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: 9MG92

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 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 428
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8030172.7161
FMO2-HF: Nuclear repulsion 7855953.416606
FMO2-HF: Total energy -174219.299494
FMO2-MP2: Total energy -174729.095557


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.
-9.949-3.5361.243-3.371-4.2850.021
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 : 0.037 / q_NPA : 0.014
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].
3A866ALA0-0.0010.0232.443-7.710-2.7421.065-2.917-3.1170.021
4A867ASN00.0590.0313.302-0.970-0.3560.016-0.136-0.4940.000
5A868ILE0-0.050-0.0105.189-0.244-0.2440.0000.0000.0000.000
6A869ASN00.014-0.0146.747-0.205-0.2050.0000.0000.0000.000
7A870ASP-1-0.875-0.9278.049-0.129-0.1290.0000.0000.0000.000
8A871SER0-0.060-0.03210.309-0.061-0.0610.0000.0000.0000.000
9A872LYS10.7880.91111.671-0.186-0.1860.0000.0000.0000.000
10A873ILE0-0.001-0.01214.0380.0300.0300.0000.0000.0000.000
11A874LEU0-0.0090.00217.3180.0110.0110.0000.0000.0000.000
12A875SER0-0.043-0.04115.122-0.010-0.0100.0000.0000.0000.000
13A876LEU00.0380.04617.1160.0280.0280.0000.0000.0000.000
14A877GLN0-0.027-0.02214.4050.0200.0200.0000.0000.0000.000
15A878ASN00.0400.03219.766-0.001-0.0010.0000.0000.0000.000
16A879ARG10.8270.90115.297-0.228-0.2280.0000.0000.0000.000
17A880LYS10.9070.93922.372-0.171-0.1710.0000.0000.0000.000
18A881ASN00.0040.00525.342-0.006-0.0060.0000.0000.0000.000
19A882THR00.0570.04425.930-0.011-0.0110.0000.0000.0000.000
20A883LEU0-0.0170.01424.1270.0150.0150.0000.0000.0000.000
21A884VAL00.009-0.00320.810-0.004-0.0040.0000.0000.0000.000
22A885ASP-1-0.683-0.82119.1610.0560.0560.0000.0000.0000.000
23A886THR0-0.084-0.05416.0450.0060.0060.0000.0000.0000.000
24A887SER0-0.064-0.06215.3920.0320.0320.0000.0000.0000.000
25A888GLY0-0.0060.01416.0390.0010.0010.0000.0000.0000.000
26A889TYR0-0.015-0.02216.507-0.016-0.0160.0000.0000.0000.000
27A890ASN0-0.100-0.04220.6750.0020.0020.0000.0000.0000.000
28A891ALA00.0170.00922.329-0.007-0.0070.0000.0000.0000.000
29A892GLU-1-0.921-0.95524.3170.0130.0130.0000.0000.0000.000
30A893VAL0-0.036-0.03024.480-0.004-0.0040.0000.0000.0000.000
31A894SER0-0.043-0.01127.8280.0020.0020.0000.0000.0000.000
32A895GLU-1-0.844-0.95029.0090.0470.0470.0000.0000.0000.000
33A896GLU-1-0.810-0.89032.4330.0060.0060.0000.0000.0000.000
34A897GLY00.0710.03535.334-0.001-0.0010.0000.0000.0000.000
35A898ASP-1-0.834-0.91036.1000.0330.0330.0000.0000.0000.000
36A899VAL0-0.037-0.02429.882-0.001-0.0010.0000.0000.0000.000
37A900GLN0-0.089-0.04431.0840.0070.0070.0000.0000.0000.000
38A901LEU0-0.0140.00426.5220.0020.0020.0000.0000.0000.000
39A902ASN0-0.024-0.01424.9650.0050.0050.0000.0000.0000.000
40A903PRO00.0170.00025.2690.0100.0100.0000.0000.0000.000
41A904ILE0-0.094-0.04923.9420.0150.0150.0000.0000.0000.000
42A905PHE00.0240.02815.953-0.004-0.0040.0000.0000.0000.000
43A906PRO0-0.032-0.02819.472-0.007-0.0070.0000.0000.0000.000
44A907PHE0-0.064-0.04318.6740.0120.0120.0000.0000.0000.000
45A908ASP-1-0.843-0.92121.8800.0700.0700.0000.0000.0000.000
46A909PHE00.0610.02723.2950.0070.0070.0000.0000.0000.000
47A910LYS10.7900.89626.615-0.037-0.0370.0000.0000.0000.000
48A911LEU00.0080.01129.4020.0010.0010.0000.0000.0000.000
49A912GLY00.0680.00031.9180.0010.0010.0000.0000.0000.000
50A913SER00.0150.01135.182-0.001-0.0010.0000.0000.0000.000
51A914SER0-0.042-0.03937.650-0.002-0.0020.0000.0000.0000.000
52A915GLY00.0120.01340.2450.0010.0010.0000.0000.0000.000
53A916GLU-1-1.003-1.00942.2970.0020.0020.0000.0000.0000.000
54A917ASP-1-0.904-0.95041.1690.0140.0140.0000.0000.0000.000
55A918ARG10.8480.92536.9080.0020.0020.0000.0000.0000.000
56A919GLY0-0.0220.00534.3430.0000.0000.0000.0000.0000.000
57A920LYS10.7950.88133.063-0.005-0.0050.0000.0000.0000.000
58A921VAL00.0140.00127.2970.0040.0040.0000.0000.0000.000
59A922ILE0-0.0090.00430.160-0.007-0.0070.0000.0000.0000.000
60A923VAL0-0.001-0.00424.3270.0070.0070.0000.0000.0000.000
61A924THR0-0.025-0.02327.744-0.008-0.0080.0000.0000.0000.000
62A925GLN00.0170.00021.6580.0030.0030.0000.0000.0000.000
63A926ASN00.0530.02124.595-0.008-0.0080.0000.0000.0000.000
64A927GLU-1-0.834-0.94225.891-0.042-0.0420.0000.0000.0000.000
65A928ASN0-0.029-0.01926.156-0.010-0.0100.0000.0000.0000.000
66A929ILE0-0.0110.00920.881-0.010-0.0100.0000.0000.0000.000
67A930VAL00.0320.02722.803-0.015-0.0150.0000.0000.0000.000
68A931TYR00.0060.00524.918-0.012-0.0120.0000.0000.0000.000
69A932ASN0-0.082-0.05623.497-0.010-0.0100.0000.0000.0000.000
70A933SER00.0110.00220.597-0.020-0.0200.0000.0000.0000.000
71A934MET0-0.056-0.02922.386-0.017-0.0170.0000.0000.0000.000
72A935TYR0-0.007-0.00524.1430.0000.0000.0000.0000.0000.000
73A936GLU-1-0.949-0.94922.894-0.166-0.1660.0000.0000.0000.000
74A937SER0-0.009-0.02619.0010.0050.0050.0000.0000.0000.000
75A938PHE0-0.0320.01118.259-0.007-0.0070.0000.0000.0000.000
76A939SER0-0.012-0.03915.334-0.031-0.0310.0000.0000.0000.000
77A940ILE00.0030.01717.4210.0190.0190.0000.0000.0000.000
78A941SER0-0.005-0.00614.604-0.028-0.0280.0000.0000.0000.000
79A942PHE00.0140.01616.6530.0280.0280.0000.0000.0000.000
80A943TRP0-0.035-0.00514.367-0.011-0.0110.0000.0000.0000.000
81A944ILE00.0400.01519.2070.0100.0100.0000.0000.0000.000
82A945ARG10.8470.93722.908-0.028-0.0280.0000.0000.0000.000
83A946ILE00.0550.02925.8100.0010.0010.0000.0000.0000.000
84A947ASN0-0.029-0.01229.4480.0040.0040.0000.0000.0000.000
85A948LYS10.8590.93632.672-0.008-0.0080.0000.0000.0000.000
86A949TRP00.0500.01927.1000.0000.0000.0000.0000.0000.000
87A950VAL00.0380.00733.539-0.002-0.0020.0000.0000.0000.000
88A951SER00.0180.00135.772-0.002-0.0020.0000.0000.0000.000
89A952ASN00.000-0.00836.791-0.002-0.0020.0000.0000.0000.000
90A953LEU0-0.0220.01234.3380.0010.0010.0000.0000.0000.000
91A954PRO00.0610.03038.196-0.003-0.0030.0000.0000.0000.000
92A955GLY00.0430.01036.817-0.001-0.0010.0000.0000.0000.000
93A956TYR00.011-0.00834.3500.0040.0040.0000.0000.0000.000
94A957THR00.0290.02432.057-0.004-0.0040.0000.0000.0000.000
95A958ILE0-0.077-0.04227.6030.0050.0050.0000.0000.0000.000
96A959ILE0-0.015-0.01924.4710.0050.0050.0000.0000.0000.000
97A960ASP-1-0.813-0.87828.431-0.046-0.0460.0000.0000.0000.000
98A961SER00.001-0.01427.8540.0030.0030.0000.0000.0000.000
99A962VAL0-0.0080.00229.950-0.006-0.0060.0000.0000.0000.000
100A963LYS10.9070.93733.2230.0340.0340.0000.0000.0000.000
101A964ASN0-0.050-0.03135.743-0.001-0.0010.0000.0000.0000.000
102A965ASN00.008-0.00437.980-0.003-0.0030.0000.0000.0000.000
103A966SER0-0.0040.00534.750-0.004-0.0040.0000.0000.0000.000
104A967GLY00.0450.02930.8620.0040.0040.0000.0000.0000.000
105A968TRP0-0.029-0.01324.731-0.007-0.0070.0000.0000.0000.000
106A969SER0-0.017-0.04728.9530.0080.0080.0000.0000.0000.000
107A970ILE0-0.001-0.00223.844-0.010-0.0100.0000.0000.0000.000
108A971GLY00.0530.02828.3020.0080.0080.0000.0000.0000.000
109A972ILE0-0.047-0.02629.613-0.005-0.0050.0000.0000.0000.000
110A973ILE00.0550.02431.9890.0030.0030.0000.0000.0000.000
111A974SER0-0.0120.00634.390-0.004-0.0040.0000.0000.0000.000
112A975ASN0-0.036-0.03432.7270.0020.0020.0000.0000.0000.000
113A976PHE0-0.024-0.00730.583-0.003-0.0030.0000.0000.0000.000
114A977LEU0-0.036-0.00624.7970.0050.0050.0000.0000.0000.000
115A978VAL00.001-0.01228.019-0.007-0.0070.0000.0000.0000.000
116A979PHE0-0.005-0.00824.7330.0010.0010.0000.0000.0000.000
117A980THR00.018-0.00327.123-0.002-0.0020.0000.0000.0000.000
118A981LEU0-0.001-0.00126.130-0.001-0.0010.0000.0000.0000.000
119A982LYS10.8620.91729.8820.0480.0480.0000.0000.0000.000
120A983GLN00.0030.01233.5070.0000.0000.0000.0000.0000.000
121A984ASN00.0290.00835.0270.0020.0020.0000.0000.0000.000
122A985GLU-1-0.840-0.92138.445-0.034-0.0340.0000.0000.0000.000
123A986ASP-1-0.886-0.93040.939-0.039-0.0390.0000.0000.0000.000
124A987SER0-0.063-0.02937.329-0.002-0.0020.0000.0000.0000.000
125A988GLU-1-0.834-0.90233.881-0.060-0.0600.0000.0000.0000.000
126A989GLN0-0.018-0.00330.402-0.004-0.0040.0000.0000.0000.000
127A990SER00.0300.00129.543-0.004-0.0040.0000.0000.0000.000
128A991ILE0-0.036-0.00523.755-0.003-0.0030.0000.0000.0000.000
129A992ASN0-0.073-0.06227.2010.0110.0110.0000.0000.0000.000
130A993PHE00.0210.00024.461-0.009-0.0090.0000.0000.0000.000
131A994SER00.0200.02826.5950.0060.0060.0000.0000.0000.000
132A995TYR0-0.056-0.03328.421-0.002-0.0020.0000.0000.0000.000
133A996ASP-1-0.777-0.86129.332-0.018-0.0180.0000.0000.0000.000
134A997ILE00.0450.00731.4380.0050.0050.0000.0000.0000.000
135A998SER0-0.089-0.05134.3970.0040.0040.0000.0000.0000.000
136A999ASN0-0.046-0.04031.4140.0070.0070.0000.0000.0000.000
137A1000ASN0-0.064-0.04429.5930.0070.0070.0000.0000.0000.000
138A1001ALA00.0620.04533.2400.0000.0000.0000.0000.0000.000
139A1002PRO0-0.055-0.02835.2720.0000.0000.0000.0000.0000.000
140A1003GLY00.0540.04834.1000.0020.0020.0000.0000.0000.000
141A1004TYR0-0.0040.00523.7250.0050.0050.0000.0000.0000.000
142A1005ASN0-0.047-0.02528.866-0.004-0.0040.0000.0000.0000.000
143A1006LYS10.7880.89024.9230.0070.0070.0000.0000.0000.000
144A1007TRP00.0090.00021.393-0.007-0.0070.0000.0000.0000.000
145A1008PHE0-0.034-0.00620.178-0.002-0.0020.0000.0000.0000.000
146A1009PHE00.0400.02012.6670.0060.0060.0000.0000.0000.000
147A1010VAL00.0470.02417.682-0.019-0.0190.0000.0000.0000.000
148A1011THR0-0.044-0.04314.110-0.033-0.0330.0000.0000.0000.000
149A1012VAL00.0390.03817.023-0.009-0.0090.0000.0000.0000.000
150A1013THR0-0.074-0.04015.602-0.014-0.0140.0000.0000.0000.000
151A1014ASN00.0670.00318.8420.0290.0290.0000.0000.0000.000
152A1015ASN00.012-0.00319.8240.0000.0000.0000.0000.0000.000
153A1016MET00.0340.04822.3480.0090.0090.0000.0000.0000.000
154A1017MET00.0190.00324.5010.0130.0130.0000.0000.0000.000
155A1018GLY0-0.033-0.00123.1680.0030.0030.0000.0000.0000.000
156A1019ASN0-0.038-0.03022.4550.0300.0300.0000.0000.0000.000
157A1020MET00.0360.04322.491-0.014-0.0140.0000.0000.0000.000
158A1021LYS10.8470.91017.7010.3030.3030.0000.0000.0000.000
159A1022ILE00.0380.02520.308-0.005-0.0050.0000.0000.0000.000
160A1023TYR0-0.002-0.01015.5640.0030.0030.0000.0000.0000.000
161A1024ILE00.0310.01718.4740.0110.0110.0000.0000.0000.000
162A1025ASN0-0.048-0.03116.450-0.003-0.0030.0000.0000.0000.000
163A1026GLY00.0360.02513.7160.0100.0100.0000.0000.0000.000
164A1027LYS10.8650.93214.4900.0690.0690.0000.0000.0000.000
165A1028LEU0-0.007-0.00217.5100.0020.0020.0000.0000.0000.000
166A1029ILE0-0.071-0.03319.3400.0190.0190.0000.0000.0000.000
167A1030ASP-1-0.760-0.87122.876-0.091-0.0910.0000.0000.0000.000
168A1031THR0-0.033-0.03422.612-0.028-0.0280.0000.0000.0000.000
169A1032ILE0-0.0120.01424.5270.0100.0100.0000.0000.0000.000
170A1033LYS10.8100.90226.4100.1270.1270.0000.0000.0000.000
171A1034VAL0-0.0160.00925.5850.0100.0100.0000.0000.0000.000
172A1035LYS10.8290.90728.4590.0710.0710.0000.0000.0000.000
173A1036GLU-1-0.791-0.88631.369-0.094-0.0940.0000.0000.0000.000
174A1037LEU0-0.031-0.02129.5960.0050.0050.0000.0000.0000.000
175A1038THR0-0.007-0.03833.4920.0030.0030.0000.0000.0000.000
176A1039GLY0-0.036-0.00935.2570.0040.0040.0000.0000.0000.000
177A1040ILE0-0.0430.00430.1220.0040.0040.0000.0000.0000.000
178A1041ASN0-0.035-0.02132.239-0.004-0.0040.0000.0000.0000.000
179A1042PHE00.011-0.00627.5750.0020.0020.0000.0000.0000.000
180A1043SER0-0.0040.01330.1580.0050.0050.0000.0000.0000.000
181A1044LYS10.9170.97827.9650.0180.0180.0000.0000.0000.000
182A1045THR0-0.018-0.00828.0900.0050.0050.0000.0000.0000.000
183A1046ILE0-0.0230.00324.098-0.007-0.0070.0000.0000.0000.000
184A1047THR00.0180.00928.3170.0090.0090.0000.0000.0000.000
185A1048PHE0-0.027-0.01923.610-0.005-0.0050.0000.0000.0000.000
186A1049GLU-1-0.748-0.87229.4850.0020.0020.0000.0000.0000.000
187A1050ILE0-0.063-0.00932.131-0.004-0.0040.0000.0000.0000.000
188A1051ASN00.001-0.01134.3050.0040.0040.0000.0000.0000.000
189A1052LYS10.8980.94236.9010.0050.0050.0000.0000.0000.000
190A1053ILE00.0260.01736.2190.0000.0000.0000.0000.0000.000
191A1054PRO0-0.012-0.00640.3390.0010.0010.0000.0000.0000.000
192A1055ASP-1-0.928-0.97143.382-0.021-0.0210.0000.0000.0000.000
193A1056THR0-0.034-0.01541.214-0.002-0.0020.0000.0000.0000.000
194A1057GLY00.021-0.00643.226-0.001-0.0010.0000.0000.0000.000
195A1058LEU0-0.054-0.01346.5570.0000.0000.0000.0000.0000.000
196A1059ILE00.0420.02547.4020.0010.0010.0000.0000.0000.000
197A1060THR0-0.029-0.01548.0540.0000.0000.0000.0000.0000.000
198A1061SER0-0.060-0.02046.5120.0010.0010.0000.0000.0000.000
199A1062ASP-1-0.856-0.91644.719-0.002-0.0020.0000.0000.0000.000
200A1063SER0-0.113-0.08442.034-0.002-0.0020.0000.0000.0000.000
201A1064ASP-1-0.892-0.93341.0490.0060.0060.0000.0000.0000.000
202A1065ASN0-0.0230.01237.135-0.002-0.0020.0000.0000.0000.000
203A1066ILE0-0.0360.00133.8110.0020.0020.0000.0000.0000.000
204A1067ASN0-0.011-0.01132.6400.0000.0000.0000.0000.0000.000
205A1068MET0-0.008-0.00427.562-0.005-0.0050.0000.0000.0000.000
206A1069TRP0-0.049-0.01625.7460.0020.0020.0000.0000.0000.000
207A1070ILE00.0300.01322.374-0.007-0.0070.0000.0000.0000.000
208A1071ARG10.8630.91214.937-0.109-0.1090.0000.0000.0000.000
209A1072ASP-1-0.809-0.88414.9160.1610.1610.0000.0000.0000.000
210A1073PHE00.0500.04016.579-0.030-0.0300.0000.0000.0000.000
211A1074TYR0-0.082-0.07411.5300.0550.0550.0000.0000.0000.000
212A1075ILE00.0540.02616.732-0.027-0.0270.0000.0000.0000.000
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