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: NNG6Q

Calculation Name: 2I3F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I3F

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-23

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2585530.77502
FMO2-HF: Nuclear repulsion 2503200.93675
FMO2-HF: Total energy -82329.83827
FMO2-MP2: Total energy -82572.756469


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:11:ASP)


Summations of interaction energy for fragment #1(A:11:ASP)
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.
-176.488-185.00233.171-13.947-10.7090.149
Interaction energy analysis for fragmet #1(A:11:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.784 / q_NPA : -0.872
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].
3A13GLY00.0370.0123.908-7.811-6.163-0.001-0.735-0.9120.002
4A14ILE00.0050.0042.902-8.741-6.9760.297-0.835-1.2270.007
5A15ILE0-0.026-0.0075.614-4.811-4.8110.0000.0000.0000.000
6A16VAL00.0130.0118.033-3.646-3.6460.0000.0000.0000.000
7A17ILE0-0.0110.0027.276-2.490-2.4900.0000.0000.0000.000
8A18LEU0-0.004-0.0067.193-2.236-2.2360.0000.0000.0000.000
9A19TRP00.006-0.01710.870-3.030-3.0300.0000.0000.0000.000
10A20LYS10.7850.89313.413-18.962-18.9620.0000.0000.0000.000
11A21GLN0-0.014-0.01612.1940.0580.0580.0000.0000.0000.000
12A22VAL0-0.069-0.00715.054-1.021-1.0210.0000.0000.0000.000
13A23THR0-0.038-0.03417.630-0.698-0.6980.0000.0000.0000.000
14A24VAL00.0500.03820.629-0.476-0.4760.0000.0000.0000.000
15A25LYS10.9050.94923.676-12.925-12.9250.0000.0000.0000.000
16A26GLU-1-0.881-0.94526.89510.05010.0500.0000.0000.0000.000
17A27ASP-1-0.857-0.91030.1909.8659.8650.0000.0000.0000.000
18A28GLY00.0020.01128.759-0.100-0.1000.0000.0000.0000.000
19A29LYS10.7930.88227.064-10.215-10.2150.0000.0000.0000.000
20A30VAL0-0.015-0.01720.8240.3790.3790.0000.0000.0000.000
21A31PRO00.0190.02019.683-0.231-0.2310.0000.0000.0000.000
22A32LEU00.018-0.00219.8410.9950.9950.0000.0000.0000.000
23A33GLU-1-0.777-0.88718.01517.17617.1760.0000.0000.0000.000
24A34PRO0-0.019-0.00715.2351.4021.4020.0000.0000.0000.000
25A35PHE00.0380.02114.6651.6121.6120.0000.0000.0000.000
26A36LEU00.005-0.00715.4361.1101.1100.0000.0000.0000.000
27A37THR0-0.032-0.02010.6451.4231.4230.0000.0000.0000.000
28A38ALA0-0.001-0.00810.7772.7812.7810.0000.0000.0000.000
29A39ALA00.005-0.00111.4681.5141.5140.0000.0000.0000.000
30A40LYS10.8870.9297.389-37.493-37.4930.0000.0000.0000.000
31A41GLU-1-0.796-0.8745.22655.37355.450-0.0010.000-0.0750.000
32A42VAL00.0190.0158.7342.0882.0880.0000.0000.0000.000
33A43LEU0-0.037-0.02810.835-1.215-1.2150.0000.0000.0000.000
34A44ARG10.7710.8461.699-126.685-138.90532.876-12.279-8.3760.139
35A45VAL00.0200.0118.534-1.084-1.0840.0000.0000.0000.000
36A46VAL0-0.028-0.01011.490-2.163-2.1630.0000.0000.0000.000
37A47ASP-1-0.824-0.89710.14025.02025.0200.0000.0000.0000.000
38A48ALA00.0130.00510.401-1.149-1.1490.0000.0000.0000.000
39A49PHE00.0160.02512.021-1.710-1.7100.0000.0000.0000.000
40A50GLY00.011-0.00215.491-0.533-0.5330.0000.0000.0000.000
41A51SER00.015-0.00416.333-0.236-0.2360.0000.0000.0000.000
42A52GLY00.0050.01219.407-0.554-0.5540.0000.0000.0000.000
43A53PHE00.0360.00516.669-0.516-0.5160.0000.0000.0000.000
44A54ARG10.9560.98519.155-12.886-12.8860.0000.0000.0000.000
45A55ILE0-0.0050.00020.5140.1650.1650.0000.0000.0000.000
46A56VAL00.0670.03517.930-0.051-0.0510.0000.0000.0000.000
47A57LYS10.8390.90812.979-23.320-23.3200.0000.0000.0000.000
48A58ASN0-0.029-0.03517.5430.8660.8660.0000.0000.0000.000
49A59ASP-1-0.825-0.90820.51113.48513.4850.0000.0000.0000.000
50A60ILE0-0.024-0.00415.085-0.083-0.0830.0000.0000.0000.000
51A61ALA00.0250.00715.9920.0980.0980.0000.0000.0000.000
52A62GLY0-0.017-0.00717.169-0.333-0.3330.0000.0000.0000.000
53A63ASN0-0.005-0.01120.767-1.140-1.1400.0000.0000.0000.000
54A64ILE00.0680.04614.689-0.469-0.4690.0000.0000.0000.000
55A65LYS10.9370.97318.804-15.229-15.2290.0000.0000.0000.000
56A66LYS10.8170.90220.301-13.585-13.5850.0000.0000.0000.000
57A67LEU00.0450.02321.132-0.484-0.4840.0000.0000.0000.000
58A68TYR0-0.031-0.03616.1800.0040.0040.0000.0000.0000.000
59A69ARG10.8850.94521.781-11.748-11.7480.0000.0000.0000.000
60A70ALA0-0.016-0.00924.964-0.423-0.4230.0000.0000.0000.000
61A71ASN00.0610.03223.481-0.885-0.8850.0000.0000.0000.000
62A72GLN0-0.060-0.02625.210-0.209-0.2090.0000.0000.0000.000
63A73THR0-0.045-0.02726.939-0.128-0.1280.0000.0000.0000.000
64A74VAL0-0.0040.00429.077-0.300-0.3000.0000.0000.0000.000
65A75HIS0-0.056-0.02526.6050.0970.0970.0000.0000.0000.000
66A76ALA00.0170.02926.899-0.048-0.0480.0000.0000.0000.000
67A77GLU-1-0.905-0.94324.83812.53012.5300.0000.0000.0000.000
68A78THR0-0.077-0.06023.7720.6650.6650.0000.0000.0000.000
69A79LEU0-0.003-0.01121.294-0.230-0.2300.0000.0000.0000.000
70A80GLN00.0500.01825.256-0.136-0.1360.0000.0000.0000.000
71A81GLU-1-0.791-0.88428.44010.74210.7420.0000.0000.0000.000
72A82LEU00.0360.02225.623-0.308-0.3080.0000.0000.0000.000
73A83ILE0-0.026-0.01727.194-0.272-0.2720.0000.0000.0000.000
74A84ILE0-0.029-0.00830.561-0.393-0.3930.0000.0000.0000.000
75A85ALA0-0.027-0.01031.979-0.320-0.3200.0000.0000.0000.000
76A86GLU-1-0.767-0.86830.52710.52210.5220.0000.0000.0000.000
77A87ASN0-0.038-0.00433.965-0.088-0.0880.0000.0000.0000.000
78A88SER00.0530.03135.019-0.293-0.2930.0000.0000.0000.000
79A89PRO00.0410.01834.1110.3460.3460.0000.0000.0000.000
80A90ASP-1-0.937-0.97133.2579.0969.0960.0000.0000.0000.000
81A91GLY0-0.033-0.00432.3610.0600.0600.0000.0000.0000.000
82A92LEU0-0.048-0.03528.8090.3290.3290.0000.0000.0000.000
83A93ALA0-0.002-0.02526.1610.5580.5580.0000.0000.0000.000
84A94THR0-0.021-0.02026.5350.4350.4350.0000.0000.0000.000
85A95VAL00.0290.01328.4040.3020.3020.0000.0000.0000.000
86A96ALA0-0.059-0.02423.7810.3380.3380.0000.0000.0000.000
87A97LEU00.011-0.00522.4800.6550.6550.0000.0000.0000.000
88A98LEU00.0290.03024.5710.3740.3740.0000.0000.0000.000
89A99TRP0-0.016-0.01624.7930.2560.2560.0000.0000.0000.000
90A100LEU0-0.043-0.01217.6590.4660.4660.0000.0000.0000.000
91A101LYS10.8540.92420.918-11.273-11.2730.0000.0000.0000.000
92A102ARG10.8020.86523.090-10.644-10.6440.0000.0000.0000.000
93A103ALA0-0.018-0.02020.1450.1300.1300.0000.0000.0000.000
94A104PHE00.006-0.00715.6070.9000.9000.0000.0000.0000.000
95A105GLN00.0350.01719.7850.2710.2710.0000.0000.0000.000
96A106PHE0-0.051-0.01619.946-0.002-0.0020.0000.0000.0000.000
97A107ILE0-0.017-0.02015.3940.0690.0690.0000.0000.0000.000
98A108ALA00.0620.03118.5420.4080.4080.0000.0000.0000.000
99A109SER0-0.033-0.04319.855-0.314-0.3140.0000.0000.0000.000
100A110PHE0-0.039-0.03316.572-0.250-0.2500.0000.0000.0000.000
101A111LEU00.0170.00114.3360.0070.0070.0000.0000.0000.000
102A112ARG10.9050.93718.211-12.837-12.8370.0000.0000.0000.000
103A113ARG10.8190.89920.999-12.637-12.6370.0000.0000.0000.000
104A114LEU0-0.0070.00716.386-0.320-0.3200.0000.0000.0000.000
105A115VAL0-0.042-0.01616.2510.2590.2590.0000.0000.0000.000
106A116VAL00.0100.01219.466-0.233-0.2330.0000.0000.0000.000
107A117THR0-0.062-0.03723.058-0.902-0.9020.0000.0000.0000.000
108A118ASP-1-0.861-0.93123.47712.65412.6540.0000.0000.0000.000
109A119LYS10.8070.90625.287-11.408-11.4080.0000.0000.0000.000
110A120SER00.0590.03223.9970.6690.6690.0000.0000.0000.000
111A121LEU00.0370.02217.433-0.035-0.0350.0000.0000.0000.000
112A122GLU-1-0.798-0.89621.86111.75211.7520.0000.0000.0000.000
113A123GLN00.0130.01024.595-0.154-0.1540.0000.0000.0000.000
114A124CYS0-0.060-0.01322.054-0.167-0.1670.0000.0000.0000.000
115A125VAL00.0210.00221.4370.0010.0010.0000.0000.0000.000
116A126THR00.008-0.01023.323-0.309-0.3090.0000.0000.0000.000
117A127GLU-1-0.798-0.87527.08210.99010.9900.0000.0000.0000.000
118A128ALA00.0080.03023.459-0.243-0.2430.0000.0000.0000.000
119A129TYR00.012-0.00325.476-0.409-0.4090.0000.0000.0000.000
120A130ASN0-0.047-0.04726.626-0.577-0.5770.0000.0000.0000.000
121A131CYS0-0.077-0.00728.218-0.242-0.2420.0000.0000.0000.000
122A132THR00.030-0.02825.0350.1920.1920.0000.0000.0000.000
123A133LEU00.0430.01023.213-0.281-0.2810.0000.0000.0000.000
124A134ARG10.8090.91527.485-10.076-10.0760.0000.0000.0000.000
125A135PRO0-0.014-0.00930.338-0.249-0.2490.0000.0000.0000.000
126A136CYS0-0.0150.02029.484-0.129-0.1290.0000.0000.0000.000
127A137HIS00.0150.02225.719-0.016-0.0160.0000.0000.0000.000
128A138SER00.0850.03931.482-0.196-0.1960.0000.0000.0000.000
129A139ALA00.0440.00833.7360.2150.2150.0000.0000.0000.000
130A140VAL0-0.0170.00233.999-0.051-0.0510.0000.0000.0000.000
131A141ILE00.0560.02228.7620.1900.1900.0000.0000.0000.000
132A142GLN00.0540.03529.6660.2640.2640.0000.0000.0000.000
133A143LYS10.8960.95130.559-8.739-8.7390.0000.0000.0000.000
134A144VAL0-0.0050.00327.1240.1480.1480.0000.0000.0000.000
135A145PHE00.0130.01123.0640.4330.4330.0000.0000.0000.000
136A146TRP0-0.004-0.01726.3200.4490.4490.0000.0000.0000.000
137A147GLY00.0030.00428.3520.0270.0270.0000.0000.0000.000
138A148GLY0-0.004-0.00224.3370.1980.1980.0000.0000.0000.000
139A149VAL00.006-0.01323.4980.5610.5610.0000.0000.0000.000
140A150LYS10.8150.89124.858-11.113-11.1130.0000.0000.0000.000
141A151LEU0-0.045-0.01322.363-0.101-0.1010.0000.0000.0000.000
142A152ALA0-0.0130.00220.9160.8360.8360.0000.0000.0000.000
143A153PRO0-0.058-0.00516.589-0.416-0.4160.0000.0000.0000.000
144A154SER00.003-0.03319.299-0.110-0.1100.0000.0000.0000.000
145A155ARG10.8980.93917.370-13.779-13.7790.0000.0000.0000.000
146A156GLU-1-0.796-0.88715.71016.85816.8580.0000.0000.0000.000
147A157ARG10.9020.96015.121-16.087-16.0870.0000.0000.0000.000
148A158PHE00.007-0.00613.3681.5281.5280.0000.0000.0000.000
149A159TYR00.0550.00111.5772.0762.0760.0000.0000.0000.000
150A160ARG10.8950.9379.834-17.002-17.0020.0000.0000.0000.000
151A161LYS10.7680.9109.125-22.282-22.2820.0000.0000.0000.000
152A162LEU0-0.0440.0036.5393.7883.7880.0000.0000.0000.000
153A163HIS00.038-0.0014.2386.1876.4030.000-0.098-0.1190.001
154A164PRO00.0210.0076.264-4.153-4.1530.0000.0000.0000.000
155A165ASP-1-0.797-0.8798.99218.73318.7330.0000.0000.0000.000
156A166LEU0-0.016-0.01510.5381.3021.3020.0000.0000.0000.000
157A167ASN0-0.042-0.02713.207-0.811-0.8110.0000.0000.0000.000
158A168ILE00.0150.0067.3230.1890.1890.0000.0000.0000.000
159A169ALA0-0.027-0.0079.0591.2301.2300.0000.0000.0000.000
160A170LYS10.8190.8969.988-16.197-16.1970.0000.0000.0000.000
161A171ALA00.0680.03611.861-0.241-0.2410.0000.0000.0000.000
162A172LYS10.7740.8606.991-26.792-26.7920.0000.0000.0000.000
163A173ILE0-0.018-0.00710.2470.4250.4250.0000.0000.0000.000
164A174GLU-1-0.832-0.90712.65616.40616.4060.0000.0000.0000.000
165A175GLU-1-0.747-0.86911.07623.80223.8020.0000.0000.0000.000
166A176PHE0-0.016-0.01211.268-0.276-0.2760.0000.0000.0000.000
167A177LEU0-0.029-0.00213.151-1.069-1.0690.0000.0000.0000.000
168A178ILE00.0130.02816.567-1.037-1.0370.0000.0000.0000.000
169A179GLU-1-0.789-0.89114.65116.94116.9410.0000.0000.0000.000
170A180LEU0-0.057-0.02015.840-0.420-0.4200.0000.0000.0000.000
171A181HIS10.8050.91017.326-14.319-14.3190.0000.0000.0000.000
172A182ASP-1-0.795-0.88021.02312.93612.9360.0000.0000.0000.000
173A183PRO00.0210.00318.656-0.652-0.6520.0000.0000.0000.000
174A184LEU0-0.0030.00620.189-0.451-0.4510.0000.0000.0000.000
175A185CYS0-0.031-0.02922.056-0.687-0.6870.0000.0000.0000.000
176A186CYS0-0.065-0.00524.729-0.575-0.5750.0000.0000.0000.000
177A187ILE00.0210.00521.647-0.465-0.4650.0000.0000.0000.000
178A188VAL0-0.029-0.01825.443-0.416-0.4160.0000.0000.0000.000
179A189GLN0-0.0180.00027.820-0.540-0.5400.0000.0000.0000.000
180A190PHE00.0350.01328.784-0.357-0.3570.0000.0000.0000.000
181A191PHE00.011-0.01827.348-0.223-0.2230.0000.0000.0000.000
182A192PHE0-0.034-0.01630.992-0.240-0.2400.0000.0000.0000.000
183A193GLN0-0.039-0.02433.158-0.136-0.1360.0000.0000.0000.000
184A194ARG10.7990.90032.727-9.510-9.5100.0000.0000.0000.000
185A195GLU-1-0.947-0.96235.4287.9427.9420.0000.0000.0000.000
186A196LEU0-0.019-0.00631.447-0.017-0.0170.0000.0000.0000.000
187A197GLU-1-0.740-0.83629.73111.26411.2640.0000.0000.0000.000
188A198ASP-1-0.794-0.88833.0089.2359.2350.0000.0000.0000.000
189A199GLN0-0.054-0.03732.6930.1430.1430.0000.0000.0000.000
190A200CYS0-0.093-0.02227.8990.2310.2310.0000.0000.0000.000
191A201TRP00.0340.02029.9540.3050.3050.0000.0000.0000.000
192A202GLY00.0420.03327.8020.2230.2230.0000.0000.0000.000
193A203ASP-1-0.776-0.84725.62112.32012.3200.0000.0000.0000.000
194A204GLU-1-0.782-0.86127.61210.47710.4770.0000.0000.0000.000
195A205VAL00.0160.01026.9700.1260.1260.0000.0000.0000.000
196A206TYR0-0.070-0.05919.3300.0000.0000.0000.0000.0000.000
197A207GLN0-0.013-0.02325.3350.5020.5020.0000.0000.0000.000
198A208ARG10.7590.85627.457-10.666-10.6660.0000.0000.0000.000
199A209LYS10.9870.98127.548-10.315-10.3150.0000.0000.0000.000
200A210ASP-1-0.791-0.88825.72212.46312.4630.0000.0000.0000.000
201A211SER00.0390.02321.393-0.055-0.0550.0000.0000.0000.000
202A212SER00.0260.00421.7090.9250.9250.0000.0000.0000.000
203A213GLU-1-0.886-0.94023.31010.44410.4440.0000.0000.0000.000
204A214TRP0-0.028-0.04518.219-0.248-0.2480.0000.0000.0000.000
205A215LEU00.0020.00819.5720.0960.0960.0000.0000.0000.000
206A216LYS10.7740.91223.716-11.900-11.9000.0000.0000.0000.000