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: QYRVY

Calculation Name: 4F47-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4F47

Chain ID: A

ChEMBL ID:

UniProt ID: B2HI06

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2780968.60263
FMO2-HF: Nuclear repulsion 2689394.601505
FMO2-HF: Total energy -91574.001125
FMO2-MP2: Total energy -91837.659764


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:15:GLY)


Summations of interaction energy for fragment #1(A:15: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.
-2.61-0.8540.13-0.964-0.9210.003
Interaction energy analysis for fragmet #1(A:15:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / 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].
3A17ASP-1-0.743-0.8393.815-4.675-3.531-0.001-0.680-0.4630.003
4A18ALA0-0.035-0.0276.3880.9560.9560.0000.0000.0000.000
5A19LEU0-0.023-0.0013.156-0.299-0.0830.043-0.082-0.1770.000
6A20VAL00.020-0.0047.0590.1600.1600.0000.0000.0000.000
7A21GLU-1-0.826-0.86710.1590.3020.3020.0000.0000.0000.000
8A22GLN00.0070.02212.335-0.061-0.0610.0000.0000.0000.000
9A23ARG10.8450.88914.136-0.099-0.0990.0000.0000.0000.000
10A24GLY00.0370.01318.122-0.017-0.0170.0000.0000.0000.000
11A25HIS0-0.027-0.01021.038-0.006-0.0060.0000.0000.0000.000
12A26THR00.0420.02418.574-0.029-0.0290.0000.0000.0000.000
13A27LEU0-0.0070.00514.8770.0180.0180.0000.0000.0000.000
14A28ILE0-0.006-0.01013.235-0.013-0.0130.0000.0000.0000.000
15A29VAL00.015-0.00411.871-0.035-0.0350.0000.0000.0000.000
16A30THR0-0.019-0.0108.9420.1290.1290.0000.0000.0000.000
17A31MET00.0030.0028.815-0.375-0.3750.0000.0000.0000.000
18A32ASN0-0.041-0.0432.6132.0092.5220.089-0.197-0.4050.000
19A33ARG10.8790.9505.1700.8210.704-0.001-0.0050.1240.000
20A34PRO00.0770.0515.4980.4430.4430.0000.0000.0000.000
21A35SER0-0.0070.0018.0870.1380.1380.0000.0000.0000.000
22A36ARG10.8680.9149.9380.6870.6870.0000.0000.0000.000
23A37ARG10.9500.98211.9000.3820.3820.0000.0000.0000.000
24A38ASN0-0.0020.0019.246-0.157-0.1570.0000.0000.0000.000
25A39ALA00.0220.01911.1330.0240.0240.0000.0000.0000.000
26A40LEU00.0490.01211.883-0.204-0.2040.0000.0000.0000.000
27A41SER0-0.067-0.0699.8390.1650.1650.0000.0000.0000.000
28A42GLY00.0500.00612.9000.0350.0350.0000.0000.0000.000
29A43GLU-1-0.836-0.9156.675-3.602-3.6020.0000.0000.0000.000
30A44MET0-0.047-0.0109.2810.1200.1200.0000.0000.0000.000
31A45MET0-0.022-0.02710.8260.1770.1770.0000.0000.0000.000
32A46GLN0-0.040-0.02212.9580.1360.1360.0000.0000.0000.000
33A47ILE00.0320.0207.6700.0990.0990.0000.0000.0000.000
34A48MET0-0.060-0.02811.9200.1210.1210.0000.0000.0000.000
35A49VAL0-0.019-0.00914.0670.1150.1150.0000.0000.0000.000
36A50GLU-1-0.826-0.89213.154-0.697-0.6970.0000.0000.0000.000
37A51ALA0-0.031-0.01613.5070.0910.0910.0000.0000.0000.000
38A52TRP0-0.036-0.03915.5380.0660.0660.0000.0000.0000.000
39A53ASP-1-0.780-0.87218.912-0.296-0.2960.0000.0000.0000.000
40A54ARG10.9110.96014.1710.2200.2200.0000.0000.0000.000
41A55VAL0-0.007-0.01118.4420.0390.0390.0000.0000.0000.000
42A56ASP-1-0.844-0.90920.827-0.207-0.2070.0000.0000.0000.000
43A57ASN0-0.076-0.04922.8780.0350.0350.0000.0000.0000.000
44A58ASP-1-0.865-0.91421.154-0.083-0.0830.0000.0000.0000.000
45A59PRO0-0.047-0.03423.6730.0000.0000.0000.0000.0000.000
46A60ASP-1-0.881-0.95223.338-0.019-0.0190.0000.0000.0000.000
47A61ILE0-0.067-0.01619.0340.0060.0060.0000.0000.0000.000
48A62ARG10.8770.92522.8790.0290.0290.0000.0000.0000.000
49A63CYS0-0.033-0.00722.422-0.001-0.0010.0000.0000.0000.000
50A64CYS00.0070.01817.693-0.016-0.0160.0000.0000.0000.000
51A65ILE0-0.0080.00917.0530.0130.0130.0000.0000.0000.000
52A66LEU0-0.0020.00914.531-0.041-0.0410.0000.0000.0000.000
53A67THR0-0.013-0.03512.8910.0690.0690.0000.0000.0000.000
54A68GLY0-0.0100.01311.471-0.142-0.1420.0000.0000.0000.000
55A69ALA00.0210.0147.8000.1710.1710.0000.0000.0000.000
56A70GLY00.003-0.0189.706-0.045-0.0450.0000.0000.0000.000
57A71GLY00.0210.02210.9050.0240.0240.0000.0000.0000.000
58A72TYR0-0.029-0.01912.159-0.005-0.0050.0000.0000.0000.000
59A73PHE00.0110.03013.682-0.034-0.0340.0000.0000.0000.000
60A74CYS0-0.014-0.02513.578-0.059-0.0590.0000.0000.0000.000
61A97ASP-1-0.797-0.88628.877-0.230-0.2300.0000.0000.0000.000
62A98PRO00.0020.00926.948-0.011-0.0110.0000.0000.0000.000
63A99SER0-0.071-0.06327.843-0.008-0.0080.0000.0000.0000.000
64A100ARG10.8760.91625.0350.2890.2890.0000.0000.0000.000
65A101ILE0-0.021-0.01121.314-0.018-0.0180.0000.0000.0000.000
66A102ASP-1-0.752-0.86721.295-0.330-0.3300.0000.0000.0000.000
67A103ALA00.0280.02016.9380.0090.0090.0000.0000.0000.000
68A104LEU0-0.014-0.02017.937-0.015-0.0150.0000.0000.0000.000
69A105LEU00.0050.02520.4280.0450.0450.0000.0000.0000.000
70A106LYS10.8160.91223.0800.3250.3250.0000.0000.0000.000
71A107GLY00.0420.01226.027-0.008-0.0080.0000.0000.0000.000
72A108ARG10.7480.84922.0240.3220.3220.0000.0000.0000.000
73A109ARG10.8170.90725.2070.1940.1940.0000.0000.0000.000
74A110LEU00.0410.03519.9780.0060.0060.0000.0000.0000.000
75A111LYS10.9060.94324.3580.1860.1860.0000.0000.0000.000
76A112LYS10.8310.93124.1080.1520.1520.0000.0000.0000.000
77A113PRO00.0030.00524.822-0.016-0.0160.0000.0000.0000.000
78A114LEU00.0150.00919.056-0.005-0.0050.0000.0000.0000.000
79A115ILE00.000-0.00321.5220.0090.0090.0000.0000.0000.000
80A116ALA0-0.019-0.00919.750-0.025-0.0250.0000.0000.0000.000
81A117ALA00.0160.00617.7400.0370.0370.0000.0000.0000.000
82A118VAL0-0.033-0.01517.447-0.040-0.0400.0000.0000.0000.000
83A119GLU-1-0.749-0.87816.1180.0020.0020.0000.0000.0000.000
84A120GLY00.0520.02917.329-0.041-0.0410.0000.0000.0000.000
85A121PRO0-0.046-0.04117.318-0.011-0.0110.0000.0000.0000.000
86A122ALA00.0560.03117.684-0.051-0.0510.0000.0000.0000.000
87A123ILE0-0.0330.00419.8010.0080.0080.0000.0000.0000.000
88A124ALA00.0110.01120.438-0.045-0.0450.0000.0000.0000.000
89A125GLY00.0180.00619.2160.0110.0110.0000.0000.0000.000
90A126GLY00.0200.01418.681-0.005-0.0050.0000.0000.0000.000
91A127THR00.051-0.00119.4110.0310.0310.0000.0000.0000.000
92A128GLU-1-0.806-0.85122.542-0.264-0.2640.0000.0000.0000.000
93A129ILE00.0120.01217.5710.0170.0170.0000.0000.0000.000
94A130LEU00.0230.02221.4390.0170.0170.0000.0000.0000.000
95A131GLN0-0.014-0.01622.7010.0340.0340.0000.0000.0000.000
96A132GLY00.0000.01024.1390.0180.0180.0000.0000.0000.000
97A133THR0-0.050-0.03521.0550.0070.0070.0000.0000.0000.000
98A134ASP-1-0.810-0.88524.164-0.161-0.1610.0000.0000.0000.000
99A135ILE00.0100.01625.5360.0140.0140.0000.0000.0000.000
100A136ARG10.7970.89824.1490.1570.1570.0000.0000.0000.000
101A137VAL00.0070.00522.6020.0170.0170.0000.0000.0000.000
102A138ALA0-0.035-0.01322.286-0.023-0.0230.0000.0000.0000.000
103A139ALA00.0430.02621.1960.0150.0150.0000.0000.0000.000
104A140GLU-1-0.911-0.97323.105-0.022-0.0220.0000.0000.0000.000
105A141SER0-0.066-0.06422.636-0.009-0.0090.0000.0000.0000.000
106A142ALA0-0.106-0.04221.676-0.016-0.0160.0000.0000.0000.000
107A143LYS10.8480.93022.0770.1320.1320.0000.0000.0000.000
108A144PHE00.0450.01322.507-0.028-0.0280.0000.0000.0000.000
109A145GLY00.0350.00824.9510.0200.0200.0000.0000.0000.000
110A146ILE00.0060.00625.066-0.025-0.0250.0000.0000.0000.000
111A147SER00.023-0.00126.2510.0190.0190.0000.0000.0000.000
112A148GLU-1-0.849-0.93024.761-0.264-0.2640.0000.0000.0000.000
113A149ALA00.0760.03728.1370.0040.0040.0000.0000.0000.000
114A150LYS10.8520.93928.7340.1670.1670.0000.0000.0000.000
115A151TRP0-0.040-0.02326.2830.0130.0130.0000.0000.0000.000
116A152SER0-0.021-0.00630.503-0.001-0.0010.0000.0000.0000.000
117A153LEU0-0.0280.00225.986-0.007-0.0070.0000.0000.0000.000
118A154TYR00.0280.00129.5690.0100.0100.0000.0000.0000.000
119A155PRO0-0.012-0.00126.892-0.019-0.0190.0000.0000.0000.000
120A156MET00.0210.00824.7400.0160.0160.0000.0000.0000.000
121A157GLY00.004-0.00524.249-0.011-0.0110.0000.0000.0000.000
122A158GLY0-0.022-0.00924.9810.0040.0040.0000.0000.0000.000
123A159SER00.017-0.03626.7710.0180.0180.0000.0000.0000.000
124A160ALA0-0.023-0.00529.1960.0130.0130.0000.0000.0000.000
125A161VAL0-0.044-0.01131.8990.0120.0120.0000.0000.0000.000
126A162ARG10.8670.90825.5720.2540.2540.0000.0000.0000.000
127A163LEU00.0540.05029.5500.0090.0090.0000.0000.0000.000
128A164VAL0-0.009-0.02832.1500.0090.0090.0000.0000.0000.000
129A165ARG10.8070.89834.3410.1460.1460.0000.0000.0000.000
130A166GLN0-0.027-0.00829.0060.0000.0000.0000.0000.0000.000
131A167ILE00.0170.03132.1380.0030.0030.0000.0000.0000.000
132A168PRO00.0260.01535.0100.0000.0000.0000.0000.0000.000
133A169TYR00.0760.02937.744-0.002-0.0020.0000.0000.0000.000
134A170THR00.0600.01438.823-0.004-0.0040.0000.0000.0000.000
135A171VAL00.0170.01634.787-0.001-0.0010.0000.0000.0000.000
136A172ALA00.0160.01534.198-0.007-0.0070.0000.0000.0000.000
137A173CYS0-0.049-0.02834.736-0.008-0.0080.0000.0000.0000.000
138A174ASP-1-0.796-0.88936.500-0.105-0.1050.0000.0000.0000.000
139A175LEU0-0.032-0.01130.598-0.005-0.0050.0000.0000.0000.000
140A176LEU0-0.041-0.02530.699-0.010-0.0100.0000.0000.0000.000
141A177LEU0-0.043-0.01532.951-0.006-0.0060.0000.0000.0000.000
142A178THR0-0.011-0.00934.8920.0000.0000.0000.0000.0000.000
143A179GLY0-0.0130.00030.802-0.002-0.0020.0000.0000.0000.000
144A180ARG10.7890.88530.0020.0900.0900.0000.0000.0000.000
145A181HIS0-0.068-0.04425.259-0.001-0.0010.0000.0000.0000.000
146A182ILE0-0.018-0.01028.0020.0110.0110.0000.0000.0000.000
147A183THR0-0.007-0.04727.278-0.010-0.0100.0000.0000.0000.000
148A184ALA00.0560.03525.684-0.006-0.0060.0000.0000.0000.000
149A185ALA00.0350.01627.5550.0000.0000.0000.0000.0000.000
150A186GLU-1-0.769-0.87031.203-0.089-0.0890.0000.0000.0000.000
151A187ALA00.003-0.00828.290-0.002-0.0020.0000.0000.0000.000
152A188LYS10.8520.92130.2000.0560.0560.0000.0000.0000.000
153A189GLU-1-0.941-0.95931.649-0.052-0.0520.0000.0000.0000.000
154A190MET0-0.100-0.04132.581-0.003-0.0030.0000.0000.0000.000
155A191GLY00.0200.01033.355-0.003-0.0030.0000.0000.0000.000
156A192LEU0-0.037-0.00327.218-0.007-0.0070.0000.0000.0000.000
157A193VAL0-0.009-0.02225.390-0.015-0.0150.0000.0000.0000.000
158A194GLY00.0310.01628.1590.0090.0090.0000.0000.0000.000
159A195HIS0-0.051-0.02527.0530.0180.0180.0000.0000.0000.000
160A196VAL00.0260.01426.896-0.013-0.0130.0000.0000.0000.000
161A197VAL0-0.063-0.02123.6690.0090.0090.0000.0000.0000.000
162A198PRO00.1010.05125.439-0.010-0.0100.0000.0000.0000.000
163A199ASP-1-0.812-0.88121.417-0.029-0.0290.0000.0000.0000.000
164A200GLY0-0.040-0.02118.5790.0240.0240.0000.0000.0000.000
165A201GLN0-0.0090.00219.4440.0250.0250.0000.0000.0000.000
166A202ALA00.0220.00719.120-0.005-0.0050.0000.0000.0000.000
167A203LEU00.017-0.00914.559-0.012-0.0120.0000.0000.0000.000
168A204THR00.0300.01118.6340.0050.0050.0000.0000.0000.000
169A205LYS10.8820.94721.1940.0070.0070.0000.0000.0000.000
170A206ALA00.012-0.00620.126-0.004-0.0040.0000.0000.0000.000
171A207LEU00.003-0.00517.620-0.005-0.0050.0000.0000.0000.000
172A208GLU-1-0.845-0.90821.6440.0150.0150.0000.0000.0000.000
173A209ILE0-0.036-0.02125.010-0.002-0.0020.0000.0000.0000.000
174A210ALA00.028-0.00122.215-0.004-0.0040.0000.0000.0000.000
175A211GLU-1-0.935-0.95723.4210.0240.0240.0000.0000.0000.000
176A212ILE0-0.040-0.01726.0070.0000.0000.0000.0000.0000.000
177A213ILE0-0.020-0.01126.090-0.001-0.0010.0000.0000.0000.000
178A214ALA0-0.0070.00325.133-0.002-0.0020.0000.0000.0000.000
179A215ALA0-0.039-0.02027.2530.0050.0050.0000.0000.0000.000
180A216ASN0-0.070-0.03930.6320.0040.0040.0000.0000.0000.000
181A217GLY00.0340.01431.7380.0000.0000.0000.0000.0000.000
182A218PRO00.0270.01629.577-0.006-0.0060.0000.0000.0000.000
183A219LEU00.0530.01631.442-0.008-0.0080.0000.0000.0000.000
184A220ALA00.0000.00134.294-0.004-0.0040.0000.0000.0000.000
185A221VAL00.006-0.00329.377-0.005-0.0050.0000.0000.0000.000
186A222GLN00.004-0.00828.591-0.009-0.0090.0000.0000.0000.000
187A223ALA00.0070.01931.624-0.008-0.0080.0000.0000.0000.000
188A224ILE00.0240.00734.481-0.003-0.0030.0000.0000.0000.000
189A225LEU0-0.025-0.00627.754-0.004-0.0040.0000.0000.0000.000
190A226ARG10.8080.87332.4370.0920.0920.0000.0000.0000.000
191A227THR00.0380.01333.964-0.004-0.0040.0000.0000.0000.000
192A228ILE0-0.0290.00733.448-0.002-0.0020.0000.0000.0000.000
193A229ARG10.7450.84627.4750.1580.1580.0000.0000.0000.000
194A230GLU-1-0.813-0.88534.108-0.112-0.1120.0000.0000.0000.000
195A231THR0-0.047-0.03837.1590.0030.0030.0000.0000.0000.000
196A232GLU-1-0.869-0.90834.820-0.137-0.1370.0000.0000.0000.000
197A233GLY0-0.039-0.02338.525-0.001-0.0010.0000.0000.0000.000
198A234MET0-0.055-0.00641.1560.0050.0050.0000.0000.0000.000
199A235HIS00.0510.02844.1930.0000.0000.0000.0000.0000.000
200A236GLU-1-0.861-0.94545.834-0.060-0.0600.0000.0000.0000.000
201A237ASN00.0240.00046.8890.0020.0020.0000.0000.0000.000
202A238GLU-1-0.886-0.92347.090-0.062-0.0620.0000.0000.0000.000
203A239ALA00.0340.02043.133-0.001-0.0010.0000.0000.0000.000
204A240PHE00.0280.01344.118-0.001-0.0010.0000.0000.0000.000
205A241LYS10.7970.88046.2550.0620.0620.0000.0000.0000.000
206A242ILE0-0.047-0.02540.7160.0010.0010.0000.0000.0000.000
207A243ASP-1-0.845-0.92841.425-0.068-0.0680.0000.0000.0000.000
208A244THR0-0.014-0.00742.3820.0020.0020.0000.0000.0000.000
209A245ARG10.8740.92843.8080.0750.0750.0000.0000.0000.000
210A246ILE0-0.041-0.00537.5590.0000.0000.0000.0000.0000.000
211A247GLY00.0450.02739.8130.0000.0000.0000.0000.0000.000
212A248ILE0-0.038-0.01741.2480.0040.0040.0000.0000.0000.000
213A249GLU-1-0.930-0.97438.757-0.067-0.0670.0000.0000.0000.000
214A250VAL00.0320.02737.9210.0030.0030.0000.0000.0000.000
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