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: 89GKY

Calculation Name: 3ER6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ER6

Chain ID: A

ChEMBL ID:

UniProt ID: Q87I90

Base Structure: X-ray

Registration Date: 2023-09-22

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2118476.172798
FMO2-HF: Nuclear repulsion 2044483.399666
FMO2-HF: Total energy -73992.773131
FMO2-MP2: Total energy -74210.767669


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:7:LYS)


Summations of interaction energy for fragment #1(A:7:LYS)
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.
-85.415-82.8360.027-1.127-1.4790
Interaction energy analysis for fragmet #1(A:7:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.926 / q_NPA : 0.948
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].
3A9LEU0-0.0210.0123.8664.6026.477-0.016-0.943-0.9160.001
4A10ARG10.8570.9296.69227.88727.8870.0000.0000.0000.000
5A11VAL00.0160.01410.4571.5371.5370.0000.0000.0000.000
6A12VAL0-0.008-0.00813.684-0.474-0.4740.0000.0000.0000.000
7A13ALA00.001-0.00516.9080.5670.5670.0000.0000.0000.000
8A14LEU00.0300.02620.0140.3130.3130.0000.0000.0000.000
9A15ALA00.0320.00523.3910.3720.3720.0000.0000.0000.000
10A16PRO0-0.014-0.00826.1770.1720.1720.0000.0000.0000.000
11A17THR00.0530.02229.3380.3020.3020.0000.0000.0000.000
12A18GLY00.0390.02831.291-0.113-0.1130.0000.0000.0000.000
13A19ARG10.8150.88632.1948.8758.8750.0000.0000.0000.000
14A20TYR00.017-0.00532.1050.3450.3450.0000.0000.0000.000
15A21PHE00.0260.02226.970-0.069-0.0690.0000.0000.0000.000
16A22ALA00.0320.01926.921-0.383-0.3830.0000.0000.0000.000
17A23SER00.0340.02326.494-0.349-0.3490.0000.0000.0000.000
18A24ILE00.0260.02321.749-0.322-0.3220.0000.0000.0000.000
19A25ILE0-0.021-0.00121.834-0.588-0.5880.0000.0000.0000.000
20A26SER00.0820.04121.982-0.321-0.3210.0000.0000.0000.000
21A27SER0-0.070-0.05320.077-0.115-0.1150.0000.0000.0000.000
22A28LEU0-0.015-0.01616.661-0.569-0.5690.0000.0000.0000.000
23A29GLU-1-0.874-0.93517.384-13.392-13.3920.0000.0000.0000.000
24A30ILE0-0.035-0.00218.076-0.269-0.2690.0000.0000.0000.000
25A31LEU0-0.017-0.01013.778-0.394-0.3940.0000.0000.0000.000
26A32GLU-1-0.859-0.91713.600-21.182-21.1820.0000.0000.0000.000
27A33THR0-0.003-0.00514.572-0.432-0.4320.0000.0000.0000.000
28A34ALA0-0.020-0.01514.154-0.057-0.0570.0000.0000.0000.000
29A35ALA0-0.011-0.01210.282-0.499-0.4990.0000.0000.0000.000
30A36GLU-1-0.951-0.96811.246-17.716-17.7160.0000.0000.0000.000
31A37PHE0-0.060-0.04613.9410.2850.2850.0000.0000.0000.000
32A38ALA0-0.042-0.0099.7810.5100.5100.0000.0000.0000.000
33A39GLU-1-0.962-0.97610.056-20.180-20.1800.0000.0000.0000.000
34A40PHE0-0.022-0.0032.980-4.583-3.8790.043-0.184-0.563-0.001
35A41GLN0-0.008-0.0176.8680.0820.0820.0000.0000.0000.000
36A42GLY0-0.018-0.0044.821-3.013-3.0130.0000.0000.0000.000
37A43PHE00.0220.0035.674-2.560-2.5600.0000.0000.0000.000
38A44MET0-0.0270.0146.8440.6510.6510.0000.0000.0000.000
39A45THR0-0.029-0.03510.7490.9390.9390.0000.0000.0000.000
40A46HIS00.024-0.00311.3981.4141.4140.0000.0000.0000.000
41A47VAL00.0090.01216.5120.5860.5860.0000.0000.0000.000
42A48VAL0-0.030-0.00819.368-0.016-0.0160.0000.0000.0000.000
43A49THR00.006-0.01322.1490.3010.3010.0000.0000.0000.000
44A50PRO00.0560.02425.876-0.195-0.1950.0000.0000.0000.000
45A51ASN00.0210.01828.046-0.198-0.1980.0000.0000.0000.000
46A52ASN0-0.005-0.01624.027-0.152-0.1520.0000.0000.0000.000
47A53ARG10.9130.97226.22610.39810.3980.0000.0000.0000.000
48A54PRO00.0100.00128.209-0.228-0.2280.0000.0000.0000.000
49A55LEU0-0.0060.01627.4400.4300.4300.0000.0000.0000.000
50A56ILE00.0190.01130.4290.0140.0140.0000.0000.0000.000
51A57GLY00.0360.03033.2980.0490.0490.0000.0000.0000.000
52A58ARG10.8600.91033.9578.8898.8890.0000.0000.0000.000
53A59GLY00.0270.00135.868-0.173-0.1730.0000.0000.0000.000
54A60GLY0-0.0050.00837.8830.0570.0570.0000.0000.0000.000
55A61ILE00.0110.02531.162-0.052-0.0520.0000.0000.0000.000
56A62SER0-0.015-0.02032.0200.0370.0370.0000.0000.0000.000
57A63VAL00.0240.01225.797-0.139-0.1390.0000.0000.0000.000
58A64GLN0-0.022-0.02324.9410.4680.4680.0000.0000.0000.000
59A65PRO00.0210.03622.241-0.360-0.3600.0000.0000.0000.000
60A66THR00.0290.00318.0980.5230.5230.0000.0000.0000.000
61A67ALA0-0.0050.00517.120-0.830-0.8300.0000.0000.0000.000
62A68GLN0-0.010-0.00819.1341.4031.4030.0000.0000.0000.000
63A69TRP00.0290.00619.395-1.077-1.0770.0000.0000.0000.000
64A70GLN00.0720.03719.722-0.939-0.9390.0000.0000.0000.000
65A71SER0-0.075-0.02616.4220.0640.0640.0000.0000.0000.000
66A72PHE0-0.053-0.03413.350-1.754-1.7540.0000.0000.0000.000
67A73ASP-1-0.800-0.89015.344-16.606-16.6060.0000.0000.0000.000
68A74PHE00.007-0.0019.1140.2310.2310.0000.0000.0000.000
69A75THR00.000-0.02312.293-1.943-1.9430.0000.0000.0000.000
70A76ASN00.0520.0567.595-0.494-0.4940.0000.0000.0000.000
71A77ILE00.0150.01611.3011.3551.3550.0000.0000.0000.000
72A78LEU00.0160.02414.198-0.722-0.7220.0000.0000.0000.000
73A79ILE0-0.0070.00217.2850.7290.7290.0000.0000.0000.000
74A80ILE0-0.007-0.00420.001-0.005-0.0050.0000.0000.0000.000
75A81GLY00.0420.00823.7420.3260.3260.0000.0000.0000.000
76A82SER0-0.042-0.04126.1070.2600.2600.0000.0000.0000.000
77A83ILE00.0230.00129.887-0.221-0.2210.0000.0000.0000.000
78A84GLY0-0.048-0.00932.3290.2530.2530.0000.0000.0000.000
79A85ASP-1-0.834-0.92735.210-7.766-7.7660.0000.0000.0000.000
80A86PRO00.004-0.00135.315-0.027-0.0270.0000.0000.0000.000
81A87LEU00.0160.01137.238-0.007-0.0070.0000.0000.0000.000
82A88GLU-1-0.884-0.90739.408-7.963-7.9630.0000.0000.0000.000
83A89SER00.001-0.02835.499-0.005-0.0050.0000.0000.0000.000
84A90LEU00.0000.00333.644-0.231-0.2310.0000.0000.0000.000
85A91ASP-1-0.844-0.92135.451-8.381-8.3810.0000.0000.0000.000
86A92LYS10.7350.84737.2318.2868.2860.0000.0000.0000.000
87A93ILE0-0.073-0.02130.814-0.193-0.1930.0000.0000.0000.000
88A94ASP-1-0.805-0.91429.423-10.462-10.4620.0000.0000.0000.000
89A95PRO00.0080.00430.896-0.248-0.2480.0000.0000.0000.000
90A96ALA00.0520.02528.033-0.233-0.2330.0000.0000.0000.000
91A97LEU0-0.022-0.00725.037-0.501-0.5010.0000.0000.0000.000
92A98PHE0-0.016-0.01926.339-0.387-0.3870.0000.0000.0000.000
93A99ASP-1-0.892-0.95027.160-10.824-10.8240.0000.0000.0000.000
94A100TRP0-0.037-0.02019.032-0.134-0.1340.0000.0000.0000.000
95A101ILE0-0.027-0.01822.304-0.619-0.6190.0000.0000.0000.000
96A102ARG10.9470.97922.86910.19610.1960.0000.0000.0000.000
97A103GLU-1-0.864-0.93521.494-14.135-14.1350.0000.0000.0000.000
98A104LEU0-0.035-0.01316.758-0.554-0.5540.0000.0000.0000.000
99A105HIS00.0070.00218.669-0.801-0.8010.0000.0000.0000.000
100A106LEU0-0.048-0.02320.384-0.063-0.0630.0000.0000.0000.000
101A107LYS10.7430.87116.72316.16416.1640.0000.0000.0000.000
102A108GLY0-0.0030.01016.264-0.877-0.8770.0000.0000.0000.000
103A109SER0-0.070-0.05314.643-0.449-0.4490.0000.0000.0000.000
104A110LYS10.7700.89013.12317.09717.0970.0000.0000.0000.000
105A111ILE00.0120.01216.291-0.358-0.3580.0000.0000.0000.000
106A112VAL00.008-0.01117.5960.5520.5520.0000.0000.0000.000
107A113ALA00.0130.02220.659-0.054-0.0540.0000.0000.0000.000
108A114ILE0-0.006-0.01823.0590.2410.2410.0000.0000.0000.000
109A115ASP-1-0.789-0.87325.993-9.281-9.2810.0000.0000.0000.000
110A116THR0-0.003-0.02429.779-0.184-0.1840.0000.0000.0000.000
111A117GLY00.0250.03127.5510.1030.1030.0000.0000.0000.000
112A118ILE0-0.053-0.04227.686-0.153-0.1530.0000.0000.0000.000
113A119PHE00.0270.00629.1330.0460.0460.0000.0000.0000.000
114A120VAL0-0.0070.00927.9270.1120.1120.0000.0000.0000.000
115A121VAL00.004-0.00824.690-0.032-0.0320.0000.0000.0000.000
116A122ALA0-0.0010.01727.8880.0070.0070.0000.0000.0000.000
117A123LYS10.8680.93531.2178.8558.8550.0000.0000.0000.000
118A124ALA0-0.041-0.01828.1250.0900.0900.0000.0000.0000.000
119A125GLY0-0.021-0.00629.632-0.115-0.1150.0000.0000.0000.000
120A126LEU0-0.070-0.03823.801-0.105-0.1050.0000.0000.0000.000
121A127LEU0-0.024-0.00526.120-0.278-0.2780.0000.0000.0000.000
122A128GLN00.0410.02926.9160.2400.2400.0000.0000.0000.000
123A129GLN0-0.118-0.08427.6070.5650.5650.0000.0000.0000.000
124A130ASN0-0.036-0.02331.0270.0750.0750.0000.0000.0000.000
125A131LYS10.8770.92831.2388.5478.5470.0000.0000.0000.000
126A132ALA00.0420.01030.489-0.348-0.3480.0000.0000.0000.000
127A133VAL0-0.064-0.01329.2430.1920.1920.0000.0000.0000.000
128A134MET00.0300.01831.852-0.175-0.1750.0000.0000.0000.000
129A135HIS0-0.034-0.01433.0160.4270.4270.0000.0000.0000.000
130A136SER00.045-0.01135.7330.0330.0330.0000.0000.0000.000
131A137TYR0-0.063-0.00938.6220.1880.1880.0000.0000.0000.000
132A138PHE00.0460.00835.8460.0590.0590.0000.0000.0000.000
133A139ALA0-0.023-0.00737.767-0.020-0.0200.0000.0000.0000.000
134A140HIS0-0.025-0.02138.670-0.027-0.0270.0000.0000.0000.000
135A141LEU00.0280.00939.2360.0270.0270.0000.0000.0000.000
136A142PHE00.010-0.01732.879-0.066-0.0660.0000.0000.0000.000
137A143GLY00.0030.00638.125-0.045-0.0450.0000.0000.0000.000
138A144GLU-1-0.887-0.94040.864-6.593-6.5930.0000.0000.0000.000
139A145LEU0-0.084-0.04238.7030.0410.0410.0000.0000.0000.000
140A146PHE0-0.005-0.00334.599-0.193-0.1930.0000.0000.0000.000
141A147PRO00.0070.02538.570-0.040-0.0400.0000.0000.0000.000
142A148GLU-1-0.916-0.96437.604-7.788-7.7880.0000.0000.0000.000
143A149ILE0-0.058-0.00932.958-0.174-0.1740.0000.0000.0000.000
144A150MET00.0330.03035.8490.0900.0900.0000.0000.0000.000
145A151LEU00.0120.00734.695-0.263-0.2630.0000.0000.0000.000
146A152MET00.0020.00332.6070.3010.3010.0000.0000.0000.000
147A153THR0-0.010-0.02334.633-0.114-0.1140.0000.0000.0000.000
148A154GLU-1-0.952-0.95936.422-7.340-7.3400.0000.0000.0000.000
149A155GLN0-0.084-0.04329.3500.0460.0460.0000.0000.0000.000
150A156LYS10.9760.97530.4498.4648.4640.0000.0000.0000.000
151A157ALA0-0.011-0.00425.704-0.168-0.1680.0000.0000.0000.000
152A158LEU00.0160.01126.4630.2660.2660.0000.0000.0000.000
153A159ILE00.0050.00120.841-0.335-0.3350.0000.0000.0000.000
154A160ASP-1-0.801-0.88623.666-9.936-9.9360.0000.0000.0000.000
155A161GLY00.0360.01822.430-0.245-0.2450.0000.0000.0000.000
156A162ASN0-0.014-0.00715.982-0.508-0.5080.0000.0000.0000.000
157A163VAL00.0050.01419.190-0.561-0.5610.0000.0000.0000.000
158A164TYR0-0.047-0.05116.6580.3870.3870.0000.0000.0000.000
159A165LEU00.0020.01422.275-0.051-0.0510.0000.0000.0000.000
160A166SER00.012-0.02724.5210.2330.2330.0000.0000.0000.000
161A167SER00.028-0.00526.4590.0170.0170.0000.0000.0000.000
162A168GLY0-0.0080.00629.0980.0300.0300.0000.0000.0000.000
163A169PRO00.000-0.00429.7910.2680.2680.0000.0000.0000.000
164A170TYR0-0.019-0.02728.505-0.321-0.3210.0000.0000.0000.000
165A171SER00.0060.00627.332-0.228-0.2280.0000.0000.0000.000
166A172HIS00.0330.02823.5050.0810.0810.0000.0000.0000.000
167A173SER00.0270.01422.923-0.382-0.3820.0000.0000.0000.000
168A174SER00.0000.01021.958-0.408-0.4080.0000.0000.0000.000
169A175VAL00.0660.03120.073-0.283-0.2830.0000.0000.0000.000
170A176MET0-0.0150.00218.147-0.790-0.7900.0000.0000.0000.000
171A177LEU0-0.006-0.00316.999-0.699-0.6990.0000.0000.0000.000
172A178GLU-1-0.825-0.87217.356-12.714-12.7140.0000.0000.0000.000
173A179ILE0-0.003-0.00113.516-0.574-0.5740.0000.0000.0000.000
174A180VAL00.0100.00512.902-1.050-1.0500.0000.0000.0000.000
175A181GLU-1-0.819-0.87412.763-13.879-13.8790.0000.0000.0000.000
176A182GLU-1-0.812-0.88912.518-16.134-16.1340.0000.0000.0000.000
177A183TYR0-0.040-0.0177.496-1.061-1.0610.0000.0000.0000.000
178A184PHE0-0.023-0.0047.075-1.549-1.5490.0000.0000.0000.000
179A185GLY00.0320.03910.3090.4950.4950.0000.0000.0000.000
180A186LYS10.8690.89713.35512.75912.7590.0000.0000.0000.000
181A187HIS00.0120.00516.1770.4720.4720.0000.0000.0000.000
182A188THR00.0570.02412.6140.5610.5610.0000.0000.0000.000
183A189ARG10.7620.84815.42612.94412.9440.0000.0000.0000.000
184A190ASN0-0.019-0.02117.5800.5140.5140.0000.0000.0000.000
185A191LEU00.0130.01517.0970.5520.5520.0000.0000.0000.000
186A192GLY00.0730.03318.5380.2800.2800.0000.0000.0000.000
187A193ASN0-0.011-0.00719.5180.4170.4170.0000.0000.0000.000
188A194GLN0-0.043-0.02122.6320.5210.5210.0000.0000.0000.000
189A195PHE0-0.002-0.00121.2460.3680.3680.0000.0000.0000.000
190A196LEU0-0.031-0.02721.7530.3430.3430.0000.0000.0000.000
191A197SER0-0.078-0.01925.0150.4330.4330.0000.0000.0000.000
192A198THR0-0.076-0.04225.7470.5400.5400.0000.0000.0000.000