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: 6Y4RZ

Calculation Name: 3C8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C8U

Chain ID: A

ChEMBL ID:

UniProt ID: Q1GJR2

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 OptH
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 -2245061.615443
FMO2-HF: Nuclear repulsion 2166897.665336
FMO2-HF: Total energy -78163.950107
FMO2-MP2: Total energy -78393.134458


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
-3.431-2.4414.39-2.553-2.827-0.021
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.007
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].
3A2THR00.0360.0183.8172.7433.589-0.011-0.339-0.4960.000
4A3LEU00.0730.0206.845-0.353-0.3530.0000.0000.0000.000
5A4ALA0-0.020-0.0029.690-0.148-0.1480.0000.0000.0000.000
6A5ALA00.0320.0087.727-0.052-0.0520.0000.0000.0000.000
7A6LEU00.0140.0088.390-0.083-0.0830.0000.0000.0000.000
8A7CYS0-0.031-0.0159.9780.0010.0010.0000.0000.0000.000
9A8GLN0-0.022-0.01113.0510.0290.0290.0000.0000.0000.000
10A9GLY00.0220.01012.3090.0000.0000.0000.0000.0000.000
11A10VAL00.009-0.00413.2010.0200.0200.0000.0000.0000.000
12A11LEU00.003-0.01115.3560.0230.0230.0000.0000.0000.000
13A12GLU-1-0.952-0.96515.609-0.386-0.3860.0000.0000.0000.000
14A13ARG10.8670.92613.1150.5140.5140.0000.0000.0000.000
15A14LEU0-0.0460.01018.8440.0190.0190.0000.0000.0000.000
16A15ASP-1-0.789-0.89921.431-0.121-0.1210.0000.0000.0000.000
17A16PRO0-0.081-0.05024.6420.0140.0140.0000.0000.0000.000
18A17ARG10.8740.93027.0450.0930.0930.0000.0000.0000.000
19A18GLN0-0.041-0.01326.2510.0010.0010.0000.0000.0000.000
20A19PRO0-0.062-0.03529.6190.0050.0050.0000.0000.0000.000
21A20GLY00.0020.01330.932-0.003-0.0030.0000.0000.0000.000
22A21ARG10.7450.85126.7260.0300.0300.0000.0000.0000.000
23A22GLN0-0.004-0.00623.279-0.014-0.0140.0000.0000.0000.000
24A23LEU0-0.026-0.01422.9150.0130.0130.0000.0000.0000.000
25A24VAL00.0210.01116.315-0.020-0.0200.0000.0000.0000.000
26A25ALA00.0100.02818.2030.0270.0270.0000.0000.0000.000
27A26LEU0-0.018-0.00911.991-0.033-0.0330.0000.0000.0000.000
28A27SER00.0290.00014.8050.0390.0390.0000.0000.0000.000
29A28GLY0-0.015-0.00614.005-0.024-0.0240.0000.0000.0000.000
30A29ALA00.0500.03415.342-0.014-0.0140.0000.0000.0000.000
31A30PRO0-0.006-0.01417.3850.0310.0310.0000.0000.0000.000
32A31GLY00.0710.03618.323-0.002-0.0020.0000.0000.0000.000
33A32SER0-0.053-0.04113.4380.0350.0350.0000.0000.0000.000
34A33GLY00.0200.00913.3260.0490.0490.0000.0000.0000.000
35A34LYS10.9420.99213.8660.0090.0090.0000.0000.0000.000
36A35SER00.013-0.00714.9440.0100.0100.0000.0000.0000.000
37A36THR0-0.104-0.06214.0500.0230.0230.0000.0000.0000.000
38A37LEU00.0100.0129.4540.0600.0600.0000.0000.0000.000
39A38SER0-0.021-0.05212.913-0.018-0.0180.0000.0000.0000.000
40A39ASN00.008-0.01015.653-0.032-0.0320.0000.0000.0000.000
41A40PRO0-0.014-0.00713.976-0.020-0.0200.0000.0000.0000.000
42A41LEU00.0210.01712.717-0.015-0.0150.0000.0000.0000.000
43A42ALA00.0470.02715.019-0.033-0.0330.0000.0000.0000.000
44A43ALA0-0.0120.00118.488-0.016-0.0160.0000.0000.0000.000
45A44ALA0-0.030-0.01915.625-0.010-0.0100.0000.0000.0000.000
46A45LEU00.0440.00416.820-0.020-0.0200.0000.0000.0000.000
47A46SER00.0410.01319.127-0.011-0.0110.0000.0000.0000.000
48A47ALA0-0.079-0.02820.379-0.004-0.0040.0000.0000.0000.000
49A48GLN0-0.077-0.03418.634-0.011-0.0110.0000.0000.0000.000
50A49GLY0-0.0050.00321.929-0.014-0.0140.0000.0000.0000.000
51A50LEU0-0.052-0.03820.962-0.006-0.0060.0000.0000.0000.000
52A51PRO0-0.039-0.01022.7770.0040.0040.0000.0000.0000.000
53A52ALA00.0160.01620.892-0.010-0.0100.0000.0000.0000.000
54A53GLU-1-0.919-0.96722.9000.0290.0290.0000.0000.0000.000
55A54VAL0-0.023-0.00919.235-0.014-0.0140.0000.0000.0000.000
56A55VAL0-0.0040.00621.8860.0050.0050.0000.0000.0000.000
57A56PRO0-0.015-0.01522.722-0.010-0.0100.0000.0000.0000.000
58A57MET00.0220.03923.146-0.005-0.0050.0000.0000.0000.000
59A58ASP-1-0.828-0.91624.5270.0300.0300.0000.0000.0000.000
60A59GLY0-0.062-0.01426.5850.0020.0020.0000.0000.0000.000
61A60PHE00.022-0.00428.658-0.001-0.0010.0000.0000.0000.000
62A61HIS0-0.075-0.01727.023-0.004-0.0040.0000.0000.0000.000
63A62LEU0-0.013-0.00631.3730.0010.0010.0000.0000.0000.000
64A63ASP-1-0.814-0.90934.7180.0140.0140.0000.0000.0000.000
65A64ASN00.0940.02036.160-0.004-0.0040.0000.0000.0000.000
66A65ARG10.8780.93838.367-0.009-0.0090.0000.0000.0000.000
67A66LEU0-0.050-0.02839.036-0.002-0.0020.0000.0000.0000.000
68A67LEU0-0.031-0.01534.086-0.002-0.0020.0000.0000.0000.000
69A68GLU-1-0.959-0.97738.4530.0030.0030.0000.0000.0000.000
70A69PRO00.0550.03141.120-0.001-0.0010.0000.0000.0000.000
71A70ARG10.8910.95138.4150.0100.0100.0000.0000.0000.000
72A71GLY00.0160.01440.222-0.002-0.0020.0000.0000.0000.000
73A72LEU0-0.010-0.01434.5360.0000.0000.0000.0000.0000.000
74A73LEU00.0060.01934.9630.0010.0010.0000.0000.0000.000
75A74PRO0-0.022-0.02434.6950.0030.0030.0000.0000.0000.000
76A75ARG10.8220.89530.1460.0190.0190.0000.0000.0000.000
77A76LYS10.8330.92530.607-0.022-0.0220.0000.0000.0000.000
78A77GLY00.0460.04027.4150.0060.0060.0000.0000.0000.000
79A78ALA00.0230.03326.363-0.005-0.0050.0000.0000.0000.000
80A79PRO00.0450.03826.0040.0030.0030.0000.0000.0000.000
81A80GLU-1-0.789-0.88228.135-0.025-0.0250.0000.0000.0000.000
82A81THR0-0.105-0.06730.0140.0050.0050.0000.0000.0000.000
83A82PHE0-0.016-0.01326.2980.0040.0040.0000.0000.0000.000
84A83ASP-1-0.868-0.94231.006-0.023-0.0230.0000.0000.0000.000
85A84PHE00.0030.00728.2250.0000.0000.0000.0000.0000.000
86A85GLU-1-0.921-0.96531.360-0.036-0.0360.0000.0000.0000.000
87A86GLY0-0.036-0.01633.941-0.002-0.0020.0000.0000.0000.000
88A87PHE00.0110.00224.1230.0000.0000.0000.0000.0000.000
89A88GLN00.0270.00729.527-0.008-0.0080.0000.0000.0000.000
90A89ARG10.9330.95930.5480.0260.0260.0000.0000.0000.000
91A90LEU0-0.0120.01028.4060.0000.0000.0000.0000.0000.000
92A91CYS0-0.015-0.00826.685-0.002-0.0020.0000.0000.0000.000
93A92HIS00.0210.00028.621-0.003-0.0030.0000.0000.0000.000
94A93ALA0-0.038-0.01031.440-0.001-0.0010.0000.0000.0000.000
95A94LEU00.010-0.00626.7630.0020.0020.0000.0000.0000.000
96A95LYS10.9721.03228.6260.0850.0850.0000.0000.0000.000
97A96HIS00.032-0.01230.3290.0020.0020.0000.0000.0000.000
98A97GLN0-0.0540.00333.7360.0010.0010.0000.0000.0000.000
99A98GLU-1-0.863-0.93633.572-0.028-0.0280.0000.0000.0000.000
100A99ARG10.8530.94433.8780.0050.0050.0000.0000.0000.000
101A100VAL0-0.035-0.01532.031-0.001-0.0010.0000.0000.0000.000
102A101ILE00.0110.02032.8390.0030.0030.0000.0000.0000.000
103A102TYR0-0.035-0.02627.443-0.003-0.0030.0000.0000.0000.000
104A103PRO0-0.009-0.00631.5720.0040.0040.0000.0000.0000.000
105A104LEU00.0260.02127.9940.0000.0000.0000.0000.0000.000
106A105PHE0-0.048-0.02528.1600.0000.0000.0000.0000.0000.000
107A106ASP-1-0.799-0.89129.3640.0510.0510.0000.0000.0000.000
108A107ARG10.8860.91224.834-0.056-0.0560.0000.0000.0000.000
109A108ALA0-0.0050.01130.168-0.001-0.0010.0000.0000.0000.000
110A109ARG10.8630.90632.983-0.037-0.0370.0000.0000.0000.000
111A110ASP-1-0.822-0.88232.9120.0220.0220.0000.0000.0000.000
112A111ILE0-0.028-0.00733.992-0.005-0.0050.0000.0000.0000.000
113A112ALA00.0090.01132.6320.0040.0040.0000.0000.0000.000
114A113ILE0-0.032-0.01133.651-0.002-0.0020.0000.0000.0000.000
115A114ALA00.016-0.00534.585-0.001-0.0010.0000.0000.0000.000
116A115GLY0-0.002-0.01336.0770.0020.0020.0000.0000.0000.000
117A116ALA0-0.034-0.00933.0930.0010.0010.0000.0000.0000.000
118A117ALA00.0150.01030.1640.0050.0050.0000.0000.0000.000
119A118GLU-1-0.871-0.97031.772-0.002-0.0020.0000.0000.0000.000
120A119VAL00.0210.03428.0540.0030.0030.0000.0000.0000.000
121A120GLY00.0700.03030.509-0.003-0.0030.0000.0000.0000.000
122A121PRO0-0.017-0.02431.334-0.003-0.0030.0000.0000.0000.000
123A122GLU-1-0.913-0.94930.119-0.003-0.0030.0000.0000.0000.000
124A123CYS0-0.072-0.00925.780-0.005-0.0050.0000.0000.0000.000
125A124ARG10.9590.98126.0010.0540.0540.0000.0000.0000.000
126A125VAL0-0.006-0.01020.382-0.012-0.0120.0000.0000.0000.000
127A126ALA00.0510.02923.4300.0140.0140.0000.0000.0000.000
128A127ILE0-0.004-0.00516.947-0.016-0.0160.0000.0000.0000.000
129A128ILE0-0.0020.01120.0850.0210.0210.0000.0000.0000.000
130A129GLU-1-0.732-0.83118.0310.0540.0540.0000.0000.0000.000
131A130GLY00.022-0.03418.7600.0110.0110.0000.0000.0000.000
132A131ASN0-0.036-0.03818.624-0.004-0.0040.0000.0000.0000.000
133A132TYR0-0.019-0.02819.859-0.012-0.0120.0000.0000.0000.000
134A133LEU00.0400.01918.8910.0010.0010.0000.0000.0000.000
135A134LEU0-0.0140.00815.435-0.012-0.0120.0000.0000.0000.000
136A135PHE0-0.0020.00519.542-0.009-0.0090.0000.0000.0000.000
137A136ASP-1-0.791-0.89122.214-0.116-0.1160.0000.0000.0000.000
138A137ALA0-0.008-0.01624.4720.0080.0080.0000.0000.0000.000
139A138PRO0-0.024-0.02627.789-0.003-0.0030.0000.0000.0000.000
140A139GLY00.0590.04930.3190.0040.0040.0000.0000.0000.000
141A140TRP00.029-0.01125.312-0.003-0.0030.0000.0000.0000.000
142A141ARG10.8550.92124.9120.0900.0900.0000.0000.0000.000
143A142ASP-1-0.914-0.95525.678-0.095-0.0950.0000.0000.0000.000
144A143LEU0-0.038-0.02924.3110.0000.0000.0000.0000.0000.000
145A144THR0-0.055-0.02521.291-0.005-0.0050.0000.0000.0000.000
146A145ALA0-0.0030.00823.073-0.010-0.0100.0000.0000.0000.000
147A146ILE0-0.077-0.03925.3420.0040.0040.0000.0000.0000.000
148A147TRP0-0.073-0.05220.0960.0110.0110.0000.0000.0000.000
149A148ASP-1-0.776-0.87421.886-0.125-0.1250.0000.0000.0000.000
150A149VAL0-0.0110.00215.329-0.027-0.0270.0000.0000.0000.000
151A150SER0-0.030-0.01816.1890.0220.0220.0000.0000.0000.000
152A151ILE00.007-0.00610.245-0.070-0.0700.0000.0000.0000.000
153A152ARG10.8730.94111.0260.4080.4080.0000.0000.0000.000
154A153LEU0-0.061-0.0239.024-0.119-0.1190.0000.0000.0000.000
155A154GLU-1-0.849-0.9337.917-0.337-0.3370.0000.0000.0000.000
156A155VAL0-0.052-0.0368.5300.0770.0770.0000.0000.0000.000
157A156PRO00.0560.0369.722-0.041-0.0410.0000.0000.0000.000
158A157MET00.0430.00412.8810.0400.0400.0000.0000.0000.000
159A158ALA00.0280.02415.7600.0140.0140.0000.0000.0000.000
160A159ASP-1-0.859-0.94011.7100.2470.2470.0000.0000.0000.000
161A160LEU0-0.074-0.04714.9260.0210.0210.0000.0000.0000.000
162A161GLU-1-0.859-0.92116.9390.0560.0560.0000.0000.0000.000
163A162ALA00.0190.01517.8700.0010.0010.0000.0000.0000.000
164A163ARG10.8960.95311.229-0.335-0.3350.0000.0000.0000.000
165A164LEU0-0.049-0.02619.115-0.004-0.0040.0000.0000.0000.000
166A165VAL00.0110.00722.025-0.006-0.0060.0000.0000.0000.000
167A166GLN00.007-0.00221.824-0.002-0.0020.0000.0000.0000.000
168A167ARG10.8730.94222.272-0.083-0.0830.0000.0000.0000.000
169A168TRP0-0.045-0.03624.552-0.008-0.0080.0000.0000.0000.000
170A169LEU0-0.020-0.01025.830-0.007-0.0070.0000.0000.0000.000
171A170ASP-1-0.880-0.92725.0850.1360.1360.0000.0000.0000.000
172A171HIS0-0.109-0.04828.390-0.002-0.0020.0000.0000.0000.000
173A172GLY00.0050.00730.851-0.007-0.0070.0000.0000.0000.000
174A173LEU0-0.104-0.03930.974-0.007-0.0070.0000.0000.0000.000
175A174ASN00.0560.03131.9040.0060.0060.0000.0000.0000.000
176A175HIS00.1050.02226.2920.0030.0030.0000.0000.0000.000
177A176ASP-1-0.895-0.94230.0170.0510.0510.0000.0000.0000.000
178A177ALA0-0.036-0.02631.904-0.003-0.0030.0000.0000.0000.000
179A178ALA0-0.020-0.01127.786-0.003-0.0030.0000.0000.0000.000
180A179VAL00.0230.00626.6170.0000.0000.0000.0000.0000.000
181A180ALA0-0.0030.00728.102-0.005-0.0050.0000.0000.0000.000
182A181ARG10.9010.95829.370-0.046-0.0460.0000.0000.0000.000
183A182ALA0-0.023-0.01524.434-0.005-0.0050.0000.0000.0000.000
184A183GLN0-0.043-0.04125.466-0.010-0.0100.0000.0000.0000.000
185A184GLY0-0.0230.01527.029-0.008-0.0080.0000.0000.0000.000
186A185ASN0-0.002-0.04227.443-0.009-0.0090.0000.0000.0000.000
187A186ASP-1-0.797-0.89323.2490.0370.0370.0000.0000.0000.000
188A187LEU00.0270.01020.790-0.009-0.0090.0000.0000.0000.000
189A188ALA0-0.033-0.01423.166-0.012-0.0120.0000.0000.0000.000
190A189ASN0-0.012-0.01423.811-0.016-0.0160.0000.0000.0000.000
191A190ALA0-0.019-0.00919.016-0.012-0.0120.0000.0000.0000.000
192A191ARG10.9620.98919.806-0.002-0.0020.0000.0000.0000.000
193A192ALA0-0.006-0.00722.002-0.013-0.0130.0000.0000.0000.000
194A193ILE0-0.030-0.02317.788-0.008-0.0080.0000.0000.0000.000
195A194GLU-1-0.878-0.93516.021-0.211-0.2110.0000.0000.0000.000
196A195ALA0-0.061-0.03018.821-0.018-0.0180.0000.0000.0000.000
197A196ALA0-0.0260.00121.229-0.001-0.0010.0000.0000.0000.000
198A197ARG10.7920.89612.4740.3160.3160.0000.0000.0000.000
199A198LEU00.0040.02019.074-0.004-0.0040.0000.0000.0000.000
200A199PRO00.001-0.00916.359-0.025-0.0250.0000.0000.0000.000
201A200ALA00.0020.00412.7420.0310.0310.0000.0000.0000.000
202A201ASP-1-0.857-0.90714.159-0.366-0.3660.0000.0000.0000.000
203A202LEU0-0.070-0.0419.855-0.117-0.1170.0000.0000.0000.000
204A203THR0-0.005-0.0017.2890.2160.2160.0000.0000.0000.000
205A204TRP0-0.006-0.0095.120-0.444-0.4440.0000.0000.0000.000
206A205PRO00.0430.0362.111-4.900-4.7564.401-2.214-2.331-0.021