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: NNY1Q

Calculation Name: 4QLP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4QLP

Chain ID: A

ChEMBL ID:

UniProt ID: O05442

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1839474.956557
FMO2-HF: Nuclear repulsion 1770146.789591
FMO2-HF: Total energy -69328.166966
FMO2-MP2: Total energy -69530.010607


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:1:THR)


Summations of interaction energy for fragment #1(A:1: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.
-8.69-2.1043.393-3.736-6.241-0.027
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.011
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].
3A3GLY00.0050.0073.871-0.3430.985-0.011-0.521-0.7950.003
4A4VAL00.010-0.0314.9900.2930.451-0.001-0.013-0.1430.000
5A5ASP-1-0.839-0.8552.471-2.813-1.9870.916-0.561-1.181-0.001
6A6LEU0-0.013-0.0142.479-4.685-2.4181.963-1.911-2.321-0.023
7A7SER0-0.016-0.0493.131-1.499-0.1640.517-0.642-1.210-0.006
8A8THR00.0370.0073.933-0.036-0.0260.0110.026-0.0460.000
9A9ASP-1-0.800-0.8526.8890.1190.1190.0000.0000.0000.000
10A10LEU00.0290.0306.288-0.028-0.0280.0000.0000.0000.000
11A11GLN0-0.016-0.0396.1010.0700.0700.0000.0000.0000.000
12A12ASP-1-0.844-0.9048.8920.0500.0500.0000.0000.0000.000
13A13TRP0-0.069-0.01911.5050.0260.0260.0000.0000.0000.000
14A14ILE00.0400.0129.4970.0020.0020.0000.0000.0000.000
15A15ARG10.8250.91311.4130.1530.1530.0000.0000.0000.000
16A16LEU0-0.062-0.04014.9250.0220.0220.0000.0000.0000.000
17A17SER0-0.058-0.03215.9420.0070.0070.0000.0000.0000.000
18A18GLY00.0250.01718.064-0.001-0.0010.0000.0000.0000.000
19A19MET0-0.119-0.03615.3960.0020.0020.0000.0000.0000.000
20A20ASN0-0.052-0.02715.3700.0250.0250.0000.0000.0000.000
21A21MET0-0.006-0.0027.3480.0190.0190.0000.0000.0000.000
22A22ILE0-0.023-0.00411.5500.0950.0950.0000.0000.0000.000
23A23GLN00.0430.0274.012-0.525-0.388-0.001-0.013-0.1220.000
24A24GLY00.0890.0437.1760.2680.2680.0000.0000.0000.000
25A25SER0-0.099-0.0765.6260.4540.4540.0000.0000.0000.000
26A26GLU-1-0.969-0.9728.271-0.006-0.0060.0000.0000.0000.000
27A27THR0-0.078-0.04611.2530.1190.1190.0000.0000.0000.000
28A28ASN0-0.032-0.02913.464-0.024-0.0240.0000.0000.0000.000
29A29ASP-1-0.898-0.95114.635-0.637-0.6370.0000.0000.0000.000
30A30GLY0-0.0030.01711.221-0.032-0.0320.0000.0000.0000.000
31A31ARG10.8030.87810.0960.3020.3020.0000.0000.0000.000
32A32THR00.008-0.0216.3910.0860.0860.0000.0000.0000.000
33A33ILE0-0.030-0.0079.5150.1460.1460.0000.0000.0000.000
34A34LEU00.0330.00710.230-0.006-0.0060.0000.0000.0000.000
35A35TRP0-0.050-0.03614.1680.0300.0300.0000.0000.0000.000
36A36ASN00.1230.06417.8500.0050.0050.0000.0000.0000.000
37A37LYS10.9800.97320.3740.0990.0990.0000.0000.0000.000
38A38GLY0-0.018-0.00923.3120.0060.0060.0000.0000.0000.000
39A39GLY0-0.010-0.00221.739-0.003-0.0030.0000.0000.0000.000
40A40GLU-1-0.941-0.95322.735-0.153-0.1530.0000.0000.0000.000
41A41VAL00.0150.00620.5260.0000.0000.0000.0000.0000.000
42A42ARG10.8690.93618.7600.2770.2770.0000.0000.0000.000
43A43TYR00.023-0.01614.6750.0300.0300.0000.0000.0000.000
44A44PHE0-0.014-0.00413.358-0.010-0.0100.0000.0000.0000.000
45A45ILE00.0060.0048.2990.0660.0660.0000.0000.0000.000
46A46ASP-1-0.805-0.91310.296-0.996-0.9960.0000.0000.0000.000
47A47ARG10.8150.9018.0271.5771.5770.0000.0000.0000.000
48A48LEU00.0240.02512.1150.0900.0900.0000.0000.0000.000
49A49ALA0-0.028-0.03315.8500.0250.0250.0000.0000.0000.000
50A50GLY00.0030.00515.8300.0470.0470.0000.0000.0000.000
51A51TRP0-0.030-0.00413.8870.0070.0070.0000.0000.0000.000
52A52TYR00.0130.0156.926-0.180-0.1800.0000.0000.0000.000
53A53VAL0-0.041-0.02911.5530.1540.1540.0000.0000.0000.000
54A54ILE00.0210.01511.766-0.108-0.1080.0000.0000.0000.000
55A55THR0-0.048-0.04714.3610.0640.0640.0000.0000.0000.000
56A56SER00.0240.00416.649-0.032-0.0320.0000.0000.0000.000
57A57SER0-0.048-0.04119.3500.0160.0160.0000.0000.0000.000
58A58ASP-1-0.725-0.80622.257-0.172-0.1720.0000.0000.0000.000
59A59ARG10.8600.87325.1760.1510.1510.0000.0000.0000.000
60A60MET0-0.045-0.00823.7930.0010.0010.0000.0000.0000.000
61A61SER0-0.064-0.02625.700-0.006-0.0060.0000.0000.0000.000
62A62ARG10.8810.93024.7890.2020.2020.0000.0000.0000.000
63A63GLU-1-0.765-0.83118.635-0.439-0.4390.0000.0000.0000.000
64A64GLY0-0.018-0.00421.8190.0280.0280.0000.0000.0000.000
65A65TYR0-0.045-0.04719.154-0.034-0.0340.0000.0000.0000.000
66A66GLU-1-0.769-0.84417.336-0.250-0.2500.0000.0000.0000.000
67A67PHE00.016-0.00212.9410.0440.0440.0000.0000.0000.000
68A68ALA00.0190.02214.660-0.060-0.0600.0000.0000.0000.000
69A69ALA00.0130.00412.3790.0770.0770.0000.0000.0000.000
70A70ALA00.0460.02812.713-0.096-0.0960.0000.0000.0000.000
71A71SER0-0.026-0.0278.3630.0130.0130.0000.0000.0000.000
72A72MET00.0710.0464.2470.1020.313-0.001-0.018-0.1920.000
73A73SER0-0.0170.0096.6800.1680.1680.0000.0000.0000.000
74A74VAL00.0190.0098.042-0.068-0.0680.0000.0000.0000.000
75A75ILE0-0.017-0.0047.796-0.009-0.0090.0000.0000.0000.000
76A76GLU-1-0.746-0.8514.031-1.047-0.7330.000-0.083-0.2310.000
77A77LYS10.7600.8747.886-0.163-0.1630.0000.0000.0000.000
78A78TYR00.0230.00611.3900.0030.0030.0000.0000.0000.000
79A79LEU0-0.014-0.0078.503-0.002-0.0020.0000.0000.0000.000
80A80TYR0-0.036-0.0658.2370.0030.0030.0000.0000.0000.000
81A81GLY00.0300.01712.6020.0190.0190.0000.0000.0000.000
82A82TYR0-0.042-0.03115.1300.0140.0140.0000.0000.0000.000
83A83PHE00.033-0.00313.135-0.007-0.0070.0000.0000.0000.000
84A84GLY00.0260.01816.1740.0180.0180.0000.0000.0000.000
85A85GLY00.010-0.00517.4580.0170.0170.0000.0000.0000.000
86A86SER00.0090.00519.5000.0050.0050.0000.0000.0000.000
87A87VAL0-0.039-0.01516.2940.0110.0110.0000.0000.0000.000
88A88ARG10.7200.83819.6520.0360.0360.0000.0000.0000.000
89A89SER00.022-0.00622.8770.0050.0050.0000.0000.0000.000
90A90GLU-1-0.914-0.93622.242-0.076-0.0760.0000.0000.0000.000
91A91ARG10.8280.91219.8800.0170.0170.0000.0000.0000.000
92A92GLU-1-0.944-0.96426.297-0.029-0.0290.0000.0000.0000.000
93A93LEU0-0.058-0.00724.8050.0050.0050.0000.0000.0000.000
94A94PRO0-0.0090.00228.346-0.007-0.0070.0000.0000.0000.000
95A95ALA00.0430.01428.2000.0000.0000.0000.0000.0000.000
96A96ILE00.0130.00023.1590.0060.0060.0000.0000.0000.000
97A97ARG10.7110.83027.3270.0300.0300.0000.0000.0000.000
98A98ALA00.0460.02223.1190.0090.0090.0000.0000.0000.000
99A99PRO0-0.038-0.02123.776-0.003-0.0030.0000.0000.0000.000
100A100PHE0-0.009-0.02324.655-0.006-0.0060.0000.0000.0000.000
101A101GLN0-0.040-0.01626.625-0.007-0.0070.0000.0000.0000.000
102A102PRO00.0300.00129.2870.0030.0030.0000.0000.0000.000
103A103GLU-1-0.849-0.92330.020-0.041-0.0410.0000.0000.0000.000
104A104GLU-1-0.746-0.83128.036-0.032-0.0320.0000.0000.0000.000
105A105LEU0-0.039-0.00124.5360.0020.0020.0000.0000.0000.000
106A106MET0-0.040-0.00322.5590.0040.0040.0000.0000.0000.000
107A107PRO00.002-0.00725.452-0.006-0.0060.0000.0000.0000.000
108A108GLU-1-0.878-0.94422.6990.0160.0160.0000.0000.0000.000
109A109TYR0-0.026-0.02319.067-0.007-0.0070.0000.0000.0000.000
110A110SER0-0.028-0.01324.7340.0000.0000.0000.0000.0000.000
111A111ILE00.012-0.00524.389-0.009-0.0090.0000.0000.0000.000
112A112GLY00.0120.01126.0810.0080.0080.0000.0000.0000.000
113A113THR0-0.040-0.02626.626-0.006-0.0060.0000.0000.0000.000
114A114MET0-0.0030.00721.3480.0040.0040.0000.0000.0000.000
115A115THR0-0.015-0.02326.265-0.003-0.0030.0000.0000.0000.000
116A116PHE00.0270.01217.949-0.006-0.0060.0000.0000.0000.000
117A117ALA00.0180.01720.8480.0110.0110.0000.0000.0000.000
118A118GLY00.0230.01722.9830.0060.0060.0000.0000.0000.000
119A119ARG10.9050.96226.4690.1790.1790.0000.0000.0000.000
120A120GLN00.0440.03626.893-0.015-0.0150.0000.0000.0000.000
121A121ARG10.8210.90122.6510.2410.2410.0000.0000.0000.000
122A122ASP-1-0.778-0.87825.105-0.128-0.1280.0000.0000.0000.000
123A123THR0-0.024-0.03522.303-0.017-0.0170.0000.0000.0000.000
124A124LEU00.0190.02718.7160.0160.0160.0000.0000.0000.000
125A125ILE0-0.030-0.01520.782-0.017-0.0170.0000.0000.0000.000
126A126ASP-1-0.730-0.83819.270-0.042-0.0420.0000.0000.0000.000
127A127SER00.0570.01721.912-0.003-0.0030.0000.0000.0000.000
128A128SER0-0.151-0.09021.444-0.003-0.0030.0000.0000.0000.000
129A129GLY0-0.006-0.00624.045-0.003-0.0030.0000.0000.0000.000
130A130THR0-0.070-0.03418.591-0.019-0.0190.0000.0000.0000.000
131A131VAL0-0.021-0.00719.0980.0080.0080.0000.0000.0000.000
132A132VAL00.0240.00616.076-0.027-0.0270.0000.0000.0000.000
133A133ALA0-0.022-0.01915.482-0.041-0.0410.0000.0000.0000.000
134A134ILE00.0030.00917.5730.0300.0300.0000.0000.0000.000
135A135THR0-0.056-0.04419.304-0.028-0.0280.0000.0000.0000.000
136A136ALA00.0090.02321.3670.0130.0130.0000.0000.0000.000
137A137ALA00.055-0.00123.4340.0000.0000.0000.0000.0000.000
138A138ASP-1-0.874-0.92625.046-0.118-0.1180.0000.0000.0000.000
139A139ARG10.8800.93219.6960.2290.2290.0000.0000.0000.000
140A140LEU0-0.060-0.01719.580-0.001-0.0010.0000.0000.0000.000
141A141VAL0-0.0100.01021.4500.0130.0130.0000.0000.0000.000
142A142GLU-1-0.853-0.87920.726-0.093-0.0930.0000.0000.0000.000
143A143LEU0-0.028-0.02514.6710.0120.0120.0000.0000.0000.000
144A144SER0-0.041-0.03517.9730.0250.0250.0000.0000.0000.000
145A145HIS10.8880.92520.1270.0320.0320.0000.0000.0000.000
146A146TYR0-0.040-0.03815.2950.0260.0260.0000.0000.0000.000
147A147LEU0-0.034-0.01014.1140.0330.0330.0000.0000.0000.000
148A148ASP-1-0.902-0.94716.1850.0980.0980.0000.0000.0000.000
149A149VAL00.0060.02917.5040.0280.0280.0000.0000.0000.000
150A150SER0-0.017-0.02115.2690.0140.0140.0000.0000.0000.000
151A151VAL00.0720.0159.980-0.026-0.0260.0000.0000.0000.000
152A152ASN0-0.0090.00113.321-0.031-0.0310.0000.0000.0000.000
153A153VAL00.0710.04415.980-0.024-0.0240.0000.0000.0000.000
154A154ILE0-0.0070.01613.733-0.022-0.0220.0000.0000.0000.000
155A155LYS10.7920.88712.374-0.188-0.1880.0000.0000.0000.000
156A156ASP-1-0.864-0.95316.9800.0930.0930.0000.0000.0000.000
157A157SER0-0.022-0.01320.345-0.009-0.0090.0000.0000.0000.000
158A158PHE0-0.013-0.00817.553-0.010-0.0100.0000.0000.0000.000
159A159LEU0-0.052-0.01719.123-0.007-0.0070.0000.0000.0000.000
160A160ASP-1-0.794-0.88322.8660.0250.0250.0000.0000.0000.000
161A161SER0-0.038-0.03425.900-0.007-0.0070.0000.0000.0000.000
162A162GLU-1-0.815-0.90329.162-0.004-0.0040.0000.0000.0000.000
163A163GLY0-0.0010.01325.697-0.006-0.0060.0000.0000.0000.000
164A164LYS10.8010.90825.368-0.010-0.0100.0000.0000.0000.000
165A165PRO00.031-0.00922.9170.0040.0040.0000.0000.0000.000
166A166LEU0-0.023-0.01719.418-0.006-0.0060.0000.0000.0000.000
167A167PHE00.0160.01920.205-0.007-0.0070.0000.0000.0000.000
168A168THR0-0.038-0.01426.2660.0070.0070.0000.0000.0000.000
169A169LEU00.0310.03229.230-0.007-0.0070.0000.0000.0000.000
170A170TRP00.013-0.00629.0410.0040.0040.0000.0000.0000.000
171A171LYS10.7550.87733.2250.0060.0060.0000.0000.0000.000
172A172ASP-1-0.819-0.89934.441-0.005-0.0050.0000.0000.0000.000
173A173TYR00.0380.02734.0810.0020.0020.0000.0000.0000.000
174A174LYS10.8270.88936.2870.0150.0150.0000.0000.0000.000
175A175GLY00.0040.02938.1700.0000.0000.0000.0000.0000.000