FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: L7ZL9

Calculation Name: 4J7R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J7R

Chain ID: A

ChEMBL ID:

UniProt ID: Q7X8Q2

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 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 800
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -21244937.508324
FMO2-HF: Nuclear repulsion 20931579.169305
FMO2-HF: Total energy -313358.339019
FMO2-MP2: Total energy -314269.495338


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:76:LEU)


Summations of interaction energy for fragment #1(A:76:LEU)
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.
-25.082-19.84710.416-7.209-8.441-0.057
Interaction energy analysis for fragmet #1(A:76:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : -0.002
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].
3A78CYS00.0010.0043.175-2.4030.7800.279-1.473-1.9900.006
4A79GLU-1-0.890-0.9381.921-22.367-20.84910.113-5.587-6.043-0.063
5A80PRO0-0.006-0.0214.6400.0660.110-0.001-0.013-0.0290.000
6A81SER00.000-0.0097.339-0.333-0.3330.0000.0000.0000.000
7A82GLY0-0.0040.0078.5060.2860.2860.0000.0000.0000.000
8A83GLN0-0.050-0.01711.5590.0190.0190.0000.0000.0000.000
9A84PRO0-0.009-0.00714.479-0.061-0.0610.0000.0000.0000.000
10A85ALA0-0.0050.00317.092-0.002-0.0020.0000.0000.0000.000
11A86SER0-0.006-0.00318.4710.0560.0560.0000.0000.0000.000
12A87THR0-0.045-0.04421.748-0.003-0.0030.0000.0000.0000.000
13A88ALA0-0.053-0.02323.0550.0250.0250.0000.0000.0000.000
14A89TYR00.0820.04317.5660.0410.0410.0000.0000.0000.000
15A90GLY00.0350.02516.0390.0080.0080.0000.0000.0000.000
16A91PRO0-0.028-0.03212.7750.0150.0150.0000.0000.0000.000
17A92ALA00.0170.02512.036-0.060-0.0600.0000.0000.0000.000
18A93LEU0-0.056-0.0217.404-0.222-0.2220.0000.0000.0000.000
19A94THR00.0200.0172.9960.1300.6200.025-0.136-0.3790.000
20A95GLY00.0130.0115.8150.9000.9000.0000.0000.0000.000
21A96ARG10.8070.8685.989-0.282-0.2820.0000.0000.0000.000
22A97PRO00.0310.0218.098-0.111-0.1110.0000.0000.0000.000
23A98ALA0-0.0080.05310.768-0.079-0.0790.0000.0000.0000.000
24A99PRO0-0.026-0.02911.6390.0400.0400.0000.0000.0000.000
25A100LEU00.005-0.00715.010-0.046-0.0460.0000.0000.0000.000
26A101GLY00.0410.02317.1110.0080.0080.0000.0000.0000.000
27A102ALA0-0.018-0.00416.564-0.032-0.0320.0000.0000.0000.000
28A103SER0-0.028-0.03014.9730.0440.0440.0000.0000.0000.000
29A104ILE0-0.040-0.01015.475-0.055-0.0550.0000.0000.0000.000
30A105ASP-1-0.765-0.84510.169-0.045-0.0450.0000.0000.0000.000
31A106ALA0-0.051-0.03513.260-0.029-0.0290.0000.0000.0000.000
32A107ASP-1-0.942-0.97010.2470.0150.0150.0000.0000.0000.000
33A108THR0-0.042-0.0499.902-0.078-0.0780.0000.0000.0000.000
34A109GLY00.0030.01112.968-0.013-0.0130.0000.0000.0000.000
35A110ALA0-0.044-0.01212.323-0.003-0.0030.0000.0000.0000.000
36A111ILE0-0.012-0.01114.4730.0880.0880.0000.0000.0000.000
37A112ASN00.0210.00710.356-0.292-0.2920.0000.0000.0000.000
38A113PHE0-0.005-0.00812.9980.1160.1160.0000.0000.0000.000
39A114SER0-0.037-0.04212.975-0.074-0.0740.0000.0000.0000.000
40A115VAL00.0370.02214.6320.0410.0410.0000.0000.0000.000
41A116PHE00.007-0.00116.458-0.003-0.0030.0000.0000.0000.000
42A117SER0-0.043-0.06218.059-0.026-0.0260.0000.0000.0000.000
43A118SER0-0.061-0.04218.526-0.003-0.0030.0000.0000.0000.000
44A119SER0-0.062-0.05420.414-0.008-0.0080.0000.0000.0000.000
45A120ALA0-0.0250.01319.651-0.012-0.0120.0000.0000.0000.000
46A121GLU-1-0.833-0.91619.750-0.078-0.0780.0000.0000.0000.000
47A122SER0-0.069-0.05118.351-0.051-0.0510.0000.0000.0000.000
48A123VAL00.0200.03016.5750.0340.0340.0000.0000.0000.000
49A124SER00.0160.00917.190-0.072-0.0720.0000.0000.0000.000
50A125LEU0-0.0030.02016.0870.0510.0510.0000.0000.0000.000
51A126VAL0-0.025-0.01218.662-0.022-0.0220.0000.0000.0000.000
52A127LEU00.0110.00119.5150.0140.0140.0000.0000.0000.000
53A128PHE00.0190.00223.5350.0040.0040.0000.0000.0000.000
54A129THR00.0630.02627.2070.0070.0070.0000.0000.0000.000
55A130GLU-1-0.779-0.88829.793-0.089-0.0890.0000.0000.0000.000
56A131ALA0-0.0170.00132.6420.0080.0080.0000.0000.0000.000
57A132ASP-1-0.768-0.84030.622-0.172-0.1720.0000.0000.0000.000
58A133LEU0-0.0050.00429.6570.0040.0040.0000.0000.0000.000
59A134ASN0-0.071-0.05632.2390.0130.0130.0000.0000.0000.000
60A135ALA0-0.050-0.02135.3030.0070.0070.0000.0000.0000.000
61A136GLY00.0220.02333.7950.0010.0010.0000.0000.0000.000
62A137ARG10.8480.90831.6390.1510.1510.0000.0000.0000.000
63A138ALA00.0380.02226.0700.0020.0020.0000.0000.0000.000
64A139THR0-0.071-0.05926.3100.0070.0070.0000.0000.0000.000
65A140PHE0-0.033-0.02922.171-0.012-0.0120.0000.0000.0000.000
66A141GLU-1-0.800-0.87821.338-0.235-0.2350.0000.0000.0000.000
67A142ILE0-0.034-0.01114.956-0.029-0.0290.0000.0000.0000.000
68A143PRO00.0090.00216.9350.0060.0060.0000.0000.0000.000
69A144LEU0-0.043-0.00112.769-0.111-0.1110.0000.0000.0000.000
70A145ASP-1-0.821-0.91610.428-0.810-0.8100.0000.0000.0000.000
71A146PRO00.013-0.00811.124-0.040-0.0400.0000.0000.0000.000
72A147TYR0-0.068-0.02910.7550.1690.1690.0000.0000.0000.000
73A148VAL0-0.0110.0015.409-0.040-0.0400.0000.0000.0000.000
74A149ASN0-0.042-0.0216.597-0.079-0.0790.0000.0000.0000.000
75A150ARG10.9951.0048.7160.1800.1800.0000.0000.0000.000
76A151THR0-0.050-0.0067.8220.0570.0570.0000.0000.0000.000
77A152GLY0-0.0130.00210.354-0.003-0.0030.0000.0000.0000.000
78A153ASP-1-0.836-0.92313.9080.0870.0870.0000.0000.0000.000
79A154VAL0-0.051-0.02213.128-0.045-0.0450.0000.0000.0000.000
80A155TRP0-0.007-0.00212.192-0.018-0.0180.0000.0000.0000.000
81A156HIS10.8060.8676.3380.6050.6050.0000.0000.0000.000
82A157ILE00.0120.0079.694-0.173-0.1730.0000.0000.0000.000
83A158MET0-0.0240.0038.5080.2730.2730.0000.0000.0000.000
84A159LEU00.0110.00711.312-0.159-0.1590.0000.0000.0000.000
85A160PRO00.0190.01212.6830.1200.1200.0000.0000.0000.000
86A161ASP-1-0.918-0.97015.077-0.471-0.4710.0000.0000.0000.000
87A162LEU0-0.041-0.00318.3690.0090.0090.0000.0000.0000.000
88A163ARG10.8730.90820.0540.2740.2740.0000.0000.0000.000
89A164ASP-1-0.929-0.97323.825-0.163-0.1630.0000.0000.0000.000
90A165ASP-1-0.875-0.91525.467-0.186-0.1860.0000.0000.0000.000
91A166LEU0-0.061-0.02523.0280.0040.0040.0000.0000.0000.000
92A167LEU0-0.051-0.02325.1110.0100.0100.0000.0000.0000.000
93A168TYR0-0.078-0.07520.170-0.025-0.0250.0000.0000.0000.000
94A169GLY00.0340.01722.6570.0340.0340.0000.0000.0000.000
95A170TYR00.017-0.00117.212-0.050-0.0500.0000.0000.0000.000
96A171ARG10.7870.87721.7840.2340.2340.0000.0000.0000.000
97A172VAL0-0.004-0.00721.153-0.028-0.0280.0000.0000.0000.000
98A173GLU-1-0.821-0.90222.201-0.136-0.1360.0000.0000.0000.000
99A174GLY00.0360.01422.815-0.002-0.0020.0000.0000.0000.000
100A175VAL0-0.0020.01625.252-0.001-0.0010.0000.0000.0000.000
101A176HIS00.0280.00028.6090.0110.0110.0000.0000.0000.000
102A177GLN00.0590.03631.7380.0020.0020.0000.0000.0000.000
103A178GLU-1-0.835-0.91234.615-0.025-0.0250.0000.0000.0000.000
104A179GLU-1-0.917-0.94931.158-0.072-0.0720.0000.0000.0000.000
105A180ASP-1-0.810-0.89733.154-0.036-0.0360.0000.0000.0000.000
106A181LYS10.7870.86134.7160.0330.0330.0000.0000.0000.000
107A182ASP-1-0.877-0.92634.227-0.005-0.0050.0000.0000.0000.000
108A183TYR0-0.061-0.03229.4080.0060.0060.0000.0000.0000.000
109A184PRO00.0150.02232.472-0.004-0.0040.0000.0000.0000.000
110A185GLY00.0560.01732.5020.0070.0070.0000.0000.0000.000
111A186MET0-0.0320.01426.2600.0020.0020.0000.0000.0000.000
112A187ARG10.8100.88129.4020.0200.0200.0000.0000.0000.000
113A188HIS00.0470.05123.844-0.013-0.0130.0000.0000.0000.000
114A189ASP-1-0.776-0.88428.065-0.090-0.0900.0000.0000.0000.000
115A190LYS10.9090.95026.4710.1610.1610.0000.0000.0000.000
116A191ARG10.8180.87527.5670.0740.0740.0000.0000.0000.000
117A192ARG10.8730.95429.0160.0880.0880.0000.0000.0000.000
118A193VAL00.0180.01224.622-0.011-0.0110.0000.0000.0000.000
119A194VAL0-0.0130.00024.0770.0120.0120.0000.0000.0000.000
120A195LEU00.0110.00024.687-0.018-0.0180.0000.0000.0000.000
121A196ASP-1-0.727-0.85420.196-0.066-0.0660.0000.0000.0000.000
122A197PRO00.0060.00222.4510.0040.0040.0000.0000.0000.000
123A198TYR0-0.038-0.05121.3180.0090.0090.0000.0000.0000.000
124A199ALA0-0.065-0.01523.436-0.004-0.0040.0000.0000.0000.000
125A200VAL00.0240.01324.1700.0130.0130.0000.0000.0000.000
126A201ALA00.004-0.01725.9720.0080.0080.0000.0000.0000.000
127A202VAL00.0130.01228.054-0.014-0.0140.0000.0000.0000.000
128A203LEU0-0.034-0.01130.3740.0070.0070.0000.0000.0000.000
129A204ASN00.008-0.01831.946-0.003-0.0030.0000.0000.0000.000
130A205ARG10.8080.89834.6770.0410.0410.0000.0000.0000.000
131A206ARG10.7760.86735.4060.0790.0790.0000.0000.0000.000
132A207ARG10.8690.92339.1600.0470.0470.0000.0000.0000.000
133A208TRP00.0100.00342.773-0.002-0.0020.0000.0000.0000.000
134A209GLY00.008-0.00644.2760.0000.0000.0000.0000.0000.000
135A210GLN0-0.070-0.02041.7080.0000.0000.0000.0000.0000.000
136A211MET0-0.0050.00843.060-0.002-0.0020.0000.0000.0000.000
137A212GLY00.0520.01940.668-0.002-0.0020.0000.0000.0000.000
138A213PRO0-0.0090.00639.0560.0040.0040.0000.0000.0000.000
139A214ASN0-0.044-0.02141.828-0.002-0.0020.0000.0000.0000.000
140A215LEU00.0150.02037.399-0.003-0.0030.0000.0000.0000.000
141A216PRO00.0160.01840.2100.0050.0050.0000.0000.0000.000
142A217TYR0-0.019-0.04537.429-0.004-0.0040.0000.0000.0000.000
143A218GLY0-0.035-0.01838.0340.0050.0050.0000.0000.0000.000
144A219GLU-1-0.983-0.98138.610-0.097-0.0970.0000.0000.0000.000
145A220GLU-1-0.887-0.95433.359-0.139-0.1390.0000.0000.0000.000
146A221GLY0-0.045-0.02032.7900.0000.0000.0000.0000.0000.000
147A222VAL0-0.084-0.02932.776-0.007-0.0070.0000.0000.0000.000
148A223LEU0-0.038-0.00928.7260.0030.0030.0000.0000.0000.000
149A224GLY00.011-0.00432.9370.0050.0050.0000.0000.0000.000
150A225VAL0-0.071-0.03734.8110.0000.0000.0000.0000.0000.000
151A226MET00.0160.00437.2880.0040.0040.0000.0000.0000.000
152A227PRO00.0380.02139.812-0.001-0.0010.0000.0000.0000.000
153A228THR00.0500.01541.469-0.002-0.0020.0000.0000.0000.000
154A229TRP0-0.034-0.00835.6260.0030.0030.0000.0000.0000.000
155A230PRO00.0000.01036.750-0.005-0.0050.0000.0000.0000.000
156A231GLN0-0.014-0.03029.1290.0050.0050.0000.0000.0000.000
157A232ALA00.0070.01130.9360.0020.0020.0000.0000.0000.000
158A233ALA00.0010.00327.025-0.011-0.0110.0000.0000.0000.000
159A234ALA00.0090.01324.1370.0160.0160.0000.0000.0000.000
160A235ALA0-0.010-0.01325.164-0.021-0.0210.0000.0000.0000.000
161A236LEU00.0470.02820.4880.0050.0050.0000.0000.0000.000
162A237PRO00.0330.02719.0710.0240.0240.0000.0000.0000.000
163A238ALA0-0.017-0.01522.410-0.016-0.0160.0000.0000.0000.000
164A239ALA00.0360.02222.4630.0000.0000.0000.0000.0000.000
165A240ARG10.9920.97618.9040.0080.0080.0000.0000.0000.000
166A241GLY0-0.022-0.01222.361-0.007-0.0070.0000.0000.0000.000
167A242SER0-0.0090.00425.450-0.002-0.0020.0000.0000.0000.000
168A243ALA0-0.039-0.01427.095-0.002-0.0020.0000.0000.0000.000
169A244PHE00.0240.01128.821-0.002-0.0020.0000.0000.0000.000
170A245ASP-1-0.863-0.92032.1180.0300.0300.0000.0000.0000.000
171A246TRP00.012-0.02231.663-0.004-0.0040.0000.0000.0000.000
172A247GLU-1-0.829-0.88236.1040.0170.0170.0000.0000.0000.000
173A248GLY0-0.041-0.02237.0860.0010.0010.0000.0000.0000.000
174A249ASP-1-0.821-0.87537.2810.0460.0460.0000.0000.0000.000
175A250THR0-0.014-0.01436.4500.0080.0080.0000.0000.0000.000
176A251PRO0-0.001-0.00535.547-0.005-0.0050.0000.0000.0000.000
177A252LEU0-0.052-0.01238.5710.0020.0020.0000.0000.0000.000
178A253ASN0-0.048-0.02040.3600.0020.0020.0000.0000.0000.000
179A254LEU0-0.0140.00242.1430.0000.0000.0000.0000.0000.000
180A255PRO00.0200.01145.2790.0020.0020.0000.0000.0000.000
181A256MET00.0470.03945.768-0.003-0.0030.0000.0000.0000.000
182A257GLU-1-0.868-0.95847.5240.0520.0520.0000.0000.0000.000
183A258SER0-0.107-0.06349.607-0.003-0.0030.0000.0000.0000.000
184A259LEU0-0.057-0.01145.767-0.002-0.0020.0000.0000.0000.000
185A260VAL0-0.015-0.02150.477-0.001-0.0010.0000.0000.0000.000
186A261ILE00.0120.01147.043-0.001-0.0010.0000.0000.0000.000
187A262TYR0-0.061-0.04949.382-0.002-0.0020.0000.0000.0000.000
188A263GLU-1-0.740-0.86547.6180.0190.0190.0000.0000.0000.000
189A264ALA0-0.001-0.01447.442-0.003-0.0030.0000.0000.0000.000
190A265HIS00.0550.02445.4470.0010.0010.0000.0000.0000.000
191A266VAL00.0220.00041.972-0.001-0.0010.0000.0000.0000.000
192A267ARG10.8380.91145.3880.0170.0170.0000.0000.0000.000
193A268GLY00.0540.01747.235-0.001-0.0010.0000.0000.0000.000
194A269PHE0-0.0210.00048.6330.0000.0000.0000.0000.0000.000
195A270THR00.022-0.00249.050-0.001-0.0010.0000.0000.0000.000
196A271ALA00.0230.03750.503-0.002-0.0020.0000.0000.0000.000
197A272HIS0-0.0100.01352.042-0.002-0.0020.0000.0000.0000.000
198A273ALA00.0390.01255.6650.0000.0000.0000.0000.0000.000
199A274SER0-0.060-0.04057.8120.0000.0000.0000.0000.0000.000
200A275SER0-0.015-0.00853.5670.0010.0010.0000.0000.0000.000
201A276GLY00.0200.00855.7910.0010.0010.0000.0000.0000.000
202A277VAL0-0.080-0.01650.4620.0000.0000.0000.0000.0000.000
203A278ALA0-0.017-0.01749.458-0.002-0.0020.0000.0000.0000.000
204A279ALA0-0.038-0.02046.164-0.003-0.0030.0000.0000.0000.000
205A280PRO00.0140.01147.6380.0020.0020.0000.0000.0000.000
206A281GLY0-0.016-0.00547.728-0.002-0.0020.0000.0000.0000.000
207A282THR0-0.048-0.03643.247-0.001-0.0010.0000.0000.0000.000
208A283TYR00.034-0.00437.7030.0050.0050.0000.0000.0000.000
209A284ALA00.0220.00742.6100.0030.0030.0000.0000.0000.000
210A285GLY00.0130.00644.2500.0010.0010.0000.0000.0000.000
211A286MET0-0.022-0.01445.2660.0020.0020.0000.0000.0000.000
212A287VAL00.0120.00143.6340.0030.0030.0000.0000.0000.000
213A288GLU-1-0.839-0.91846.751-0.007-0.0070.0000.0000.0000.000
214A289ARG10.8090.91150.0030.0030.0030.0000.0000.0000.000
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