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: 7G9GK

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2206606.328794
FMO2-HF: Nuclear repulsion 2130542.823217
FMO2-HF: Total energy -76063.505577
FMO2-MP2: Total energy -76287.599713


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.
-26.364-18.22617.613-12.299-13.452-0.046
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 : -0.004 / q_NPA : -0.004
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].
3A5LEU0-0.009-0.0113.805-1.4041.186-0.021-1.367-1.2030.005
4A6LEU00.0160.0066.0930.0550.0550.0000.0000.0000.000
5A7TYR00.001-0.0199.2890.0840.0840.0000.0000.0000.000
6A8ILE00.0270.01112.3720.0110.0110.0000.0000.0000.000
7A9HIS00.0110.00215.6310.0120.0120.0000.0000.0000.000
8A10GLY00.0280.00618.8910.0010.0010.0000.0000.0000.000
9A11PHE00.0770.02122.249-0.003-0.0030.0000.0000.0000.000
10A12ASN00.0220.02825.7340.0010.0010.0000.0000.0000.000
11A13SER0-0.0060.01822.3980.0000.0000.0000.0000.0000.000
12A14SER00.0460.00521.5980.0020.0020.0000.0000.0000.000
13A15PRO00.0240.00717.6820.0010.0010.0000.0000.0000.000
14A16SER0-0.020-0.00618.6390.0030.0030.0000.0000.0000.000
15A17SER0-0.050-0.00519.0960.0140.0140.0000.0000.0000.000
16A18ALA00.0650.02019.487-0.005-0.0050.0000.0000.0000.000
17A19LYS10.8700.93317.5030.1540.1540.0000.0000.0000.000
18A20ALA00.0290.02715.086-0.009-0.0090.0000.0000.0000.000
19A21THR00.0220.01014.7400.0010.0010.0000.0000.0000.000
20A22THR0-0.022-0.02416.3960.0070.0070.0000.0000.0000.000
21A23PHE00.0280.01810.1920.0140.0140.0000.0000.0000.000
22A24LYS11.0000.98211.5640.1770.1770.0000.0000.0000.000
23A25SER0-0.062-0.02812.3080.0300.0300.0000.0000.0000.000
24A26TRP00.0460.0239.3600.0120.0120.0000.0000.0000.000
25A27LEU00.017-0.0106.614-0.036-0.0360.0000.0000.0000.000
26A28GLN0-0.0320.0099.2920.0410.0410.0000.0000.0000.000
27A29GLN0-0.046-0.02211.5110.0170.0170.0000.0000.0000.000
28A30HIS0-0.077-0.05210.7580.0210.0210.0000.0000.0000.000
29A31HIS0-0.017-0.0055.448-0.211-0.2110.0000.0000.0000.000
30A32PRO00.0200.0136.7000.2710.2710.0000.0000.0000.000
31A33HIS0-0.022-0.0164.453-0.247-0.158-0.001-0.007-0.0800.000
32A34ILE0-0.0260.0122.079-3.393-2.3474.200-2.182-3.0650.014
33A35GLU-1-0.892-0.9433.838-2.916-2.2010.014-0.199-0.5290.001
34A36MET0-0.043-0.0115.795-0.034-0.0340.0000.0000.0000.000
35A37GLN00.0190.0048.576-0.068-0.0680.0000.0000.0000.000
36A38ILE0-0.037-0.01510.5280.0320.0320.0000.0000.0000.000
37A39PRO00.0110.01513.4420.0400.0400.0000.0000.0000.000
38A40GLN0-0.026-0.02716.2950.0160.0160.0000.0000.0000.000
39A41LEU0-0.014-0.02317.4170.0010.0010.0000.0000.0000.000
40A42PRO00.0160.02821.0780.0110.0110.0000.0000.0000.000
41A43PRO0-0.025-0.01924.461-0.005-0.0050.0000.0000.0000.000
42A44TYR0-0.006-0.00127.0740.0060.0060.0000.0000.0000.000
43A45PRO00.017-0.00424.982-0.008-0.0080.0000.0000.0000.000
44A46ALA00.0560.03423.988-0.010-0.0100.0000.0000.0000.000
45A47GLU-1-0.853-0.93723.613-0.102-0.1020.0000.0000.0000.000
46A48ALA0-0.018-0.02321.244-0.013-0.0130.0000.0000.0000.000
47A49ALA0-0.014-0.01519.531-0.024-0.0240.0000.0000.0000.000
48A50GLU-1-0.927-0.94918.923-0.122-0.1220.0000.0000.0000.000
49A51MET0-0.032-0.00817.165-0.008-0.0080.0000.0000.0000.000
50A52LEU0-0.048-0.03414.915-0.037-0.0370.0000.0000.0000.000
51A53GLU-1-0.898-0.95814.074-0.174-0.1740.0000.0000.0000.000
52A54SER0-0.011-0.00914.5650.0060.0060.0000.0000.0000.000
53A55ILE0-0.032-0.00410.276-0.011-0.0110.0000.0000.0000.000
54A56VAL0-0.014-0.0109.999-0.085-0.0850.0000.0000.0000.000
55A57MET0-0.022-0.0119.892-0.001-0.0010.0000.0000.0000.000
56A58ASP-1-0.935-0.95010.806-0.177-0.1770.0000.0000.0000.000
57A59LYS10.8510.9075.4881.1251.1250.0000.0000.0000.000
58A60ALA0-0.0180.0016.0780.0520.0520.0000.0000.0000.000
59A61GLY0-0.052-0.0078.3150.0760.0760.0000.0000.0000.000
60A62GLN0-0.047-0.0243.415-0.240-0.0260.015-0.089-0.1410.000
61A63SER00.0240.0162.135-1.021-0.9472.426-1.218-1.2820.001
62A64ILE00.0390.0152.335-4.628-3.1694.029-3.093-2.394-0.030
63A65GLY00.0250.0204.7290.2800.344-0.001-0.009-0.0530.000
64A66ILE0-0.037-0.0176.576-0.021-0.0210.0000.0000.0000.000
65A67VAL0-0.0030.0149.7440.0440.0440.0000.0000.0000.000
66A68GLY00.0370.01512.3550.0010.0010.0000.0000.0000.000
67A69SER0-0.031-0.00315.8320.0110.0110.0000.0000.0000.000
68A70SER00.0220.00319.1330.0010.0010.0000.0000.0000.000
69A71LEU0-0.002-0.00421.984-0.004-0.0040.0000.0000.0000.000
70A72GLY00.0560.02718.799-0.001-0.0010.0000.0000.0000.000
71A73GLY0-0.008-0.00717.839-0.021-0.0210.0000.0000.0000.000
72A74TYR0-0.027-0.01618.968-0.003-0.0030.0000.0000.0000.000
73A75PHE00.003-0.01018.1750.0020.0020.0000.0000.0000.000
74A76ALA00.0230.00714.632-0.009-0.0090.0000.0000.0000.000
75A77THR00.0220.01715.565-0.012-0.0120.0000.0000.0000.000
76A78TRP00.0110.00818.0550.0010.0010.0000.0000.0000.000
77A79LEU0-0.013-0.01913.8970.0070.0070.0000.0000.0000.000
78A80SER0-0.069-0.03313.7200.0190.0190.0000.0000.0000.000
79A81GLN00.0230.01414.7520.0260.0260.0000.0000.0000.000
80A82ARG10.9080.96317.9140.1210.1210.0000.0000.0000.000
81A83PHE0-0.034-0.03113.8300.0230.0230.0000.0000.0000.000
82A84SER0-0.023-0.00413.6120.0100.0100.0000.0000.0000.000
83A85ILE0-0.020-0.0058.694-0.006-0.0060.0000.0000.0000.000
84A86PRO00.0160.0258.3910.0340.0340.0000.0000.0000.000
85A87ALA00.0470.0019.979-0.064-0.0640.0000.0000.0000.000
86A88VAL0-0.028-0.00411.8150.0370.0370.0000.0000.0000.000
87A89VAL0-0.025-0.00913.904-0.002-0.0020.0000.0000.0000.000
88A90VAL00.009-0.01916.5790.0140.0140.0000.0000.0000.000
89A91ASN00.007-0.01419.1970.0050.0050.0000.0000.0000.000
90A92PRO0-0.021-0.00520.3970.0030.0030.0000.0000.0000.000
91A93ALA00.0040.00422.3150.0110.0110.0000.0000.0000.000
92A94VAL00.0330.00724.290-0.005-0.0050.0000.0000.0000.000
93A95ARG10.8710.93126.3760.0750.0750.0000.0000.0000.000
94A96PRO00.0300.02525.6070.0050.0050.0000.0000.0000.000
95A97PHE0-0.001-0.00328.5710.0040.0040.0000.0000.0000.000
96A98GLU-1-0.892-0.94731.138-0.064-0.0640.0000.0000.0000.000
97A99LEU00.0450.02530.0120.0020.0020.0000.0000.0000.000
98A100LEU0-0.005-0.01928.2960.0010.0010.0000.0000.0000.000
99A101SER0-0.037-0.01832.4410.0030.0030.0000.0000.0000.000
100A102ASP-1-0.907-0.94535.703-0.056-0.0560.0000.0000.0000.000
101A103TYR0-0.104-0.05730.370-0.001-0.0010.0000.0000.0000.000
102A104LEU0-0.051-0.01335.135-0.001-0.0010.0000.0000.0000.000
103A105GLY00.0320.02437.0530.0030.0030.0000.0000.0000.000
104A106GLU-1-0.989-1.00036.713-0.050-0.0500.0000.0000.0000.000
105A107ASN0-0.034-0.01332.997-0.002-0.0020.0000.0000.0000.000
106A108GLN00.006-0.02333.0350.0030.0030.0000.0000.0000.000
107A109ASN0-0.0030.02725.6320.0010.0010.0000.0000.0000.000
108A110PRO0-0.036-0.02429.2120.0020.0020.0000.0000.0000.000
109A111TYR00.011-0.00525.4300.0010.0010.0000.0000.0000.000
110A112THR0-0.0280.00025.4630.0030.0030.0000.0000.0000.000
111A113GLY0-0.0030.00328.2160.0040.0040.0000.0000.0000.000
112A114GLN0-0.010-0.00827.3970.0070.0070.0000.0000.0000.000
113A115LYS10.9360.96531.4180.0510.0510.0000.0000.0000.000
114A116TYR0-0.022-0.03330.008-0.001-0.0010.0000.0000.0000.000
115A117VAL00.0300.01434.0730.0010.0010.0000.0000.0000.000
116A118LEU0-0.0280.00230.967-0.002-0.0020.0000.0000.0000.000
117A119GLU-1-0.835-0.95734.236-0.050-0.0500.0000.0000.0000.000
118A120SER00.052-0.00134.596-0.004-0.0040.0000.0000.0000.000
119A121ARG10.9140.97032.7700.0590.0590.0000.0000.0000.000
120A122HIS00.0700.06330.753-0.003-0.0030.0000.0000.0000.000
121A123ILE00.0150.01730.262-0.006-0.0060.0000.0000.0000.000
122A124TYR0-0.067-0.02831.322-0.002-0.0020.0000.0000.0000.000
123A125ASP-1-0.849-0.94028.127-0.077-0.0770.0000.0000.0000.000
124A126LEU0-0.019-0.00424.955-0.005-0.0050.0000.0000.0000.000
125A127LYS10.8980.95227.0700.0620.0620.0000.0000.0000.000
126A128ALA0-0.031-0.01528.7940.0000.0000.0000.0000.0000.000
127A129MET0-0.048-0.00621.6350.0010.0010.0000.0000.0000.000
128A130GLN00.0100.00624.300-0.009-0.0090.0000.0000.0000.000
129A131ILE00.0220.02521.3900.0060.0060.0000.0000.0000.000
130A132GLU-1-0.965-0.97125.555-0.066-0.0660.0000.0000.0000.000
131A133LYS10.9190.95226.8250.0700.0700.0000.0000.0000.000
132A134LEU00.0020.00721.1010.0000.0000.0000.0000.0000.000
133A135GLU-1-0.880-0.94820.774-0.099-0.0990.0000.0000.0000.000
134A136SER0-0.020-0.01317.7560.0120.0120.0000.0000.0000.000
135A137PRO00.011-0.00917.962-0.022-0.0220.0000.0000.0000.000
136A138ASP-1-0.902-0.94217.302-0.138-0.1380.0000.0000.0000.000
137A139LEU0-0.068-0.01212.650-0.027-0.0270.0000.0000.0000.000
138A140LEU0-0.001-0.00613.705-0.043-0.0430.0000.0000.0000.000
139A141TRP0-0.064-0.03213.8050.0040.0040.0000.0000.0000.000
140A142LEU0-0.028-0.00316.774-0.010-0.0100.0000.0000.0000.000
141A143LEU0-0.0050.00416.6080.0070.0070.0000.0000.0000.000
142A144GLN00.036-0.00220.343-0.004-0.0040.0000.0000.0000.000
143A145GLN00.0340.03623.9220.0080.0080.0000.0000.0000.000
144A146THR0-0.018-0.02726.8560.0010.0010.0000.0000.0000.000
145A147GLY0-0.044-0.01830.1250.0040.0040.0000.0000.0000.000
146A148ASP-1-0.833-0.90627.372-0.100-0.1000.0000.0000.0000.000
147A149GLU-1-0.925-0.96129.956-0.063-0.0630.0000.0000.0000.000
148A150VAL0-0.090-0.03329.2290.0030.0030.0000.0000.0000.000
149A151LEU0-0.059-0.03626.0340.0010.0010.0000.0000.0000.000
150A152ASP-1-0.837-0.91430.145-0.072-0.0720.0000.0000.0000.000
151A153TYR00.040-0.00728.501-0.001-0.0010.0000.0000.0000.000
152A154ARG10.8970.96328.8510.0590.0590.0000.0000.0000.000
153A155GLN00.0170.00929.355-0.001-0.0010.0000.0000.0000.000
154A156ALA00.0380.02124.630-0.002-0.0020.0000.0000.0000.000
155A157VAL0-0.017-0.00825.699-0.004-0.0040.0000.0000.0000.000
156A158ALA00.0000.00027.3670.0000.0000.0000.0000.0000.000
157A159TYR0-0.047-0.04622.692-0.002-0.0020.0000.0000.0000.000
158A160TYR0-0.001-0.03220.1400.0020.0020.0000.0000.0000.000
159A161THR0-0.0070.01323.652-0.003-0.0030.0000.0000.0000.000
160A162PRO0-0.096-0.04423.5650.0010.0010.0000.0000.0000.000
161A163CYS0-0.0080.01819.623-0.005-0.0050.0000.0000.0000.000
162A164ARG10.9691.00815.1820.2540.2540.0000.0000.0000.000
163A165GLN0-0.042-0.05120.155-0.005-0.0050.0000.0000.0000.000
164A166THR0-0.043-0.01120.599-0.003-0.0030.0000.0000.0000.000
165A167VAL0-0.004-0.00122.499-0.003-0.0030.0000.0000.0000.000
166A168GLU-1-0.830-0.86423.698-0.121-0.1210.0000.0000.0000.000
167A169SER00.011-0.00427.2300.0000.0000.0000.0000.0000.000
168A170GLY0-0.0120.00830.3760.0000.0000.0000.0000.0000.000
169A171GLY00.0380.01828.362-0.005-0.0050.0000.0000.0000.000
170A172ASN00.0430.00027.4150.0000.0000.0000.0000.0000.000
171A173HIS00.0360.01325.657-0.010-0.0100.0000.0000.0000.000
172A174ALA0-0.042-0.00424.494-0.009-0.0090.0000.0000.0000.000
173A175PHE00.0410.03120.996-0.013-0.0130.0000.0000.0000.000
174A176VAL0-0.050-0.03323.300-0.002-0.0020.0000.0000.0000.000
175A177GLY00.0500.02922.885-0.002-0.0020.0000.0000.0000.000
176A178PHE00.004-0.01114.668-0.007-0.0070.0000.0000.0000.000
177A179ASP-1-0.856-0.93917.140-0.140-0.1400.0000.0000.0000.000
178A180HIS0-0.046-0.00716.896-0.007-0.0070.0000.0000.0000.000
179A181TYR0-0.060-0.10915.774-0.015-0.0150.0000.0000.0000.000
180A182PHE0-0.0080.02112.456-0.035-0.0350.0000.0000.0000.000
181A183SER00.0280.00310.936-0.076-0.0760.0000.0000.0000.000
182A184PRO00.0290.01111.003-0.078-0.0780.0000.0000.0000.000
183A185ILE00.0120.0279.663-0.043-0.0430.0000.0000.0000.000
184A186VAL00.0080.0165.335-0.056-0.0560.0000.0000.0000.000
185A187THR0-0.093-0.0607.098-0.260-0.2600.0000.0000.0000.000
186A188PHE0-0.025-0.0179.437-0.009-0.0090.0000.0000.0000.000
187A189LEU0-0.053-0.0226.4670.0350.0350.0000.0000.0000.000
188A190GLY00.0130.0246.380-0.032-0.0320.0000.0000.0000.000
189A191LEU0-0.039-0.0232.107-1.786-0.4162.150-1.250-2.2700.002
190A192ALA00.0140.0121.968-12.594-12.1334.803-2.875-2.389-0.039
191A193THR00.010-0.0084.6550.6080.664-0.001-0.010-0.0460.000
192A194ALA00.0480.0027.6270.0960.0960.0000.0000.0000.000
193A195LEU0-0.085-0.0199.1360.0260.0260.0000.0000.0000.000
194A196GLU-1-0.864-0.93510.9090.6620.6620.0000.0000.0000.000
195A197HIS0-0.128-0.04510.348-0.009-0.0090.0000.0000.0000.000