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: 85Z1Y

Calculation Name: 4AO6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AO6

Chain ID: A

ChEMBL ID:

UniProt ID:

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2650740.179216
FMO2-HF: Nuclear repulsion 2565513.731691
FMO2-HF: Total energy -85226.447525
FMO2-MP2: Total energy -85473.767046


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:5:MET)


Summations of interaction energy for fragment #1(A:5: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.
-11.452-20.93828.575-9.487-9.602-0.052
Interaction energy analysis for fragmet #1(A:5:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / 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].
3A7TRP0-0.046-0.0503.814-1.0601.231-0.028-1.250-1.0130.004
4A8ASN0-0.133-0.0716.8500.2520.2520.0000.0000.0000.000
5A9GLY00.0280.0097.130-0.317-0.3170.0000.0000.0000.000
6A10LYS10.8760.9409.3770.9330.9330.0000.0000.0000.000
7A11ASP-1-0.909-0.94212.436-0.755-0.7550.0000.0000.0000.000
8A12GLU-1-0.862-0.91014.575-0.267-0.2670.0000.0000.0000.000
9A13ARG10.8200.88818.1160.2200.2200.0000.0000.0000.000
10A14LYS10.8160.90619.8730.3150.3150.0000.0000.0000.000
11A15LEU00.005-0.00923.4050.0070.0070.0000.0000.0000.000
12A16SER00.0090.00324.891-0.012-0.0120.0000.0000.0000.000
13A17VAL00.0070.00719.5290.0030.0030.0000.0000.0000.000
14A18GLN0-0.038-0.01816.1610.0350.0350.0000.0000.0000.000
15A19GLU-1-0.853-0.91015.363-0.341-0.3410.0000.0000.0000.000
16A20ARG10.8350.88211.3130.6790.6790.0000.0000.0000.000
17A21GLY00.0720.03810.2060.0330.0330.0000.0000.0000.000
18A22PHE0-0.027-0.0194.844-0.226-0.2260.0000.0000.0000.000
19A23SER00.0190.0164.0140.4181.220-0.001-0.465-0.335-0.001
20A24LEU00.0220.0081.784-7.327-17.61327.896-12.356-5.255-0.053
21A25GLU-1-0.889-0.9232.8120.218-4.1950.1875.270-1.0440.003
22A26VAL0-0.025-0.0154.786-0.2170.010-0.001-0.011-0.2150.000
23A27ASP-1-0.950-0.9677.0980.2420.2420.0000.0000.0000.000
24A28GLY0-0.041-0.0259.294-0.114-0.1140.0000.0000.0000.000
25A29ARG10.7940.86410.084-0.692-0.6920.0000.0000.0000.000
26A30THR00.0240.0197.0230.3590.3590.0000.0000.0000.000
27A31VAL0-0.022-0.0246.069-0.265-0.2650.0000.0000.0000.000
28A32PRO00.0010.0155.846-0.108-0.1080.0000.0000.0000.000
29A33GLY00.0600.0117.8230.1800.1800.0000.0000.0000.000
30A34VAL0-0.042-0.0139.054-0.201-0.2010.0000.0000.0000.000
31A35TYR0-0.017-0.03410.3140.1010.1010.0000.0000.0000.000
32A36TRP00.001-0.02012.313-0.027-0.0270.0000.0000.0000.000
33A37SER00.0520.01015.6880.0040.0040.0000.0000.0000.000
34A38PRO00.0200.00317.563-0.003-0.0030.0000.0000.0000.000
35A39ALA0-0.068-0.02519.875-0.020-0.0200.0000.0000.0000.000
36A40GLU-1-0.838-0.88521.526-0.199-0.1990.0000.0000.0000.000
37A41GLY0-0.063-0.02922.7610.0160.0160.0000.0000.0000.000
38A42SER00.037-0.01918.984-0.017-0.0170.0000.0000.0000.000
39A43SER0-0.037-0.02218.5520.0030.0030.0000.0000.0000.000
40A44ASP-1-0.850-0.91918.924-0.081-0.0810.0000.0000.0000.000
41A45ARG10.7830.89019.3920.0830.0830.0000.0000.0000.000
42A46LEU00.0070.01912.659-0.028-0.0280.0000.0000.0000.000
43A47VAL0-0.036-0.02317.2570.0320.0320.0000.0000.0000.000
44A48LEU00.0090.01712.647-0.031-0.0310.0000.0000.0000.000
45A49LEU0-0.043-0.02815.5250.0200.0200.0000.0000.0000.000
46A50GLY00.0330.00916.2880.0010.0010.0000.0000.0000.000
47A51HIS0-0.026-0.04215.3630.0120.0120.0000.0000.0000.000
48A60GLU-1-0.846-0.91622.395-0.114-0.1140.0000.0000.0000.000
49A61TYR00.026-0.00623.581-0.006-0.0060.0000.0000.0000.000
50A62ILE00.0160.01218.2360.0000.0000.0000.0000.0000.000
51A63GLU-1-0.735-0.83119.740-0.224-0.2240.0000.0000.0000.000
52A64GLN0-0.082-0.06021.4400.0030.0030.0000.0000.0000.000
53A65VAL00.018-0.00322.0560.0000.0000.0000.0000.0000.000
54A66ALA00.0330.02518.9600.0030.0030.0000.0000.0000.000
55A67LYS10.8350.89520.7890.1680.1680.0000.0000.0000.000
56A68LEU0-0.049-0.02623.3420.0040.0040.0000.0000.0000.000
57A69LEU0-0.009-0.00520.4120.0080.0080.0000.0000.0000.000
58A70VAL00.0600.04019.5900.0050.0050.0000.0000.0000.000
59A71GLY0-0.031-0.00622.2510.0040.0040.0000.0000.0000.000
60A72ARG10.7090.82625.2000.0720.0720.0000.0000.0000.000
61A73GLY00.0190.00623.4750.0100.0100.0000.0000.0000.000
62A74ILE0-0.116-0.03120.0070.0030.0030.0000.0000.0000.000
63A75SER00.0420.00815.680-0.020-0.0200.0000.0000.0000.000
64A76ALA0-0.023-0.01616.1910.0360.0360.0000.0000.0000.000
65A77MET0-0.0260.0198.868-0.036-0.0360.0000.0000.0000.000
66A78ALA0-0.019-0.00512.4170.0710.0710.0000.0000.0000.000
67A79ILE00.0340.0218.443-0.085-0.0850.0000.0000.0000.000
68A80ASP-1-0.905-0.94211.220-0.116-0.1160.0000.0000.0000.000
69A81GLY00.016-0.00712.5540.0750.0750.0000.0000.0000.000
70A82PRO0-0.080-0.02415.280-0.026-0.0260.0000.0000.0000.000
71A83GLY00.0140.00317.535-0.014-0.0140.0000.0000.0000.000
72A97THR0-0.001-0.00729.7790.0010.0010.0000.0000.0000.000
73A98ASP-1-0.794-0.88426.442-0.014-0.0140.0000.0000.0000.000
74A99VAL00.0730.03622.6430.0030.0030.0000.0000.0000.000
75A100VAL0-0.019-0.01525.1530.0050.0050.0000.0000.0000.000
76A101GLY0-0.026-0.00427.3120.0040.0040.0000.0000.0000.000
77A102LEU0-0.052-0.01526.554-0.002-0.0020.0000.0000.0000.000
78A103ASP-1-0.796-0.88729.6240.0180.0180.0000.0000.0000.000
79A104ALA0-0.019-0.02327.3160.0050.0050.0000.0000.0000.000
80A105PHE00.0140.00822.2360.0060.0060.0000.0000.0000.000
81A106PRO00.0320.00124.7920.0090.0090.0000.0000.0000.000
82A107ARG10.8270.89225.346-0.014-0.0140.0000.0000.0000.000
83A108MET00.0310.02121.6370.0060.0060.0000.0000.0000.000
84A109TRP00.0280.02120.0170.0170.0170.0000.0000.0000.000
85A110HIS0-0.011-0.02520.3950.0280.0280.0000.0000.0000.000
86A111GLU-1-0.955-0.96720.9730.0940.0940.0000.0000.0000.000
87A112GLY0-0.034-0.00617.0750.0130.0130.0000.0000.0000.000
88A113GLY00.008-0.00816.2080.0420.0420.0000.0000.0000.000
89A114GLY0-0.001-0.00218.0860.0040.0040.0000.0000.0000.000
90A115THR0-0.026-0.06718.2200.0170.0170.0000.0000.0000.000
91A116ALA0-0.006-0.00516.8970.0100.0100.0000.0000.0000.000
92A117ALA00.0230.03214.0060.0270.0270.0000.0000.0000.000
93A118VAL00.0270.02113.1610.0540.0540.0000.0000.0000.000
94A119ILE0-0.052-0.02813.5530.0130.0130.0000.0000.0000.000
95A120ALA00.0310.01910.154-0.011-0.0110.0000.0000.0000.000
96A121ASP-1-0.789-0.8618.8650.7190.7190.0000.0000.0000.000
97A122TRP00.008-0.0378.8340.0580.0580.0000.0000.0000.000
98A123ALA0-0.0230.0039.387-0.063-0.0630.0000.0000.0000.000
99A124ALA00.0400.0264.794-0.160-0.083-0.001-0.003-0.0730.000
100A125ALA00.013-0.0125.253-0.214-0.2140.0000.0000.0000.000
101A126LEU0-0.053-0.0296.836-0.302-0.3020.0000.0000.0000.000
102A127ASP-1-0.817-0.9025.0180.0770.0770.0000.0000.0000.000
103A128PHE0-0.030-0.0162.841-2.104-0.3500.524-0.665-1.613-0.005
104A129ILE00.0130.0034.616-0.0620.000-0.001-0.007-0.0540.000
105A130GLU-1-0.891-0.9448.2120.1120.1120.0000.0000.0000.000
106A131ALA0-0.042-0.0116.0510.0790.0790.0000.0000.0000.000
107A132GLU-1-0.900-0.9336.011-1.223-1.2230.0000.0000.0000.000
108A133GLU-1-0.856-0.8908.697-0.493-0.4930.0000.0000.0000.000
109A134GLY0-0.0100.01511.4110.0480.0480.0000.0000.0000.000
110A135PRO0-0.017-0.01912.532-0.035-0.0350.0000.0000.0000.000
111A136ARG10.8390.92713.3070.1990.1990.0000.0000.0000.000
112A137PRO0-0.082-0.03916.7830.0140.0140.0000.0000.0000.000
113A138THR00.0880.03714.805-0.028-0.0280.0000.0000.0000.000
114A139GLY0-0.025-0.00817.8960.0190.0190.0000.0000.0000.000
115A140TRP00.0060.04015.249-0.012-0.0120.0000.0000.0000.000
116A141TRP00.012-0.01219.5030.0010.0010.0000.0000.0000.000
117A142GLY00.0610.01720.235-0.005-0.0050.0000.0000.0000.000
118A143LEU0-0.0290.01422.1330.0100.0100.0000.0000.0000.000
119A144SER00.020-0.02024.2310.0010.0010.0000.0000.0000.000
120A145MET00.0540.05118.2390.0010.0010.0000.0000.0000.000
121A146GLY00.0360.01520.3400.0130.0130.0000.0000.0000.000
122A147THR0-0.024-0.02921.0790.0050.0050.0000.0000.0000.000
123A148MET0-0.039-0.00722.5570.0030.0030.0000.0000.0000.000
124A149MET00.0040.02516.6700.0240.0240.0000.0000.0000.000
125A150GLY00.0770.01418.9800.0120.0120.0000.0000.0000.000
126A151LEU0-0.060-0.00420.1770.0010.0010.0000.0000.0000.000
127A152PRO00.015-0.01419.0920.0020.0020.0000.0000.0000.000
128A153VAL00.0370.04314.9690.0090.0090.0000.0000.0000.000
129A154THR0-0.002-0.01717.179-0.003-0.0030.0000.0000.0000.000
130A155ALA0-0.090-0.03119.6210.0000.0000.0000.0000.0000.000
131A156SER0-0.029-0.02316.1950.0030.0030.0000.0000.0000.000
132A157ASP-1-0.781-0.86812.5370.1390.1390.0000.0000.0000.000
133A158LYS10.8180.89515.853-0.106-0.1060.0000.0000.0000.000
134A159ARG10.7520.8459.197-0.149-0.1490.0000.0000.0000.000
135A160ILE0-0.052-0.01415.781-0.021-0.0210.0000.0000.0000.000
136A161LYS10.8600.90518.706-0.019-0.0190.0000.0000.0000.000
137A162VAL0-0.057-0.03521.992-0.002-0.0020.0000.0000.0000.000
138A163ALA00.0160.01722.377-0.003-0.0030.0000.0000.0000.000
139A164LEU0-0.053-0.01723.6300.0000.0000.0000.0000.0000.000
140A165LEU00.002-0.00422.7380.0010.0010.0000.0000.0000.000
141A166GLY00.055-0.00326.097-0.005-0.0050.0000.0000.0000.000
142A167LEU0-0.055-0.01827.6920.0020.0020.0000.0000.0000.000
143A168MET00.0410.02426.6100.0020.0020.0000.0000.0000.000
144A169GLY00.0750.02529.660-0.002-0.0020.0000.0000.0000.000
145A170VAL0-0.029-0.01330.6010.0040.0040.0000.0000.0000.000
146A171GLU-1-0.876-0.92632.4400.0230.0230.0000.0000.0000.000
147A172GLY00.0160.01129.097-0.002-0.0020.0000.0000.0000.000
148A173VAL00.0240.01325.7600.0030.0030.0000.0000.0000.000
149A174ASN0-0.034-0.02122.694-0.006-0.0060.0000.0000.0000.000
150A175GLY00.0400.02126.3620.0030.0030.0000.0000.0000.000
151A176GLU-1-0.913-0.96528.4580.0660.0660.0000.0000.0000.000
152A177ASP-1-0.786-0.85323.3900.1100.1100.0000.0000.0000.000
153A178LEU0-0.026-0.00724.3180.0010.0010.0000.0000.0000.000
154A179VAL0-0.009-0.01626.464-0.003-0.0030.0000.0000.0000.000
155A180ARG10.8520.91421.723-0.111-0.1110.0000.0000.0000.000
156A181LEU0-0.001-0.01121.0210.0020.0020.0000.0000.0000.000
157A182ALA00.0380.03624.941-0.001-0.0010.0000.0000.0000.000
158A183PRO00.0080.00327.229-0.003-0.0030.0000.0000.0000.000
159A184GLN0-0.050-0.02723.2130.0040.0040.0000.0000.0000.000
160A185VAL00.0150.01623.4060.0030.0030.0000.0000.0000.000
161A186THR0-0.022-0.03024.574-0.003-0.0030.0000.0000.0000.000
162A187CYS0-0.0360.00923.669-0.002-0.0020.0000.0000.0000.000
163A188PRO0-0.013-0.01425.8000.0000.0000.0000.0000.0000.000
164A189VAL00.0030.00626.224-0.001-0.0010.0000.0000.0000.000
165A190ARG10.9000.97328.2120.0160.0160.0000.0000.0000.000
166A191TYR00.000-0.02328.1990.0000.0000.0000.0000.0000.000
167A192LEU00.0070.00529.651-0.002-0.0020.0000.0000.0000.000
168A193LEU0-0.022-0.00331.6730.0030.0030.0000.0000.0000.000
169A194GLN00.002-0.00634.297-0.003-0.0030.0000.0000.0000.000
170A195TRP0-0.029-0.02336.4690.0030.0030.0000.0000.0000.000
171A196ASP-1-0.861-0.93439.856-0.007-0.0070.0000.0000.0000.000
172A197ASP-1-0.805-0.89433.533-0.005-0.0050.0000.0000.0000.000
173A198GLU-1-0.775-0.89335.686-0.012-0.0120.0000.0000.0000.000
174A199LEU0-0.076-0.03030.9290.0010.0010.0000.0000.0000.000
175A200VAL0-0.0310.00631.0730.0040.0040.0000.0000.0000.000
176A201SER0-0.0050.00734.355-0.002-0.0020.0000.0000.0000.000
177A202LEU00.0730.02236.8780.0020.0020.0000.0000.0000.000
178A203GLN00.005-0.01138.0570.0030.0030.0000.0000.0000.000
179A204SER00.0370.02935.0010.0030.0030.0000.0000.0000.000
180A205GLY00.014-0.00133.6110.0030.0030.0000.0000.0000.000
181A206LEU0-0.041-0.03534.3410.0020.0020.0000.0000.0000.000
182A207GLU-1-0.850-0.90935.8370.0340.0340.0000.0000.0000.000
183A208LEU0-0.0020.00128.3630.0030.0030.0000.0000.0000.000
184A209PHE00.0400.01631.7330.0020.0020.0000.0000.0000.000
185A210GLY0-0.008-0.00533.0410.0010.0010.0000.0000.0000.000
186A211LYS10.8140.89231.545-0.037-0.0370.0000.0000.0000.000
187A212LEU0-0.0340.00427.4240.0040.0040.0000.0000.0000.000
188A213GLY00.0640.04428.836-0.003-0.0030.0000.0000.0000.000
189A214THR0-0.091-0.04528.464-0.003-0.0030.0000.0000.0000.000
190A215LYS10.9350.95830.384-0.037-0.0370.0000.0000.0000.000
191A216GLN0-0.032-0.00230.869-0.001-0.0010.0000.0000.0000.000
192A217LYS10.8280.91531.132-0.029-0.0290.0000.0000.0000.000
193A218THR0-0.041-0.02732.588-0.001-0.0010.0000.0000.0000.000
194A219LEU00.0000.01233.248-0.001-0.0010.0000.0000.0000.000
195A220HIS0-0.099-0.06234.4930.0010.0010.0000.0000.0000.000
196A221VAL00.008-0.01035.3690.0000.0000.0000.0000.0000.000
197A222ASN0-0.026-0.00336.220-0.001-0.0010.0000.0000.0000.000
198A223PRO00.0430.02038.9890.0010.0010.0000.0000.0000.000
199A224GLY00.0150.01239.589-0.003-0.0030.0000.0000.0000.000
200A225LYS10.8460.91337.1850.0160.0160.0000.0000.0000.000
201A226HIS10.8110.87128.7890.0050.0050.0000.0000.0000.000
202A227SER0-0.041-0.02631.8580.0000.0000.0000.0000.0000.000
203A228ALA0-0.058-0.02532.898-0.004-0.0040.0000.0000.0000.000
204A229VAL00.0440.03731.3800.0010.0010.0000.0000.0000.000
205A230PRO0-0.0090.00334.178-0.004-0.0040.0000.0000.0000.000
206A231THR00.0670.02233.1440.0010.0010.0000.0000.0000.000
207A232TRP00.0150.00932.942-0.004-0.0040.0000.0000.0000.000
208A233GLU-1-0.808-0.88632.716-0.020-0.0200.0000.0000.0000.000
209A234MET0-0.010-0.01628.238-0.002-0.0020.0000.0000.0000.000
210A235PHE00.0170.02327.133-0.002-0.0020.0000.0000.0000.000
211A236ALA00.0120.00629.5120.0000.0000.0000.0000.0000.000
212A237GLY00.0370.02431.4550.0010.0010.0000.0000.0000.000
213A238THR0-0.053-0.03826.9230.0020.0020.0000.0000.0000.000
214A239VAL00.0530.03125.8130.0020.0020.0000.0000.0000.000
215A240ASP-1-0.821-0.89127.618-0.045-0.0450.0000.0000.0000.000
216A241TYR0-0.082-0.04027.2120.0040.0040.0000.0000.0000.000
217A242LEU00.0400.00322.6100.0060.0060.0000.0000.0000.000
218A243ASP-1-0.746-0.85026.017-0.056-0.0560.0000.0000.0000.000
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