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: 943K2

Calculation Name: 5D93-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D93

Chain ID: A

ChEMBL ID:

UniProt ID: Q8BND5

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2918113.153087
FMO2-HF: Nuclear repulsion 2824799.8993
FMO2-HF: Total energy -93313.253787
FMO2-MP2: Total energy -93585.543519


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:35:MET)


Summations of interaction energy for fragment #1(A:35:MET)
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.
-9.083-3.0183.935-3.359-6.643-0.026
Interaction energy analysis for fragmet #1(A:35:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.019
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].
3A37VAL00.0310.0142.555-5.839-2.2722.129-2.390-3.306-0.019
4A38LEU00.0300.0242.9000.4621.2740.2620.122-1.1980.000
5A39TYR0-0.071-0.0564.4730.6650.771-0.001-0.013-0.0920.000
6A40SER0-0.024-0.0237.375-0.273-0.2730.0000.0000.0000.000
7A41SER00.0660.0179.7780.1090.1090.0000.0000.0000.000
8A42SER0-0.038-0.02711.8510.1350.1350.0000.0000.0000.000
9A43ASP-1-0.832-0.89110.532-0.943-0.9430.0000.0000.0000.000
10A44PRO0-0.048-0.02213.8940.0030.0030.0000.0000.0000.000
11A45LEU0-0.033-0.01811.7290.0480.0480.0000.0000.0000.000
12A46THR0-0.018-0.01714.924-0.016-0.0160.0000.0000.0000.000
13A47LEU0-0.020-0.0189.814-0.012-0.0120.0000.0000.0000.000
14A48LEU0-0.024-0.00912.3470.0880.0880.0000.0000.0000.000
15A49ASP-1-0.820-0.87912.196-0.675-0.6750.0000.0000.0000.000
16A50ALA00.013-0.01914.2610.0660.0660.0000.0000.0000.000
17A51ASP-1-0.935-0.95217.164-0.285-0.2850.0000.0000.0000.000
18A52SER0-0.021-0.05316.5320.0220.0220.0000.0000.0000.000
19A53VAL0-0.0110.00216.8930.0300.0300.0000.0000.0000.000
20A54ARG10.8450.88818.7390.2340.2340.0000.0000.0000.000
21A55PRO0-0.008-0.00521.7700.0170.0170.0000.0000.0000.000
22A56THR0-0.0100.00519.4680.0030.0030.0000.0000.0000.000
23A57VAL0-0.038-0.01920.3990.0140.0140.0000.0000.0000.000
24A58LEU0-0.052-0.01223.3750.0220.0220.0000.0000.0000.000
25A59GLY0-0.035-0.02426.501-0.002-0.0020.0000.0000.0000.000
26A60SER00.0090.01224.9890.0100.0100.0000.0000.0000.000
27A61SER00.0230.01127.8050.0050.0050.0000.0000.0000.000
28A62SER0-0.025-0.01024.8660.0070.0070.0000.0000.0000.000
29A63ALA00.0190.01526.1550.0000.0000.0000.0000.0000.000
30A64TRP0-0.013-0.01819.147-0.030-0.0300.0000.0000.0000.000
31A65ALA00.0080.00319.6590.0260.0260.0000.0000.0000.000
32A66VAL00.0080.00915.058-0.038-0.0380.0000.0000.0000.000
33A67GLU-1-0.825-0.89110.814-0.487-0.4870.0000.0000.0000.000
34A68PHE00.0400.01112.419-0.094-0.0940.0000.0000.0000.000
35A69PHE00.013-0.0195.0030.1660.1660.0000.0000.0000.000
36A70ALA00.0470.0207.511-0.026-0.0260.0000.0000.0000.000
37A71SER00.007-0.0372.227-2.531-1.3891.545-1.016-1.670-0.007
38A72TRP00.0060.0114.1781.0681.4370.001-0.060-0.3110.000
39A73CYS0-0.0480.0146.745-0.212-0.2120.0000.0000.0000.000
40A74GLY00.0160.0079.141-0.038-0.0380.0000.0000.0000.000
41A75HIS00.0380.00111.235-0.049-0.0490.0000.0000.0000.000
42A77ILE00.0030.0076.089-0.183-0.1830.0000.0000.0000.000
43A78ALA0-0.021-0.0148.388-0.118-0.1180.0000.0000.0000.000
44A79PHE0-0.025-0.00211.661-0.031-0.0310.0000.0000.0000.000
45A80ALA00.0560.0308.175-0.044-0.0440.0000.0000.0000.000
46A81PRO0-0.021-0.01210.186-0.075-0.0750.0000.0000.0000.000
47A82THR00.0310.01412.405-0.006-0.0060.0000.0000.0000.000
48A83TRP00.016-0.00412.0280.0580.0580.0000.0000.0000.000
49A84LYS10.8630.9337.9551.2031.2030.0000.0000.0000.000
50A85GLU-1-0.944-0.95913.681-0.180-0.1800.0000.0000.0000.000
51A86LEU00.004-0.00716.9040.0220.0220.0000.0000.0000.000
52A87ALA00.0170.00815.8740.0210.0210.0000.0000.0000.000
53A88ASN0-0.058-0.04116.1650.0430.0430.0000.0000.0000.000
54A89ASP-1-0.778-0.84519.341-0.156-0.1560.0000.0000.0000.000
55A90VAL00.0230.02120.7990.0230.0230.0000.0000.0000.000
56A91LYS10.8760.95220.1860.2890.2890.0000.0000.0000.000
57A92ASP-1-0.821-0.90522.486-0.203-0.2030.0000.0000.0000.000
58A93TRP0-0.002-0.02325.2810.0110.0110.0000.0000.0000.000
59A94ARG10.8910.97919.9830.3400.3400.0000.0000.0000.000
60A95PRO0-0.039-0.02225.4270.0080.0080.0000.0000.0000.000
61A96ALA00.0160.00527.0310.0050.0050.0000.0000.0000.000
62A97LEU00.019-0.00523.1240.0060.0060.0000.0000.0000.000
63A98ASN0-0.033-0.02820.600-0.025-0.0250.0000.0000.0000.000
64A99LEU00.0070.01316.9890.0140.0140.0000.0000.0000.000
65A100ALA00.0310.01014.991-0.030-0.0300.0000.0000.0000.000
66A101VAL0-0.036-0.0049.7760.0320.0320.0000.0000.0000.000
67A102LEU00.0100.01310.989-0.032-0.0320.0000.0000.0000.000
68A103ASP-1-0.746-0.8474.902-1.550-1.481-0.001-0.002-0.0660.000
69A104CYS00.002-0.0138.4440.0380.0380.0000.0000.0000.000
70A105ALA0-0.050-0.0226.7340.1550.1550.0000.0000.0000.000
71A106GLU-1-0.922-0.9467.728-1.128-1.1280.0000.0000.0000.000
72A107GLU-1-0.905-0.9519.806-0.094-0.0940.0000.0000.0000.000
73A108THR0-0.003-0.00113.3090.0460.0460.0000.0000.0000.000
74A109ASN00.018-0.00710.4990.1080.1080.0000.0000.0000.000
75A110SER0-0.040-0.02914.0420.0550.0550.0000.0000.0000.000
76A111ALA0-0.087-0.02815.5090.0390.0390.0000.0000.0000.000
77A112VAL00.0960.04715.9720.0220.0220.0000.0000.0000.000
78A114ARG10.9510.97816.7500.1390.1390.0000.0000.0000.000
79A115GLU-1-0.846-0.90219.989-0.183-0.1830.0000.0000.0000.000
80A116PHE0-0.015-0.01018.9370.0090.0090.0000.0000.0000.000
81A117ASN0-0.0180.00021.000-0.004-0.0040.0000.0000.0000.000
82A118ILE0-0.0160.00315.2020.0100.0100.0000.0000.0000.000
83A119ALA0-0.016-0.00917.9410.0110.0110.0000.0000.0000.000
84A120GLY00.0120.01116.5020.0300.0300.0000.0000.0000.000
85A121PHE0-0.0300.01111.695-0.043-0.0430.0000.0000.0000.000
86A122PRO00.003-0.01011.8810.0630.0630.0000.0000.0000.000
87A123THR0-0.051-0.05013.4210.0410.0410.0000.0000.0000.000
88A124VAL00.0160.01815.893-0.042-0.0420.0000.0000.0000.000
89A125ARG10.7840.88117.4540.2030.2030.0000.0000.0000.000
90A126PHE00.0340.01020.089-0.028-0.0280.0000.0000.0000.000
91A127PHE0-0.010-0.01519.8850.0160.0160.0000.0000.0000.000
92A128GLN00.0510.03424.7380.0010.0010.0000.0000.0000.000
93A129ALA00.0710.05828.041-0.007-0.0070.0000.0000.0000.000
94A130PHE0-0.032-0.02429.6620.0110.0110.0000.0000.0000.000
95A131THR0-0.039-0.02526.8550.0140.0140.0000.0000.0000.000
96A132LYS10.9120.95528.9940.1040.1040.0000.0000.0000.000
97A133ASN0-0.009-0.00928.382-0.001-0.0010.0000.0000.0000.000
98A134GLY00.0210.01226.8880.0040.0040.0000.0000.0000.000
99A135SER0-0.013-0.01722.193-0.013-0.0130.0000.0000.0000.000
100A136GLY00.0580.04222.001-0.014-0.0140.0000.0000.0000.000
101A137ALA0-0.022-0.00823.9760.0130.0130.0000.0000.0000.000
102A138THR0-0.014-0.01620.850-0.021-0.0210.0000.0000.0000.000
103A139LEU00.0030.01620.8950.0130.0130.0000.0000.0000.000
104A140PRO0-0.021-0.02420.5290.0010.0010.0000.0000.0000.000
105A141GLY00.0830.03716.979-0.027-0.0270.0000.0000.0000.000
106A142ALA00.0110.00116.2570.0030.0030.0000.0000.0000.000
107A143GLY0-0.016-0.00217.1330.0050.0050.0000.0000.0000.000
108A144ALA0-0.0220.00818.9580.0030.0030.0000.0000.0000.000
109A145ASN00.0500.02818.934-0.014-0.0140.0000.0000.0000.000
110A146VAL00.0770.03118.673-0.003-0.0030.0000.0000.0000.000
111A147GLN00.0040.00921.013-0.003-0.0030.0000.0000.0000.000
112A148THR00.017-0.01623.4760.0040.0040.0000.0000.0000.000
113A149LEU0-0.033-0.01317.9580.0000.0000.0000.0000.0000.000
114A150ARG10.8110.87322.2240.1460.1460.0000.0000.0000.000
115A151MET0-0.051-0.01624.3420.0040.0040.0000.0000.0000.000
116A152ARG10.8830.92724.6050.0970.0970.0000.0000.0000.000
117A153LEU0-0.0050.00420.848-0.002-0.0020.0000.0000.0000.000
118A154ILE0-0.0080.00425.2530.0010.0010.0000.0000.0000.000
119A155ASP-1-0.773-0.86428.812-0.096-0.0960.0000.0000.0000.000
120A156ALA0-0.017-0.00126.7000.0050.0050.0000.0000.0000.000
121A157LEU0-0.046-0.01927.759-0.002-0.0020.0000.0000.0000.000
122A158GLU-1-0.830-0.92830.205-0.092-0.0920.0000.0000.0000.000
123A159SER0-0.035-0.00731.4130.0060.0060.0000.0000.0000.000
124A160HIS0-0.026-0.00828.720-0.008-0.0080.0000.0000.0000.000
125A161ARG10.8760.94333.0220.0930.0930.0000.0000.0000.000
126A162ASP-1-0.899-0.96135.191-0.097-0.0970.0000.0000.0000.000
127A163THR0-0.051-0.02632.3040.0020.0020.0000.0000.0000.000
128A164TRP0-0.007-0.02133.6900.0020.0020.0000.0000.0000.000
129A165PRO00.0370.02129.812-0.001-0.0010.0000.0000.0000.000
130A166PRO0-0.038-0.02231.9670.0050.0050.0000.0000.0000.000
131A167ALA0-0.0030.01330.9810.0050.0050.0000.0000.0000.000
132A168CYS0-0.007-0.00231.601-0.004-0.0040.0000.0000.0000.000
133A169PRO0-0.0090.01133.1450.0070.0070.0000.0000.0000.000
134A170PRO00.019-0.01035.749-0.002-0.0020.0000.0000.0000.000
135A171LEU00.0550.03132.0860.0010.0010.0000.0000.0000.000
136A172GLU-1-0.804-0.86136.648-0.070-0.0700.0000.0000.0000.000
137A173PRO0-0.011-0.00439.864-0.001-0.0010.0000.0000.0000.000
138A174ALA0-0.031-0.01542.0380.0010.0010.0000.0000.0000.000
139A175LYS10.8670.90544.9100.0670.0670.0000.0000.0000.000
140A176LEU00.0170.00548.621-0.002-0.0020.0000.0000.0000.000
141A177ASN0-0.024-0.02651.035-0.002-0.0020.0000.0000.0000.000
142A178ASP-1-0.763-0.84746.323-0.066-0.0660.0000.0000.0000.000
143A179ILE0-0.010-0.00346.803-0.002-0.0020.0000.0000.0000.000
144A180ASP-1-0.764-0.86550.032-0.045-0.0450.0000.0000.0000.000
145A181GLY00.0390.02353.8280.0000.0000.0000.0000.0000.000
146A182PHE00.0140.02044.508-0.001-0.0010.0000.0000.0000.000
147A183PHE00.0170.00747.180-0.001-0.0010.0000.0000.0000.000
148A184THR0-0.073-0.03850.8290.0000.0000.0000.0000.0000.000
149A185ARG10.8350.91849.8510.0560.0560.0000.0000.0000.000
150A186ASN0-0.010-0.01243.485-0.004-0.0040.0000.0000.0000.000
151A187LYS10.9170.94645.4160.0740.0740.0000.0000.0000.000
152A188ALA00.0350.04943.0460.0000.0000.0000.0000.0000.000
153A189ASP-1-0.887-0.95044.766-0.065-0.0650.0000.0000.0000.000
154A190TYR0-0.041-0.03742.9280.0050.0050.0000.0000.0000.000
155A191LEU0-0.026-0.01743.184-0.003-0.0030.0000.0000.0000.000
156A192ALA00.0240.01940.2210.0030.0030.0000.0000.0000.000
157A193LEU0-0.011-0.01542.114-0.002-0.0020.0000.0000.0000.000
158A194VAL00.0330.01037.5460.0020.0020.0000.0000.0000.000
159A195PHE00.0130.01940.8100.0000.0000.0000.0000.0000.000
160A196GLU-1-0.777-0.87637.363-0.081-0.0810.0000.0000.0000.000
161A197ARG10.9280.96240.0290.0500.0500.0000.0000.0000.000
162A198GLU-1-0.939-0.97839.602-0.052-0.0520.0000.0000.0000.000
163A199ASP-1-0.925-0.95836.620-0.060-0.0600.0000.0000.0000.000
164A200SER0-0.042-0.04335.154-0.005-0.0050.0000.0000.0000.000
165A201TYR0-0.026-0.05230.5820.0000.0000.0000.0000.0000.000
166A202LEU00.0040.01933.014-0.006-0.0060.0000.0000.0000.000
167A203GLY00.0370.00234.076-0.005-0.0050.0000.0000.0000.000
168A204ARG10.7700.88432.7210.0910.0910.0000.0000.0000.000
169A205GLU-1-0.818-0.91828.986-0.126-0.1260.0000.0000.0000.000
170A206VAL0-0.012-0.00330.892-0.007-0.0070.0000.0000.0000.000
171A207THR0-0.024-0.03033.3280.0000.0000.0000.0000.0000.000
172A208LEU00.0080.00628.634-0.003-0.0030.0000.0000.0000.000
173A209ASP-1-0.780-0.80828.474-0.161-0.1610.0000.0000.0000.000
174A210LEU0-0.024-0.01930.227-0.003-0.0030.0000.0000.0000.000
175A211SER0-0.016-0.00130.3560.0020.0020.0000.0000.0000.000
176A212GLN0-0.014-0.01026.6580.0100.0100.0000.0000.0000.000
177A213TYR0-0.055-0.03929.6950.0030.0030.0000.0000.0000.000
178A214HIS00.003-0.00834.6610.0060.0060.0000.0000.0000.000
179A215ALA00.0100.02338.4650.0050.0050.0000.0000.0000.000
180A216VAL0-0.007-0.00837.9960.0060.0060.0000.0000.0000.000
181A217ALA0-0.0210.00439.221-0.005-0.0050.0000.0000.0000.000
182A218VAL0-0.003-0.00736.6820.0030.0030.0000.0000.0000.000
183A219ARG10.7600.86139.6760.0750.0750.0000.0000.0000.000
184A220ARG10.8590.93637.2980.0830.0830.0000.0000.0000.000
185A221VAL00.0100.00640.8100.0010.0010.0000.0000.0000.000
186A222LEU00.0430.03341.2380.0000.0000.0000.0000.0000.000
187A223ASN00.001-0.01144.3700.0000.0000.0000.0000.0000.000
188A224THR00.001-0.01046.6460.0020.0020.0000.0000.0000.000
189A225GLU-1-0.850-0.91447.680-0.047-0.0470.0000.0000.0000.000
190A226SER00.005-0.01449.4150.0000.0000.0000.0000.0000.000
191A227ASP-1-0.884-0.92352.788-0.040-0.0400.0000.0000.0000.000
192A228LEU0-0.023-0.01347.9380.0000.0000.0000.0000.0000.000
193A229VAL00.0080.00648.6020.0000.0000.0000.0000.0000.000
194A230ASN0-0.057-0.03850.9990.0020.0020.0000.0000.0000.000
195A231LYS10.7890.89353.5580.0450.0450.0000.0000.0000.000
196A232PHE0-0.025-0.01950.4270.0000.0000.0000.0000.0000.000
197A233GLY00.0010.00851.7660.0000.0000.0000.0000.0000.000
198A234VAL0-0.047-0.01746.8630.0010.0010.0000.0000.0000.000
199A235THR00.013-0.02449.7580.0010.0010.0000.0000.0000.000
200A236ASP-1-0.852-0.86945.334-0.042-0.0420.0000.0000.0000.000
201A237PHE00.0120.02743.045-0.003-0.0030.0000.0000.0000.000
202A238PRO0-0.025-0.02337.8760.0020.0020.0000.0000.0000.000
203A239SER0-0.001-0.01640.7820.0030.0030.0000.0000.0000.000
204A240CYS0-0.043-0.00339.608-0.003-0.0030.0000.0000.0000.000
205A241TYR00.0240.00742.3330.0030.0030.0000.0000.0000.000
206A242LEU0-0.016-0.00843.240-0.004-0.0040.0000.0000.0000.000
207A243LEU0-0.0050.00345.6680.0040.0040.0000.0000.0000.000
208A244LEU00.023-0.00247.046-0.004-0.0040.0000.0000.0000.000
209A245ARG10.8590.91848.6480.0660.0660.0000.0000.0000.000
210A246ASN0-0.0280.00650.9190.0010.0010.0000.0000.0000.000
211A247GLY00.0140.01453.1160.0020.0020.0000.0000.0000.000
212A248SER0-0.056-0.04451.6670.0020.0020.0000.0000.0000.000
213A249VAL00.008-0.00750.578-0.002-0.0020.0000.0000.0000.000
214A250SER0-0.052-0.01248.0900.0010.0010.0000.0000.0000.000
215A251ARG10.8060.88444.5570.0480.0480.0000.0000.0000.000
216A252VAL0-0.010-0.02140.7000.0010.0010.0000.0000.0000.000
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