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: 379NL

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 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 800
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -21241907.743948
FMO2-HF: Nuclear repulsion 20928551.690629
FMO2-HF: Total energy -313356.053319
FMO2-MP2: Total energy -314267.137624


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.
-25.852-21.11810.98-7.041-8.674-0.064
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 : -0.028 / q_NPA : -0.021
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].
3A78CYS00.0000.0023.127-2.2470.3300.261-1.057-1.7820.003
4A79GLU-1-0.884-0.9392.002-24.225-22.48110.719-5.875-6.588-0.067
5A80PRO0-0.012-0.0224.5210.6520.706-0.001-0.014-0.0390.000
6A81SER00.012-0.0047.519-0.307-0.3070.0000.0000.0000.000
7A82GLY0-0.0130.0038.5580.2010.2010.0000.0000.0000.000
8A83GLN0-0.053-0.02911.956-0.041-0.0410.0000.0000.0000.000
9A84PRO0-0.006-0.00214.451-0.061-0.0610.0000.0000.0000.000
10A85ALA0-0.006-0.00117.0030.0160.0160.0000.0000.0000.000
11A86SER0-0.007-0.00318.3500.0350.0350.0000.0000.0000.000
12A87THR0-0.042-0.04021.762-0.007-0.0070.0000.0000.0000.000
13A88ALA0-0.055-0.02723.0440.0130.0130.0000.0000.0000.000
14A89TYR00.0720.03917.5580.0450.0450.0000.0000.0000.000
15A90GLY00.0380.02715.937-0.009-0.0090.0000.0000.0000.000
16A91PRO0-0.028-0.03312.6890.0330.0330.0000.0000.0000.000
17A92ALA00.0160.02712.272-0.050-0.0500.0000.0000.0000.000
18A93LEU0-0.044-0.0167.286-0.232-0.2320.0000.0000.0000.000
19A94THR00.0110.0164.0840.1160.4750.001-0.095-0.2650.000
20A95GLY00.0230.0166.3570.6080.6080.0000.0000.0000.000
21A96ARG10.8840.9196.029-0.342-0.3420.0000.0000.0000.000
22A97PRO00.0300.0258.135-0.258-0.2580.0000.0000.0000.000
23A98ALA00.0010.06110.800-0.179-0.1790.0000.0000.0000.000
24A99PRO0-0.021-0.02711.6600.0810.0810.0000.0000.0000.000
25A100LEU00.002-0.00815.039-0.001-0.0010.0000.0000.0000.000
26A101GLY00.0440.02517.147-0.027-0.0270.0000.0000.0000.000
27A102ALA0-0.020-0.00616.5950.0210.0210.0000.0000.0000.000
28A103SER0-0.030-0.03114.9220.0100.0100.0000.0000.0000.000
29A104ILE0-0.024-0.00815.482-0.023-0.0230.0000.0000.0000.000
30A105ASP-1-0.856-0.9379.7860.2140.2140.0000.0000.0000.000
31A106ALA0-0.052-0.03913.270-0.056-0.0560.0000.0000.0000.000
32A107ASP-1-0.924-0.95310.4490.1200.1200.0000.0000.0000.000
33A108THR0-0.027-0.0189.942-0.067-0.0670.0000.0000.0000.000
34A109GLY00.0030.01012.947-0.028-0.0280.0000.0000.0000.000
35A110ALA0-0.044-0.01212.320-0.009-0.0090.0000.0000.0000.000
36A111ILE0-0.019-0.00814.4440.0800.0800.0000.0000.0000.000
37A112ASN00.0290.01010.212-0.080-0.0800.0000.0000.0000.000
38A113PHE0-0.024-0.01713.1970.0200.0200.0000.0000.0000.000
39A114SER0-0.060-0.06213.1450.0470.0470.0000.0000.0000.000
40A115VAL00.0400.02314.897-0.033-0.0330.0000.0000.0000.000
41A116PHE00.0080.00317.1830.0370.0370.0000.0000.0000.000
42A117SER0-0.046-0.06718.815-0.048-0.0480.0000.0000.0000.000
43A118SER0-0.085-0.07619.2960.0170.0170.0000.0000.0000.000
44A119SER0-0.047-0.02521.122-0.011-0.0110.0000.0000.0000.000
45A120ALA0-0.0130.01520.504-0.024-0.0240.0000.0000.0000.000
46A121GLU-1-0.878-0.95720.6030.0850.0850.0000.0000.0000.000
47A122SER0-0.057-0.04519.109-0.023-0.0230.0000.0000.0000.000
48A123VAL00.0030.02017.3890.0060.0060.0000.0000.0000.000
49A124SER00.0250.01217.894-0.031-0.0310.0000.0000.0000.000
50A125LEU0-0.0050.01916.8380.0270.0270.0000.0000.0000.000
51A126VAL0-0.029-0.01619.334-0.034-0.0340.0000.0000.0000.000
52A127LEU00.0050.00020.0890.0150.0150.0000.0000.0000.000
53A128PHE00.0180.00424.076-0.008-0.0080.0000.0000.0000.000
54A129THR00.0760.05227.7380.0050.0050.0000.0000.0000.000
55A130GLU-1-0.785-0.89330.2470.0000.0000.0000.0000.0000.000
56A131ALA0-0.033-0.01733.0630.0040.0040.0000.0000.0000.000
57A132ASP-1-0.800-0.87630.847-0.064-0.0640.0000.0000.0000.000
58A133LEU0-0.023-0.01130.3410.0030.0030.0000.0000.0000.000
59A134ASN0-0.035-0.02932.8370.0080.0080.0000.0000.0000.000
60A135ALA0-0.049-0.02335.8570.0020.0020.0000.0000.0000.000
61A136GLY00.0170.01934.427-0.001-0.0010.0000.0000.0000.000
62A137ARG10.9060.95132.1750.0520.0520.0000.0000.0000.000
63A138ALA00.0360.02126.5730.0040.0040.0000.0000.0000.000
64A139THR0-0.078-0.07426.7820.0000.0000.0000.0000.0000.000
65A140PHE0-0.038-0.02722.431-0.018-0.0180.0000.0000.0000.000
66A141GLU-1-0.829-0.92221.864-0.046-0.0460.0000.0000.0000.000
67A142ILE0-0.035-0.01215.300-0.034-0.0340.0000.0000.0000.000
68A143PRO00.0200.00917.4930.0360.0360.0000.0000.0000.000
69A144LEU0-0.0520.00113.422-0.068-0.0680.0000.0000.0000.000
70A145ASP-1-0.821-0.91910.908-0.279-0.2790.0000.0000.0000.000
71A146PRO00.009-0.00311.7950.1160.1160.0000.0000.0000.000
72A147TYR0-0.063-0.02811.3340.1420.1420.0000.0000.0000.000
73A148VAL00.0010.0115.9780.0540.0540.0000.0000.0000.000
74A149ASN0-0.035-0.0237.4360.3840.3840.0000.0000.0000.000
75A150ARG11.0081.0169.599-0.431-0.4310.0000.0000.0000.000
76A151THR0-0.065-0.0158.3420.3120.3120.0000.0000.0000.000
77A152GLY0-0.024-0.00310.935-0.090-0.0900.0000.0000.0000.000
78A153ASP-1-0.844-0.92914.4230.3440.3440.0000.0000.0000.000
79A154VAL0-0.048-0.01713.305-0.059-0.0590.0000.0000.0000.000
80A155TRP00.0040.00512.9260.1560.1560.0000.0000.0000.000
81A156HIS10.7970.8607.112-1.300-1.3000.0000.0000.0000.000
82A157ILE00.0190.01310.392-0.029-0.0290.0000.0000.0000.000
83A158MET0-0.0280.0028.4660.1480.1480.0000.0000.0000.000
84A159LEU00.0100.00211.508-0.162-0.1620.0000.0000.0000.000
85A160PRO00.0310.01512.6280.0860.0860.0000.0000.0000.000
86A161ASP-1-0.932-0.97214.998-0.302-0.3020.0000.0000.0000.000
87A162LEU0-0.039-0.00518.4010.0030.0030.0000.0000.0000.000
88A163ARG10.8710.91519.9910.1280.1280.0000.0000.0000.000
89A164ASP-1-0.925-0.97023.765-0.039-0.0390.0000.0000.0000.000
90A165ASP-1-0.878-0.92225.432-0.062-0.0620.0000.0000.0000.000
91A166LEU0-0.054-0.02623.3360.0020.0020.0000.0000.0000.000
92A167LEU0-0.064-0.02825.3260.0120.0120.0000.0000.0000.000
93A168TYR0-0.075-0.07821.017-0.022-0.0220.0000.0000.0000.000
94A169GLY00.0330.01323.3550.0160.0160.0000.0000.0000.000
95A170TYR00.0410.01017.795-0.011-0.0110.0000.0000.0000.000
96A171ARG10.8050.91022.5200.0360.0360.0000.0000.0000.000
97A172VAL00.003-0.00621.844-0.001-0.0010.0000.0000.0000.000
98A173GLU-1-0.837-0.92023.0060.0030.0030.0000.0000.0000.000
99A174GLY00.0290.00823.6330.0180.0180.0000.0000.0000.000
100A175VAL00.0090.02526.074-0.010-0.0100.0000.0000.0000.000
101A176HIS00.0350.01829.4450.0090.0090.0000.0000.0000.000
102A177GLN00.0500.03632.6080.0000.0000.0000.0000.0000.000
103A178GLU-1-0.939-0.97635.4670.0350.0350.0000.0000.0000.000
104A179GLU-1-0.935-0.97031.9510.0250.0250.0000.0000.0000.000
105A180ASP-1-0.816-0.90633.9920.0370.0370.0000.0000.0000.000
106A181LYS10.7820.87035.544-0.030-0.0300.0000.0000.0000.000
107A182ASP-1-0.886-0.92835.0380.0500.0500.0000.0000.0000.000
108A183TYR0-0.067-0.03929.8300.0100.0100.0000.0000.0000.000
109A184PRO00.0150.02833.2670.0020.0020.0000.0000.0000.000
110A185GLY00.0530.00933.2520.0090.0090.0000.0000.0000.000
111A186MET0-0.0290.01126.6660.0110.0110.0000.0000.0000.000
112A187ARG10.9130.94030.244-0.074-0.0740.0000.0000.0000.000
113A188HIS00.0510.04524.949-0.008-0.0080.0000.0000.0000.000
114A189ASP-1-0.788-0.90428.9600.0120.0120.0000.0000.0000.000
115A190LYS10.9260.97426.8590.0240.0240.0000.0000.0000.000
116A191ARG10.8460.91428.322-0.022-0.0220.0000.0000.0000.000
117A192ARG10.8780.95429.874-0.025-0.0250.0000.0000.0000.000
118A193VAL00.0180.01425.3530.0000.0000.0000.0000.0000.000
119A194VAL0-0.0090.00524.880-0.001-0.0010.0000.0000.0000.000
120A195LEU00.010-0.00525.548-0.002-0.0020.0000.0000.0000.000
121A196ASP-1-0.760-0.85920.9010.2010.2010.0000.0000.0000.000
122A197PRO0-0.0010.00022.735-0.011-0.0110.0000.0000.0000.000
123A198TYR0-0.032-0.04321.356-0.002-0.0020.0000.0000.0000.000
124A199ALA0-0.065-0.01523.465-0.003-0.0030.0000.0000.0000.000
125A200VAL00.0220.01224.136-0.001-0.0010.0000.0000.0000.000
126A201ALA0-0.002-0.02225.994-0.007-0.0070.0000.0000.0000.000
127A202VAL00.0300.02228.108-0.002-0.0020.0000.0000.0000.000
128A203LEU0-0.038-0.01430.563-0.003-0.0030.0000.0000.0000.000
129A204ASN00.0400.00632.413-0.002-0.0020.0000.0000.0000.000
130A205ARG10.8280.92835.170-0.033-0.0330.0000.0000.0000.000
131A206ARG10.7740.88335.316-0.002-0.0020.0000.0000.0000.000
132A207ARG10.9430.96039.407-0.012-0.0120.0000.0000.0000.000
133A208TRP0-0.002-0.00843.0080.0000.0000.0000.0000.0000.000
134A209GLY00.006-0.01044.527-0.002-0.0020.0000.0000.0000.000
135A210GLN0-0.069-0.02741.843-0.001-0.0010.0000.0000.0000.000
136A211MET00.0020.01143.5820.0020.0020.0000.0000.0000.000
137A212GLY00.0500.01741.389-0.002-0.0020.0000.0000.0000.000
138A213PRO0-0.0210.00639.6020.0000.0000.0000.0000.0000.000
139A214ASN0-0.047-0.03742.5160.0000.0000.0000.0000.0000.000
140A215LEU00.0200.01937.993-0.003-0.0030.0000.0000.0000.000
141A216PRO00.0120.01540.8720.0040.0040.0000.0000.0000.000
142A217TYR0-0.004-0.02038.114-0.001-0.0010.0000.0000.0000.000
143A218GLY0-0.035-0.01938.7370.0010.0010.0000.0000.0000.000
144A219GLU-1-0.990-0.98339.289-0.029-0.0290.0000.0000.0000.000
145A220GLU-1-0.886-0.95234.052-0.033-0.0330.0000.0000.0000.000
146A221GLY0-0.035-0.01633.326-0.003-0.0030.0000.0000.0000.000
147A222VAL0-0.088-0.02833.343-0.001-0.0010.0000.0000.0000.000
148A223LEU0-0.044-0.01429.6220.0050.0050.0000.0000.0000.000
149A224GLY00.006-0.00733.6200.0000.0000.0000.0000.0000.000
150A225VAL0-0.071-0.03335.567-0.002-0.0020.0000.0000.0000.000
151A226MET00.0230.00438.094-0.002-0.0020.0000.0000.0000.000
152A227PRO00.0300.01840.6010.0010.0010.0000.0000.0000.000
153A228THR00.0460.01042.250-0.001-0.0010.0000.0000.0000.000
154A229TRP0-0.030-0.01036.1260.0050.0050.0000.0000.0000.000
155A230PRO0-0.0060.00637.436-0.002-0.0020.0000.0000.0000.000
156A231GLN00.008-0.01029.6840.0030.0030.0000.0000.0000.000
157A232ALA0-0.0150.00031.565-0.002-0.0020.0000.0000.0000.000
158A233ALA00.003-0.00327.575-0.003-0.0030.0000.0000.0000.000
159A234ALA00.0090.01424.5220.0040.0040.0000.0000.0000.000
160A235ALA0-0.007-0.01325.446-0.014-0.0140.0000.0000.0000.000
161A236LEU00.0470.02920.5140.0170.0170.0000.0000.0000.000
162A237PRO00.0100.01819.0930.0030.0030.0000.0000.0000.000
163A238ALA0-0.024-0.02122.419-0.019-0.0190.0000.0000.0000.000
164A239ALA00.0400.02522.4520.0080.0080.0000.0000.0000.000
165A240ARG10.9950.97919.057-0.107-0.1070.0000.0000.0000.000
166A241GLY0-0.031-0.01722.366-0.013-0.0130.0000.0000.0000.000
167A242SER0-0.0250.00025.460-0.006-0.0060.0000.0000.0000.000
168A243ALA0-0.012-0.00427.1710.0070.0070.0000.0000.0000.000
169A244PHE00.0110.00228.841-0.006-0.0060.0000.0000.0000.000
170A245ASP-1-0.859-0.92032.1480.0670.0670.0000.0000.0000.000
171A246TRP00.005-0.03031.634-0.006-0.0060.0000.0000.0000.000
172A247GLU-1-0.893-0.93036.0960.0500.0500.0000.0000.0000.000
173A248GLY0-0.048-0.02537.127-0.001-0.0010.0000.0000.0000.000
174A249ASP-1-0.834-0.89737.2340.0870.0870.0000.0000.0000.000
175A250THR0-0.025-0.01936.4440.0090.0090.0000.0000.0000.000
176A251PRO00.002-0.00335.562-0.005-0.0050.0000.0000.0000.000
177A252LEU0-0.059-0.00938.573-0.001-0.0010.0000.0000.0000.000
178A253ASN0-0.039-0.01240.5670.0000.0000.0000.0000.0000.000
179A254LEU0-0.019-0.00642.147-0.002-0.0020.0000.0000.0000.000
180A255PRO00.0290.01045.2870.0030.0030.0000.0000.0000.000
181A256MET00.0310.03345.498-0.003-0.0030.0000.0000.0000.000
182A257GLU-1-0.871-0.96147.5370.0710.0710.0000.0000.0000.000
183A258SER0-0.101-0.05049.605-0.004-0.0040.0000.0000.0000.000
184A259LEU0-0.054-0.01145.818-0.002-0.0020.0000.0000.0000.000
185A260VAL0-0.014-0.02450.491-0.002-0.0020.0000.0000.0000.000
186A261ILE00.0220.01447.1660.0000.0000.0000.0000.0000.000
187A262TYR0-0.056-0.04749.404-0.003-0.0030.0000.0000.0000.000
188A263GLU-1-0.728-0.86247.6890.0600.0600.0000.0000.0000.000
189A264ALA00.007-0.02047.463-0.004-0.0040.0000.0000.0000.000
190A265HIS00.0590.03245.6330.0010.0010.0000.0000.0000.000
191A266VAL00.016-0.00142.029-0.003-0.0030.0000.0000.0000.000
192A267ARG10.8600.93745.411-0.033-0.0330.0000.0000.0000.000
193A268GLY00.0450.01447.260-0.003-0.0030.0000.0000.0000.000
194A269PHE0-0.0180.00048.803-0.002-0.0020.0000.0000.0000.000
195A270THR00.0240.01349.004-0.002-0.0020.0000.0000.0000.000
196A271ALA00.0340.03550.572-0.002-0.0020.0000.0000.0000.000
197A272HIS00.0000.01652.064-0.002-0.0020.0000.0000.0000.000
198A273ALA00.0450.01355.6840.0000.0000.0000.0000.0000.000
199A274SER0-0.063-0.02857.8320.0000.0000.0000.0000.0000.000
200A275SER0-0.005-0.00453.5890.0000.0000.0000.0000.0000.000
201A276GLY0-0.003-0.01055.8040.0010.0010.0000.0000.0000.000
202A277VAL0-0.065-0.00550.5480.0000.0000.0000.0000.0000.000
203A278ALA0-0.013-0.02049.452-0.002-0.0020.0000.0000.0000.000
204A279ALA0-0.044-0.02246.184-0.002-0.0020.0000.0000.0000.000
205A280PRO00.0130.01647.6530.0030.0030.0000.0000.0000.000
206A281GLY0-0.026-0.01947.749-0.001-0.0010.0000.0000.0000.000
207A282THR0-0.047-0.04443.2870.0020.0020.0000.0000.0000.000
208A283TYR00.0270.00337.6070.0020.0020.0000.0000.0000.000
209A284ALA00.0210.00542.6250.0010.0010.0000.0000.0000.000
210A285GLY00.0100.00744.261-0.001-0.0010.0000.0000.0000.000
211A286MET0-0.008-0.01245.2970.0000.0000.0000.0000.0000.000
212A287VAL00.0070.00143.6900.0010.0010.0000.0000.0000.000
213A288GLU-1-0.849-0.91646.7590.0260.0260.0000.0000.0000.000
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