
172A220LYS10.8050.89238.958-0.073-0.0730.0000.0000.0000.000
173A221LEU0-0.0320.00036.306-0.002-0.0020.0000.0000.0000.000
174A222GLY00.0060.01540.2690.0000.0000.0000.0000.0000.000
175A223TYR0-0.099-0.05136.4230.0000.0000.0000.0000.0000.000
176A224SER00.0010.01339.460-0.001-0.0010.0000.0000.0000.000
177A225VAL00.004-0.01934.0820.0060.0060.0000.0000.0000.000
178A226LYS10.9360.98134.814-0.104-0.1040.0000.0000.0000.000
179A227ASP-1-0.775-0.87429.4550.1290.1290.0000.0000.0000.000
180A228ILE0-0.0140.00329.160-0.007-0.0070.0000.0000.0000.000
181A229LYS10.8550.92024.515-0.111-0.1110.0000.0000.0000.000
182A230PHE00.006-0.00623.210-0.005-0.0050.0000.0000.0000.000
183A231LYS10.9220.94319.244-0.145-0.1450.0000.0000.0000.000
184A232VAL00.0160.02620.393-0.006-0.0060.0000.0000.0000.000
185A233GLY00.1110.04017.0110.0310.0310.0000.0000.0000.000
186A234THR0-0.060-0.01911.980-0.041-0.0410.0000.0000.0000.000
187A235ARG10.8130.88915.433-0.162-0.1620.0000.0000.0000.000
188A236TRP00.0180.00718.4060.0090.0090.0000.0000.0000.000
189A237ARG10.8480.94515.838-0.299-0.2990.0000.0000.0000.000
190A238HIS00.018-0.00521.643-0.020-0.0200.0000.0000.0000.000
191A239SER00.0030.00624.5340.0190.0190.0000.0000.0000.000
192A240LEU0-0.0240.01227.257-0.011-0.0110.0000.0000.0000.000
193A241ILE0-0.004-0.01129.8350.0080.0080.0000.0000.0000.000
194A242PHE00.0320.01530.977-0.008-0.0080.0000.0000.0000.000
195A243PHE0-0.012-0.02335.2150.0050.0050.0000.0000.0000.000
196A244LYS10.8670.92938.542-0.090-0.0900.0000.0000.0000.000
197A245GLY0-0.0070.01140.991-0.004-0.0040.0000.0000.0000.000
198A246ILE00.0550.02843.7640.0010.0010.0000.0000.0000.000