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: 6Y68Z

Calculation Name: 1SUL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SUL

Chain ID: A

ChEMBL ID:

UniProt ID: P38424

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptHSide
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2104577.752801
FMO2-HF: Nuclear repulsion 2031421.371835
FMO2-HF: Total energy -73156.380966
FMO2-MP2: Total energy -73372.750291


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-19.561-12.74723.002-9.413-20.403-0.067
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.073 / q_NPA : -0.011
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].
3A3VAL0-0.0020.0042.1640.2422.5241.473-1.085-2.6710.002
4A4THR0-0.033-0.0184.505-0.1040.0570.000-0.025-0.1360.000
5A5LYS10.7530.8556.0980.5190.5190.0000.0000.0000.000
6A6SER0-0.029-0.0086.233-0.616-0.6160.0000.0000.0000.000
7A7GLU-1-0.838-0.8988.550-0.380-0.3800.0000.0000.0000.000
8A8ILE00.000-0.00311.560-0.126-0.1260.0000.0000.0000.000
9A9VAL0-0.040-0.01812.6520.0600.0600.0000.0000.0000.000
10A10ILE00.0130.00615.4160.0730.0730.0000.0000.0000.000
11A11SER0-0.036-0.02117.781-0.065-0.0650.0000.0000.0000.000
12A12ALA0-0.023-0.00620.2090.0450.0450.0000.0000.0000.000
13A13VAL0-0.008-0.02821.934-0.020-0.0200.0000.0000.0000.000
14A14LYS10.8060.89224.3770.2270.2270.0000.0000.0000.000
15A15PRO00.0960.02622.976-0.013-0.0130.0000.0000.0000.000
16A16GLU-1-0.823-0.89123.166-0.219-0.2190.0000.0000.0000.000
17A17GLN0-0.003-0.00422.829-0.008-0.0080.0000.0000.0000.000
18A18TYR0-0.0030.00918.591-0.042-0.0420.0000.0000.0000.000
19A19PRO00.0110.00915.0860.0390.0390.0000.0000.0000.000
20A20GLU-1-0.884-0.93217.529-0.169-0.1690.0000.0000.0000.000
21A21GLY0-0.022-0.02615.123-0.042-0.0420.0000.0000.0000.000
22A22GLY0-0.0070.00215.1070.0460.0460.0000.0000.0000.000
23A23LEU0-0.060-0.0139.1370.0200.0200.0000.0000.0000.000
24A24PRO00.0270.0128.254-0.047-0.0470.0000.0000.0000.000
25A25GLU-1-0.709-0.8279.521-0.870-0.8700.0000.0000.0000.000
26A26ILE0-0.043-0.0097.5480.0220.0220.0000.0000.0000.000
27A27ALA00.0470.04010.395-0.100-0.1000.0000.0000.0000.000
28A28LEU0-0.044-0.02410.355-0.058-0.0580.0000.0000.0000.000
29A29ALA00.0580.02614.3000.0910.0910.0000.0000.0000.000
30A30GLY00.0390.00417.974-0.042-0.0420.0000.0000.0000.000
31A31ARG10.8510.93620.2380.4210.4210.0000.0000.0000.000
32A32SER0-0.034-0.02922.2020.0240.0240.0000.0000.0000.000
33A33ASN00.1090.04920.373-0.080-0.0800.0000.0000.0000.000
34A34VAL00.0410.03119.290-0.055-0.0550.0000.0000.0000.000
35A35GLY0-0.036-0.02319.064-0.039-0.0390.0000.0000.0000.000
36A36LYS10.8320.92215.6930.6310.6310.0000.0000.0000.000
37A37SER00.0860.03614.710-0.099-0.0990.0000.0000.0000.000
38A38SER0-0.044-0.01614.181-0.123-0.1230.0000.0000.0000.000
39A39PHE00.0170.00110.136-0.085-0.0850.0000.0000.0000.000
40A40ILE00.0570.0329.506-0.220-0.2200.0000.0000.0000.000
41A41ASN0-0.001-0.0039.215-0.297-0.2970.0000.0000.0000.000
42A42SER0-0.040-0.02210.294-0.077-0.0770.0000.0000.0000.000
43A43LEU00.0260.0176.174-0.065-0.0650.0000.0000.0000.000
44A44ILE00.0190.0144.886-1.034-1.0340.0000.0000.0000.000
45A45ASN0-0.0460.0066.6250.1640.1640.0000.0000.0000.000
46A46ARG10.9530.9799.5191.0531.0530.0000.0000.0000.000
47A47LYS10.9290.94312.0790.5640.5640.0000.0000.0000.000
48A48ASN00.009-0.01515.179-0.001-0.0010.0000.0000.0000.000
49A49LEU0-0.0090.04410.7630.0460.0460.0000.0000.0000.000
50A50ALA00.0240.01212.9720.1000.1000.0000.0000.0000.000
51A60GLN0-0.094-0.07324.982-0.028-0.0280.0000.0000.0000.000
52A61THR00.016-0.00621.1210.0290.0290.0000.0000.0000.000
53A62LEU00.0140.01718.229-0.036-0.0360.0000.0000.0000.000
54A63ASN0-0.0130.01716.5980.0730.0730.0000.0000.0000.000
55A64PHE00.0260.02213.728-0.106-0.1060.0000.0000.0000.000
56A65TYR0-0.012-0.01510.2900.0890.0890.0000.0000.0000.000
57A66ILE00.0610.0668.191-0.233-0.2330.0000.0000.0000.000
58A67ILE0-0.021-0.0382.851-0.533-0.1190.187-0.104-0.4970.000
59A68ASN0-0.025-0.0452.366-2.100-1.3792.173-0.804-2.089-0.007
60A69ASP-1-0.825-0.8994.6580.1530.217-0.001-0.006-0.0560.000
61A70GLU-1-0.773-0.8842.539-1.4801.7502.373-2.516-3.087-0.035
62A71LEU0-0.0130.0043.147-0.569-0.1760.067-0.083-0.377-0.001
63A72HIS00.0550.0227.084-0.358-0.3580.0000.0000.0000.000
64A73PHE0-0.051-0.0275.921-0.210-0.2100.0000.0000.0000.000
65A74VAL00.0170.0019.6470.1560.1560.0000.0000.0000.000
66A75ASP-1-0.875-0.93213.376-0.777-0.7770.0000.0000.0000.000
67A76VAL00.0620.02715.4570.0850.0850.0000.0000.0000.000
68A77PRO0-0.028-0.01318.632-0.016-0.0160.0000.0000.0000.000
69A78GLY0-0.011-0.01621.6690.0080.0080.0000.0000.0000.000
70A79TYR00.021-0.01521.1200.0150.0150.0000.0000.0000.000
71A80GLY0-0.0150.00225.3190.0220.0220.0000.0000.0000.000
72A81PHE00.043-0.01227.2880.0160.0160.0000.0000.0000.000
73A82ALA0-0.0160.00930.9930.0170.0170.0000.0000.0000.000
74A83LYS10.9340.95532.9770.2370.2370.0000.0000.0000.000
75A84VAL00.0170.04530.2830.0030.0030.0000.0000.0000.000
76A85SER00.0370.01633.3650.0070.0070.0000.0000.0000.000
77A86LYS10.9180.92734.4900.1590.1590.0000.0000.0000.000
78A87SER00.0060.00735.158-0.005-0.0050.0000.0000.0000.000
79A88GLU-1-0.796-0.90230.655-0.275-0.2750.0000.0000.0000.000
80A89ARG10.8840.95930.5100.2130.2130.0000.0000.0000.000
81A90GLU-1-0.807-0.88030.405-0.192-0.1920.0000.0000.0000.000
82A91ALA0-0.042-0.01930.511-0.001-0.0010.0000.0000.0000.000
83A92TRP0-0.030-0.01922.9780.0030.0030.0000.0000.0000.000
84A93GLY00.0160.00226.162-0.019-0.0190.0000.0000.0000.000
85A94ARG10.9480.95427.4810.2050.2050.0000.0000.0000.000
86A95MET0-0.0240.02223.019-0.003-0.0030.0000.0000.0000.000
87A96ILE00.0220.00119.848-0.018-0.0180.0000.0000.0000.000
88A97GLU-1-0.842-0.90822.783-0.269-0.2690.0000.0000.0000.000
89A98THR0-0.039-0.00724.9590.0160.0160.0000.0000.0000.000
90A99TYR0-0.087-0.05514.951-0.009-0.0090.0000.0000.0000.000
91A100ILE0-0.030-0.02618.971-0.008-0.0080.0000.0000.0000.000
92A101THR0-0.039-0.03221.2410.0150.0150.0000.0000.0000.000
93A102THR0-0.080-0.04822.9110.0220.0220.0000.0000.0000.000
94A103ARG10.7540.86715.5370.4650.4650.0000.0000.0000.000
95A104GLU-1-0.896-0.93618.509-0.179-0.1790.0000.0000.0000.000
96A105GLU-1-0.841-0.93613.729-0.337-0.3370.0000.0000.0000.000
97A106LEU0-0.057-0.02213.410-0.101-0.1010.0000.0000.0000.000
98A107LYS10.8650.92711.4370.3930.3930.0000.0000.0000.000
99A108ALA0-0.008-0.00811.9080.0370.0370.0000.0000.0000.000
100A109VAL00.0020.01113.147-0.084-0.0840.0000.0000.0000.000
101A110VAL0-0.016-0.00610.386-0.003-0.0030.0000.0000.0000.000
102A111GLN0-0.002-0.01213.7660.0370.0370.0000.0000.0000.000
103A112ILE0-0.039-0.02414.240-0.003-0.0030.0000.0000.0000.000
104A113VAL00.0300.01317.5010.0770.0770.0000.0000.0000.000
105A114ASP-1-0.802-0.86319.656-0.513-0.5130.0000.0000.0000.000
106A115LEU00.0280.01719.7980.0330.0330.0000.0000.0000.000
107A116ARG10.7980.85422.4740.4290.4290.0000.0000.0000.000
108A117HIS0-0.040-0.01425.7590.0190.0190.0000.0000.0000.000
109A118ALA00.0370.01726.519-0.021-0.0210.0000.0000.0000.000
110A119PRO0-0.041-0.00924.352-0.001-0.0010.0000.0000.0000.000
111A120SER0-0.031-0.03226.6560.0280.0280.0000.0000.0000.000
112A121ASN00.0880.02428.361-0.004-0.0040.0000.0000.0000.000
113A122ASP-1-0.851-0.93327.838-0.299-0.2990.0000.0000.0000.000
114A123ASP-1-0.776-0.83823.969-0.448-0.4480.0000.0000.0000.000
115A124VAL00.0510.02424.895-0.020-0.0200.0000.0000.0000.000
116A125GLN00.0380.03527.2180.0130.0130.0000.0000.0000.000
117A126MET0-0.044-0.01520.8580.0080.0080.0000.0000.0000.000
118A127TYR0-0.039-0.04220.341-0.003-0.0030.0000.0000.0000.000
119A128GLU-1-0.900-0.95723.766-0.246-0.2460.0000.0000.0000.000
120A129PHE0-0.059-0.02622.7980.0070.0070.0000.0000.0000.000
121A130LEU0-0.026-0.02319.121-0.002-0.0020.0000.0000.0000.000
122A131LYS10.8220.88120.2030.4020.4020.0000.0000.0000.000
123A132TYR0-0.0360.00924.1530.0270.0270.0000.0000.0000.000
124A133TYR0-0.087-0.06623.3720.0220.0220.0000.0000.0000.000
125A134GLY0-0.0070.01023.2420.0060.0060.0000.0000.0000.000
126A135ILE0-0.024-0.00217.258-0.007-0.0070.0000.0000.0000.000
127A136PRO00.0250.01615.477-0.009-0.0090.0000.0000.0000.000
128A137VAL0-0.008-0.01016.229-0.077-0.0770.0000.0000.0000.000
129A138ILE0-0.019-0.00310.186-0.002-0.0020.0000.0000.0000.000
130A139VAL00.0260.01214.325-0.051-0.0510.0000.0000.0000.000
131A140ILE0-0.006-0.00111.455-0.021-0.0210.0000.0000.0000.000
132A141ALA00.0190.01015.4270.0620.0620.0000.0000.0000.000
133A142THR0-0.025-0.03915.8300.0080.0080.0000.0000.0000.000
134A143LYS10.8440.90918.2370.6370.6370.0000.0000.0000.000
135A144ALA00.0740.03417.8410.0580.0580.0000.0000.0000.000
136A145ASP-1-0.845-0.88219.264-0.486-0.4860.0000.0000.0000.000
137A146LYS10.8500.90720.7980.4370.4370.0000.0000.0000.000
138A147ILE0-0.0120.01722.9430.0310.0310.0000.0000.0000.000
139A148PRO00.0410.01923.893-0.010-0.0100.0000.0000.0000.000
140A149LYS11.0501.01520.3600.2710.2710.0000.0000.0000.000
141A150GLY00.0150.01724.240-0.002-0.0020.0000.0000.0000.000
142A151LYS10.9020.94126.5900.1910.1910.0000.0000.0000.000
143A152TRP00.0540.02718.716-0.020-0.0200.0000.0000.0000.000
144A153ASP-1-0.778-0.86723.537-0.268-0.2680.0000.0000.0000.000
145A154LYS10.9720.98524.8020.1950.1950.0000.0000.0000.000
146A155HIS0-0.038-0.03224.4700.0090.0090.0000.0000.0000.000
147A156ALA00.0210.00121.819-0.016-0.0160.0000.0000.0000.000
148A157LYS10.8540.92023.2450.2330.2330.0000.0000.0000.000
149A158VAL00.0050.01726.2830.0060.0060.0000.0000.0000.000
150A159VAL00.0290.01921.4580.0010.0010.0000.0000.0000.000
151A160ARG10.9140.95519.9260.3700.3700.0000.0000.0000.000
152A161GLN0-0.025-0.02724.6330.0080.0080.0000.0000.0000.000
153A162THR0-0.055-0.03127.2380.0170.0170.0000.0000.0000.000
154A163LEU0-0.038-0.02222.0900.0030.0030.0000.0000.0000.000
155A164ASN0-0.0180.00526.0760.0100.0100.0000.0000.0000.000
156A165ILE0-0.074-0.04020.453-0.001-0.0010.0000.0000.0000.000
157A166ASP-1-0.812-0.90222.339-0.244-0.2440.0000.0000.0000.000
158A167PRO0-0.044-0.04222.029-0.030-0.0300.0000.0000.0000.000
159A168GLU-1-0.848-0.90319.352-0.243-0.2430.0000.0000.0000.000
160A169ASP-1-0.734-0.80417.590-0.492-0.4920.0000.0000.0000.000
161A170GLU-1-0.853-0.92812.964-0.691-0.6910.0000.0000.0000.000
162A171LEU0-0.065-0.03016.385-0.026-0.0260.0000.0000.0000.000
163A172ILE0-0.014-0.00410.8200.0270.0270.0000.0000.0000.000
164A173LEU0-0.049-0.02014.764-0.008-0.0080.0000.0000.0000.000
165A174PHE00.0550.0129.8480.0090.0090.0000.0000.0000.000
166A175SER0-0.095-0.07213.9970.1290.1290.0000.0000.0000.000
167A176SER00.0740.03113.787-0.092-0.0920.0000.0000.0000.000
168A177GLU-1-0.952-0.96414.874-0.515-0.5150.0000.0000.0000.000
169A178THR00.000-0.02115.900-0.014-0.0140.0000.0000.0000.000
170A179LYS10.8580.93010.4520.8950.8950.0000.0000.0000.000
171A180LYS10.9500.98510.8540.5300.5300.0000.0000.0000.000
172A181GLY00.0590.02111.060-0.011-0.0110.0000.0000.0000.000
173A182LYS10.8160.9095.4012.9972.9970.0000.0000.0000.000
174A183ASP-1-0.885-0.9364.852-3.049-3.0490.0000.0000.0000.000
175A184GLU-1-0.886-0.9545.546-1.393-1.3930.0000.0000.0000.000
176A185ALA0-0.0040.0027.9260.1230.1230.0000.0000.0000.000
177A186TRP00.004-0.0242.584-6.371-3.4226.379-2.203-7.126-0.030
178A187GLY00.0210.0154.5530.3200.497-0.001-0.009-0.1670.000
179A188ALA0-0.028-0.0216.3640.4370.4370.0000.0000.0000.000
180A189ILE00.0210.0095.0350.1760.1760.0000.0000.0000.000
181A190LYS10.7860.8592.437-8.662-12.23910.352-2.578-4.1970.004
182A191LYS10.8430.9206.6690.9760.9760.0000.0000.0000.000
183A192MET0-0.024-0.0099.9950.1530.1530.0000.0000.0000.000
184A193ILE0-0.012-0.0075.6370.0310.0310.0000.0000.0000.000
185A194ASN0-0.111-0.0619.5970.2480.2480.0000.0000.0000.000
186A195ARG10.8770.95611.5480.3240.3240.0000.0000.0000.000