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: 8937Y

Calculation Name: 4BEJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BEJ

Chain ID: A

ChEMBL ID:

UniProt ID: O00429

Base Structure: X-ray

Registration Date: 2023-09-24

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 565
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -9848501.954697
FMO2-HF: Nuclear repulsion 9625981.587092
FMO2-HF: Total energy -222520.367605
FMO2-MP2: Total energy -223168.043597


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.
-18.466-21.33316.381-5.085-8.430.026
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 : -0.002 / q_NPA : -0.024
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].
3A3ALA00.0420.0102.491-1.0731.1211.112-1.057-2.2490.001
4A4LEU00.008-0.0062.715-0.9650.6250.677-0.467-1.800-0.003
5A5ILE00.0220.0174.4020.1740.3500.000-0.026-0.1500.000
6A6PRO0-0.023-0.0116.2510.1380.1380.0000.0000.0000.000
7A7VAL00.0300.0206.1620.1590.1590.0000.0000.0000.000
8A8ILE00.0350.0198.7530.1100.1100.0000.0000.0000.000
9A9ASN00.0600.04010.8730.0900.0900.0000.0000.0000.000
10A10LYS10.9300.97210.0750.7610.7610.0000.0000.0000.000
11A11LEU00.003-0.00610.9260.0450.0450.0000.0000.0000.000
12A12GLN0-0.004-0.01714.3260.0090.0090.0000.0000.0000.000
13A13ASP-1-0.891-0.95116.843-0.220-0.2200.0000.0000.0000.000
14A14VAL0-0.111-0.05316.6430.0170.0170.0000.0000.0000.000
15A15PHE0-0.046-0.02917.1230.0100.0100.0000.0000.0000.000
16A16ASN00.0720.03721.2900.0250.0250.0000.0000.0000.000
17A17THR0-0.052-0.01223.3770.0130.0130.0000.0000.0000.000
18A18VAL00.0290.02024.1320.0080.0080.0000.0000.0000.000
19A19GLY00.0350.00824.980-0.002-0.0020.0000.0000.0000.000
20A20ALA00.037-0.00521.022-0.001-0.0010.0000.0000.0000.000
21A21ASP-1-0.983-0.97621.757-0.008-0.0080.0000.0000.0000.000
22A22ILE00.0000.00223.6940.0110.0110.0000.0000.0000.000
23A23ILE0-0.044-0.02417.4570.0070.0070.0000.0000.0000.000
24A24GLN0-0.031-0.01919.1540.0240.0240.0000.0000.0000.000
25A25LEU00.0210.01014.2420.0190.0190.0000.0000.0000.000
26A26PRO00.014-0.00111.5010.0240.0240.0000.0000.0000.000
27A27GLN00.0130.01713.339-0.055-0.0550.0000.0000.0000.000
28A28ILE00.0080.00414.4080.0350.0350.0000.0000.0000.000
29A29VAL00.0210.02317.562-0.037-0.0370.0000.0000.0000.000
30A30VAL00.0310.02121.2760.0200.0200.0000.0000.0000.000
31A31VAL00.0250.03523.567-0.016-0.0160.0000.0000.0000.000
32A32GLY00.023-0.01227.0260.0080.0080.0000.0000.0000.000
33A33THR00.0080.02329.721-0.007-0.0070.0000.0000.0000.000
34A34GLN00.0500.01732.5080.0000.0000.0000.0000.0000.000
35A35SER0-0.034-0.00234.397-0.001-0.0010.0000.0000.0000.000
36A36SER0-0.077-0.06530.0550.0010.0010.0000.0000.0000.000
37A37GLY00.0400.03230.8740.0030.0030.0000.0000.0000.000
38A38LYS10.8350.94426.774-0.040-0.0400.0000.0000.0000.000
39A39SER00.0900.03926.5820.0010.0010.0000.0000.0000.000
40A40SER0-0.059-0.07127.330-0.003-0.0030.0000.0000.0000.000
41A41VAL00.0050.00122.853-0.003-0.0030.0000.0000.0000.000
42A42LEU0-0.004-0.00422.0760.0000.0000.0000.0000.0000.000
43A43GLU-1-0.786-0.92122.923-0.027-0.0270.0000.0000.0000.000
44A44SER0-0.041-0.03824.291-0.011-0.0110.0000.0000.0000.000
45A45LEU0-0.068-0.01417.8690.0010.0010.0000.0000.0000.000
46A46VAL0-0.041-0.00619.904-0.014-0.0140.0000.0000.0000.000
47A47GLY00.0250.01421.391-0.010-0.0100.0000.0000.0000.000
48A48ARG10.8450.88923.9920.0720.0720.0000.0000.0000.000
49A49ASP-1-0.906-0.95226.790-0.020-0.0200.0000.0000.0000.000
50A50LEU00.0290.01524.192-0.005-0.0050.0000.0000.0000.000
51A51LEU0-0.0140.00026.916-0.002-0.0020.0000.0000.0000.000
52A52PRO00.0040.02829.6600.0030.0030.0000.0000.0000.000
53A53ARG10.8800.92832.0700.0160.0160.0000.0000.0000.000
54A54GLY00.0310.00435.5080.0030.0030.0000.0000.0000.000
55A55THR0-0.081-0.06038.8930.0030.0030.0000.0000.0000.000
56A56GLY00.0590.04440.1180.0010.0010.0000.0000.0000.000
57A57ILE0-0.0260.00536.368-0.002-0.0020.0000.0000.0000.000
58A58VAL0-0.008-0.00836.1400.0040.0040.0000.0000.0000.000
59A59THR00.0390.02930.869-0.002-0.0020.0000.0000.0000.000
60A60ARG10.9010.95033.3480.0220.0220.0000.0000.0000.000
61A61ARG10.8780.92328.2550.0530.0530.0000.0000.0000.000
62A62PRO0-0.0050.01425.0310.0010.0010.0000.0000.0000.000
63A63LEU00.0230.01223.335-0.011-0.0110.0000.0000.0000.000
64A64ILE0-0.040-0.01718.6390.0130.0130.0000.0000.0000.000
65A65LEU00.0090.00620.134-0.019-0.0190.0000.0000.0000.000
66A66GLN0-0.029-0.03015.601-0.014-0.0140.0000.0000.0000.000
67A67LEU00.002-0.00615.645-0.012-0.0120.0000.0000.0000.000
68A68VAL0-0.010-0.01212.869-0.040-0.0400.0000.0000.0000.000
69A69HIS0-0.027-0.01312.1270.0400.0400.0000.0000.0000.000
70A70VAL00.005-0.00113.861-0.051-0.0510.0000.0000.0000.000
71A71SER0-0.0120.00614.566-0.012-0.0120.0000.0000.0000.000
72A85VAL0-0.039-0.01524.120-0.002-0.0020.0000.0000.0000.000
73A86GLU-1-0.948-0.98027.326-0.090-0.0900.0000.0000.0000.000
74A87ALA0-0.013-0.00827.130-0.001-0.0010.0000.0000.0000.000
75A88GLU-1-0.904-0.95923.296-0.150-0.1500.0000.0000.0000.000
76A89GLU-1-0.925-0.94722.532-0.108-0.1080.0000.0000.0000.000
77A90TRP0-0.015-0.01720.0980.0050.0050.0000.0000.0000.000
78A91GLY00.0560.03622.310-0.015-0.0150.0000.0000.0000.000
79A92LYS10.9421.00419.1380.2420.2420.0000.0000.0000.000
80A93PHE00.0170.01622.549-0.007-0.0070.0000.0000.0000.000
81A94LEU0-0.059-0.02221.116-0.006-0.0060.0000.0000.0000.000
82A95HIS00.0330.00423.728-0.009-0.0090.0000.0000.0000.000
83A96THR0-0.0180.00427.4240.0020.0020.0000.0000.0000.000
84A97LYS10.9730.97725.0990.1200.1200.0000.0000.0000.000
85A98ASN0-0.107-0.06424.2250.0090.0090.0000.0000.0000.000
86A99LYS11.0121.03225.2210.0940.0940.0000.0000.0000.000
87A100LEU0-0.033-0.02523.530-0.005-0.0050.0000.0000.0000.000
88A101TYR0-0.029-0.02726.4600.0080.0080.0000.0000.0000.000
89A102THR00.0720.01126.844-0.008-0.0080.0000.0000.0000.000
90A103ASP-1-0.855-0.91529.137-0.059-0.0590.0000.0000.0000.000
91A104PHE0-0.016-0.04424.3160.0000.0000.0000.0000.0000.000
92A105ASP-1-0.877-0.92630.067-0.039-0.0390.0000.0000.0000.000
93A106GLU-1-0.909-0.96331.789-0.077-0.0770.0000.0000.0000.000
94A107ILE0-0.053-0.02125.859-0.001-0.0010.0000.0000.0000.000
95A108ARG10.9100.95229.6580.0390.0390.0000.0000.0000.000
96A109GLN0-0.015-0.00531.4630.0050.0050.0000.0000.0000.000
97A110GLU-1-0.852-0.91430.038-0.067-0.0670.0000.0000.0000.000
98A111ILE0-0.031-0.01127.3540.0010.0010.0000.0000.0000.000
99A112GLU-1-0.931-0.96930.804-0.027-0.0270.0000.0000.0000.000
100A113ASN00.0530.02234.4050.0060.0060.0000.0000.0000.000
101A114GLU-1-0.929-0.97029.486-0.060-0.0600.0000.0000.0000.000
102A115THR0-0.055-0.03832.2900.0040.0040.0000.0000.0000.000
103A116GLU-1-0.991-1.00633.905-0.030-0.0300.0000.0000.0000.000
104A117ARG10.9941.02434.4820.0570.0570.0000.0000.0000.000
105A118ILE0-0.033-0.00233.5410.0010.0010.0000.0000.0000.000
106A119SER0-0.016-0.00436.7320.0040.0040.0000.0000.0000.000
107A120GLY0-0.021-0.03539.2490.0010.0010.0000.0000.0000.000
108A121ASN0-0.0050.01841.8900.0010.0010.0000.0000.0000.000
109A122ASN0-0.021-0.02142.7370.0010.0010.0000.0000.0000.000
110A123LYS10.9040.96036.0930.0260.0260.0000.0000.0000.000
111A124GLY0-0.0050.00939.123-0.003-0.0030.0000.0000.0000.000
112A125VAL0-0.015-0.01633.251-0.003-0.0030.0000.0000.0000.000
113A126SER0-0.009-0.01132.370-0.001-0.0010.0000.0000.0000.000
114A127PRO00.041-0.01129.5380.0020.0020.0000.0000.0000.000
115A128GLU-1-0.932-0.94127.571-0.060-0.0600.0000.0000.0000.000
116A129PRO0-0.0200.00623.3950.0030.0030.0000.0000.0000.000
117A130ILE00.0390.04725.364-0.010-0.0100.0000.0000.0000.000
118A131HIS0-0.041-0.04320.3000.0010.0010.0000.0000.0000.000
119A132LEU00.0180.02221.898-0.012-0.0120.0000.0000.0000.000
120A133LYS10.9130.97515.3420.3060.3060.0000.0000.0000.000
121A134ILE00.003-0.01019.0560.0080.0080.0000.0000.0000.000
122A135PHE0-0.038-0.02816.037-0.026-0.0260.0000.0000.0000.000
123A136SER00.0580.00918.1140.0250.0250.0000.0000.0000.000
124A137PRO0-0.0290.00617.450-0.030-0.0300.0000.0000.0000.000
125A138ASN00.011-0.00617.711-0.006-0.0060.0000.0000.0000.000
126A139VAL0-0.0150.02115.8610.0260.0260.0000.0000.0000.000
127A140VAL0-0.024-0.01311.893-0.032-0.0320.0000.0000.0000.000
128A141ASN00.004-0.0149.2360.0510.0510.0000.0000.0000.000
129A142LEU0-0.022-0.00910.6550.0730.0730.0000.0000.0000.000
130A143THR0-0.008-0.01612.908-0.050-0.0500.0000.0000.0000.000
131A144LEU0-0.048-0.01615.0660.0610.0610.0000.0000.0000.000
132A145VAL00.0230.01518.280-0.027-0.0270.0000.0000.0000.000
133A146ASP-1-0.863-0.94720.9700.0330.0330.0000.0000.0000.000
134A147LEU0-0.016-0.01124.357-0.007-0.0070.0000.0000.0000.000
135A148PRO00.0320.01027.3180.0040.0040.0000.0000.0000.000
136A149GLY0-0.0010.00831.0930.0060.0060.0000.0000.0000.000
137A150MET0-0.014-0.00431.960-0.003-0.0030.0000.0000.0000.000
138A151THR0-0.034-0.05435.359-0.001-0.0010.0000.0000.0000.000
139A152LYS10.9571.03037.643-0.047-0.0470.0000.0000.0000.000
140A161ASP-1-0.900-0.95842.5640.0090.0090.0000.0000.0000.000
141A162ILE0-0.002-0.00839.216-0.001-0.0010.0000.0000.0000.000
142A163GLU-1-0.858-0.94638.0270.0270.0270.0000.0000.0000.000
143A164LEU00.0070.00536.9230.0030.0030.0000.0000.0000.000
144A165GLN00.0400.02736.7190.0000.0000.0000.0000.0000.000
145A166ILE00.0260.02432.5890.0000.0000.0000.0000.0000.000
146A167ARG10.9110.95532.474-0.041-0.0410.0000.0000.0000.000
147A168GLU-1-0.913-0.96632.4020.0210.0210.0000.0000.0000.000
148A169LEU00.0150.00029.3760.0020.0020.0000.0000.0000.000
149A170ILE0-0.039-0.03127.7210.0030.0030.0000.0000.0000.000
150A171LEU0-0.020-0.00927.4120.0080.0080.0000.0000.0000.000
151A172ARG10.9180.98327.224-0.002-0.0020.0000.0000.0000.000
152A173PHE0-0.013-0.00222.6340.0010.0010.0000.0000.0000.000
153A174ILE0-0.001-0.01523.2710.0130.0130.0000.0000.0000.000
154A175SER00.004-0.01024.4980.0180.0180.0000.0000.0000.000
155A176ASN0-0.049-0.01518.404-0.015-0.0150.0000.0000.0000.000
156A177PRO00.0560.05020.1980.0200.0200.0000.0000.0000.000
157A178ASN0-0.032-0.01015.232-0.005-0.0050.0000.0000.0000.000
158A179SER0-0.064-0.04116.1500.0290.0290.0000.0000.0000.000
159A180ILE00.0120.01914.0370.0020.0020.0000.0000.0000.000
160A181ILE00.0100.00318.392-0.033-0.0330.0000.0000.0000.000
161A182LEU0-0.010-0.00119.5100.0170.0170.0000.0000.0000.000
162A183ALA00.0310.01322.005-0.023-0.0230.0000.0000.0000.000
163A184VAL00.0210.01024.7730.0060.0060.0000.0000.0000.000
164A185THR0-0.060-0.02927.100-0.009-0.0090.0000.0000.0000.000
165A186ALA00.0100.01630.1180.0020.0020.0000.0000.0000.000
166A187ALA00.041-0.00532.5090.0020.0020.0000.0000.0000.000
167A188ASN0-0.032-0.01033.879-0.001-0.0010.0000.0000.0000.000
168A189THR0-0.049-0.00635.723-0.003-0.0030.0000.0000.0000.000
169A190ASP-1-0.836-0.92536.5170.0700.0700.0000.0000.0000.000
170A191MET0-0.002-0.01930.7920.0020.0020.0000.0000.0000.000
171A192ALA00.0650.05033.6640.0040.0040.0000.0000.0000.000
172A193THR0-0.067-0.03335.484-0.001-0.0010.0000.0000.0000.000
173A194SER0-0.021-0.00531.710-0.007-0.0070.0000.0000.0000.000
174A195GLU-1-0.783-0.92434.1650.0460.0460.0000.0000.0000.000
175A196ALA0-0.007-0.00129.3230.0010.0010.0000.0000.0000.000
176A197LEU00.017-0.00729.4580.0070.0070.0000.0000.0000.000
177A198LYS10.8860.94330.723-0.054-0.0540.0000.0000.0000.000
178A199ILE00.0190.01629.5900.0020.0020.0000.0000.0000.000
179A200SER00.0020.00726.4220.0070.0070.0000.0000.0000.000
180A201ARG10.8910.96028.070-0.105-0.1050.0000.0000.0000.000
181A202GLU-1-0.896-0.95230.5100.0600.0600.0000.0000.0000.000
182A203VAL0-0.0180.00626.381-0.002-0.0020.0000.0000.0000.000
183A204ASP-1-0.877-0.95724.3490.1980.1980.0000.0000.0000.000
184A205PRO0-0.0180.01727.0740.0010.0010.0000.0000.0000.000
185A206ASP-1-0.913-0.96427.0780.1650.1650.0000.0000.0000.000
186A207GLY00.0590.04725.8870.0020.0020.0000.0000.0000.000
187A208ARG10.8840.93621.487-0.182-0.1820.0000.0000.0000.000
188A209ARG10.8390.92719.428-0.128-0.1280.0000.0000.0000.000
189A210THR00.0520.01320.683-0.005-0.0050.0000.0000.0000.000
190A211LEU0-0.054-0.02317.4480.0120.0120.0000.0000.0000.000
191A212ALA00.0120.01621.405-0.022-0.0220.0000.0000.0000.000
192A213VAL00.000-0.01622.2640.0090.0090.0000.0000.0000.000
193A214ILE00.0150.00924.865-0.010-0.0100.0000.0000.0000.000
194A215THR00.004-0.00127.398-0.001-0.0010.0000.0000.0000.000
195A216LYS10.9170.94529.407-0.034-0.0340.0000.0000.0000.000
196A217LEU00.0510.03528.0720.0000.0000.0000.0000.0000.000
197A218ASP-1-0.930-0.97132.4260.0370.0370.0000.0000.0000.000
198A219LEU0-0.087-0.03635.359-0.003-0.0030.0000.0000.0000.000
199A220MET0-0.037-0.00331.8620.0020.0020.0000.0000.0000.000
200A221ASP-1-0.927-0.97036.7240.0460.0460.0000.0000.0000.000
201A222ALA0-0.035-0.03739.0270.0030.0030.0000.0000.0000.000
202A223GLY0-0.0140.01740.2880.0030.0030.0000.0000.0000.000
203A224THR00.0070.00336.9720.0000.0000.0000.0000.0000.000
204A225ASP-1-0.867-0.93834.9520.0920.0920.0000.0000.0000.000
205A226ALA00.012-0.00132.5260.0070.0070.0000.0000.0000.000
206A227MET0-0.006-0.01331.8940.0080.0080.0000.0000.0000.000
207A228ASP-1-0.815-0.92432.5280.0900.0900.0000.0000.0000.000
208A229VAL00.0100.01228.4200.0080.0080.0000.0000.0000.000
209A230LEU0-0.0010.00126.5680.0130.0130.0000.0000.0000.000
210A231MET00.0000.01127.4810.0110.0110.0000.0000.0000.000
211A232GLY0-0.052-0.04028.7070.0050.0050.0000.0000.0000.000
212A233ARG10.8590.92229.468-0.100-0.1000.0000.0000.0000.000
213A234VAL0-0.0060.01530.9610.0090.0090.0000.0000.0000.000
214A235ILE00.0110.00027.0500.0020.0020.0000.0000.0000.000
215A236PRO0-0.0200.00828.2340.0000.0000.0000.0000.0000.000
216A237VAL00.022-0.01023.9810.0010.0010.0000.0000.0000.000
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