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: 85Y4Y

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2339223.16497
FMO2-HF: Nuclear repulsion 2261831.472734
FMO2-HF: Total energy -77391.692236
FMO2-MP2: Total energy -77621.683379


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.
-25.115-16.0445.133-4.969-9.2350.045
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 : 0.083 / q_NPA : 0.010
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].
3A36ASN00.0400.0332.596-7.079-2.0914.172-3.516-5.6430.035
4A37ARG10.8600.9132.660-8.534-5.8040.866-1.143-2.4530.009
5A38GLN00.0610.0384.262-0.992-0.4040.003-0.120-0.4720.000
6A39ALA00.0450.0366.383-0.266-0.2660.0000.0000.0000.000
7A40ARG10.9230.9492.808-3.584-2.9120.093-0.184-0.5810.001
8A41ILE0-0.017-0.0057.219-0.223-0.2230.0000.0000.0000.000
9A42LEU00.0230.0159.839-0.180-0.1800.0000.0000.0000.000
10A43TYR0-0.021-0.00411.931-0.094-0.0940.0000.0000.0000.000
11A44ASN00.015-0.03411.380-0.194-0.1940.0000.0000.0000.000
12A45LYS10.9080.98713.982-0.453-0.4530.0000.0000.0000.000
13A46ALA00.0160.01015.739-0.068-0.0680.0000.0000.0000.000
14A47ILE0-0.014-0.00317.297-0.045-0.0450.0000.0000.0000.000
15A48ALA0-0.019-0.02018.221-0.038-0.0380.0000.0000.0000.000
16A49LYS10.9880.99819.948-0.238-0.2380.0000.0000.0000.000
17A50ALA0-0.026-0.00521.768-0.027-0.0270.0000.0000.0000.000
18A51LEU0-0.019-0.01322.019-0.018-0.0180.0000.0000.0000.000
19A52PHE00.0040.00021.544-0.009-0.0090.0000.0000.0000.000
20A53GLY00.0400.03125.037-0.012-0.0120.0000.0000.0000.000
21A54LEU0-0.054-0.03121.950-0.010-0.0100.0000.0000.0000.000
22A55ASP-1-0.901-0.95419.5150.3120.3120.0000.0000.0000.000
23A56ILE0-0.020-0.00816.0620.0080.0080.0000.0000.0000.000
24A57GLU-1-0.798-0.85714.9940.3980.3980.0000.0000.0000.000
25A58TYR0-0.045-0.03810.8660.0310.0310.0000.0000.0000.000
26A59HIS00.0690.02911.4490.2400.2400.0000.0000.0000.000
27A60PRO00.0260.0076.6920.3250.3250.0000.0000.0000.000
28A61LYS10.8380.9024.787-3.019-2.926-0.001-0.006-0.0860.000
29A62GLY00.0910.0708.801-0.190-0.1900.0000.0000.0000.000
30A63LEU0-0.012-0.0029.2410.3400.3400.0000.0000.0000.000
31A64VAL0-0.014-0.0107.098-0.010-0.0100.0000.0000.0000.000
32A65THR00.0200.00810.272-0.079-0.0790.0000.0000.0000.000
33A66THR00.0200.01412.844-0.011-0.0110.0000.0000.0000.000
34A67PRO00.0280.01515.269-0.049-0.0490.0000.0000.0000.000
35A68ILE00.0620.03518.750-0.035-0.0350.0000.0000.0000.000
36A69SER0-0.014-0.01018.433-0.030-0.0300.0000.0000.0000.000
37A70ARG10.9710.98015.644-0.578-0.5780.0000.0000.0000.000
38A71TYR00.0780.04521.443-0.030-0.0300.0000.0000.0000.000
39A72ILE0-0.011-0.01523.651-0.022-0.0220.0000.0000.0000.000
40A73PHE0-0.029-0.02523.630-0.015-0.0150.0000.0000.0000.000
41A74LEU00.0380.03225.415-0.016-0.0160.0000.0000.0000.000
42A75LYS10.8740.95627.644-0.201-0.2010.0000.0000.0000.000
43A76THR0-0.041-0.00128.501-0.021-0.0210.0000.0000.0000.000
44A77PHE0-0.040-0.03327.570-0.011-0.0110.0000.0000.0000.000
45A78LEU0-0.0240.01229.915-0.008-0.0080.0000.0000.0000.000
46A79ARG10.7560.84433.045-0.154-0.1540.0000.0000.0000.000
47A80GLY00.0270.02135.837-0.005-0.0050.0000.0000.0000.000
48A81GLY0-0.018-0.00336.773-0.006-0.0060.0000.0000.0000.000
49A82GLU-1-0.826-0.91135.1090.1540.1540.0000.0000.0000.000
50A83VAL00.0280.02136.0060.0060.0060.0000.0000.0000.000
51A84ALA0-0.020-0.02731.5650.0000.0000.0000.0000.0000.000
52A85LEU00.0040.01330.2740.0020.0020.0000.0000.0000.000
53A86GLU-1-0.824-0.94923.0160.3440.3440.0000.0000.0000.000
54A87ILE0-0.015-0.02025.450-0.001-0.0010.0000.0000.0000.000
55A88GLY0-0.0020.01422.5330.0170.0170.0000.0000.0000.000
56A89THR0-0.027-0.01421.2120.0210.0210.0000.0000.0000.000
57A90GLY0-0.015-0.00217.8720.0420.0420.0000.0000.0000.000
58A91HIS0-0.039-0.02912.440-0.050-0.0500.0000.0000.0000.000
59A92THR0-0.065-0.02415.3910.0070.0070.0000.0000.0000.000
60A93ALA00.1020.05417.440-0.039-0.0390.0000.0000.0000.000
61A94MET0-0.008-0.01117.790-0.035-0.0350.0000.0000.0000.000
62A95MET0-0.066-0.03020.893-0.024-0.0240.0000.0000.0000.000
63A96ALA00.0910.05723.565-0.024-0.0240.0000.0000.0000.000
64A97LEU00.0360.02122.085-0.020-0.0200.0000.0000.0000.000
65A98MET0-0.093-0.04322.105-0.016-0.0160.0000.0000.0000.000
66A99ALA00.0290.00026.325-0.018-0.0180.0000.0000.0000.000
67A100GLU-1-0.780-0.85828.9720.1750.1750.0000.0000.0000.000
68A101LYS10.8520.93426.966-0.225-0.2250.0000.0000.0000.000
69A102PHE0-0.071-0.04326.696-0.008-0.0080.0000.0000.0000.000
70A103PHE0-0.017-0.01628.379-0.006-0.0060.0000.0000.0000.000
71A104ASN00.0390.03033.214-0.008-0.0080.0000.0000.0000.000
72A105CYS0-0.0340.01832.349-0.005-0.0050.0000.0000.0000.000
73A106LYS10.9950.99633.795-0.122-0.1220.0000.0000.0000.000
74A107VAL0-0.012-0.00928.546-0.001-0.0010.0000.0000.0000.000
75A108THR0-0.0080.00230.985-0.007-0.0070.0000.0000.0000.000
76A109ALA0-0.0050.00925.6410.0050.0050.0000.0000.0000.000
77A110THR00.0680.03826.4680.0010.0010.0000.0000.0000.000
78A111GLU-1-0.855-0.92220.3540.4500.4500.0000.0000.0000.000
79A112VAL00.0170.01021.272-0.027-0.0270.0000.0000.0000.000
80A113ASP-1-0.838-0.89917.7230.4580.4580.0000.0000.0000.000
81A114GLU-1-0.789-0.89920.3940.2700.2700.0000.0000.0000.000
82A115GLU-1-0.856-0.90214.6410.4880.4880.0000.0000.0000.000
83A116PHE0-0.107-0.08213.0740.0490.0490.0000.0000.0000.000
84A117PHE00.0440.00717.765-0.004-0.0040.0000.0000.0000.000
85A118GLU-1-0.746-0.83519.3220.2310.2310.0000.0000.0000.000
86A119TYR0-0.015-0.01512.9850.0100.0100.0000.0000.0000.000
87A120ALA00.0040.02018.545-0.013-0.0130.0000.0000.0000.000
88A121ARG10.8130.87121.063-0.231-0.2310.0000.0000.0000.000
89A122ARG10.8540.89916.249-0.339-0.3390.0000.0000.0000.000
90A123ASN0-0.058-0.03117.265-0.030-0.0300.0000.0000.0000.000
91A124ILE00.0180.01321.574-0.011-0.0110.0000.0000.0000.000
92A125GLU-1-0.842-0.91024.8880.1710.1710.0000.0000.0000.000
93A126ARG10.7770.85618.874-0.322-0.3220.0000.0000.0000.000
94A127ASN0-0.118-0.08222.207-0.011-0.0110.0000.0000.0000.000
95A128ASN0-0.046-0.01226.277-0.010-0.0100.0000.0000.0000.000
96A129SER0-0.046-0.03927.703-0.002-0.0020.0000.0000.0000.000
97A130ASN0-0.027-0.02029.682-0.011-0.0110.0000.0000.0000.000
98A131VAL0-0.054-0.01526.628-0.002-0.0020.0000.0000.0000.000
99A132ARG10.9690.98730.031-0.154-0.1540.0000.0000.0000.000
100A133LEU0-0.009-0.00423.9270.0070.0070.0000.0000.0000.000
101A134VAL0-0.046-0.02528.093-0.014-0.0140.0000.0000.0000.000
102A135LYS10.8420.90224.171-0.232-0.2320.0000.0000.0000.000
103A136SER0-0.005-0.00426.252-0.020-0.0200.0000.0000.0000.000
104A137ASN0-0.013-0.02026.5980.0200.0200.0000.0000.0000.000
105A138GLY00.019-0.00326.498-0.006-0.0060.0000.0000.0000.000
106A139GLY0-0.0020.02127.5830.0040.0040.0000.0000.0000.000
107A140ILE0-0.046-0.02127.9190.0190.0190.0000.0000.0000.000
108A141ILE0-0.007-0.03129.4800.0090.0090.0000.0000.0000.000
109A142LYS10.8420.91232.531-0.129-0.1290.0000.0000.0000.000
110A143GLY00.0180.00934.1450.0040.0040.0000.0000.0000.000
111A144VAL0-0.113-0.03629.4950.0040.0040.0000.0000.0000.000
112A145VAL0-0.032-0.02931.7430.0000.0000.0000.0000.0000.000
113A146GLU-1-0.912-0.95534.5140.1100.1100.0000.0000.0000.000
114A147GLY0-0.012-0.00137.7540.0030.0030.0000.0000.0000.000
115A148THR0-0.045-0.03839.0710.0030.0030.0000.0000.0000.000
116A149PHE0-0.031-0.02234.8560.0030.0030.0000.0000.0000.000
117A150ASP-1-0.783-0.86837.3110.1210.1210.0000.0000.0000.000
118A151VAL0-0.073-0.04631.7250.0010.0010.0000.0000.0000.000
119A152ILE00.0450.05030.5560.0050.0050.0000.0000.0000.000
120A153PHE0-0.014-0.01525.487-0.001-0.0010.0000.0000.0000.000
121A154SER00.015-0.00324.1650.0100.0100.0000.0000.0000.000
122A155ALA0-0.036-0.01619.629-0.008-0.0080.0000.0000.0000.000
123A156PRO00.0170.02620.1430.0330.0330.0000.0000.0000.000
124A157PRO00.0570.01418.2230.0210.0210.0000.0000.0000.000
125A158TYR0-0.022-0.02315.4730.0430.0430.0000.0000.0000.000
126A159TYR00.0330.03013.471-0.047-0.0470.0000.0000.0000.000
127A175GLY00.0910.05024.0760.0070.0070.0000.0000.0000.000
128A176GLY0-0.005-0.00725.0500.0010.0010.0000.0000.0000.000
129A177LYS10.8840.93026.573-0.131-0.1310.0000.0000.0000.000
130A178TYR0-0.045-0.04025.562-0.005-0.0050.0000.0000.0000.000
131A179GLY00.0300.03023.1460.0140.0140.0000.0000.0000.000
132A180GLU-1-0.855-0.95124.0650.1920.1920.0000.0000.0000.000
133A181GLU-1-0.832-0.90026.8170.1900.1900.0000.0000.0000.000
134A182PHE00.0710.02724.807-0.003-0.0030.0000.0000.0000.000
135A183SER00.009-0.00125.6780.0020.0020.0000.0000.0000.000
136A184VAL0-0.003-0.00427.791-0.008-0.0080.0000.0000.0000.000
137A185LYS10.8780.93628.501-0.195-0.1950.0000.0000.0000.000
138A186LEU00.0170.01627.497-0.005-0.0050.0000.0000.0000.000
139A187LEU0-0.030-0.02030.868-0.006-0.0060.0000.0000.0000.000
140A188GLU-1-0.851-0.92133.3040.1250.1250.0000.0000.0000.000
141A189GLU-1-0.834-0.89833.1260.1590.1590.0000.0000.0000.000
142A190ALA0-0.001-0.01233.350-0.004-0.0040.0000.0000.0000.000
143A191PHE00.0520.03835.375-0.005-0.0050.0000.0000.0000.000
144A192ASP-1-0.815-0.89338.7590.1060.1060.0000.0000.0000.000
145A193HIS0-0.046-0.02636.842-0.004-0.0040.0000.0000.0000.000
146A194LEU0-0.040-0.00135.6530.0040.0040.0000.0000.0000.000
147A195ASN00.0340.01939.410-0.010-0.0100.0000.0000.0000.000
148A196PRO00.0400.01141.7140.0030.0030.0000.0000.0000.000
149A197GLY0-0.056-0.03342.4140.0010.0010.0000.0000.0000.000
150A198GLY0-0.0080.01038.8430.0050.0050.0000.0000.0000.000
151A199LYS10.8210.89633.897-0.149-0.1490.0000.0000.0000.000
152A200VAL00.0850.04030.4320.0060.0060.0000.0000.0000.000
153A201ALA0-0.025-0.00329.075-0.005-0.0050.0000.0000.0000.000
154A202LEU00.021-0.00425.9170.0150.0150.0000.0000.0000.000
155A203TYR0-0.053-0.02517.9470.0160.0160.0000.0000.0000.000
156A204LEU00.023-0.00921.7730.0250.0250.0000.0000.0000.000
157A205PRO0-0.087-0.04018.5250.0030.0030.0000.0000.0000.000
158A206ASP-1-0.750-0.86420.2810.1950.1950.0000.0000.0000.000
159A207LYS10.9190.96417.428-0.306-0.3060.0000.0000.0000.000
160A208GLU-1-0.748-0.85323.1760.1260.1260.0000.0000.0000.000
161A209LYS10.9190.92526.776-0.122-0.1220.0000.0000.0000.000
162A210LEU0-0.0060.00222.769-0.003-0.0030.0000.0000.0000.000
163A211LEU0-0.024-0.01324.979-0.003-0.0030.0000.0000.0000.000
164A212ASN0-0.018-0.02027.989-0.003-0.0030.0000.0000.0000.000
165A213VAL00.0300.02430.019-0.006-0.0060.0000.0000.0000.000
166A214ILE00.0000.01026.418-0.003-0.0030.0000.0000.0000.000
167A215LYS10.8500.92330.664-0.155-0.1550.0000.0000.0000.000
168A216GLU-1-0.855-0.92533.3930.1020.1020.0000.0000.0000.000
169A217ARG10.8390.91033.584-0.133-0.1330.0000.0000.0000.000
170A218GLY00.0380.01834.621-0.003-0.0030.0000.0000.0000.000
171A219ILE00.003-0.00535.779-0.004-0.0040.0000.0000.0000.000
172A220LYS10.8260.90938.749-0.105-0.1050.0000.0000.0000.000
173A221LEU00.0030.01635.888-0.003-0.0030.0000.0000.0000.000
174A222GLY00.0150.02339.912-0.002-0.0020.0000.0000.0000.000
175A223TYR0-0.102-0.05536.262-0.001-0.0010.0000.0000.0000.000
176A224SER00.0260.02239.481-0.002-0.0020.0000.0000.0000.000
177A225VAL0-0.021-0.02833.4390.0070.0070.0000.0000.0000.000
178A226LYS10.9320.98734.531-0.138-0.1380.0000.0000.0000.000
179A227ASP-1-0.784-0.87829.2330.1850.1850.0000.0000.0000.000
180A228ILE00.0180.02329.014-0.008-0.0080.0000.0000.0000.000
181A229LYS10.8620.92824.523-0.173-0.1730.0000.0000.0000.000
182A230PHE00.010-0.01122.752-0.007-0.0070.0000.0000.0000.000
183A231LYS10.8950.94018.376-0.244-0.2440.0000.0000.0000.000
184A232VAL0-0.0170.00520.189-0.006-0.0060.0000.0000.0000.000
185A233GLY00.0850.01916.8540.0200.0200.0000.0000.0000.000
186A234THR00.0330.03411.632-0.019-0.0190.0000.0000.0000.000
187A235ARG10.8460.89814.988-0.305-0.3050.0000.0000.0000.000
188A236TRP0-0.0290.00018.2090.0170.0170.0000.0000.0000.000
189A237ARG10.8470.93415.811-0.419-0.4190.0000.0000.0000.000
190A238HIS00.0390.01021.679-0.020-0.0200.0000.0000.0000.000
191A239SER0-0.009-0.00924.6300.0220.0220.0000.0000.0000.000
192A240LEU0-0.0190.00827.136-0.014-0.0140.0000.0000.0000.000
193A241ILE0-0.004-0.00929.6000.0080.0080.0000.0000.0000.000
194A242PHE00.0390.01330.658-0.009-0.0090.0000.0000.0000.000
195A243PHE0-0.026-0.03434.9760.0040.0040.0000.0000.0000.000
196A244LYS10.8770.93938.334-0.113-0.1130.0000.0000.0000.000
197A245GLY0-0.022-0.00140.602-0.005-0.0050.0000.0000.0000.000
198A246ILE00.0720.03843.4570.0010.0010.0000.0000.0000.000