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: L7J49

Calculation Name: 3R4U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R4U

Chain ID: A

ChEMBL ID:

UniProt ID: P18640

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 428
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8028059.260274
FMO2-HF: Nuclear repulsion 7853840.495292
FMO2-HF: Total energy -174218.764982
FMO2-MP2: Total energy -174728.493865


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:864:SER)


Summations of interaction energy for fragment #1(A:864:SER)
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.
-10.837-4.2941.109-3.295-4.3590.021
Interaction energy analysis for fragmet #1(A:864:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / 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].
3A866ALA0-0.043-0.0052.496-8.488-3.2640.808-2.827-3.2050.022
4A867ASN00.0750.0274.292-1.115-0.7130.003-0.071-0.3350.000
5A868ILE0-0.055-0.0115.081-0.026-0.0260.0000.0000.0000.000
6A869ASN00.002-0.0327.138-0.227-0.2270.0000.0000.0000.000
7A870ASP-1-0.863-0.9008.7780.0200.0200.0000.0000.0000.000
8A871SER0-0.057-0.02410.754-0.044-0.0440.0000.0000.0000.000
9A872LYS10.7980.91011.626-0.243-0.2430.0000.0000.0000.000
10A873ILE00.010-0.00714.0560.0370.0370.0000.0000.0000.000
11A874LEU0-0.031-0.00717.2360.0120.0120.0000.0000.0000.000
12A875SER0-0.036-0.03215.182-0.009-0.0090.0000.0000.0000.000
13A876LEU00.0260.03917.0630.0280.0280.0000.0000.0000.000
14A877GLN0-0.020-0.02714.2790.0300.0300.0000.0000.0000.000
15A878ASN00.0460.03219.617-0.004-0.0040.0000.0000.0000.000
16A879ARG10.8400.90714.954-0.292-0.2920.0000.0000.0000.000
17A880LYS10.9100.94121.862-0.212-0.2120.0000.0000.0000.000
18A881ASN00.002-0.00124.826-0.007-0.0070.0000.0000.0000.000
19A882THR00.0610.04325.371-0.014-0.0140.0000.0000.0000.000
20A883LEU00.0000.02123.9240.0180.0180.0000.0000.0000.000
21A884VAL00.010-0.00620.840-0.003-0.0030.0000.0000.0000.000
22A885ASP-1-0.688-0.83119.5170.0920.0920.0000.0000.0000.000
23A886THR0-0.090-0.05516.2390.0040.0040.0000.0000.0000.000
24A887SER0-0.050-0.04315.4880.0420.0420.0000.0000.0000.000
25A888GLY00.0010.01316.0750.0110.0110.0000.0000.0000.000
26A889TYR0-0.025-0.02016.826-0.022-0.0220.0000.0000.0000.000
27A890ASN0-0.103-0.04020.998-0.001-0.0010.0000.0000.0000.000
28A891ALA00.0220.00822.884-0.009-0.0090.0000.0000.0000.000
29A892GLU-1-0.943-0.96324.8900.0320.0320.0000.0000.0000.000
30A893VAL0-0.034-0.02824.340-0.007-0.0070.0000.0000.0000.000
31A894SER0-0.027-0.00627.7510.0030.0030.0000.0000.0000.000
32A895GLU-1-0.905-0.96929.2900.0590.0590.0000.0000.0000.000
33A896GLU-1-0.818-0.89632.3450.0130.0130.0000.0000.0000.000
34A897GLY00.0430.02235.172-0.001-0.0010.0000.0000.0000.000
35A898ASP-1-0.832-0.92035.8630.0400.0400.0000.0000.0000.000
36A899VAL0-0.039-0.00929.713-0.002-0.0020.0000.0000.0000.000
37A900GLN0-0.103-0.05431.1950.0090.0090.0000.0000.0000.000
38A901LEU00.0260.01626.3560.0020.0020.0000.0000.0000.000
39A902ASN0-0.046-0.02424.8540.0050.0050.0000.0000.0000.000
40A903PRO00.0220.00024.9940.0120.0120.0000.0000.0000.000
41A904ILE0-0.088-0.04523.7730.0180.0180.0000.0000.0000.000
42A905PHE00.0170.03515.605-0.004-0.0040.0000.0000.0000.000
43A906PRO0-0.035-0.03819.170-0.008-0.0080.0000.0000.0000.000
44A907PHE0-0.055-0.04018.0910.0150.0150.0000.0000.0000.000
45A908ASP-1-0.827-0.90621.9390.0780.0780.0000.0000.0000.000
46A909PHE00.0490.02623.2590.0050.0050.0000.0000.0000.000
47A910LYS10.8330.90326.245-0.043-0.0430.0000.0000.0000.000
48A911LEU00.0070.01129.2300.0010.0010.0000.0000.0000.000
49A912GLY00.0610.01731.825-0.001-0.0010.0000.0000.0000.000
50A913SER00.0100.00035.1060.0000.0000.0000.0000.0000.000
51A914SER0-0.001-0.00137.177-0.002-0.0020.0000.0000.0000.000
52A915GLY00.0210.01440.3260.0020.0020.0000.0000.0000.000
53A916GLU-1-0.976-0.99541.5900.0070.0070.0000.0000.0000.000
54A917ASP-1-0.951-0.96340.8100.0200.0200.0000.0000.0000.000
55A918ARG10.8620.93836.5570.0000.0000.0000.0000.0000.000
56A919GLY0-0.0110.00333.9730.0000.0000.0000.0000.0000.000
57A920LYS10.8070.88732.703-0.013-0.0130.0000.0000.0000.000
58A921VAL00.0030.00126.7780.0050.0050.0000.0000.0000.000
59A922ILE0-0.020-0.00329.499-0.008-0.0080.0000.0000.0000.000
60A923VAL0-0.004-0.00624.0150.0080.0080.0000.0000.0000.000
61A924THR00.0100.00327.419-0.013-0.0130.0000.0000.0000.000
62A925GLN00.009-0.01122.3990.0020.0020.0000.0000.0000.000
63A926ASN00.0570.01625.070-0.011-0.0110.0000.0000.0000.000
64A927GLU-1-0.831-0.94726.348-0.028-0.0280.0000.0000.0000.000
65A928ASN0-0.028-0.01626.681-0.011-0.0110.0000.0000.0000.000
66A929ILE00.0140.02321.187-0.010-0.0100.0000.0000.0000.000
67A930VAL00.0130.02522.969-0.014-0.0140.0000.0000.0000.000
68A931TYR0-0.024-0.00225.045-0.014-0.0140.0000.0000.0000.000
69A932ASN0-0.066-0.05223.526-0.011-0.0110.0000.0000.0000.000
70A933SER0-0.015-0.01120.687-0.018-0.0180.0000.0000.0000.000
71A934MET0-0.032-0.02122.355-0.021-0.0210.0000.0000.0000.000
72A935TYR0-0.0030.00124.109-0.002-0.0020.0000.0000.0000.000
73A936GLU-1-0.935-0.94522.971-0.162-0.1620.0000.0000.0000.000
74A937SER0-0.004-0.02619.0170.0010.0010.0000.0000.0000.000
75A938PHE0-0.0290.01218.4790.0030.0030.0000.0000.0000.000
76A939SER0-0.013-0.03715.215-0.041-0.0410.0000.0000.0000.000
77A940ILE0-0.0010.02217.2990.0240.0240.0000.0000.0000.000
78A941SER00.0170.00214.345-0.042-0.0420.0000.0000.0000.000
79A942PHE00.0250.01316.4360.0370.0370.0000.0000.0000.000
80A943TRP0-0.0440.00013.946-0.016-0.0160.0000.0000.0000.000
81A944ILE00.0460.01618.8910.0130.0130.0000.0000.0000.000
82A945ARG10.8650.94122.586-0.030-0.0300.0000.0000.0000.000
83A946ILE00.0490.03325.3710.0030.0030.0000.0000.0000.000
84A947ASN0-0.068-0.00128.9500.0000.0000.0000.0000.0000.000
85A948LYS10.9090.96132.045-0.003-0.0030.0000.0000.0000.000
86A949TRP00.0590.00826.587-0.001-0.0010.0000.0000.0000.000
87A950VAL00.0340.01532.826-0.003-0.0030.0000.0000.0000.000
88A951SER00.0370.00935.517-0.002-0.0020.0000.0000.0000.000
89A952ASN0-0.022-0.01436.524-0.003-0.0030.0000.0000.0000.000
90A953LEU0-0.0220.01333.6110.0020.0020.0000.0000.0000.000
91A954PRO00.0470.02637.477-0.003-0.0030.0000.0000.0000.000
92A955GLY00.0370.01136.268-0.001-0.0010.0000.0000.0000.000
93A956TYR00.015-0.00233.9450.0050.0050.0000.0000.0000.000
94A957THR00.0420.02931.996-0.005-0.0050.0000.0000.0000.000
95A958ILE0-0.071-0.03827.1290.0050.0050.0000.0000.0000.000
96A959ILE0-0.012-0.01224.0750.0050.0050.0000.0000.0000.000
97A960ASP-1-0.797-0.87428.157-0.043-0.0430.0000.0000.0000.000
98A961SER0-0.016-0.01727.7680.0040.0040.0000.0000.0000.000
99A962VAL0-0.0090.00129.846-0.007-0.0070.0000.0000.0000.000
100A963LYS10.9240.94933.1200.0270.0270.0000.0000.0000.000
101A964ASN0-0.049-0.02935.745-0.001-0.0010.0000.0000.0000.000
102A965ASN00.007-0.00937.903-0.003-0.0030.0000.0000.0000.000
103A966SER00.0370.02134.715-0.005-0.0050.0000.0000.0000.000
104A967GLY00.0330.03130.7540.0050.0050.0000.0000.0000.000
105A968TRP0-0.031-0.01724.644-0.010-0.0100.0000.0000.0000.000
106A969SER0-0.010-0.04528.7070.0080.0080.0000.0000.0000.000
107A970ILE00.0010.00123.596-0.010-0.0100.0000.0000.0000.000
108A971GLY00.0630.03228.0470.0090.0090.0000.0000.0000.000
109A972ILE0-0.052-0.02629.086-0.006-0.0060.0000.0000.0000.000
110A973ILE00.0560.02431.5210.0040.0040.0000.0000.0000.000
111A974SER00.0000.01433.870-0.005-0.0050.0000.0000.0000.000
112A975ASN0-0.049-0.03032.2360.0030.0030.0000.0000.0000.000
113A976PHE00.003-0.01130.198-0.005-0.0050.0000.0000.0000.000
114A977LEU0-0.050-0.01324.3470.0050.0050.0000.0000.0000.000
115A978VAL00.000-0.01927.427-0.010-0.0100.0000.0000.0000.000
116A979PHE0-0.0040.00324.4110.0020.0020.0000.0000.0000.000
117A980THR00.023-0.01026.926-0.004-0.0040.0000.0000.0000.000
118A981LEU0-0.0020.00026.1750.0020.0020.0000.0000.0000.000
119A982LYS10.8600.93029.8390.0480.0480.0000.0000.0000.000
120A983GLN00.0060.01933.3530.0000.0000.0000.0000.0000.000
121A984ASN00.0480.00734.9230.0030.0030.0000.0000.0000.000
122A985GLU-1-0.887-0.94638.221-0.032-0.0320.0000.0000.0000.000
123A986ASP-1-0.906-0.93840.863-0.038-0.0380.0000.0000.0000.000
124A987SER0-0.068-0.03437.259-0.003-0.0030.0000.0000.0000.000
125A988GLU-1-0.856-0.91533.994-0.062-0.0620.0000.0000.0000.000
126A989GLN0-0.010-0.00330.339-0.003-0.0030.0000.0000.0000.000
127A990SER00.0370.00729.663-0.004-0.0040.0000.0000.0000.000
128A991ILE0-0.0350.00223.688-0.004-0.0040.0000.0000.0000.000
129A992ASN0-0.056-0.04127.0660.0100.0100.0000.0000.0000.000
130A993PHE00.0250.02024.112-0.009-0.0090.0000.0000.0000.000
131A994SER00.0260.01426.2410.0080.0080.0000.0000.0000.000
132A995TYR0-0.064-0.03428.046-0.003-0.0030.0000.0000.0000.000
133A996ASP-1-0.777-0.86628.954-0.033-0.0330.0000.0000.0000.000
134A997ILE00.0500.00931.0960.0060.0060.0000.0000.0000.000
135A998SER0-0.091-0.04434.3430.0050.0050.0000.0000.0000.000
136A999ASN0-0.049-0.04431.0000.0080.0080.0000.0000.0000.000
137A1000ASN0-0.074-0.04829.3380.0070.0070.0000.0000.0000.000
138A1001ALA00.0580.04433.0570.0000.0000.0000.0000.0000.000
139A1002PRO0-0.045-0.02434.6330.0000.0000.0000.0000.0000.000
140A1003GLY00.0410.03933.6080.0030.0030.0000.0000.0000.000
141A1004TYR0-0.009-0.00323.4340.0030.0030.0000.0000.0000.000
142A1005ASN0-0.015-0.02328.708-0.004-0.0040.0000.0000.0000.000
143A1006LYS10.8050.90824.1390.0220.0220.0000.0000.0000.000
144A1007TRP00.000-0.00120.789-0.009-0.0090.0000.0000.0000.000
145A1008PHE0-0.043-0.00619.883-0.003-0.0030.0000.0000.0000.000
146A1009PHE00.0490.01312.4410.0080.0080.0000.0000.0000.000
147A1010VAL00.0530.03617.431-0.026-0.0260.0000.0000.0000.000
148A1011THR0-0.057-0.04613.970-0.036-0.0360.0000.0000.0000.000
149A1012VAL00.0340.02916.951-0.005-0.0050.0000.0000.0000.000
150A1013THR0-0.023-0.01315.698-0.021-0.0210.0000.0000.0000.000
151A1014ASN00.020-0.01318.8760.0220.0220.0000.0000.0000.000
152A1015ASN00.0140.00620.2740.0080.0080.0000.0000.0000.000
153A1016MET00.0530.05522.6720.0080.0080.0000.0000.0000.000
154A1017MET0-0.0190.00025.1010.0130.0130.0000.0000.0000.000
155A1018GLY0-0.045-0.02723.783-0.005-0.0050.0000.0000.0000.000
156A1019ASN0-0.034-0.01722.6340.0300.0300.0000.0000.0000.000
157A1020MET00.0400.04722.749-0.013-0.0130.0000.0000.0000.000
158A1021LYS10.8500.91017.8350.3300.3300.0000.0000.0000.000
159A1022ILE00.0360.02220.269-0.006-0.0060.0000.0000.0000.000
160A1023TYR0-0.011-0.02515.706-0.011-0.0110.0000.0000.0000.000
161A1024ILE00.0310.01918.4370.0170.0170.0000.0000.0000.000
162A1025ASN0-0.059-0.04415.808-0.004-0.0040.0000.0000.0000.000
163A1026GLY00.0250.02113.484-0.004-0.0040.0000.0000.0000.000
164A1027LYS10.8780.94714.1800.1150.1150.0000.0000.0000.000
165A1028LEU0-0.013-0.00317.3000.0080.0080.0000.0000.0000.000
166A1029ILE0-0.067-0.03319.2690.0190.0190.0000.0000.0000.000
167A1030ASP-1-0.785-0.89722.654-0.105-0.1050.0000.0000.0000.000
168A1031THR0-0.024-0.02922.886-0.029-0.0290.0000.0000.0000.000
169A1032ILE0-0.0070.01824.7360.0120.0120.0000.0000.0000.000
170A1033LYS10.8380.91126.6150.1320.1320.0000.0000.0000.000
171A1034VAL0-0.0040.00525.8500.0100.0100.0000.0000.0000.000
172A1035LYS10.8160.90628.7790.0740.0740.0000.0000.0000.000
173A1036GLU-1-0.847-0.93131.679-0.097-0.0970.0000.0000.0000.000
174A1037LEU0-0.020-0.01129.8590.0060.0060.0000.0000.0000.000
175A1038THR00.005-0.01833.6750.0030.0030.0000.0000.0000.000
176A1039GLY0-0.009-0.00335.2870.0040.0040.0000.0000.0000.000
177A1040ILE0-0.0430.00530.0850.0040.0040.0000.0000.0000.000
178A1041ASN0-0.046-0.03032.790-0.003-0.0030.0000.0000.0000.000
179A1042PHE00.000-0.01327.4010.0020.0020.0000.0000.0000.000
180A1043SER00.0040.01530.1040.0060.0060.0000.0000.0000.000
181A1044LYS10.9250.97628.0900.0060.0060.0000.0000.0000.000
182A1045THR0-0.031-0.00928.3280.0060.0060.0000.0000.0000.000
183A1046ILE0-0.0200.00424.046-0.008-0.0080.0000.0000.0000.000
184A1047THR00.0140.00328.1930.0110.0110.0000.0000.0000.000
185A1048PHE0-0.037-0.02223.337-0.006-0.0060.0000.0000.0000.000
186A1049GLU-1-0.760-0.88129.2930.0070.0070.0000.0000.0000.000
187A1050ILE0-0.068-0.01731.743-0.005-0.0050.0000.0000.0000.000
188A1051ASN00.005-0.01433.9030.0040.0040.0000.0000.0000.000
189A1052LYS10.9020.94836.6910.0060.0060.0000.0000.0000.000
190A1053ILE00.0290.01635.8880.0000.0000.0000.0000.0000.000
191A1054PRO0-0.021-0.02139.9990.0000.0000.0000.0000.0000.000
192A1055ASP-1-0.927-0.96143.419-0.022-0.0220.0000.0000.0000.000
193A1056THR0-0.025-0.00140.950-0.002-0.0020.0000.0000.0000.000
194A1057GLY00.003-0.00943.419-0.001-0.0010.0000.0000.0000.000
195A1058LEU0-0.029-0.01846.1380.0000.0000.0000.0000.0000.000
196A1059ILE00.0450.02747.1440.0010.0010.0000.0000.0000.000
197A1060THR0-0.025-0.01447.6670.0000.0000.0000.0000.0000.000
198A1061SER0-0.085-0.03745.9840.0010.0010.0000.0000.0000.000
199A1062ASP-1-0.861-0.92644.788-0.001-0.0010.0000.0000.0000.000
200A1063SER0-0.098-0.07041.827-0.002-0.0020.0000.0000.0000.000
201A1064ASP-1-0.895-0.92340.4170.0050.0050.0000.0000.0000.000
202A1065ASN0-0.017-0.00836.533-0.002-0.0020.0000.0000.0000.000
203A1066ILE0-0.067-0.02233.1620.0000.0000.0000.0000.0000.000
204A1067ASN0-0.042-0.03431.8780.0020.0020.0000.0000.0000.000
205A1068MET00.0210.01627.125-0.007-0.0070.0000.0000.0000.000
206A1069TRP0-0.055-0.03125.4680.0030.0030.0000.0000.0000.000
207A1070ILE00.0310.01022.095-0.011-0.0110.0000.0000.0000.000
208A1071ARG10.8420.91114.722-0.101-0.1010.0000.0000.0000.000
209A1072ASP-1-0.823-0.89114.9740.1720.1720.0000.0000.0000.000
210A1073PHE00.0550.04016.692-0.034-0.0340.0000.0000.0000.000
211A1074TYR0-0.086-0.07511.3960.0650.0650.0000.0000.0000.000
212A1075ILE00.0470.02716.556-0.031-0.0310.0000.0000.0000.000
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