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: VQ991

Calculation Name: 1J2W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1J2W

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SJ28

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2372307.686311
FMO2-HF: Nuclear repulsion 2293795.809861
FMO2-HF: Total energy -78511.87645
FMO2-MP2: Total energy -78743.390743


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.
-6.423-0.5713.5-4.421-4.927-0.013
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 : 0.060 / q_NPA : 0.013
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].
3A3LEU0-0.008-0.0093.235-1.3990.6370.007-0.847-1.1960.002
4A4ALA00.0480.0333.3190.4741.0960.030-0.180-0.4720.000
5A5ALA00.0340.0124.8850.6330.749-0.001-0.009-0.1060.000
6A6HIS10.8280.9017.7141.3511.3510.0000.0000.0000.000
7A7ILE00.0040.0095.9780.2320.2320.0000.0000.0000.000
8A8ASP-1-0.703-0.8049.741-0.629-0.6290.0000.0000.0000.000
9A9HIS0-0.047-0.04210.617-0.007-0.0070.0000.0000.0000.000
10A10THR0-0.060-0.04512.2770.0950.0950.0000.0000.0000.000
11A11LEU00.0130.01015.7250.0050.0050.0000.0000.0000.000
12A12LEU00.002-0.02018.5120.0170.0170.0000.0000.0000.000
13A13LYS10.8230.92721.7500.2430.2430.0000.0000.0000.000
14A14PRO00.0580.00623.761-0.002-0.0020.0000.0000.0000.000
15A15THR0-0.013-0.00726.8330.0030.0030.0000.0000.0000.000
16A16ALA0-0.0270.00322.8150.0030.0030.0000.0000.0000.000
17A17THR00.0530.04224.5420.0040.0040.0000.0000.0000.000
18A18LEU00.0590.01323.919-0.017-0.0170.0000.0000.0000.000
19A19GLU-1-0.943-0.96123.342-0.175-0.1750.0000.0000.0000.000
20A20GLU-1-0.782-0.89020.710-0.243-0.2430.0000.0000.0000.000
21A21VAL0-0.019-0.01419.223-0.037-0.0370.0000.0000.0000.000
22A22ALA0-0.027-0.01518.936-0.035-0.0350.0000.0000.0000.000
23A23LYS10.9080.95714.2130.3340.3340.0000.0000.0000.000
24A24ALA00.0180.00314.882-0.044-0.0440.0000.0000.0000.000
25A25ALA0-0.006-0.02114.017-0.079-0.0790.0000.0000.0000.000
26A26GLU-1-0.934-0.97214.318-0.323-0.3230.0000.0000.0000.000
27A27GLU-1-0.801-0.88210.914-0.540-0.5400.0000.0000.0000.000
28A28ALA0-0.029-0.0209.833-0.150-0.1500.0000.0000.0000.000
29A29LEU0-0.067-0.0319.812-0.158-0.1580.0000.0000.0000.000
30A30GLU-1-0.931-0.9338.746-0.436-0.4360.0000.0000.0000.000
31A31TYR0-0.083-0.0835.026-0.042-0.0420.0000.0000.0000.000
32A32GLY0-0.0070.0134.891-0.878-0.792-0.001-0.002-0.0820.000
33A33PHE0-0.070-0.0335.222-0.253-0.2530.0000.0000.0000.000
34A34TYR0-0.0220.0008.3440.2180.2180.0000.0000.0000.000
35A35GLY00.0130.00410.8930.1530.1530.0000.0000.0000.000
36A36LEU0-0.0190.01512.548-0.075-0.0750.0000.0000.0000.000
37A37CYS0-0.066-0.02815.0800.0640.0640.0000.0000.0000.000
38A38ILE00.0240.01717.7350.0020.0020.0000.0000.0000.000
39A39PRO00.0550.02720.4790.0110.0110.0000.0000.0000.000
40A40PRO00.0970.04624.238-0.003-0.0030.0000.0000.0000.000
41A41SER0-0.055-0.02426.5230.0020.0020.0000.0000.0000.000
42A42TYR0-0.045-0.05123.9020.0130.0130.0000.0000.0000.000
43A43VAL0-0.0160.00423.542-0.011-0.0110.0000.0000.0000.000
44A44ALA00.0380.01624.808-0.005-0.0050.0000.0000.0000.000
45A45TRP00.0070.00921.296-0.003-0.0030.0000.0000.0000.000
46A46VAL00.0300.00919.5510.0000.0000.0000.0000.0000.000
47A47ARG10.8470.92719.7220.3150.3150.0000.0000.0000.000
48A48ALA0-0.015-0.00723.4220.0060.0060.0000.0000.0000.000
49A49ARG10.8770.96020.2630.2400.2400.0000.0000.0000.000
50A50TYR0-0.035-0.03418.1870.0070.0070.0000.0000.0000.000
51A51PRO00.0350.02120.307-0.023-0.0230.0000.0000.0000.000
52A52HIS0-0.015-0.01619.388-0.009-0.0090.0000.0000.0000.000
53A53ALA0-0.0200.00016.146-0.020-0.0200.0000.0000.0000.000
54A54PRO00.0030.01111.4950.0090.0090.0000.0000.0000.000
55A55PHE0-0.020-0.00712.457-0.040-0.0400.0000.0000.0000.000
56A56ARG10.9240.96513.7010.6690.6690.0000.0000.0000.000
57A57LEU0-0.036-0.01916.446-0.034-0.0340.0000.0000.0000.000
58A58VAL0-0.020-0.01417.1050.0310.0310.0000.0000.0000.000
59A59THR00.025-0.01119.7640.0110.0110.0000.0000.0000.000
60A60VAL0-0.081-0.03622.262-0.005-0.0050.0000.0000.0000.000
61A61VAL00.0360.02124.7480.0110.0110.0000.0000.0000.000
62A62GLY00.019-0.00428.378-0.001-0.0010.0000.0000.0000.000
63A63PHE0-0.0320.00523.411-0.001-0.0010.0000.0000.0000.000
64A64PRO0-0.015-0.02127.0020.0060.0060.0000.0000.0000.000
65A65LEU00.016-0.02728.5870.0010.0010.0000.0000.0000.000
66A66GLY00.0560.05231.7720.0050.0050.0000.0000.0000.000
67A67TYR0-0.030-0.01432.7790.0030.0030.0000.0000.0000.000
68A68GLN0-0.0060.00033.7350.0030.0030.0000.0000.0000.000
69A69GLU-1-0.847-0.93436.929-0.101-0.1010.0000.0000.0000.000
70A70LYS10.8890.92736.7650.0950.0950.0000.0000.0000.000
71A71GLU-1-0.785-0.88836.925-0.108-0.1080.0000.0000.0000.000
72A72VAL0-0.029-0.01135.542-0.002-0.0020.0000.0000.0000.000
73A73LYS10.7710.86832.5210.1430.1430.0000.0000.0000.000
74A74ALA00.0180.01332.716-0.010-0.0100.0000.0000.0000.000
75A75LEU00.0170.00033.957-0.005-0.0050.0000.0000.0000.000
76A76GLU-1-0.884-0.93130.380-0.182-0.1820.0000.0000.0000.000
77A77ALA00.018-0.00229.379-0.011-0.0110.0000.0000.0000.000
78A78ALA00.0380.01729.794-0.009-0.0090.0000.0000.0000.000
79A79LEU0-0.050-0.02131.804-0.002-0.0020.0000.0000.0000.000
80A80ALA0-0.007-0.00526.767-0.004-0.0040.0000.0000.0000.000
81A81CYS00.007-0.00126.163-0.012-0.0120.0000.0000.0000.000
82A82ALA0-0.0210.01028.137-0.002-0.0020.0000.0000.0000.000
83A83ARG10.8820.93028.8660.1620.1620.0000.0000.0000.000
84A84GLY00.0300.00825.317-0.003-0.0030.0000.0000.0000.000
85A85ALA0-0.036-0.01123.052-0.024-0.0240.0000.0000.0000.000
86A86ASP-1-0.777-0.87119.631-0.362-0.3620.0000.0000.0000.000
87A87GLU-1-0.766-0.86318.293-0.485-0.4850.0000.0000.0000.000
88A88VAL00.0190.01522.1960.0000.0000.0000.0000.0000.000
89A89ASP-1-0.726-0.84120.264-0.387-0.3870.0000.0000.0000.000
90A90MET00.0150.01923.6900.0070.0070.0000.0000.0000.000
91A91VAL0-0.0130.00526.965-0.008-0.0080.0000.0000.0000.000
92A92LEU00.0230.02828.8230.0090.0090.0000.0000.0000.000
93A93HIS00.0330.01231.816-0.002-0.0020.0000.0000.0000.000
94A94LEU00.021-0.01130.7860.0050.0050.0000.0000.0000.000
95A95GLY00.0040.01334.9240.0050.0050.0000.0000.0000.000
96A96ARG10.8750.93038.3100.0970.0970.0000.0000.0000.000
97A97ALA00.0260.01735.0990.0040.0040.0000.0000.0000.000
98A98LYS10.7690.87336.4150.1060.1060.0000.0000.0000.000
99A99ALA0-0.039-0.01738.6430.0040.0040.0000.0000.0000.000
100A100GLY0-0.0090.00240.0990.0040.0040.0000.0000.0000.000
101A101ASP-1-0.854-0.92440.793-0.088-0.0880.0000.0000.0000.000
102A102LEU00.006-0.02837.167-0.005-0.0050.0000.0000.0000.000
103A103ASP-1-0.867-0.92338.720-0.091-0.0910.0000.0000.0000.000
104A104TYR0-0.033-0.01037.632-0.002-0.0020.0000.0000.0000.000
105A105LEU0-0.052-0.02834.691-0.005-0.0050.0000.0000.0000.000
106A106GLU-1-0.877-0.94635.388-0.116-0.1160.0000.0000.0000.000
107A107ALA00.0120.00636.382-0.004-0.0040.0000.0000.0000.000
108A108GLU-1-0.787-0.89234.367-0.140-0.1400.0000.0000.0000.000
109A109VAL0-0.048-0.02430.744-0.007-0.0070.0000.0000.0000.000
110A110ARG10.8990.95932.9690.1190.1190.0000.0000.0000.000
111A111ALA00.0000.00235.400-0.001-0.0010.0000.0000.0000.000
112A112VAL0-0.003-0.01630.006-0.002-0.0020.0000.0000.0000.000
113A113ARG10.7530.85927.3480.1960.1960.0000.0000.0000.000
114A114GLU-1-0.927-0.98332.081-0.120-0.1200.0000.0000.0000.000
115A115ALA0-0.0450.00033.5030.0040.0040.0000.0000.0000.000
116A116VAL0-0.057-0.02728.656-0.002-0.0020.0000.0000.0000.000
117A117PRO00.0200.01329.629-0.014-0.0140.0000.0000.0000.000
118A118GLN0-0.041-0.02427.8790.0010.0010.0000.0000.0000.000
119A119ALA00.0030.01825.273-0.015-0.0150.0000.0000.0000.000
120A120VAL0-0.0230.00520.5980.0080.0080.0000.0000.0000.000
121A121LEU0-0.006-0.01223.611-0.008-0.0080.0000.0000.0000.000
122A122LYS10.7560.86117.8140.4390.4390.0000.0000.0000.000
123A123VAL00.0230.00823.7980.0090.0090.0000.0000.0000.000
124A124ILE0-0.059-0.04223.468-0.010-0.0100.0000.0000.0000.000
125A125LEU00.024-0.00425.8760.0150.0150.0000.0000.0000.000
126A126GLU-1-0.782-0.85026.227-0.197-0.1970.0000.0000.0000.000
127A127THR0-0.012-0.03925.4160.0130.0130.0000.0000.0000.000
128A128GLY0-0.035-0.00427.8830.0110.0110.0000.0000.0000.000
129A129TYR0-0.008-0.00329.2100.0120.0120.0000.0000.0000.000
130A130PHE0-0.088-0.04131.2140.0110.0110.0000.0000.0000.000
131A131SER00.019-0.00732.111-0.002-0.0020.0000.0000.0000.000
132A132PRO00.0370.00031.440-0.006-0.0060.0000.0000.0000.000
133A133GLU-1-0.861-0.94732.500-0.092-0.0920.0000.0000.0000.000
134A134GLU-1-0.788-0.86034.991-0.102-0.1020.0000.0000.0000.000
135A135ILE00.0000.00528.490-0.005-0.0050.0000.0000.0000.000
136A136ALA0-0.010-0.00231.450-0.007-0.0070.0000.0000.0000.000
137A137ARG10.9630.98432.6460.0900.0900.0000.0000.0000.000
138A138LEU00.0100.00931.711-0.001-0.0010.0000.0000.0000.000
139A139ALA0-0.002-0.00629.249-0.006-0.0060.0000.0000.0000.000
140A140GLU-1-0.786-0.85730.562-0.120-0.1200.0000.0000.0000.000
141A141ALA00.0120.00733.3350.0000.0000.0000.0000.0000.000
142A142ALA00.0270.00629.546-0.001-0.0010.0000.0000.0000.000
143A143ILE0-0.010-0.00728.456-0.005-0.0050.0000.0000.0000.000
144A144ARG10.8220.91831.0070.1020.1020.0000.0000.0000.000
145A145GLY00.0330.02433.6600.0050.0050.0000.0000.0000.000
146A146GLY0-0.023-0.02331.4810.0000.0000.0000.0000.0000.000
147A147ALA0-0.046-0.01627.034-0.011-0.0110.0000.0000.0000.000
148A148ASP-1-0.768-0.85223.739-0.235-0.2350.0000.0000.0000.000
149A149PHE0-0.071-0.05717.577-0.021-0.0210.0000.0000.0000.000
150A150LEU00.0270.03422.9320.0150.0150.0000.0000.0000.000
151A151LYS10.8110.88719.9240.3160.3160.0000.0000.0000.000
152A152THR00.0220.01121.1730.0080.0080.0000.0000.0000.000
153A153SER00.013-0.01921.5410.0280.0280.0000.0000.0000.000
154A154THR0-0.047-0.05722.220-0.028-0.0280.0000.0000.0000.000
155A155GLY0-0.059-0.03421.964-0.021-0.0210.0000.0000.0000.000
156A156PHE0-0.074-0.04422.7490.0040.0040.0000.0000.0000.000
157A157GLY00.0460.04426.1140.0150.0150.0000.0000.0000.000
158A158PRO0-0.052-0.02527.728-0.002-0.0020.0000.0000.0000.000
159A159ARG10.8250.87824.8100.1780.1780.0000.0000.0000.000
160A160GLY0-0.024-0.00621.471-0.009-0.0090.0000.0000.0000.000
161A161ALA0-0.023-0.00318.8300.0200.0200.0000.0000.0000.000
162A162SER0-0.007-0.02320.579-0.001-0.0010.0000.0000.0000.000
163A163LEU00.034-0.00617.499-0.013-0.0130.0000.0000.0000.000
164A164GLU-1-0.839-0.90621.004-0.142-0.1420.0000.0000.0000.000
165A165ASP-1-0.755-0.82022.975-0.186-0.1860.0000.0000.0000.000
166A166VAL0-0.015-0.01118.599-0.001-0.0010.0000.0000.0000.000
167A167ALA00.0410.02221.8500.0060.0060.0000.0000.0000.000
168A168LEU0-0.084-0.03623.6690.0110.0110.0000.0000.0000.000
169A169LEU00.0290.00623.6670.0070.0070.0000.0000.0000.000
170A170VAL00.0030.01821.2050.0030.0030.0000.0000.0000.000
171A171ARG10.9070.96624.5460.1230.1230.0000.0000.0000.000
172A172VAL00.0130.00727.8340.0090.0090.0000.0000.0000.000
173A173ALA00.0420.02526.0680.0070.0070.0000.0000.0000.000
174A174GLN0-0.098-0.04328.0500.0080.0080.0000.0000.0000.000
175A175GLY00.001-0.00325.5390.0060.0060.0000.0000.0000.000
176A176ARG10.7720.85926.6260.1220.1220.0000.0000.0000.000
177A177ALA00.0330.02425.082-0.004-0.0040.0000.0000.0000.000
178A178GLN0-0.0060.02518.455-0.033-0.0330.0000.0000.0000.000
179A179VAL00.0430.02219.9340.0100.0100.0000.0000.0000.000
180A180LYS10.7550.85616.0190.4390.4390.0000.0000.0000.000
181A181ALA00.0290.02216.1480.0420.0420.0000.0000.0000.000
182A182ALA00.017-0.00216.211-0.067-0.0670.0000.0000.0000.000
183A183GLY00.0460.03917.6170.0440.0440.0000.0000.0000.000
184A184GLY00.030-0.00118.4180.0090.0090.0000.0000.0000.000
185A185ILE0-0.0080.01412.0110.0140.0140.0000.0000.0000.000
186A186ARG10.8970.94613.5160.3530.3530.0000.0000.0000.000
187A187ASP-1-0.769-0.84210.714-0.373-0.3730.0000.0000.0000.000
188A188ARG10.9200.9244.130-0.0420.047-0.001-0.008-0.0790.000
189A189GLU-1-0.824-0.8988.235-0.098-0.0980.0000.0000.0000.000
190A190THR0-0.050-0.07211.2240.0300.0300.0000.0000.0000.000
191A191ALA00.003-0.0038.9640.0220.0220.0000.0000.0000.000
192A192LEU00.010-0.0017.4000.0140.0140.0000.0000.0000.000
193A193ARG10.8170.90110.7220.2590.2590.0000.0000.0000.000
194A194MET0-0.020-0.00613.8000.0360.0360.0000.0000.0000.000
195A195LEU0-0.025-0.0119.6600.0010.0010.0000.0000.0000.000
196A196LYS10.9310.97813.8380.0870.0870.0000.0000.0000.000
197A197ALA0-0.047-0.02015.7370.0310.0310.0000.0000.0000.000
198A198GLY00.0230.00217.3020.0220.0220.0000.0000.0000.000
199A199ALA0-0.048-0.00515.771-0.007-0.0070.0000.0000.0000.000
200A200SER0-0.020-0.03114.762-0.028-0.0280.0000.0000.0000.000
201A201ARG10.7450.82613.1610.4950.4950.0000.0000.0000.000
202A202LEU00.0190.0059.8090.0830.0830.0000.0000.0000.000
203A203GLY0-0.0010.00012.830-0.058-0.0580.0000.0000.0000.000
204A204THR0-0.032-0.05210.9940.0550.0550.0000.0000.0000.000
205A205SER00.0580.03913.267-0.041-0.0410.0000.0000.0000.000
206A206SER0-0.022-0.01011.9750.0460.0460.0000.0000.0000.000
207A207GLY00.0600.0378.289-0.057-0.0570.0000.0000.0000.000
208A208VAL00.0690.0296.714-0.277-0.2770.0000.0000.0000.000
209A209ALA0-0.008-0.0027.267-0.124-0.1240.0000.0000.0000.000
210A210LEU0-0.074-0.0246.4420.0040.0040.0000.0000.0000.000
211A211VAL0-0.044-0.0212.092-2.016-0.9953.299-2.391-1.928-0.004
212A212ALA0-0.0160.0142.889-3.790-1.9080.167-0.984-1.064-0.011