Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: YY362

Calculation Name: 4EJS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EJS

Chain ID: A

ChEMBL ID:

UniProt ID: Q02884

Base Structure: X-ray

Registration Date: 2023-06-20

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2873964.977982
FMO2-HF: Nuclear repulsion 2785322.39493
FMO2-HF: Total energy -88642.583051
FMO2-MP2: Total energy -88901.525717


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:67:GLY)


Summations of interaction energy for fragment #1(A:67:GLY)
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.
-3.0640.880.543-2.078-2.4110.006
Interaction energy analysis for fragmet #1(A:67:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.013
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].
3A69ASP-1-0.854-0.9173.816-1.360-0.117-0.013-0.643-0.5880.002
4A70SER00.0150.0087.1760.2860.2860.0000.0000.0000.000
5A71SER0-0.118-0.0439.4480.1360.1360.0000.0000.0000.000
6A72HIS00.0700.0419.0440.0590.0590.0000.0000.0000.000
7A73VAL0-0.024-0.02411.6500.0580.0580.0000.0000.0000.000
8A74GLY00.004-0.01413.2640.0360.0360.0000.0000.0000.000
9A75VAL0-0.029-0.0168.7050.0590.0590.0000.0000.0000.000
10A76ARG10.8960.94612.073-0.081-0.0810.0000.0000.0000.000
11A77PRO0-0.0180.00113.6730.0320.0320.0000.0000.0000.000
12A78SER0-0.0180.00814.911-0.023-0.0230.0000.0000.0000.000
13A79PRO00.001-0.00717.586-0.003-0.0030.0000.0000.0000.000
14A80ALA00.0010.01020.701-0.004-0.0040.0000.0000.0000.000
15A81THR0-0.041-0.01816.1400.0090.0090.0000.0000.0000.000
16A82SER00.0240.01414.932-0.003-0.0030.0000.0000.0000.000
17A83GLN0-0.029-0.02012.409-0.034-0.0340.0000.0000.0000.000
18A84PRO00.0540.0178.379-0.045-0.0450.0000.0000.0000.000
19A85THR0-0.0220.01311.1320.0580.0580.0000.0000.0000.000
20A86THR00.0440.02112.381-0.032-0.0320.0000.0000.0000.000
21A87SER0-0.007-0.00714.4290.0080.0080.0000.0000.0000.000
22A88THR00.005-0.05817.8850.0060.0060.0000.0000.0000.000
23A89GLY0-0.032-0.02719.9580.0000.0000.0000.0000.0000.000
24A90SER0-0.041-0.01421.771-0.013-0.0130.0000.0000.0000.000
25A91ALA00.0410.01924.2990.0050.0050.0000.0000.0000.000
26A92ASP-1-0.873-0.93425.4370.0450.0450.0000.0000.0000.000
27A93LEU00.0730.03022.8070.0050.0050.0000.0000.0000.000
28A94ASP-1-0.727-0.80920.6380.0940.0940.0000.0000.0000.000
29A95SER0-0.100-0.07022.6120.0060.0060.0000.0000.0000.000
30A96ILE00.0190.01725.1150.0030.0030.0000.0000.0000.000
31A97LEU0-0.030-0.00619.7190.0060.0060.0000.0000.0000.000
32A98GLY0-0.052-0.01422.7870.0090.0090.0000.0000.0000.000
33A99HIS0-0.042-0.03117.807-0.003-0.0030.0000.0000.0000.000
34A100MET0-0.016-0.01418.750-0.004-0.0040.0000.0000.0000.000
35A101GLY00.0380.03717.821-0.012-0.0120.0000.0000.0000.000
36A102LEU0-0.021-0.01615.3920.0040.0040.0000.0000.0000.000
37A103PRO0-0.034-0.02813.5570.0130.0130.0000.0000.0000.000
38A104LEU0-0.008-0.0217.1720.0020.0020.0000.0000.0000.000
39A105GLY00.0180.00710.4600.0170.0170.0000.0000.0000.000
40A106ASN0-0.077-0.02411.056-0.029-0.0290.0000.0000.0000.000
41A107SER0-0.032-0.03114.7420.0080.0080.0000.0000.0000.000
42A108VAL0-0.007-0.00217.569-0.015-0.0150.0000.0000.0000.000
43A109LEU0-0.017-0.00320.9530.0040.0040.0000.0000.0000.000
44A110VAL0-0.005-0.01424.159-0.006-0.0060.0000.0000.0000.000
45A111GLU-1-0.813-0.91226.7360.0930.0930.0000.0000.0000.000
46A112GLU-1-0.761-0.89430.3140.0580.0580.0000.0000.0000.000
47A113GLN0-0.050-0.03033.213-0.001-0.0010.0000.0000.0000.000
48A114SER0-0.021-0.04136.3030.0000.0000.0000.0000.0000.000
49A115THR0-0.091-0.05737.909-0.001-0.0010.0000.0000.0000.000
50A116THR0-0.0050.05335.4670.0010.0010.0000.0000.0000.000
51A117GLU-1-0.887-0.99233.2120.0440.0440.0000.0000.0000.000
52A118PHE00.0360.02332.3850.0020.0020.0000.0000.0000.000
53A119HIS00.0540.01729.0580.0080.0080.0000.0000.0000.000
54A120SER0-0.086-0.03827.8090.0070.0070.0000.0000.0000.000
55A121ILE00.0240.00428.2570.0010.0010.0000.0000.0000.000
56A122LEU00.0350.02225.4780.0000.0000.0000.0000.0000.000
57A123GLY00.0450.01923.7100.0080.0080.0000.0000.0000.000
58A124LYS10.8750.93823.171-0.047-0.0470.0000.0000.0000.000
59A125LEU00.0150.02224.021-0.004-0.0040.0000.0000.0000.000
60A126PHE00.0570.03716.447-0.002-0.0020.0000.0000.0000.000
61A127ALA0-0.040-0.02519.1870.0060.0060.0000.0000.0000.000
62A128ALA00.0140.00219.937-0.008-0.0080.0000.0000.0000.000
63A129GLN00.008-0.00418.198-0.010-0.0100.0000.0000.0000.000
64A130GLY00.0030.00316.278-0.011-0.0110.0000.0000.0000.000
65A131ILE0-0.0100.01316.679-0.025-0.0250.0000.0000.0000.000
66A132VAL00.009-0.00419.278-0.022-0.0220.0000.0000.0000.000
67A133HIS0-0.0430.00614.917-0.008-0.0080.0000.0000.0000.000
68A134ASN00.0260.01914.969-0.059-0.0590.0000.0000.0000.000
69A135ARG10.7320.87516.4330.0130.0130.0000.0000.0000.000
70A136ILE00.0100.01118.4080.0100.0100.0000.0000.0000.000
71A145ARG10.9400.97715.1200.2100.2100.0000.0000.0000.000
72A146ASN0-0.102-0.08810.939-0.002-0.0020.0000.0000.0000.000
73A147GLY00.1350.04012.6630.0050.0050.0000.0000.0000.000
74A148ASP-1-0.923-0.92810.534-0.347-0.3470.0000.0000.0000.000
75A149THR0-0.070-0.06310.7060.0110.0110.0000.0000.0000.000
76A150HIS0-0.044-0.02412.555-0.023-0.0230.0000.0000.0000.000
77A151VAL00.0240.01813.9500.0670.0670.0000.0000.0000.000
78A152ILE00.0150.00814.015-0.020-0.0200.0000.0000.0000.000
79A153VAL0-0.021-0.01317.8900.0090.0090.0000.0000.0000.000
80A154LEU0-0.0100.00421.471-0.007-0.0070.0000.0000.0000.000
81A155SER00.017-0.01923.282-0.008-0.0080.0000.0000.0000.000
82A156LEU00.000-0.01226.8220.0000.0000.0000.0000.0000.000
83A157ASN00.0160.01129.549-0.010-0.0100.0000.0000.0000.000
84A158GLN00.015-0.00427.6370.0080.0080.0000.0000.0000.000
85A159MET0-0.043-0.01828.903-0.004-0.0040.0000.0000.0000.000
86A160PHE00.0280.01523.225-0.003-0.0030.0000.0000.0000.000
87A161ALA00.027-0.00325.352-0.001-0.0010.0000.0000.0000.000
88A162LYS10.8840.93926.685-0.023-0.0230.0000.0000.0000.000
89A163GLU-1-0.790-0.86529.5470.0230.0230.0000.0000.0000.000
90A164LEU0-0.081-0.02823.5990.0020.0020.0000.0000.0000.000
91A165PRO00.0210.01826.518-0.006-0.0060.0000.0000.0000.000
92A166GLY00.0010.00727.126-0.001-0.0010.0000.0000.0000.000
93A167ILE0-0.065-0.04325.5410.0030.0030.0000.0000.0000.000
94A168TYR0-0.0070.00628.257-0.002-0.0020.0000.0000.0000.000
95A235LYS10.8110.86318.8480.0810.0810.0000.0000.0000.000
96A236ASP-1-0.804-0.86220.155-0.070-0.0700.0000.0000.0000.000
97A237TYR0-0.034-0.03215.054-0.003-0.0030.0000.0000.0000.000
98A238ASN0-0.016-0.01518.7290.0080.0080.0000.0000.0000.000
99A239HIS0-0.0110.00220.422-0.002-0.0020.0000.0000.0000.000
100A240GLN00.0390.01724.3220.0070.0070.0000.0000.0000.000
101A241PHE0-0.029-0.01422.660-0.006-0.0060.0000.0000.0000.000
102A242ASP-1-0.808-0.90728.4480.0120.0120.0000.0000.0000.000
103A243ILE0-0.012-0.01131.0470.0000.0000.0000.0000.0000.000
104A244THR0-0.006-0.00532.6670.0000.0000.0000.0000.0000.000
105A245THR0-0.0400.01032.211-0.002-0.0020.0000.0000.0000.000
106A246ARG10.8270.88530.942-0.020-0.0200.0000.0000.0000.000
107A247LEU00.0080.00024.032-0.005-0.0050.0000.0000.0000.000
108A248MET0-0.015-0.01628.556-0.004-0.0040.0000.0000.0000.000
109A249PRO00.0000.01826.3260.0010.0010.0000.0000.0000.000
110A250ALA00.0370.00426.7380.0030.0030.0000.0000.0000.000
111A251PRO00.0070.00322.628-0.007-0.0070.0000.0000.0000.000
112A252ILE00.0050.01821.7470.0050.0050.0000.0000.0000.000
113A253ALA00.010-0.00321.3840.0060.0060.0000.0000.0000.000
114A254SER0-0.040-0.02017.8660.0130.0130.0000.0000.0000.000
115A255GLU-1-0.804-0.90416.709-0.040-0.0400.0000.0000.0000.000
116A256LEU0-0.018-0.00917.4340.0200.0200.0000.0000.0000.000
117A257THR0-0.015-0.00517.042-0.015-0.0150.0000.0000.0000.000
118A258PHE0-0.016-0.00620.0810.0170.0170.0000.0000.0000.000
119A259ILE00.0030.00018.8090.0000.0000.0000.0000.0000.000
120A260ALA00.0320.01523.1810.0010.0010.0000.0000.0000.000
121A261PRO00.0190.00726.2320.0060.0060.0000.0000.0000.000
122A262THR00.000-0.00227.4820.0000.0000.0000.0000.0000.000
123A263GLN0-0.050-0.02224.878-0.012-0.0120.0000.0000.0000.000
124A264PRO00.0290.00827.6550.0040.0040.0000.0000.0000.000
125A265VAL00.1140.06624.0500.0080.0080.0000.0000.0000.000
126A266SER0-0.008-0.01023.3910.0140.0140.0000.0000.0000.000
127A267THR0-0.027-0.00822.3180.0090.0090.0000.0000.0000.000
128A268ILE00.0450.02521.2480.0100.0100.0000.0000.0000.000
129A269LEU00.0080.01118.5860.0190.0190.0000.0000.0000.000
130A270SER0-0.0020.01117.5140.0370.0370.0000.0000.0000.000
131A271GLN0-0.007-0.01017.3390.0090.0090.0000.0000.0000.000
132A272ILE00.0320.02314.6880.0070.0070.0000.0000.0000.000
133A273GLU-1-0.776-0.88512.2730.5160.5160.0000.0000.0000.000
134A274GLN0-0.021-0.01712.4960.0280.0280.0000.0000.0000.000
135A275THR0-0.054-0.04213.320-0.041-0.0410.0000.0000.0000.000
136A276ILE00.0260.0098.623-0.038-0.0380.0000.0000.0000.000
137A277LYS10.8870.9448.569-0.231-0.2310.0000.0000.0000.000
138A278ARG10.9170.9758.931-0.200-0.2000.0000.0000.0000.000
139A279ASN0-0.091-0.0399.849-0.171-0.1710.0000.0000.0000.000
140A280ASP-1-0.798-0.9163.9150.1290.3150.000-0.066-0.1200.000
141A281LYS10.8960.9604.1551.2141.374-0.001-0.048-0.1110.000
142A282LYS10.8340.9295.014-0.0130.044-0.001-0.007-0.0490.000
143A283LEU0-0.003-0.0057.6400.4000.4000.0000.0000.0000.000
144A284ILE0-0.029-0.0188.859-0.085-0.0850.0000.0000.0000.000
145A285ARG10.8280.93511.060-0.077-0.0770.0000.0000.0000.000
146A286ILE00.0210.01013.921-0.030-0.0300.0000.0000.0000.000
147A287VAL00.0200.01116.630-0.006-0.0060.0000.0000.0000.000
148A288ILE0-0.013-0.02320.180-0.008-0.0080.0000.0000.0000.000
149A289PRO0-0.031-0.02023.134-0.004-0.0040.0000.0000.0000.000
150A290SER00.004-0.00326.019-0.009-0.0090.0000.0000.0000.000
151A291LEU00.0440.01925.390-0.004-0.0040.0000.0000.0000.000
152A292LEU0-0.025-0.01828.070-0.005-0.0050.0000.0000.0000.000
153A293HIS00.0900.05931.149-0.006-0.0060.0000.0000.0000.000
154A294PRO00.0620.01633.2180.0010.0010.0000.0000.0000.000
155A295ALA0-0.048-0.01535.875-0.002-0.0020.0000.0000.0000.000
156A296MET0-0.063-0.01829.352-0.001-0.0010.0000.0000.0000.000
157A297TYR00.0070.00726.0610.0040.0040.0000.0000.0000.000
158A298PRO00.0350.01431.847-0.005-0.0050.0000.0000.0000.000
159A299PRO00.0950.03534.5090.0040.0040.0000.0000.0000.000
160A300LYS10.9720.97333.956-0.060-0.0600.0000.0000.0000.000
161A301MET0-0.0240.00428.3840.0050.0050.0000.0000.0000.000
162A302PHE0-0.023-0.01831.6360.0070.0070.0000.0000.0000.000
163A303GLU-1-0.940-0.95234.0050.0740.0740.0000.0000.0000.000
164A304SER00.020-0.01632.2890.0050.0050.0000.0000.0000.000
165A305SER0-0.009-0.00330.1690.0090.0090.0000.0000.0000.000
166A306GLU-1-0.916-0.94128.7470.1060.1060.0000.0000.0000.000
167A307ILE00.0210.01427.2840.0140.0140.0000.0000.0000.000
168A308ILE00.0120.00126.4690.0130.0130.0000.0000.0000.000
169A309GLY00.0420.03125.2010.0140.0140.0000.0000.0000.000
170A310LEU0-0.033-0.03322.2760.0190.0190.0000.0000.0000.000
171A311MET0-0.019-0.00921.3890.0220.0220.0000.0000.0000.000
172A312HIS00.0080.01020.9590.0340.0340.0000.0000.0000.000
173A313GLY00.010-0.00219.3370.0270.0270.0000.0000.0000.000
174A314VAL0-0.001-0.01517.2880.0420.0420.0000.0000.0000.000
175A315ARG10.9120.96516.163-0.194-0.1940.0000.0000.0000.000
176A316SER0-0.049-0.03015.6150.0670.0670.0000.0000.0000.000
177A317LEU0-0.010-0.00612.6740.0630.0630.0000.0000.0000.000
178A318VAL0-0.023-0.00211.2840.1690.1690.0000.0000.0000.000
179A319LYS10.8120.88610.906-0.284-0.2840.0000.0000.0000.000
180A320LYS10.8580.9459.451-0.415-0.4150.0000.0000.0000.000
181A321TYR0-0.066-0.0425.947-0.091-0.0910.0000.0000.0000.000
182A322TYR00.0620.0147.3430.1780.1780.0000.0000.0000.000
183A323GLU-1-0.962-0.9802.5442.8874.0110.478-0.729-0.873-0.001
184A324ARG10.8040.9103.451-6.593-5.4190.080-0.585-0.6700.005
185A325VAL00.0020.0206.138-0.330-0.3300.0000.0000.0000.000
186A326VAL00.0150.0319.575-0.041-0.0410.0000.0000.0000.000
187A327LEU0-0.047-0.02312.911-0.014-0.0140.0000.0000.0000.000
188A328PHE00.0330.03216.478-0.014-0.0140.0000.0000.0000.000
189A329ALA0-0.019-0.01819.8460.0000.0000.0000.0000.0000.000
190A330SER00.0640.05823.085-0.001-0.0010.0000.0000.0000.000
191A331ILE0-0.034-0.02726.7270.0030.0030.0000.0000.0000.000
192A332SER00.0430.03429.847-0.001-0.0010.0000.0000.0000.000
193A333ILE00.002-0.01831.8750.0010.0010.0000.0000.0000.000
194A334ASP-1-0.847-0.90935.1440.0550.0550.0000.0000.0000.000
195A335ILE0-0.039-0.01634.170-0.003-0.0030.0000.0000.0000.000
196A336ILE0-0.043-0.01632.7510.0030.0030.0000.0000.0000.000
197A337THR0-0.0040.00835.998-0.001-0.0010.0000.0000.0000.000
198A338PRO00.0730.01436.0150.0050.0050.0000.0000.0000.000
199A339PRO00.013-0.00135.4300.0040.0040.0000.0000.0000.000
200A340LEU00.0380.02731.8240.0050.0050.0000.0000.0000.000
201A341LEU00.0140.01630.5950.0080.0080.0000.0000.0000.000
202A342VAL0-0.019-0.01130.6200.0070.0070.0000.0000.0000.000
203A343LEU0-0.025-0.01729.8790.0070.0070.0000.0000.0000.000
204A344LEU00.009-0.00526.7850.0110.0110.0000.0000.0000.000
205A345ARG10.8730.91225.811-0.079-0.0790.0000.0000.0000.000
206A346ASN0-0.058-0.01125.4520.0100.0100.0000.0000.0000.000
207A347MET0-0.047-0.01822.2800.0170.0170.0000.0000.0000.000
208A348PHE00.014-0.00120.7460.0300.0300.0000.0000.0000.000
209A349ASP-1-0.842-0.89617.2300.3010.3010.0000.0000.0000.000
210A350SER0-0.035-0.01820.420-0.015-0.0150.0000.0000.0000.000
211A351VAL00.0120.00922.7880.0080.0080.0000.0000.0000.000
212A352ILE00.0230.01624.221-0.005-0.0050.0000.0000.0000.000
213A353ASN0-0.0220.00627.768-0.004-0.0040.0000.0000.0000.000
214A354LEU00.0090.00129.578-0.002-0.0020.0000.0000.0000.000
215A355GLU-1-0.807-0.90533.0140.0460.0460.0000.0000.0000.000
216A356PRO0-0.0070.01536.762-0.001-0.0010.0000.0000.0000.000
217A357PHE0-0.068-0.04238.545-0.004-0.0040.0000.0000.0000.000
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