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: VQJR1

Calculation Name: 3A1Y-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A1Y

Chain ID: G

ChEMBL ID:

UniProt ID: O74109

Base Structure: X-ray

Registration Date: 2023-09-23

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1981417.389575
FMO2-HF: Nuclear repulsion 1898367.057004
FMO2-HF: Total energy -83050.33257
FMO2-MP2: Total energy -83293.615322


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(G:1:MET)


Summations of interaction energy for fragment #1(G:1: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.
-3.1530.391-0.03-1.776-1.737-0.002
Interaction energy analysis for fragmet #1(G:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.043
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].
3G3HIS0-0.0160.0083.409-2.2681.163-0.028-1.764-1.639-0.002
4G4VAL00.003-0.0205.1400.2800.2800.0000.0000.0000.000
5G5ALA0-0.0390.0126.669-0.052-0.0520.0000.0000.0000.000
6G6GLU-1-0.865-0.9355.026-1.774-1.816-0.001-0.0050.0480.000
7G7TRP0-0.031-0.0197.5570.1760.1760.0000.0000.0000.000
8G8LYS10.9890.9839.2330.4440.4440.0000.0000.0000.000
9G9LYS10.9200.94612.4140.2210.2210.0000.0000.0000.000
10G10LYS10.9310.9814.7660.3910.546-0.001-0.007-0.1460.000
11G11GLU-1-0.865-0.9307.064-0.764-0.7640.0000.0000.0000.000
12G12VAL0-0.011-0.0179.9860.0670.0670.0000.0000.0000.000
13G13GLU-1-0.896-0.90910.4590.0250.0250.0000.0000.0000.000
14G14GLU-1-0.854-0.9129.3770.1300.1300.0000.0000.0000.000
15G15LEU00.014-0.00112.1000.0270.0270.0000.0000.0000.000
16G16ALA00.044-0.01214.2980.0250.0250.0000.0000.0000.000
17G17LYS10.8440.89711.957-0.100-0.1000.0000.0000.0000.000
18G18LEU0-0.0240.01413.7460.0110.0110.0000.0000.0000.000
19G19ILE00.0580.02016.9670.0100.0100.0000.0000.0000.000
20G20LYS10.8490.93119.9950.0350.0350.0000.0000.0000.000
21G21SER0-0.064-0.03219.1690.0140.0140.0000.0000.0000.000
22G22TYR0-0.066-0.02618.5100.0090.0090.0000.0000.0000.000
23G23PRO00.0120.01923.242-0.007-0.0070.0000.0000.0000.000
24G24VAL00.0170.02325.515-0.005-0.0050.0000.0000.0000.000
25G25ILE0-0.054-0.03421.863-0.004-0.0040.0000.0000.0000.000
26G26ALA00.0220.01623.2960.0000.0000.0000.0000.0000.000
27G27LEU00.0010.00922.285-0.012-0.0120.0000.0000.0000.000
28G28VAL00.003-0.01120.8660.0100.0100.0000.0000.0000.000
29G29ASP-1-0.743-0.84022.084-0.086-0.0860.0000.0000.0000.000
30G30VAL0-0.056-0.05717.7460.0090.0090.0000.0000.0000.000
31G31SER0-0.099-0.06820.9790.0100.0100.0000.0000.0000.000
32G32SER00.0260.02322.3540.0070.0070.0000.0000.0000.000
33G33MET0-0.036-0.00520.5930.0100.0100.0000.0000.0000.000
34G34PRO00.0060.00520.141-0.004-0.0040.0000.0000.0000.000
35G35ALA00.0310.00315.3290.0010.0010.0000.0000.0000.000
36G36TYR00.001-0.00216.5080.0000.0000.0000.0000.0000.000
37G37PRO00.0590.01818.3590.0030.0030.0000.0000.0000.000
38G38LEU00.0750.05015.827-0.004-0.0040.0000.0000.0000.000
39G39SER0-0.063-0.03614.550-0.012-0.0120.0000.0000.0000.000
40G40GLN0-0.016-0.01516.3580.0160.0160.0000.0000.0000.000
41G41MET00.0900.05419.6830.0010.0010.0000.0000.0000.000
42G42ARG10.8620.93412.6490.1100.1100.0000.0000.0000.000
43G43ARG10.7830.87016.860-0.098-0.0980.0000.0000.0000.000
44G44LEU00.0690.04818.4160.0030.0030.0000.0000.0000.000
45G45ILE00.0060.00819.372-0.001-0.0010.0000.0000.0000.000
46G46ARG10.9050.94912.075-0.040-0.0400.0000.0000.0000.000
47G47GLU-1-0.886-0.91619.3020.0830.0830.0000.0000.0000.000
48G48ASN0-0.065-0.03422.401-0.001-0.0010.0000.0000.0000.000
49G49GLY00.0310.03122.871-0.006-0.0060.0000.0000.0000.000
50G50GLY00.0560.02120.730-0.004-0.0040.0000.0000.0000.000
51G51LEU0-0.085-0.05215.1060.0070.0070.0000.0000.0000.000
52G52LEU00.0400.03115.947-0.009-0.0090.0000.0000.0000.000
53G53ARG10.8020.88010.3900.0960.0960.0000.0000.0000.000
54G54VAL00.0560.03412.3070.0260.0260.0000.0000.0000.000
55G55SER00.010-0.00212.306-0.099-0.0990.0000.0000.0000.000
56G56ARG10.8960.94314.3560.2290.2290.0000.0000.0000.000
57G57ASN00.019-0.00317.3350.0030.0030.0000.0000.0000.000
58G58THR0-0.001-0.01313.3430.0270.0270.0000.0000.0000.000
59G59LEU00.0590.04116.2390.0060.0060.0000.0000.0000.000
60G60ILE00.0410.02917.6150.0180.0180.0000.0000.0000.000
61G61GLU-1-0.894-0.98016.148-0.202-0.2020.0000.0000.0000.000
62G62LEU00.1310.05620.4210.0110.0110.0000.0000.0000.000
63G63ALA00.0210.01422.2870.0130.0130.0000.0000.0000.000
64G64ILE0-0.036-0.02418.7570.0060.0060.0000.0000.0000.000
65G65LYN0-0.0460.02417.2990.0190.0190.0000.0000.0000.000
66G66LYS10.8880.96122.5190.0650.0650.0000.0000.0000.000
67G67ALA0-0.024-0.00925.1280.0060.0060.0000.0000.0000.000
68G68ALA0-0.070-0.03922.8460.0060.0060.0000.0000.0000.000
69G69LYN0-0.012-0.00323.8600.0050.0050.0000.0000.0000.000
70G70GLU-1-0.905-0.94727.945-0.027-0.0270.0000.0000.0000.000
71G71LEU00.0080.00827.497-0.001-0.0010.0000.0000.0000.000
72G72GLY00.0400.00031.078-0.002-0.0020.0000.0000.0000.000
73G73LYS10.8300.92923.6510.0570.0570.0000.0000.0000.000
74G74PRO0-0.116-0.04526.038-0.005-0.0050.0000.0000.0000.000
75G75GLU-1-0.858-0.92726.344-0.114-0.1140.0000.0000.0000.000
76G76LEU0-0.096-0.08328.0610.0060.0060.0000.0000.0000.000
77G77GLU-1-0.914-0.94530.936-0.047-0.0470.0000.0000.0000.000
78G78LYN0-0.0560.00728.6450.0060.0060.0000.0000.0000.000
79G79LEU00.0180.00732.2350.0010.0010.0000.0000.0000.000
80G80VAL0-0.010-0.02732.2810.0000.0000.0000.0000.0000.000
81G81GLU-1-0.900-0.94524.245-0.115-0.1150.0000.0000.0000.000
82G82TYR00.0440.03028.383-0.005-0.0050.0000.0000.0000.000
83G83ILE0-0.078-0.03421.041-0.003-0.0030.0000.0000.0000.000
84G84ASP-1-0.757-0.88224.675-0.085-0.0850.0000.0000.0000.000
85G85ARG10.9140.93022.8850.0910.0910.0000.0000.0000.000
86G86GLY0-0.018-0.01019.4820.0070.0070.0000.0000.0000.000
87G87ALA00.0750.05520.5390.0110.0110.0000.0000.0000.000
88G88GLY0-0.081-0.04917.815-0.030-0.0300.0000.0000.0000.000
89G89ILE0-0.028-0.02016.6420.0130.0130.0000.0000.0000.000
90G90LEU0-0.009-0.01117.720-0.006-0.0060.0000.0000.0000.000
91G91VAL00.0060.02218.0220.0040.0040.0000.0000.0000.000
92G92THR00.0500.00120.6190.0110.0110.0000.0000.0000.000
93G93ASN00.000-0.01023.235-0.003-0.0030.0000.0000.0000.000
94G94MET0-0.072-0.01326.0020.0000.0000.0000.0000.0000.000
95G95ASN00.1030.04128.036-0.005-0.0050.0000.0000.0000.000
96G96PRO00.0780.04029.7230.0010.0010.0000.0000.0000.000
97G97PHE00.0410.03430.794-0.001-0.0010.0000.0000.0000.000
98G98LYS10.8330.91730.334-0.007-0.0070.0000.0000.0000.000
99G99LEU00.0200.00424.5740.0020.0020.0000.0000.0000.000
100G100TYR00.0540.03328.4890.0010.0010.0000.0000.0000.000
101G101LYN00.0790.04630.5670.0010.0010.0000.0000.0000.000
102G102PHE0-0.053-0.03424.2100.0020.0020.0000.0000.0000.000
103G103LEU00.0290.00524.1420.0030.0030.0000.0000.0000.000
104G104GLN0-0.065-0.02727.7340.0000.0000.0000.0000.0000.000
105G105GLN0-0.007-0.01031.0450.0020.0020.0000.0000.0000.000
106G106ASN0-0.091-0.03826.8060.0090.0090.0000.0000.0000.000
107G107ARG10.8560.93926.6020.0090.0090.0000.0000.0000.000
108G108GLN00.0160.00826.3330.0020.0020.0000.0000.0000.000
109G109PRO0-0.060-0.02922.9690.0020.0020.0000.0000.0000.000
110G183GLN0-0.003-0.02831.8320.0020.0020.0000.0000.0000.000
111G184PRO0-0.0010.01632.2880.0000.0000.0000.0000.0000.000
112G185LEU0-0.046-0.01728.989-0.003-0.0030.0000.0000.0000.000
113G186GLU-1-0.874-0.94829.7740.0170.0170.0000.0000.0000.000
114G187VAL0-0.063-0.03224.873-0.004-0.0040.0000.0000.0000.000
115G188GLY00.026-0.01125.0650.0060.0060.0000.0000.0000.000
116G189LEU0-0.031-0.00520.589-0.006-0.0060.0000.0000.0000.000
117G190ASP-1-0.776-0.86124.603-0.023-0.0230.0000.0000.0000.000
118G191VAL0-0.031-0.02226.006-0.008-0.0080.0000.0000.0000.000
119G192LEU0-0.030-0.00124.8130.0020.0020.0000.0000.0000.000
120G193ALA00.015-0.00827.5440.0020.0020.0000.0000.0000.000
121G194VAL0-0.044-0.02527.160-0.004-0.0040.0000.0000.0000.000
122G195TYR00.0050.02826.7110.0010.0010.0000.0000.0000.000
123G196GLU-1-0.892-0.97327.972-0.008-0.0080.0000.0000.0000.000
124G197ASP-1-0.949-0.96530.332-0.015-0.0150.0000.0000.0000.000
125G198GLY00.022-0.00231.6150.0010.0010.0000.0000.0000.000
126G199ILE0-0.014-0.00533.126-0.003-0.0030.0000.0000.0000.000
127G200VAL0-0.038-0.02930.196-0.002-0.0020.0000.0000.0000.000
128G201TYR0-0.006-0.00131.8060.0020.0020.0000.0000.0000.000
129G202THR00.005-0.03131.891-0.004-0.0040.0000.0000.0000.000
130G203PRO00.010-0.01731.3210.0040.0040.0000.0000.0000.000
131G204ASP-1-0.877-0.91833.795-0.026-0.0260.0000.0000.0000.000
132G205VAL0-0.0020.01336.5460.0030.0030.0000.0000.0000.000
133G206LEU0-0.056-0.03731.2520.0020.0020.0000.0000.0000.000
134G207ALA0-0.046-0.02035.4600.0030.0030.0000.0000.0000.000
135G208ILE0-0.0060.00537.1140.0000.0000.0000.0000.0000.000
136G209ASP-1-0.859-0.92239.819-0.003-0.0030.0000.0000.0000.000
137G210GLU-1-0.916-0.98041.7380.0030.0030.0000.0000.0000.000
138G211GLN0-0.070-0.05243.5950.0020.0020.0000.0000.0000.000
139G212GLU-1-0.916-0.94346.502-0.007-0.0070.0000.0000.0000.000
140G213TYR00.018-0.00443.4770.0000.0000.0000.0000.0000.000
141G214ILE0-0.039-0.01146.8210.0010.0010.0000.0000.0000.000
142G215ASP-1-0.842-0.91649.3070.0000.0000.0000.0000.0000.000
143G216MET0-0.068-0.03850.2770.0000.0000.0000.0000.0000.000
144G217LEU0-0.0040.00949.6320.0000.0000.0000.0000.0000.000
145G218GLN00.0040.00052.4840.0000.0000.0000.0000.0000.000
146G219LYS10.9190.96255.1950.0020.0020.0000.0000.0000.000
147G220ALA00.0040.00555.0390.0000.0000.0000.0000.0000.000
148G221TYR00.0110.00856.5350.0000.0000.0000.0000.0000.000
149G222MET0-0.001-0.00658.2660.0000.0000.0000.0000.0000.000
150G223HIS0-0.028-0.01559.4040.0000.0000.0000.0000.0000.000
151G224ALA00.0130.01160.5610.0000.0000.0000.0000.0000.000
152G225PHE00.0230.01662.4200.0000.0000.0000.0000.0000.000
153G226ASN00.003-0.02064.3670.0000.0000.0000.0000.0000.000
154G227LEU0-0.0070.01365.0280.0000.0000.0000.0000.0000.000
155G228ALA00.0370.01566.4540.0000.0000.0000.0000.0000.000
156G229VAL00.0110.00268.1970.0000.0000.0000.0000.0000.000
157G230ASN0-0.089-0.06269.4930.0000.0000.0000.0000.0000.000
158G231ILE0-0.043-0.01369.3660.0000.0000.0000.0000.0000.000
159G232ALA0-0.032-0.01172.7740.0000.0000.0000.0000.0000.000
160G233TYR00.0010.00666.4140.0000.0000.0000.0000.0000.000
161G234PRO0-0.031-0.00969.9830.0000.0000.0000.0000.0000.000
162G235THR00.013-0.00766.1800.0000.0000.0000.0000.0000.000
163G236PRO00.008-0.01266.1150.0000.0000.0000.0000.0000.000
164G237GLU-1-0.875-0.93562.4550.0050.0050.0000.0000.0000.000
165G238THR0-0.014-0.00766.0040.0000.0000.0000.0000.0000.000
166G239ILE00.0040.00268.8580.0000.0000.0000.0000.0000.000
167G240GLU-1-0.905-0.95771.5090.0050.0050.0000.0000.0000.000
168G241ALA00.0190.00770.1720.0000.0000.0000.0000.0000.000
169G242ILE0-0.0250.00271.3610.0000.0000.0000.0000.0000.000
170G243ILE0-0.026-0.00874.2820.0000.0000.0000.0000.0000.000
171G244GLN0-0.004-0.00473.3040.0000.0000.0000.0000.0000.000
172G245LYS10.9270.98173.591-0.001-0.0010.0000.0000.0000.000
173G246ALA00.0210.01076.6760.0000.0000.0000.0000.0000.000
174G247PHE00.0040.00279.7560.0000.0000.0000.0000.0000.000
175G248LEU0-0.0060.00578.0940.0000.0000.0000.0000.0000.000
176G249ASN0-0.001-0.00278.4500.0000.0000.0000.0000.0000.000
177G250ALA00.0080.01081.5990.0000.0000.0000.0000.0000.000
178G251LYS10.8530.91683.809-0.002-0.0020.0000.0000.0000.000
179G252THR0-0.031-0.03782.0020.0000.0000.0000.0000.0000.000
180G253VAL00.0010.00184.5460.0000.0000.0000.0000.0000.000
181G254ALA0-0.0050.00286.8040.0000.0000.0000.0000.0000.000
182G255ILE0-0.033-0.01986.2570.0000.0000.0000.0000.0000.000
183G256GLU-1-0.842-0.87286.6030.0000.0000.0000.0000.0000.000
184G257ALA0-0.033-0.01089.2020.0000.0000.0000.0000.0000.000
185G258GLY0-0.029-0.00392.1160.0000.0000.0000.0000.0000.000
186G259TYR0-0.045-0.03092.9730.0000.0000.0000.0000.0000.000
187G260ILE0-0.002-0.00593.3700.0000.0000.0000.0000.0000.000
188G261THR0-0.008-0.01191.0370.0000.0000.0000.0000.0000.000
189G262LYS10.9720.98090.536-0.003-0.0030.0000.0000.0000.000
190G263GLU-1-0.881-0.94387.5670.0030.0030.0000.0000.0000.000
191G264THR00.0330.00888.3100.0000.0000.0000.0000.0000.000
192G265ILE00.0110.01390.3110.0000.0000.0000.0000.0000.000
193G266GLN00.0060.00489.7120.0000.0000.0000.0000.0000.000
194G267ASP-1-0.781-0.88485.9790.0020.0020.0000.0000.0000.000
195G268ILE0-0.010-0.00489.3620.0000.0000.0000.0000.0000.000
196G269ILE00.003-0.00292.5150.0000.0000.0000.0000.0000.000
197G270GLY00.0150.01590.7850.0000.0000.0000.0000.0000.000
198G271ARG10.7600.82986.614-0.001-0.0010.0000.0000.0000.000
199G272ALA00.0200.01892.1240.0000.0000.0000.0000.0000.000
200G273PHE0-0.004-0.00793.2000.0000.0000.0000.0000.0000.000
201G274ARG10.9720.97588.428-0.002-0.0020.0000.0000.0000.000
202G275ALA00.0110.01893.5320.0000.0000.0000.0000.0000.000
203G276MET0-0.0220.00695.8180.0000.0000.0000.0000.0000.000
204G277LEU00.012-0.00493.5710.0000.0000.0000.0000.0000.000
205G278LEU0-0.004-0.00792.7620.0000.0000.0000.0000.0000.000
206G279LEU0-0.013-0.00595.9590.0000.0000.0000.0000.0000.000
207G280ALA00.006-0.01399.4710.0000.0000.0000.0000.0000.000
208G281GLN0-0.032-0.01194.4110.0000.0000.0000.0000.0000.000
209G282GLN0-0.078-0.02898.1370.0000.0000.0000.0000.0000.000
210G283LEU0-0.052-0.014101.5930.0000.0000.0000.0000.0000.000
211G284PRO0-0.0110.006103.0470.0000.0000.0000.0000.0000.000