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: RY8M8

Calculation Name: 2AHE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AHE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y696

Base Structure: X-ray

Registration Date: 2023-09-27

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2814571.8689
FMO2-HF: Nuclear repulsion 2723992.03464
FMO2-HF: Total energy -90579.83426
FMO2-MP2: Total energy -90844.426835


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:16:GLU)


Summations of interaction energy for fragment #1(A:16:GLU)
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.
-142.917-150.55447.592-20.884-19.0730.24
Interaction energy analysis for fragmet #1(A:16:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.751 / q_NPA : -0.853
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].
3A18LEU00.0340.0183.4572.6275.1030.043-1.292-1.2270.004
4A19ILE0-0.007-0.0135.308-2.928-2.9280.0000.0000.0000.000
5A20GLU-1-0.836-0.8787.71420.33620.3360.0000.0000.0000.000
6A21LEU0-0.036-0.01411.210-1.051-1.0510.0000.0000.0000.000
7A22PHE00.0010.00913.538-0.746-0.7460.0000.0000.0000.000
8A23VAL00.015-0.01617.052-0.411-0.4110.0000.0000.0000.000
9A24LYS10.9040.94619.723-11.889-11.8890.0000.0000.0000.000
10A25ALA00.0350.02923.2180.2740.2740.0000.0000.0000.000
11A26GLY0-0.003-0.01424.829-0.347-0.3470.0000.0000.0000.000
12A27SER0-0.142-0.10427.365-0.250-0.2500.0000.0000.0000.000
13A28ASP-1-0.800-0.87227.94511.03311.0330.0000.0000.0000.000
14A29GLY0-0.076-0.03928.355-0.078-0.0780.0000.0000.0000.000
15A30GLU-1-0.916-0.95524.95712.10712.1070.0000.0000.0000.000
16A31SER0-0.071-0.05423.3250.7590.7590.0000.0000.0000.000
17A32ILE00.0430.01318.0930.0550.0550.0000.0000.0000.000
18A33GLY00.0280.01722.501-0.474-0.4740.0000.0000.0000.000
19A34ASN0-0.039-0.02624.1450.6300.6300.0000.0000.0000.000
20A35CYS0-0.025-0.00823.152-0.174-0.1740.0000.0000.0000.000
21A36PRO00.0330.02622.7540.5740.5740.0000.0000.0000.000
22A37PHE00.002-0.01221.5380.4430.4430.0000.0000.0000.000
23A38SER00.0880.00418.8640.7120.7120.0000.0000.0000.000
24A39GLN0-0.028-0.02017.5270.3520.3520.0000.0000.0000.000
25A40ARG10.8620.91517.375-14.546-14.5460.0000.0000.0000.000
26A41LEU0-0.004-0.00914.6010.9420.9420.0000.0000.0000.000
27A42PHE00.0480.02312.8431.6691.6690.0000.0000.0000.000
28A43MET0-0.034-0.01412.6341.2831.2830.0000.0000.0000.000
29A44ILE0-0.0040.00311.7871.2421.2420.0000.0000.0000.000
30A45LEU00.0020.0038.1152.0352.0350.0000.0000.0000.000
31A46TRP00.0140.0048.1463.9613.9610.0000.0000.0000.000
32A47LEU0-0.039-0.0339.5451.8511.8510.0000.0000.0000.000
33A48LYS10.7030.8336.956-30.719-30.7190.0000.0000.0000.000
34A49GLY0-0.0090.0096.3774.6224.6220.0000.0000.0000.000
35A50VAL0-0.069-0.0122.5074.6727.3853.462-2.536-3.6390.029
36A51VAL00.000-0.0141.896-26.212-28.0277.498-2.040-3.6420.037
37A52PHE0-0.045-0.0254.000-3.701-3.4790.002-0.077-0.1480.001
38A53SER00.0240.0237.384-0.934-0.9340.0000.0000.0000.000
39A54VAL0-0.020-0.02710.909-0.017-0.0170.0000.0000.0000.000
40A55THR00.002-0.01214.180-0.848-0.8480.0000.0000.0000.000
41A56THR0-0.055-0.02917.4490.0710.0710.0000.0000.0000.000
42A57VAL00.0080.00020.734-0.364-0.3640.0000.0000.0000.000
43A58ASP-1-0.775-0.87823.36510.18910.1890.0000.0000.0000.000
44A59LEU0-0.032-0.03725.512-0.207-0.2070.0000.0000.0000.000
45A60LYS10.8540.92128.723-10.332-10.3320.0000.0000.0000.000
46A61ARG10.8850.94229.720-10.363-10.3630.0000.0000.0000.000
47A62LYS10.8830.97224.300-11.774-11.7740.0000.0000.0000.000
48A63PRO00.0480.03124.256-0.362-0.3620.0000.0000.0000.000
49A64ALA00.018-0.00126.0660.1980.1980.0000.0000.0000.000
50A65ASP-1-0.872-0.94422.24412.47312.4730.0000.0000.0000.000
51A66LEU00.0600.02319.8810.2980.2980.0000.0000.0000.000
52A67GLN0-0.013-0.00122.8790.4350.4350.0000.0000.0000.000
53A68ASN0-0.025-0.02224.531-0.307-0.3070.0000.0000.0000.000
54A69LEU0-0.0080.01717.0840.0110.0110.0000.0000.0000.000
55A70ALA0-0.003-0.00420.2420.2910.2910.0000.0000.0000.000
56A71PRO00.0050.00822.303-0.257-0.2570.0000.0000.0000.000
57A72GLY0-0.040-0.03226.083-0.048-0.0480.0000.0000.0000.000
58A73THR0-0.0160.00121.408-0.253-0.2530.0000.0000.0000.000
59A74HIS0-0.042-0.02624.159-0.180-0.1800.0000.0000.0000.000
60A75PRO0-0.0090.03321.0170.3580.3580.0000.0000.0000.000
61A76PRO0-0.089-0.05818.057-0.660-0.6600.0000.0000.0000.000
62A77PHE0-0.026-0.02517.007-0.456-0.4560.0000.0000.0000.000
63A78ILE00.0290.01110.6010.5000.5000.0000.0000.0000.000
64A79THR00.0060.00712.433-0.903-0.9030.0000.0000.0000.000
65A80PHE00.0410.0086.8561.9001.9000.0000.0000.0000.000
66A81ASN00.002-0.0146.683-0.275-0.2750.0000.0000.0000.000
67A82SER0-0.002-0.0079.541-0.998-0.9980.0000.0000.0000.000
68A83GLU-1-0.835-0.87912.71716.48316.4830.0000.0000.0000.000
69A84VAL00.0080.00313.7911.1441.1440.0000.0000.0000.000
70A85LYS10.8050.90512.891-19.379-19.3790.0000.0000.0000.000
71A86THR00.0420.00016.3630.1190.1190.0000.0000.0000.000
72A87ASP-1-0.856-0.92919.18513.77313.7730.0000.0000.0000.000
73A88VAL00.0260.00318.6810.6080.6080.0000.0000.0000.000
74A89ASN00.009-0.00818.4660.8860.8860.0000.0000.0000.000
75A90LYS10.8120.90018.973-13.826-13.8260.0000.0000.0000.000
76A91ILE0-0.0060.00813.5190.7710.7710.0000.0000.0000.000
77A92GLU-1-0.827-0.91414.09518.56318.5630.0000.0000.0000.000
78A93GLU-1-0.845-0.90314.97316.10716.1070.0000.0000.0000.000
79A94PHE00.0290.01910.4420.8430.8430.0000.0000.0000.000
80A95LEU00.0160.0028.8831.6741.6740.0000.0000.0000.000
81A96GLU-1-0.746-0.84010.68825.76525.7650.0000.0000.0000.000
82A97GLU-1-0.978-0.97812.56920.07220.0720.0000.0000.0000.000
83A98VAL0-0.017-0.0117.6350.6610.6610.0000.0000.0000.000
84A99LEU0-0.0300.0025.2692.9372.9370.0000.0000.0000.000
85A100CYS0-0.025-0.0078.112-1.325-1.3250.0000.0000.0000.000
86A101PRO00.0040.0169.2642.4922.4920.0000.0000.0000.000
87A102PRO0-0.022-0.03411.152-0.932-0.9320.0000.0000.0000.000
88A103LYS10.8150.9041.759-125.889-129.85016.756-7.595-5.2010.091
89A104TYR00.000-0.0171.634-23.397-30.66919.831-7.344-5.2160.078
90A105LEU00.0230.0137.746-4.484-4.4840.0000.0000.0000.000
91A106LYS10.9740.99311.085-16.638-16.6380.0000.0000.0000.000
92A107LEU0-0.008-0.01211.855-1.045-1.0450.0000.0000.0000.000
93A108SER0-0.075-0.07315.144-1.511-1.5110.0000.0000.0000.000
94A109PRO0-0.069-0.02718.303-0.002-0.0020.0000.0000.0000.000
95A110LYS10.8450.91920.584-15.439-15.4390.0000.0000.0000.000
96A111HIS0-0.014-0.01723.526-0.832-0.8320.0000.0000.0000.000
97A112PRO00.0100.00126.2320.2560.2560.0000.0000.0000.000
98A113GLU-1-0.847-0.93427.48310.28310.2830.0000.0000.0000.000
99A114SER0-0.062-0.05025.075-0.288-0.2880.0000.0000.0000.000
100A115ASN0-0.032-0.01623.2960.7230.7230.0000.0000.0000.000
101A116THR0-0.0120.00125.9910.0270.0270.0000.0000.0000.000
102A117ALA00.0420.03028.864-0.372-0.3720.0000.0000.0000.000
103A118GLY00.014-0.00729.1290.3410.3410.0000.0000.0000.000
104A119MET0-0.026-0.00726.2260.0400.0400.0000.0000.0000.000
105A120ASP-1-0.855-0.91930.7069.1919.1910.0000.0000.0000.000
106A121ILE00.0040.00731.977-0.299-0.2990.0000.0000.0000.000
107A122PHE00.0290.01530.090-0.256-0.2560.0000.0000.0000.000
108A123ALA00.0390.02433.038-0.220-0.2200.0000.0000.0000.000
109A124LYS10.9270.97035.885-8.248-8.2480.0000.0000.0000.000
110A125PHE00.0570.03233.028-0.254-0.2540.0000.0000.0000.000
111A126SER0-0.007-0.01034.868-0.127-0.1270.0000.0000.0000.000
112A127ALA0-0.029-0.02037.193-0.184-0.1840.0000.0000.0000.000
113A128TYR0-0.062-0.06239.811-0.146-0.1460.0000.0000.0000.000
114A129ILE00.0060.00737.189-0.202-0.2020.0000.0000.0000.000
115A130LYS10.9530.97638.167-8.356-8.3560.0000.0000.0000.000
116A131ASN0-0.034-0.01541.863-0.248-0.2480.0000.0000.0000.000
117A132SER00.0250.00445.3290.0210.0210.0000.0000.0000.000
118A133ARG10.8520.89948.092-6.113-6.1130.0000.0000.0000.000
119A134PRO00.0520.01950.3300.1070.1070.0000.0000.0000.000
120A135GLU-1-0.803-0.87651.8396.0076.0070.0000.0000.0000.000
121A136ALA00.0010.00749.141-0.004-0.0040.0000.0000.0000.000
122A137ASN00.001-0.00246.4380.2160.2160.0000.0000.0000.000
123A138GLU-1-0.821-0.91846.9826.7356.7350.0000.0000.0000.000
124A139ALA00.0300.01747.8130.0940.0940.0000.0000.0000.000
125A140LEU0-0.052-0.03143.7070.1580.1580.0000.0000.0000.000
126A141GLU-1-0.828-0.88643.1457.4077.4070.0000.0000.0000.000
127A142ARG10.8970.94643.192-6.782-6.7820.0000.0000.0000.000
128A143GLY0-0.043-0.01543.1340.0950.0950.0000.0000.0000.000
129A144LEU00.0110.00336.6470.1910.1910.0000.0000.0000.000
130A145LEU00.0410.01739.0610.2090.2090.0000.0000.0000.000
131A146LYS10.9780.99540.449-7.264-7.2640.0000.0000.0000.000
132A147THR0-0.082-0.04436.4070.1040.1040.0000.0000.0000.000
133A148LEU00.0160.00034.5430.2330.2330.0000.0000.0000.000
134A149GLN0-0.044-0.03936.4510.0770.0770.0000.0000.0000.000
135A150LYS10.9040.95536.593-8.660-8.6600.0000.0000.0000.000
136A151LEU0-0.0160.00230.0560.1420.1420.0000.0000.0000.000
137A152ASP-1-0.806-0.90733.4679.2759.2750.0000.0000.0000.000
138A153GLU-1-0.827-0.91735.5078.2688.2680.0000.0000.0000.000
139A154TYR0-0.023-0.00728.028-0.097-0.0970.0000.0000.0000.000
140A155LEU0-0.014-0.00128.6920.1940.1940.0000.0000.0000.000
141A156ASN00.0070.00732.1800.3500.3500.0000.0000.0000.000
142A157SER0-0.034-0.01434.861-0.329-0.3290.0000.0000.0000.000
143A158PRO0-0.062-0.03333.4340.3740.3740.0000.0000.0000.000
144A159LEU0-0.0050.01827.358-0.230-0.2300.0000.0000.0000.000
145A174SER0-0.016-0.01231.6580.1270.1270.0000.0000.0000.000
146A175THR0-0.002-0.00532.305-0.046-0.0460.0000.0000.0000.000
147A176ARG10.7730.91027.245-10.984-10.9840.0000.0000.0000.000
148A177LYS10.9680.98623.364-14.105-14.1050.0000.0000.0000.000
149A178PHE0-0.005-0.01821.4500.0710.0710.0000.0000.0000.000
150A179LEU00.0180.00924.315-0.509-0.5090.0000.0000.0000.000
151A180ASP-1-0.699-0.83422.52113.49213.4920.0000.0000.0000.000
152A181GLY00.0170.00324.270-0.123-0.1230.0000.0000.0000.000
153A182ASN0-0.011-0.01223.376-0.333-0.3330.0000.0000.0000.000
154A183GLU-1-0.851-0.92217.79015.98715.9870.0000.0000.0000.000
155A184MET0-0.061-0.01017.252-0.531-0.5310.0000.0000.0000.000
156A185THR00.017-0.00617.0810.7710.7710.0000.0000.0000.000
157A186LEU00.0570.01215.124-0.186-0.1860.0000.0000.0000.000
158A187ALA00.0210.01318.380-0.480-0.4800.0000.0000.0000.000
159A188ASP-1-0.765-0.86420.24714.31714.3170.0000.0000.0000.000
160A189CYS00.0150.01816.9260.0450.0450.0000.0000.0000.000
161A190ASN0-0.0090.00019.351-0.900-0.9000.0000.0000.0000.000
162A191LEU0-0.006-0.00722.234-0.515-0.5150.0000.0000.0000.000
163A192LEU00.0200.02121.649-0.558-0.5580.0000.0000.0000.000
164A193PRO00.0560.03021.275-0.646-0.6460.0000.0000.0000.000
165A194LYS10.8140.91524.111-12.954-12.9540.0000.0000.0000.000
166A195LEU00.002-0.00927.375-0.520-0.5200.0000.0000.0000.000
167A196HIS00.1110.07426.068-0.598-0.5980.0000.0000.0000.000
168A197ILE00.0020.00426.595-0.469-0.4690.0000.0000.0000.000
169A198VAL0-0.047-0.02229.891-0.431-0.4310.0000.0000.0000.000
170A199LYS10.8850.95230.190-10.884-10.8840.0000.0000.0000.000
171A200VAL00.0000.00430.392-0.357-0.3570.0000.0000.0000.000
172A201VAL0-0.027-0.00932.757-0.373-0.3730.0000.0000.0000.000
173A202ALA00.009-0.00735.271-0.329-0.3290.0000.0000.0000.000
174A203LYS10.8570.93236.901-8.232-8.2320.0000.0000.0000.000
175A204LYS10.8170.89837.210-8.720-8.7200.0000.0000.0000.000
176A205TYR0-0.114-0.09436.818-0.387-0.3870.0000.0000.0000.000
177A206ARG10.7620.88341.053-7.653-7.6530.0000.0000.0000.000
178A207ASN0-0.0170.01042.225-0.015-0.0150.0000.0000.0000.000
179A208PHE00.0090.01438.083-0.082-0.0820.0000.0000.0000.000
180A209ASP-1-0.843-0.90838.9118.2488.2480.0000.0000.0000.000
181A210ILE00.0170.00133.854-0.116-0.1160.0000.0000.0000.000
182A211PRO00.021-0.00238.0690.0290.0290.0000.0000.0000.000
183A212LYS10.9751.00439.148-7.154-7.1540.0000.0000.0000.000
184A213GLU-1-0.886-0.97139.8047.6547.6540.0000.0000.0000.000
185A214MET0-0.073-0.00737.2650.0500.0500.0000.0000.0000.000
186A215THR00.0510.00736.5560.3220.3220.0000.0000.0000.000
187A216GLY00.0310.02334.0640.2440.2440.0000.0000.0000.000
188A217ILE0-0.020-0.03332.0480.4330.4330.0000.0000.0000.000
189A218TRP0-0.041-0.01631.4330.5160.5160.0000.0000.0000.000
190A219ARG10.8060.92230.339-10.317-10.3170.0000.0000.0000.000
191A220TYR0-0.018-0.03024.2530.2840.2840.0000.0000.0000.000
192A221LEU00.012-0.00326.9860.5070.5070.0000.0000.0000.000
193A222THR0-0.048-0.02827.4390.2570.2570.0000.0000.0000.000
194A223ASN0-0.031-0.02425.3100.1150.1150.0000.0000.0000.000
195A224ALA00.0320.02923.0650.5840.5840.0000.0000.0000.000
196A225TYR0-0.036-0.04422.9410.2770.2770.0000.0000.0000.000
197A226SER0-0.096-0.04524.334-0.102-0.1020.0000.0000.0000.000
198A227ARG10.7980.86616.294-18.321-18.3210.0000.0000.0000.000
199A228ASP-1-0.790-0.88016.90417.01417.0140.0000.0000.0000.000
200A229GLU-1-0.782-0.86014.16920.45120.4510.0000.0000.0000.000
201A230PHE0-0.020-0.00816.378-0.162-0.1620.0000.0000.0000.000
202A231THR00.0510.01719.754-0.278-0.2780.0000.0000.0000.000
203A232ASN0-0.078-0.04416.856-1.375-1.3750.0000.0000.0000.000
204A233THR0-0.034-0.02015.692-0.227-0.2270.0000.0000.0000.000
205A234CYS0-0.088-0.01218.634-0.440-0.4400.0000.0000.0000.000
206A235PRO00.0110.01322.444-0.154-0.1540.0000.0000.0000.000
207A236SER00.014-0.00124.732-0.397-0.3970.0000.0000.0000.000
208A237ASP-1-0.795-0.92827.71610.42910.4290.0000.0000.0000.000
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210A239GLU-1-0.775-0.84527.65110.44210.4420.0000.0000.0000.000
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