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: QV65Y

Calculation Name: 3PKV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PKV

Chain ID: A

ChEMBL ID:

UniProt ID: E3SET7

Base Structure: X-ray

Registration Date: 2023-09-23

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2693579.915227
FMO2-HF: Nuclear repulsion 2608398.79727
FMO2-HF: Total energy -85181.117956
FMO2-MP2: Total energy -85433.057778


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:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-30.302-56.28365.597-28.109-11.507-0.075
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.069 / q_NPA : -0.072
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].
3A4ILE00.0360.0093.6040.0033.4230.013-1.874-1.5590.006
4A5LYS10.9480.9935.469-0.274-0.2740.0000.0000.0000.000
5A6GLN0-0.059-0.0637.647-0.021-0.0210.0000.0000.0000.000
6A7LEU00.0170.0259.6950.1620.1620.0000.0000.0000.000
7A8THR0-0.019-0.00411.613-0.037-0.0370.0000.0000.0000.000
8A9LEU0-0.009-0.00414.1750.0270.0270.0000.0000.0000.000
9A10TYR0-0.007-0.01317.3030.0050.0050.0000.0000.0000.000
10A11THR00.044-0.00921.039-0.015-0.0150.0000.0000.0000.000
11A12ALA0-0.027-0.01823.8640.0120.0120.0000.0000.0000.000
12A13GLU-1-0.930-0.96926.555-0.082-0.0820.0000.0000.0000.000
13A14LEU00.0180.00524.073-0.013-0.0130.0000.0000.0000.000
14A15ASP-1-0.864-0.92027.047-0.089-0.0890.0000.0000.0000.000
15A16ARG10.8890.93729.4900.1060.1060.0000.0000.0000.000
16A17MET0-0.0520.02221.546-0.015-0.0150.0000.0000.0000.000
17A18LEU00.0480.03925.306-0.022-0.0220.0000.0000.0000.000
18A19ALA0-0.017-0.01126.384-0.013-0.0130.0000.0000.0000.000
19A20PHE0-0.003-0.00923.162-0.005-0.0050.0000.0000.0000.000
20A21TYR00.034-0.02920.342-0.027-0.0270.0000.0000.0000.000
21A22THR0-0.040-0.01424.137-0.019-0.0190.0000.0000.0000.000
22A23ASN0-0.096-0.05026.445-0.011-0.0110.0000.0000.0000.000
23A24MET00.0060.01722.335-0.018-0.0180.0000.0000.0000.000
24A25LEU0-0.042-0.03119.591-0.022-0.0220.0000.0000.0000.000
25A26GLY00.0260.02423.450-0.010-0.0100.0000.0000.0000.000
26A27ALA00.007-0.02124.755-0.008-0.0080.0000.0000.0000.000
27A28GLN0-0.028-0.00723.3480.0320.0320.0000.0000.0000.000
28A29HIS0-0.082-0.04020.219-0.016-0.0160.0000.0000.0000.000
29A30VAL0-0.009-0.00620.401-0.021-0.0210.0000.0000.0000.000
30A31HIS0-0.047-0.01221.7690.0090.0090.0000.0000.0000.000
31A32GLU-1-0.904-0.95323.252-0.094-0.0940.0000.0000.0000.000
32A33GLN0-0.074-0.05221.989-0.003-0.0030.0000.0000.0000.000
33A34ALA0-0.008-0.01126.531-0.002-0.0020.0000.0000.0000.000
34A35ASP-1-0.912-0.95725.900-0.007-0.0070.0000.0000.0000.000
35A36ALA0-0.016-0.01521.9850.0060.0060.0000.0000.0000.000
36A37PHE0-0.0050.01321.857-0.001-0.0010.0000.0000.0000.000
37A38THR0-0.024-0.01117.948-0.005-0.0050.0000.0000.0000.000
38A39ILE00.0300.01816.7100.0040.0040.0000.0000.0000.000
39A40GLN0-0.047-0.04012.9740.0680.0680.0000.0000.0000.000
40A41LEU0-0.008-0.01913.3560.0230.0230.0000.0000.0000.000
41A42GLY00.0800.04912.875-0.169-0.1690.0000.0000.0000.000
42A43VAL0-0.074-0.0367.8910.1670.1670.0000.0000.0000.000
43A44SER0-0.022-0.0068.313-0.108-0.1080.0000.0000.0000.000
44A45GLN0-0.0090.03210.6380.1580.1580.0000.0000.0000.000
45A46ILE00.0280.01312.2000.0200.0200.0000.0000.0000.000
46A47GLN0-0.014-0.00214.6570.0360.0360.0000.0000.0000.000
47A48PHE00.0270.01017.3850.0210.0210.0000.0000.0000.000
48A49ARG10.9080.94319.837-0.005-0.0050.0000.0000.0000.000
49A50ALA00.0540.02122.300-0.009-0.0090.0000.0000.0000.000
50A51ALA0-0.038-0.01024.7340.0140.0140.0000.0000.0000.000
51A52ALA00.0060.00825.6010.0030.0030.0000.0000.0000.000
52A53ASP-1-0.845-0.92028.180-0.021-0.0210.0000.0000.0000.000
53A54GLY0-0.074-0.03831.4650.0060.0060.0000.0000.0000.000
54A55THR0-0.086-0.04326.895-0.001-0.0010.0000.0000.0000.000
55A56LYS10.9710.96327.1810.0580.0580.0000.0000.0000.000
56A57PRO0-0.005-0.00621.890-0.006-0.0060.0000.0000.0000.000
57A58PHE0-0.039-0.01221.392-0.004-0.0040.0000.0000.0000.000
58A59TYR0-0.043-0.04016.1570.0220.0220.0000.0000.0000.000
59A60HIS0-0.045-0.01814.6190.0590.0590.0000.0000.0000.000
60A61ILE00.005-0.01113.309-0.026-0.0260.0000.0000.0000.000
61A62ALA00.0330.03613.2050.0340.0340.0000.0000.0000.000
62A63ILE0-0.010-0.01312.404-0.168-0.1680.0000.0000.0000.000
63A64ASN00.0040.0028.8410.3610.3610.0000.0000.0000.000
64A65ILE0-0.003-0.00213.1340.0510.0510.0000.0000.0000.000
65A66ALA00.0320.00615.424-0.059-0.0590.0000.0000.0000.000
66A67ALA00.0260.02816.6180.0580.0580.0000.0000.0000.000
67A68ASN0-0.013-0.02117.9140.0080.0080.0000.0000.0000.000
68A69HIS00.011-0.01019.7890.0010.0010.0000.0000.0000.000
69A70PHE0-0.0030.01620.4540.0180.0180.0000.0000.0000.000
70A71GLN00.014-0.01022.1800.0220.0220.0000.0000.0000.000
71A72GLU-1-0.866-0.92524.659-0.328-0.3280.0000.0000.0000.000
72A73GLY00.0160.01222.2670.0110.0110.0000.0000.0000.000
73A74LYS10.8400.88723.2820.2720.2720.0000.0000.0000.000
74A75ALA0-0.021-0.01025.3180.0190.0190.0000.0000.0000.000
75A76TRP0-0.030-0.00421.4810.0080.0080.0000.0000.0000.000
76A77LEU00.0300.00822.0420.0120.0120.0000.0000.0000.000
77A78SER0-0.050-0.03325.4680.0220.0220.0000.0000.0000.000
78A79GLY0-0.032-0.00528.7500.0190.0190.0000.0000.0000.000
79A80PHE0-0.057-0.03425.9980.0120.0120.0000.0000.0000.000
80A81GLY0-0.013-0.01528.6710.0110.0110.0000.0000.0000.000
81A82GLU-1-0.975-0.97329.618-0.177-0.1770.0000.0000.0000.000
82A83LEU0-0.035-0.01626.218-0.010-0.0100.0000.0000.0000.000
83A84LEU0-0.028-0.00324.2670.0140.0140.0000.0000.0000.000
84A85THR0-0.023-0.02627.715-0.010-0.0100.0000.0000.0000.000
85A86GLU-1-0.781-0.87926.664-0.160-0.1600.0000.0000.0000.000
86A87ASN0-0.077-0.04729.0440.0050.0050.0000.0000.0000.000
87A88ASP-1-0.931-0.95932.022-0.128-0.1280.0000.0000.0000.000
88A89GLU-1-0.956-0.96229.152-0.184-0.1840.0000.0000.0000.000
89A90ASP-1-0.819-0.90828.659-0.231-0.2310.0000.0000.0000.000
90A91GLN0-0.002-0.00524.792-0.025-0.0250.0000.0000.0000.000
91A92ALA00.0180.01822.4580.0240.0240.0000.0000.0000.000
92A93TYR0-0.047-0.03820.752-0.018-0.0180.0000.0000.0000.000
93A94PHE00.001-0.00218.1080.0430.0430.0000.0000.0000.000
94A95PRO00.030-0.00418.713-0.037-0.0370.0000.0000.0000.000
95A96PHE0-0.088-0.03113.6360.0040.0040.0000.0000.0000.000
96A97PHE00.0580.02211.839-0.028-0.0280.0000.0000.0000.000
97A98ASN0-0.0300.01514.999-0.041-0.0410.0000.0000.0000.000
98A99ALA00.0230.01315.426-0.049-0.0490.0000.0000.0000.000
99A100TYR0-0.036-0.00317.5660.0680.0680.0000.0000.0000.000
100A101SER0-0.009-0.01117.925-0.066-0.0660.0000.0000.0000.000
101A102CYS0-0.040-0.00920.2680.0540.0540.0000.0000.0000.000
102A103TYR00.0550.01519.654-0.037-0.0370.0000.0000.0000.000
103A104VAL00.0270.02922.6830.0250.0250.0000.0000.0000.000
104A105GLU-1-0.918-0.94823.093-0.181-0.1810.0000.0000.0000.000
105A106ASP-1-0.715-0.83121.894-0.216-0.2160.0000.0000.0000.000
106A107PRO0-0.034-0.03924.8090.0180.0180.0000.0000.0000.000
107A108SER0-0.034-0.02423.5960.0240.0240.0000.0000.0000.000
108A109GLY00.000-0.00525.2680.0150.0150.0000.0000.0000.000
109A110ASN0-0.074-0.04219.6580.0120.0120.0000.0000.0000.000
110A111ILE00.0160.01019.7100.0030.0030.0000.0000.0000.000
111A112ILE0-0.0180.00118.506-0.039-0.0390.0000.0000.0000.000
112A113GLU-1-0.777-0.89817.037-0.529-0.5290.0000.0000.0000.000
113A114LEU0-0.050-0.01417.013-0.076-0.0760.0000.0000.0000.000
114A115ILE00.0450.01313.3470.0420.0420.0000.0000.0000.000
115A116SER0-0.056-0.03315.213-0.086-0.0860.0000.0000.0000.000
116A117ARG10.9160.95310.0551.4951.4950.0000.0000.0000.000
117A118GLN0-0.065-0.04614.9110.0250.0250.0000.0000.0000.000
118A119GLN0-0.059-0.03915.7180.0570.0570.0000.0000.0000.000
119A120ALA0-0.0280.00210.2400.0210.0210.0000.0000.0000.000
120A121ALA00.0680.03110.764-0.275-0.2750.0000.0000.0000.000
121A122PRO0-0.0130.00612.0290.1390.1390.0000.0000.0000.000
122A123VAL00.0230.00814.8230.0270.0270.0000.0000.0000.000
123A124LEU0-0.055-0.03216.3600.0130.0130.0000.0000.0000.000
124A125ASP-1-0.951-0.96119.916-0.287-0.2870.0000.0000.0000.000
125A126LYS10.8790.93519.8320.5150.5150.0000.0000.0000.000
126A127PRO00.0030.00724.183-0.019-0.0190.0000.0000.0000.000
127A128PHE00.0170.00919.615-0.021-0.0210.0000.0000.0000.000
128A129SER0-0.011-0.02022.5890.0280.0280.0000.0000.0000.000
129A130ALA00.0870.04521.743-0.042-0.0420.0000.0000.0000.000
130A131ASP-1-0.906-0.94020.089-0.414-0.4140.0000.0000.0000.000
131A132GLN0-0.089-0.04718.542-0.078-0.0780.0000.0000.0000.000
132A133LEU0-0.0090.01216.256-0.062-0.0620.0000.0000.0000.000
133A134LEU0-0.021-0.01711.875-0.012-0.0120.0000.0000.0000.000
134A135SER00.0340.0158.667-0.006-0.0060.0000.0000.0000.000
135A136ILE0-0.0030.0058.6830.2040.2040.0000.0000.0000.000
136A137GLY0-0.010-0.0088.074-0.475-0.4750.0000.0000.0000.000
137A138GLU-1-0.899-0.9599.420-0.768-0.7680.0000.0000.0000.000
138A139ILE00.0140.0168.7680.0680.0680.0000.0000.0000.000
139A140ASN0-0.0030.00611.346-0.009-0.0090.0000.0000.0000.000
140A141ILE0-0.004-0.00810.1480.0520.0520.0000.0000.0000.000
141A142THR00.0100.00313.7220.0000.0000.0000.0000.0000.000
142A143THR0-0.015-0.02116.5160.0260.0260.0000.0000.0000.000
143A144SER0-0.031-0.03118.569-0.016-0.0160.0000.0000.0000.000
144A145ASP-1-0.887-0.94419.7260.1730.1730.0000.0000.0000.000
145A146VAL00.0160.01316.8070.0310.0310.0000.0000.0000.000
146A147GLU-1-0.897-0.93816.6350.2130.2130.0000.0000.0000.000
147A148GLN00.003-0.00317.1820.0460.0460.0000.0000.0000.000
148A149ALA00.003-0.00513.8750.0640.0640.0000.0000.0000.000
149A150ALA00.0330.01212.6760.0860.0860.0000.0000.0000.000
150A151THR0-0.039-0.03112.5400.0900.0900.0000.0000.0000.000
151A152ARG10.7900.86913.066-0.303-0.3030.0000.0000.0000.000
152A153LEU00.0250.0167.6440.1440.1440.0000.0000.0000.000
153A154LYS10.8970.9548.420-0.395-0.3950.0000.0000.0000.000
154A155GLN0-0.071-0.04210.5970.1180.1180.0000.0000.0000.000
155A156ALA0-0.0320.0007.8660.0080.0080.0000.0000.0000.000
156A157GLU-1-0.987-0.9927.0752.2332.2330.0000.0000.0000.000
157A158LEU0-0.0080.0083.6670.2280.4940.003-0.033-0.2360.000
158A159PRO0-0.023-0.0095.341-0.232-0.2320.0000.0000.0000.000
159A160VAL00.0420.0148.425-0.253-0.2530.0000.0000.0000.000
160A161LYS10.9120.95111.395-0.052-0.0520.0000.0000.0000.000
161A162LEU00.0520.00714.928-0.038-0.0380.0000.0000.0000.000
162A163ASP-1-0.957-0.96816.8670.1510.1510.0000.0000.0000.000
163A164GLN0-0.033-0.02517.288-0.036-0.0360.0000.0000.0000.000
164A165ILE0-0.0380.00214.296-0.023-0.0230.0000.0000.0000.000
165A166GLU-1-0.882-0.94618.2660.0320.0320.0000.0000.0000.000
166A167PRO0-0.008-0.01420.195-0.013-0.0130.0000.0000.0000.000
167A168ALA0-0.027-0.01621.523-0.003-0.0030.0000.0000.0000.000
168A169GLY0-0.040-0.02421.414-0.016-0.0160.0000.0000.0000.000
169A170LEU0-0.041-0.01816.4420.0180.0180.0000.0000.0000.000
170A171ASN0-0.017-0.00514.7870.0130.0130.0000.0000.0000.000
171A172PHE00.0030.00512.143-0.015-0.0150.0000.0000.0000.000
172A173ILE0-0.024-0.0127.4990.0600.0600.0000.0000.0000.000
173A174GLY00.0140.0055.862-0.144-0.1440.0000.0000.0000.000
174A175ASP-1-0.898-0.9605.6420.0820.0820.0000.0000.0000.000
175A176GLN0-0.091-0.0414.251-1.806-1.669-0.001-0.011-0.1240.000
176A177ASP-1-0.895-0.9535.639-3.917-3.9170.0000.0000.0000.000
177A178LEU00.0040.0212.855-0.0480.4600.234-0.161-0.5820.000
178A179PHE0-0.044-0.0266.0180.2060.2060.0000.0000.0000.000
179A180LEU00.0070.0016.0150.1050.1050.0000.0000.0000.000
180A181LEU0-0.006-0.0069.2600.0900.0900.0000.0000.0000.000
181A182LEU0-0.0040.01112.5180.0510.0510.0000.0000.0000.000
182A183GLY00.0360.00414.267-0.008-0.0080.0000.0000.0000.000
183A184PRO0-0.0040.02618.0490.0140.0140.0000.0000.0000.000
184A185PRO0-0.006-0.01321.244-0.024-0.0240.0000.0000.0000.000
185A186GLY0-0.028-0.02223.2420.0070.0070.0000.0000.0000.000
186A187ARG10.9290.96723.7900.0840.0840.0000.0000.0000.000
187A188ARG10.7750.87124.6860.1400.1400.0000.0000.0000.000
188A189TRP00.0330.01816.877-0.006-0.0060.0000.0000.0000.000
189A190LEU0-0.018-0.01722.3510.0090.0090.0000.0000.0000.000
190A191PHE0-0.008-0.00523.146-0.020-0.0200.0000.0000.0000.000
191A192SER00.0680.05424.2480.0100.0100.0000.0000.0000.000
192A193GLU-1-0.910-0.95926.249-0.099-0.0990.0000.0000.0000.000
193A194ARG10.8290.93424.9850.1220.1220.0000.0000.0000.000
194A195VAL00.003-0.00825.410-0.011-0.0110.0000.0000.0000.000
195A196ALA0-0.0130.00121.3440.0020.0020.0000.0000.0000.000
196A197VAL0-0.006-0.01022.2460.0190.0190.0000.0000.0000.000
197A198ILE0-0.0190.00320.251-0.011-0.0110.0000.0000.0000.000
198A199TYR00.0080.01019.864-0.002-0.0020.0000.0000.0000.000
199A200PRO0-0.0050.01818.5620.0030.0030.0000.0000.0000.000
200A201LEU00.0040.01312.234-0.037-0.0370.0000.0000.0000.000
201A202GLN0-0.007-0.01013.1870.0020.0020.0000.0000.0000.000
202A203MET00.0050.0106.168-0.259-0.2590.0000.0000.0000.000
203A204GLU-1-0.928-0.9607.7370.7350.7350.0000.0000.0000.000
204A205LEU00.006-0.0082.192-3.019-1.8772.620-1.142-2.6200.011
205A206ASP-1-0.795-0.8631.342-16.701-51.62062.098-23.210-3.969-0.097
206A207ASN00.0030.0042.587-5.120-1.7730.627-1.638-2.3360.005
207A208GLY0-0.020-0.0104.106-0.789-0.6710.003-0.040-0.0810.000
208A209VAL0-0.023-0.0015.240-0.794-0.7940.0000.0000.0000.000
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