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: 22Y2R

Calculation Name: 4FLE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FLE

Chain ID: A

ChEMBL ID:

UniProt ID: A1JQU0

Base Structure: X-ray

Registration Date: 2023-06-20

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2207047.536616
FMO2-HF: Nuclear repulsion 2130983.40187
FMO2-HF: Total energy -76064.134746
FMO2-MP2: Total energy -76288.20525


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:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
-29.439-21.27919.819-13.625-14.351-0.049
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.017
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].
3A5LEU0-0.012-0.0093.805-1.2611.396-0.022-1.388-1.2470.005
4A6LEU00.0100.0046.318-0.117-0.1170.0000.0000.0000.000
5A7TYR0-0.011-0.0309.4380.0780.0780.0000.0000.0000.000
6A8ILE00.0330.01412.568-0.018-0.0180.0000.0000.0000.000
7A9HIS00.0150.00515.7840.0130.0130.0000.0000.0000.000
8A10GLY00.0260.00619.077-0.002-0.0020.0000.0000.0000.000
9A11PHE00.0670.01322.416-0.005-0.0050.0000.0000.0000.000
10A12ASN00.0060.02725.8930.0000.0000.0000.0000.0000.000
11A13SER00.0040.01522.5810.0020.0020.0000.0000.0000.000
12A14SER00.0510.01921.853-0.003-0.0030.0000.0000.0000.000
13A15PRO00.015-0.00117.5850.0080.0080.0000.0000.0000.000
14A16SER0-0.029-0.00818.6230.0070.0070.0000.0000.0000.000
15A17SER0-0.0340.00219.1810.0130.0130.0000.0000.0000.000
16A18ALA00.0700.02219.4390.0010.0010.0000.0000.0000.000
17A19LYS10.8760.94517.5130.0680.0680.0000.0000.0000.000
18A20ALA00.0230.02315.0060.0090.0090.0000.0000.0000.000
19A21THR00.0280.01014.7130.0150.0150.0000.0000.0000.000
20A22THR0-0.031-0.02716.4220.0110.0110.0000.0000.0000.000
21A23PHE00.0190.0189.8450.0230.0230.0000.0000.0000.000
22A24LYS10.9910.98111.5960.1350.1350.0000.0000.0000.000
23A25SER0-0.067-0.03912.3950.0170.0170.0000.0000.0000.000
24A26TRP00.0560.0259.2800.0120.0120.0000.0000.0000.000
25A27LEU00.0270.0026.250-0.057-0.0570.0000.0000.0000.000
26A28GLN0-0.050-0.0059.4720.0150.0150.0000.0000.0000.000
27A29GLN0-0.032-0.01711.672-0.002-0.0020.0000.0000.0000.000
28A30HIS0-0.086-0.05510.792-0.009-0.0090.0000.0000.0000.000
29A31HIS0-0.011-0.0055.650-0.182-0.1820.0000.0000.0000.000
30A32PRO00.0150.0086.8910.2550.2550.0000.0000.0000.000
31A33HIS0-0.020-0.0134.396-0.264-0.178-0.001-0.008-0.0770.000
32A34ILE0-0.0350.0062.329-5.449-2.8182.714-2.169-3.1760.016
33A35GLU-1-0.823-0.8783.835-3.064-2.3710.006-0.230-0.4680.001
34A36MET0-0.030-0.0025.9380.1680.1680.0000.0000.0000.000
35A37GLN00.0120.0068.598-0.151-0.1510.0000.0000.0000.000
36A38ILE0-0.028-0.01410.5280.0570.0570.0000.0000.0000.000
37A39PRO00.0230.01813.4230.0210.0210.0000.0000.0000.000
38A40GLN0-0.041-0.03316.2950.0240.0240.0000.0000.0000.000
39A41LEU0-0.004-0.01217.624-0.005-0.0050.0000.0000.0000.000
40A42PRO00.0110.02121.1010.0110.0110.0000.0000.0000.000
41A43PRO0-0.025-0.01624.449-0.002-0.0020.0000.0000.0000.000
42A44TYR0-0.019-0.00427.0630.0070.0070.0000.0000.0000.000
43A45PRO00.020-0.00225.015-0.008-0.0080.0000.0000.0000.000
44A46ALA00.0530.03323.991-0.008-0.0080.0000.0000.0000.000
45A47GLU-1-0.850-0.93323.608-0.092-0.0920.0000.0000.0000.000
46A48ALA0-0.016-0.02021.261-0.013-0.0130.0000.0000.0000.000
47A49ALA0-0.007-0.01119.527-0.020-0.0200.0000.0000.0000.000
48A50GLU-1-0.934-0.95718.921-0.119-0.1190.0000.0000.0000.000
49A51MET0-0.031-0.00717.015-0.013-0.0130.0000.0000.0000.000
50A52LEU0-0.053-0.03915.001-0.037-0.0370.0000.0000.0000.000
51A53GLU-1-0.892-0.95414.069-0.167-0.1670.0000.0000.0000.000
52A54SER0-0.007-0.00714.553-0.002-0.0020.0000.0000.0000.000
53A55ILE0-0.032-0.01210.333-0.025-0.0250.0000.0000.0000.000
54A56VAL00.001-0.0069.981-0.103-0.1030.0000.0000.0000.000
55A57MET0-0.021-0.0089.879-0.030-0.0300.0000.0000.0000.000
56A58ASP-1-0.945-0.95510.849-0.282-0.2820.0000.0000.0000.000
57A59LYS10.7870.8665.5271.5081.5080.0000.0000.0000.000
58A60ALA0-0.027-0.0046.0630.0100.0100.0000.0000.0000.000
59A61GLY0-0.050-0.0068.2990.0910.0910.0000.0000.0000.000
60A62GLN0-0.046-0.0263.525-0.348-0.1410.013-0.086-0.1340.000
61A63SER00.0280.0182.164-0.748-0.9972.992-1.413-1.3310.001
62A64ILE00.0350.0122.378-4.307-2.8264.008-3.018-2.470-0.033
63A65GLY00.0170.0194.5970.1790.256-0.001-0.010-0.0660.000
64A66ILE0-0.037-0.0226.5800.0000.0000.0000.0000.0000.000
65A67VAL00.0040.0189.8230.0340.0340.0000.0000.0000.000
66A68GLY00.0460.02612.506-0.014-0.0140.0000.0000.0000.000
67A69SER0-0.037-0.00215.9710.0100.0100.0000.0000.0000.000
68A70SER00.017-0.00919.302-0.005-0.0050.0000.0000.0000.000
69A71LEU00.0020.00022.103-0.002-0.0020.0000.0000.0000.000
70A72GLY00.0530.02518.935-0.004-0.0040.0000.0000.0000.000
71A73GLY0-0.007-0.00617.930-0.012-0.0120.0000.0000.0000.000
72A74TYR0-0.025-0.01919.060-0.002-0.0020.0000.0000.0000.000
73A75PHE00.004-0.00818.1810.0000.0000.0000.0000.0000.000
74A76ALA00.0160.00514.787-0.010-0.0100.0000.0000.0000.000
75A77THR00.0130.01015.547-0.006-0.0060.0000.0000.0000.000
76A78TRP00.0180.00818.024-0.001-0.0010.0000.0000.0000.000
77A79LEU0-0.013-0.01714.1230.0030.0030.0000.0000.0000.000
78A80SER0-0.055-0.02513.6170.0070.0070.0000.0000.0000.000
79A81GLN00.005-0.00414.6580.0150.0150.0000.0000.0000.000
80A82ARG10.9040.96917.7790.0970.0970.0000.0000.0000.000
81A83PHE0-0.034-0.02713.8750.0100.0100.0000.0000.0000.000
82A84SER0-0.029-0.00613.5370.0040.0040.0000.0000.0000.000
83A85ILE0-0.017-0.0038.556-0.005-0.0050.0000.0000.0000.000
84A86PRO00.0170.0218.3570.0230.0230.0000.0000.0000.000
85A87ALA00.039-0.0019.946-0.024-0.0240.0000.0000.0000.000
86A88VAL0-0.037-0.01211.6160.0140.0140.0000.0000.0000.000
87A89VAL0-0.014-0.00513.9930.0000.0000.0000.0000.0000.000
88A90VAL0-0.006-0.02016.7430.0070.0070.0000.0000.0000.000
89A91ASN0-0.001-0.01619.3520.0000.0000.0000.0000.0000.000
90A92PRO00.0020.00620.5320.0000.0000.0000.0000.0000.000
91A93ALA0-0.006-0.00122.4210.0050.0050.0000.0000.0000.000
92A94VAL00.0340.00724.350-0.004-0.0040.0000.0000.0000.000
93A95ARG10.8500.89926.4200.0440.0440.0000.0000.0000.000
94A96PRO00.0310.02425.5520.0030.0030.0000.0000.0000.000
95A97PHE0-0.009-0.00228.4940.0020.0020.0000.0000.0000.000
96A98GLU-1-0.833-0.89831.185-0.040-0.0400.0000.0000.0000.000
97A99LEU00.0310.02030.0170.0010.0010.0000.0000.0000.000
98A100LEU00.000-0.01428.2920.0000.0000.0000.0000.0000.000
99A101SER0-0.037-0.02032.5400.0010.0010.0000.0000.0000.000
100A102ASP-1-0.912-0.94835.791-0.035-0.0350.0000.0000.0000.000
101A103TYR0-0.100-0.05830.478-0.001-0.0010.0000.0000.0000.000
102A104LEU0-0.050-0.00935.469-0.002-0.0020.0000.0000.0000.000
103A105GLY00.0330.02437.1570.0020.0020.0000.0000.0000.000
104A106GLU-1-0.988-0.99436.835-0.039-0.0390.0000.0000.0000.000
105A107ASN0-0.040-0.02033.114-0.001-0.0010.0000.0000.0000.000
106A108GLN00.001-0.02333.2270.0010.0010.0000.0000.0000.000
107A109ASN00.0180.03025.7760.0030.0030.0000.0000.0000.000
108A110PRO0-0.030-0.02129.3990.0000.0000.0000.0000.0000.000
109A111TYR00.0210.00525.7840.0020.0020.0000.0000.0000.000
110A112THR0-0.021-0.00725.3710.0000.0000.0000.0000.0000.000
111A113GLY0-0.016-0.00128.2160.0020.0020.0000.0000.0000.000
112A114GLN0-0.026-0.01827.2080.0050.0050.0000.0000.0000.000
113A115LYS10.9520.97931.4180.0420.0420.0000.0000.0000.000
114A116TYR0-0.025-0.04029.912-0.001-0.0010.0000.0000.0000.000
115A117VAL00.0260.00934.0840.0020.0020.0000.0000.0000.000
116A118LEU0-0.0210.00930.949-0.002-0.0020.0000.0000.0000.000
117A119GLU-1-0.754-0.86734.311-0.042-0.0420.0000.0000.0000.000
118A120SER00.047-0.00134.649-0.002-0.0020.0000.0000.0000.000
119A121ARG10.8200.88033.2110.0500.0500.0000.0000.0000.000
120A122HIS00.0850.06130.685-0.001-0.0010.0000.0000.0000.000
121A123ILE0-0.0030.00630.291-0.004-0.0040.0000.0000.0000.000
122A124TYR0-0.049-0.02031.3340.0000.0000.0000.0000.0000.000
123A125ASP-1-0.847-0.94128.147-0.063-0.0630.0000.0000.0000.000
124A126LEU0-0.014-0.00524.901-0.004-0.0040.0000.0000.0000.000
125A127LYS10.9030.96227.0620.0430.0430.0000.0000.0000.000
126A128ALA0-0.017-0.01028.7780.0010.0010.0000.0000.0000.000
127A129MET0-0.058-0.00921.6360.0000.0000.0000.0000.0000.000
128A130GLN0-0.043-0.02224.249-0.003-0.0030.0000.0000.0000.000
129A131ILE00.0160.02121.2830.0030.0030.0000.0000.0000.000
130A132GLU-1-0.923-0.95525.477-0.041-0.0410.0000.0000.0000.000
131A133LYS10.9020.94426.1180.0430.0430.0000.0000.0000.000
132A134LEU00.0140.01620.866-0.001-0.0010.0000.0000.0000.000
133A135GLU-1-0.877-0.94920.675-0.059-0.0590.0000.0000.0000.000
134A136SER0-0.033-0.02017.4850.0070.0070.0000.0000.0000.000
135A137PRO00.0250.00117.829-0.012-0.0120.0000.0000.0000.000
136A138ASP-1-0.883-0.93517.305-0.069-0.0690.0000.0000.0000.000
137A139LEU0-0.041-0.00312.553-0.014-0.0140.0000.0000.0000.000
138A140LEU0-0.005-0.00813.644-0.018-0.0180.0000.0000.0000.000
139A141TRP0-0.066-0.04113.7080.0020.0020.0000.0000.0000.000
140A142LEU0-0.0320.00016.807-0.002-0.0020.0000.0000.0000.000
141A143LEU00.0080.00716.5350.0040.0040.0000.0000.0000.000
142A144GLN0-0.002-0.02620.474-0.003-0.0030.0000.0000.0000.000
143A145GLN00.0410.02224.0620.0030.0030.0000.0000.0000.000
144A146THR0-0.011-0.02127.0250.0000.0000.0000.0000.0000.000
145A147GLY0-0.046-0.01830.2990.0010.0010.0000.0000.0000.000
146A148ASP-1-0.820-0.90427.294-0.050-0.0500.0000.0000.0000.000
147A149GLU-1-0.925-0.95930.134-0.032-0.0320.0000.0000.0000.000
148A150VAL0-0.087-0.02929.4120.0010.0010.0000.0000.0000.000
149A151LEU0-0.051-0.02926.178-0.001-0.0010.0000.0000.0000.000
150A152ASP-1-0.797-0.89230.278-0.037-0.0370.0000.0000.0000.000
151A153TYR00.052-0.00128.607-0.001-0.0010.0000.0000.0000.000
152A154ARG10.8900.95728.9330.0300.0300.0000.0000.0000.000
153A155GLN0-0.023-0.01329.343-0.001-0.0010.0000.0000.0000.000
154A156ALA00.0400.02024.697-0.001-0.0010.0000.0000.0000.000
155A157VAL0-0.017-0.00525.735-0.002-0.0020.0000.0000.0000.000
156A158ALA00.0050.00727.4100.0000.0000.0000.0000.0000.000
157A159TYR0-0.053-0.04122.783-0.001-0.0010.0000.0000.0000.000
158A160TYR00.002-0.02520.2500.0010.0010.0000.0000.0000.000
159A161THR0-0.0120.00123.6390.0000.0000.0000.0000.0000.000
160A162PRO0-0.085-0.03423.6670.0010.0010.0000.0000.0000.000
161A163CYS0-0.050-0.00119.645-0.002-0.0020.0000.0000.0000.000
162A164ARG10.9500.99915.1390.1170.1170.0000.0000.0000.000
163A165GLN0-0.016-0.03820.179-0.001-0.0010.0000.0000.0000.000
164A166THR0-0.050-0.01620.616-0.001-0.0010.0000.0000.0000.000
165A167VAL0-0.0030.00022.585-0.001-0.0010.0000.0000.0000.000
166A168GLU-1-0.813-0.86623.447-0.047-0.0470.0000.0000.0000.000
167A169SER0-0.002-0.00127.1810.0000.0000.0000.0000.0000.000
168A170GLY0-0.0120.00130.2600.0010.0010.0000.0000.0000.000
169A171GLY00.0440.02128.363-0.002-0.0020.0000.0000.0000.000
170A172ASN00.037-0.00427.725-0.001-0.0010.0000.0000.0000.000
171A173HIS00.0380.02325.709-0.005-0.0050.0000.0000.0000.000
172A174ALA0-0.028-0.00224.702-0.004-0.0040.0000.0000.0000.000
173A175PHE00.0030.01821.317-0.003-0.0030.0000.0000.0000.000
174A176VAL0-0.051-0.03223.2520.0010.0010.0000.0000.0000.000
175A177GLY00.0620.03422.858-0.001-0.0010.0000.0000.0000.000
176A178PHE00.008-0.01014.689-0.002-0.0020.0000.0000.0000.000
177A179ASP-1-0.878-0.95417.133-0.035-0.0350.0000.0000.0000.000
178A180HIS0-0.038-0.00416.8780.0000.0000.0000.0000.0000.000
179A181TYR0-0.055-0.07915.727-0.009-0.0090.0000.0000.0000.000
180A182PHE00.0000.02112.496-0.010-0.0100.0000.0000.0000.000
181A183SER00.0580.01110.8740.0010.0010.0000.0000.0000.000
182A184PRO0-0.012-0.00310.905-0.050-0.0500.0000.0000.0000.000
183A185ILE00.0120.0189.740-0.037-0.0370.0000.0000.0000.000
184A186VAL00.0170.0195.207-0.026-0.0260.0000.0000.0000.000
185A187THR0-0.071-0.0436.914-0.236-0.2360.0000.0000.0000.000
186A188PHE0-0.043-0.0269.266-0.028-0.0280.0000.0000.0000.000
187A189LEU0-0.044-0.0176.5480.0170.0170.0000.0000.0000.000
188A190GLY00.0170.0286.301-0.001-0.0010.0000.0000.0000.000
189A191LEU0-0.049-0.0242.280-2.644-0.6082.097-1.482-2.6500.008
190A192ALA00.0200.0171.849-13.370-14.8918.014-3.805-2.687-0.047
191A193THR00.012-0.0084.5800.5490.611-0.001-0.016-0.0450.000
192A194ALA00.0490.0107.5630.1020.1020.0000.0000.0000.000
193A195LEU0-0.072-0.0139.3050.0200.0200.0000.0000.0000.000
194A196GLU-1-0.852-0.92310.7850.6070.6070.0000.0000.0000.000
195A197HIS0-0.156-0.06910.191-0.038-0.0380.0000.0000.0000.000