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: LZ219

Calculation Name: 3QIV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QIV

Chain ID: A

ChEMBL ID:

UniProt ID: Q743I2

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2060669.408585
FMO2-HF: Nuclear repulsion 1986590.366872
FMO2-HF: Total energy -74079.041713
FMO2-MP2: Total energy -74292.90778


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-1.513.4876.164-3.615-7.545-0.029
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / 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].
3A3PHE0-0.071-0.0343.256-2.362-0.4140.003-0.867-1.0830.002
4A4GLU-1-0.874-0.9322.626-2.979-1.8520.182-0.324-0.984-0.002
5A5ASN0-0.049-0.0234.4460.0320.102-0.001-0.015-0.0540.000
6A6LYS10.9020.9797.7090.0580.0580.0000.0000.0000.000
7A7VAL00.0050.0029.6430.0920.0920.0000.0000.0000.000
8A8GLY00.0000.00312.204-0.006-0.0060.0000.0000.0000.000
9A9ILE00.0000.00513.032-0.016-0.0160.0000.0000.0000.000
10A10VAL00.0150.01114.1150.0290.0290.0000.0000.0000.000
11A11THR00.0340.02917.050-0.030-0.0300.0000.0000.0000.000
12A12GLY00.006-0.00920.4590.0230.0230.0000.0000.0000.000
13A13SER0-0.036-0.04417.4480.0060.0060.0000.0000.0000.000
14A14GLY00.0280.01418.9220.0090.0090.0000.0000.0000.000
15A15GLY00.0330.01521.080-0.023-0.0230.0000.0000.0000.000
16A16GLY0-0.021-0.00921.2520.0180.0180.0000.0000.0000.000
17A17ILE00.020-0.00317.9530.0160.0160.0000.0000.0000.000
18A18GLY00.0470.02117.2210.0640.0640.0000.0000.0000.000
19A19GLN0-0.031-0.00216.3730.0360.0360.0000.0000.0000.000
20A20ALA00.0360.01814.8020.0450.0450.0000.0000.0000.000
21A21TYR0-0.056-0.04912.8640.1500.1500.0000.0000.0000.000
22A22ALA00.0010.00011.5640.1550.1550.0000.0000.0000.000
23A23GLU-1-0.834-0.93110.8900.5250.5250.0000.0000.0000.000
24A24ALA0-0.048-0.0218.9510.1280.1280.0000.0000.0000.000
25A25LEU0-0.018-0.0166.9120.6230.6230.0000.0000.0000.000
26A26ALA00.0180.0146.2060.4130.4130.0000.0000.0000.000
27A27ARG10.9290.9774.949-1.134-1.1340.0000.0000.0000.000
28A28GLU-1-0.850-0.9182.4776.7978.2832.666-1.507-2.645-0.005
29A29GLY00.0600.0102.450-3.747-3.2263.264-1.107-2.678-0.024
30A30ALA0-0.052-0.0074.177-1.043-1.1980.0500.205-0.1010.000
31A31ALA00.0030.0017.4560.0050.0050.0000.0000.0000.000
32A32VAL0-0.034-0.02410.082-0.002-0.0020.0000.0000.0000.000
33A33VAL0-0.032-0.02112.673-0.074-0.0740.0000.0000.0000.000
34A34VAL0-0.017-0.01515.5080.0340.0340.0000.0000.0000.000
35A35ALA00.0350.01017.887-0.043-0.0430.0000.0000.0000.000
36A36ASP-1-0.824-0.92621.1040.2230.2230.0000.0000.0000.000
37A37ILE0-0.0020.01323.962-0.016-0.0160.0000.0000.0000.000
38A38ASN0-0.056-0.03326.125-0.024-0.0240.0000.0000.0000.000
39A39ALA00.0420.00525.0150.0100.0100.0000.0000.0000.000
40A40GLU-1-0.905-0.94124.0750.0740.0740.0000.0000.0000.000
41A41ALA0-0.029-0.01323.385-0.001-0.0010.0000.0000.0000.000
42A42ALA00.0430.01220.5380.0140.0140.0000.0000.0000.000
43A43GLU-1-0.802-0.86019.2740.0830.0830.0000.0000.0000.000
44A44ALA0-0.022-0.01019.192-0.008-0.0080.0000.0000.0000.000
45A45VAL0-0.019-0.00215.461-0.008-0.0080.0000.0000.0000.000
46A46ALA00.012-0.00314.9360.0150.0150.0000.0000.0000.000
47A47LYS10.8370.89814.450-0.059-0.0590.0000.0000.0000.000
48A48GLN0-0.055-0.03412.2900.0030.0030.0000.0000.0000.000
49A49ILE00.0610.0299.436-0.024-0.0240.0000.0000.0000.000
50A50VAL0-0.064-0.0209.854-0.073-0.0730.0000.0000.0000.000
51A51ALA0-0.059-0.03511.261-0.078-0.0780.0000.0000.0000.000
52A52ASP-1-0.919-0.9498.696-0.152-0.1520.0000.0000.0000.000
53A53GLY0-0.055-0.0087.164-0.179-0.1790.0000.0000.0000.000
54A54GLY0-0.0060.0066.192-0.167-0.1670.0000.0000.0000.000
55A55THR0-0.029-0.0217.527-0.073-0.0730.0000.0000.0000.000
56A56ALA00.012-0.00810.1620.1230.1230.0000.0000.0000.000
57A57ILE0-0.0280.01313.198-0.056-0.0560.0000.0000.0000.000
58A58SER0-0.004-0.01316.9720.0400.0400.0000.0000.0000.000
59A59VAL0-0.069-0.04319.721-0.023-0.0230.0000.0000.0000.000
60A60ALA00.0260.01822.8600.0160.0160.0000.0000.0000.000
61A61VAL0-0.039-0.04223.619-0.004-0.0040.0000.0000.0000.000
62A62ASP-1-0.766-0.86526.7960.1210.1210.0000.0000.0000.000
63A63VAL00.0050.04825.172-0.004-0.0040.0000.0000.0000.000
64A64SER0-0.064-0.05928.167-0.003-0.0030.0000.0000.0000.000
65A65ASP-1-0.868-0.92931.1660.0810.0810.0000.0000.0000.000
66A66PRO0-0.013-0.03030.7270.0050.0050.0000.0000.0000.000
67A67GLU-1-0.886-0.94630.3430.0740.0740.0000.0000.0000.000
68A68SER00.0110.03929.1850.0030.0030.0000.0000.0000.000
69A69ALA00.0360.01026.2230.0070.0070.0000.0000.0000.000
70A70LYS10.8850.93125.628-0.069-0.0690.0000.0000.0000.000
71A71ALA00.0360.03126.520-0.001-0.0010.0000.0000.0000.000
72A72MET00.0080.02321.8010.0020.0020.0000.0000.0000.000
73A73ALA0-0.021-0.01121.9500.0060.0060.0000.0000.0000.000
74A74ASP-1-0.920-0.97622.3500.0670.0670.0000.0000.0000.000
75A75ARG10.9410.97821.888-0.084-0.0840.0000.0000.0000.000
76A76THR00.0210.00717.2630.0030.0030.0000.0000.0000.000
77A77LEU0-0.066-0.02019.053-0.008-0.0080.0000.0000.0000.000
78A78ALA0-0.064-0.02220.597-0.016-0.0160.0000.0000.0000.000
79A79GLU-1-0.948-0.96417.6400.0140.0140.0000.0000.0000.000
80A80PHE00.038-0.00114.478-0.001-0.0010.0000.0000.0000.000
81A81GLY0-0.0100.00315.907-0.017-0.0170.0000.0000.0000.000
82A82GLY0-0.081-0.07117.293-0.016-0.0160.0000.0000.0000.000
83A83ILE0-0.017-0.01216.1820.0160.0160.0000.0000.0000.000
84A84ASP-1-0.777-0.85312.5630.0750.0750.0000.0000.0000.000
85A85TYR00.019-0.0109.3200.0130.0130.0000.0000.0000.000
86A86LEU0-0.035-0.00714.600-0.026-0.0260.0000.0000.0000.000
87A87VAL00.0150.01114.4990.0100.0100.0000.0000.0000.000
88A88ASN0-0.033-0.03917.538-0.038-0.0380.0000.0000.0000.000
89A89ASN00.016-0.00719.6850.0120.0120.0000.0000.0000.000
90A90ALA0-0.035-0.00421.633-0.015-0.0150.0000.0000.0000.000
91A91ALA00.0160.00424.468-0.004-0.0040.0000.0000.0000.000
92A92ILE0-0.045-0.00727.617-0.006-0.0060.0000.0000.0000.000
93A93PHE00.0360.00926.032-0.002-0.0020.0000.0000.0000.000
94A94GLY00.0090.00331.820-0.008-0.0080.0000.0000.0000.000
95A95GLY0-0.028-0.02135.109-0.006-0.0060.0000.0000.0000.000
96A96MET00.0810.02436.467-0.003-0.0030.0000.0000.0000.000
97A97LYS10.9420.98537.999-0.105-0.1050.0000.0000.0000.000
98A98LEU0-0.032-0.02537.908-0.005-0.0050.0000.0000.0000.000
99A99ASP-1-0.889-0.92340.9900.1020.1020.0000.0000.0000.000
100A100PHE0-0.071-0.03943.694-0.005-0.0050.0000.0000.0000.000
101A101LEU00.016-0.00942.250-0.002-0.0020.0000.0000.0000.000
102A102LEU0-0.029-0.01145.906-0.002-0.0020.0000.0000.0000.000
103A103THR00.0130.00147.989-0.003-0.0030.0000.0000.0000.000
104A104ILE0-0.096-0.01440.7590.0000.0000.0000.0000.0000.000
105A105ASP-1-0.824-0.92643.2390.0700.0700.0000.0000.0000.000
106A106PRO00.011-0.00443.2040.0050.0050.0000.0000.0000.000
107A107GLU-1-0.891-0.94841.5490.0760.0760.0000.0000.0000.000
108A108TYR0-0.015-0.00435.6360.0070.0070.0000.0000.0000.000
109A109TYR00.006-0.00538.2600.0070.0070.0000.0000.0000.000
110A110LYS10.9840.98238.682-0.069-0.0690.0000.0000.0000.000
111A111LYS10.8690.94033.576-0.099-0.0990.0000.0000.0000.000
112A112PHE0-0.006-0.01834.0630.0090.0090.0000.0000.0000.000
113A113MET0-0.034-0.02033.7750.0110.0110.0000.0000.0000.000
114A114SER00.0020.01634.2110.0060.0060.0000.0000.0000.000
115A115VAL0-0.011-0.01628.7810.0060.0060.0000.0000.0000.000
116A116ASN0-0.006-0.00929.4920.0210.0210.0000.0000.0000.000
117A117LEU0-0.077-0.02629.8370.0110.0110.0000.0000.0000.000
118A118ASP-1-0.870-0.93531.0140.1260.1260.0000.0000.0000.000
119A119GLY00.010-0.03528.033-0.001-0.0010.0000.0000.0000.000
120A120ALA00.023-0.00225.0500.0030.0030.0000.0000.0000.000
121A121LEU0-0.0020.01925.7310.0020.0020.0000.0000.0000.000
122A122TRP00.000-0.00728.041-0.008-0.0080.0000.0000.0000.000
123A123CYS00.0230.01523.106-0.007-0.0070.0000.0000.0000.000
124A124THR00.0210.00623.4630.0070.0070.0000.0000.0000.000
125A125ARG10.8840.92924.527-0.112-0.1120.0000.0000.0000.000
126A126ALA0-0.0310.00125.012-0.012-0.0120.0000.0000.0000.000
127A127VAL00.0470.02020.476-0.013-0.0130.0000.0000.0000.000
128A128TYR00.0240.02222.174-0.015-0.0150.0000.0000.0000.000
129A129LYS10.9170.97123.628-0.079-0.0790.0000.0000.0000.000
130A130LYS10.9050.96321.487-0.104-0.1040.0000.0000.0000.000
131A131MET00.0540.04017.307-0.020-0.0200.0000.0000.0000.000
132A132THR0-0.020-0.02920.136-0.012-0.0120.0000.0000.0000.000
133A133LYS10.8950.95322.342-0.018-0.0180.0000.0000.0000.000
134A134ARG10.8240.90213.111-0.048-0.0480.0000.0000.0000.000
135A135GLY0-0.0070.01617.754-0.021-0.0210.0000.0000.0000.000
136A136GLY0-0.007-0.01118.7170.0010.0010.0000.0000.0000.000
137A137GLY00.0080.00015.968-0.009-0.0090.0000.0000.0000.000
138A138ALA0-0.0320.00214.619-0.004-0.0040.0000.0000.0000.000
139A139ILE0-0.003-0.00716.2970.0140.0140.0000.0000.0000.000
140A140VAL00.0210.01115.951-0.004-0.0040.0000.0000.0000.000
141A141ASN0-0.025-0.01918.803-0.008-0.0080.0000.0000.0000.000
142A142GLN00.0810.05920.2750.0340.0340.0000.0000.0000.000
143A143SER0-0.028-0.02522.658-0.027-0.0270.0000.0000.0000.000
144A144SER0-0.009-0.00625.796-0.005-0.0050.0000.0000.0000.000
145A156LEU00.0370.00336.0090.0030.0030.0000.0000.0000.000
146A157ALA00.0420.01734.7660.0030.0030.0000.0000.0000.000
147A158LYS11.0081.00828.931-0.211-0.2110.0000.0000.0000.000
148A159VAL00.007-0.00630.8600.0090.0090.0000.0000.0000.000
149A160GLY00.0140.02532.969-0.002-0.0020.0000.0000.0000.000
150A161ILE00.0650.03626.385-0.003-0.0030.0000.0000.0000.000
151A162ASN00.0060.01828.2470.0200.0200.0000.0000.0000.000
152A163GLY00.0110.00129.5970.0010.0010.0000.0000.0000.000
153A164LEU0-0.006-0.00728.373-0.003-0.0030.0000.0000.0000.000
154A165THR00.008-0.01424.5640.0040.0040.0000.0000.0000.000
155A166GLN0-0.0010.00226.974-0.009-0.0090.0000.0000.0000.000
156A167GLN00.0040.01129.313-0.011-0.0110.0000.0000.0000.000
157A168LEU00.0300.00626.440-0.007-0.0070.0000.0000.0000.000
158A169SER00.0230.02925.707-0.002-0.0020.0000.0000.0000.000
159A170ARG10.8470.91626.670-0.129-0.1290.0000.0000.0000.000
160A171GLU-1-0.947-0.97329.8570.1020.1020.0000.0000.0000.000
161A172LEU0-0.066-0.03223.555-0.011-0.0110.0000.0000.0000.000
162A173GLY00.0420.02625.8390.0010.0010.0000.0000.0000.000
163A174GLY0-0.034-0.02626.774-0.009-0.0090.0000.0000.0000.000
164A175ARG10.8790.94024.043-0.101-0.1010.0000.0000.0000.000
165A176ASN0-0.010-0.00718.2700.0160.0160.0000.0000.0000.000
166A177ILE0-0.0040.00419.6770.0090.0090.0000.0000.0000.000
167A178ARG10.8120.93514.906-0.429-0.4290.0000.0000.0000.000
168A179ILE0-0.0060.00219.7110.0160.0160.0000.0000.0000.000
169A180ASN0-0.004-0.01319.128-0.046-0.0460.0000.0000.0000.000
170A181ALA00.0110.01521.4330.0100.0100.0000.0000.0000.000
171A182ILE00.0510.03617.7170.0040.0040.0000.0000.0000.000
172A183ALA0-0.024-0.01522.334-0.022-0.0220.0000.0000.0000.000
173A184PRO00.0000.01923.446-0.015-0.0150.0000.0000.0000.000
174A216PRO0-0.015-0.03319.622-0.006-0.0060.0000.0000.0000.000
175A217ASP-1-0.903-0.94314.5940.5900.5900.0000.0000.0000.000
176A218ASP-1-0.850-0.92914.9150.6390.6390.0000.0000.0000.000
177A219LEU0-0.071-0.03816.6420.0340.0340.0000.0000.0000.000
178A220VAL00.0210.01111.5580.0270.0270.0000.0000.0000.000
179A221GLY00.0330.02211.7160.1530.1530.0000.0000.0000.000
180A222MET0-0.019-0.00412.6070.0650.0650.0000.0000.0000.000
181A223CYS0-0.043-0.02513.951-0.025-0.0250.0000.0000.0000.000
182A224LEU00.0410.0077.594-0.077-0.0770.0000.0000.0000.000
183A225PHE00.0160.01510.733-0.018-0.0180.0000.0000.0000.000
184A226LEU0-0.034-0.01212.204-0.119-0.1190.0000.0000.0000.000
185A227LEU0-0.024-0.00311.195-0.127-0.1270.0000.0000.0000.000
186A228SER0-0.047-0.0239.596-0.086-0.0860.0000.0000.0000.000
187A229ASP-1-0.874-0.94510.9000.0900.0900.0000.0000.0000.000
188A230GLU-1-0.930-0.9789.6120.9780.9780.0000.0000.0000.000
189A231ALA0-0.056-0.01113.657-0.053-0.0530.0000.0000.0000.000
190A232SER0-0.001-0.00816.151-0.051-0.0510.0000.0000.0000.000
191A233TRP0-0.014-0.01018.071-0.036-0.0360.0000.0000.0000.000
192A234ILE0-0.056-0.01518.188-0.021-0.0210.0000.0000.0000.000
193A235THR00.042-0.00220.3810.0250.0250.0000.0000.0000.000
194A236GLY0-0.054-0.02822.925-0.020-0.0200.0000.0000.0000.000
195A237GLN0-0.026-0.00423.439-0.018-0.0180.0000.0000.0000.000
196A238ILE0-0.025-0.01824.0000.0150.0150.0000.0000.0000.000
197A239PHE00.0170.00420.853-0.005-0.0050.0000.0000.0000.000
198A240ASN0-0.040-0.02223.7640.0060.0060.0000.0000.0000.000
199A241VAL00.0220.01120.7990.0040.0040.0000.0000.0000.000