FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 1N8KZ

Calculation Name: 3RD3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RD3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I1S1

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:

Apendix: None


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 186
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1965725.514587
FMO2-HF: Nuclear repulsion 1890887.97017
FMO2-HF: Total energy -74837.544417
FMO2-MP2: Total energy -75050.737642


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:ASP)


Summations of interaction energy for fragment #1(A:7: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.
-65.156-60.490.069-2.251-2.4840.011
Interaction energy analysis for fragmet #1(A:7:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.847 / q_NPA : -0.915
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].
3A9ARG10.8860.9443.310-49.092-45.5890.051-1.886-1.6680.011
4A10GLN00.000-0.0193.518-6.776-6.1360.020-0.184-0.4760.000
5A11HIS00.0290.0124.187-5.379-5.004-0.001-0.172-0.2020.000
6A12LEU0-0.016-0.0046.179-5.907-5.9070.0000.0000.0000.000
7A13LEU0-0.010-0.0027.838-3.625-3.6250.0000.0000.0000.000
8A14ASP-1-0.823-0.9107.74926.56626.5660.0000.0000.0000.000
9A15THR0-0.061-0.05110.012-2.853-2.8530.0000.0000.0000.000
10A16GLY0-0.006-0.00511.851-1.816-1.8160.0000.0000.0000.000
11A17TYR0-0.031-0.01913.132-1.634-1.6340.0000.0000.0000.000
12A18ARG10.9540.99111.036-23.351-23.3510.0000.0000.0000.000
13A19ILE0-0.008-0.00515.534-1.057-1.0570.0000.0000.0000.000
14A20MET0-0.0150.01317.505-0.994-0.9940.0000.0000.0000.000
15A21ALA00.0390.01618.882-0.886-0.8860.0000.0000.0000.000
16A22VAL00.0000.01220.554-0.835-0.8350.0000.0000.0000.000
17A23LYS10.8470.90721.863-14.286-14.2860.0000.0000.0000.000
18A24GLY00.0320.04122.312-0.558-0.5580.0000.0000.0000.000
19A25PHE0-0.069-0.06718.3941.0231.0230.0000.0000.0000.000
20A26SER0-0.029-0.04622.2630.4700.4700.0000.0000.0000.000
21A27GLY00.0030.00625.3560.0890.0890.0000.0000.0000.000
22A28VAL0-0.0270.00019.7000.1080.1080.0000.0000.0000.000
23A29GLY00.0220.01522.0550.1370.1370.0000.0000.0000.000
24A30LEU0-0.008-0.02315.5060.5150.5150.0000.0000.0000.000
25A31ASN00.0230.00017.4541.2341.2340.0000.0000.0000.000
26A32GLU-1-0.759-0.86018.60514.66014.6600.0000.0000.0000.000
27A33ILE00.0080.02313.6840.6700.6700.0000.0000.0000.000
28A34LEU0-0.038-0.01813.4511.2601.2600.0000.0000.0000.000
29A35GLN0-0.026-0.01814.0700.7360.7360.0000.0000.0000.000
30A36SER0-0.034-0.02715.729-0.103-0.1030.0000.0000.0000.000
31A37ALA0-0.0200.00410.3510.3290.3290.0000.0000.0000.000
32A38GLY00.0210.03010.7152.2252.2250.0000.0000.0000.000
33A39VAL0-0.031-0.0148.2841.9161.9160.0000.0000.0000.000
34A40PRO00.0310.00510.182-2.563-2.5630.0000.0000.0000.000
35A41LYS10.9630.97711.933-16.296-16.2960.0000.0000.0000.000
36A42GLY0-0.006-0.00913.3830.1640.1640.0000.0000.0000.000
37A43SER00.0400.0097.865-0.593-0.5930.0000.0000.0000.000
38A44PHE00.0390.0258.7182.9112.9110.0000.0000.0000.000
39A45TYR00.014-0.01411.045-0.072-0.0720.0000.0000.0000.000
40A46HIS0-0.0500.0008.030-2.057-2.0570.0000.0000.0000.000
41A47TYR0-0.025-0.0124.4720.9451.093-0.001-0.009-0.1380.000
42A48PHE0-0.031-0.0138.583-1.758-1.7580.0000.0000.0000.000
43A49LYS10.9390.96312.678-20.341-20.3410.0000.0000.0000.000
44A50SER00.005-0.00616.135-1.041-1.0410.0000.0000.0000.000
45A51LYS10.8810.94116.570-13.456-13.4560.0000.0000.0000.000
46A52GLU-1-0.745-0.84717.88814.23914.2390.0000.0000.0000.000
47A53GLN0-0.023-0.01213.200-0.044-0.0440.0000.0000.0000.000
48A54PHE00.0030.00110.8180.4150.4150.0000.0000.0000.000
49A55GLY00.0620.02814.7240.3940.3940.0000.0000.0000.000
50A56GLN0-0.005-0.03217.725-0.554-0.5540.0000.0000.0000.000
51A57ALA0-0.0090.00112.291-0.111-0.1110.0000.0000.0000.000
52A58LEU0-0.0120.00012.7080.3530.3530.0000.0000.0000.000
53A59LEU0-0.008-0.00114.774-0.369-0.3690.0000.0000.0000.000
54A60GLU-1-0.874-0.91915.20918.50218.5020.0000.0000.0000.000
55A61ASP-1-0.788-0.88411.20724.08624.0860.0000.0000.0000.000
56A62TYR0-0.0230.00314.099-0.451-0.4510.0000.0000.0000.000
57A63PHE00.0190.00216.579-0.570-0.5700.0000.0000.0000.000
58A64ARG10.7480.84912.237-20.832-20.8320.0000.0000.0000.000
59A65VAL0-0.014-0.00314.083-0.372-0.3720.0000.0000.0000.000
60A66TYR0-0.037-0.03417.249-0.557-0.5570.0000.0000.0000.000
61A67LEU0-0.008-0.01720.557-0.605-0.6050.0000.0000.0000.000
62A68ALA00.0320.02919.430-0.484-0.4840.0000.0000.0000.000
63A69ASP-1-0.857-0.91221.02111.78511.7850.0000.0000.0000.000
64A70MET0-0.007-0.00122.487-0.631-0.6310.0000.0000.0000.000
65A71ASP-1-0.798-0.85424.38711.00611.0060.0000.0000.0000.000
66A72GLN0-0.057-0.00222.769-0.358-0.3580.0000.0000.0000.000
67A73ARG10.7880.88324.895-11.388-11.3880.0000.0000.0000.000
68A74PHE0-0.018-0.03028.199-0.367-0.3670.0000.0000.0000.000
69A75SER0-0.039-0.03828.319-0.292-0.2920.0000.0000.0000.000
70A76ALA00.0070.01629.443-0.178-0.1780.0000.0000.0000.000
71A77PRO00.0290.01730.883-0.313-0.3130.0000.0000.0000.000
72A78GLY0-0.040-0.02233.9060.0940.0940.0000.0000.0000.000
73A79LEU0-0.037-0.00232.191-0.156-0.1560.0000.0000.0000.000
74A80ASN0-0.001-0.00936.2490.1080.1080.0000.0000.0000.000
75A81ALA00.0380.01236.8080.2250.2250.0000.0000.0000.000
76A82ARG10.8140.87836.842-7.007-7.0070.0000.0000.0000.000
77A83GLU-1-0.841-0.91535.6537.8427.8420.0000.0000.0000.000
78A84ARG10.8230.91132.755-8.295-8.2950.0000.0000.0000.000
79A85LEU00.0440.02332.2670.3080.3080.0000.0000.0000.000
80A86MET0-0.030-0.01833.2850.2190.2190.0000.0000.0000.000
81A87SER0-0.016-0.01630.5840.2710.2710.0000.0000.0000.000
82A88TYR0-0.0060.01526.3130.4750.4750.0000.0000.0000.000
83A89TRP00.0430.00229.3370.2930.2930.0000.0000.0000.000
84A90GLN0-0.013-0.01731.378-0.211-0.2110.0000.0000.0000.000
85A91LYS10.8810.94622.903-11.922-11.9220.0000.0000.0000.000
86A92TRP0-0.005-0.00326.4350.4190.4190.0000.0000.0000.000
87A93LEU00.000-0.00327.8960.1900.1900.0000.0000.0000.000
88A94ASP-1-0.850-0.90927.8069.9029.9020.0000.0000.0000.000
89A95ASN0-0.054-0.04022.6670.7990.7990.0000.0000.0000.000
90A96ALA0-0.0440.00424.1200.4310.4310.0000.0000.0000.000
91A97CYS0-0.0020.00623.9920.0490.0490.0000.0000.0000.000
92A98PRO0-0.005-0.00426.8280.2480.2480.0000.0000.0000.000
93A99PRO00.0250.00028.9280.0580.0580.0000.0000.0000.000
94A101ASP-1-0.791-0.88024.58911.15811.1580.0000.0000.0000.000
95A102GLU-1-0.930-0.96918.52115.86515.8650.0000.0000.0000.000
96A103GLN0-0.029-0.00722.775-0.103-0.1030.0000.0000.0000.000
97A104ARG10.9920.97517.863-14.767-14.7670.0000.0000.0000.000
98A105CYS00.0050.03520.7940.4100.4100.0000.0000.0000.000
99A106LEU00.0620.01417.949-0.321-0.3210.0000.0000.0000.000
100A107VAL00.0520.03922.554-0.168-0.1680.0000.0000.0000.000
101A108VAL00.0030.00525.890-0.294-0.2940.0000.0000.0000.000
102A109LYS10.7520.87923.045-12.680-12.6800.0000.0000.0000.000
103A110LEU00.013-0.00921.433-0.170-0.1700.0000.0000.0000.000
104A111SER0-0.021-0.03325.983-0.242-0.2420.0000.0000.0000.000
105A112ALA0-0.041-0.01429.355-0.322-0.3220.0000.0000.0000.000
106A113GLU-1-0.769-0.87025.23412.30212.3020.0000.0000.0000.000
107A114VAL00.0220.01128.362-0.028-0.0280.0000.0000.0000.000
108A115ALA0-0.028-0.00829.7880.0240.0240.0000.0000.0000.000
109A116ASP-1-0.858-0.89029.49510.45610.4560.0000.0000.0000.000
110A117LEU0-0.062-0.01824.5240.5320.5320.0000.0000.0000.000
111A118SER0-0.024-0.04724.298-0.398-0.3980.0000.0000.0000.000
112A119GLU-1-0.795-0.89326.90310.00810.0080.0000.0000.0000.000
113A120SER0-0.031-0.01423.642-0.228-0.2280.0000.0000.0000.000
114A121MET00.0260.04120.5000.2520.2520.0000.0000.0000.000
115A122ARG10.8030.89024.190-10.160-10.1600.0000.0000.0000.000
116A123ILE00.004-0.00326.913-0.148-0.1480.0000.0000.0000.000
117A124THR00.007-0.00820.9170.1040.1040.0000.0000.0000.000
118A125LEU0-0.025-0.00823.8300.1320.1320.0000.0000.0000.000
119A126ARG10.7400.85225.249-10.045-10.0450.0000.0000.0000.000
120A127ASP-1-0.803-0.89526.46210.39010.3900.0000.0000.0000.000
121A128GLY0-0.002-0.00224.327-0.065-0.0650.0000.0000.0000.000
122A129SER00.0000.00025.176-0.102-0.1020.0000.0000.0000.000
123A130ASP-1-0.813-0.90027.8939.2899.2890.0000.0000.0000.000
124A131GLY0-0.0080.00327.258-0.241-0.2410.0000.0000.0000.000
125A132ILE0-0.026-0.01625.0340.0770.0770.0000.0000.0000.000
126A133ILE0-0.009-0.00228.479-0.246-0.2460.0000.0000.0000.000
127A134GLU-1-0.881-0.94931.7738.3508.3500.0000.0000.0000.000
128A135ARG10.7700.84825.604-11.285-11.2850.0000.0000.0000.000
129A136LEU0-0.0110.00531.376-0.191-0.1910.0000.0000.0000.000
130A137VAL0-0.022-0.00633.601-0.287-0.2870.0000.0000.0000.000
131A138GLY00.0050.00235.028-0.241-0.2410.0000.0000.0000.000
132A139CYS0-0.044-0.01633.638-0.147-0.1470.0000.0000.0000.000
133A140LEU00.004-0.01335.745-0.191-0.1910.0000.0000.0000.000
134A141GLY0-0.067-0.03538.868-0.227-0.2270.0000.0000.0000.000
135A142GLN00.0720.04134.862-0.178-0.1780.0000.0000.0000.000
136A143GLY00.0420.00839.776-0.101-0.1010.0000.0000.0000.000
137A144ARG10.8040.90641.329-7.134-7.1340.0000.0000.0000.000
138A145ASP-1-0.935-0.96142.2376.9656.9650.0000.0000.0000.000
139A146ASP-1-0.823-0.89440.6577.3057.3050.0000.0000.0000.000
140A147GLY0-0.0130.00144.000-0.083-0.0830.0000.0000.0000.000
141A148SER0-0.067-0.05441.619-0.080-0.0800.0000.0000.0000.000
142A149LEU0-0.052-0.03939.2250.0710.0710.0000.0000.0000.000
143A150ALA00.0350.02843.936-0.107-0.1070.0000.0000.0000.000
144A151PRO0-0.003-0.01145.7700.1250.1250.0000.0000.0000.000
145A152CYS0-0.0100.00343.982-0.005-0.0050.0000.0000.0000.000
146A153ASP-1-0.824-0.91143.9457.0987.0980.0000.0000.0000.000
147A154ALA00.0310.01239.9080.0730.0730.0000.0000.0000.000
148A155ARG10.9770.98939.408-7.267-7.2670.0000.0000.0000.000
149A156HIS00.0130.01439.6440.2560.2560.0000.0000.0000.000
150A157MET0-0.0020.01040.1320.1440.1440.0000.0000.0000.000
151A158ALA00.0100.00835.7360.1190.1190.0000.0000.0000.000
152A159SER0-0.011-0.01535.9980.2890.2890.0000.0000.0000.000
153A160ALA00.0010.00436.9360.1410.1410.0000.0000.0000.000
154A161LEU00.0050.00436.3940.0590.0590.0000.0000.0000.000
155A162TYR00.047-0.00628.8620.2540.2540.0000.0000.0000.000
156A163GLN0-0.028-0.02633.3450.1890.1890.0000.0000.0000.000
157A164LEU0-0.0230.00635.5900.0720.0720.0000.0000.0000.000
158A165TRP00.0360.00031.5700.1260.1260.0000.0000.0000.000
159A166LEU0-0.0040.01429.5520.2810.2810.0000.0000.0000.000
160A167GLY0-0.0010.00432.0460.1390.1390.0000.0000.0000.000
161A168ALA00.005-0.00234.3220.0040.0040.0000.0000.0000.000
162A169SER0-0.007-0.01929.0280.1850.1850.0000.0000.0000.000
163A170LEU0-0.025-0.01130.8700.1820.1820.0000.0000.0000.000
164A171LEU00.0110.00232.0550.0150.0150.0000.0000.0000.000
165A172SER0-0.005-0.02931.849-0.119-0.1190.0000.0000.0000.000
166A173LYS10.7300.85625.594-11.245-11.2450.0000.0000.0000.000
167A174LEU0-0.041-0.00730.8140.0040.0040.0000.0000.0000.000
168A175HIS0-0.009-0.01433.879-0.071-0.0710.0000.0000.0000.000
169A176ARG10.8450.92729.487-10.187-10.1870.0000.0000.0000.000
170A177SER00.0270.02232.9750.0170.0170.0000.0000.0000.000
171A178PRO00.0460.02433.4300.1350.1350.0000.0000.0000.000
172A179GLY00.0800.05434.525-0.013-0.0130.0000.0000.0000.000
173A180PRO0-0.033-0.01535.541-0.147-0.1470.0000.0000.0000.000
174A181LEU00.0170.01230.570-0.047-0.0470.0000.0000.0000.000
175A182GLU-1-0.898-0.95034.8148.0738.0730.0000.0000.0000.000
176A183THR00.005-0.00937.337-0.212-0.2120.0000.0000.0000.000
177A184ALA00.0120.01635.735-0.162-0.1620.0000.0000.0000.000
178A185MET0-0.0080.01635.472-0.018-0.0180.0000.0000.0000.000
179A186GLN0-0.018-0.01137.447-0.041-0.0410.0000.0000.0000.000
180A187THR0-0.002-0.00940.524-0.201-0.2010.0000.0000.0000.000
181A188THR00.015-0.01736.696-0.056-0.0560.0000.0000.0000.000
182A189ARG10.8610.91936.236-8.035-8.0350.0000.0000.0000.000
183A190SER0-0.034-0.00941.840-0.191-0.1910.0000.0000.0000.000
184A191LEU0-0.058-0.02541.976-0.135-0.1350.0000.0000.0000.000
185A192LEU0-0.026-0.00538.464-0.023-0.0230.0000.0000.0000.000
186A193GLU-1-0.831-0.87241.9277.0567.0560.0000.0000.0000.000