Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: QNN8Y

Calculation Name: 3I82-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3I82

Chain ID: A

ChEMBL ID:

UniProt ID: P76541

Base Structure: X-ray

Registration Date: 2023-09-27

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2234732.447847
FMO2-HF: Nuclear repulsion 2155707.805331
FMO2-HF: Total energy -79024.642516
FMO2-MP2: Total energy -79254.424136


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-33.224-42.27536.887-14.827-13.01-0.058
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.075 / q_NPA : -0.033
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].
3A4LEU0-0.066-0.0423.669-2.117-1.0530.000-0.473-0.5920.001
4A5ASP-1-0.835-0.8891.902-21.887-22.36512.489-6.498-5.512-0.076
5A6LEU0-0.056-0.0464.4801.5061.591-0.001-0.014-0.0700.000
6A7ILE00.0100.0236.9950.1370.1370.0000.0000.0000.000
7A8ARG10.8720.9268.8810.3270.3270.0000.0000.0000.000
8A9PRO00.0100.02811.6680.1160.1160.0000.0000.0000.000
9A10SER0-0.016-0.01814.888-0.035-0.0350.0000.0000.0000.000
10A11VAL0-0.014-0.01017.9650.0170.0170.0000.0000.0000.000
11A12THR0-0.023-0.01720.9090.0090.0090.0000.0000.0000.000
12A13ALA0-0.054-0.03523.2850.0060.0060.0000.0000.0000.000
13A14MET00.0320.03526.974-0.011-0.0110.0000.0000.0000.000
14A15ARG10.8500.91929.351-0.026-0.0260.0000.0000.0000.000
15A16VAL00.0280.02633.113-0.004-0.0040.0000.0000.0000.000
16A17ILE0-0.0320.00435.8090.0040.0040.0000.0000.0000.000
17A18ALA00.001-0.01739.085-0.004-0.0040.0000.0000.0000.000
18A19SER0-0.0020.00141.457-0.003-0.0030.0000.0000.0000.000
19A20VAL00.0020.01040.7650.0040.0040.0000.0000.0000.000
20A21ASN00.0230.01243.439-0.001-0.0010.0000.0000.0000.000
21A22ALA00.024-0.00445.8600.0000.0000.0000.0000.0000.000
22A23ASP-1-0.951-0.97447.8190.0140.0140.0000.0000.0000.000
23A24PHE00.0770.02739.060-0.001-0.0010.0000.0000.0000.000
24A25ALA00.0160.00643.5370.0000.0000.0000.0000.0000.000
25A26ARG10.9030.94944.494-0.006-0.0060.0000.0000.0000.000
26A27GLU-1-0.937-0.96843.6790.0170.0170.0000.0000.0000.000
27A28LEU0-0.042-0.01038.6110.0000.0000.0000.0000.0000.000
28A29LYS10.8940.95541.158-0.006-0.0060.0000.0000.0000.000
29A30LEU0-0.0020.01339.721-0.003-0.0030.0000.0000.0000.000
30A31PRO00.0310.01941.8480.0010.0010.0000.0000.0000.000
31A32PRO0-0.039-0.03144.8810.0010.0010.0000.0000.0000.000
32A33HIS00.0110.00441.7120.0030.0030.0000.0000.0000.000
33A34ILE0-0.0120.03238.932-0.001-0.0010.0000.0000.0000.000
34A35ARG10.9030.94342.8010.0140.0140.0000.0000.0000.000
35A36SER0-0.032-0.00439.7290.0020.0020.0000.0000.0000.000
36A37LEU00.022-0.00836.185-0.003-0.0030.0000.0000.0000.000
37A38GLY00.0100.00133.5350.0040.0040.0000.0000.0000.000
38A39LEU0-0.034-0.01431.767-0.001-0.0010.0000.0000.0000.000
39A40ILE00.027-0.00524.9510.0010.0010.0000.0000.0000.000
40A41SER00.0190.00425.527-0.006-0.0060.0000.0000.0000.000
41A42ALA00.0440.02820.273-0.005-0.0050.0000.0000.0000.000
42A43ASP-1-0.842-0.92116.5160.1890.1890.0000.0000.0000.000
43A44SER00.0310.02115.9830.0130.0130.0000.0000.0000.000
44A45ASP-1-0.813-0.94017.9490.0030.0030.0000.0000.0000.000
45A46ASP-1-0.756-0.85618.476-0.057-0.0570.0000.0000.0000.000
46A47VAL0-0.0010.01215.435-0.026-0.0260.0000.0000.0000.000
47A48THR0-0.009-0.02718.774-0.016-0.0160.0000.0000.0000.000
48A49TYR0-0.033-0.02421.904-0.002-0.0020.0000.0000.0000.000
49A50ILE0-0.006-0.00419.546-0.007-0.0070.0000.0000.0000.000
50A51ALA00.0160.02322.031-0.006-0.0060.0000.0000.0000.000
51A52ALA00.003-0.00723.7590.0030.0030.0000.0000.0000.000
52A53ASP-1-0.760-0.88626.476-0.114-0.1140.0000.0000.0000.000
53A54GLU-1-0.827-0.91525.048-0.177-0.1770.0000.0000.0000.000
54A55ALA00.015-0.00327.2200.0020.0020.0000.0000.0000.000
55A56THR0-0.128-0.06529.4330.0050.0050.0000.0000.0000.000
56A57LYS10.7620.88627.2160.1660.1660.0000.0000.0000.000
57A58GLN0-0.096-0.04428.5730.0080.0080.0000.0000.0000.000
58A59ALA0-0.0020.01332.1000.0040.0040.0000.0000.0000.000
59A60MET0-0.085-0.02734.8320.0010.0010.0000.0000.0000.000
60A61VAL0-0.056-0.04132.6930.0080.0080.0000.0000.0000.000
61A62GLU-1-0.898-0.95834.610-0.043-0.0430.0000.0000.0000.000
62A63VAL0-0.007-0.00630.1860.0050.0050.0000.0000.0000.000
63A64VAL0-0.044-0.00233.3960.0020.0020.0000.0000.0000.000
64A65TYR0-0.004-0.02731.8770.0030.0030.0000.0000.0000.000
65A66GLY00.0370.01029.554-0.004-0.0040.0000.0000.0000.000
66A67ARG10.8410.94628.675-0.045-0.0450.0000.0000.0000.000
67A68SER00.0760.04323.9430.0040.0040.0000.0000.0000.000
68A69LEU0-0.065-0.02924.563-0.001-0.0010.0000.0000.0000.000
69A70TYR0-0.009-0.02024.4400.0040.0040.0000.0000.0000.000
70A71ALA0-0.033-0.01323.0190.0100.0100.0000.0000.0000.000
71A72GLY00.0420.02820.1590.0380.0380.0000.0000.0000.000
72A73ALA0-0.0060.00217.9550.0040.0040.0000.0000.0000.000
73A74ALA0-0.051-0.02116.8960.0020.0020.0000.0000.0000.000
74A75HIS0-0.087-0.04618.9340.0360.0360.0000.0000.0000.000
75A76GLY00.0540.04422.303-0.033-0.0330.0000.0000.0000.000
76A77PRO0-0.066-0.03324.1880.0070.0070.0000.0000.0000.000
77A78SER0-0.007-0.02326.103-0.007-0.0070.0000.0000.0000.000
78A79PRO00.0510.02023.061-0.001-0.0010.0000.0000.0000.000
79A80THR0-0.014-0.01123.408-0.010-0.0100.0000.0000.0000.000
80A81ALA0-0.0220.00325.502-0.018-0.0180.0000.0000.0000.000
81A82GLY00.0460.03821.298-0.014-0.0140.0000.0000.0000.000
82A83GLU-1-0.799-0.92018.9170.1990.1990.0000.0000.0000.000
83A84VAL00.0020.01821.942-0.016-0.0160.0000.0000.0000.000
84A85LEU0-0.060-0.01524.7320.0040.0040.0000.0000.0000.000
85A86ILE00.0050.01026.472-0.006-0.0060.0000.0000.0000.000
86A87MET0-0.076-0.03929.0540.0020.0020.0000.0000.0000.000
87A88LEU00.0560.02730.042-0.003-0.0030.0000.0000.0000.000
88A89GLY00.012-0.01233.4760.0060.0060.0000.0000.0000.000
89A90GLY00.0690.01937.217-0.006-0.0060.0000.0000.0000.000
90A91PRO0-0.005-0.00139.1010.0050.0050.0000.0000.0000.000
91A92ASN00.000-0.00141.0260.0020.0020.0000.0000.0000.000
92A93PRO00.025-0.00839.128-0.002-0.0020.0000.0000.0000.000
93A94ALA0-0.0210.00337.745-0.001-0.0010.0000.0000.0000.000
94A95GLU-1-0.800-0.90936.871-0.064-0.0640.0000.0000.0000.000
95A96VAL0-0.0070.00734.477-0.004-0.0040.0000.0000.0000.000
96A97ARG10.9110.94333.3430.0230.0230.0000.0000.0000.000
97A98ALA00.0690.06232.090-0.003-0.0030.0000.0000.0000.000
98A99GLY00.0280.00930.999-0.009-0.0090.0000.0000.0000.000
99A100LEU0-0.025-0.03628.985-0.005-0.0050.0000.0000.0000.000
100A101ASP-1-0.908-0.94827.463-0.069-0.0690.0000.0000.0000.000
101A102ALA0-0.035-0.01726.447-0.013-0.0130.0000.0000.0000.000
102A103MET0-0.042-0.01924.944-0.012-0.0120.0000.0000.0000.000
103A104ILE00.0300.00923.060-0.005-0.0050.0000.0000.0000.000
104A105ALA0-0.0050.00321.538-0.012-0.0120.0000.0000.0000.000
105A106HIS0-0.035-0.02020.517-0.042-0.0420.0000.0000.0000.000
106A107ILE0-0.011-0.00118.729-0.019-0.0190.0000.0000.0000.000
107A108GLU-1-0.971-0.98117.060-0.103-0.1030.0000.0000.0000.000
108A109ASN0-0.119-0.06915.854-0.110-0.1100.0000.0000.0000.000
109A110GLY00.0340.01316.758-0.007-0.0070.0000.0000.0000.000
110A111ALA0-0.048-0.00515.667-0.074-0.0740.0000.0000.0000.000
111A112ALA00.005-0.01711.6670.0570.0570.0000.0000.0000.000
112A113PHE00.0190.01611.480-0.103-0.1030.0000.0000.0000.000
113A114GLN0-0.066-0.0417.9380.1610.1610.0000.0000.0000.000
114A115TRP00.0300.0323.9190.5250.8640.000-0.047-0.2930.000
115A116ALA0-0.013-0.0186.616-0.931-0.9310.0000.0000.0000.000
116A117ASN0-0.012-0.0355.8510.0060.0060.0000.0000.0000.000
117A118ASP-1-0.845-0.9292.065-2.453-0.3773.133-3.045-2.164-0.014
118A119ALA0-0.076-0.0363.1002.7342.5570.0010.599-0.423-0.002
119A120GLN0-0.056-0.0411.830-11.607-23.56721.265-5.349-3.9560.033
120A121ASP-1-0.862-0.9176.0190.7780.7780.0000.0000.0000.000
121A122THR0-0.040-0.0158.654-0.381-0.3810.0000.0000.0000.000
122A123ALA0-0.0070.0048.9130.0230.0230.0000.0000.0000.000
123A124PHE0-0.022-0.0179.1160.0150.0150.0000.0000.0000.000
124A125LEU00.0060.01112.255-0.099-0.0990.0000.0000.0000.000
125A126ALA00.0440.02614.6510.0580.0580.0000.0000.0000.000
126A127HIS00.0030.00116.049-0.113-0.1130.0000.0000.0000.000
127A128VAL0-0.005-0.00918.1190.0470.0470.0000.0000.0000.000
128A129VAL00.0020.01921.405-0.013-0.0130.0000.0000.0000.000
129A130SER0-0.021-0.02923.9090.0190.0190.0000.0000.0000.000
130A131ARG10.9170.96226.1900.1410.1410.0000.0000.0000.000
131A132THR00.0100.01427.6210.0030.0030.0000.0000.0000.000
132A133GLY00.0290.01129.4390.0040.0040.0000.0000.0000.000
133A134SER00.015-0.00431.4800.0020.0020.0000.0000.0000.000
134A135TYR0-0.0080.00927.2490.0070.0070.0000.0000.0000.000
135A136LEU00.0440.00825.1940.0060.0060.0000.0000.0000.000
136A137SER0-0.090-0.05029.5660.0050.0050.0000.0000.0000.000
137A138SER0-0.019-0.01632.7780.0070.0070.0000.0000.0000.000
138A139THR0-0.064-0.02030.7380.0100.0100.0000.0000.0000.000
139A140ALA0-0.015-0.01633.229-0.006-0.0060.0000.0000.0000.000
140A141GLY00.0160.00634.272-0.001-0.0010.0000.0000.0000.000
141A142ILE0-0.046-0.01629.154-0.008-0.0080.0000.0000.0000.000
142A143THR00.0200.01633.2870.0090.0090.0000.0000.0000.000
143A144LEU0-0.027-0.00733.827-0.008-0.0080.0000.0000.0000.000
144A145GLY0-0.040-0.02033.0330.0020.0020.0000.0000.0000.000
145A146ASP-1-0.897-0.94932.257-0.127-0.1270.0000.0000.0000.000
146A147PRO0-0.060-0.03327.608-0.005-0.0050.0000.0000.0000.000
147A148MET0-0.0030.00524.0440.0190.0190.0000.0000.0000.000
148A149ALA0-0.044-0.01521.982-0.027-0.0270.0000.0000.0000.000
149A150TYR0-0.038-0.07620.2330.0240.0240.0000.0000.0000.000
150A151LEU0-0.024-0.01718.897-0.041-0.0410.0000.0000.0000.000
151A152VAL00.0070.01117.3020.0360.0360.0000.0000.0000.000
152A153ALA00.0270.00916.125-0.037-0.0370.0000.0000.0000.000
153A154PRO00.0610.03714.8600.0020.0020.0000.0000.0000.000
154A155PRO00.0160.00417.913-0.036-0.0360.0000.0000.0000.000
155A156LEU0-0.0140.00719.583-0.026-0.0260.0000.0000.0000.000
156A157GLU-1-0.820-0.92614.5120.1220.1220.0000.0000.0000.000
157A158ALA0-0.0060.00417.922-0.047-0.0470.0000.0000.0000.000
158A159THR0-0.038-0.03520.068-0.022-0.0220.0000.0000.0000.000
159A160TYR0-0.028-0.01519.408-0.003-0.0030.0000.0000.0000.000
160A161GLY00.0770.02219.458-0.019-0.0190.0000.0000.0000.000
161A162ILE0-0.024-0.01320.331-0.023-0.0230.0000.0000.0000.000
162A163ASP-1-0.871-0.93423.373-0.099-0.0990.0000.0000.0000.000
163A164ALA00.013-0.00221.315-0.006-0.0060.0000.0000.0000.000
164A165ALA0-0.0200.00121.849-0.018-0.0180.0000.0000.0000.000
165A166LEU0-0.029-0.02223.399-0.005-0.0050.0000.0000.0000.000
166A167LYS10.8270.92326.3350.1040.1040.0000.0000.0000.000
167A168SER0-0.098-0.03723.415-0.010-0.0100.0000.0000.0000.000
168A169ALA0-0.018-0.02225.204-0.012-0.0120.0000.0000.0000.000
169A170ASP-1-0.954-0.96527.123-0.122-0.1220.0000.0000.0000.000
170A171VAL0-0.044-0.02526.634-0.006-0.0060.0000.0000.0000.000
171A172GLN0-0.014-0.00929.7970.0090.0090.0000.0000.0000.000
172A173LEU00.0090.00127.788-0.009-0.0090.0000.0000.0000.000
173A174ALA0-0.036-0.00329.6000.0080.0080.0000.0000.0000.000
174A175THR0-0.020-0.01127.9750.0140.0140.0000.0000.0000.000
175A176TYR00.027-0.00425.628-0.007-0.0070.0000.0000.0000.000
176A177VAL00.0120.01725.8530.0090.0090.0000.0000.0000.000
177A178PRO00.0080.00825.9140.0010.0010.0000.0000.0000.000
178A179PRO0-0.0370.02123.7530.0070.0070.0000.0000.0000.000
179A180PRO0-0.043-0.03124.754-0.001-0.0010.0000.0000.0000.000
180A181SER00.0920.04322.631-0.004-0.0040.0000.0000.0000.000
181A182GLU-1-0.877-0.95325.4360.0710.0710.0000.0000.0000.000
182A183THR00.0410.01320.2020.0170.0170.0000.0000.0000.000
183A184ASN0-0.094-0.04120.7940.0140.0140.0000.0000.0000.000
184A185TYR00.0120.01614.9530.0220.0220.0000.0000.0000.000
185A186SER0-0.061-0.03920.457-0.007-0.0070.0000.0000.0000.000
186A187ALA00.0400.00520.930-0.014-0.0140.0000.0000.0000.000
187A188ALA0-0.003-0.00522.7210.0110.0110.0000.0000.0000.000
188A189PHE0-0.0420.00123.524-0.021-0.0210.0000.0000.0000.000
189A190LEU00.000-0.00524.5030.0130.0130.0000.0000.0000.000
190A191THR00.0750.02426.981-0.016-0.0160.0000.0000.0000.000
191A192GLY00.0800.03929.5780.0020.0020.0000.0000.0000.000
192A193SER00.0230.01229.561-0.009-0.0090.0000.0000.0000.000
193A194GLN00.0900.03625.326-0.030-0.0300.0000.0000.0000.000
194A195ALA0-0.016-0.01125.220-0.020-0.0200.0000.0000.0000.000
195A196ALA00.0180.01324.677-0.022-0.0220.0000.0000.0000.000
196A197CYS00.0310.02124.140-0.004-0.0040.0000.0000.0000.000
197A198LYS10.9370.96416.2820.5760.5760.0000.0000.0000.000
198A199ALA0-0.015-0.00420.142-0.039-0.0390.0000.0000.0000.000
199A200ALA00.0420.02420.929-0.018-0.0180.0000.0000.0000.000
200A201CYS0-0.035-0.01417.6830.0030.0030.0000.0000.0000.000
201A202ASN0-0.025-0.01116.294-0.084-0.0840.0000.0000.0000.000
202A203ALA00.0590.03816.646-0.029-0.0290.0000.0000.0000.000
203A204PHE0-0.053-0.01416.4840.0170.0170.0000.0000.0000.000
204A205THR0-0.001-0.02711.9790.0080.0080.0000.0000.0000.000
205A206ASP-1-0.927-0.95813.439-0.582-0.5820.0000.0000.0000.000
206A207ALA0-0.0060.00615.1470.0390.0390.0000.0000.0000.000
207A208VAL0-0.005-0.00811.9830.0610.0610.0000.0000.0000.000
208A209LEU0-0.006-0.0088.5610.0500.0500.0000.0000.0000.000
209A210GLU-1-1.010-1.00311.713-0.131-0.1310.0000.0000.0000.000
210A211ILE0-0.023-0.00514.5890.0600.0600.0000.0000.0000.000
211A212ALA00.0100.0089.6100.0800.0800.0000.0000.0000.000
212A213ARG10.8650.9419.7430.5370.5370.0000.0000.0000.000
213A214ASN0-0.067-0.03612.0180.0970.0970.0000.0000.0000.000
214A215PRO00.0460.04714.114-0.037-0.0370.0000.0000.0000.000
215A216ILE0-0.040-0.02916.718-0.020-0.0200.0000.0000.0000.000
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