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: KGQ93

Calculation Name: 4BVY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4BVY

Chain ID: A

ChEMBL ID:

UniProt ID: O43324

Base Structure: X-ray

Registration Date: 2023-09-23

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2434741.568586
FMO2-HF: Nuclear repulsion 2353402.473637
FMO2-HF: Total energy -81339.094949
FMO2-MP2: Total energy -81577.687748


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.
-48.255-42.94542.353-18.949-28.714-0.085
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 : -0.032 / q_NPA : 0.018
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].
3A3LEU0-0.034-0.0153.761-0.8961.638-0.033-1.226-1.2760.006
4A4PHE0-0.001-0.0105.888-0.264-0.2640.0000.0000.0000.000
5A5VAL00.040-0.0039.3340.1520.1520.0000.0000.0000.000
6A6SER0-0.046-0.05612.365-0.033-0.0330.0000.0000.0000.000
7A7ASP-1-0.801-0.90616.111-0.048-0.0480.0000.0000.0000.000
8A8GLY00.0070.01219.3130.0170.0170.0000.0000.0000.000
9A9VAL0-0.045-0.02117.0820.0180.0180.0000.0000.0000.000
10A10PRO00.0650.03117.793-0.001-0.0010.0000.0000.0000.000
11A11GLY00.0400.01816.3110.0040.0040.0000.0000.0000.000
12A12CYS0-0.033-0.02713.2300.0790.0790.0000.0000.0000.000
13A13LEU00.0140.01213.348-0.036-0.0360.0000.0000.0000.000
14A14PRO00.0420.03114.036-0.032-0.0320.0000.0000.0000.000
15A15VAL0-0.051-0.0528.9150.0070.0070.0000.0000.0000.000
16A16LEU0-0.0070.0099.260-0.071-0.0710.0000.0000.0000.000
17A17ALA00.0270.02811.029-0.103-0.1030.0000.0000.0000.000
18A18ALA0-0.014-0.0089.495-0.046-0.0460.0000.0000.0000.000
19A19ALA00.0250.0126.513-0.009-0.0090.0000.0000.0000.000
20A20GLY0-0.035-0.0196.470-0.387-0.3870.0000.0000.0000.000
21A21ARG10.8530.9077.870-0.167-0.1670.0000.0000.0000.000
22A22ALA00.0350.0253.347-0.0940.1560.025-0.062-0.2130.000
23A23ARG10.9370.9635.2610.9000.941-0.0010.001-0.0400.000
24A24GLY00.0110.0108.2440.2770.2770.0000.0000.0000.000
25A25ARG10.8390.9286.1670.0000.0000.0000.0000.0000.000
26A26ALA00.0190.0042.544-0.545-0.0671.105-0.386-1.197-0.001
27A27GLU-1-0.954-0.9633.787-2.172-1.3030.012-0.203-0.678-0.001
28A28VAL0-0.025-0.0202.096-10.720-9.5985.849-2.839-4.132-0.030
29A29LEU00.0070.0113.5251.1842.1540.008-0.256-0.7220.001
30A30ILE0-0.001-0.0045.5660.1740.1740.0000.0000.0000.000
31A31SER0-0.015-0.0078.3900.0920.0920.0000.0000.0000.000
32A32THR0-0.005-0.00410.4720.0680.0680.0000.0000.0000.000
33A33VAL0-0.029-0.00212.980-0.003-0.0030.0000.0000.0000.000
34A34GLY00.0560.04315.5090.0030.0030.0000.0000.0000.000
35A35PRO0-0.019-0.02217.7480.0260.0260.0000.0000.0000.000
36A36GLN00.006-0.00619.8180.0270.0270.0000.0000.0000.000
37A37ASP-1-0.796-0.88716.6410.0700.0700.0000.0000.0000.000
38A38CYS0-0.057-0.02616.6250.0330.0330.0000.0000.0000.000
39A39VAL00.0350.01511.045-0.010-0.0100.0000.0000.0000.000
40A40VAL0-0.045-0.01111.1300.0220.0220.0000.0000.0000.000
41A41PRO00.0190.01112.096-0.033-0.0330.0000.0000.0000.000
42A42PHE00.009-0.00112.678-0.033-0.0330.0000.0000.0000.000
43A43LEU0-0.048-0.01614.804-0.005-0.0050.0000.0000.0000.000
44A44THR00.0060.00017.946-0.019-0.0190.0000.0000.0000.000
45A45ARG10.9330.96820.373-0.224-0.2240.0000.0000.0000.000
46A46PRO00.0400.02917.6860.0340.0340.0000.0000.0000.000
47A47LYS10.9210.95714.365-0.429-0.4290.0000.0000.0000.000
48A48VAL0-0.0090.01812.5620.0240.0240.0000.0000.0000.000
49A49PRO00.007-0.00810.332-0.038-0.0380.0000.0000.0000.000
50A50VAL0-0.055-0.0218.2250.0950.0950.0000.0000.0000.000
51A51LEU00.0020.0122.436-2.172-1.0951.120-0.458-1.7390.003
52A52GLN0-0.015-0.0144.411-0.0060.260-0.001-0.040-0.2250.000
53A53LEU00.028-0.0042.571-3.347-0.5872.798-1.913-3.644-0.014
54A54ASP-1-0.794-0.8921.881-23.580-23.24613.522-6.066-7.790-0.074
55A55SER0-0.049-0.0153.5840.6150.8150.018-0.024-0.1950.000
56A56GLY00.003-0.0015.8580.0840.0840.0000.0000.0000.000
57A57ASN0-0.054-0.0277.679-0.074-0.0740.0000.0000.0000.000
58A58TYR00.0460.0007.1790.1900.1900.0000.0000.0000.000
59A59LEU0-0.0190.0116.977-0.127-0.1270.0000.0000.0000.000
60A60PHE00.0570.0039.098-0.109-0.1090.0000.0000.0000.000
61A61SER0-0.0080.00711.903-0.167-0.1670.0000.0000.0000.000
62A62THR00.0870.03212.0610.1980.1980.0000.0000.0000.000
63A63SER00.0830.03911.9840.0930.0930.0000.0000.0000.000
64A64ALA0-0.0130.00111.7130.0340.0340.0000.0000.0000.000
65A65ILE0-0.020-0.0076.6490.3520.3520.0000.0000.0000.000
66A66CYS0-0.028-0.0077.5320.1620.1620.0000.0000.0000.000
67A67ARG10.8520.9069.338-0.816-0.8160.0000.0000.0000.000
68A68TYR00.001-0.0202.194-5.632-12.54817.263-5.183-5.1640.026
69A69PHE00.011-0.0092.548-0.6490.0290.388-0.116-0.9500.001
70A70PHE00.0520.0235.951-0.335-0.3350.0000.0000.0000.000
71A71LEU00.0090.0248.686-0.125-0.1250.0000.0000.0000.000
72A72LEU0-0.052-0.0142.693-1.203-0.5560.280-0.178-0.749-0.002
73A73SER0-0.095-0.0587.156-0.331-0.3310.0000.0000.0000.000
74A74GLY0-0.007-0.0079.678-0.103-0.1030.0000.0000.0000.000
75A75TRP0-0.016-0.01011.8980.0330.0330.0000.0000.0000.000
76A76GLU-1-0.883-0.94913.5110.5290.5290.0000.0000.0000.000
77A77GLN0-0.039-0.01415.0140.0620.0620.0000.0000.0000.000
78A78ASP-1-0.764-0.84217.2630.2640.2640.0000.0000.0000.000
79A79ASP-1-0.882-0.96020.6740.3030.3030.0000.0000.0000.000
80A80LEU0-0.0320.00423.3790.0080.0080.0000.0000.0000.000
81A81THR0-0.019-0.04816.9550.0010.0010.0000.0000.0000.000
82A82ASN0-0.003-0.00618.6780.0870.0870.0000.0000.0000.000
83A83GLN00.0110.01720.483-0.006-0.0060.0000.0000.0000.000
84A84TRP00.0150.00221.398-0.005-0.0050.0000.0000.0000.000
85A85LEU0-0.032-0.03015.3470.0110.0110.0000.0000.0000.000
86A86GLU-1-0.948-0.95819.9410.3360.3360.0000.0000.0000.000
87A87TRP0-0.0010.00922.545-0.018-0.0180.0000.0000.0000.000
88A88GLU-1-0.861-0.93919.4090.3630.3630.0000.0000.0000.000
89A89ALA0-0.004-0.01020.580-0.013-0.0130.0000.0000.0000.000
90A90THR0-0.084-0.05922.399-0.022-0.0220.0000.0000.0000.000
91A91GLU-1-0.899-0.94425.9760.1550.1550.0000.0000.0000.000
92A92LEU0-0.080-0.03223.665-0.018-0.0180.0000.0000.0000.000
93A93GLN00.013-0.00120.404-0.038-0.0380.0000.0000.0000.000
94A94PRO0-0.0230.01424.926-0.017-0.0170.0000.0000.0000.000
95A95ALA00.0340.02028.129-0.015-0.0150.0000.0000.0000.000
96A96LEU00.019-0.00924.196-0.017-0.0170.0000.0000.0000.000
97A97SER0-0.022-0.02225.912-0.010-0.0100.0000.0000.0000.000
98A98ALA0-0.033-0.01427.824-0.012-0.0120.0000.0000.0000.000
99A99ALA00.0130.01630.595-0.010-0.0100.0000.0000.0000.000
100A100LEU00.0280.00025.605-0.012-0.0120.0000.0000.0000.000
101A101TYR0-0.028-0.01729.885-0.012-0.0120.0000.0000.0000.000
102A102TYR00.006-0.01031.878-0.009-0.0090.0000.0000.0000.000
103A103LEU0-0.0130.01230.850-0.008-0.0080.0000.0000.0000.000
104A104VAL0-0.035-0.03028.849-0.007-0.0070.0000.0000.0000.000
105A105VAL0-0.102-0.04631.114-0.005-0.0050.0000.0000.0000.000
106A106GLN0-0.021-0.01533.603-0.005-0.0050.0000.0000.0000.000
107A107GLY0-0.0200.00536.082-0.004-0.0040.0000.0000.0000.000
108A108LYS10.8690.93637.509-0.072-0.0720.0000.0000.0000.000
109A109LYS10.9220.94037.396-0.039-0.0390.0000.0000.0000.000
110A110GLY00.0590.04238.6460.0010.0010.0000.0000.0000.000
111A111GLU-1-0.743-0.88238.3100.0660.0660.0000.0000.0000.000
112A112ASP-1-0.872-0.91739.5820.0650.0650.0000.0000.0000.000
113A113VAL0-0.083-0.02633.5050.0050.0050.0000.0000.0000.000
114A114LEU00.018-0.00634.0560.0090.0090.0000.0000.0000.000
115A115GLY00.0230.01835.8020.0050.0050.0000.0000.0000.000
116A116SER0-0.036-0.02333.6240.0020.0020.0000.0000.0000.000
117A117VAL00.0000.00130.1870.0100.0100.0000.0000.0000.000
118A118ARG10.8170.90932.614-0.060-0.0600.0000.0000.0000.000
119A119ARG10.9520.99134.525-0.116-0.1160.0000.0000.0000.000
120A120ALA00.0430.01529.3810.0010.0010.0000.0000.0000.000
121A121LEU00.0430.01229.2770.0040.0040.0000.0000.0000.000
122A122THR00.017-0.01131.422-0.004-0.0040.0000.0000.0000.000
123A123HIS0-0.084-0.03328.822-0.009-0.0090.0000.0000.0000.000
124A124ILE00.0380.02726.7180.0020.0020.0000.0000.0000.000
125A125ASP-1-0.777-0.89329.4440.0710.0710.0000.0000.0000.000
126A126HIS0-0.081-0.06232.064-0.006-0.0060.0000.0000.0000.000
127A127SER0-0.031-0.02329.199-0.001-0.0010.0000.0000.0000.000
128A128LEU0-0.017-0.01526.346-0.001-0.0010.0000.0000.0000.000
129A129SER0-0.034-0.01530.176-0.009-0.0090.0000.0000.0000.000
130A130ARG10.8630.93933.559-0.092-0.0920.0000.0000.0000.000
131A131GLN0-0.043-0.00626.6410.0040.0040.0000.0000.0000.000
132A132ASN0-0.021-0.02131.873-0.006-0.0060.0000.0000.0000.000
133A133CYS0-0.0290.00826.885-0.008-0.0080.0000.0000.0000.000
134A134PRO00.0020.00326.5030.0030.0030.0000.0000.0000.000
135A135PHE0-0.039-0.02822.457-0.005-0.0050.0000.0000.0000.000
136A136LEU0-0.006-0.01921.7850.0030.0030.0000.0000.0000.000
137A137ALA0-0.016-0.00521.3710.0080.0080.0000.0000.0000.000
138A138GLY00.0020.00822.3630.0020.0020.0000.0000.0000.000
139A139GLU-1-0.872-0.95023.3090.0730.0730.0000.0000.0000.000
140A140THR0-0.061-0.01219.318-0.020-0.0200.0000.0000.0000.000
141A141GLU-1-0.809-0.85317.0460.0380.0380.0000.0000.0000.000
142A142SER00.003-0.02116.1860.0140.0140.0000.0000.0000.000
143A143LEU0-0.018-0.00512.0300.0050.0050.0000.0000.0000.000
144A144ALA00.0460.00715.0460.0100.0100.0000.0000.0000.000
145A145ASP-1-0.725-0.85118.4330.1490.1490.0000.0000.0000.000
146A146ILE00.0210.01213.343-0.014-0.0140.0000.0000.0000.000
147A147VAL0-0.002-0.00914.772-0.004-0.0040.0000.0000.0000.000
148A148LEU00.0090.00816.903-0.016-0.0160.0000.0000.0000.000
149A149TRP0-0.037-0.02416.887-0.017-0.0170.0000.0000.0000.000
150A150GLY0-0.039-0.03617.527-0.022-0.0220.0000.0000.0000.000
151A151ALA0-0.029-0.01218.522-0.013-0.0130.0000.0000.0000.000
152A152LEU00.014-0.00220.990-0.019-0.0190.0000.0000.0000.000
153A153TYR0-0.0220.00521.361-0.022-0.0220.0000.0000.0000.000
154A154PRO0-0.037-0.03121.778-0.016-0.0160.0000.0000.0000.000
155A155LEU0-0.0130.00024.633-0.009-0.0090.0000.0000.0000.000
156A156LEU00.0230.00026.832-0.010-0.0100.0000.0000.0000.000
157A157GLN0-0.045-0.01525.718-0.010-0.0100.0000.0000.0000.000
158A158ASP-1-0.924-0.95427.7180.0240.0240.0000.0000.0000.000
159A159PRO00.032-0.00131.3460.0060.0060.0000.0000.0000.000
160A160ALA0-0.0230.00433.6700.0020.0020.0000.0000.0000.000
161A161TYR0-0.069-0.04932.0980.0040.0040.0000.0000.0000.000
162A162LEU0-0.017-0.00629.9460.0090.0090.0000.0000.0000.000
163A163PRO0-0.0040.00033.211-0.005-0.0050.0000.0000.0000.000
164A164GLU-1-0.917-0.95735.9740.0300.0300.0000.0000.0000.000
165A165GLU-1-0.874-0.93837.6620.0520.0520.0000.0000.0000.000
166A166LEU0-0.100-0.02633.8270.0030.0030.0000.0000.0000.000
167A167SER00.0440.00533.8780.0010.0010.0000.0000.0000.000
168A168ALA00.0230.02031.875-0.004-0.0040.0000.0000.0000.000
169A169LEU0-0.021-0.01828.0600.0020.0020.0000.0000.0000.000
170A170HIS00.0480.02629.1290.0000.0000.0000.0000.0000.000
171A171SER00.0180.00830.063-0.007-0.0070.0000.0000.0000.000
172A172TRP0-0.022-0.00222.119-0.008-0.0080.0000.0000.0000.000
173A173PHE00.010-0.00723.922-0.002-0.0020.0000.0000.0000.000
174A174GLN0-0.013-0.00325.281-0.013-0.0130.0000.0000.0000.000
175A175THR0-0.020-0.01424.269-0.016-0.0160.0000.0000.0000.000
176A176LEU0-0.016-0.01019.698-0.013-0.0130.0000.0000.0000.000
177A177SER00.0080.00721.259-0.011-0.0110.0000.0000.0000.000
178A178THR0-0.088-0.04622.613-0.019-0.0190.0000.0000.0000.000
179A179GLN0-0.029-0.01218.717-0.022-0.0220.0000.0000.0000.000
180A180GLU-1-0.777-0.85816.786-0.311-0.3110.0000.0000.0000.000
181A181PRO00.0300.00613.739-0.013-0.0130.0000.0000.0000.000
182A182CYS0-0.026-0.00715.6210.0140.0140.0000.0000.0000.000
183A183GLN00.0220.01917.831-0.007-0.0070.0000.0000.0000.000
184A184ARG10.8250.86613.2460.3750.3750.0000.0000.0000.000
185A185ALA0-0.0070.01314.605-0.008-0.0080.0000.0000.0000.000
186A186ALA00.0540.01316.0450.0180.0180.0000.0000.0000.000
187A187GLN0-0.012-0.00219.607-0.013-0.0130.0000.0000.0000.000
188A188THR0-0.045-0.01614.638-0.013-0.0130.0000.0000.0000.000
189A189VAL0-0.033-0.02216.1900.0100.0100.0000.0000.0000.000
190A190LEU0-0.018-0.01118.6010.0160.0160.0000.0000.0000.000
191A191LYS10.8070.91419.2440.0680.0680.0000.0000.0000.000
192A192GLN0-0.005-0.02223.1010.0060.0060.0000.0000.0000.000
193A193GLN0-0.065-0.03125.994-0.002-0.0020.0000.0000.0000.000
194A194GLY00.0360.04626.8250.0060.0060.0000.0000.0000.000
195A195VAL00.1020.02826.6310.0010.0010.0000.0000.0000.000
196A196LEU0-0.016-0.01127.7690.0090.0090.0000.0000.0000.000
197A197ALA0-0.038-0.00624.2500.0030.0030.0000.0000.0000.000
198A198LEU00.0500.01522.3450.0040.0040.0000.0000.0000.000
199A199ARG10.9170.97825.299-0.028-0.0280.0000.0000.0000.000
200A200PRO0-0.008-0.01625.3080.0070.0070.0000.0000.0000.000
201A201TYR00.0340.01620.2080.0130.0130.0000.0000.0000.000
202A202LEU00.0340.00424.3530.0140.0140.0000.0000.0000.000
203A203GLN0-0.053-0.02127.0270.0030.0030.0000.0000.0000.000
204A204LYS10.8630.92723.324-0.115-0.1150.0000.0000.0000.000
205A205GLN0-0.054-0.00723.2600.0270.0270.0000.0000.0000.000
206A206PRO0-0.017-0.00526.872-0.011-0.0110.0000.0000.0000.000
207A207GLN00.0320.02730.045-0.004-0.0040.0000.0000.0000.000
208A208PRO00.0160.01332.7270.0070.0070.0000.0000.0000.000
209A209SER00.0320.00133.780-0.001-0.0010.0000.0000.0000.000
210A210PRO0-0.067-0.01536.877-0.004-0.0040.0000.0000.0000.000
211A211ALA00.0400.02639.5630.0020.0020.0000.0000.0000.000