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: 2N28R

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2102757.084455
FMO2-HF: Nuclear repulsion 2029602.639063
FMO2-HF: Total energy -73154.445392
FMO2-MP2: Total energy -73370.916373


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.
-26.939-21.05226.051-11.654-20.28-0.067
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 : -0.046 / q_NPA : -0.001
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].
3A3VAL0-0.0050.0002.292-0.1592.3860.695-0.887-2.3520.002
4A4THR0-0.031-0.0154.3550.1920.3900.000-0.034-0.1630.000
5A5LYS10.9180.9606.0590.7940.7940.0000.0000.0000.000
6A6SER0-0.015-0.0066.317-0.537-0.5370.0000.0000.0000.000
7A7GLU-1-0.930-0.9578.463-0.400-0.4000.0000.0000.0000.000
8A8ILE0-0.032-0.00711.661-0.136-0.1360.0000.0000.0000.000
9A9VAL0-0.012-0.00712.6750.0560.0560.0000.0000.0000.000
10A10ILE00.000-0.00115.3940.0820.0820.0000.0000.0000.000
11A11SER0-0.036-0.01417.713-0.068-0.0680.0000.0000.0000.000
12A12ALA0-0.0100.00420.0010.0470.0470.0000.0000.0000.000
13A13VAL0-0.014-0.03121.739-0.017-0.0170.0000.0000.0000.000
14A14LYS10.8750.93124.1550.2410.2410.0000.0000.0000.000
15A15PRO00.1150.01822.847-0.020-0.0200.0000.0000.0000.000
16A16GLU-1-0.849-0.87522.912-0.239-0.2390.0000.0000.0000.000
17A17GLN0-0.058-0.05222.766-0.016-0.0160.0000.0000.0000.000
18A18TYR0-0.0260.00118.301-0.041-0.0410.0000.0000.0000.000
19A19PRO00.0130.01114.8130.0410.0410.0000.0000.0000.000
20A20GLU-1-0.883-0.93517.232-0.189-0.1890.0000.0000.0000.000
21A21GLY0-0.028-0.02714.743-0.057-0.0570.0000.0000.0000.000
22A22GLY00.0000.00914.6530.0490.0490.0000.0000.0000.000
23A23LEU0-0.070-0.0198.6170.0320.0320.0000.0000.0000.000
24A24PRO00.0260.0098.209-0.036-0.0360.0000.0000.0000.000
25A25GLU-1-0.722-0.8319.472-0.951-0.9510.0000.0000.0000.000
26A26ILE0-0.035-0.0057.3300.0660.0660.0000.0000.0000.000
27A27ALA00.0500.03810.201-0.133-0.1330.0000.0000.0000.000
28A28LEU0-0.039-0.02710.160-0.032-0.0320.0000.0000.0000.000
29A29ALA00.0650.03514.0110.0820.0820.0000.0000.0000.000
30A30GLY00.0350.00217.681-0.036-0.0360.0000.0000.0000.000
31A31ARG10.8510.93119.9390.4110.4110.0000.0000.0000.000
32A32SER0-0.036-0.02822.1370.0150.0150.0000.0000.0000.000
33A33ASN00.1320.05520.463-0.073-0.0730.0000.0000.0000.000
34A34VAL00.0280.02219.564-0.061-0.0610.0000.0000.0000.000
35A35GLY0-0.037-0.02319.434-0.043-0.0430.0000.0000.0000.000
36A36LYS10.8710.94815.6930.6590.6590.0000.0000.0000.000
37A37SER00.0600.02614.980-0.119-0.1190.0000.0000.0000.000
38A38SER0-0.055-0.02314.513-0.128-0.1280.0000.0000.0000.000
39A39PHE00.0230.01110.102-0.100-0.1000.0000.0000.0000.000
40A40ILE00.0620.0359.756-0.235-0.2350.0000.0000.0000.000
41A41ASN00.0200.0149.556-0.374-0.3740.0000.0000.0000.000
42A42SER0-0.034-0.02810.595-0.038-0.0380.0000.0000.0000.000
43A43LEU00.0050.0075.787-0.059-0.0590.0000.0000.0000.000
44A44ILE00.0040.0125.112-0.995-0.9950.0000.0000.0000.000
45A45ASN0-0.066-0.0156.8720.2410.2410.0000.0000.0000.000
46A46ARG10.9600.9769.5221.2441.2440.0000.0000.0000.000
47A47LYS10.9190.93412.2420.6830.6830.0000.0000.0000.000
48A48ASN00.011-0.00915.3500.0110.0110.0000.0000.0000.000
49A49LEU0-0.0080.04110.3200.0510.0510.0000.0000.0000.000
50A50ALA00.0320.01713.2650.0900.0900.0000.0000.0000.000
51A60GLN0-0.041-0.04124.794-0.011-0.0110.0000.0000.0000.000
52A61THR0-0.009-0.01620.9440.0320.0320.0000.0000.0000.000
53A62LEU00.0000.01217.990-0.036-0.0360.0000.0000.0000.000
54A63ASN00.0460.04016.5570.0800.0800.0000.0000.0000.000
55A64PHE00.0170.01513.512-0.108-0.1080.0000.0000.0000.000
56A65TYR0-0.016-0.01710.2130.0860.0860.0000.0000.0000.000
57A66ILE00.0640.0648.020-0.258-0.2580.0000.0000.0000.000
58A67ILE0-0.031-0.0382.853-0.549-0.1410.279-0.120-0.568-0.001
59A68ASN0-0.004-0.0392.609-2.807-1.6851.007-0.564-1.565-0.002
60A69ASP-1-0.922-0.9544.771-0.0060.058-0.001-0.003-0.0590.000
61A70GLU-1-0.862-0.9492.357-6.102-1.5073.312-3.857-4.050-0.058
62A71LEU0-0.025-0.0052.907-0.4320.0300.147-0.106-0.502-0.001
63A72HIS00.0720.0336.724-0.455-0.4550.0000.0000.0000.000
64A73PHE0-0.063-0.0335.735-0.197-0.1970.0000.0000.0000.000
65A74VAL00.021-0.0039.4030.1390.1390.0000.0000.0000.000
66A75ASP-1-0.900-0.94913.134-0.819-0.8190.0000.0000.0000.000
67A76VAL00.0590.03015.1720.0890.0890.0000.0000.0000.000
68A77PRO0-0.044-0.02018.352-0.015-0.0150.0000.0000.0000.000
69A78GLY0-0.009-0.01921.4000.0110.0110.0000.0000.0000.000
70A79TYR00.006-0.04820.9850.0170.0170.0000.0000.0000.000
71A80GLY0-0.014-0.00125.0200.0240.0240.0000.0000.0000.000
72A81PHE00.044-0.05926.6370.0170.0170.0000.0000.0000.000
73A82ALA0-0.0040.00330.6880.0160.0160.0000.0000.0000.000
74A83LYS10.9250.95132.8220.2450.2450.0000.0000.0000.000
75A84VAL0-0.0080.09329.956-0.001-0.0010.0000.0000.0000.000
76A85SER00.0250.01333.1240.0100.0100.0000.0000.0000.000
77A86LYS10.9700.96634.2030.1500.1500.0000.0000.0000.000
78A87SER00.0700.03134.887-0.003-0.0030.0000.0000.0000.000
79A88GLU-1-0.911-0.96029.654-0.291-0.2910.0000.0000.0000.000
80A89ARG10.9070.96230.2350.2140.2140.0000.0000.0000.000
81A90GLU-1-0.890-0.94830.142-0.193-0.1930.0000.0000.0000.000
82A91ALA0-0.047-0.02130.1980.0000.0000.0000.0000.0000.000
83A92TRP0-0.009-0.00822.6960.0020.0020.0000.0000.0000.000
84A93GLY00.0210.00125.915-0.018-0.0180.0000.0000.0000.000
85A94ARG10.9890.98927.2580.2120.2120.0000.0000.0000.000
86A95MET0-0.0320.01022.442-0.003-0.0030.0000.0000.0000.000
87A96ILE00.007-0.00720.015-0.019-0.0190.0000.0000.0000.000
88A97GLU-1-0.909-0.95622.581-0.250-0.2500.0000.0000.0000.000
89A98THR0-0.0420.00324.5010.0190.0190.0000.0000.0000.000
90A99TYR0-0.044-0.01814.839-0.006-0.0060.0000.0000.0000.000
91A100ILE0-0.047-0.03518.734-0.004-0.0040.0000.0000.0000.000
92A101THR0-0.063-0.04121.0780.0200.0200.0000.0000.0000.000
93A102THR0-0.070-0.04822.7880.0210.0210.0000.0000.0000.000
94A103ARG10.7700.86015.3520.4780.4780.0000.0000.0000.000
95A104GLU-1-0.917-0.94818.340-0.140-0.1400.0000.0000.0000.000
96A105GLU-1-0.877-0.95213.698-0.317-0.3170.0000.0000.0000.000
97A106LEU0-0.067-0.02613.357-0.094-0.0940.0000.0000.0000.000
98A107LYS10.9280.96511.2680.2470.2470.0000.0000.0000.000
99A108ALA0-0.023-0.02011.7400.0600.0600.0000.0000.0000.000
100A109VAL00.0080.01712.964-0.103-0.1030.0000.0000.0000.000
101A110VAL0-0.014-0.00510.1500.0130.0130.0000.0000.0000.000
102A111GLN0-0.004-0.01113.5270.0170.0170.0000.0000.0000.000
103A112ILE0-0.045-0.02614.0070.0010.0010.0000.0000.0000.000
104A113VAL00.0330.01317.4570.0680.0680.0000.0000.0000.000
105A114ASP-1-0.816-0.88519.575-0.502-0.5020.0000.0000.0000.000
106A115LEU00.0280.02020.0050.0350.0350.0000.0000.0000.000
107A116ARG10.7980.85022.5120.4310.4310.0000.0000.0000.000
108A117HIS0-0.037-0.01225.7970.0170.0170.0000.0000.0000.000
109A118ALA00.0210.01126.474-0.019-0.0190.0000.0000.0000.000
110A119PRO0-0.0280.00024.439-0.004-0.0040.0000.0000.0000.000
111A120SER0-0.014-0.00126.6530.0270.0270.0000.0000.0000.000
112A121ASN00.1090.02928.382-0.006-0.0060.0000.0000.0000.000
113A122ASP-1-0.869-0.93127.431-0.291-0.2910.0000.0000.0000.000
114A123ASP-1-0.790-0.84123.966-0.440-0.4400.0000.0000.0000.000
115A124VAL00.0430.02424.827-0.018-0.0180.0000.0000.0000.000
116A125GLN00.0500.03827.1220.0110.0110.0000.0000.0000.000
117A126MET0-0.048-0.01920.6810.0070.0070.0000.0000.0000.000
118A127TYR0-0.052-0.06820.509-0.001-0.0010.0000.0000.0000.000
119A128GLU-1-0.900-0.95923.611-0.213-0.2130.0000.0000.0000.000
120A129PHE0-0.043-0.01822.8730.0080.0080.0000.0000.0000.000
121A130LEU0-0.018-0.01919.0970.0000.0000.0000.0000.0000.000
122A131LYS10.8300.88520.3070.3210.3210.0000.0000.0000.000
123A132TYR0-0.0270.01323.9820.0280.0280.0000.0000.0000.000
124A133TYR0-0.047-0.02923.0860.0170.0170.0000.0000.0000.000
125A134GLY0-0.0020.01123.1220.0070.0070.0000.0000.0000.000
126A135ILE0-0.0250.00217.2200.0030.0030.0000.0000.0000.000
127A136PRO00.0140.01215.410-0.009-0.0090.0000.0000.0000.000
128A137VAL00.0020.00316.088-0.079-0.0790.0000.0000.0000.000
129A138ILE0-0.022-0.00210.3260.0060.0060.0000.0000.0000.000
130A139VAL00.0340.01714.521-0.069-0.0690.0000.0000.0000.000
131A140ILE0-0.002-0.00111.468-0.013-0.0130.0000.0000.0000.000
132A141ALA00.0220.01115.4420.0490.0490.0000.0000.0000.000
133A142THR0-0.040-0.04715.7700.0000.0000.0000.0000.0000.000
134A143LYS10.8830.94318.1190.6310.6310.0000.0000.0000.000
135A144ALA00.0580.02617.9530.0560.0560.0000.0000.0000.000
136A145ASP-1-0.891-0.91719.357-0.493-0.4930.0000.0000.0000.000
137A146LYS10.9100.95220.8660.4200.4200.0000.0000.0000.000
138A147ILE0-0.0010.01423.0320.0320.0320.0000.0000.0000.000
139A148PRO00.0410.02123.984-0.010-0.0100.0000.0000.0000.000
140A149LYS11.0511.01120.4470.2610.2610.0000.0000.0000.000
141A150GLY00.0160.01724.3570.0010.0010.0000.0000.0000.000
142A151LYS10.8850.93726.6900.1830.1830.0000.0000.0000.000
143A152TRP00.0560.01719.298-0.016-0.0160.0000.0000.0000.000
144A153ASP-1-0.807-0.87823.630-0.223-0.2230.0000.0000.0000.000
145A154LYS10.9780.99024.9070.1760.1760.0000.0000.0000.000
146A155HIS0-0.040-0.02324.6120.0050.0050.0000.0000.0000.000
147A156ALA00.0200.00521.915-0.015-0.0150.0000.0000.0000.000
148A157LYS10.8770.92023.3180.2020.2020.0000.0000.0000.000
149A158VAL0-0.0010.01826.3560.0070.0070.0000.0000.0000.000
150A159VAL00.0390.01921.5170.0010.0010.0000.0000.0000.000
151A160ARG10.9750.98020.3630.2840.2840.0000.0000.0000.000
152A161GLN0-0.034-0.03124.7300.0150.0150.0000.0000.0000.000
153A162THR0-0.056-0.02627.2780.0150.0150.0000.0000.0000.000
154A163LEU0-0.034-0.02122.1240.0010.0010.0000.0000.0000.000
155A164ASN0-0.0150.00926.2030.0070.0070.0000.0000.0000.000
156A165ILE0-0.074-0.03920.585-0.001-0.0010.0000.0000.0000.000
157A166ASP-1-0.799-0.88522.618-0.166-0.1660.0000.0000.0000.000
158A167PRO0-0.059-0.04322.312-0.022-0.0220.0000.0000.0000.000
159A168GLU-1-0.978-0.98720.371-0.104-0.1040.0000.0000.0000.000
160A169ASP-1-0.766-0.81717.891-0.370-0.3700.0000.0000.0000.000
161A170GLU-1-0.905-0.96612.965-0.466-0.4660.0000.0000.0000.000
162A171LEU0-0.070-0.03616.526-0.036-0.0360.0000.0000.0000.000
163A172ILE0-0.021-0.00410.7220.0240.0240.0000.0000.0000.000
164A173LEU0-0.063-0.03514.829-0.021-0.0210.0000.0000.0000.000
165A174PHE00.0480.0159.928-0.008-0.0080.0000.0000.0000.000
166A175SER0-0.098-0.08314.0410.1110.1110.0000.0000.0000.000
167A176SER00.0480.01214.125-0.068-0.0680.0000.0000.0000.000
168A177GLU-1-0.981-0.97815.216-0.540-0.5400.0000.0000.0000.000
169A178THR00.003-0.01515.967-0.030-0.0300.0000.0000.0000.000
170A179LYS10.9060.95410.5601.0541.0540.0000.0000.0000.000
171A180LYS10.9590.99010.9360.4180.4180.0000.0000.0000.000
172A181GLY00.0610.02711.150-0.017-0.0170.0000.0000.0000.000
173A182LYS10.8900.9575.6083.4253.4250.0000.0000.0000.000
174A183ASP-1-0.888-0.9334.988-2.995-2.9950.0000.0000.0000.000
175A184GLU-1-0.885-0.9585.670-1.157-1.1570.0000.0000.0000.000
176A185ALA0-0.0050.0037.8590.1670.1670.0000.0000.0000.000
177A186TRP0-0.019-0.0262.609-6.233-3.2725.289-1.994-6.256-0.025
178A187GLY00.0180.0134.7070.7070.883-0.001-0.009-0.1660.000
179A188ALA0-0.011-0.0096.4690.4730.4730.0000.0000.0000.000
180A189ILE00.0200.0075.1610.1480.1480.0000.0000.0000.000
181A190LYS10.8630.9162.348-11.641-18.28515.324-4.080-4.5990.018
182A191LYS10.8800.9406.6590.3980.3980.0000.0000.0000.000
183A192MET0-0.035-0.01710.0270.0790.0790.0000.0000.0000.000
184A193ILE00.0280.0075.683-0.007-0.0070.0000.0000.0000.000
185A194ASN0-0.128-0.0569.6410.1470.1470.0000.0000.0000.000
186A195ARG11.0021.02811.6830.1030.1030.0000.0000.0000.000