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

tag_button

FMODB ID: 14ZMZ

Calculation Name: 4E72-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E72

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HUJ3

Base Structure: X-ray

Registration Date: 2023-06-20

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2576758.266298
FMO2-HF: Nuclear repulsion 2489477.605961
FMO2-HF: Total energy -87280.660336
FMO2-MP2: Total energy -87538.146172


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:26:GLY)


Summations of interaction energy for fragment #1(A:26:GLY)
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.
-8.435-3.1782.288-3.915-3.629-0.03
Interaction energy analysis for fragmet #1(A:26:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.025
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].
3A28ASP-1-0.913-0.9673.856-1.830-0.707-0.001-0.500-0.6220.001
4A29ASP-1-0.931-0.9422.445-9.891-6.1152.285-3.168-2.893-0.031
5A30PRO0-0.058-0.0314.5000.2610.194-0.001-0.0200.0880.000
6A31LEU0-0.005-0.0235.176-0.206-0.2060.0000.0000.0000.000
7A32PRO00.0100.0105.8100.0600.0600.0000.0000.0000.000
8A33THR0-0.076-0.0529.0860.1730.1730.0000.0000.0000.000
9A34GLU-1-0.929-0.95612.426-0.101-0.1010.0000.0000.0000.000
10A35ARG10.8620.92515.8760.1280.1280.0000.0000.0000.000
11A36LEU0-0.015-0.01119.0080.0130.0130.0000.0000.0000.000
12A37ALA0-0.003-0.00322.0180.0000.0000.0000.0000.0000.000
13A38SER0-0.019-0.00725.1820.0040.0040.0000.0000.0000.000
14A39GLU-1-0.857-0.92528.829-0.043-0.0430.0000.0000.0000.000
15A40HIS0-0.095-0.05930.8430.0000.0000.0000.0000.0000.000
16A41LEU00.0340.00935.007-0.001-0.0010.0000.0000.0000.000
17A42LYS10.9290.97038.7170.0000.0000.0000.0000.0000.000
18A43PRO00.022-0.01040.235-0.002-0.0020.0000.0000.0000.000
19A44GLY0-0.026-0.01442.6100.0010.0010.0000.0000.0000.000
20A45CYS0-0.055-0.01144.562-0.001-0.0010.0000.0000.0000.000
21A46GLN00.008-0.00345.127-0.003-0.0030.0000.0000.0000.000
22A47GLY00.0260.00046.1950.0010.0010.0000.0000.0000.000
23A48GLU-1-0.945-0.97044.727-0.025-0.0250.0000.0000.0000.000
24A49GLN00.0060.00044.257-0.002-0.0020.0000.0000.0000.000
25A50CYS0-0.0190.01141.5910.0030.0030.0000.0000.0000.000
26A51PRO0-0.0270.00841.372-0.002-0.0020.0000.0000.0000.000
27A52LEU00.0070.01234.9310.0020.0020.0000.0000.0000.000
28A53VAL00.001-0.01231.9350.0000.0000.0000.0000.0000.000
29A54ASN0-0.096-0.05129.455-0.003-0.0030.0000.0000.0000.000
30A55ILE00.0270.00525.6560.0000.0000.0000.0000.0000.000
31A56ASP-1-0.841-0.91722.779-0.099-0.0990.0000.0000.0000.000
32A57THR00.0490.00021.256-0.008-0.0080.0000.0000.0000.000
33A58LEU0-0.040-0.01415.727-0.023-0.0230.0000.0000.0000.000
34A59LYS10.9330.98115.850-0.087-0.0870.0000.0000.0000.000
35A60PHE00.020-0.00710.271-0.099-0.0990.0000.0000.0000.000
36A61PRO0-0.025-0.01010.5130.1010.1010.0000.0000.0000.000
37A62ASP-1-0.886-0.9476.2151.0471.0470.0000.0000.0000.000
38A63GLU-1-0.817-0.8818.3141.5651.5650.0000.0000.0000.000
39A64PRO00.0790.03310.129-0.199-0.1990.0000.0000.0000.000
40A65GLN0-0.046-0.03112.375-0.007-0.0070.0000.0000.0000.000
41A66LEU0-0.005-0.00711.568-0.072-0.0720.0000.0000.0000.000
42A67ASP-1-0.790-0.88315.0960.1690.1690.0000.0000.0000.000
43A68PRO0-0.010-0.01317.306-0.038-0.0380.0000.0000.0000.000
44A69ILE0-0.048-0.02016.675-0.024-0.0240.0000.0000.0000.000
45A70VAL00.0130.00017.155-0.028-0.0280.0000.0000.0000.000
46A71GLU-1-0.886-0.94820.0850.0640.0640.0000.0000.0000.000
47A72ARG10.9210.95623.034-0.089-0.0890.0000.0000.0000.000
48A73ALA0-0.007-0.00722.609-0.009-0.0090.0000.0000.0000.000
49A74LEU0-0.006-0.01323.160-0.010-0.0100.0000.0000.0000.000
50A75LEU00.0030.00425.973-0.005-0.0050.0000.0000.0000.000
51A76GLU-1-0.836-0.91627.7470.0390.0390.0000.0000.0000.000
52A77MET0-0.121-0.03427.180-0.005-0.0050.0000.0000.0000.000
53A78THR0-0.075-0.05530.447-0.004-0.0040.0000.0000.0000.000
54A79ARG10.8290.93731.929-0.031-0.0310.0000.0000.0000.000
55A80GLU-1-0.840-0.88435.1590.0090.0090.0000.0000.0000.000
56A81ASN0-0.052-0.03237.400-0.001-0.0010.0000.0000.0000.000
57A82ASN0-0.031-0.05136.8340.0010.0010.0000.0000.0000.000
58A83GLU-1-0.873-0.92537.2860.0250.0250.0000.0000.0000.000
59A84THR0-0.056-0.03638.0970.0040.0040.0000.0000.0000.000
60A85PRO0-0.050-0.02235.9750.0020.0020.0000.0000.0000.000
61A86LEU0-0.0010.00630.307-0.003-0.0030.0000.0000.0000.000
62A87PRO00.0080.00332.1790.0050.0050.0000.0000.0000.000
63A88ALA0-0.024-0.01930.7210.0030.0030.0000.0000.0000.000
64A89SER00.0270.00827.8420.0050.0050.0000.0000.0000.000
65A90LEU00.0520.03224.556-0.008-0.0080.0000.0000.0000.000
66A91ALA00.0220.01728.487-0.006-0.0060.0000.0000.0000.000
67A92ALA0-0.077-0.04430.575-0.004-0.0040.0000.0000.0000.000
68A93TYR00.021-0.01931.331-0.002-0.0020.0000.0000.0000.000
69A94GLU-1-0.837-0.89932.0370.0020.0020.0000.0000.0000.000
70A95ARG10.9490.97733.771-0.041-0.0410.0000.0000.0000.000
71A96GLN00.0170.00436.3190.0010.0010.0000.0000.0000.000
72A97PHE00.0110.00436.464-0.003-0.0030.0000.0000.0000.000
73A98LEU0-0.007-0.01536.455-0.002-0.0020.0000.0000.0000.000
74A99ASP-1-1.021-1.00839.6670.0140.0140.0000.0000.0000.000
75A100SER0-0.055-0.03141.4100.0000.0000.0000.0000.0000.000
76A101ALA0-0.0500.00041.080-0.001-0.0010.0000.0000.0000.000
77A102GLU-1-0.911-0.95243.126-0.003-0.0030.0000.0000.0000.000
78A103PRO0-0.043-0.05444.926-0.001-0.0010.0000.0000.0000.000
79A104GLY00.0100.00444.4320.0000.0000.0000.0000.0000.000
80A105TRP0-0.0340.01141.196-0.002-0.0020.0000.0000.0000.000
81A106SER00.011-0.00137.099-0.001-0.0010.0000.0000.0000.000
82A107SER00.0380.04233.0740.0020.0020.0000.0000.0000.000
83A108TYR0-0.0300.00330.8470.0010.0010.0000.0000.0000.000
84A109LEU0-0.007-0.01027.2260.0000.0000.0000.0000.0000.000
85A110GLN0-0.010-0.00923.492-0.011-0.0110.0000.0000.0000.000
86A111ALA00.0150.01920.0050.0010.0010.0000.0000.0000.000
87A112LYS11.0011.00018.7190.1740.1740.0000.0000.0000.000
88A113VAL00.0140.00412.9650.0070.0070.0000.0000.0000.000
89A114ARG10.7000.85416.1960.1770.1770.0000.0000.0000.000
90A115GLU-1-0.857-0.96515.167-0.353-0.3530.0000.0000.0000.000
91A116GLN00.0050.0238.558-0.088-0.0880.0000.0000.0000.000
92A117HIS10.8290.90311.0710.4090.4090.0000.0000.0000.000
93A118ASP-1-0.730-0.8529.985-0.504-0.5040.0000.0000.0000.000
94A119GLY00.0310.0287.5970.1750.1750.0000.0000.0000.000
95A120LEU0-0.060-0.0288.5600.3100.3100.0000.0000.0000.000
96A121VAL0-0.006-0.0099.820-0.153-0.1530.0000.0000.0000.000
97A122ILE0-0.049-0.01912.4400.0870.0870.0000.0000.0000.000
98A123ILE00.0210.01114.720-0.031-0.0310.0000.0000.0000.000
99A124GLU-1-0.875-0.95717.749-0.126-0.1260.0000.0000.0000.000
100A125LEU0-0.001-0.00121.3110.0010.0010.0000.0000.0000.000
101A126SER0-0.042-0.03123.946-0.004-0.0040.0000.0000.0000.000
102A127SER00.0430.02927.2290.0020.0020.0000.0000.0000.000
103A128TYR0-0.024-0.01730.288-0.005-0.0050.0000.0000.0000.000
104A129LEU00.0620.05033.7290.0020.0020.0000.0000.0000.000
105A130PHE0-0.023-0.01536.626-0.002-0.0020.0000.0000.0000.000
106A131THR00.0320.00440.1160.0010.0010.0000.0000.0000.000
107A132GLY00.0360.02042.9260.0020.0020.0000.0000.0000.000
108A133GLY0-0.0010.01744.9080.0010.0010.0000.0000.0000.000
109A134ALA0-0.016-0.02246.478-0.001-0.0010.0000.0000.0000.000
110A135HIS10.8520.90741.3140.0270.0270.0000.0000.0000.000
111A136GLY00.0390.04039.2960.0030.0030.0000.0000.0000.000
112A137MET0-0.020-0.01137.809-0.002-0.0020.0000.0000.0000.000
113A138PRO0-0.039-0.01833.6560.0000.0000.0000.0000.0000.000
114A139GLY00.0730.04331.6010.0030.0030.0000.0000.0000.000
115A140ARG10.8430.91227.3670.0680.0680.0000.0000.0000.000
116A141GLY00.0960.04625.8460.0100.0100.0000.0000.0000.000
117A142PHE0-0.062-0.03321.463-0.019-0.0190.0000.0000.0000.000
118A143ILE00.0330.02517.3680.0230.0230.0000.0000.0000.000
119A144ASN00.009-0.00517.113-0.066-0.0660.0000.0000.0000.000
120A145TYR0-0.016-0.01811.057-0.001-0.0010.0000.0000.0000.000
121A146ASP-1-0.789-0.88712.279-0.052-0.0520.0000.0000.0000.000
122A147ARG10.9100.9293.1881.5121.9370.005-0.227-0.2020.000
123A148ARG10.9120.9729.0300.1660.1660.0000.0000.0000.000
124A149GLN0-0.107-0.0859.9370.1120.1120.0000.0000.0000.000
125A150HIS10.8000.9008.851-1.103-1.1030.0000.0000.0000.000
126A151LYS10.9500.98713.244-0.168-0.1680.0000.0000.0000.000
127A152VAL00.0320.02616.009-0.036-0.0360.0000.0000.0000.000
128A153LEU0-0.044-0.02516.5400.0110.0110.0000.0000.0000.000
129A154SER00.0140.00120.009-0.021-0.0210.0000.0000.0000.000
130A155LEU00.0470.00223.388-0.006-0.0060.0000.0000.0000.000
131A156GLN00.014-0.00125.650-0.007-0.0070.0000.0000.0000.000
132A157ASP-1-0.846-0.91921.1680.0710.0710.0000.0000.0000.000
133A158MET0-0.032-0.00620.648-0.006-0.0060.0000.0000.0000.000
134A159LEU0-0.0170.00722.625-0.013-0.0130.0000.0000.0000.000
135A160VAL0-0.011-0.00325.8060.0130.0130.0000.0000.0000.000
136A161PRO00.028-0.00826.881-0.001-0.0010.0000.0000.0000.000
137A162GLY00.0210.00929.803-0.002-0.0020.0000.0000.0000.000
138A163GLN0-0.061-0.01930.061-0.008-0.0080.0000.0000.0000.000
139A164GLU-1-0.856-0.92931.341-0.014-0.0140.0000.0000.0000.000
140A165GLU-1-0.836-0.91632.271-0.029-0.0290.0000.0000.0000.000
141A166ALA00.0540.02233.059-0.004-0.0040.0000.0000.0000.000
142A167PHE00.006-0.00526.938-0.007-0.0070.0000.0000.0000.000
143A168TRP0-0.021-0.03430.928-0.009-0.0090.0000.0000.0000.000
144A169LYS10.8950.94934.2150.0250.0250.0000.0000.0000.000
145A170GLN0-0.029-0.02131.750-0.008-0.0080.0000.0000.0000.000
146A171ALA00.0060.00832.325-0.006-0.0060.0000.0000.0000.000
147A172GLU-1-0.895-0.95033.412-0.039-0.0390.0000.0000.0000.000
148A173LEU0-0.073-0.03034.856-0.001-0.0010.0000.0000.0000.000
149A174ALA00.014-0.00432.347-0.002-0.0020.0000.0000.0000.000
150A175HIS00.0540.02734.279-0.006-0.0060.0000.0000.0000.000
151A176LYS10.9600.97636.8330.0480.0480.0000.0000.0000.000
152A177ALA0-0.014-0.00335.3080.0000.0000.0000.0000.0000.000
153A178TRP00.0390.01934.146-0.001-0.0010.0000.0000.0000.000
154A179LEU00.0140.01136.6180.0000.0000.0000.0000.0000.000
155A180LEU0-0.0080.00839.9680.0010.0010.0000.0000.0000.000
156A181ALA0-0.051-0.02436.7800.0000.0000.0000.0000.0000.000
157A182ASN0-0.067-0.04236.742-0.002-0.0020.0000.0000.0000.000
158A183LYS10.9100.95940.4640.0660.0660.0000.0000.0000.000
159A184LEU00.0220.00941.4160.0030.0030.0000.0000.0000.000
160A185ASP-1-0.960-0.98443.954-0.050-0.0500.0000.0000.0000.000
161A186GLN00.002-0.00145.2640.0020.0020.0000.0000.0000.000
162A187ASP-1-0.905-0.94047.319-0.038-0.0380.0000.0000.0000.000
163A188ALA00.002-0.02048.0460.0000.0000.0000.0000.0000.000
164A189ASP-1-0.883-0.94650.007-0.028-0.0280.0000.0000.0000.000
165A190PHE00.0370.02641.7040.0010.0010.0000.0000.0000.000
166A191GLN0-0.069-0.04944.7280.0020.0020.0000.0000.0000.000
167A192LYS10.8420.92946.2060.0320.0320.0000.0000.0000.000
168A193THR0-0.0040.00646.6910.0020.0020.0000.0000.0000.000
169A194TRP0-0.064-0.02442.2570.0010.0010.0000.0000.0000.000
170A195PRO0-0.0130.01243.051-0.003-0.0030.0000.0000.0000.000
171A196PHE0-0.012-0.01934.800-0.001-0.0010.0000.0000.0000.000
172A197GLN00.0590.02737.6390.0030.0030.0000.0000.0000.000
173A198ARG10.9270.97734.0710.0120.0120.0000.0000.0000.000
174A199THR00.002-0.02129.9660.0030.0030.0000.0000.0000.000
175A200PRO00.0210.01229.3420.0000.0000.0000.0000.0000.000
176A201HIS0-0.0270.00326.3720.0000.0000.0000.0000.0000.000
177A202VAL00.008-0.00424.173-0.010-0.0100.0000.0000.0000.000
178A203ALA00.0120.01020.6580.0030.0030.0000.0000.0000.000
179A204LEU00.0360.01818.168-0.001-0.0010.0000.0000.0000.000
180A205THR0-0.0170.01417.981-0.034-0.0340.0000.0000.0000.000
181A206PHE00.0110.00815.5290.0250.0250.0000.0000.0000.000
182A207GLY0-0.0020.00118.7920.0140.0140.0000.0000.0000.000
183A208ALA0-0.055-0.03822.3390.0190.0190.0000.0000.0000.000
184A209VAL00.0410.04022.821-0.014-0.0140.0000.0000.0000.000
185A210THR0-0.031-0.04323.3880.0090.0090.0000.0000.0000.000
186A211LEU0-0.034-0.00525.4650.0070.0070.0000.0000.0000.000
187A212LYS10.8880.95226.5590.1060.1060.0000.0000.0000.000
188A213TYR0-0.044-0.02128.9210.0060.0060.0000.0000.0000.000
189A214ASP-1-0.832-0.90532.369-0.042-0.0420.0000.0000.0000.000
190A215ALA00.0240.00533.769-0.001-0.0010.0000.0000.0000.000
191A216TYR0-0.066-0.03036.4890.0040.0040.0000.0000.0000.000
192A217SER0-0.010-0.00436.1560.0020.0020.0000.0000.0000.000
193A218ILE00.0090.00235.2410.0010.0010.0000.0000.0000.000
194A219ALA0-0.018-0.01038.740-0.002-0.0020.0000.0000.0000.000
195A220PRO00.0100.02040.3570.0020.0020.0000.0000.0000.000
196A221TYR00.0570.00538.609-0.004-0.0040.0000.0000.0000.000
197A222SER0-0.0190.00438.963-0.002-0.0020.0000.0000.0000.000
198A223TYR00.004-0.00337.817-0.002-0.0020.0000.0000.0000.000
199A224ALA0-0.027-0.01634.097-0.006-0.0060.0000.0000.0000.000
200A225HIS00.0140.00831.0860.0040.0040.0000.0000.0000.000
201A226PRO00.0090.01231.611-0.010-0.0100.0000.0000.0000.000
202A227GLU-1-0.747-0.86926.814-0.145-0.1450.0000.0000.0000.000
203A228LEU0-0.0110.00530.331-0.002-0.0020.0000.0000.0000.000
204A229LYS10.8740.93825.2790.1540.1540.0000.0000.0000.000
205A230ILE00.0160.01527.8480.0070.0070.0000.0000.0000.000
206A231PRO00.0120.00626.817-0.012-0.0120.0000.0000.0000.000
207A232TYR00.0870.02420.3680.0210.0210.0000.0000.0000.000
208A233PRO0-0.040-0.02025.3980.0120.0120.0000.0000.0000.000
209A234ARG10.8740.94528.1340.0870.0870.0000.0000.0000.000
210A235LEU00.0260.01125.5470.0100.0100.0000.0000.0000.000
211A236ASN0-0.0050.00426.955-0.003-0.0030.0000.0000.0000.000
212A237GLY00.0220.01427.2550.0060.0060.0000.0000.0000.000
213A238ILE0-0.0210.00127.9750.0080.0080.0000.0000.0000.000
214A239VAL00.0200.01022.2440.0090.0090.0000.0000.0000.000
215A240LYS10.8670.92721.101-0.026-0.0260.0000.0000.0000.000
216A241PRO00.0500.00921.215-0.017-0.0170.0000.0000.0000.000
217A242ASN0-0.047-0.02716.393-0.013-0.0130.0000.0000.0000.000
218A243LEU0-0.0230.00215.920-0.017-0.0170.0000.0000.0000.000
219A244PHE0-0.054-0.01917.732-0.019-0.0190.0000.0000.0000.000
220A245PRO0-0.046-0.00116.225-0.020-0.0200.0000.0000.0000.000
221A246GLY00.0310.01414.3410.0530.0530.0000.0000.0000.000
222A247ARG10.9020.95315.4100.1860.1860.0000.0000.0000.000