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: N9MRQ

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2653266.05212
FMO2-HF: Nuclear repulsion 2568039.128378
FMO2-HF: Total energy -85226.923742
FMO2-MP2: Total energy -85474.133641


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.
-17.084-13.19910.947-5.914-8.918-0.025
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 : -0.016 / q_NPA : -0.001
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].
3A7TRP0-0.037-0.0403.870-0.9201.258-0.021-1.223-0.9350.004
4A8ASN0-0.062-0.0276.9330.0860.0860.0000.0000.0000.000
5A9GLY00.0630.0416.731-0.437-0.4370.0000.0000.0000.000
6A10LYS10.7970.8769.6320.9900.9900.0000.0000.0000.000
7A11ASP-1-0.862-0.91812.765-0.928-0.9280.0000.0000.0000.000
8A12GLU-1-0.870-0.91814.911-0.334-0.3340.0000.0000.0000.000
9A13ARG10.7700.84218.5120.2500.2500.0000.0000.0000.000
10A14LYS10.8070.88819.8390.4010.4010.0000.0000.0000.000
11A15LEU00.001-0.01223.5710.0120.0120.0000.0000.0000.000
12A16SER00.0060.00625.188-0.008-0.0080.0000.0000.0000.000
13A17VAL00.0190.02019.5420.0030.0030.0000.0000.0000.000
14A18GLN0-0.031-0.00716.3760.0380.0380.0000.0000.0000.000
15A19GLU-1-0.850-0.90715.973-0.427-0.4270.0000.0000.0000.000
16A20ARG10.8160.86811.5040.7000.7000.0000.0000.0000.000
17A21GLY00.0460.02410.6540.0000.0000.0000.0000.0000.000
18A22PHE0-0.050-0.0375.266-0.136-0.1360.0000.0000.0000.000
19A23SER0-0.001-0.0033.7900.9411.2900.000-0.135-0.2140.000
20A24LEU0-0.0010.0102.112-9.323-9.2999.849-5.494-4.379-0.034
21A25GLU-1-0.865-0.9282.838-3.450-4.0100.6851.395-1.5200.007
22A26VAL0-0.019-0.0084.790-0.573-0.370-0.001-0.016-0.1860.000
23A27ASP-1-0.889-0.9447.0590.3280.3280.0000.0000.0000.000
24A28GLY0-0.040-0.0159.206-0.150-0.1500.0000.0000.0000.000
25A29ARG10.7450.8299.726-0.740-0.7400.0000.0000.0000.000
26A30THR00.0160.0166.9040.3750.3750.0000.0000.0000.000
27A31VAL0-0.023-0.0086.175-0.254-0.2540.0000.0000.0000.000
28A32PRO00.0010.0086.195-0.211-0.2110.0000.0000.0000.000
29A33GLY00.0550.0098.1690.2230.2230.0000.0000.0000.000
30A34VAL0-0.053-0.0129.725-0.205-0.2050.0000.0000.0000.000
31A35TYR0-0.011-0.03210.6190.1030.1030.0000.0000.0000.000
32A36TRP0-0.009-0.02212.574-0.026-0.0260.0000.0000.0000.000
33A37SER00.0420.01616.2070.0110.0110.0000.0000.0000.000
34A38PRO00.0250.00217.983-0.004-0.0040.0000.0000.0000.000
35A39ALA0-0.043-0.01620.029-0.029-0.0290.0000.0000.0000.000
36A40GLU-1-0.801-0.85621.637-0.230-0.2300.0000.0000.0000.000
37A41GLY0-0.033-0.01822.7340.0140.0140.0000.0000.0000.000
38A42SER0-0.007-0.02119.193-0.005-0.0050.0000.0000.0000.000
39A43SER0-0.028-0.03318.584-0.003-0.0030.0000.0000.0000.000
40A44ASP-1-0.844-0.90218.939-0.081-0.0810.0000.0000.0000.000
41A45ARG10.7520.85919.1530.0970.0970.0000.0000.0000.000
42A46LEU00.0320.02612.502-0.033-0.0330.0000.0000.0000.000
43A47VAL0-0.055-0.03117.1430.0380.0380.0000.0000.0000.000
44A48LEU00.0140.01512.606-0.041-0.0410.0000.0000.0000.000
45A49LEU0-0.044-0.02815.7880.0360.0360.0000.0000.0000.000
46A50GLY00.0420.01716.756-0.017-0.0170.0000.0000.0000.000
47A51HIS0-0.051-0.06915.6240.0430.0430.0000.0000.0000.000
48A60GLU-1-0.834-0.90822.911-0.166-0.1660.0000.0000.0000.000
49A61TYR00.022-0.00523.825-0.009-0.0090.0000.0000.0000.000
50A62ILE00.0220.01118.5760.0030.0030.0000.0000.0000.000
51A63GLU-1-0.724-0.82920.056-0.292-0.2920.0000.0000.0000.000
52A64GLN0-0.109-0.07421.6360.0070.0070.0000.0000.0000.000
53A65VAL00.018-0.00121.9840.0050.0050.0000.0000.0000.000
54A66ALA00.0290.02319.1230.0060.0060.0000.0000.0000.000
55A67LYS10.8280.89020.8960.2180.2180.0000.0000.0000.000
56A68LEU0-0.034-0.01823.6750.0090.0090.0000.0000.0000.000
57A69LEU0-0.009-0.00320.5460.0140.0140.0000.0000.0000.000
58A70VAL00.0480.03720.0850.0100.0100.0000.0000.0000.000
59A71GLY0-0.034-0.01222.7440.0080.0080.0000.0000.0000.000
60A72ARG10.7190.82725.5820.0930.0930.0000.0000.0000.000
61A73GLY00.0190.01224.0020.0120.0120.0000.0000.0000.000
62A74ILE0-0.104-0.01620.1460.0020.0020.0000.0000.0000.000
63A75SER00.0380.00815.903-0.025-0.0250.0000.0000.0000.000
64A76ALA0-0.031-0.02116.5870.0410.0410.0000.0000.0000.000
65A77MET0-0.0220.0099.305-0.053-0.0530.0000.0000.0000.000
66A78ALA0-0.026-0.01412.5240.0930.0930.0000.0000.0000.000
67A79ILE00.0440.0218.388-0.138-0.1380.0000.0000.0000.000
68A80ASP-1-0.895-0.93211.414-0.238-0.2380.0000.0000.0000.000
69A81GLY00.0330.00512.6140.0630.0630.0000.0000.0000.000
70A82PRO0-0.0420.00315.161-0.026-0.0260.0000.0000.0000.000
71A83GLY0-0.026-0.02317.881-0.007-0.0070.0000.0000.0000.000
72A97THR00.001-0.00430.3350.0010.0010.0000.0000.0000.000
73A98ASP-1-0.802-0.88626.841-0.051-0.0510.0000.0000.0000.000
74A99VAL00.0570.02722.8920.0060.0060.0000.0000.0000.000
75A100VAL0-0.013-0.01225.5540.0070.0070.0000.0000.0000.000
76A101GLY0-0.0080.00527.6360.0060.0060.0000.0000.0000.000
77A102LEU0-0.067-0.02126.7530.0000.0000.0000.0000.0000.000
78A103ASP-1-0.788-0.87629.3240.0040.0040.0000.0000.0000.000
79A104ALA00.0140.00126.7840.0060.0060.0000.0000.0000.000
80A105PHE00.0230.01222.1240.0070.0070.0000.0000.0000.000
81A106PRO00.007-0.01324.8960.0090.0090.0000.0000.0000.000
82A107ARG10.8010.88125.950-0.001-0.0010.0000.0000.0000.000
83A108MET00.0220.00221.4770.0070.0070.0000.0000.0000.000
84A109TRP00.0440.01520.0320.0110.0110.0000.0000.0000.000
85A110HIS0-0.003-0.01820.3890.0280.0280.0000.0000.0000.000
86A111GLU-1-0.946-0.96720.8220.0890.0890.0000.0000.0000.000
87A112GLY0-0.043-0.01216.8900.0150.0150.0000.0000.0000.000
88A113GLY00.016-0.00115.9270.0410.0410.0000.0000.0000.000
89A114GLY00.0010.00017.8770.0100.0100.0000.0000.0000.000
90A115THR0-0.045-0.06917.6100.0090.0090.0000.0000.0000.000
91A116ALA0-0.025-0.00516.6230.0030.0030.0000.0000.0000.000
92A117ALA00.0430.03713.4040.0220.0220.0000.0000.0000.000
93A118VAL00.0280.02012.4090.0280.0280.0000.0000.0000.000
94A119ILE0-0.053-0.02812.979-0.016-0.0160.0000.0000.0000.000
95A120ALA00.0240.0199.531-0.020-0.0200.0000.0000.0000.000
96A121ASP-1-0.789-0.8648.3230.5380.5380.0000.0000.0000.000
97A122TRP00.006-0.0408.462-0.082-0.0820.0000.0000.0000.000
98A123ALA0-0.0190.0089.129-0.063-0.0630.0000.0000.0000.000
99A124ALA00.0480.0254.142-0.130-0.028-0.001-0.009-0.0910.000
100A125ALA00.019-0.0074.815-0.410-0.327-0.001-0.003-0.0780.000
101A126LEU0-0.059-0.0277.085-0.196-0.1960.0000.0000.0000.000
102A127ASP-1-0.818-0.9034.8970.3030.3030.0000.0000.0000.000
103A128PHE0-0.012-0.0042.768-1.494-0.0550.438-0.422-1.456-0.002
104A129ILE00.008-0.0024.622-0.072-0.005-0.001-0.007-0.0590.000
105A130GLU-1-0.874-0.9438.2340.2060.2060.0000.0000.0000.000
106A131ALA0-0.054-0.0226.1040.0720.0720.0000.0000.0000.000
107A132GLU-1-0.910-0.9395.832-1.207-1.2070.0000.0000.0000.000
108A133GLU-1-0.826-0.8698.560-0.518-0.5180.0000.0000.0000.000
109A134GLY0-0.0120.01211.5760.0300.0300.0000.0000.0000.000
110A135PRO0-0.012-0.01712.649-0.047-0.0470.0000.0000.0000.000
111A136ARG10.8270.92013.2370.1770.1770.0000.0000.0000.000
112A137PRO0-0.084-0.03716.7220.0100.0100.0000.0000.0000.000
113A138THR00.0830.04114.621-0.035-0.0350.0000.0000.0000.000
114A139GLY0-0.028-0.01617.7090.0230.0230.0000.0000.0000.000
115A140TRP0-0.0020.03215.185-0.018-0.0180.0000.0000.0000.000
116A141TRP00.007-0.01819.8410.0070.0070.0000.0000.0000.000
117A142GLY00.0620.02420.321-0.014-0.0140.0000.0000.0000.000
118A143LEU0-0.0360.01822.1820.0160.0160.0000.0000.0000.000
119A144SER00.021-0.02524.250-0.001-0.0010.0000.0000.0000.000
120A145MET00.0460.05218.4400.0030.0030.0000.0000.0000.000
121A146GLY00.0370.02320.2480.0090.0090.0000.0000.0000.000
122A147THR0-0.030-0.04421.0040.0060.0060.0000.0000.0000.000
123A148MET0-0.050-0.01222.6280.0050.0050.0000.0000.0000.000
124A149MET00.0170.04616.8720.0220.0220.0000.0000.0000.000
125A150GLY00.0780.02018.5010.0130.0130.0000.0000.0000.000
126A151LEU0-0.062-0.00619.7870.0070.0070.0000.0000.0000.000
127A152PRO00.018-0.01218.7280.0070.0070.0000.0000.0000.000
128A153VAL00.0320.04114.4450.0160.0160.0000.0000.0000.000
129A154THR0-0.003-0.02116.7730.0060.0060.0000.0000.0000.000
130A155ALA0-0.075-0.03219.2190.0060.0060.0000.0000.0000.000
131A156SER0-0.033-0.02415.6770.0110.0110.0000.0000.0000.000
132A157ASP-1-0.798-0.88612.4010.1630.1630.0000.0000.0000.000
133A158LYS10.7890.89315.651-0.117-0.1170.0000.0000.0000.000
134A159ARG10.7580.8449.213-0.237-0.2370.0000.0000.0000.000
135A160ILE0-0.033-0.00415.060-0.026-0.0260.0000.0000.0000.000
136A161LYS10.8940.93118.363-0.029-0.0290.0000.0000.0000.000
137A162VAL0-0.066-0.04121.5670.0000.0000.0000.0000.0000.000
138A163ALA00.0270.02921.897-0.007-0.0070.0000.0000.0000.000
139A164LEU0-0.055-0.02223.4820.0030.0030.0000.0000.0000.000
140A165LEU00.0090.00622.427-0.004-0.0040.0000.0000.0000.000
141A166GLY00.048-0.00326.168-0.002-0.0020.0000.0000.0000.000
142A167LEU0-0.052-0.01427.805-0.001-0.0010.0000.0000.0000.000
143A168MET00.0430.02826.4430.0020.0020.0000.0000.0000.000
144A169GLY00.0550.01729.5760.0000.0000.0000.0000.0000.000
145A170VAL0-0.024-0.01530.3140.0030.0030.0000.0000.0000.000
146A171GLU-1-0.855-0.90731.8230.0110.0110.0000.0000.0000.000
147A172GLY00.0220.01528.717-0.002-0.0020.0000.0000.0000.000
148A173VAL00.0030.00525.4790.0050.0050.0000.0000.0000.000
149A174ASN0-0.013-0.01222.049-0.004-0.0040.0000.0000.0000.000
150A175GLY00.0410.02025.8270.0040.0040.0000.0000.0000.000
151A176GLU-1-0.923-0.96527.9840.0640.0640.0000.0000.0000.000
152A177ASP-1-0.766-0.85022.7700.1080.1080.0000.0000.0000.000
153A178LEU0-0.031-0.01423.9060.0010.0010.0000.0000.0000.000
154A179VAL0-0.016-0.02326.115-0.002-0.0020.0000.0000.0000.000
155A180ARG10.8340.91020.902-0.115-0.1150.0000.0000.0000.000
156A181LEU0-0.005-0.00520.6010.0060.0060.0000.0000.0000.000
157A182ALA00.0620.04024.537-0.001-0.0010.0000.0000.0000.000
158A183PRO0-0.007-0.00526.842-0.002-0.0020.0000.0000.0000.000
159A184GLN0-0.031-0.01823.3370.0080.0080.0000.0000.0000.000
160A185VAL0-0.0070.01122.7940.0050.0050.0000.0000.0000.000
161A186THR0-0.014-0.02723.956-0.003-0.0030.0000.0000.0000.000
162A187CYS0-0.0290.01523.0400.0000.0000.0000.0000.0000.000
163A188PRO00.000-0.00825.182-0.001-0.0010.0000.0000.0000.000
164A189VAL00.0070.00825.626-0.002-0.0020.0000.0000.0000.000
165A190ARG10.8470.94927.9740.0340.0340.0000.0000.0000.000
166A191TYR0-0.011-0.03427.650-0.001-0.0010.0000.0000.0000.000
167A192LEU00.0110.00129.567-0.001-0.0010.0000.0000.0000.000
168A193LEU0-0.034-0.00731.7450.0020.0020.0000.0000.0000.000
169A194GLN00.016-0.00234.371-0.003-0.0030.0000.0000.0000.000
170A195TRP0-0.037-0.02236.6910.0040.0040.0000.0000.0000.000
171A196ASP-1-0.859-0.92939.884-0.019-0.0190.0000.0000.0000.000
172A197ASP-1-0.812-0.90233.810-0.025-0.0250.0000.0000.0000.000
173A198GLU-1-0.806-0.90535.803-0.030-0.0300.0000.0000.0000.000
174A199LEU0-0.055-0.02331.0750.0000.0000.0000.0000.0000.000
175A200VAL0-0.030-0.00131.0630.0040.0040.0000.0000.0000.000
176A201SER0-0.012-0.01334.430-0.002-0.0020.0000.0000.0000.000
177A202LEU00.0440.00536.7530.0020.0020.0000.0000.0000.000
178A203GLN00.014-0.00437.7650.0030.0030.0000.0000.0000.000
179A204SER00.0520.04034.3400.0040.0040.0000.0000.0000.000
180A205GLY00.0280.01233.0270.0030.0030.0000.0000.0000.000
181A206LEU0-0.028-0.02233.6460.0020.0020.0000.0000.0000.000
182A207GLU-1-0.842-0.90935.4030.0290.0290.0000.0000.0000.000
183A208LEU0-0.020-0.00127.8240.0040.0040.0000.0000.0000.000
184A209PHE00.0370.01131.0590.0030.0030.0000.0000.0000.000
185A210GLY00.003-0.00232.3660.0020.0020.0000.0000.0000.000
186A211LYS10.8010.88630.991-0.032-0.0320.0000.0000.0000.000
187A212LEU0-0.0330.00627.0010.0050.0050.0000.0000.0000.000
188A213GLY00.0590.04128.420-0.003-0.0030.0000.0000.0000.000
189A214THR0-0.071-0.04727.942-0.001-0.0010.0000.0000.0000.000
190A215LYS10.8900.93229.865-0.037-0.0370.0000.0000.0000.000
191A216GLN0-0.0110.01530.220-0.002-0.0020.0000.0000.0000.000
192A217LYS10.8110.90630.819-0.027-0.0270.0000.0000.0000.000
193A218THR0-0.030-0.02632.1780.0000.0000.0000.0000.0000.000
194A219LEU00.0020.01733.049-0.003-0.0030.0000.0000.0000.000
195A220HIS0-0.068-0.05034.3250.0030.0030.0000.0000.0000.000
196A221VAL00.004-0.01435.4310.0000.0000.0000.0000.0000.000
197A222ASN0-0.0050.00736.6610.0000.0000.0000.0000.0000.000
198A223PRO00.0290.00939.2730.0010.0010.0000.0000.0000.000
199A224GLY00.0200.01939.695-0.004-0.0040.0000.0000.0000.000
200A225LYS10.8430.90837.4310.0310.0310.0000.0000.0000.000
201A226HIS10.8210.88129.1880.0290.0290.0000.0000.0000.000
202A227SER0-0.038-0.02332.204-0.001-0.0010.0000.0000.0000.000
203A228ALA0-0.048-0.01933.286-0.005-0.0050.0000.0000.0000.000
204A229VAL00.0350.02731.5720.0030.0030.0000.0000.0000.000
205A230PRO0-0.0040.00834.020-0.006-0.0060.0000.0000.0000.000
206A231THR00.0480.01733.1910.0010.0010.0000.0000.0000.000
207A232TRP00.0270.01033.198-0.005-0.0050.0000.0000.0000.000
208A233GLU-1-0.810-0.87832.596-0.038-0.0380.0000.0000.0000.000
209A234MET0-0.006-0.01228.568-0.005-0.0050.0000.0000.0000.000
210A235PHE00.0090.02726.969-0.004-0.0040.0000.0000.0000.000
211A236ALA00.0260.01529.587-0.001-0.0010.0000.0000.0000.000
212A237GLY00.0370.02031.6300.0020.0020.0000.0000.0000.000
213A238THR0-0.030-0.03827.1060.0030.0030.0000.0000.0000.000
214A239VAL00.0510.03525.9060.0030.0030.0000.0000.0000.000
215A240ASP-1-0.830-0.89727.914-0.060-0.0600.0000.0000.0000.000
216A241TYR0-0.081-0.03626.8580.0080.0080.0000.0000.0000.000
217A242LEU00.0290.00022.9750.0080.0080.0000.0000.0000.000
218A243ASP-1-0.740-0.85026.116-0.066-0.0660.0000.0000.0000.000
219A244GLN0-0.039-0.01427.2750.0110.0110.0000.0000.0000.000
220A245ARG10.8690.92927.4950.0260.0260.0000.0000.0000.000
221A246LEU0-0.0200.01620.5230.0120.0120.0000.0000.0000.000
222A247LYS10.9150.96624.2650.0460.0460.0000.0000.0000.000