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: G63Z1

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2337510.868104
FMO2-HF: Nuclear repulsion 2260121.313473
FMO2-HF: Total energy -77389.554631
FMO2-MP2: Total energy -77619.588612


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.
-16.87-9.226.704-4.558-9.7960.035
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 : 0.053 / q_NPA : 0.002
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].
3A36ASN00.0540.0212.366-7.018-3.1074.834-3.257-5.4880.027
4A37ARG10.8440.9142.199-5.068-2.6611.828-1.072-3.1630.008
5A38GLN00.0420.0414.023-1.172-0.5610.006-0.098-0.5180.000
6A39ALA00.0600.0466.212-0.113-0.1130.0000.0000.0000.000
7A40ARG10.9710.9893.049-2.451-1.8490.037-0.124-0.5160.000
8A41ILE0-0.0160.0077.026-0.134-0.1340.0000.0000.0000.000
9A42LEU00.0410.0209.683-0.063-0.0630.0000.0000.0000.000
10A43TYR0-0.016-0.00211.642-0.050-0.0500.0000.0000.0000.000
11A44ASN0-0.001-0.04711.152-0.090-0.0900.0000.0000.0000.000
12A45LYS10.9421.00013.336-0.196-0.1960.0000.0000.0000.000
13A46ALA00.0160.01315.594-0.026-0.0260.0000.0000.0000.000
14A47ILE0-0.012-0.00217.029-0.021-0.0210.0000.0000.0000.000
15A48ALA0-0.019-0.01918.075-0.018-0.0180.0000.0000.0000.000
16A49LYS10.9980.99919.804-0.135-0.1350.0000.0000.0000.000
17A50ALA0-0.038-0.01021.599-0.011-0.0110.0000.0000.0000.000
18A51LEU0-0.017-0.01522.017-0.008-0.0080.0000.0000.0000.000
19A52PHE00.0040.00221.367-0.006-0.0060.0000.0000.0000.000
20A53GLY00.0090.01524.867-0.008-0.0080.0000.0000.0000.000
21A54LEU0-0.049-0.02521.755-0.005-0.0050.0000.0000.0000.000
22A55ASP-1-0.957-0.96819.0340.1310.1310.0000.0000.0000.000
23A56ILE00.003-0.00515.508-0.005-0.0050.0000.0000.0000.000
24A57GLU-1-0.836-0.91714.3260.1020.1020.0000.0000.0000.000
25A58TYR0-0.066-0.05010.3640.0040.0040.0000.0000.0000.000
26A59HIS00.1270.08010.408-0.036-0.0360.0000.0000.0000.000
27A60PRO00.0270.0066.134-0.024-0.0240.0000.0000.0000.000
28A61LYS10.8340.8874.3870.1650.284-0.001-0.007-0.1110.000
29A62GLY00.0900.0698.3440.0680.0680.0000.0000.0000.000
30A63LEU0-0.024-0.0219.2580.0540.0540.0000.0000.0000.000
31A64VAL0-0.025-0.0177.326-0.008-0.0080.0000.0000.0000.000
32A65THR00.0120.00510.3890.0230.0230.0000.0000.0000.000
33A66THR00.0190.01112.9070.0050.0050.0000.0000.0000.000
34A67PRO00.0240.02315.237-0.021-0.0210.0000.0000.0000.000
35A68ILE00.0770.03718.667-0.014-0.0140.0000.0000.0000.000
36A69SER00.006-0.03418.243-0.018-0.0180.0000.0000.0000.000
37A70ARG10.9130.96816.475-0.176-0.1760.0000.0000.0000.000
38A71TYR00.0650.04221.491-0.012-0.0120.0000.0000.0000.000
39A72ILE0-0.022-0.01523.627-0.009-0.0090.0000.0000.0000.000
40A73PHE0-0.040-0.02623.634-0.006-0.0060.0000.0000.0000.000
41A74LEU00.0550.03525.442-0.006-0.0060.0000.0000.0000.000
42A75LYS10.9570.98927.714-0.074-0.0740.0000.0000.0000.000
43A76THR0-0.0480.03528.538-0.007-0.0070.0000.0000.0000.000
44A77PHE0-0.035-0.04027.858-0.005-0.0050.0000.0000.0000.000
45A78LEU0-0.0220.00929.659-0.003-0.0030.0000.0000.0000.000
46A79ARG10.7410.83733.130-0.052-0.0520.0000.0000.0000.000
47A80GLY0-0.015-0.00235.968-0.001-0.0010.0000.0000.0000.000
48A81GLY0-0.016-0.00236.788-0.002-0.0020.0000.0000.0000.000
49A82GLU-1-0.790-0.88735.0930.0480.0480.0000.0000.0000.000
50A83VAL00.0020.00635.9660.0020.0020.0000.0000.0000.000
51A84ALA0-0.015-0.02831.5520.0000.0000.0000.0000.0000.000
52A85LEU00.0060.01630.1700.0000.0000.0000.0000.0000.000
53A86GLU-1-0.824-0.95422.8980.0890.0890.0000.0000.0000.000
54A87ILE0-0.021-0.02225.652-0.003-0.0030.0000.0000.0000.000
55A88GLY0-0.0080.01122.5750.0060.0060.0000.0000.0000.000
56A89THR0-0.0130.00521.2240.0070.0070.0000.0000.0000.000
57A90GLY0-0.030-0.01317.8860.0130.0130.0000.0000.0000.000
58A91HIS0-0.034-0.01511.782-0.022-0.0220.0000.0000.0000.000
59A92THR0-0.043-0.01615.1670.0070.0070.0000.0000.0000.000
60A93ALA00.0920.04617.2530.0000.0000.0000.0000.0000.000
61A94MET0-0.021-0.02317.362-0.002-0.0020.0000.0000.0000.000
62A95MET0-0.049-0.02520.8440.0020.0020.0000.0000.0000.000
63A96ALA00.0760.04923.621-0.004-0.0040.0000.0000.0000.000
64A97LEU00.0360.02221.784-0.003-0.0030.0000.0000.0000.000
65A98MET0-0.092-0.04022.0280.0010.0010.0000.0000.0000.000
66A99ALA00.0210.00226.229-0.003-0.0030.0000.0000.0000.000
67A100GLU-1-0.756-0.84628.9080.0570.0570.0000.0000.0000.000
68A101LYS10.8630.95027.030-0.087-0.0870.0000.0000.0000.000
69A102PHE0-0.076-0.05226.652-0.001-0.0010.0000.0000.0000.000
70A103PHE0-0.035-0.02128.585-0.001-0.0010.0000.0000.0000.000
71A104ASN00.0240.02333.242-0.003-0.0030.0000.0000.0000.000
72A105CYS0-0.0290.01832.298-0.002-0.0020.0000.0000.0000.000
73A106LYS10.9941.00033.738-0.037-0.0370.0000.0000.0000.000
74A107VAL0-0.017-0.00728.467-0.001-0.0010.0000.0000.0000.000
75A108THR0-0.013-0.00430.882-0.002-0.0020.0000.0000.0000.000
76A109ALA0-0.0120.00925.5610.0020.0020.0000.0000.0000.000
77A110THR00.0560.03626.438-0.001-0.0010.0000.0000.0000.000
78A111GLU-1-0.839-0.93119.7260.0690.0690.0000.0000.0000.000
79A112VAL00.0160.00621.500-0.004-0.0040.0000.0000.0000.000
80A113ASP-1-0.836-0.89017.0210.0190.0190.0000.0000.0000.000
81A114GLU-1-0.877-0.95419.8050.0230.0230.0000.0000.0000.000
82A115GLU-1-0.901-0.95014.349-0.007-0.0070.0000.0000.0000.000
83A116PHE0-0.119-0.09212.5270.0110.0110.0000.0000.0000.000
84A117PHE00.030-0.00117.0690.0080.0080.0000.0000.0000.000
85A118GLU-1-0.765-0.86418.2880.0530.0530.0000.0000.0000.000
86A119TYR0-0.020-0.01612.229-0.002-0.0020.0000.0000.0000.000
87A120ALA00.0120.02517.7080.0070.0070.0000.0000.0000.000
88A121ARG10.8790.92920.368-0.048-0.0480.0000.0000.0000.000
89A122ARG10.8590.93815.796-0.061-0.0610.0000.0000.0000.000
90A123ASN0-0.038-0.02716.5290.0100.0100.0000.0000.0000.000
91A124ILE00.0180.01020.7680.0030.0030.0000.0000.0000.000
92A125GLU-1-0.911-0.95424.3640.0570.0570.0000.0000.0000.000
93A126ARG10.8020.89018.059-0.094-0.0940.0000.0000.0000.000
94A127ASN0-0.104-0.06921.6270.0060.0060.0000.0000.0000.000
95A128ASN0-0.033-0.00525.555-0.002-0.0020.0000.0000.0000.000
96A129SER0-0.065-0.05827.004-0.002-0.0020.0000.0000.0000.000
97A130ASN00.003-0.00629.082-0.004-0.0040.0000.0000.0000.000
98A131VAL0-0.090-0.03526.694-0.002-0.0020.0000.0000.0000.000
99A132ARG10.9860.99029.499-0.037-0.0370.0000.0000.0000.000
100A133LEU00.0260.00023.3550.0010.0010.0000.0000.0000.000
101A134VAL0-0.066-0.02727.638-0.003-0.0030.0000.0000.0000.000
102A135LYS10.9240.96223.203-0.026-0.0260.0000.0000.0000.000
103A136SER0-0.0130.00026.042-0.003-0.0030.0000.0000.0000.000
104A137ASN0-0.003-0.01526.2630.0010.0010.0000.0000.0000.000
105A138GLY00.010-0.01126.546-0.003-0.0030.0000.0000.0000.000
106A139GLY0-0.0020.02127.6150.0010.0010.0000.0000.0000.000
107A140ILE0-0.053-0.02528.3090.0030.0030.0000.0000.0000.000
108A141ILE00.010-0.02229.5740.0030.0030.0000.0000.0000.000
109A142LYS10.9270.97032.583-0.026-0.0260.0000.0000.0000.000
110A143GLY00.0140.01134.2240.0000.0000.0000.0000.0000.000
111A144VAL0-0.114-0.03329.6020.0000.0000.0000.0000.0000.000
112A145VAL0-0.030-0.02531.7150.0010.0010.0000.0000.0000.000
113A146GLU-1-0.892-0.95534.4980.0230.0230.0000.0000.0000.000
114A147GLY0-0.028-0.00637.7830.0010.0010.0000.0000.0000.000
115A148THR0-0.043-0.03039.0920.0000.0000.0000.0000.0000.000
116A149PHE0-0.039-0.02434.9110.0010.0010.0000.0000.0000.000
117A150ASP-1-0.778-0.86437.4340.0360.0360.0000.0000.0000.000
118A151VAL0-0.081-0.04631.9120.0010.0010.0000.0000.0000.000
119A152ILE00.0480.04730.9070.0010.0010.0000.0000.0000.000
120A153PHE0-0.006-0.01625.8990.0010.0010.0000.0000.0000.000
121A154SER00.017-0.00624.5060.0000.0000.0000.0000.0000.000
122A155ALA0-0.030-0.01419.8290.0020.0020.0000.0000.0000.000
123A156PRO00.0130.02120.4640.0050.0050.0000.0000.0000.000
124A157PRO00.0390.00518.6090.0100.0100.0000.0000.0000.000
125A158TYR0-0.055-0.03415.7280.0220.0220.0000.0000.0000.000
126A159TYR00.0330.03014.3020.0020.0020.0000.0000.0000.000
127A175GLY00.0760.04724.5600.0010.0010.0000.0000.0000.000
128A176GLY0-0.013-0.01325.5410.0030.0030.0000.0000.0000.000
129A177LYS10.9240.95727.042-0.012-0.0120.0000.0000.0000.000
130A178TYR0-0.061-0.05726.151-0.003-0.0030.0000.0000.0000.000
131A179GLY00.0260.02723.5670.0060.0060.0000.0000.0000.000
132A180GLU-1-0.854-0.95524.4940.0360.0360.0000.0000.0000.000
133A181GLU-1-0.881-0.93827.2230.0260.0260.0000.0000.0000.000
134A182PHE00.004-0.00425.2220.0000.0000.0000.0000.0000.000
135A183SER00.0340.01226.1300.0010.0010.0000.0000.0000.000
136A184VAL00.010-0.00128.173-0.001-0.0010.0000.0000.0000.000
137A185LYS10.9700.99328.451-0.032-0.0320.0000.0000.0000.000
138A186LEU00.0210.02128.022-0.001-0.0010.0000.0000.0000.000
139A187LEU0-0.039-0.02631.256-0.001-0.0010.0000.0000.0000.000
140A188GLU-1-0.920-0.96033.6620.0220.0220.0000.0000.0000.000
141A189GLU-1-0.850-0.92133.3160.0290.0290.0000.0000.0000.000
142A190ALA00.002-0.01133.7450.0000.0000.0000.0000.0000.000
143A191PHE00.0520.03835.7250.0000.0000.0000.0000.0000.000
144A192ASP-1-0.871-0.92839.1010.0220.0220.0000.0000.0000.000
145A193HIS0-0.079-0.03637.013-0.001-0.0010.0000.0000.0000.000
146A194LEU0-0.053-0.01435.9140.0020.0020.0000.0000.0000.000
147A195ASN00.0500.01939.698-0.004-0.0040.0000.0000.0000.000
148A196PRO00.0360.01341.9640.0010.0010.0000.0000.0000.000
149A197GLY0-0.056-0.03542.6240.0010.0010.0000.0000.0000.000
150A198GLY0-0.0020.01239.0590.0020.0020.0000.0000.0000.000
151A199LYS10.8730.92634.540-0.045-0.0450.0000.0000.0000.000
152A200VAL00.0730.04330.7090.0010.0010.0000.0000.0000.000
153A201ALA0-0.027-0.00629.297-0.001-0.0010.0000.0000.0000.000
154A202LEU00.019-0.00226.1470.0030.0030.0000.0000.0000.000
155A203TYR0-0.037-0.01218.2670.0100.0100.0000.0000.0000.000
156A204LEU00.018-0.01122.0400.0050.0050.0000.0000.0000.000
157A205PRO0-0.073-0.03718.9700.0050.0050.0000.0000.0000.000
158A206ASP-1-0.815-0.91720.8180.0640.0640.0000.0000.0000.000
159A207LYS10.8870.94818.093-0.095-0.0950.0000.0000.0000.000
160A208GLU-1-0.842-0.91223.7390.0290.0290.0000.0000.0000.000
161A209LYS10.9850.97427.324-0.018-0.0180.0000.0000.0000.000
162A210LEU00.0070.00623.049-0.001-0.0010.0000.0000.0000.000
163A211LEU0-0.021-0.01125.454-0.001-0.0010.0000.0000.0000.000
164A212ASN00.003-0.00328.4870.0000.0000.0000.0000.0000.000
165A213VAL00.0130.02030.354-0.002-0.0020.0000.0000.0000.000
166A214ILE0-0.0060.00226.813-0.001-0.0010.0000.0000.0000.000
167A215LYS10.9010.95631.225-0.041-0.0410.0000.0000.0000.000
168A216GLU-1-0.895-0.94833.6790.0250.0250.0000.0000.0000.000
169A217ARG10.8610.93633.774-0.025-0.0250.0000.0000.0000.000
170A218GLY00.0550.02534.950-0.001-0.0010.0000.0000.0000.000
171A219ILE00.0160.00336.103-0.001-0.0010.0000.0000.0000.000
172A220LYS10.8890.93839.088-0.020-0.0200.0000.0000.0000.000
173A221LEU0-0.0020.01436.302-0.001-0.0010.0000.0000.0000.000
174A222GLY00.0130.02440.2640.0000.0000.0000.0000.0000.000
175A223TYR0-0.096-0.05336.5660.0010.0010.0000.0000.0000.000
176A224SER00.0350.02739.7180.0000.0000.0000.0000.0000.000
177A225VAL0-0.016-0.02633.7990.0020.0020.0000.0000.0000.000
178A226LYS10.9250.98434.545-0.045-0.0450.0000.0000.0000.000
179A227ASP-1-0.803-0.89929.5650.0560.0560.0000.0000.0000.000
180A228ILE00.0170.02729.141-0.002-0.0020.0000.0000.0000.000
181A229LYS10.9720.99725.566-0.053-0.0530.0000.0000.0000.000
182A230PHE00.016-0.00722.370-0.001-0.0010.0000.0000.0000.000
183A231LYS10.8520.97818.160-0.108-0.1080.0000.0000.0000.000
184A232VAL00.0020.03020.4080.0000.0000.0000.0000.0000.000
185A233GLY00.0920.02217.0470.0060.0060.0000.0000.0000.000
186A234THR00.1310.09911.769-0.006-0.0060.0000.0000.0000.000
187A235ARG10.7680.82015.202-0.133-0.1330.0000.0000.0000.000
188A236TRP00.003-0.01218.1070.0070.0070.0000.0000.0000.000
189A237ARG10.8840.95116.279-0.148-0.1480.0000.0000.0000.000
190A238HIS00.016-0.01022.091-0.005-0.0050.0000.0000.0000.000
191A239SER0-0.064-0.06124.7910.0050.0050.0000.0000.0000.000
192A240LEU0-0.0100.00827.282-0.004-0.0040.0000.0000.0000.000
193A241ILE00.004-0.01029.8030.0020.0020.0000.0000.0000.000
194A242PHE00.0350.01230.931-0.002-0.0020.0000.0000.0000.000
195A243PHE0-0.035-0.04435.2170.0020.0020.0000.0000.0000.000
196A244LYS10.8860.95038.562-0.028-0.0280.0000.0000.0000.000
197A245GLY0-0.018-0.00340.864-0.001-0.0010.0000.0000.0000.000
198A246ILE00.0690.03643.6870.0000.0000.0000.0000.0000.000