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: 1N83Z

Calculation Name: 3JSY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JSY

Chain ID: A

ChEMBL ID:

UniProt ID: P54049

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2200485.517223
FMO2-HF: Nuclear repulsion 2119356.93203
FMO2-HF: Total energy -81128.585194
FMO2-MP2: Total energy -81366.181636


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:9:MET)


Summations of interaction energy for fragment #1(A:9: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.
-15.836-15.94522.443-9.06-13.2690.02
Interaction energy analysis for fragmet #1(A:9:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.037
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].
3A11PRO00.1260.0373.442-1.7221.2140.016-1.541-1.4110.006
4A12TRP00.0460.0196.0970.9730.9730.0000.0000.0000.000
5A13LYS10.9310.9782.123-4.578-3.5033.539-1.197-3.417-0.002
6A14ILE00.0180.0173.0230.3971.3810.109-0.212-0.881-0.001
7A15GLU-1-0.793-0.8815.1300.1720.240-0.001-0.004-0.0620.000
8A16GLU-1-0.851-0.9017.3481.4811.4810.0000.0000.0000.000
9A17VAL00.0270.0034.292-0.501-0.2080.010-0.068-0.2340.000
10A18LYS10.8350.9077.551-0.701-0.7010.0000.0000.0000.000
11A19THR0-0.075-0.04110.540-0.230-0.2300.0000.0000.0000.000
12A20LEU0-0.031-0.0168.091-0.154-0.1540.0000.0000.0000.000
13A21LYS10.8060.8759.180-1.377-1.3770.0000.0000.0000.000
14A22GLY0-0.0070.00612.520-0.122-0.1220.0000.0000.0000.000
15A23LEU0-0.063-0.03315.143-0.078-0.0780.0000.0000.0000.000
16A24ILE00.0100.00711.602-0.058-0.0580.0000.0000.0000.000
17A25LYS10.8600.91714.475-0.554-0.5540.0000.0000.0000.000
18A26SER0-0.108-0.04718.088-0.051-0.0510.0000.0000.0000.000
19A27LYS10.7650.86320.565-0.236-0.2360.0000.0000.0000.000
20A28PRO00.0410.03621.4290.0190.0190.0000.0000.0000.000
21A29VAL00.0090.02122.7670.0040.0040.0000.0000.0000.000
22A30VAL0-0.026-0.01716.0590.0240.0240.0000.0000.0000.000
23A31ALA00.0270.00719.013-0.017-0.0170.0000.0000.0000.000
24A32ILE0-0.034-0.00813.5080.0500.0500.0000.0000.0000.000
25A33VAL00.0170.00216.943-0.037-0.0370.0000.0000.0000.000
26A34ASP-1-0.775-0.90117.3820.2950.2950.0000.0000.0000.000
27A35MET0-0.075-0.04417.986-0.015-0.0150.0000.0000.0000.000
28A36MET0-0.006-0.01219.610-0.002-0.0020.0000.0000.0000.000
29A37ASP-1-0.865-0.91121.1410.1550.1550.0000.0000.0000.000
30A38VAL00.0070.00324.166-0.012-0.0120.0000.0000.0000.000
31A39PRO0-0.0030.00326.2290.0060.0060.0000.0000.0000.000
32A40ALA00.0350.00828.4140.0020.0020.0000.0000.0000.000
33A41PRO00.0180.00329.3890.0040.0040.0000.0000.0000.000
34A42GLN00.0730.02130.2400.0030.0030.0000.0000.0000.000
35A43LEU0-0.0030.01123.6490.0040.0040.0000.0000.0000.000
36A44GLN0-0.073-0.05128.0410.0100.0100.0000.0000.0000.000
37A45GLU-1-0.788-0.86930.3930.1150.1150.0000.0000.0000.000
38A46ILE00.0020.00326.321-0.001-0.0010.0000.0000.0000.000
39A47ARG10.9310.96525.726-0.182-0.1820.0000.0000.0000.000
40A48ASP-1-0.796-0.89128.7270.1270.1270.0000.0000.0000.000
41A49LYS10.8430.94131.281-0.132-0.1320.0000.0000.0000.000
42A50ILE00.0240.00525.004-0.002-0.0020.0000.0000.0000.000
43A51ARG10.8010.90328.104-0.129-0.1290.0000.0000.0000.000
44A52ASP-1-0.855-0.91228.0590.1500.1500.0000.0000.0000.000
45A53LYS10.8280.90528.789-0.140-0.1400.0000.0000.0000.000
46A54VAL00.0030.02323.5500.0060.0060.0000.0000.0000.000
47A55LYS10.9120.97320.850-0.308-0.3080.0000.0000.0000.000
48A56LEU00.0240.01718.6590.0130.0130.0000.0000.0000.000
49A57ARG10.8970.94713.721-0.547-0.5470.0000.0000.0000.000
50A58MET00.0340.02314.6150.0100.0100.0000.0000.0000.000
51A59SER00.002-0.0449.2280.1320.1320.0000.0000.0000.000
52A60ARG10.9760.9937.317-1.131-1.1310.0000.0000.0000.000
53A61ASN00.0970.0367.8630.1840.1840.0000.0000.0000.000
54A62THR0-0.009-0.0102.841-0.2490.1340.174-0.085-0.4710.000
55A63LEU0-0.062-0.0273.307-1.254-0.1660.258-0.409-0.937-0.002
56A64ILE00.0450.0284.7980.0490.095-0.001-0.003-0.0410.000
57A65ILE00.0200.0116.023-0.038-0.0380.0000.0000.0000.000
58A66ARG10.7910.8462.241-8.856-15.86118.340-5.539-5.7960.019
59A67ALA00.0150.0025.1010.0930.116-0.001-0.002-0.0190.000
60A68LEU00.0330.0158.007-0.152-0.1520.0000.0000.0000.000
61A69LYS10.9530.9727.769-0.384-0.3840.0000.0000.0000.000
62A70GLU-1-0.744-0.8426.9292.5922.5920.0000.0000.0000.000
63A71ALA00.0000.00010.209-0.127-0.1270.0000.0000.0000.000
64A72ALA0-0.013-0.00312.789-0.088-0.0880.0000.0000.0000.000
65A73GLU-1-0.949-0.96512.3240.3330.3330.0000.0000.0000.000
66A74GLU-1-0.811-0.88712.2760.6820.6820.0000.0000.0000.000
67A75LEU0-0.043-0.01516.014-0.043-0.0430.0000.0000.0000.000
68A76ASN0-0.045-0.01018.333-0.034-0.0340.0000.0000.0000.000
69A77ASN00.0200.02418.383-0.029-0.0290.0000.0000.0000.000
70A78PRO00.0900.02716.8620.0310.0310.0000.0000.0000.000
71A79LYS10.8600.92316.801-0.160-0.1600.0000.0000.0000.000
72A80LEU00.0280.02214.7390.0090.0090.0000.0000.0000.000
73A81ALA00.009-0.00712.7610.0330.0330.0000.0000.0000.000
74A82GLU-1-0.858-0.91513.1890.1970.1970.0000.0000.0000.000
75A83LEU00.0320.01514.376-0.009-0.0090.0000.0000.0000.000
76A84ALA0-0.037-0.02510.0470.0060.0060.0000.0000.0000.000
77A85ASN0-0.072-0.04211.839-0.011-0.0110.0000.0000.0000.000
78A86TYR00.0160.01414.363-0.025-0.0250.0000.0000.0000.000
79A87VAL0-0.067-0.02010.1010.0140.0140.0000.0000.0000.000
80A88GLU-1-0.833-0.89813.4110.1930.1930.0000.0000.0000.000
81A89ARG10.8110.88115.110-0.199-0.1990.0000.0000.0000.000
82A90GLY00.0250.02914.6990.0430.0430.0000.0000.0000.000
83A91ALA0-0.025-0.00512.560-0.005-0.0050.0000.0000.0000.000
84A92ALA0-0.028-0.01613.8070.0620.0620.0000.0000.0000.000
85A93ILE00.0050.00310.911-0.017-0.0170.0000.0000.0000.000
86A94LEU00.0090.00615.304-0.008-0.0080.0000.0000.0000.000
87A95VAL0-0.030-0.01117.8200.0020.0020.0000.0000.0000.000
88A96THR00.008-0.03320.568-0.018-0.0180.0000.0000.0000.000
89A97ASP-1-0.746-0.86624.3110.1950.1950.0000.0000.0000.000
90A98MET0-0.094-0.01027.301-0.016-0.0160.0000.0000.0000.000
91A99ASN00.0530.01427.2390.0140.0140.0000.0000.0000.000
92A100PRO00.0620.01125.3190.0010.0010.0000.0000.0000.000
93A101PHE00.0560.04127.0490.0040.0040.0000.0000.0000.000
94A102LYS10.9700.98930.296-0.132-0.1320.0000.0000.0000.000
95A103LEU0-0.014-0.01623.2700.0010.0010.0000.0000.0000.000
96A104TYR00.0420.00126.6270.0000.0000.0000.0000.0000.000
97A105LYS10.7930.89628.351-0.103-0.1030.0000.0000.0000.000
98A106LEU0-0.065-0.02628.336-0.003-0.0030.0000.0000.0000.000
99A107LEU0-0.070-0.04424.1480.0010.0010.0000.0000.0000.000
100A108GLU-1-0.834-0.92026.2800.1650.1650.0000.0000.0000.000
101A109GLU-1-0.903-0.94829.8660.1050.1050.0000.0000.0000.000
102A110ASN0-0.095-0.03632.440-0.012-0.0120.0000.0000.0000.000
103A111LYS10.8660.94029.002-0.136-0.1360.0000.0000.0000.000
104A112SER0-0.020-0.04931.294-0.007-0.0070.0000.0000.0000.000
105A113PRO0-0.021-0.00332.7320.0030.0030.0000.0000.0000.000
106A114ALA00.0150.00232.3300.0020.0020.0000.0000.0000.000
107A115PRO00.0070.01234.100-0.003-0.0030.0000.0000.0000.000
108A116VAL0-0.016-0.00334.0910.0060.0060.0000.0000.0000.000
109A117ARG10.8590.90627.153-0.142-0.1420.0000.0000.0000.000
110A118GLY00.003-0.01634.073-0.003-0.0030.0000.0000.0000.000
111A119GLY0-0.034-0.01833.9040.0030.0030.0000.0000.0000.000
112A120GLN00.0100.02130.6810.0010.0010.0000.0000.0000.000
113A121ILE00.0160.00332.007-0.006-0.0060.0000.0000.0000.000
114A122ALA00.0210.01533.1570.0060.0060.0000.0000.0000.000
115A123PRO00.0220.01532.179-0.002-0.0020.0000.0000.0000.000
116A124CYS0-0.026-0.03534.1400.0010.0010.0000.0000.0000.000
117A125ASP-1-0.797-0.89337.6710.0670.0670.0000.0000.0000.000
118A126ILE0-0.0100.00237.4900.0020.0020.0000.0000.0000.000
119A127LYS10.9120.95641.762-0.059-0.0590.0000.0000.0000.000
120A128VAL0-0.029-0.01144.8790.0020.0020.0000.0000.0000.000
121A129GLU-1-0.903-0.95947.5240.0600.0600.0000.0000.0000.000
122A130LYS10.8570.93250.288-0.042-0.0420.0000.0000.0000.000
123A131GLY00.0340.01453.8190.0000.0000.0000.0000.0000.000
124A132SER0-0.054-0.03654.4840.0000.0000.0000.0000.0000.000
125A133THR00.032-0.00851.3220.0010.0010.0000.0000.0000.000
126A134GLY0-0.0020.00852.0120.0010.0010.0000.0000.0000.000
127A135MET0-0.023-0.00549.7890.0000.0000.0000.0000.0000.000
128A136PRO00.0270.00354.299-0.001-0.0010.0000.0000.0000.000
129A137PRO00.0060.00756.2560.0010.0010.0000.0000.0000.000
130A138GLY00.0550.01856.2130.0000.0000.0000.0000.0000.000
131A139PRO00.0240.00252.9280.0000.0000.0000.0000.0000.000
132A140PHE00.0500.02547.8840.0000.0000.0000.0000.0000.000
133A141LEU00.0190.01752.1910.0010.0010.0000.0000.0000.000
134A142GLY00.000-0.00654.4030.0000.0000.0000.0000.0000.000
135A143GLU-1-0.870-0.94248.1540.0500.0500.0000.0000.0000.000
136A144LEU00.0390.03949.2980.0010.0010.0000.0000.0000.000
137A145LYS10.9560.98450.774-0.036-0.0360.0000.0000.0000.000
138A146SER0-0.066-0.03449.9620.0000.0000.0000.0000.0000.000
139A147VAL0-0.020-0.00945.8560.0000.0000.0000.0000.0000.000
140A148GLY00.0440.03247.8750.0020.0020.0000.0000.0000.000
141A149ILE00.0240.01946.8920.0000.0000.0000.0000.0000.000
142A150PRO0-0.047-0.01651.352-0.001-0.0010.0000.0000.0000.000
143A151ALA00.0600.02754.2440.0010.0010.0000.0000.0000.000
144A152ALA0-0.067-0.05256.341-0.002-0.0020.0000.0000.0000.000
145A153ILE00.0080.01258.8500.0010.0010.0000.0000.0000.000
146A154GLU-1-0.838-0.91360.1490.0370.0370.0000.0000.0000.000
147A155LYS10.8950.92961.234-0.036-0.0360.0000.0000.0000.000
148A156GLY00.0070.00362.5410.0000.0000.0000.0000.0000.000
149A157LYS10.9100.96757.240-0.038-0.0380.0000.0000.0000.000
150A158ILE0-0.0020.00953.898-0.001-0.0010.0000.0000.0000.000
151A159ALA0-0.0010.02155.4560.0020.0020.0000.0000.0000.000
152A160ILE00.0440.01949.986-0.001-0.0010.0000.0000.0000.000
153A161LYS10.9200.96154.439-0.037-0.0370.0000.0000.0000.000
154A162GLU-1-0.881-0.96354.6110.0420.0420.0000.0000.0000.000
155A163ASP-1-0.790-0.89151.0550.0510.0510.0000.0000.0000.000
156A164LYS10.7960.90149.881-0.048-0.0480.0000.0000.0000.000
157A165VAL00.0180.02244.5040.0020.0020.0000.0000.0000.000
158A166VAL0-0.037-0.03443.659-0.002-0.0020.0000.0000.0000.000
159A167VAL0-0.014-0.00840.204-0.001-0.0010.0000.0000.0000.000
160A168LYS10.8650.92841.960-0.056-0.0560.0000.0000.0000.000
161A169LYS10.9060.94834.449-0.088-0.0880.0000.0000.0000.000
162A170GLY0-0.032-0.01935.637-0.003-0.0030.0000.0000.0000.000
163A171GLU-1-0.813-0.88736.7240.0590.0590.0000.0000.0000.000
164A172VAL0-0.013-0.00635.4020.0040.0040.0000.0000.0000.000
165A173VAL00.0220.02036.696-0.005-0.0050.0000.0000.0000.000
166A174SER00.0130.00937.7710.0020.0020.0000.0000.0000.000
167A175PRO00.1010.01937.4500.0010.0010.0000.0000.0000.000
168A176LYS10.8990.96039.411-0.047-0.0470.0000.0000.0000.000
169A177LEU00.0330.01942.0580.0000.0000.0000.0000.0000.000
170A178ALA00.0090.00537.8370.0000.0000.0000.0000.0000.000
171A179ALA00.0070.00639.9290.0010.0010.0000.0000.0000.000
172A180VAL0-0.026-0.01741.607-0.001-0.0010.0000.0000.0000.000
173A181LEU0-0.002-0.01041.017-0.001-0.0010.0000.0000.0000.000
174A182ASP-1-0.813-0.91538.1430.0870.0870.0000.0000.0000.000
175A183ARG10.8100.91541.133-0.053-0.0530.0000.0000.0000.000
176A184LEU0-0.060-0.02744.424-0.002-0.0020.0000.0000.0000.000
177A185GLY0-0.0060.00242.431-0.001-0.0010.0000.0000.0000.000
178A186ILE0-0.027-0.01041.3670.0020.0020.0000.0000.0000.000
179A187LYS10.8220.90337.210-0.085-0.0850.0000.0000.0000.000
180A188PRO00.0080.01137.5220.0010.0010.0000.0000.0000.000
181A189ILE0-0.0090.01031.6480.0010.0010.0000.0000.0000.000
182A190LYS10.9120.95732.382-0.109-0.1090.0000.0000.0000.000
183A191VAL00.001-0.00328.0630.0040.0040.0000.0000.0000.000
184A192GLY00.026-0.01726.915-0.007-0.0070.0000.0000.0000.000
185A193LEU0-0.050-0.00821.3530.0080.0080.0000.0000.0000.000
186A194ASN00.0130.01722.668-0.021-0.0210.0000.0000.0000.000
187A195ILE00.0120.01321.5000.0240.0240.0000.0000.0000.000
188A196LEU0-0.049-0.01816.749-0.013-0.0130.0000.0000.0000.000
189A197ALA00.017-0.00218.450-0.015-0.0150.0000.0000.0000.000
190A198VAL0-0.026-0.01519.7500.0250.0250.0000.0000.0000.000
191A199TYR0-0.039-0.01919.085-0.015-0.0150.0000.0000.0000.000
192A200GLU-1-0.776-0.91321.0580.1670.1670.0000.0000.0000.000
193A201ASP-1-0.895-0.93323.9610.1520.1520.0000.0000.0000.000
194A202GLY0-0.018-0.01722.636-0.010-0.0100.0000.0000.0000.000
195A203ILE0-0.011-0.00223.665-0.008-0.0080.0000.0000.0000.000
196A204ILE0-0.060-0.03418.7600.0170.0170.0000.0000.0000.000
197A205TYR0-0.014-0.01022.461-0.018-0.0180.0000.0000.0000.000
198A206THR00.0340.00422.8930.0130.0130.0000.0000.0000.000
199A207PRO00.0490.00423.198-0.008-0.0080.0000.0000.0000.000
200A208ASP-1-0.893-0.94226.2510.1180.1180.0000.0000.0000.000
201A209VAL00.0050.00927.882-0.006-0.0060.0000.0000.0000.000
202A210LEU0-0.038-0.01625.153-0.003-0.0030.0000.0000.0000.000
203A211LYS10.8310.90829.608-0.126-0.1260.0000.0000.0000.000
204A212VAL0-0.060-0.02532.046-0.006-0.0060.0000.0000.0000.000
205A213ASP-1-0.886-0.93532.8380.1040.1040.0000.0000.0000.000
206A214GLU-1-0.914-0.93233.5910.0890.0890.0000.0000.0000.000
207A215GLU-1-0.890-0.95734.5210.0990.0990.0000.0000.0000.000
208A216LYS10.8580.93429.700-0.138-0.1380.0000.0000.0000.000
209A217LEU00.0310.00034.192-0.005-0.0050.0000.0000.0000.000
210A218LEU0-0.048-0.03036.3960.0020.0020.0000.0000.0000.000
211A219ALA0-0.0060.01436.601-0.001-0.0010.0000.0000.0000.000
212A220ASP-1-0.916-0.95633.6480.1270.1270.0000.0000.0000.000
213A221ILE0-0.0060.00831.997-0.006-0.0060.0000.0000.0000.000