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: 94GR2

Calculation Name: 3F84-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F84

Chain ID: A

ChEMBL ID:

UniProt ID: E3PPC4

Base Structure: X-ray

Registration Date: 2023-06-21

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 302
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3259391.91095
FMO2-HF: Nuclear repulsion 3150109.319226
FMO2-HF: Total energy -109282.591724
FMO2-MP2: Total energy -109601.776139


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.
-8.138-2.6714.333-3.152-6.648-0.003
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 : -0.009 / q_NPA : -0.003
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].
3A3ASP-1-0.781-0.8603.880-2.781-0.266-0.021-1.351-1.1430.000
4A4LEU0-0.043-0.0126.5210.1160.1160.0000.0000.0000.000
5A5LEU0-0.014-0.0019.8770.1120.1120.0000.0000.0000.000
6A6GLN00.005-0.03012.4720.0660.0660.0000.0000.0000.000
7A7ALA0-0.031-0.03515.269-0.051-0.0510.0000.0000.0000.000
8A8ASP-1-0.899-0.91117.195-0.313-0.3130.0000.0000.0000.000
9A9GLY0-0.0020.00614.0260.0040.0040.0000.0000.0000.000
10A10ASN0-0.062-0.05114.258-0.034-0.0340.0000.0000.0000.000
11A11ALA00.0210.00713.620-0.061-0.0610.0000.0000.0000.000
12A12LEU00.0050.00413.4930.0610.0610.0000.0000.0000.000
13A13PRO0-0.018-0.00116.0140.0080.0080.0000.0000.0000.000
14A14SER00.0590.03818.226-0.010-0.0100.0000.0000.0000.000
15A15ALA0-0.027-0.00419.2230.0250.0250.0000.0000.0000.000
16A16VAL00.0050.01022.230-0.012-0.0120.0000.0000.0000.000
17A17LYS10.8530.94124.9060.0910.0910.0000.0000.0000.000
18A18LEU00.0070.01226.895-0.007-0.0070.0000.0000.0000.000
19A19ALA00.0120.00530.4020.0090.0090.0000.0000.0000.000
20A20TYR00.0520.02833.6860.0010.0010.0000.0000.0000.000
21A21SER00.007-0.00536.693-0.001-0.0010.0000.0000.0000.000
22A22PRO00.0340.00539.9690.0020.0020.0000.0000.0000.000
23A23ALA0-0.0100.00043.0570.0030.0030.0000.0000.0000.000
24A24SER00.000-0.00439.5280.0030.0030.0000.0000.0000.000
25A25LYS10.8930.95741.1070.0400.0400.0000.0000.0000.000
26A26THR00.0210.01636.5000.0000.0000.0000.0000.0000.000
27A27PHE0-0.036-0.02332.4630.0010.0010.0000.0000.0000.000
28A28GLU-1-0.945-0.96231.288-0.104-0.1040.0000.0000.0000.000
29A29SER0-0.076-0.05227.999-0.001-0.0010.0000.0000.0000.000
30A30TYR00.0620.02420.734-0.009-0.0090.0000.0000.0000.000
31A31ARG10.8780.92224.2500.1390.1390.0000.0000.0000.000
32A32VAL00.0190.01719.133-0.001-0.0010.0000.0000.0000.000
33A33MET00.0130.03420.103-0.015-0.0150.0000.0000.0000.000
34A34THR0-0.004-0.00814.769-0.026-0.0260.0000.0000.0000.000
35A35GLN0-0.018-0.01112.8500.0500.0500.0000.0000.0000.000
36A36VAL00.0250.0058.306-0.101-0.1010.0000.0000.0000.000
37A37HIS00.0270.0156.5990.1060.1060.0000.0000.0000.000
38A38THR00.007-0.0084.246-1.380-1.300-0.001-0.036-0.0430.000
39A39ASN00.0260.0013.131-1.1500.2860.143-0.617-0.962-0.005
40A40ASP-1-0.844-0.9144.8460.8100.955-0.001-0.005-0.1390.000
41A41ALA00.0370.0296.665-0.139-0.1390.0000.0000.0000.000
42A42THR0-0.069-0.0529.9430.1280.1280.0000.0000.0000.000
43A43LYS10.9590.9938.631-0.799-0.7990.0000.0000.0000.000
44A44LYS10.8620.92211.161-0.254-0.2540.0000.0000.0000.000
45A45VAL00.0150.0049.5380.0500.0500.0000.0000.0000.000
46A46ILE0-0.049-0.01810.5050.0410.0410.0000.0000.0000.000
47A47VAL00.0200.00311.398-0.013-0.0130.0000.0000.0000.000
48A48LYS10.9540.97613.914-0.160-0.1600.0000.0000.0000.000
49A49LEU0-0.0150.00015.496-0.036-0.0360.0000.0000.0000.000
50A50ALA0-0.013-0.01615.8290.0320.0320.0000.0000.0000.000
51A51ASP-1-0.938-0.96417.5010.0360.0360.0000.0000.0000.000
52A52THR0-0.044-0.03721.272-0.017-0.0170.0000.0000.0000.000
53A53PRO00.0220.04022.5650.0030.0030.0000.0000.0000.000
54A54GLN00.012-0.01324.497-0.003-0.0030.0000.0000.0000.000
55A55LEU0-0.0200.00127.554-0.003-0.0030.0000.0000.0000.000
56A56THR00.000-0.00229.8250.0070.0070.0000.0000.0000.000
57A57ASP-1-0.817-0.91832.076-0.034-0.0340.0000.0000.0000.000
58A58VAL0-0.043-0.03932.2630.0030.0030.0000.0000.0000.000
59A59LEU0-0.050-0.01934.5390.0020.0020.0000.0000.0000.000
60A60ASN0-0.012-0.00237.0990.0050.0050.0000.0000.0000.000
61A61SER00.0670.02034.855-0.001-0.0010.0000.0000.0000.000
62A62THR0-0.039-0.02335.3260.0020.0020.0000.0000.0000.000
63A63VAL0-0.068-0.01037.2060.0000.0000.0000.0000.0000.000
64A64GLN0-0.007-0.01530.7970.0000.0000.0000.0000.0000.000
65A65MET0-0.074-0.02932.3480.0000.0000.0000.0000.0000.000
66A66PRO00.0080.02029.575-0.001-0.0010.0000.0000.0000.000
67A67ILE0-0.006-0.00824.402-0.006-0.0060.0000.0000.0000.000
68A68SER0-0.058-0.02526.0330.0090.0090.0000.0000.0000.000
69A69VAL00.0390.00419.710-0.012-0.0120.0000.0000.0000.000
70A70SER0-0.073-0.01821.9720.0120.0120.0000.0000.0000.000
71A71TRP00.0690.00213.976-0.012-0.0120.0000.0000.0000.000
72A72GLY00.0620.04119.2790.0160.0160.0000.0000.0000.000
73A73GLY0-0.023-0.00620.0640.0180.0180.0000.0000.0000.000
74A74GLN0-0.0180.00420.3960.0400.0400.0000.0000.0000.000
75A75VAL00.014-0.00321.600-0.014-0.0140.0000.0000.0000.000
76A76LEU00.0080.01417.3760.0090.0090.0000.0000.0000.000
77A77SER00.0420.00520.4370.0090.0090.0000.0000.0000.000
78A78THR00.0510.02819.518-0.006-0.0060.0000.0000.0000.000
79A79THR0-0.069-0.02419.3360.0310.0310.0000.0000.0000.000
80A80ALA0-0.011-0.00215.486-0.019-0.0190.0000.0000.0000.000
81A81LYS10.8440.91416.9930.0720.0720.0000.0000.0000.000
82A82GLU-1-0.828-0.90415.1520.1060.1060.0000.0000.0000.000
83A83PHE0-0.024-0.00414.590-0.002-0.0020.0000.0000.0000.000
84A84GLU-1-0.856-0.94314.583-0.043-0.0430.0000.0000.0000.000
85A85ALA0-0.001-0.01012.823-0.045-0.0450.0000.0000.0000.000
86A86ALA00.005-0.01514.171-0.045-0.0450.0000.0000.0000.000
87A87ALA0-0.0210.00017.359-0.006-0.0060.0000.0000.0000.000
88A88LEU00.0020.01112.855-0.008-0.0080.0000.0000.0000.000
89A89GLY00.0110.03315.900-0.051-0.0510.0000.0000.0000.000
90A90TYR0-0.021-0.0249.957-0.071-0.0710.0000.0000.0000.000
91A91SER0-0.0290.00113.9540.0860.0860.0000.0000.0000.000
92A92ALA00.056-0.01313.143-0.079-0.0790.0000.0000.0000.000
93A93SER0-0.045-0.01414.9210.0460.0460.0000.0000.0000.000
94A94GLY00.0250.00216.9760.0340.0340.0000.0000.0000.000
95A95VAL0-0.0200.00013.3320.0090.0090.0000.0000.0000.000
96A96ASN0-0.041-0.01411.037-0.057-0.0570.0000.0000.0000.000
97A97GLY00.0300.0318.258-0.037-0.0370.0000.0000.0000.000
98A98VAL00.0210.0108.290-0.368-0.3680.0000.0000.0000.000
99A99SER0-0.0190.00011.0070.1200.1200.0000.0000.0000.000
100A100SER00.017-0.00613.3740.0180.0180.0000.0000.0000.000
101A101SER0-0.006-0.01016.189-0.038-0.0380.0000.0000.0000.000
102A102GLN0-0.0100.00616.7890.0780.0780.0000.0000.0000.000
103A103GLU-1-0.799-0.89918.633-0.208-0.2080.0000.0000.0000.000
104A104LEU0-0.053-0.02717.3010.0040.0040.0000.0000.0000.000
105A105VAL0-0.019-0.00320.4440.0130.0130.0000.0000.0000.000
106A106ILE00.0010.00020.3240.0080.0080.0000.0000.0000.000
107A107SER00.0130.00224.4850.0020.0020.0000.0000.0000.000
108A108ALA00.0480.02027.6700.0030.0030.0000.0000.0000.000
109A109ALA00.0190.01230.370-0.002-0.0020.0000.0000.0000.000
110A110PRO00.0420.01433.6580.0020.0020.0000.0000.0000.000
111A111LYS10.9710.98734.3540.0100.0100.0000.0000.0000.000
112A112THR0-0.054-0.01435.9770.0030.0030.0000.0000.0000.000
113A113ALA00.0350.00837.358-0.002-0.0020.0000.0000.0000.000
114A114GLY00.0240.00839.1150.0020.0020.0000.0000.0000.000
115A115THR0-0.039-0.00741.1560.0010.0010.0000.0000.0000.000
116A116ALA00.0280.01040.849-0.003-0.0030.0000.0000.0000.000
117A117PRO0-0.013-0.00737.7090.0020.0020.0000.0000.0000.000
118A118THR00.0140.01139.6990.0000.0000.0000.0000.0000.000
119A119ALA0-0.020-0.00739.571-0.003-0.0030.0000.0000.0000.000
120A120GLY00.0620.04638.6940.0030.0030.0000.0000.0000.000
121A121ASN0-0.054-0.01134.891-0.009-0.0090.0000.0000.0000.000
122A122TYR00.020-0.00431.9980.0040.0040.0000.0000.0000.000
123A123SER0-0.026-0.02827.908-0.007-0.0070.0000.0000.0000.000
124A124GLY00.0500.02326.1900.0100.0100.0000.0000.0000.000
125A125VAL0-0.0020.00119.673-0.013-0.0130.0000.0000.0000.000
126A126VAL0-0.0090.00518.3280.0140.0140.0000.0000.0000.000
127A127SER00.0470.01516.290-0.026-0.0260.0000.0000.0000.000
128A128LEU0-0.043-0.01913.6230.0350.0350.0000.0000.0000.000
129A129VAL00.015-0.00110.955-0.018-0.0180.0000.0000.0000.000
130A130MET0-0.027-0.0019.055-0.097-0.0970.0000.0000.0000.000
131A131THR00.003-0.0066.8030.1160.1160.0000.0000.0000.000
132A132LEU0-0.0160.0054.212-0.371-0.252-0.001-0.019-0.0990.000
133A133GLY0-0.045-0.0337.4690.3820.3820.0000.0000.0000.000
134A134SER0-0.038-0.01210.214-0.035-0.0350.0000.0000.0000.000
135A135ASP-1-0.886-0.9397.5151.5821.5820.0000.0000.0000.000
136A136ASN0-0.065-0.0526.737-0.430-0.4300.0000.0000.0000.000
137A137LYS10.8210.9182.229-2.114-0.8354.218-1.562-3.9350.002
138A138GLN00.021-0.0033.888-2.103-2.338-0.0030.445-0.2070.000
139A139VAL0-0.0150.0075.0800.0390.167-0.001-0.007-0.1200.000
140A140GLU-1-0.880-0.9337.0610.0750.0750.0000.0000.0000.000
141A141LYS10.8040.8959.6310.7900.7900.0000.0000.0000.000
142A142ASN0-0.007-0.00512.9520.0490.0490.0000.0000.0000.000
143A143ILE0-0.019-0.00616.404-0.025-0.0250.0000.0000.0000.000
144A144THR0-0.002-0.01419.3430.0280.0280.0000.0000.0000.000
145A145VAL00.002-0.00222.734-0.014-0.0140.0000.0000.0000.000
146A146THR0-0.002-0.00725.4250.0140.0140.0000.0000.0000.000
147A147ALA00.029-0.00229.029-0.007-0.0070.0000.0000.0000.000
148A148SER0-0.011-0.03132.3260.0020.0020.0000.0000.0000.000
149A149VAL0-0.0360.01236.026-0.003-0.0030.0000.0000.0000.000
150A150ASP-1-0.830-0.91539.152-0.038-0.0380.0000.0000.0000.000
151A151PRO00.0530.02942.1930.0010.0010.0000.0000.0000.000
152A152VAL00.000-0.00445.103-0.001-0.0010.0000.0000.0000.000
153A153ILE00.0150.00447.9070.0010.0010.0000.0000.0000.000
154A154GLU-1-0.806-0.88451.481-0.027-0.0270.0000.0000.0000.000
155A155LEU0-0.047-0.02954.1880.0010.0010.0000.0000.0000.000
156A156LEU0-0.0090.00355.2430.0000.0000.0000.0000.0000.000
157A157GLN0-0.004-0.02859.0980.0020.0020.0000.0000.0000.000
158A158ALA0-0.030-0.02160.234-0.001-0.0010.0000.0000.0000.000
159A159ASP-1-0.816-0.88860.167-0.020-0.0200.0000.0000.0000.000
160A160GLY0-0.026-0.00857.995-0.001-0.0010.0000.0000.0000.000
161A161ASN0-0.078-0.03858.317-0.002-0.0020.0000.0000.0000.000
162A162ALA00.014-0.00260.2770.0000.0000.0000.0000.0000.000
163A163LEU00.004-0.00561.2340.0010.0010.0000.0000.0000.000
164A164PRO0-0.019-0.00463.796-0.001-0.0010.0000.0000.0000.000
165A165SER00.0470.03165.9510.0000.0000.0000.0000.0000.000
166A166ALA0-0.044-0.02267.4570.0000.0000.0000.0000.0000.000
167A167VAL00.0100.01070.7080.0000.0000.0000.0000.0000.000
168A168LYS10.8800.94373.4120.0130.0130.0000.0000.0000.000
169A169LEU00.0120.01375.7950.0000.0000.0000.0000.0000.000
170A170ALA0-0.014-0.01079.0810.0000.0000.0000.0000.0000.000
171A171TYR00.0290.01582.3630.0000.0000.0000.0000.0000.000
172A172SER00.0120.00285.4390.0000.0000.0000.0000.0000.000
173A173PRO00.0660.01587.7530.0000.0000.0000.0000.0000.000
174A174ALA0-0.023-0.00591.2630.0000.0000.0000.0000.0000.000
175A175SER0-0.014-0.01587.3780.0000.0000.0000.0000.0000.000
176A176LYS10.8620.94189.8330.0080.0080.0000.0000.0000.000
177A177THR00.0210.02084.7020.0000.0000.0000.0000.0000.000
178A178PHE0-0.029-0.01981.1470.0000.0000.0000.0000.0000.000
179A179GLU-1-0.930-0.95679.231-0.010-0.0100.0000.0000.0000.000
180A180SER0-0.074-0.04975.7690.0000.0000.0000.0000.0000.000
181A181TYR00.0620.02969.1820.0000.0000.0000.0000.0000.000
182A182ARG10.8880.92771.2630.0110.0110.0000.0000.0000.000
183A183VAL0-0.0070.01166.0340.0000.0000.0000.0000.0000.000
184A184MET00.0080.01964.7370.0000.0000.0000.0000.0000.000
185A185THR0-0.005-0.02661.496-0.001-0.0010.0000.0000.0000.000
186A186GLN0-0.038-0.01956.9710.0000.0000.0000.0000.0000.000
187A187VAL00.0350.01853.656-0.001-0.0010.0000.0000.0000.000
188A188HIS0-0.0130.00451.569-0.001-0.0010.0000.0000.0000.000
189A189THR0-0.026-0.03149.336-0.001-0.0010.0000.0000.0000.000
190A190ASN0-0.005-0.01244.0730.0010.0010.0000.0000.0000.000
191A191ASP-1-0.794-0.89144.334-0.023-0.0230.0000.0000.0000.000
192A192ALA00.0050.00146.2750.0010.0010.0000.0000.0000.000
193A193THR0-0.057-0.02145.3450.0020.0020.0000.0000.0000.000
194A194LYS10.7880.90144.2430.0230.0230.0000.0000.0000.000
195A195LYS10.8020.87749.9080.0100.0100.0000.0000.0000.000
196A196VAL00.0110.00853.169-0.001-0.0010.0000.0000.0000.000
197A197ILE00.0030.00355.0790.0010.0010.0000.0000.0000.000
198A198VAL0-0.007-0.00157.985-0.001-0.0010.0000.0000.0000.000
199A199LYS10.8760.93761.0500.0170.0170.0000.0000.0000.000
200A200LEU00.0000.00263.726-0.001-0.0010.0000.0000.0000.000
201A201ALA0-0.017-0.01664.0770.0000.0000.0000.0000.0000.000
202A202ASP-1-0.859-0.92565.546-0.015-0.0150.0000.0000.0000.000
203A203THR0-0.059-0.04069.3620.0000.0000.0000.0000.0000.000
204A204PRO0-0.0160.01271.3040.0000.0000.0000.0000.0000.000
205A205GLN00.037-0.00473.6380.0010.0010.0000.0000.0000.000
206A206LEU0-0.044-0.00977.0230.0000.0000.0000.0000.0000.000
207A207THR0-0.014-0.02279.2770.0010.0010.0000.0000.0000.000
208A208ASP-1-0.808-0.90881.460-0.011-0.0110.0000.0000.0000.000
209A209VAL0-0.065-0.04681.2140.0000.0000.0000.0000.0000.000
210A210LEU0-0.038-0.01383.6810.0000.0000.0000.0000.0000.000
211A211ASN0-0.0100.01186.5440.0000.0000.0000.0000.0000.000
212A212SER00.0530.02183.8950.0000.0000.0000.0000.0000.000
213A213THR0-0.046-0.03184.0230.0000.0000.0000.0000.0000.000
214A214VAL0-0.035-0.01186.5320.0000.0000.0000.0000.0000.000
215A215GLN0-0.012-0.00280.8880.0000.0000.0000.0000.0000.000
216A216MET0-0.096-0.04481.7780.0010.0010.0000.0000.0000.000
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