Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 3Q39L

Calculation Name: 3NI7-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NI7

Chain ID: A

ChEMBL ID:

UniProt ID: Q82XH4

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 180
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1971859.144424
FMO2-HF: Nuclear repulsion 1898139.211015
FMO2-HF: Total energy -73719.933409
FMO2-MP2: Total energy -73933.306385


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:5:ACE )


Summations of interaction energy for fragment #1(A:5:ACE )
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.
1.2182.570.095-0.69-0.756-0.001
Interaction energy analysis for fragmet #1(A:5:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.034
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].
3A7PRO 0-0.0100.0093.1620.5261.8780.095-0.690-0.756-0.001
4A8MET 00.0150.0096.0790.2510.2510.0000.0000.0000.000
5A9ARG 10.9720.9867.4601.1911.1910.0000.0000.0000.000
6A10ASP -1-0.876-0.9617.026-0.841-0.8410.0000.0000.0000.000
7A11ALA 00.0660.0329.6840.1670.1670.0000.0000.0000.000
8A12ILE 0-0.0290.02111.9250.1000.1000.0000.0000.0000.000
9A13VAL 00.0020.00312.7240.0810.0810.0000.0000.0000.000
10A14ASP -1-0.814-0.89413.122-0.218-0.2180.0000.0000.0000.000
11A15THR 0-0.021-0.01115.5240.0610.0610.0000.0000.0000.000
12A16ALA 0-0.034-0.03617.3560.0340.0340.0000.0000.0000.000
13A17VAL 0-0.030-0.01118.0240.0330.0330.0000.0000.0000.000
14A18GLU -1-0.921-0.97718.304-0.103-0.1030.0000.0000.0000.000
15A19LEU 0-0.013-0.00321.5930.0160.0160.0000.0000.0000.000
16A20ALA 00.0210.01223.0980.0130.0130.0000.0000.0000.000
17A21ALA 0-0.058-0.02124.2150.0140.0140.0000.0000.0000.000
18A22HIS 0-0.025-0.01724.6980.0030.0030.0000.0000.0000.000
19A23THR 0-0.0170.00627.4130.0050.0050.0000.0000.0000.000
20A24SER 0-0.009-0.02828.4420.0040.0040.0000.0000.0000.000
21A25TRP 00.1300.06520.957-0.002-0.0020.0000.0000.0000.000
22A26GLU -1-0.940-0.95026.566-0.098-0.0980.0000.0000.0000.000
23A27ALA 00.0590.03429.069-0.004-0.0040.0000.0000.0000.000
24A28VAL 00.0000.00522.338-0.001-0.0010.0000.0000.0000.000
25A29ARG 10.8200.89725.0480.1150.1150.0000.0000.0000.000
26A30LEU 00.0780.02319.5670.0010.0010.0000.0000.0000.000
27A31TYR 00.0290.01121.419-0.010-0.0100.0000.0000.0000.000
28A32ASP -1-0.828-0.91123.368-0.116-0.1160.0000.0000.0000.000
29A33ILE 0-0.051-0.01217.5220.0050.0050.0000.0000.0000.000
30A34ALA 00.0210.00219.152-0.005-0.0050.0000.0000.0000.000
31A35ALA 0-0.0050.00620.2000.0100.0100.0000.0000.0000.000
32A36ARG 10.8440.91219.7070.1380.1380.0000.0000.0000.000
33A37LEU 0-0.035-0.02514.6350.0070.0070.0000.0000.0000.000
34A38ALA 0-0.061-0.00617.8020.0050.0050.0000.0000.0000.000
35A39VAL 0-0.0030.00515.5260.0020.0020.0000.0000.0000.000
36A40SER 00.001-0.00118.9160.0030.0030.0000.0000.0000.000
37A41LEU 00.018-0.00819.169-0.025-0.0250.0000.0000.0000.000
38A42ASP -1-0.916-0.96419.962-0.186-0.1860.0000.0000.0000.000
39A43GLU -1-0.891-0.96214.771-0.264-0.2640.0000.0000.0000.000
40A44ILE 0-0.025-0.01015.207-0.063-0.0630.0000.0000.0000.000
41A45ARG 10.8800.92915.8940.1700.1700.0000.0000.0000.000
42A46LEU 0-0.052-0.00613.743-0.001-0.0010.0000.0000.0000.000
43A47TYR 0-0.049-0.0108.5360.0160.0160.0000.0000.0000.000
44A48PHE 00.025-0.00912.474-0.013-0.0130.0000.0000.0000.000
45A49ARG 10.9320.96716.4560.2850.2850.0000.0000.0000.000
46A50GLU -1-0.943-0.97819.721-0.158-0.1580.0000.0000.0000.000
47A51LYS 10.8300.90720.0630.1240.1240.0000.0000.0000.000
48A52ASP -1-0.845-0.92820.903-0.190-0.1900.0000.0000.0000.000
49A53GLU -1-0.844-0.91916.999-0.360-0.3600.0000.0000.0000.000
50A54LEU 0-0.010-0.00615.879-0.039-0.0390.0000.0000.0000.000
51A55ILE 0-0.053-0.02817.152-0.001-0.0010.0000.0000.0000.000
52A56ASP -1-0.865-0.93516.603-0.271-0.2710.0000.0000.0000.000
53A57ALA 00.001-0.00512.775-0.008-0.0080.0000.0000.0000.000
54A58TRP 0-0.059-0.02213.819-0.014-0.0140.0000.0000.0000.000
55A59PHE 0-0.050-0.04816.2360.0330.0330.0000.0000.0000.000
56A60ASP -1-0.798-0.88912.825-0.338-0.3380.0000.0000.0000.000
57A61ARG 10.7810.91210.5650.4280.4280.0000.0000.0000.000
58A62ALA 0-0.006-0.01013.1980.0490.0490.0000.0000.0000.000
59A63ASP -1-0.818-0.89715.573-0.155-0.1550.0000.0000.0000.000
60A64SER 0-0.026-0.00611.2540.0460.0460.0000.0000.0000.000
61A65ARG 10.9090.96113.3020.0740.0740.0000.0000.0000.000
62A66MET 0-0.004-0.00315.0270.0360.0360.0000.0000.0000.000
63A67LEU 00.0080.00412.7590.0150.0150.0000.0000.0000.000
64A68LYS 10.8320.90710.812-0.110-0.1100.0000.0000.0000.000
65A69GLU -1-0.910-0.95915.0080.0450.0450.0000.0000.0000.000
66A70ALA 0-0.008-0.00318.6100.0110.0110.0000.0000.0000.000
67A71GLU -1-0.877-0.92814.2560.0930.0930.0000.0000.0000.000
68A72SER 0-0.046-0.01619.0400.0190.0190.0000.0000.0000.000
69A73ALA 00.015-0.01920.019-0.010-0.0100.0000.0000.0000.000
70A74GLY 00.0370.02123.070-0.006-0.0060.0000.0000.0000.000
71A75PHE 00.0180.01222.600-0.010-0.0100.0000.0000.0000.000
72A76LEU 0-0.060-0.05123.644-0.007-0.0070.0000.0000.0000.000
73A77ASP -1-0.907-0.94226.5510.0380.0380.0000.0000.0000.000
74A78LEU 0-0.069-0.01826.441-0.005-0.0050.0000.0000.0000.000
75A79VAL 00.0310.02029.969-0.001-0.0010.0000.0000.0000.000
76A80ALA 00.0400.01331.127-0.002-0.0020.0000.0000.0000.000
77A81SER 00.0210.00631.090-0.003-0.0030.0000.0000.0000.000
78A82GLU -1-0.965-1.00430.5860.0020.0020.0000.0000.0000.000
79A83ARG 10.8750.95627.260-0.012-0.0120.0000.0000.0000.000
80A84ILE 00.0640.03626.503-0.004-0.0040.0000.0000.0000.000
81A85HIS 0-0.076-0.05127.228-0.003-0.0030.0000.0000.0000.000
82A86HIS 00.0120.01222.750-0.009-0.0090.0000.0000.0000.000
83A87LEU 00.0290.01521.184-0.005-0.0050.0000.0000.0000.000
84A88ILE 00.0150.00722.579-0.010-0.0100.0000.0000.0000.000
85A89MET 0-0.043-0.02424.120-0.008-0.0080.0000.0000.0000.000
86A90ILE 0-0.0040.02018.624-0.003-0.0030.0000.0000.0000.000
87A91TRP 0-0.017-0.02719.210-0.003-0.0030.0000.0000.0000.000
88A92LEU 00.011-0.02820.809-0.011-0.0110.0000.0000.0000.000
89A93ASP -1-0.878-0.93821.720-0.040-0.0400.0000.0000.0000.000
90A94ALA 0-0.039-0.01517.066-0.005-0.0050.0000.0000.0000.000
91A95LEU 0-0.024-0.01418.810-0.011-0.0110.0000.0000.0000.000
92A96ALA 0-0.063-0.03020.677-0.002-0.0020.0000.0000.0000.000
93A97VAL 0-0.0200.00817.8580.0070.0070.0000.0000.0000.000
94A98GLN 00.005-0.00320.8550.0120.0120.0000.0000.0000.000
95A99ARG 10.8800.95722.8520.0480.0480.0000.0000.0000.000
96A100LYS 10.8420.92525.6300.0860.0860.0000.0000.0000.000
97A101VAL 00.0210.01622.2430.0010.0010.0000.0000.0000.000
98A102THR 00.0740.03922.568-0.010-0.0100.0000.0000.0000.000
99A103ARG 10.8990.94524.2140.0700.0700.0000.0000.0000.000
100A104GLN 0-0.002-0.00627.240-0.004-0.0040.0000.0000.0000.000
101A105MET 00.0070.01019.7950.0020.0020.0000.0000.0000.000
102A106ILE 0-0.033-0.01524.997-0.005-0.0050.0000.0000.0000.000
103A107MET 0-0.064-0.05027.7420.0060.0060.0000.0000.0000.000
104A108SER 00.0270.03227.8570.0030.0030.0000.0000.0000.000
105A109LYS 10.8590.95924.0290.1580.1580.0000.0000.0000.000
106A110LEU 00.0120.02929.9870.0020.0020.0000.0000.0000.000
107A111GLU -1-0.883-0.94233.519-0.062-0.0620.0000.0000.0000.000
108A112PHE 0-0.081-0.10833.292-0.002-0.0020.0000.0000.0000.000
109A113GLY 00.1010.03334.0320.0030.0030.0000.0000.0000.000
110A114HIS 0-0.1200.02230.124-0.004-0.0040.0000.0000.0000.000
111A115ILE 00.030-0.00531.351-0.004-0.0040.0000.0000.0000.000
112A116HIS 00.0390.00727.8160.0070.0070.0000.0000.0000.000
113A117ILE 00.0610.01825.602-0.004-0.0040.0000.0000.0000.000
114A118GLN 00.000-0.01527.152-0.005-0.0050.0000.0000.0000.000
115A119ILE 0-0.0340.00128.6040.0010.0010.0000.0000.0000.000
116A120PRO 0-0.0050.00924.0680.0020.0020.0000.0000.0000.000
117A121ALA 00.014-0.00124.873-0.004-0.0040.0000.0000.0000.000
118A122VAL 00.0100.02325.9240.0030.0030.0000.0000.0000.000
119A123MET 00.0240.00225.4460.0080.0080.0000.0000.0000.000
120A124ARG 10.8430.92016.6870.2480.2480.0000.0000.0000.000
121A125VAL 00.0030.03223.5380.0060.0060.0000.0000.0000.000
122A126SER 00.0190.02126.0460.0090.0090.0000.0000.0000.000
123A127ARG 10.9941.00918.7410.1340.1340.0000.0000.0000.000
124A128THR 0-0.011-0.05021.6820.0030.0030.0000.0000.0000.000
125A129VAL 0-0.004-0.00723.3320.0110.0110.0000.0000.0000.000
126A130GLN 0-0.071-0.05926.4200.0050.0050.0000.0000.0000.000
127A131TRP 0-0.0010.01118.6740.0040.0040.0000.0000.0000.000
128A132VAL 00.003-0.01623.5940.0100.0100.0000.0000.0000.000
129A133ARG 10.8560.91524.8260.0450.0450.0000.0000.0000.000
130A134GLU -1-0.937-0.97325.620-0.028-0.0280.0000.0000.0000.000
131A135ALA 0-0.042-0.00622.7820.0080.0080.0000.0000.0000.000
132A136ALA 0-0.020-0.00824.4550.0090.0090.0000.0000.0000.000
133A137GLN 00.0130.01327.4950.0070.0070.0000.0000.0000.000
134A138ARG 10.8170.89622.738-0.009-0.0090.0000.0000.0000.000
135A139NME 00.0300.04428.867-0.001-0.0010.0000.0000.0000.000
136A145ACE 00.0260.00337.7650.0000.0000.0000.0000.0000.000
137A146ALA 0-0.024-0.02134.3070.0000.0000.0000.0000.0000.000
138A147LEU 00.0380.02533.2450.0010.0010.0000.0000.0000.000
139A148GLU -1-0.878-0.91635.358-0.029-0.0290.0000.0000.0000.000
140A149GLU -1-0.857-0.93832.097-0.053-0.0530.0000.0000.0000.000
141A150SER 00.0670.03233.688-0.003-0.0030.0000.0000.0000.000
142A151THR 0-0.0010.03035.955-0.002-0.0020.0000.0000.0000.000
143A152LEU 00.0590.01729.690-0.001-0.0010.0000.0000.0000.000
144A153THR 00.0200.00931.085-0.005-0.0050.0000.0000.0000.000
145A154THR 0-0.052-0.04232.294-0.004-0.0040.0000.0000.0000.000
146A155ILE 0-0.014-0.01332.563-0.001-0.0010.0000.0000.0000.000
147A156TYR 0-0.0100.01423.6580.0000.0000.0000.0000.0000.000
148A157LEU 00.0360.01229.594-0.004-0.0040.0000.0000.0000.000
149A158MET 0-0.011-0.01031.3550.0000.0000.0000.0000.0000.000
150A159THR 0-0.019-0.03530.2670.0030.0030.0000.0000.0000.000
151A160PHE 0-0.0030.02225.2280.0000.0000.0000.0000.0000.000
152A161PHE 00.042-0.01129.427-0.002-0.0020.0000.0000.0000.000
153A162PHE 0-0.058-0.01932.0180.0010.0010.0000.0000.0000.000
154A163TRP 00.0660.01424.478-0.001-0.0010.0000.0000.0000.000
155A164MET 0-0.052-0.00528.0790.0000.0000.0000.0000.0000.000
156A165ARG 10.8780.93130.2200.0550.0550.0000.0000.0000.000
157A166ASP -1-0.747-0.84531.949-0.031-0.0310.0000.0000.0000.000
158A167GLU -1-0.884-0.95632.003-0.050-0.0500.0000.0000.0000.000
159A168SER 0-0.076-0.02933.9860.0040.0040.0000.0000.0000.000
160A169GLU -1-0.731-0.85331.838-0.019-0.0190.0000.0000.0000.000
161A170ASN 0-0.068-0.04626.7320.0050.0050.0000.0000.0000.000
162A171SER 00.0470.02628.767-0.002-0.0020.0000.0000.0000.000
163A172ARG 10.8800.91430.6970.0110.0110.0000.0000.0000.000
164A173HIS 0-0.036-0.01133.3630.0030.0030.0000.0000.0000.000
165A174THR 00.0170.00029.558-0.001-0.0010.0000.0000.0000.000
166A175ARG 10.9180.97926.3690.0210.0210.0000.0000.0000.000
167A176GLN 00.007-0.01731.9100.0030.0030.0000.0000.0000.000
168A177PHE 00.0060.00633.9520.0020.0020.0000.0000.0000.000
169A178LEU 00.0370.02629.1360.0010.0010.0000.0000.0000.000
170A179LYS 10.9711.00132.8170.0110.0110.0000.0000.0000.000
171A180ARG 10.9531.01334.8600.0180.0180.0000.0000.0000.000
172A181HIS 0-0.017-0.00836.1770.0010.0010.0000.0000.0000.000
173A182LEU 0-0.021-0.00631.0150.0000.0000.0000.0000.0000.000
174A183THR 0-0.041-0.06435.7600.0020.0020.0000.0000.0000.000
175A184MET 0-0.051-0.03338.4690.0010.0010.0000.0000.0000.000
176A185ALA 0-0.0010.00037.9650.0000.0000.0000.0000.0000.000
177A186ALA 0-0.0090.00337.6550.0000.0000.0000.0000.0000.000
178A187TRP 0-0.069-0.03839.4730.0010.0010.0000.0000.0000.000
179A188LEU 0-0.041-0.00542.8950.0010.0010.0000.0000.0000.000
180A189NME 00.0070.01641.3920.0000.0000.0000.0000.0000.000