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

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FMODB ID: GN9J1

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 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 -2580195.628954
FMO2-HF: Nuclear repulsion 2492914.14373
FMO2-HF: Total energy -87281.485223
FMO2-MP2: Total energy -87539.021334


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.
-8.453-4.0673.37-4.056-3.701-0.031
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 : 0.048 / q_NPA : 0.020
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-1-0.919-0.9693.856-1.774-0.645-0.001-0.502-0.6270.001
4A29ASP-1-0.915-0.9372.336-9.680-6.6793.369-3.380-2.990-0.032
5A30PRO0-0.057-0.0264.5380.3960.335-0.001-0.0190.0810.000
6A31LEU0-0.001-0.0135.117-0.122-0.1220.0000.0000.0000.000
7A32PRO00.0140.0095.8390.0110.0110.0000.0000.0000.000
8A33THR0-0.081-0.0589.1130.1660.1660.0000.0000.0000.000
9A34GLU-1-0.889-0.94012.470-0.068-0.0680.0000.0000.0000.000
10A35ARG10.8030.86615.9150.0960.0960.0000.0000.0000.000
11A36LEU0-0.029-0.01619.0510.0100.0100.0000.0000.0000.000
12A37ALA0-0.008-0.00522.069-0.001-0.0010.0000.0000.0000.000
13A38SER0-0.013-0.00225.2300.0040.0040.0000.0000.0000.000
14A39GLU-1-0.836-0.91828.878-0.030-0.0300.0000.0000.0000.000
15A40HIS0-0.083-0.04530.714-0.001-0.0010.0000.0000.0000.000
16A41LEU00.0390.01235.062-0.001-0.0010.0000.0000.0000.000
17A42LYS10.9050.95038.772-0.008-0.0080.0000.0000.0000.000
18A43PRO00.020-0.01140.181-0.002-0.0020.0000.0000.0000.000
19A44GLY0-0.030-0.01442.6660.0010.0010.0000.0000.0000.000
20A45CYS0-0.0310.00844.558-0.001-0.0010.0000.0000.0000.000
21A46GLN0-0.017-0.00945.177-0.003-0.0030.0000.0000.0000.000
22A47GLY00.0290.00146.2520.0000.0000.0000.0000.0000.000
23A48GLU-1-0.948-0.97244.784-0.017-0.0170.0000.0000.0000.000
24A49GLN00.0150.00444.311-0.002-0.0020.0000.0000.0000.000
25A50CYS0-0.017-0.00141.6150.0030.0030.0000.0000.0000.000
26A51PRO0-0.0350.00441.377-0.001-0.0010.0000.0000.0000.000
27A52LEU0-0.0030.00534.9380.0020.0020.0000.0000.0000.000
28A53VAL0-0.005-0.00932.0780.0000.0000.0000.0000.0000.000
29A54ASN0-0.088-0.05029.507-0.001-0.0010.0000.0000.0000.000
30A55ILE00.0190.00325.7640.0000.0000.0000.0000.0000.000
31A56ASP-1-0.754-0.83523.163-0.069-0.0690.0000.0000.0000.000
32A57THR00.0490.00021.334-0.006-0.0060.0000.0000.0000.000
33A58LEU0-0.038-0.01115.553-0.023-0.0230.0000.0000.0000.000
34A59LYS10.8620.92915.917-0.149-0.1490.0000.0000.0000.000
35A60PHE00.016-0.00510.411-0.086-0.0860.0000.0000.0000.000
36A61PRO0-0.026-0.01110.5650.0930.0930.0000.0000.0000.000
37A62ASP-1-0.879-0.9416.2581.0581.0580.0000.0000.0000.000
38A63GLU-1-0.819-0.8608.3791.4781.4780.0000.0000.0000.000
39A64PRO00.0740.03110.220-0.204-0.2040.0000.0000.0000.000
40A65GLN0-0.023-0.02611.819-0.060-0.0600.0000.0000.0000.000
41A66LEU00.002-0.00411.669-0.077-0.0770.0000.0000.0000.000
42A67ASP-1-0.752-0.84315.2180.1880.1880.0000.0000.0000.000
43A68PRO0-0.008-0.01317.394-0.039-0.0390.0000.0000.0000.000
44A69ILE0-0.041-0.01616.854-0.027-0.0270.0000.0000.0000.000
45A70VAL00.012-0.00117.254-0.030-0.0300.0000.0000.0000.000
46A71GLU-1-0.846-0.91420.1770.0810.0810.0000.0000.0000.000
47A72ARG10.8950.93623.123-0.101-0.1010.0000.0000.0000.000
48A73ALA0-0.007-0.01122.684-0.011-0.0110.0000.0000.0000.000
49A74LEU0-0.010-0.01223.351-0.012-0.0120.0000.0000.0000.000
50A75LEU00.0050.00326.061-0.006-0.0060.0000.0000.0000.000
51A76GLU-1-0.787-0.86027.9090.0500.0500.0000.0000.0000.000
52A77MET0-0.128-0.03527.267-0.006-0.0060.0000.0000.0000.000
53A78THR0-0.071-0.04930.532-0.005-0.0050.0000.0000.0000.000
54A79ARG10.7840.88132.032-0.042-0.0420.0000.0000.0000.000
55A80GLU-1-0.842-0.88835.2540.0170.0170.0000.0000.0000.000
56A81ASN0-0.055-0.03337.4990.0000.0000.0000.0000.0000.000
57A82ASN0-0.036-0.05336.8330.0010.0010.0000.0000.0000.000
58A83GLU-1-0.866-0.91837.1610.0310.0310.0000.0000.0000.000
59A84THR0-0.045-0.03038.1950.0040.0040.0000.0000.0000.000
60A85PRO0-0.053-0.01436.0770.0020.0020.0000.0000.0000.000
61A86LEU00.0160.01130.186-0.002-0.0020.0000.0000.0000.000
62A87PRO00.000-0.00332.3060.0050.0050.0000.0000.0000.000
63A88ALA0-0.028-0.01930.8110.0040.0040.0000.0000.0000.000
64A89SER00.004-0.00627.7660.0060.0060.0000.0000.0000.000
65A90LEU00.0550.02124.594-0.009-0.0090.0000.0000.0000.000
66A91ALA00.0190.01628.567-0.007-0.0070.0000.0000.0000.000
67A92ALA0-0.084-0.04530.649-0.005-0.0050.0000.0000.0000.000
68A93TYR00.028-0.00931.410-0.003-0.0030.0000.0000.0000.000
69A94GLU-1-0.846-0.91031.9640.0140.0140.0000.0000.0000.000
70A95ARG10.9430.96833.703-0.050-0.0500.0000.0000.0000.000
71A96GLN00.0230.00936.4000.0010.0010.0000.0000.0000.000
72A97PHE00.0120.00736.515-0.003-0.0030.0000.0000.0000.000
73A98LEU00.002-0.00836.504-0.002-0.0020.0000.0000.0000.000
74A99ASP-1-0.991-0.99139.7380.0200.0200.0000.0000.0000.000
75A100SER0-0.066-0.03741.457-0.001-0.0010.0000.0000.0000.000
76A101ALA0-0.0480.00441.131-0.001-0.0010.0000.0000.0000.000
77A102GLU-1-0.890-0.94343.2010.0030.0030.0000.0000.0000.000
78A103PRO0-0.038-0.05244.996-0.001-0.0010.0000.0000.0000.000
79A104GLY00.0100.00244.498-0.001-0.0010.0000.0000.0000.000
80A105TRP0-0.052-0.00241.258-0.002-0.0020.0000.0000.0000.000
81A106SER00.004-0.00437.156-0.001-0.0010.0000.0000.0000.000
82A107SER0-0.0140.02034.0550.0020.0020.0000.0000.0000.000
83A108TYR00.0090.01430.9350.0000.0000.0000.0000.0000.000
84A109LEU0-0.006-0.00727.4050.0000.0000.0000.0000.0000.000
85A110GLN0-0.052-0.03723.627-0.007-0.0070.0000.0000.0000.000
86A111ALA00.0040.01120.1270.0000.0000.0000.0000.0000.000
87A112LYS10.9970.99918.7910.1350.1350.0000.0000.0000.000
88A113VAL00.0160.00312.9180.0070.0070.0000.0000.0000.000
89A114ARG10.7130.83616.2580.1480.1480.0000.0000.0000.000
90A115GLU-1-0.834-0.94615.240-0.312-0.3120.0000.0000.0000.000
91A116GLN00.0070.0148.782-0.030-0.0300.0000.0000.0000.000
92A117HIS10.8120.87711.1110.3600.3600.0000.0000.0000.000
93A118ASP-1-0.736-0.8479.963-0.482-0.4820.0000.0000.0000.000
94A119GLY00.0360.0287.5950.1610.1610.0000.0000.0000.000
95A120LEU0-0.064-0.0308.5600.3150.3150.0000.0000.0000.000
96A121VAL00.000-0.0069.921-0.139-0.1390.0000.0000.0000.000
97A122ILE0-0.052-0.01712.5240.0770.0770.0000.0000.0000.000
98A123ILE00.0320.01214.819-0.029-0.0290.0000.0000.0000.000
99A124GLU-1-0.813-0.89617.829-0.105-0.1050.0000.0000.0000.000
100A125LEU00.000-0.00221.2420.0030.0030.0000.0000.0000.000
101A126SER0-0.045-0.03624.025-0.006-0.0060.0000.0000.0000.000
102A127SER00.0510.03227.3030.0030.0030.0000.0000.0000.000
103A128TYR0-0.015-0.02130.364-0.006-0.0060.0000.0000.0000.000
104A129LEU00.0430.04233.8010.0020.0020.0000.0000.0000.000
105A130PHE0-0.020-0.01136.702-0.002-0.0020.0000.0000.0000.000
106A131THR00.0310.00640.1890.0010.0010.0000.0000.0000.000
107A132GLY00.0460.02743.0030.0010.0010.0000.0000.0000.000
108A133GLY0-0.0040.01444.9840.0000.0000.0000.0000.0000.000
109A134ALA0-0.016-0.02246.553-0.001-0.0010.0000.0000.0000.000
110A135HIS10.8550.90841.4060.0190.0190.0000.0000.0000.000
111A136GLY00.0420.04439.3740.0020.0020.0000.0000.0000.000
112A137MET0-0.022-0.01137.956-0.002-0.0020.0000.0000.0000.000
113A138PRO0-0.045-0.02033.6830.0000.0000.0000.0000.0000.000
114A139GLY00.0750.04831.6750.0030.0030.0000.0000.0000.000
115A140ARG10.8230.90427.5160.0480.0480.0000.0000.0000.000
116A141GLY00.1000.04925.9320.0080.0080.0000.0000.0000.000
117A142PHE0-0.079-0.04121.579-0.018-0.0180.0000.0000.0000.000
118A143ILE00.0320.02517.9850.0210.0210.0000.0000.0000.000
119A144ASN0-0.005-0.01317.225-0.060-0.0600.0000.0000.0000.000
120A145TYR0-0.016-0.03511.347-0.016-0.0160.0000.0000.0000.000
121A146ASP-1-0.789-0.89212.0740.0120.0120.0000.0000.0000.000
122A147ARG10.9120.9303.3101.1951.5120.003-0.155-0.1650.000
123A148ARG10.9160.9689.0230.1830.1830.0000.0000.0000.000
124A149GLN0-0.105-0.0739.9290.1020.1020.0000.0000.0000.000
125A150HIS10.7860.8868.623-1.173-1.1730.0000.0000.0000.000
126A151LYS10.9020.94913.233-0.166-0.1660.0000.0000.0000.000
127A152VAL00.0300.03016.017-0.031-0.0310.0000.0000.0000.000
128A153LEU0-0.057-0.03116.6740.0060.0060.0000.0000.0000.000
129A154SER00.018-0.01920.009-0.020-0.0200.0000.0000.0000.000
130A155LEU00.0570.00323.388-0.006-0.0060.0000.0000.0000.000
131A156GLN00.012-0.00225.650-0.008-0.0080.0000.0000.0000.000
132A157ASP-1-0.794-0.85821.1170.0810.0810.0000.0000.0000.000
133A158MET0-0.0100.01620.856-0.006-0.0060.0000.0000.0000.000
134A159LEU0-0.0260.00622.635-0.014-0.0140.0000.0000.0000.000
135A160VAL0-0.0010.01725.7990.0140.0140.0000.0000.0000.000
136A161PRO00.028-0.00726.855-0.001-0.0010.0000.0000.0000.000
137A162GLY00.0250.01329.797-0.003-0.0030.0000.0000.0000.000
138A163GLN0-0.049-0.01430.081-0.006-0.0060.0000.0000.0000.000
139A164GLU-1-0.768-0.86230.952-0.012-0.0120.0000.0000.0000.000
140A165GLU-1-0.814-0.89632.271-0.024-0.0240.0000.0000.0000.000
141A166ALA00.0610.02933.133-0.004-0.0040.0000.0000.0000.000
142A167PHE00.010-0.00426.773-0.007-0.0070.0000.0000.0000.000
143A168TRP0-0.007-0.03131.049-0.009-0.0090.0000.0000.0000.000
144A169LYS10.8500.91834.2150.0200.0200.0000.0000.0000.000
145A170GLN0-0.027-0.01431.778-0.008-0.0080.0000.0000.0000.000
146A171ALA00.0160.01132.207-0.006-0.0060.0000.0000.0000.000
147A172GLU-1-0.822-0.91333.412-0.035-0.0350.0000.0000.0000.000
148A173LEU0-0.074-0.02835.222-0.001-0.0010.0000.0000.0000.000
149A174ALA00.0150.00032.341-0.002-0.0020.0000.0000.0000.000
150A175HIS00.0560.02534.279-0.005-0.0050.0000.0000.0000.000
151A176LYS10.8770.93536.8960.0410.0410.0000.0000.0000.000
152A177ALA0-0.012-0.00135.3200.0000.0000.0000.0000.0000.000
153A178TRP00.0350.01533.947-0.001-0.0010.0000.0000.0000.000
154A179LEU00.0260.01436.6710.0000.0000.0000.0000.0000.000
155A180LEU0-0.0150.00540.0100.0010.0010.0000.0000.0000.000
156A181ALA0-0.052-0.02336.7950.0000.0000.0000.0000.0000.000
157A182ASN0-0.061-0.03936.770-0.001-0.0010.0000.0000.0000.000
158A183LYS10.9070.95740.5110.0610.0610.0000.0000.0000.000
159A184LEU00.0290.01541.5410.0030.0030.0000.0000.0000.000
160A185ASP-1-0.913-0.94743.965-0.045-0.0450.0000.0000.0000.000
161A186GLN0-0.044-0.04145.3170.0040.0040.0000.0000.0000.000
162A187ASP-1-0.882-0.91847.368-0.033-0.0330.0000.0000.0000.000
163A188ALA00.007-0.01548.1070.0000.0000.0000.0000.0000.000
164A189ASP-1-0.850-0.92850.074-0.024-0.0240.0000.0000.0000.000
165A190PHE00.0300.02041.9180.0010.0010.0000.0000.0000.000
166A191GLN0-0.089-0.06344.9340.0020.0020.0000.0000.0000.000
167A192LYS10.8080.91046.2790.0280.0280.0000.0000.0000.000
168A193THR0-0.0110.00246.8770.0020.0020.0000.0000.0000.000
169A194TRP0-0.067-0.02742.3560.0010.0010.0000.0000.0000.000
170A195PRO0-0.0070.01343.124-0.003-0.0030.0000.0000.0000.000
171A196PHE0-0.018-0.02234.887-0.001-0.0010.0000.0000.0000.000
172A197GLN00.0250.01036.4980.0050.0050.0000.0000.0000.000
173A198ARG10.8440.91934.2020.0060.0060.0000.0000.0000.000
174A199THR00.005-0.01230.0490.0030.0030.0000.0000.0000.000
175A200PRO00.0130.00729.4780.0000.0000.0000.0000.0000.000
176A201HIS0-0.047-0.01826.4610.0020.0020.0000.0000.0000.000
177A202VAL00.004-0.00724.270-0.011-0.0110.0000.0000.0000.000
178A203ALA00.0160.01820.7510.0050.0050.0000.0000.0000.000
179A204LEU00.0320.01617.997-0.004-0.0040.0000.0000.0000.000
180A205THR0-0.0310.00018.000-0.031-0.0310.0000.0000.0000.000
181A206PHE00.007-0.00315.1860.0230.0230.0000.0000.0000.000
182A207GLY0-0.006-0.00118.7920.0110.0110.0000.0000.0000.000
183A208ALA0-0.055-0.03622.3520.0170.0170.0000.0000.0000.000
184A209VAL00.0430.04322.959-0.012-0.0120.0000.0000.0000.000
185A210THR0-0.025-0.01823.6120.0080.0080.0000.0000.0000.000
186A211LEU0-0.026-0.00825.5310.0080.0080.0000.0000.0000.000
187A212LYS10.8350.91426.4790.0910.0910.0000.0000.0000.000
188A213TYR0-0.036-0.03228.9950.0060.0060.0000.0000.0000.000
189A214ASP-1-0.800-0.87932.397-0.030-0.0300.0000.0000.0000.000
190A215ALA00.0160.00733.849-0.001-0.0010.0000.0000.0000.000
191A216TYR0-0.054-0.02636.5640.0030.0030.0000.0000.0000.000
192A217SER0-0.009-0.00736.2200.0020.0020.0000.0000.0000.000
193A218ILE00.002-0.00535.3920.0010.0010.0000.0000.0000.000
194A219ALA0-0.013-0.00638.771-0.002-0.0020.0000.0000.0000.000
195A220PRO00.0190.02140.4280.0020.0020.0000.0000.0000.000
196A221TYR00.0610.00738.626-0.003-0.0030.0000.0000.0000.000
197A222SER0-0.0170.00539.026-0.002-0.0020.0000.0000.0000.000
198A223TYR00.001-0.00537.900-0.002-0.0020.0000.0000.0000.000
199A224ALA0-0.029-0.02134.277-0.005-0.0050.0000.0000.0000.000
200A225HIS00.0200.01031.1840.0040.0040.0000.0000.0000.000
201A226PRO00.0040.01431.675-0.008-0.0080.0000.0000.0000.000
202A227GLU-1-0.731-0.83126.621-0.127-0.1270.0000.0000.0000.000
203A228LEU0-0.0160.00430.408-0.003-0.0030.0000.0000.0000.000
204A229LYS10.8450.90225.4640.1330.1330.0000.0000.0000.000
205A230ILE00.0280.01627.8530.0060.0060.0000.0000.0000.000
206A231PRO00.0050.00326.817-0.011-0.0110.0000.0000.0000.000
207A232TYR00.0880.02320.3020.0210.0210.0000.0000.0000.000
208A233PRO0-0.038-0.02025.3980.0110.0110.0000.0000.0000.000
209A234ARG10.8820.94528.1340.0800.0800.0000.0000.0000.000
210A235LEU00.0230.00625.9310.0100.0100.0000.0000.0000.000
211A236ASN0-0.0130.00026.951-0.001-0.0010.0000.0000.0000.000
212A237GLY00.0250.01527.2530.0050.0050.0000.0000.0000.000
213A238ILE0-0.033-0.00227.9700.0080.0080.0000.0000.0000.000
214A239VAL00.0320.01522.2080.0100.0100.0000.0000.0000.000
215A240LYS10.8110.87521.185-0.022-0.0220.0000.0000.0000.000
216A241PRO00.0500.00821.211-0.015-0.0150.0000.0000.0000.000
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