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: K22G3

Calculation Name: 3Q9S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q9S

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RRR8

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 OptAll
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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2435032.333906
FMO2-HF: Nuclear repulsion 2352674.419705
FMO2-HF: Total energy -82357.914201
FMO2-MP2: Total energy -82601.040496


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:3:GLU)


Summations of interaction energy for fragment #1(A:3:GLU)
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.
97.017100.9691.371-2.077-3.2470.003
Interaction energy analysis for fragmet #1(A:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.978 / q_NPA : -0.999
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].
3A5ARG10.8070.8743.866-29.035-27.474-0.013-0.739-0.8090.004
4A6ILE0-0.022-0.0146.327-3.023-3.0230.0000.0000.0000.000
5A7LEU0-0.0210.0029.4040.2900.2900.0000.0000.0000.000
6A8VAL0-0.001-0.00912.608-1.143-1.1430.0000.0000.0000.000
7A9ILE0-0.016-0.01015.025-0.419-0.4190.0000.0000.0000.000
8A10GLH0-0.055-0.07818.561-0.605-0.6050.0000.0000.0000.000
9A11ASP-1-0.858-0.92420.63812.13312.1330.0000.0000.0000.000
10A12ASP-1-0.871-0.92123.42912.22712.2270.0000.0000.0000.000
11A13HIS00.038-0.00921.3631.0391.0390.0000.0000.0000.000
12A14ASP-1-0.903-0.92820.83213.39313.3930.0000.0000.0000.000
13A15ILE0-0.037-0.03220.1690.7000.7000.0000.0000.0000.000
14A16ALA0-0.024-0.01017.7760.8290.8290.0000.0000.0000.000
15A17ASN0-0.043-0.02916.2282.0882.0880.0000.0000.0000.000
16A18VAL0-0.0020.00716.2230.9910.9910.0000.0000.0000.000
17A19LEU00.0060.00015.0120.9480.9480.0000.0000.0000.000
18A20ARG10.8650.92611.170-22.248-22.2480.0000.0000.0000.000
19A21MET0-0.0250.00211.5251.9821.9820.0000.0000.0000.000
20A22ASP-1-0.846-0.92912.13519.75619.7560.0000.0000.0000.000
21A23LEU0-0.063-0.0399.5740.8320.8320.0000.0000.0000.000
22A24THR0-0.018-0.0296.9283.5433.5430.0000.0000.0000.000
23A25ASP-1-0.937-0.9607.37829.11729.1170.0000.0000.0000.000
24A26ALA0-0.103-0.0478.9070.0640.0640.0000.0000.0000.000
25A27GLY0-0.037-0.0144.815-0.115-0.1150.0000.0000.0000.000
26A28TYR0-0.067-0.0343.3933.6344.9110.061-0.533-0.806-0.004
27A29VAL00.0290.0092.185-2.389-1.2771.324-0.797-1.6390.003
28A30VAL00.0020.0114.772-5.128-5.126-0.001-0.0080.0070.000
29A31ASP-1-0.807-0.8898.55721.63921.6390.0000.0000.0000.000
30A32HIS0-0.056-0.02811.375-0.317-0.3170.0000.0000.0000.000
31A33ALA0-0.024-0.00715.069-0.195-0.1950.0000.0000.0000.000
32A34ASP-1-0.797-0.86718.43713.03413.0340.0000.0000.0000.000
33A35SER00.019-0.01321.621-0.764-0.7640.0000.0000.0000.000
34A36ALA00.0650.02422.1120.4740.4740.0000.0000.0000.000
35A37MET0-0.047-0.01923.2100.0710.0710.0000.0000.0000.000
36A38ASN00.012-0.01520.3530.1100.1100.0000.0000.0000.000
37A39GLY00.0420.01418.6040.7030.7030.0000.0000.0000.000
38A40LEU0-0.043-0.03418.9330.4030.4030.0000.0000.0000.000
39A41ILE0-0.033-0.00820.015-0.005-0.0050.0000.0000.0000.000
40A42LYS10.8970.92814.830-18.532-18.5320.0000.0000.0000.000
41A43ALA00.000-0.01215.8130.8080.8080.0000.0000.0000.000
42A44ARG10.8430.93016.926-12.647-12.6470.0000.0000.0000.000
43A45GLU-1-0.976-0.98217.23713.86413.8640.0000.0000.0000.000
44A46ASP-1-0.844-0.92312.14222.35422.3540.0000.0000.0000.000
45A47HIS0-0.049-0.00211.7031.7471.7470.0000.0000.0000.000
46A48PRO0-0.0060.0059.8762.0732.0730.0000.0000.0000.000
47A49ASP-1-0.814-0.8986.64129.28529.2850.0000.0000.0000.000
48A50LEU0-0.051-0.0379.555-1.520-1.5200.0000.0000.0000.000
49A51ILE0-0.0170.00511.7220.5580.5580.0000.0000.0000.000
50A52LEU0-0.006-0.00213.264-0.624-0.6240.0000.0000.0000.000
51A53LEU00.0000.00616.366-0.032-0.0320.0000.0000.0000.000
52A54ASP-1-0.771-0.83720.01912.46512.4650.0000.0000.0000.000
53A55LEU0-0.052-0.02622.486-0.253-0.2530.0000.0000.0000.000
54A56GLY00.0550.04426.088-0.256-0.2560.0000.0000.0000.000
55A57LEU0-0.055-0.02527.215-0.300-0.3000.0000.0000.0000.000
56A58PRO00.0110.01229.964-0.074-0.0740.0000.0000.0000.000
57A59ASP-1-0.750-0.87031.4549.6149.6140.0000.0000.0000.000
58A60PHE0-0.068-0.00732.6030.0440.0440.0000.0000.0000.000
59A61ASP-1-0.816-0.92330.7959.2809.2800.0000.0000.0000.000
60A62GLY0-0.012-0.00428.1200.3410.3410.0000.0000.0000.000
61A63GLY00.006-0.00627.6900.3560.3560.0000.0000.0000.000
62A64ASP-1-0.792-0.85628.70010.11510.1150.0000.0000.0000.000
63A65VAL00.0340.00624.0790.2770.2770.0000.0000.0000.000
64A66VAL00.0230.01523.8580.4620.4620.0000.0000.0000.000
65A67GLN00.0190.00024.3710.1830.1830.0000.0000.0000.000
66A68ARG10.6980.80325.845-9.792-9.7920.0000.0000.0000.000
67A69LEU00.0320.02119.3650.1370.1370.0000.0000.0000.000
68A70ARG10.7950.88319.231-13.099-13.0990.0000.0000.0000.000
69A71LYS10.8190.89823.077-11.366-11.3660.0000.0000.0000.000
70A72ASN0-0.053-0.02724.0900.1500.1500.0000.0000.0000.000
71A73SER00.0480.04019.1060.4060.4060.0000.0000.0000.000
72A74ALA00.0460.01417.651-0.235-0.2350.0000.0000.0000.000
73A75LEU00.0230.02513.3010.3430.3430.0000.0000.0000.000
74A76PRO00.0060.01013.005-1.150-1.1500.0000.0000.0000.000
75A77ILE0-0.012-0.01115.3420.5410.5410.0000.0000.0000.000
76A78ILE0-0.033-0.01114.818-0.718-0.7180.0000.0000.0000.000
77A79VAL0-0.007-0.00518.3250.1800.1800.0000.0000.0000.000
78A80LEU0-0.0100.00118.471-0.233-0.2330.0000.0000.0000.000
79A81THR00.014-0.02922.381-0.401-0.4010.0000.0000.0000.000
80A82ALA00.0260.02326.2320.1170.1170.0000.0000.0000.000
81A83ARG10.7530.83929.047-9.839-9.8390.0000.0000.0000.000
82A84ASP-1-0.777-0.88129.8889.9329.9320.0000.0000.0000.000
83A85THR0-0.063-0.04431.010-0.052-0.0520.0000.0000.0000.000
84A86VAL00.0320.00931.9080.2790.2790.0000.0000.0000.000
85A87GLU-1-0.819-0.91232.7568.3848.3840.0000.0000.0000.000
86A88GLU-1-0.703-0.79828.84710.06810.0680.0000.0000.0000.000
87A89LYS10.8140.90227.781-9.578-9.5780.0000.0000.0000.000
88A90VAL0-0.007-0.00828.4300.2010.2010.0000.0000.0000.000
89A91ARG10.7890.87230.036-9.571-9.5710.0000.0000.0000.000
90A92LEU00.0010.00025.3930.1170.1170.0000.0000.0000.000
91A93LEU00.0070.01623.7910.2510.2510.0000.0000.0000.000
92A94GLY0-0.032-0.02026.4290.0390.0390.0000.0000.0000.000
93A95LEU0-0.091-0.03827.809-0.139-0.1390.0000.0000.0000.000
94A96GLY00.0050.01425.2450.1310.1310.0000.0000.0000.000
95A97ALA00.0150.02021.8100.5300.5300.0000.0000.0000.000
96A98ASP-1-0.781-0.87718.32714.05714.0570.0000.0000.0000.000
97A99ASP-1-0.767-0.87218.89613.52713.5270.0000.0000.0000.000
98A100TYR0-0.050-0.04220.733-0.031-0.0310.0000.0000.0000.000
99A101LEU0-0.024-0.01518.6940.2120.2120.0000.0000.0000.000
100A102ILE0-0.0100.00322.125-0.124-0.1240.0000.0000.0000.000
101A103LYS10.8650.92723.432-11.868-11.8680.0000.0000.0000.000
102A104PRO0-0.029-0.04225.663-0.412-0.4120.0000.0000.0000.000
103A105PHE00.0360.01718.793-0.229-0.2290.0000.0000.0000.000
104A106HIS0-0.0060.00320.1610.3040.3040.0000.0000.0000.000
105A107PRO00.0650.02116.8150.1150.1150.0000.0000.0000.000
106A108ASP-1-0.846-0.93616.38217.48217.4820.0000.0000.0000.000
107A109GLU-1-0.929-0.95917.07012.80312.8030.0000.0000.0000.000
108A110LEU00.0020.00514.353-0.008-0.0080.0000.0000.0000.000
109A111LEU00.0090.00911.0750.7030.7030.0000.0000.0000.000
110A112ALA0-0.044-0.01712.9490.6640.6640.0000.0000.0000.000
111A113ARG10.8290.89015.195-14.101-14.1010.0000.0000.0000.000
112A114VAL00.0450.0209.751-0.154-0.1540.0000.0000.0000.000
113A115LYS10.9730.98710.034-20.626-20.6260.0000.0000.0000.000
114A116VAL0-0.055-0.02311.711-0.212-0.2120.0000.0000.0000.000
115A117GLN00.007-0.00113.630-0.780-0.7800.0000.0000.0000.000
116A118LEU0-0.0010.0177.195-0.247-0.2470.0000.0000.0000.000
117A119ARG10.7680.8969.590-14.052-14.0520.0000.0000.0000.000
118A120GLN00.0440.0198.521-1.651-1.6510.0000.0000.0000.000
119A121ARG10.8280.89211.882-16.768-16.7680.0000.0000.0000.000
120A122THR0-0.007-0.01914.794-0.199-0.1990.0000.0000.0000.000
121A123SER0-0.065-0.03918.233-0.189-0.1890.0000.0000.0000.000
122A124GLU-1-0.789-0.85719.67914.61014.6100.0000.0000.0000.000
123A125SER00.008-0.00621.475-0.025-0.0250.0000.0000.0000.000
124A126LEU0-0.0220.01122.959-0.379-0.3790.0000.0000.0000.000
125A127SER0-0.030-0.03426.1520.0930.0930.0000.0000.0000.000
126A128MET0-0.041-0.01329.260-0.253-0.2530.0000.0000.0000.000
127A129GLY00.0220.02032.559-0.146-0.1460.0000.0000.0000.000
128A130ASP-1-0.860-0.95132.4178.6668.6660.0000.0000.0000.000
129A131LEU0-0.0190.01328.6480.2340.2340.0000.0000.0000.000
130A132THR0-0.034-0.01826.0650.0940.0940.0000.0000.0000.000
131A133LEU00.019-0.00223.2750.1590.1590.0000.0000.0000.000
132A134ASP-1-0.736-0.86217.70014.63414.6340.0000.0000.0000.000
133A135PRO0-0.057-0.04918.7130.4310.4310.0000.0000.0000.000
134A136GLN0-0.060-0.03313.6901.0011.0010.0000.0000.0000.000
135A137LYS10.8970.94313.463-13.971-13.9710.0000.0000.0000.000
136A138ARG10.7830.89515.092-14.881-14.8810.0000.0000.0000.000
137A139LEU00.0420.04617.318-0.342-0.3420.0000.0000.0000.000
138A140VAL00.000-0.02319.808-0.221-0.2210.0000.0000.0000.000
139A141THR0-0.042-0.01223.626-0.023-0.0230.0000.0000.0000.000
140A142TYR0-0.003-0.03226.593-0.136-0.1360.0000.0000.0000.000
141A143LYS10.8210.91030.392-7.927-7.9270.0000.0000.0000.000
142A144GLY0-0.037-0.01130.465-0.176-0.1760.0000.0000.0000.000
143A145GLU-1-0.861-0.90628.66710.33110.3310.0000.0000.0000.000
144A146GLU-1-0.894-0.93921.77512.43812.4380.0000.0000.0000.000
145A147LEU00.007-0.01024.532-0.253-0.2530.0000.0000.0000.000
146A148ARG10.8090.89622.446-10.753-10.7530.0000.0000.0000.000
147A149LEU0-0.054-0.01623.079-0.380-0.3800.0000.0000.0000.000
148A150SER00.0590.02621.1580.6020.6020.0000.0000.0000.000
149A151PRO00.0330.00717.481-0.361-0.3610.0000.0000.0000.000
150A152LYS10.8680.93119.039-14.024-14.0240.0000.0000.0000.000
151A153GLU-1-0.810-0.88823.06310.49510.4950.0000.0000.0000.000
152A154PHE00.0080.00220.918-0.303-0.3030.0000.0000.0000.000
153A155ASP-1-0.810-0.89520.58713.25413.2540.0000.0000.0000.000
154A156ILE0-0.023-0.01223.653-0.388-0.3880.0000.0000.0000.000
155A157LEU00.0070.00526.424-0.330-0.3300.0000.0000.0000.000
156A158ALA00.0250.00524.127-0.253-0.2530.0000.0000.0000.000
157A159LEU0-0.061-0.02326.135-0.140-0.1400.0000.0000.0000.000
158A160LEU0-0.0090.00128.129-0.306-0.3060.0000.0000.0000.000
159A161ILE00.008-0.00428.473-0.230-0.2300.0000.0000.0000.000
160A162ARG10.9360.97422.523-11.624-11.6240.0000.0000.0000.000
161A163GLN0-0.032-0.00429.901-0.364-0.3640.0000.0000.0000.000
162A164PRO00.0400.02033.401-0.182-0.1820.0000.0000.0000.000
163A165GLY0-0.0060.00835.506-0.140-0.1400.0000.0000.0000.000
164A166ARG10.7820.88133.597-8.748-8.7480.0000.0000.0000.000
165A167VAL0-0.001-0.00636.4700.1550.1550.0000.0000.0000.000
166A168TYR0-0.020-0.02031.055-0.106-0.1060.0000.0000.0000.000
167A169SER0-0.033-0.05135.931-0.034-0.0340.0000.0000.0000.000
168A170ARG10.8900.90834.832-7.565-7.5650.0000.0000.0000.000
169A171GLN0-0.034-0.01533.8110.2160.2160.0000.0000.0000.000
170A172GLU-1-0.723-0.81632.7668.4388.4380.0000.0000.0000.000
171A173ILE0-0.008-0.00329.7760.3290.3290.0000.0000.0000.000
172A174GLY00.010-0.00228.9230.3540.3540.0000.0000.0000.000
173A175GLN00.0080.00427.9420.2110.2110.0000.0000.0000.000
174A176GLU-1-0.921-0.96125.85011.14311.1430.0000.0000.0000.000
175A177ILE0-0.037-0.01124.3440.5080.5080.0000.0000.0000.000
176A178TRP00.012-0.01023.2430.3170.3170.0000.0000.0000.000
177A179GLN0-0.016-0.01320.5690.8610.8610.0000.0000.0000.000
178A180GLY00.0110.01424.5320.1170.1170.0000.0000.0000.000
179A181ARG10.7940.89921.765-12.601-12.6010.0000.0000.0000.000
180A182LEU00.0160.02425.807-0.068-0.0680.0000.0000.0000.000
181A183PRO0-0.0110.00128.491-0.221-0.2210.0000.0000.0000.000
182A184GLU-1-0.838-0.90932.0228.2548.2540.0000.0000.0000.000
183A185GLY0-0.026-0.01334.808-0.075-0.0750.0000.0000.0000.000
184A186SER0-0.027-0.01133.199-0.083-0.0830.0000.0000.0000.000
185A187ASN00.008-0.00935.220-0.019-0.0190.0000.0000.0000.000
186A188VAL00.0340.02928.524-0.023-0.0230.0000.0000.0000.000
187A189VAL00.0400.02730.8060.1790.1790.0000.0000.0000.000
188A190ASP-1-0.845-0.91431.9558.0838.0830.0000.0000.0000.000
189A191VAL00.0140.00931.030-0.097-0.0970.0000.0000.0000.000
190A192HIS00.0000.01126.2210.3440.3440.0000.0000.0000.000
191A193MET0-0.004-0.00830.2330.0720.0720.0000.0000.0000.000
192A194ALA0-0.074-0.03532.899-0.158-0.1580.0000.0000.0000.000
193A195ASN0-0.025-0.01929.806-0.087-0.0870.0000.0000.0000.000
194A196LEU00.0420.02028.084-0.009-0.0090.0000.0000.0000.000
195A197ARG10.9150.95030.996-8.157-8.1570.0000.0000.0000.000
196A198ALA0-0.012-0.00933.413-0.130-0.1300.0000.0000.0000.000
197A199LYS10.7960.89026.103-10.822-10.8220.0000.0000.0000.000
198A200LEU00.0200.01428.8660.1340.1340.0000.0000.0000.000
199A201ARG10.8060.90832.909-7.479-7.4790.0000.0000.0000.000
200A202ASP-1-0.732-0.80536.5637.7287.7280.0000.0000.0000.000
201A203LEU00.005-0.00239.016-0.119-0.1190.0000.0000.0000.000
202A204ASP-1-0.900-0.94841.9486.3496.3490.0000.0000.0000.000
203A205GLY0-0.019-0.00245.3340.0050.0050.0000.0000.0000.000
204A206TYR0-0.059-0.05140.5310.0650.0650.0000.0000.0000.000
205A207GLY00.032-0.00345.816-0.174-0.1740.0000.0000.0000.000
206A208LEU0-0.018-0.01245.7850.1440.1440.0000.0000.0000.000
207A209LEU0-0.021-0.02345.4420.1320.1320.0000.0000.0000.000
208A210ARG10.9160.97839.648-7.207-7.2070.0000.0000.0000.000
209A211THR00.0440.01842.5470.1200.1200.0000.0000.0000.000
210A212VAL00.0090.02037.3160.1590.1590.0000.0000.0000.000