FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: J2LM9

Calculation Name: 4J87-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J87

Chain ID: A

ChEMBL ID:

UniProt ID: Q96WV5

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptAll
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 316
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5122249.826898
FMO2-HF: Nuclear repulsion 4993182.045623
FMO2-HF: Total energy -129067.781275
FMO2-MP2: Total energy -129439.120502


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.
-32.829-20.92820.513-11.845-20.569-0.078
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 : -0.012 / 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].
3A3MET0-0.029-0.0083.870-0.6920.729-0.007-0.638-0.7770.003
4A4LEU0-0.011-0.0095.8600.0610.0610.0000.0000.0000.000
5A5THR00.007-0.0188.7690.1110.1110.0000.0000.0000.000
6A6LYS10.8020.90211.6110.2510.2510.0000.0000.0000.000
7A7PHE00.0570.04214.716-0.002-0.0020.0000.0000.0000.000
8A8GLU-1-0.771-0.85716.3450.1080.1080.0000.0000.0000.000
9A9SER0-0.0030.01218.685-0.017-0.0170.0000.0000.0000.000
10A10ARG10.8350.89017.915-0.040-0.0400.0000.0000.0000.000
11A11SER00.000-0.01023.481-0.009-0.0090.0000.0000.0000.000
12A12SER00.0240.01025.2500.0040.0040.0000.0000.0000.000
13A13ARG10.8090.90223.644-0.144-0.1440.0000.0000.0000.000
14A14ALA00.0160.02421.620-0.010-0.0100.0000.0000.0000.000
15A15LYS10.8000.90022.716-0.186-0.1860.0000.0000.0000.000
16A16GLY00.0710.04721.0540.0230.0230.0000.0000.0000.000
17A17VAL0-0.041-0.02918.192-0.022-0.0220.0000.0000.0000.000
18A18ALA00.0140.01019.5250.0230.0230.0000.0000.0000.000
19A19PHE00.003-0.00413.807-0.031-0.0310.0000.0000.0000.000
20A20HIS00.0500.04819.3810.0010.0010.0000.0000.0000.000
21A21PRO0-0.005-0.00720.270-0.005-0.0050.0000.0000.0000.000
22A22THR0-0.041-0.03120.885-0.012-0.0120.0000.0000.0000.000
23A23GLN0-0.0030.00822.831-0.016-0.0160.0000.0000.0000.000
24A24PRO0-0.0060.00620.8910.0080.0080.0000.0000.0000.000
25A25TRP0-0.010-0.02021.7930.0060.0060.0000.0000.0000.000
26A26ILE0-0.038-0.02318.3870.0100.0100.0000.0000.0000.000
27A27LEU00.0300.02821.658-0.012-0.0120.0000.0000.0000.000
28A28THR0-0.032-0.02921.5270.0180.0180.0000.0000.0000.000
29A29SER00.0160.00623.949-0.011-0.0110.0000.0000.0000.000
30A30LEU00.0310.01725.2970.0160.0160.0000.0000.0000.000
31A31HIS00.0790.02727.4500.0060.0060.0000.0000.0000.000
32A32ASN0-0.016-0.02129.148-0.004-0.0040.0000.0000.0000.000
33A33GLY00.0490.04231.579-0.008-0.0080.0000.0000.0000.000
34A34ARG10.7620.87731.555-0.071-0.0710.0000.0000.0000.000
35A35ILE00.0210.00627.8910.0110.0110.0000.0000.0000.000
36A36GLN0-0.0090.00525.804-0.003-0.0030.0000.0000.0000.000
37A37LEU00.0110.01625.7430.0090.0090.0000.0000.0000.000
38A38TRP00.0140.00122.898-0.010-0.0100.0000.0000.0000.000
39A39ASP-1-0.743-0.87323.313-0.015-0.0150.0000.0000.0000.000
40A40TYR0-0.020-0.00816.675-0.015-0.0150.0000.0000.0000.000
41A41ARG10.8140.89218.0910.0500.0500.0000.0000.0000.000
42A42MET00.002-0.00620.970-0.010-0.0100.0000.0000.0000.000
43A43GLY00.0050.00822.690-0.001-0.0010.0000.0000.0000.000
44A44THR00.0010.00223.5250.0080.0080.0000.0000.0000.000
45A45LEU0-0.026-0.01226.3710.0060.0060.0000.0000.0000.000
46A46LEU0-0.034-0.02426.809-0.005-0.0050.0000.0000.0000.000
47A47ASP-1-0.797-0.89429.7040.0310.0310.0000.0000.0000.000
48A48ARG10.8870.93730.195-0.043-0.0430.0000.0000.0000.000
49A49PHE0-0.0020.02229.894-0.003-0.0030.0000.0000.0000.000
50A50ASP-1-0.817-0.91733.1420.0630.0630.0000.0000.0000.000
51A51GLY00.0320.01635.826-0.004-0.0040.0000.0000.0000.000
52A52HIS0-0.052-0.02233.0780.0030.0030.0000.0000.0000.000
53A53ASP-1-0.864-0.92036.1970.0600.0600.0000.0000.0000.000
54A54GLY00.0220.00535.072-0.001-0.0010.0000.0000.0000.000
55A55PRO0-0.083-0.03529.5460.0010.0010.0000.0000.0000.000
56A56VAL00.0050.02528.6080.0010.0010.0000.0000.0000.000
57A57ARG10.7730.85726.305-0.131-0.1310.0000.0000.0000.000
58A58GLY00.0290.02724.9260.0190.0190.0000.0000.0000.000
59A59ILE0-0.020-0.02723.204-0.016-0.0160.0000.0000.0000.000
60A60ALA00.0110.00723.6360.0170.0170.0000.0000.0000.000
61A61PHE00.011-0.00323.093-0.015-0.0150.0000.0000.0000.000
62A62HIS00.0830.06025.4630.0060.0060.0000.0000.0000.000
63A63PRO0-0.016-0.01823.900-0.005-0.0050.0000.0000.0000.000
64A64THR0-0.024-0.01925.508-0.007-0.0070.0000.0000.0000.000
65A65GLN00.0530.03928.580-0.009-0.0090.0000.0000.0000.000
66A66PRO0-0.054-0.02530.1670.0020.0020.0000.0000.0000.000
67A67ILE0-0.011-0.01830.965-0.001-0.0010.0000.0000.0000.000
68A68PHE0-0.010-0.01227.9930.0020.0020.0000.0000.0000.000
69A69VAL0-0.0050.00628.126-0.006-0.0060.0000.0000.0000.000
70A70SER00.027-0.02528.3610.0060.0060.0000.0000.0000.000
71A71GLY00.0370.01029.488-0.008-0.0080.0000.0000.0000.000
72A72GLY00.0240.00129.8510.0100.0100.0000.0000.0000.000
73A73ASP-1-0.757-0.85232.0270.1180.1180.0000.0000.0000.000
74A74ASP-1-0.734-0.84034.3630.0780.0780.0000.0000.0000.000
75A75TYR0-0.046-0.01235.856-0.006-0.0060.0000.0000.0000.000
76A76LYS10.7710.89436.027-0.068-0.0680.0000.0000.0000.000
77A77VAL00.006-0.01032.0410.0080.0080.0000.0000.0000.000
78A78ASN00.0050.02033.860-0.010-0.0100.0000.0000.0000.000
79A79VAL00.0140.00833.0420.0060.0060.0000.0000.0000.000
80A80TRP00.0260.00032.320-0.009-0.0090.0000.0000.0000.000
81A81ASN00.0300.01933.664-0.002-0.0020.0000.0000.0000.000
82A82TYR00.0330.01829.043-0.006-0.0060.0000.0000.0000.000
83A83LYS10.9270.96732.391-0.020-0.0200.0000.0000.0000.000
84A84SER0-0.030-0.03434.842-0.002-0.0020.0000.0000.0000.000
85A85ARG10.7970.88931.715-0.027-0.0270.0000.0000.0000.000
86A86LYS10.9911.01336.216-0.028-0.0280.0000.0000.0000.000
87A87LEU00.0150.01736.3840.0020.0020.0000.0000.0000.000
88A88LEU0-0.076-0.04737.004-0.005-0.0050.0000.0000.0000.000
89A89PHE0-0.005-0.03137.361-0.003-0.0030.0000.0000.0000.000
90A90SER00.0570.01737.8640.0020.0020.0000.0000.0000.000
91A91LEU0-0.0410.00835.124-0.003-0.0030.0000.0000.0000.000
92A92CYS0-0.011-0.01737.7010.0040.0040.0000.0000.0000.000
93A93GLY00.0580.01340.000-0.002-0.0020.0000.0000.0000.000
94A94HIS0-0.068-0.03833.7750.0040.0040.0000.0000.0000.000
95A95MET0-0.028-0.02537.887-0.004-0.0040.0000.0000.0000.000
96A96ASP-1-0.739-0.86936.3520.0970.0970.0000.0000.0000.000
97A97TYR0-0.051-0.01232.4050.0030.0030.0000.0000.0000.000
98A98VAL0-0.032-0.00130.0190.0050.0050.0000.0000.0000.000
99A99ARG10.7080.82427.034-0.158-0.1580.0000.0000.0000.000
100A100VAL00.003-0.01223.7470.0120.0120.0000.0000.0000.000
101A101CYS0-0.045-0.00526.193-0.014-0.0140.0000.0000.0000.000
102A102THR0-0.030-0.00823.1760.0030.0030.0000.0000.0000.000
103A103PHE00.001-0.00925.899-0.012-0.0120.0000.0000.0000.000
104A104HIS00.0580.05926.0850.0060.0060.0000.0000.0000.000
105A105HIS0-0.050-0.03424.673-0.001-0.0010.0000.0000.0000.000
106A106GLU-1-0.979-0.98326.8000.0450.0450.0000.0000.0000.000
107A107TYR0-0.026-0.04130.232-0.005-0.0050.0000.0000.0000.000
108A108PRO00.0100.01931.9290.0040.0040.0000.0000.0000.000
109A109TRP0-0.063-0.06131.8350.0020.0020.0000.0000.0000.000
110A110ILE0-0.029-0.01830.5230.0020.0020.0000.0000.0000.000
111A111LEU0-0.0020.01626.440-0.005-0.0050.0000.0000.0000.000
112A112SER0-0.010-0.02629.1240.0020.0020.0000.0000.0000.000
113A113CYS0-0.0390.00427.8890.0000.0000.0000.0000.0000.000
114A114SER00.0080.00530.4520.0010.0010.0000.0000.0000.000
115A115ASP-1-0.682-0.81631.5060.1450.1450.0000.0000.0000.000
116A116ASP-1-0.776-0.84933.7930.0960.0960.0000.0000.0000.000
117A117GLN0-0.011-0.00334.137-0.005-0.0050.0000.0000.0000.000
118A118THR0-0.084-0.06234.8290.0000.0000.0000.0000.0000.000
119A119ILE00.005-0.01229.7200.0090.0090.0000.0000.0000.000
120A120ARG10.8570.94332.564-0.088-0.0880.0000.0000.0000.000
121A121ILE00.0350.01532.2790.0060.0060.0000.0000.0000.000
122A122TRP0-0.006-0.01733.576-0.010-0.0100.0000.0000.0000.000
123A123ASN00.0370.03535.0530.0000.0000.0000.0000.0000.000
124A124TRP00.0260.00332.450-0.006-0.0060.0000.0000.0000.000
125A125GLN0-0.037-0.02236.723-0.002-0.0020.0000.0000.0000.000
126A126SER0-0.032-0.02539.398-0.002-0.0020.0000.0000.0000.000
127A127ARG10.9010.95639.618-0.044-0.0440.0000.0000.0000.000
128A128ASN00.0350.02740.6810.0020.0020.0000.0000.0000.000
129A129CYS0-0.0190.00137.6540.0040.0040.0000.0000.0000.000
130A130ILE0-0.044-0.03036.083-0.004-0.0040.0000.0000.0000.000
131A131ALA00.0120.00536.311-0.001-0.0010.0000.0000.0000.000
132A132ILE00.006-0.01137.0540.0030.0030.0000.0000.0000.000
133A133LEU0-0.0090.01532.225-0.004-0.0040.0000.0000.0000.000
134A134THR00.019-0.00435.3880.0050.0050.0000.0000.0000.000
135A135GLY00.0440.00736.345-0.001-0.0010.0000.0000.0000.000
136A136HIS0-0.091-0.02929.1640.0040.0040.0000.0000.0000.000
137A137SER0-0.024-0.01434.381-0.007-0.0070.0000.0000.0000.000
138A138HIS00.0420.02132.875-0.004-0.0040.0000.0000.0000.000
139A139TYR0-0.029-0.02131.1740.0050.0050.0000.0000.0000.000
140A140VAL0-0.0100.00628.4570.0110.0110.0000.0000.0000.000
141A141MET0-0.0180.01025.396-0.009-0.0090.0000.0000.0000.000
142A142CYS0-0.055-0.02621.7720.0120.0120.0000.0000.0000.000
143A143ALA00.0590.01324.698-0.009-0.0090.0000.0000.0000.000
144A144ALA0-0.055-0.01722.0320.0030.0030.0000.0000.0000.000
145A145PHE00.0720.02023.974-0.006-0.0060.0000.0000.0000.000
146A146HIS00.0020.01522.8270.0210.0210.0000.0000.0000.000
147A147PRO0-0.017-0.01519.691-0.013-0.0130.0000.0000.0000.000
148A148SER0-0.041-0.03522.779-0.012-0.0120.0000.0000.0000.000
149A149GLU-1-0.886-0.92725.3450.1030.1030.0000.0000.0000.000
150A150ASP-1-0.777-0.84627.7710.0770.0770.0000.0000.0000.000
151A151LEU0-0.038-0.03326.6160.0000.0000.0000.0000.0000.000
152A152ILE0-0.014-0.01026.4700.0030.0030.0000.0000.0000.000
153A153VAL0-0.020-0.00221.882-0.003-0.0030.0000.0000.0000.000
154A154SER00.024-0.01825.374-0.003-0.0030.0000.0000.0000.000
155A155ALA00.0050.00523.7460.0040.0040.0000.0000.0000.000
156A156SER00.0280.01025.814-0.008-0.0080.0000.0000.0000.000
157A157LEU00.0150.00527.5780.0100.0100.0000.0000.0000.000
158A158ASP-1-0.726-0.83329.6800.1380.1380.0000.0000.0000.000
159A159GLN0-0.020-0.00228.024-0.006-0.0060.0000.0000.0000.000
160A160THR0-0.054-0.03427.7450.0100.0100.0000.0000.0000.000
161A161VAL00.003-0.00723.1030.0110.0110.0000.0000.0000.000
162A162ARG10.8440.92326.401-0.143-0.1430.0000.0000.0000.000
163A163VAL00.010-0.00125.7190.0120.0120.0000.0000.0000.000
164A164TRP0-0.036-0.02828.278-0.017-0.0170.0000.0000.0000.000
165A165ASP-1-0.812-0.87730.0700.0890.0890.0000.0000.0000.000
166A166ILE00.024-0.00229.957-0.003-0.0030.0000.0000.0000.000
167A167SER00.002-0.01433.962-0.006-0.0060.0000.0000.0000.000
168A168GLY00.0190.01335.557-0.005-0.0050.0000.0000.0000.000
169A169LEU0-0.004-0.00934.959-0.004-0.0040.0000.0000.0000.000
170A170ARG10.8760.92033.587-0.064-0.0640.0000.0000.0000.000
171A171MET0-0.014-0.00436.765-0.004-0.0040.0000.0000.0000.000
172A172LYS10.8000.87540.007-0.057-0.0570.0000.0000.0000.000
173A173ASN0-0.0120.00838.5880.0000.0000.0000.0000.0000.000
174A174ALA00.0090.01138.272-0.001-0.0010.0000.0000.0000.000
175A175ALA0-0.0140.00340.333-0.003-0.0030.0000.0000.0000.000
176A176PRO0-0.0220.00543.8990.0000.0000.0000.0000.0000.000
177A177VAL00.008-0.01146.443-0.001-0.0010.0000.0000.0000.000
178A178SER0-0.019-0.00349.781-0.001-0.0010.0000.0000.0000.000
179A179MET0-0.046-0.03549.6160.0010.0010.0000.0000.0000.000
180A180SER0-0.003-0.00954.665-0.001-0.0010.0000.0000.0000.000
181A181LYS10.8950.93257.273-0.020-0.0200.0000.0000.0000.000
182A182GLU-1-0.844-0.92458.2890.0220.0220.0000.0000.0000.000
183A183ASP-1-0.874-0.89859.6940.0220.0220.0000.0000.0000.000
184A184GLN0-0.083-0.04554.4020.0020.0020.0000.0000.0000.000
185A185LYS10.9540.96753.265-0.035-0.0350.0000.0000.0000.000
186A186ALA00.0350.01255.6780.0010.0010.0000.0000.0000.000
187A187GLN0-0.025-0.00753.1610.0000.0000.0000.0000.0000.000
188A188ALA0-0.0170.00950.4390.0020.0020.0000.0000.0000.000
189A200ALA00.010-0.01241.1420.0000.0000.0000.0000.0000.000
190A201ASP-1-0.815-0.88439.5960.0590.0590.0000.0000.0000.000
191A202ALA00.003-0.01034.9920.0020.0020.0000.0000.0000.000
192A203ILE0-0.0250.00135.349-0.002-0.0020.0000.0000.0000.000
193A204VAL00.0280.01132.7480.0050.0050.0000.0000.0000.000
194A205LYS10.8530.93030.095-0.100-0.1000.0000.0000.0000.000
195A206PHE0-0.030-0.03228.155-0.002-0.0020.0000.0000.0000.000
196A207VAL00.0230.01530.4130.0050.0050.0000.0000.0000.000
197A208LEU0-0.061-0.02024.550-0.003-0.0030.0000.0000.0000.000
198A209GLU-1-0.884-0.94627.5360.1380.1380.0000.0000.0000.000
199A210GLY00.0490.00426.2010.0000.0000.0000.0000.0000.000
200A211HIS0-0.068-0.02420.6980.0160.0160.0000.0000.0000.000
201A212ASP-1-0.781-0.86925.5930.1770.1770.0000.0000.0000.000
202A213ARG10.7630.86324.839-0.211-0.2110.0000.0000.0000.000
203A214GLY00.0410.03127.0910.0030.0030.0000.0000.0000.000
204A215VAL0-0.047-0.01822.6300.0240.0240.0000.0000.0000.000
205A216ASN0-0.046-0.04421.283-0.032-0.0320.0000.0000.0000.000
206A217TRP00.025-0.01717.394-0.015-0.0150.0000.0000.0000.000
207A218CYS00.0110.00319.712-0.002-0.0020.0000.0000.0000.000
208A219ALA0-0.033-0.00116.394-0.007-0.0070.0000.0000.0000.000
209A220PHE00.0870.03618.4590.0080.0080.0000.0000.0000.000
210A221HIS00.0080.00512.3930.0140.0140.0000.0000.0000.000
211A222PRO0-0.032-0.02313.848-0.036-0.0360.0000.0000.0000.000
212A223THR0-0.020-0.01716.190-0.021-0.0210.0000.0000.0000.000
213A224LEU00.0220.02315.127-0.022-0.0220.0000.0000.0000.000
214A225PRO00.0180.02518.8090.0200.0200.0000.0000.0000.000
215A226LEU0-0.055-0.04015.5750.0020.0020.0000.0000.0000.000
216A227ILE00.0170.00219.013-0.004-0.0040.0000.0000.0000.000
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