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: K23K3

Calculation Name: 3BEW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BEW

Chain ID: A

ChEMBL ID:

UniProt ID: P21611

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 269
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3439090.585569
FMO2-HF: Nuclear repulsion 3330619.035752
FMO2-HF: Total energy -108471.549816
FMO2-MP2: Total energy -108788.885414


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:GLU)


Summations of interaction energy for fragment #1(A:1:GLU)
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.
-14.144-17.08920.785-8.098-9.7410.089
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.836 / q_NPA : -0.912
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].
3A3HIS10.7740.8501.712-93.499-93.86415.274-7.898-7.0110.089
4A4THR0-0.026-0.0096.023-6.524-6.5240.0000.0000.0000.000
5A5LEU00.0210.0139.7630.2260.2260.0000.0000.0000.000
6A6ARG10.7710.85012.854-23.749-23.7490.0000.0000.0000.000
7A7TYR00.001-0.01816.1010.4040.4040.0000.0000.0000.000
8A8ILE0-0.020-0.01517.652-0.381-0.3810.0000.0000.0000.000
9A9ARG10.8550.91321.667-13.882-13.8820.0000.0000.0000.000
10A10THR0-0.049-0.03825.4670.0120.0120.0000.0000.0000.000
11A11ALA00.0090.01428.510-0.081-0.0810.0000.0000.0000.000
12A12MET00.0000.00431.413-0.021-0.0210.0000.0000.0000.000
13A13THR0-0.063-0.05234.924-0.023-0.0230.0000.0000.0000.000
14A14ASP-1-0.893-0.92337.3038.0348.0340.0000.0000.0000.000
15A15PRO0-0.0310.00634.9500.1460.1460.0000.0000.0000.000
16A16GLY00.0830.04634.3360.2590.2590.0000.0000.0000.000
17A17PRO0-0.028-0.04937.8690.0080.0080.0000.0000.0000.000
18A18GLY00.0050.01137.8150.1270.1270.0000.0000.0000.000
19A19LEU0-0.0190.00832.1710.1990.1990.0000.0000.0000.000
20A20PRO0-0.043-0.01431.089-0.216-0.2160.0000.0000.0000.000
21A21TRP00.0240.00233.0070.1990.1990.0000.0000.0000.000
22A22PHE00.005-0.00128.6410.0420.0420.0000.0000.0000.000
23A23VAL00.004-0.00425.775-0.074-0.0740.0000.0000.0000.000
24A24ASP-1-0.823-0.91323.34913.46813.4680.0000.0000.0000.000
25A25VAL0-0.0040.00020.801-0.163-0.1630.0000.0000.0000.000
26A26GLY00.0460.02318.3810.1920.1920.0000.0000.0000.000
27A27TYR0-0.041-0.03314.120-0.266-0.2660.0000.0000.0000.000
28A28VAL00.0510.0119.290-0.415-0.4150.0000.0000.0000.000
29A29ASP-1-0.783-0.8776.47746.00146.0010.0000.0000.0000.000
30A30GLY0-0.019-0.0028.6530.7880.7880.0000.0000.0000.000
31A31GLU-1-0.781-0.87210.43723.28223.2820.0000.0000.0000.000
32A32LEU0-0.050-0.03013.010-0.356-0.3560.0000.0000.0000.000
33A33PHE00.0240.01614.715-0.255-0.2550.0000.0000.0000.000
34A34MET0-0.0290.00816.814-0.980-0.9800.0000.0000.0000.000
35A35HIS00.0500.00720.188-0.063-0.0630.0000.0000.0000.000
36A36TYR0-0.004-0.00623.433-0.359-0.3590.0000.0000.0000.000
37A37ASN00.0280.00026.970-0.225-0.2250.0000.0000.0000.000
38A38SER00.0390.01229.924-0.112-0.1120.0000.0000.0000.000
39A39THR0-0.052-0.02233.225-0.300-0.3000.0000.0000.0000.000
40A40ALA0-0.005-0.00730.796-0.176-0.1760.0000.0000.0000.000
41A41ARG10.7860.87832.473-9.131-9.1310.0000.0000.0000.000
42A42ARG10.8590.90629.934-10.305-10.3050.0000.0000.0000.000
43A43ALA0-0.027-0.00225.1490.2140.2140.0000.0000.0000.000
44A44VAL0-0.062-0.03224.939-0.305-0.3050.0000.0000.0000.000
45A45PRO00.0470.02721.2260.4740.4740.0000.0000.0000.000
46A46ARG10.8490.91719.209-14.530-14.5300.0000.0000.0000.000
47A47THR00.0490.02614.851-0.125-0.1250.0000.0000.0000.000
48A48GLU-1-0.887-0.95118.02514.41514.4150.0000.0000.0000.000
49A49TRP00.0560.04512.500-0.646-0.6460.0000.0000.0000.000
50A50ILE0-0.034-0.00316.421-0.243-0.2430.0000.0000.0000.000
51A51ALA0-0.0200.00517.622-0.716-0.7160.0000.0000.0000.000
52A52ALA0-0.0120.00119.188-0.654-0.6540.0000.0000.0000.000
53A53ASN0-0.069-0.03016.931-0.612-0.6120.0000.0000.0000.000
54A54THR0-0.050-0.04119.705-0.037-0.0370.0000.0000.0000.000
55A55ASP-1-0.770-0.88822.22711.44111.4410.0000.0000.0000.000
56A56GLN0-0.039-0.03326.0480.2400.2400.0000.0000.0000.000
57A57GLN0-0.0070.00426.9020.0760.0760.0000.0000.0000.000
58A58TYR0-0.001-0.01419.9620.2840.2840.0000.0000.0000.000
59A59TRP00.0730.02020.774-0.030-0.0300.0000.0000.0000.000
60A60ASP-1-0.809-0.87126.4959.8349.8340.0000.0000.0000.000
61A61ARG10.8920.96026.052-11.574-11.5740.0000.0000.0000.000
62A62GLU-1-0.764-0.86321.63614.15214.1520.0000.0000.0000.000
63A63THR0-0.033-0.03026.143-0.147-0.1470.0000.0000.0000.000
64A64GLN0-0.023-0.01129.307-0.141-0.1410.0000.0000.0000.000
65A65ILE0-0.0050.00625.925-0.258-0.2580.0000.0000.0000.000
66A66VAL00.0070.00025.560-0.156-0.1560.0000.0000.0000.000
67A67GLN00.0050.00928.761-0.466-0.4660.0000.0000.0000.000
68A68GLY00.0140.01332.079-0.308-0.3080.0000.0000.0000.000
69A69SER0-0.011-0.01027.620-0.250-0.2500.0000.0000.0000.000
70A70GLU-1-0.740-0.82630.6389.0789.0780.0000.0000.0000.000
71A71GLN0-0.002-0.00732.741-0.188-0.1880.0000.0000.0000.000
72A72ILE00.0330.01232.629-0.177-0.1770.0000.0000.0000.000
73A73ASN0-0.004-0.01729.895-0.145-0.1450.0000.0000.0000.000
74A74ARG10.8160.90333.883-8.673-8.6730.0000.0000.0000.000
75A75GLU-1-0.905-0.93137.2128.0608.0600.0000.0000.0000.000
76A76ASN0-0.041-0.04032.833-0.333-0.3330.0000.0000.0000.000
77A77LEU00.0010.00635.481-0.116-0.1160.0000.0000.0000.000
78A78ASP-1-0.752-0.83937.7947.1577.1570.0000.0000.0000.000
79A79ILE0-0.016-0.01239.219-0.181-0.1810.0000.0000.0000.000
80A80LEU00.003-0.00534.885-0.144-0.1440.0000.0000.0000.000
81A81ARG10.8200.90239.405-7.349-7.3490.0000.0000.0000.000
82A82ARG10.8010.87841.807-7.201-7.2010.0000.0000.0000.000
83A83ARG10.8500.91837.384-8.483-8.4830.0000.0000.0000.000
84A84TYR0-0.037-0.03837.4690.0030.0030.0000.0000.0000.000
85A85ASN0-0.064-0.02842.901-0.210-0.2100.0000.0000.0000.000
86A86GLN00.0230.03839.977-0.086-0.0860.0000.0000.0000.000
87A87THR00.002-0.01645.356-0.059-0.0590.0000.0000.0000.000
88A88GLY00.0050.01745.569-0.050-0.0500.0000.0000.0000.000
89A89GLY00.0310.01343.7610.0980.0980.0000.0000.0000.000
90A90SER0-0.030-0.02038.5830.1510.1510.0000.0000.0000.000
91A91HIS10.8010.88037.495-8.183-8.1830.0000.0000.0000.000
92A92THR00.007-0.00331.9680.1080.1080.0000.0000.0000.000
93A93VAL0-0.0080.01431.101-0.051-0.0510.0000.0000.0000.000
94A94GLN0-0.028-0.01627.059-0.010-0.0100.0000.0000.0000.000
95A95TRP00.0130.00325.999-0.133-0.1330.0000.0000.0000.000
96A96MET0-0.0340.00118.6100.5260.5260.0000.0000.0000.000
97A97SER00.005-0.01020.775-0.588-0.5880.0000.0000.0000.000
98A98GLY00.0270.01016.6570.5570.5570.0000.0000.0000.000
99A99CYS0-0.037-0.01013.3740.0430.0430.0000.0000.0000.000
100A100ASP-1-0.747-0.8379.38626.79026.7900.0000.0000.0000.000
101A101ILE0-0.045-0.0124.983-3.013-3.0130.0000.0000.0000.000
102A102LEU00.0180.0065.5934.0514.0510.0000.0000.0000.000
103A103GLU-1-0.890-0.9571.88235.02534.5385.562-2.921-2.1530.004
104A104ASP-1-0.826-0.8862.66327.50725.414-0.0512.721-0.577-0.004
105A105GLY0-0.027-0.0105.278-1.923-1.9230.0000.0000.0000.000
106A106THR0-0.096-0.0746.667-2.119-2.1190.0000.0000.0000.000
107A107ILE0-0.019-0.0138.7211.7581.7580.0000.0000.0000.000
108A108ARG10.8900.95411.290-21.673-21.6730.0000.0000.0000.000
109A109GLY00.0400.01213.4900.7340.7340.0000.0000.0000.000
110A110TYR0-0.085-0.05613.327-1.168-1.1680.0000.0000.0000.000
111A111HIS00.0540.02919.1470.4960.4960.0000.0000.0000.000
112A112GLN0-0.006-0.00121.3010.1150.1150.0000.0000.0000.000
113A113ALA00.0180.01025.1390.1990.1990.0000.0000.0000.000
114A114ALA00.0240.01227.923-0.093-0.0930.0000.0000.0000.000
115A115TYR0-0.008-0.03429.810-0.051-0.0510.0000.0000.0000.000
116A116ASP-1-0.797-0.88433.3578.6578.6570.0000.0000.0000.000
117A117GLY00.0280.01630.586-0.156-0.1560.0000.0000.0000.000
118A118ARG10.8770.94630.783-9.116-9.1160.0000.0000.0000.000
119A119ASP-1-0.877-0.93426.79411.78611.7860.0000.0000.0000.000
120A120PHE0-0.028-0.01629.743-0.437-0.4370.0000.0000.0000.000
121A121VAL0-0.023-0.02728.916-0.320-0.3200.0000.0000.0000.000
122A122ALA00.0380.02024.6060.4390.4390.0000.0000.0000.000
123A123PHE0-0.024-0.01922.461-0.462-0.4620.0000.0000.0000.000
124A124ASP-1-0.834-0.90022.98812.99212.9920.0000.0000.0000.000
125A125LYS10.8860.90716.368-16.000-16.0000.0000.0000.0000.000
126A126GLY0-0.025-0.00222.2920.0400.0400.0000.0000.0000.000
127A127THR0-0.051-0.03922.875-0.468-0.4680.0000.0000.0000.000
128A128MET0-0.0340.00224.684-0.220-0.2200.0000.0000.0000.000
129A129THR0-0.0060.00226.397-0.572-0.5720.0000.0000.0000.000
130A130LEU00.0010.00227.3250.3720.3720.0000.0000.0000.000
131A131THR00.0300.00427.510-0.558-0.5580.0000.0000.0000.000
132A132ALA0-0.016-0.01129.8600.2020.2020.0000.0000.0000.000
133A133ALA0-0.0070.00130.626-0.075-0.0750.0000.0000.0000.000
134A134VAL00.0200.01632.453-0.158-0.1580.0000.0000.0000.000
135A135PRO00.0470.01636.2230.0310.0310.0000.0000.0000.000
136A136GLU-1-0.814-0.89338.6078.1438.1430.0000.0000.0000.000
137A137ALA00.0010.00834.1080.0160.0160.0000.0000.0000.000
138A138VAL00.0000.00235.7970.1230.1230.0000.0000.0000.000
139A139PRO0-0.011-0.01837.7840.0070.0070.0000.0000.0000.000
140A140THR0-0.024-0.00433.220-0.129-0.1290.0000.0000.0000.000
141A141LYS10.8480.93732.363-9.200-9.2000.0000.0000.0000.000
142A142ARG10.8820.91634.813-8.019-8.0190.0000.0000.0000.000
143A143LYS10.9971.00536.248-8.476-8.4760.0000.0000.0000.000
144A144TRP0-0.011-0.01327.2110.1420.1420.0000.0000.0000.000
145A145GLU-1-0.865-0.89633.2208.6818.6810.0000.0000.0000.000
146A146GLU-1-0.950-0.97535.0207.5687.5680.0000.0000.0000.000
147A147GLY0-0.031-0.00835.651-0.085-0.0850.0000.0000.0000.000
148A148GLY00.0270.01233.1380.0910.0910.0000.0000.0000.000
149A149TYR0-0.032-0.02930.1250.2080.2080.0000.0000.0000.000
150A150ALA00.0230.01027.4540.3880.3880.0000.0000.0000.000
151A151GLU-1-0.808-0.87426.04011.64911.6490.0000.0000.0000.000
152A152GLY00.0270.01925.4480.3630.3630.0000.0000.0000.000
153A153LEU0-0.037-0.01722.8590.4570.4570.0000.0000.0000.000
154A154LYS10.8870.92421.451-11.432-11.4320.0000.0000.0000.000
155A155GLN0-0.043-0.02020.5550.3410.3410.0000.0000.0000.000
156A156TYR0-0.018-0.01319.5360.8060.8060.0000.0000.0000.000
157A157LEU0-0.048-0.03917.9880.8810.8810.0000.0000.0000.000
158A158GLU-1-0.872-0.92616.02515.72415.7240.0000.0000.0000.000
159A159GLU-1-0.861-0.91315.97213.46213.4620.0000.0000.0000.000
160A160THR0-0.020-0.01216.5470.6900.6900.0000.0000.0000.000
161A162VAL00.0560.02111.0561.5691.5690.0000.0000.0000.000
162A163GLU-1-0.862-0.91112.18016.96716.9670.0000.0000.0000.000
163A164TRP0-0.017-0.01913.5130.9620.9620.0000.0000.0000.000
164A165LEU0-0.0190.0078.7520.4260.4260.0000.0000.0000.000
165A166ARG10.9290.9707.417-23.084-23.0840.0000.0000.0000.000
166A167ARG10.7920.88610.108-15.910-15.9100.0000.0000.0000.000
167A168TYR0-0.008-0.03011.9710.0300.0300.0000.0000.0000.000
168A169VAL00.0110.0035.5400.4710.4710.0000.0000.0000.000
169A170GLU-1-0.876-0.9148.84628.51228.5120.0000.0000.0000.000
170A171TYR0-0.068-0.04910.554-0.751-0.7510.0000.0000.0000.000
171A172GLY00.0570.03211.578-1.686-1.6860.0000.0000.0000.000
172A173LYS10.8530.9207.191-26.756-26.7560.0000.0000.0000.000
173A174ALA0-0.044-0.0188.1973.1803.1800.0000.0000.0000.000
174A175GLU-1-0.840-0.94710.33023.79323.7930.0000.0000.0000.000
175A176LEU0-0.0090.0086.393-0.037-0.0370.0000.0000.0000.000
176A177GLY0-0.0070.0055.6466.4646.4640.0000.0000.0000.000
177A178ARG10.7170.8486.591-26.127-26.1270.0000.0000.0000.000
178A179ARG10.8580.9196.367-36.022-36.0220.0000.0000.0000.000
179A180GLU-1-0.827-0.89311.75519.20519.2050.0000.0000.0000.000
180A181ARG10.9390.95215.044-16.715-16.7150.0000.0000.0000.000
181A182PRO0-0.0080.01116.617-0.657-0.6570.0000.0000.0000.000
182A183GLU-1-0.836-0.90519.29011.75611.7560.0000.0000.0000.000
183A184VAL0-0.068-0.03221.513-0.147-0.1470.0000.0000.0000.000
184A185ARG10.8570.92023.976-11.580-11.5800.0000.0000.0000.000
185A186VAL00.0150.00227.3690.2260.2260.0000.0000.0000.000
186A187TRP0-0.050-0.03529.627-0.231-0.2310.0000.0000.0000.000
187A188GLY00.0580.03632.8760.1900.1900.0000.0000.0000.000
188A189LYS10.8720.92835.783-8.423-8.4230.0000.0000.0000.000
189A190GLU-1-0.845-0.92138.4407.5677.5670.0000.0000.0000.000
190A191ALA00.004-0.00641.5050.0400.0400.0000.0000.0000.000
191A192ASP-1-0.971-0.99244.6936.9596.9590.0000.0000.0000.000
192A193GLY00.0450.02943.452-0.078-0.0780.0000.0000.0000.000
193A194ILE0-0.101-0.05337.2740.1690.1690.0000.0000.0000.000
194A195LEU00.0050.03438.6360.0850.0850.0000.0000.0000.000
195A196THR00.003-0.01633.9480.1230.1230.0000.0000.0000.000
196A197LEU0-0.031-0.01431.917-0.046-0.0460.0000.0000.0000.000
197A198SER0-0.033-0.02529.5920.3210.3210.0000.0000.0000.000
198A199CYS0-0.046-0.00424.5590.3580.3580.0000.0000.0000.000
199A200ARG10.8640.94424.419-11.638-11.6380.0000.0000.0000.000
200A201ALA00.0570.03219.876-0.112-0.1120.0000.0000.0000.000
201A202HIS0-0.013-0.02921.272-0.050-0.0500.0000.0000.0000.000
202A203GLY00.0790.04919.4060.0460.0460.0000.0000.0000.000
203A204PHE0-0.061-0.00814.2470.2030.2030.0000.0000.0000.000
204A205TYR0-0.004-0.0128.5771.3121.3120.0000.0000.0000.000
205A206PRO00.0480.0167.178-1.115-1.1150.0000.0000.0000.000
206A207ARG10.8960.9459.746-23.854-23.8540.0000.0000.0000.000
207A208PRO0-0.012-0.0137.382-2.626-2.6260.0000.0000.0000.000
208A209ILE0-0.010-0.00210.6790.2490.2490.0000.0000.0000.000
209A210VAL00.0050.01613.738-0.492-0.4920.0000.0000.0000.000
210A211VAL00.0100.00216.465-0.254-0.2540.0000.0000.0000.000
211A212SER0-0.029-0.00820.052-0.405-0.4050.0000.0000.0000.000
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234A235GLY00.0250.02716.2470.3920.3920.0000.0000.0000.000
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