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: 94632

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 OptHSide
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 -2062389.708447
FMO2-HF: Nuclear repulsion 1988310.042932
FMO2-HF: Total energy -74079.665515
FMO2-MP2: Total energy -74293.595996


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.
0.382.5899.994-2.707-9.498-0.035
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 : -0.039 / q_NPA : -0.019
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].
3A3PHE0-0.084-0.0423.248-2.407-0.4500.004-0.863-1.0990.002
4A4GLU-1-0.842-0.9122.674-2.017-0.9250.150-0.289-0.953-0.001
5A5ASN0-0.104-0.0504.465-0.0140.041-0.001-0.016-0.0380.000
6A6LYS10.8590.9467.725-0.254-0.2540.0000.0000.0000.000
7A7VAL00.0020.0029.6630.0820.0820.0000.0000.0000.000
8A8GLY0-0.014-0.00112.208-0.005-0.0050.0000.0000.0000.000
9A9ILE00.0000.00213.032-0.027-0.0270.0000.0000.0000.000
10A10VAL00.0160.01314.1150.0310.0310.0000.0000.0000.000
11A11THR00.0340.02717.038-0.036-0.0360.0000.0000.0000.000
12A12GLY0-0.001-0.01020.4410.0220.0220.0000.0000.0000.000
13A13SER0-0.044-0.04317.0460.0030.0030.0000.0000.0000.000
14A14GLY00.0300.01118.2900.0000.0000.0000.0000.0000.000
15A15GLY00.0340.01420.454-0.025-0.0250.0000.0000.0000.000
16A16GLY0-0.021-0.00820.8460.0200.0200.0000.0000.0000.000
17A17ILE00.020-0.00317.5110.0110.0110.0000.0000.0000.000
18A18GLY00.0510.02317.1910.0610.0610.0000.0000.0000.000
19A19GLN0-0.029-0.00715.7380.0400.0400.0000.0000.0000.000
20A20ALA00.0150.00614.2510.0300.0300.0000.0000.0000.000
21A21TYR0-0.051-0.05212.8370.1350.1350.0000.0000.0000.000
22A22ALA00.0080.00111.5410.1540.1540.0000.0000.0000.000
23A23GLU-1-0.783-0.88810.2740.3710.3710.0000.0000.0000.000
24A24ALA0-0.045-0.0158.3660.0400.0400.0000.0000.0000.000
25A25LEU0-0.015-0.0146.8880.6040.6040.0000.0000.0000.000
26A26ALA00.0080.0086.2020.5260.5260.0000.0000.0000.000
27A27ARG10.8620.9294.327-0.944-0.631-0.001-0.046-0.2660.000
28A28GLU-1-0.801-0.8842.4616.4277.0164.965-1.968-3.586-0.010
29A29GLY00.0610.0102.462-1.938-3.1584.776-0.171-3.386-0.026
30A30ALA0-0.058-0.0073.928-0.801-1.3780.1010.646-0.1700.000
31A31ALA00.004-0.0017.473-0.083-0.0830.0000.0000.0000.000
32A32VAL0-0.031-0.0239.9250.0100.0100.0000.0000.0000.000
33A33VAL0-0.025-0.02112.498-0.082-0.0820.0000.0000.0000.000
34A34VAL0-0.017-0.01314.9120.0350.0350.0000.0000.0000.000
35A35ALA00.0210.00717.286-0.040-0.0400.0000.0000.0000.000
36A36ASP-1-0.822-0.92420.8760.1930.1930.0000.0000.0000.000
37A37ILE0-0.0030.01023.530-0.014-0.0140.0000.0000.0000.000
38A38ASN0-0.063-0.03225.561-0.021-0.0210.0000.0000.0000.000
39A39ALA00.0530.00924.4190.0080.0080.0000.0000.0000.000
40A40GLU-1-0.900-0.94523.5210.0380.0380.0000.0000.0000.000
41A41ALA0-0.033-0.01322.819-0.004-0.0040.0000.0000.0000.000
42A42ALA00.0390.01119.9390.0070.0070.0000.0000.0000.000
43A43GLU-1-0.791-0.85818.7090.0360.0360.0000.0000.0000.000
44A44ALA0-0.028-0.01118.691-0.014-0.0140.0000.0000.0000.000
45A45VAL0-0.008-0.00914.781-0.016-0.0160.0000.0000.0000.000
46A46ALA00.0170.00414.393-0.003-0.0030.0000.0000.0000.000
47A47LYS10.8390.89813.975-0.026-0.0260.0000.0000.0000.000
48A48GLN0-0.045-0.02311.2400.0080.0080.0000.0000.0000.000
49A49ILE00.0420.0218.924-0.045-0.0450.0000.0000.0000.000
50A50VAL0-0.055-0.0189.439-0.113-0.1130.0000.0000.0000.000
51A51ALA0-0.060-0.03311.011-0.079-0.0790.0000.0000.0000.000
52A52ASP-1-0.909-0.9498.370-0.354-0.3540.0000.0000.0000.000
53A53GLY0-0.061-0.0147.066-0.243-0.2430.0000.0000.0000.000
54A54GLY0-0.0030.0096.010-0.229-0.2290.0000.0000.0000.000
55A55THR0-0.029-0.0217.1320.0220.0220.0000.0000.0000.000
56A56ALA00.014-0.0069.7730.1270.1270.0000.0000.0000.000
57A57ILE0-0.0580.00212.711-0.053-0.0530.0000.0000.0000.000
58A58SER00.001-0.00716.4870.0400.0400.0000.0000.0000.000
59A59VAL0-0.052-0.04019.182-0.017-0.0170.0000.0000.0000.000
60A60ALA00.0250.01722.3110.0140.0140.0000.0000.0000.000
61A61VAL0-0.027-0.03223.681-0.002-0.0020.0000.0000.0000.000
62A62ASP-1-0.758-0.84026.7550.1100.1100.0000.0000.0000.000
63A63VAL00.0110.02425.110-0.003-0.0030.0000.0000.0000.000
64A64SER0-0.043-0.04928.157-0.001-0.0010.0000.0000.0000.000
65A65ASP-1-0.858-0.92531.1560.0780.0780.0000.0000.0000.000
66A66PRO0-0.018-0.02930.7230.0060.0060.0000.0000.0000.000
67A67GLU-1-0.816-0.88830.3420.0780.0780.0000.0000.0000.000
68A68SER00.0290.03729.4070.0020.0020.0000.0000.0000.000
69A69ALA00.0200.00826.2220.0060.0060.0000.0000.0000.000
70A70LYS10.8060.86525.630-0.069-0.0690.0000.0000.0000.000
71A71ALA00.0170.01826.5280.0000.0000.0000.0000.0000.000
72A72MET00.0090.02821.8390.0040.0040.0000.0000.0000.000
73A73ALA0-0.014-0.00421.9550.0070.0070.0000.0000.0000.000
74A74ASP-1-0.862-0.94122.3630.0780.0780.0000.0000.0000.000
75A75ARG10.8420.92020.610-0.075-0.0750.0000.0000.0000.000
76A76THR00.0190.00217.2830.0020.0020.0000.0000.0000.000
77A77LEU0-0.070-0.02518.994-0.004-0.0040.0000.0000.0000.000
78A78ALA0-0.050-0.01620.609-0.012-0.0120.0000.0000.0000.000
79A79GLU-1-0.843-0.90017.6100.0200.0200.0000.0000.0000.000
80A80PHE00.032-0.00914.2160.0000.0000.0000.0000.0000.000
81A81GLY0-0.0050.01015.919-0.006-0.0060.0000.0000.0000.000
82A82GLY0-0.078-0.06117.313-0.014-0.0140.0000.0000.0000.000
83A83ILE0-0.022-0.01816.1830.0140.0140.0000.0000.0000.000
84A84ASP-1-0.752-0.83112.5190.1650.1650.0000.0000.0000.000
85A85TYR0-0.001-0.0119.2230.0090.0090.0000.0000.0000.000
86A86LEU0-0.030-0.00614.591-0.030-0.0300.0000.0000.0000.000
87A87VAL00.0120.00914.4500.0100.0100.0000.0000.0000.000
88A88ASN0-0.029-0.03417.517-0.039-0.0390.0000.0000.0000.000
89A89ASN00.018-0.01019.7150.0130.0130.0000.0000.0000.000
90A90ALA0-0.0270.00421.608-0.016-0.0160.0000.0000.0000.000
91A91ALA00.0140.00524.448-0.002-0.0020.0000.0000.0000.000
92A92ILE0-0.047-0.01527.593-0.008-0.0080.0000.0000.0000.000
93A93PHE00.0410.01125.953-0.002-0.0020.0000.0000.0000.000
94A94GLY0-0.007-0.00231.792-0.008-0.0080.0000.0000.0000.000
95A95GLY0-0.016-0.01735.076-0.006-0.0060.0000.0000.0000.000
96A96MET00.0750.02336.435-0.002-0.0020.0000.0000.0000.000
97A97LYS10.9130.97237.309-0.093-0.0930.0000.0000.0000.000
98A98LEU0-0.042-0.02737.408-0.004-0.0040.0000.0000.0000.000
99A99ASP-1-0.875-0.92340.9590.0910.0910.0000.0000.0000.000
100A100PHE0-0.064-0.03543.661-0.005-0.0050.0000.0000.0000.000
101A101LEU00.015-0.00742.131-0.002-0.0020.0000.0000.0000.000
102A102LEU0-0.030-0.01145.877-0.001-0.0010.0000.0000.0000.000
103A103THR00.0120.00048.071-0.002-0.0020.0000.0000.0000.000
104A104ILE0-0.093-0.01240.7570.0000.0000.0000.0000.0000.000
105A105ASP-1-0.807-0.91243.2590.0620.0620.0000.0000.0000.000
106A106PRO00.0200.00243.1830.0040.0040.0000.0000.0000.000
107A107GLU-1-0.801-0.89241.5940.0690.0690.0000.0000.0000.000
108A108TYR00.003-0.00235.4030.0060.0060.0000.0000.0000.000
109A109TYR00.007-0.00538.2390.0060.0060.0000.0000.0000.000
110A110LYS10.8740.91738.660-0.062-0.0620.0000.0000.0000.000
111A111LYS10.8310.90933.570-0.090-0.0900.0000.0000.0000.000
112A112PHE0-0.003-0.01534.0470.0090.0090.0000.0000.0000.000
113A113MET0-0.038-0.01833.7510.0110.0110.0000.0000.0000.000
114A114SER0-0.025-0.00934.1880.0060.0060.0000.0000.0000.000
115A115VAL0-0.023-0.02228.7960.0070.0070.0000.0000.0000.000
116A116ASN0-0.011-0.00629.4700.0200.0200.0000.0000.0000.000
117A117LEU0-0.067-0.02429.8100.0110.0110.0000.0000.0000.000
118A118ASP-1-0.826-0.90630.9900.1210.1210.0000.0000.0000.000
119A119GLY00.019-0.01128.0030.0000.0000.0000.0000.0000.000
120A120ALA00.0290.00325.0170.0040.0040.0000.0000.0000.000
121A121LEU00.0010.02325.7140.0050.0050.0000.0000.0000.000
122A122TRP0-0.002-0.00928.028-0.004-0.0040.0000.0000.0000.000
123A123CYS00.0150.01023.160-0.007-0.0070.0000.0000.0000.000
124A124THR00.0300.00323.4530.0100.0100.0000.0000.0000.000
125A125ARG10.8700.93124.515-0.113-0.1130.0000.0000.0000.000
126A126ALA0-0.0230.00025.018-0.010-0.0100.0000.0000.0000.000
127A127VAL00.0460.01820.407-0.011-0.0110.0000.0000.0000.000
128A128TYR00.0310.02222.175-0.012-0.0120.0000.0000.0000.000
129A129LYS10.9050.95923.627-0.091-0.0910.0000.0000.0000.000
130A130LYS10.8220.91621.722-0.108-0.1080.0000.0000.0000.000
131A131MET00.0600.04117.199-0.017-0.0170.0000.0000.0000.000
132A132THR0-0.027-0.02420.140-0.010-0.0100.0000.0000.0000.000
133A133LYS10.8970.95422.456-0.043-0.0430.0000.0000.0000.000
134A134ARG10.8370.89812.958-0.121-0.1210.0000.0000.0000.000
135A135GLY0-0.0010.02017.779-0.014-0.0140.0000.0000.0000.000
136A136GLY0-0.002-0.00418.7150.0010.0010.0000.0000.0000.000
137A137GLY00.0100.00415.960-0.005-0.0050.0000.0000.0000.000
138A138ALA0-0.048-0.00614.605-0.007-0.0070.0000.0000.0000.000
139A139ILE00.006-0.00516.2800.0130.0130.0000.0000.0000.000
140A140VAL00.0180.01015.935-0.005-0.0050.0000.0000.0000.000
141A141ASN0-0.024-0.02518.773-0.012-0.0120.0000.0000.0000.000
142A142GLN00.0780.06520.4440.0370.0370.0000.0000.0000.000
143A143SER0-0.028-0.02422.624-0.024-0.0240.0000.0000.0000.000
144A144SER0-0.007-0.00625.591-0.001-0.0010.0000.0000.0000.000
145A156LEU00.029-0.00136.1120.0040.0040.0000.0000.0000.000
146A157ALA00.0460.01934.9830.0030.0030.0000.0000.0000.000
147A158LYS10.9931.00128.563-0.201-0.2010.0000.0000.0000.000
148A159VAL00.010-0.00130.8230.0100.0100.0000.0000.0000.000
149A160GLY00.0150.02632.934-0.001-0.0010.0000.0000.0000.000
150A161ILE00.0650.03526.320-0.002-0.0020.0000.0000.0000.000
151A162ASN0-0.0010.00928.2150.0190.0190.0000.0000.0000.000
152A163GLY00.0180.00629.5610.0020.0020.0000.0000.0000.000
153A164LEU0-0.006-0.00528.318-0.002-0.0020.0000.0000.0000.000
154A165THR00.014-0.00524.4380.0050.0050.0000.0000.0000.000
155A166GLN0-0.008-0.00126.946-0.007-0.0070.0000.0000.0000.000
156A167GLN0-0.033-0.01329.282-0.008-0.0080.0000.0000.0000.000
157A168LEU00.0440.01326.361-0.005-0.0050.0000.0000.0000.000
158A169SER00.0060.01625.6880.0000.0000.0000.0000.0000.000
159A170ARG10.8630.91826.645-0.134-0.1340.0000.0000.0000.000
160A171GLU-1-0.925-0.94929.8290.1130.1130.0000.0000.0000.000
161A172LEU0-0.062-0.03323.578-0.010-0.0100.0000.0000.0000.000
162A173GLY00.0470.02725.8260.0030.0030.0000.0000.0000.000
163A174GLY0-0.032-0.02626.748-0.009-0.0090.0000.0000.0000.000
164A175ARG10.8730.94124.136-0.119-0.1190.0000.0000.0000.000
165A176ASN0-0.026-0.02218.1910.0160.0160.0000.0000.0000.000
166A177ILE00.0010.00719.6660.0120.0120.0000.0000.0000.000
167A178ARG10.8060.93514.808-0.460-0.4600.0000.0000.0000.000
168A179ILE0-0.0040.00019.6880.0150.0150.0000.0000.0000.000
169A180ASN0-0.004-0.01319.094-0.047-0.0470.0000.0000.0000.000
170A181ALA00.0120.01521.4000.0090.0090.0000.0000.0000.000
171A182ILE00.0420.03117.6210.0040.0040.0000.0000.0000.000
172A183ALA0-0.013-0.01222.293-0.022-0.0220.0000.0000.0000.000
173A184PRO00.0100.02123.282-0.014-0.0140.0000.0000.0000.000
174A216PRO0-0.015-0.03519.9210.0020.0020.0000.0000.0000.000
175A217ASP-1-0.893-0.94014.7090.5240.5240.0000.0000.0000.000
176A218ASP-1-0.858-0.92714.9490.5960.5960.0000.0000.0000.000
177A219LEU0-0.077-0.04116.6420.0400.0400.0000.0000.0000.000
178A220VAL00.0250.01211.4600.0320.0320.0000.0000.0000.000
179A221GLY00.0470.03111.7160.1550.1550.0000.0000.0000.000
180A222MET0-0.023-0.00712.6070.0670.0670.0000.0000.0000.000
181A223CYS0-0.054-0.03213.944-0.017-0.0170.0000.0000.0000.000
182A224LEU00.0580.0187.522-0.070-0.0700.0000.0000.0000.000
183A225PHE00.0050.00910.693-0.006-0.0060.0000.0000.0000.000
184A226LEU0-0.021-0.00512.204-0.108-0.1080.0000.0000.0000.000
185A227LEU0-0.0160.00111.200-0.123-0.1230.0000.0000.0000.000
186A228SER0-0.055-0.0249.638-0.084-0.0840.0000.0000.0000.000
187A229ASP-1-0.841-0.93410.8910.1940.1940.0000.0000.0000.000
188A230GLU-1-0.869-0.9439.3851.0701.0700.0000.0000.0000.000
189A231ALA0-0.046-0.00813.600-0.060-0.0600.0000.0000.0000.000
190A232SER0-0.001-0.01616.151-0.055-0.0550.0000.0000.0000.000
191A233TRP0-0.036-0.01918.071-0.040-0.0400.0000.0000.0000.000
192A234ILE0-0.050-0.01218.157-0.025-0.0250.0000.0000.0000.000
193A235THR00.0640.01720.3490.0270.0270.0000.0000.0000.000
194A236GLY0-0.041-0.01522.893-0.021-0.0210.0000.0000.0000.000
195A237GLN0-0.059-0.02523.372-0.021-0.0210.0000.0000.0000.000
196A238ILE0-0.026-0.02223.9620.0150.0150.0000.0000.0000.000
197A239PHE00.0230.01021.206-0.005-0.0050.0000.0000.0000.000
198A240ASN0-0.047-0.02423.7640.0020.0020.0000.0000.0000.000
199A241VAL00.0260.01520.7310.0040.0040.0000.0000.0000.000