Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 52G8Z

Calculation Name: 3AAZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AAZ

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2433704.164068
FMO2-HF: Nuclear repulsion 2346531.700298
FMO2-HF: Total energy -87172.463769
FMO2-MP2: Total energy -87426.68343


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:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-0.6993.8670.549-2.117-2.9980.008
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.032
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].
3A3THR00.0170.0082.518-1.6962.7160.552-2.064-2.9000.008
4A4LEU0-0.032-0.0235.272-0.818-0.805-0.001-0.003-0.0090.000
5A5LYS10.8920.9468.9620.8980.8980.0000.0000.0000.000
6A6GLU-1-0.745-0.86311.2020.0910.0910.0000.0000.0000.000
7A7SER0-0.071-0.03514.985-0.038-0.0380.0000.0000.0000.000
8A8GLY00.0470.01417.3820.0040.0040.0000.0000.0000.000
9A9PRO00.0000.00321.1890.0010.0010.0000.0000.0000.000
10A10THR00.0110.01722.5820.0180.0180.0000.0000.0000.000
11A11LEU0-0.048-0.03124.0630.0240.0240.0000.0000.0000.000
12A12VAL0-0.0020.01327.908-0.018-0.0180.0000.0000.0000.000
13A13LYS10.8940.94930.2340.0800.0800.0000.0000.0000.000
14A14PRO00.0430.00633.965-0.003-0.0030.0000.0000.0000.000
15A15THR0-0.029-0.02335.611-0.004-0.0040.0000.0000.0000.000
16A16GLN0-0.032-0.01033.249-0.008-0.0080.0000.0000.0000.000
17A17THR00.0180.00329.5770.0130.0130.0000.0000.0000.000
18A18LEU0-0.0160.00624.564-0.012-0.0120.0000.0000.0000.000
19A19THR00.0110.00224.4490.0050.0050.0000.0000.0000.000
20A20LEU0-0.022-0.00720.104-0.013-0.0130.0000.0000.0000.000
21A21THR0-0.005-0.00616.481-0.012-0.0120.0000.0000.0000.000
22A22CYS0-0.062-0.00513.551-0.039-0.0390.0000.0000.0000.000
23A23THR00.0050.00711.116-0.028-0.0280.0000.0000.0000.000
24A24PHE00.0330.0129.1000.0640.0640.0000.0000.0000.000
25A25SER0-0.018-0.0175.5210.0280.0280.0000.0000.0000.000
26A26GLY00.0600.0274.314-0.500-0.477-0.001-0.0430.0210.000
27A27PHE0-0.019-0.0184.9810.6510.769-0.001-0.007-0.1100.000
28A28SER00.0160.0207.8670.0230.0230.0000.0000.0000.000
29A29LEU00.0070.00311.5900.1780.1780.0000.0000.0000.000
30A30ARG10.9960.98914.3020.5010.5010.0000.0000.0000.000
31A31THR0-0.044-0.03214.2060.0830.0830.0000.0000.0000.000
32A32SER0-0.0370.00212.8160.0660.0660.0000.0000.0000.000
33A33ARG10.9630.97014.8210.2700.2700.0000.0000.0000.000
34A34VAL0-0.041-0.00711.8180.0530.0530.0000.0000.0000.000
35A35GLY00.0030.01315.273-0.033-0.0330.0000.0000.0000.000
36A36VAL0-0.018-0.01614.491-0.001-0.0010.0000.0000.0000.000
37A37SER00.013-0.01216.839-0.005-0.0050.0000.0000.0000.000
38A38TRP00.0170.00917.5580.0170.0170.0000.0000.0000.000
39A39ILE0-0.048-0.02817.5190.0030.0030.0000.0000.0000.000
40A40ARG10.8060.89520.256-0.073-0.0730.0000.0000.0000.000
41A41GLN00.007-0.00220.9160.0480.0480.0000.0000.0000.000
42A42PRO00.0560.03423.412-0.003-0.0030.0000.0000.0000.000
43A43PRO00.0340.00925.3420.0250.0250.0000.0000.0000.000
44A44GLY00.0060.00525.948-0.014-0.0140.0000.0000.0000.000
45A45LYS10.8950.96026.798-0.144-0.1440.0000.0000.0000.000
46A46ALA00.0440.01925.6290.0260.0260.0000.0000.0000.000
47A47LEU0-0.006-0.00519.821-0.017-0.0170.0000.0000.0000.000
48A48GLU-1-0.788-0.88323.7040.0880.0880.0000.0000.0000.000
49A49TRP0-0.044-0.03021.476-0.005-0.0050.0000.0000.0000.000
50A50LEU00.0190.01223.179-0.017-0.0170.0000.0000.0000.000
51A51ALA00.017-0.00223.232-0.020-0.0200.0000.0000.0000.000
52A52HIS0-0.0190.02218.4600.0350.0350.0000.0000.0000.000
53A53ILE0-0.0210.00719.713-0.009-0.0090.0000.0000.0000.000
54A54TYR00.0270.00519.7780.0000.0000.0000.0000.0000.000
55A55TRP00.0370.00618.542-0.046-0.0460.0000.0000.0000.000
56A56ASP-1-0.856-0.93919.978-0.148-0.1480.0000.0000.0000.000
57A57ASP-1-0.826-0.88523.252-0.230-0.2300.0000.0000.0000.000
58A58ASP-1-0.746-0.81724.651-0.035-0.0350.0000.0000.0000.000
59A59LYS10.7700.85224.7310.1400.1400.0000.0000.0000.000
60A60ARG10.7720.86825.6380.0240.0240.0000.0000.0000.000
61A61TYR00.0550.00826.271-0.009-0.0090.0000.0000.0000.000
62A62ASN00.0250.02827.846-0.002-0.0020.0000.0000.0000.000
63A63PRO00.0370.00629.464-0.012-0.0120.0000.0000.0000.000
64A64SER0-0.044-0.01732.335-0.008-0.0080.0000.0000.0000.000
65A65LEU00.0360.00629.251-0.005-0.0050.0000.0000.0000.000
66A66LYS10.9350.96831.3140.0170.0170.0000.0000.0000.000
67A67SER0-0.027-0.00332.348-0.010-0.0100.0000.0000.0000.000
68A68ARG10.8470.91231.8600.0010.0010.0000.0000.0000.000
69A69LEU0-0.025-0.01126.678-0.009-0.0090.0000.0000.0000.000
70A70THR0-0.036-0.02427.071-0.005-0.0050.0000.0000.0000.000
71A71ILE0-0.0060.00920.580-0.008-0.0080.0000.0000.0000.000
72A72SER0-0.009-0.01622.741-0.002-0.0020.0000.0000.0000.000
73A73LYS10.8600.91218.4250.2640.2640.0000.0000.0000.000
74A74ASP-1-0.719-0.83419.214-0.500-0.5000.0000.0000.0000.000
75A75THR0-0.035-0.02617.556-0.072-0.0720.0000.0000.0000.000
76A76SER0-0.063-0.02517.324-0.081-0.0810.0000.0000.0000.000
77A77LYS10.8780.92116.8240.4770.4770.0000.0000.0000.000
78A78ASN0-0.032-0.01510.7830.1030.1030.0000.0000.0000.000
79A79GLN00.021-0.00313.5220.0070.0070.0000.0000.0000.000
80A80VAL00.002-0.00215.9050.0400.0400.0000.0000.0000.000
81A81VAL0-0.029-0.01617.9230.0020.0020.0000.0000.0000.000
82A82LEU00.0000.00520.7440.0300.0300.0000.0000.0000.000
83A83THR0-0.002-0.00523.085-0.017-0.0170.0000.0000.0000.000
84A84MET0-0.032-0.01026.5330.0150.0150.0000.0000.0000.000
85A85THR00.0360.01428.764-0.005-0.0050.0000.0000.0000.000
86A86ASN0-0.0090.00232.3710.0090.0090.0000.0000.0000.000
87A87MET0-0.035-0.01327.9670.0090.0090.0000.0000.0000.000
88A88ASP-1-0.744-0.87032.5790.0120.0120.0000.0000.0000.000
89A89PRO00.0260.00332.4060.0040.0040.0000.0000.0000.000
90A90VAL0-0.031-0.00932.0820.0100.0100.0000.0000.0000.000
91A91ASP-1-0.777-0.85328.9990.0270.0270.0000.0000.0000.000
92A92THR0-0.0280.00027.632-0.007-0.0070.0000.0000.0000.000
93A93ALA0-0.033-0.02424.2750.0190.0190.0000.0000.0000.000
94A94THR0-0.0120.01118.328-0.043-0.0430.0000.0000.0000.000
95A95TYR0-0.030-0.03720.0880.0150.0150.0000.0000.0000.000
96A96TYR00.023-0.00914.944-0.006-0.0060.0000.0000.0000.000
97A98ALA00.0340.01313.1440.1150.1150.0000.0000.0000.000
98A99ARG10.8350.9038.1390.0200.0200.0000.0000.0000.000
99A100ARG10.8640.93613.164-0.037-0.0370.0000.0000.0000.000
100A101GLY00.0100.01411.914-0.112-0.1120.0000.0000.0000.000
101A102PHE0-0.024-0.03412.9040.0540.0540.0000.0000.0000.000
102A103TYR0-0.072-0.07010.1350.0600.0600.0000.0000.0000.000
103A104GLY00.0740.04714.5130.0010.0010.0000.0000.0000.000
104A105ARG10.9130.95216.727-0.075-0.0750.0000.0000.0000.000
105A106LYS10.9951.00518.275-0.130-0.1300.0000.0000.0000.000
106A107TYR0-0.001-0.01816.6440.0000.0000.0000.0000.0000.000
107A108GLU-1-0.883-0.95419.5360.1730.1730.0000.0000.0000.000
108A109VAL00.0310.03216.6250.0140.0140.0000.0000.0000.000
109A110ASN00.0250.01916.235-0.011-0.0110.0000.0000.0000.000
110A111HIS10.9010.94612.413-0.658-0.6580.0000.0000.0000.000
111A112PHE00.032-0.00414.526-0.025-0.0250.0000.0000.0000.000
112A113ASP-1-0.751-0.8079.6890.4850.4850.0000.0000.0000.000
113A114TYR0-0.001-0.0034.817-0.426-0.4260.0000.0000.0000.000
114A115TRP00.0470.0109.276-0.413-0.4130.0000.0000.0000.000
115A116GLY00.0270.0159.7880.2870.2870.0000.0000.0000.000
116A117GLN0-0.030-0.01110.474-0.002-0.0020.0000.0000.0000.000
117A118GLY00.0140.01111.889-0.011-0.0110.0000.0000.0000.000
118A119THR0-0.051-0.03215.444-0.062-0.0620.0000.0000.0000.000
119A120THR00.0010.00818.1240.0210.0210.0000.0000.0000.000
120A121VAL0-0.015-0.01521.463-0.039-0.0390.0000.0000.0000.000
121A122THR00.0420.01924.5260.0290.0290.0000.0000.0000.000
122A123VAL0-0.0120.00427.959-0.021-0.0210.0000.0000.0000.000
123A124SER00.025-0.00131.2050.0080.0080.0000.0000.0000.000
124A125SER00.0290.00333.840-0.009-0.0090.0000.0000.0000.000
125A126ALA00.0020.02934.443-0.008-0.0080.0000.0000.0000.000
126A127SER00.007-0.01333.839-0.006-0.0060.0000.0000.0000.000
127A128THR0-0.005-0.00228.4780.0120.0120.0000.0000.0000.000
128A129LYS10.8430.92130.5830.0380.0380.0000.0000.0000.000
129A130GLY00.0510.03129.0700.0050.0050.0000.0000.0000.000
130A131PRO0-0.018-0.00626.7770.0080.0080.0000.0000.0000.000
131A132SER0-0.042-0.01230.105-0.011-0.0110.0000.0000.0000.000
132A133VAL00.017-0.00127.9570.0100.0100.0000.0000.0000.000
133A134PHE00.006-0.00631.196-0.009-0.0090.0000.0000.0000.000
134A135PRO00.0310.02132.5090.0070.0070.0000.0000.0000.000
135A136LEU0-0.0270.00331.8110.0020.0020.0000.0000.0000.000
136A137ALA00.025-0.00134.1210.0050.0050.0000.0000.0000.000
137A138PRO00.0290.02234.3310.0040.0040.0000.0000.0000.000
138A139SER0-0.009-0.01236.897-0.007-0.0070.0000.0000.0000.000
139A140SER00.0210.00139.9530.0050.0050.0000.0000.0000.000
140A141LYS10.9630.97442.367-0.045-0.0450.0000.0000.0000.000
141A142SER0-0.0040.02036.5980.0010.0010.0000.0000.0000.000
142A143THR0-0.005-0.01537.0300.0040.0040.0000.0000.0000.000
143A144SER0-0.019-0.01338.209-0.002-0.0020.0000.0000.0000.000
144A145GLY00.0190.01238.4630.0060.0060.0000.0000.0000.000
145A146GLY00.0150.00838.2000.0070.0070.0000.0000.0000.000
146A147THR0-0.0020.01132.9780.0060.0060.0000.0000.0000.000
147A148ALA0-0.007-0.00434.151-0.006-0.0060.0000.0000.0000.000
148A149ALA0-0.0010.00932.3400.0090.0090.0000.0000.0000.000
149A150LEU0-0.0070.00829.260-0.013-0.0130.0000.0000.0000.000
150A151GLY00.0470.00329.2940.0150.0150.0000.0000.0000.000
151A152CYS0-0.094-0.03224.720-0.025-0.0250.0000.0000.0000.000
152A153LEU00.0210.02429.6100.0130.0130.0000.0000.0000.000
153A154VAL0-0.029-0.02226.565-0.016-0.0160.0000.0000.0000.000
154A155LYS10.9270.93429.7630.0040.0040.0000.0000.0000.000
155A156ASP-1-0.827-0.89432.270-0.014-0.0140.0000.0000.0000.000
156A157TYR0-0.005-0.00826.313-0.014-0.0140.0000.0000.0000.000
157A158PHE00.0380.04429.8330.0150.0150.0000.0000.0000.000
158A159PRO00.0310.00626.246-0.017-0.0170.0000.0000.0000.000
159A160GLU-1-0.776-0.88123.9060.0660.0660.0000.0000.0000.000
160A161PRO0-0.017-0.00820.037-0.014-0.0140.0000.0000.0000.000
161A162VAL0-0.015-0.02122.537-0.036-0.0360.0000.0000.0000.000
162A163THR0-0.033-0.01516.8330.0190.0190.0000.0000.0000.000
163A164VAL00.029-0.00319.969-0.039-0.0390.0000.0000.0000.000
164A165SER0-0.048-0.00817.6880.0280.0280.0000.0000.0000.000
165A166TRP0-0.016-0.03019.680-0.022-0.0220.0000.0000.0000.000
166A167ASN00.0540.00620.7460.0050.0050.0000.0000.0000.000
167A168SER0-0.018-0.01120.744-0.004-0.0040.0000.0000.0000.000
168A169GLY00.0320.01116.758-0.053-0.0530.0000.0000.0000.000
169A170ALA0-0.093-0.04215.5120.0330.0330.0000.0000.0000.000
170A171LEU00.0340.04517.3590.0230.0230.0000.0000.0000.000
171A172THR00.008-0.02818.323-0.002-0.0020.0000.0000.0000.000
172A173SER00.0090.01121.110-0.019-0.0190.0000.0000.0000.000
173A174GLY00.0380.03123.5150.0200.0200.0000.0000.0000.000
174A175VAL0-0.046-0.01821.546-0.025-0.0250.0000.0000.0000.000
175A176HIS00.0060.00723.4450.0350.0350.0000.0000.0000.000
176A177THR00.0140.00922.080-0.038-0.0380.0000.0000.0000.000
177A178PHE0-0.018-0.00124.5130.0250.0250.0000.0000.0000.000
178A179PRO00.0210.00325.797-0.012-0.0120.0000.0000.0000.000
179A180ALA0-0.0040.00326.711-0.012-0.0120.0000.0000.0000.000
180A181VAL0-0.021-0.00828.5450.0080.0080.0000.0000.0000.000
181A182LEU0-0.010-0.00232.090-0.011-0.0110.0000.0000.0000.000
182A183GLN0-0.015-0.01533.8140.0090.0090.0000.0000.0000.000
183A184SER00.0730.02936.970-0.002-0.0020.0000.0000.0000.000
184A185SER0-0.030-0.01638.0960.0000.0000.0000.0000.0000.000
185A186GLY00.0220.01936.894-0.006-0.0060.0000.0000.0000.000
186A187LEU0-0.087-0.03333.839-0.006-0.0060.0000.0000.0000.000
187A188TYR00.0170.00129.5430.0030.0030.0000.0000.0000.000
188A189SER0-0.015-0.02631.422-0.015-0.0150.0000.0000.0000.000
189A190LEU0-0.0100.01924.9410.0090.0090.0000.0000.0000.000
190A191SER00.0160.00829.571-0.017-0.0170.0000.0000.0000.000
191A192SER0-0.017-0.01524.1650.0130.0130.0000.0000.0000.000
192A193VAL00.0430.00626.879-0.021-0.0210.0000.0000.0000.000
193A194VAL00.0100.01425.5850.0180.0180.0000.0000.0000.000
194A195THR0-0.018-0.01427.694-0.011-0.0110.0000.0000.0000.000
195A196VAL0-0.026-0.01328.2980.0120.0120.0000.0000.0000.000
196A197PRO00.0680.02230.298-0.001-0.0010.0000.0000.0000.000
197A198SER00.0250.01033.495-0.006-0.0060.0000.0000.0000.000
198A199SER0-0.058-0.02736.673-0.006-0.0060.0000.0000.0000.000
199A200SER00.0570.02533.048-0.001-0.0010.0000.0000.0000.000
200A201LEU0-0.037-0.02134.245-0.005-0.0050.0000.0000.0000.000
201A202GLY00.011-0.00434.801-0.005-0.0050.0000.0000.0000.000
202A203THR0-0.0120.00434.104-0.005-0.0050.0000.0000.0000.000
203A204GLN0-0.0300.00128.810-0.010-0.0100.0000.0000.0000.000
204A205THR0-0.0030.00928.999-0.006-0.0060.0000.0000.0000.000
205A206TYR00.0270.00027.3980.0090.0090.0000.0000.0000.000
206A207ILE00.004-0.00225.447-0.001-0.0010.0000.0000.0000.000
207A209ASN00.0560.02420.8370.0060.0060.0000.0000.0000.000
208A210VAL0-0.019-0.00621.8860.0190.0190.0000.0000.0000.000
209A211ASN0-0.020-0.01718.161-0.053-0.0530.0000.0000.0000.000
210A212HIS00.0360.04221.6970.0120.0120.0000.0000.0000.000
211A213LYS10.9840.97116.7120.3150.3150.0000.0000.0000.000
212A214PRO00.0050.01721.601-0.023-0.0230.0000.0000.0000.000
213A215SER0-0.010-0.03024.582-0.011-0.0110.0000.0000.0000.000
214A216ASN0-0.067-0.03823.976-0.027-0.0270.0000.0000.0000.000
215A217THR00.0070.02125.018-0.011-0.0110.0000.0000.0000.000
216A218LYS10.9430.95918.9950.2790.2790.0000.0000.0000.000
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219A221LYS10.8290.90726.8080.0410.0410.0000.0000.0000.000
220A222LYS10.8770.92829.1240.0390.0390.0000.0000.0000.000
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