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: 37Q7L

Calculation Name: 3AEV-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3AEV

Chain ID: B

ChEMBL ID:

UniProt ID: O58655

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptH
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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1917756.293448
FMO2-HF: Nuclear repulsion 1846245.079698
FMO2-HF: Total energy -71511.21375
FMO2-MP2: Total energy -71725.505066


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(B:26:ASP)


Summations of interaction energy for fragment #1(B:26:ASP)
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.
-19.738-12.0253.057-4.936-5.8330.023
Interaction energy analysis for fragmet #1(B:26:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.929 / q_NPA : -0.983
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].
3B28TRP0-0.041-0.0353.401-8.215-5.7810.058-1.171-1.3200.008
4B29GLU-1-0.957-0.9852.19248.15051.3622.896-2.948-3.1610.008
5B30GLU-1-0.908-0.9493.11547.95649.9040.104-0.810-1.2420.007
6B31PHE0-0.057-0.0105.399-8.246-8.127-0.001-0.007-0.1100.000
7B32PHE0-0.088-0.0627.321-4.191-4.1910.0000.0000.0000.000
8B33LYS10.8340.9506.459-41.108-41.1080.0000.0000.0000.000
9B34GLN00.0530.0268.798-1.249-1.2490.0000.0000.0000.000
10B35GLU-1-0.969-1.0099.95629.52429.5240.0000.0000.0000.000
11B36GLU-1-0.886-0.94413.37415.40915.4090.0000.0000.0000.000
12B37TYR0-0.063-0.02616.9130.0030.0030.0000.0000.0000.000
13B38VAL0-0.024-0.01518.815-0.898-0.8980.0000.0000.0000.000
14B39LYS10.9870.99622.187-11.777-11.7770.0000.0000.0000.000
15B40ILE0-0.061-0.01924.995-0.573-0.5730.0000.0000.0000.000
16B41PRO0-0.054-0.04927.697-0.036-0.0360.0000.0000.0000.000
17B42LYN00.1680.08030.4180.0290.0290.0000.0000.0000.000
18B43ASP-1-0.928-0.95831.4858.9958.9950.0000.0000.0000.000
19B44ARG10.8200.90630.703-9.524-9.5240.0000.0000.0000.000
20B45ILE00.0450.03726.5820.1630.1630.0000.0000.0000.000
21B46ALA00.002-0.00428.2940.1970.1970.0000.0000.0000.000
22B47VAL0-0.072-0.03830.0430.0270.0270.0000.0000.0000.000
23B48LEU00.0250.01823.550-0.040-0.0400.0000.0000.0000.000
24B49ILE00.0350.03124.7730.2760.2760.0000.0000.0000.000
25B50GLY00.0460.02526.3110.0540.0540.0000.0000.0000.000
26B51LYS10.9820.96628.710-8.473-8.4730.0000.0000.0000.000
27B52LYS10.9320.95228.333-9.837-9.8370.0000.0000.0000.000
28B53GLY00.0460.03024.7410.3080.3080.0000.0000.0000.000
29B54GLN0-0.050-0.02924.5950.2710.2710.0000.0000.0000.000
30B55THR00.0160.02126.106-0.040-0.0400.0000.0000.0000.000
31B56LYS10.8970.95218.009-15.728-15.7280.0000.0000.0000.000
32B57LYS10.9510.96821.060-12.674-12.6740.0000.0000.0000.000
33B58GLU-1-0.882-0.94122.05411.05211.0520.0000.0000.0000.000
34B59ILE00.0110.01521.3100.0220.0220.0000.0000.0000.000
35B60GLU-1-0.851-0.90617.40316.44816.4480.0000.0000.0000.000
36B61LYS10.9380.96419.018-11.405-11.4050.0000.0000.0000.000
37B62ARG10.8650.91720.970-10.517-10.5170.0000.0000.0000.000
38B63THR0-0.032-0.00719.8130.0680.0680.0000.0000.0000.000
39B64LYS10.9841.01016.103-13.998-13.9980.0000.0000.0000.000
40B65THR0-0.0150.01014.7501.0361.0360.0000.0000.0000.000
41B66LYS10.9430.98510.895-24.382-24.3820.0000.0000.0000.000
42B67ILE00.009-0.01414.5270.2400.2400.0000.0000.0000.000
43B68THR0-0.046-0.02914.799-0.118-0.1180.0000.0000.0000.000
44B69ILE0-0.011-0.01617.403-0.209-0.2090.0000.0000.0000.000
45B70ASP-1-0.832-0.90620.87014.27714.2770.0000.0000.0000.000
46B71SER0-0.074-0.06622.305-0.364-0.3640.0000.0000.0000.000
47B72GLU-1-0.905-0.92425.43110.53610.5360.0000.0000.0000.000
48B73THR0-0.020-0.01023.200-0.536-0.5360.0000.0000.0000.000
49B74GLY0-0.024-0.01225.566-0.324-0.3240.0000.0000.0000.000
50B75GLU-1-0.941-0.96520.63814.71814.7180.0000.0000.0000.000
51B76VAL0-0.041-0.03419.7790.0370.0370.0000.0000.0000.000
52B77TRP00.0510.02414.751-0.058-0.0580.0000.0000.0000.000
53B78ILE0-0.058-0.02316.189-0.305-0.3050.0000.0000.0000.000
54B79THR00.0330.01110.8810.5270.5270.0000.0000.0000.000
55B80SER00.0290.03110.467-1.311-1.3110.0000.0000.0000.000
56B81THR0-0.066-0.0549.4581.3101.3100.0000.0000.0000.000
57B82LYS11.0341.0068.379-23.428-23.4280.0000.0000.0000.000
58B83GLU-1-0.952-0.9749.84617.14517.1450.0000.0000.0000.000
59B84THR0-0.101-0.05912.959-0.685-0.6850.0000.0000.0000.000
60B85GLU-1-0.910-0.94114.90314.37614.3760.0000.0000.0000.000
61B86ASP-1-0.851-0.92617.98812.84412.8440.0000.0000.0000.000
62B87PRO00.0320.00417.7480.6050.6050.0000.0000.0000.000
63B88LEU00.0370.00318.3570.4620.4620.0000.0000.0000.000
64B89ALA0-0.018-0.00418.282-0.285-0.2850.0000.0000.0000.000
65B90VAL00.0200.01814.661-0.366-0.3660.0000.0000.0000.000
66B91TRP00.0250.00816.597-0.622-0.6220.0000.0000.0000.000
67B92LYS10.9360.97021.112-12.631-12.6310.0000.0000.0000.000
68B93ALA0-0.014-0.00419.758-0.515-0.5150.0000.0000.0000.000
69B94ARG10.9120.95620.366-13.863-13.8630.0000.0000.0000.000
70B95ASP-1-0.830-0.91322.00811.67711.6770.0000.0000.0000.000
71B96ILE0-0.021-0.01224.846-0.546-0.5460.0000.0000.0000.000
72B97VAL0-0.0080.00221.881-0.475-0.4750.0000.0000.0000.000
73B98LEU00.0300.01125.273-0.479-0.4790.0000.0000.0000.000
74B99ALA0-0.001-0.00327.524-0.494-0.4940.0000.0000.0000.000
75B100ILE0-0.038-0.01227.169-0.441-0.4410.0000.0000.0000.000
76B101GLY00.0310.02229.031-0.319-0.3190.0000.0000.0000.000
77B102ARG10.8300.90130.157-9.760-9.7600.0000.0000.0000.000
78B103GLY0-0.0090.00633.215-0.340-0.3400.0000.0000.0000.000
79B104PHE0-0.026-0.00632.900-0.294-0.2940.0000.0000.0000.000
80B105SER0-0.016-0.01333.2590.2280.2280.0000.0000.0000.000
81B106PRO00.0900.02629.602-0.016-0.0160.0000.0000.0000.000
82B107GLU-1-0.935-0.95531.1458.4458.4450.0000.0000.0000.000
83B108ARG10.8210.87733.363-8.087-8.0870.0000.0000.0000.000
84B109ALA00.014-0.00129.707-0.012-0.0120.0000.0000.0000.000
85B110PHE00.003-0.00526.0840.2290.2290.0000.0000.0000.000
86B111ARG10.7870.88630.142-8.375-8.3750.0000.0000.0000.000
87B112LEU0-0.054-0.03128.237-0.072-0.0720.0000.0000.0000.000
88B113LEU0-0.049-0.01324.8570.3170.3170.0000.0000.0000.000
89B114ASN0-0.037-0.00528.1220.2150.2150.0000.0000.0000.000
90B115GLU-1-0.903-0.94929.70410.47310.4730.0000.0000.0000.000
91B116GLY0-0.019-0.00130.595-0.314-0.3140.0000.0000.0000.000
92B117GLU-1-0.913-0.95931.2608.3258.3250.0000.0000.0000.000
93B118TYR00.0220.01029.1180.2040.2040.0000.0000.0000.000
94B119LEU00.006-0.01128.899-0.356-0.3560.0000.0000.0000.000
95B120GLU-1-0.894-0.94131.3719.0879.0870.0000.0000.0000.000
96B121ILE0-0.040-0.03330.426-0.226-0.2260.0000.0000.0000.000
97B122ILE00.0370.03434.394-0.035-0.0350.0000.0000.0000.000
98B123ASN00.025-0.01735.261-0.171-0.1710.0000.0000.0000.000
99B124LEU00.0050.00538.624-0.192-0.1920.0000.0000.0000.000
100B125THR0-0.051-0.03940.147-0.171-0.1710.0000.0000.0000.000
101B126ASP-1-0.884-0.92438.7458.1318.1310.0000.0000.0000.000
102B127ILE0-0.077-0.03342.291-0.137-0.1370.0000.0000.0000.000
103B128ILE0-0.067-0.04145.270-0.138-0.1380.0000.0000.0000.000
104B129ILE00.0800.04446.648-0.128-0.1280.0000.0000.0000.000
105B130GLY0-0.044-0.02048.778-0.104-0.1040.0000.0000.0000.000
106B131ASN00.0130.00150.243-0.162-0.1620.0000.0000.0000.000
107B132GLU-1-0.775-0.85853.0395.6065.6060.0000.0000.0000.000
108B133LYS10.9110.94352.543-5.429-5.4290.0000.0000.0000.000
109B134ASN00.020-0.01350.8770.0270.0270.0000.0000.0000.000
110B135ALA00.0330.01550.1340.0180.0180.0000.0000.0000.000
111B136LEU00.0610.03342.8560.0190.0190.0000.0000.0000.000
112B137PRO0-0.034-0.02747.2560.0300.0300.0000.0000.0000.000
113B138ARG10.8920.94848.244-5.945-5.9450.0000.0000.0000.000
114B139VAL00.0370.01946.514-0.056-0.0560.0000.0000.0000.000
115B140ARG10.9550.98742.901-7.304-7.3040.0000.0000.0000.000
116B141GLY00.0090.01146.7040.0220.0220.0000.0000.0000.000
117B142ARG10.8090.90549.844-6.147-6.1470.0000.0000.0000.000
118B143ILE00.0400.02344.587-0.059-0.0590.0000.0000.0000.000
119B144ILE0-0.0050.00345.248-0.007-0.0070.0000.0000.0000.000
120B145GLY00.0550.04147.868-0.049-0.0490.0000.0000.0000.000
121B146ARG10.9870.97951.369-5.646-5.6460.0000.0000.0000.000
122B147LYS10.9280.95251.803-5.684-5.6840.0000.0000.0000.000
123B148GLY00.0340.01748.7550.0400.0400.0000.0000.0000.000
124B149ARG10.9050.94349.020-5.796-5.7960.0000.0000.0000.000
125B150THR0-0.026-0.00949.287-0.033-0.0330.0000.0000.0000.000
126B151ARG10.9290.97542.507-7.299-7.2990.0000.0000.0000.000
127B152GLN00.0950.07146.138-0.047-0.0470.0000.0000.0000.000
128B153ILE0-0.029-0.01447.7340.0150.0150.0000.0000.0000.000
129B154ILE00.001-0.01044.7420.0100.0100.0000.0000.0000.000
130B155GLU-1-0.786-0.87541.7567.5947.5940.0000.0000.0000.000
131B156GLU-1-0.939-0.97444.7356.5116.5110.0000.0000.0000.000
132B157MET0-0.087-0.03747.330-0.080-0.0800.0000.0000.0000.000
133B158SER0-0.049-0.01643.7080.0560.0560.0000.0000.0000.000
134B159GLY00.0480.02843.2200.0760.0760.0000.0000.0000.000
135B160ALA0-0.0090.01739.3760.1930.1930.0000.0000.0000.000
136B161SER0-0.028-0.01337.087-0.231-0.2310.0000.0000.0000.000
137B162VAL00.006-0.01538.4230.1400.1400.0000.0000.0000.000
138B163SER0-0.079-0.02836.692-0.198-0.1980.0000.0000.0000.000
139B164VAL0-0.001-0.00838.7500.0300.0300.0000.0000.0000.000
140B165TYR00.0070.00534.950-0.163-0.1630.0000.0000.0000.000
141B166GLY00.0230.01338.3190.1370.1370.0000.0000.0000.000
142B167LYS10.9560.95237.499-8.479-8.4790.0000.0000.0000.000
143B168THR00.0470.04935.0100.0630.0630.0000.0000.0000.000
144B169VAL0-0.052-0.02238.173-0.130-0.1300.0000.0000.0000.000
145B170ALA00.0020.00634.3480.0920.0920.0000.0000.0000.000
146B171ILE00.004-0.00635.917-0.217-0.2170.0000.0000.0000.000
147B172ILE00.0300.01332.1940.2400.2400.0000.0000.0000.000
148B173GLY00.0290.01034.847-0.319-0.3190.0000.0000.0000.000
149B174ASN00.1370.08535.0750.1460.1460.0000.0000.0000.000
150B175PRO00.0640.01735.332-0.169-0.1690.0000.0000.0000.000
151B176ILE00.0160.01437.736-0.160-0.1600.0000.0000.0000.000
152B177GLN00.0260.00939.1690.0390.0390.0000.0000.0000.000
153B178ILE0-0.020-0.01535.097-0.159-0.1590.0000.0000.0000.000
154B179GLU-1-0.904-0.95239.4857.0747.0740.0000.0000.0000.000
155B180ILE00.0000.01441.997-0.200-0.2000.0000.0000.0000.000
156B181ALA00.005-0.00941.692-0.141-0.1410.0000.0000.0000.000
157B182LYS10.9420.97939.212-8.137-8.1370.0000.0000.0000.000
158B183THR00.0310.02742.592-0.142-0.1420.0000.0000.0000.000
159B184ALA0-0.043-0.02846.015-0.153-0.1530.0000.0000.0000.000
160B185ILE0-0.013-0.01942.182-0.135-0.1350.0000.0000.0000.000
161B186GLU-1-0.882-0.94943.3617.2037.2030.0000.0000.0000.000
162B187LYS10.8850.94646.508-6.262-6.2620.0000.0000.0000.000
163B188LEU0-0.063-0.03248.522-0.151-0.1510.0000.0000.0000.000
164B189ALA0-0.015-0.01146.678-0.101-0.1010.0000.0000.0000.000
165B190ARG10.9670.97848.697-6.444-6.4440.0000.0000.0000.000
166B191GLY00.0170.02351.079-0.114-0.1140.0000.0000.0000.000
167B192SER0-0.031-0.00153.432-0.144-0.1440.0000.0000.0000.000
168B193PRO00.0340.01454.9080.0730.0730.0000.0000.0000.000
169B194HIS00.028-0.00652.566-0.067-0.0670.0000.0000.0000.000
170B195GLY00.0190.02255.7010.0320.0320.0000.0000.0000.000
171B196SER0-0.065-0.03056.6820.0280.0280.0000.0000.0000.000
172B197VAL00.0600.03350.7230.0380.0380.0000.0000.0000.000
173B198TYR00.0490.01952.3930.0970.0970.0000.0000.0000.000
174B199ARG11.0241.00854.575-5.315-5.3150.0000.0000.0000.000
175B200TYR0-0.037-0.01648.207-0.038-0.0380.0000.0000.0000.000
176B201LEU00.0380.00148.2780.0380.0380.0000.0000.0000.000
177B202GLU-1-0.953-0.98151.6815.6925.6920.0000.0000.0000.000
178B203ARG10.8720.93954.148-5.800-5.8000.0000.0000.0000.000
179B204ARG10.9480.97246.334-6.639-6.6390.0000.0000.0000.000
180B205LYS11.0471.03750.345-5.987-5.9870.0000.0000.0000.000
181B206LYS10.8720.93151.315-5.354-5.3540.0000.0000.0000.000
182B207ASP-1-0.947-0.95551.3645.8855.8850.0000.0000.0000.000
183B208LEU0-0.021-0.00547.5680.1070.1070.0000.0000.0000.000