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: N1K6Q

Calculation Name: 3GR0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GR0

Chain ID: A

ChEMBL ID:

UniProt ID: P41783

Base Structure: X-ray

Registration Date: 2023-06-19

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2026470.256462
FMO2-HF: Nuclear repulsion 1950743.790601
FMO2-HF: Total energy -75726.465861
FMO2-MP2: Total energy -75950.186402


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:177:LEU)


Summations of interaction energy for fragment #1(A:177:LEU)
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.
-12.531-4.8178.36-3.892-12.182-0.016
Interaction energy analysis for fragmet #1(A:177:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : -0.006
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].
3A179GLN0-0.005-0.0053.823-0.3121.169-0.013-0.600-0.8690.002
4A180GLU-1-0.844-0.9332.442-3.269-2.0330.642-0.485-1.392-0.002
5A181LYS10.8740.9252.289-8.779-5.7704.320-2.738-4.591-0.003
6A182GLU-1-0.889-0.9423.2171.8210.4880.1191.693-0.479-0.001
7A183ARG10.8240.9264.8811.1271.1270.0000.0000.0000.000
8A184PHE0-0.031-0.0172.426-0.5360.4600.823-0.373-1.445-0.001
9A185GLN00.0020.0002.810-1.2320.3390.736-0.962-1.345-0.010
10A186VAL00.0060.0112.147-1.318-0.8191.733-0.390-1.842-0.001
11A187LEU0-0.053-0.0294.3840.3340.409-0.001-0.014-0.0610.000
12A188PRO00.0110.0098.060-0.095-0.0950.0000.0000.0000.000
13A189GLY00.0560.02811.152-0.010-0.0100.0000.0000.0000.000
14A190ARG10.7850.85514.1770.0010.0010.0000.0000.0000.000
15A191ASP-1-0.776-0.85316.070-0.076-0.0760.0000.0000.0000.000
16A192LYS10.8930.93916.202-0.069-0.0690.0000.0000.0000.000
17A193MET0-0.0200.02513.471-0.003-0.0030.0000.0000.0000.000
18A194LEU0-0.018-0.0088.2650.0520.0520.0000.0000.0000.000
19A195TYR0-0.050-0.0739.090-0.079-0.0790.0000.0000.0000.000
20A196VAL00.0050.0044.006-0.1410.0390.001-0.023-0.1580.000
21A197ALA0-0.014-0.0116.0480.0690.0690.0000.0000.0000.000
22A198ALA00.0410.0176.531-0.264-0.2640.0000.0000.0000.000
23A199GLN00.0670.0298.6980.1260.1260.0000.0000.0000.000
24A200ASN0-0.011-0.00211.0770.0670.0670.0000.0000.0000.000
25A201GLU-1-0.805-0.89312.484-0.425-0.4250.0000.0000.0000.000
26A202ARG10.9670.97713.1690.4990.4990.0000.0000.0000.000
27A203ASP-1-0.859-0.9358.462-1.094-1.0940.0000.0000.0000.000
28A204THR0-0.009-0.0169.187-0.121-0.1210.0000.0000.0000.000
29A205LEU0-0.016-0.01411.089-0.004-0.0040.0000.0000.0000.000
30A206TRP00.0030.0135.4680.0760.0760.0000.0000.0000.000
31A207ALA00.0190.0046.984-0.032-0.0320.0000.0000.0000.000
32A208ARG10.7750.8308.4470.4860.4860.0000.0000.0000.000
33A209GLN0-0.0110.00411.4260.0860.0860.0000.0000.0000.000
34A210VAL0-0.030-0.0086.9640.0680.0680.0000.0000.0000.000
35A211LEU0-0.029-0.0237.1810.0410.0410.0000.0000.0000.000
36A212ALA00.0180.01210.6760.0580.0580.0000.0000.0000.000
37A213ARG10.8690.94712.7210.6460.6460.0000.0000.0000.000
38A214GLY0-0.0040.00212.0830.0390.0390.0000.0000.0000.000
39A215ASP-1-0.877-0.92713.079-0.243-0.2430.0000.0000.0000.000
40A216TYR0-0.005-0.0149.3800.0010.0010.0000.0000.0000.000
41A217ASP-1-0.871-0.93612.686-0.368-0.3680.0000.0000.0000.000
42A218LYS10.8600.92814.4230.2830.2830.0000.0000.0000.000
43A219ASN0-0.053-0.03313.4280.0210.0210.0000.0000.0000.000
44A220ALA0-0.0020.0048.8440.0300.0300.0000.0000.0000.000
45A221ARG10.9400.97210.4030.1850.1850.0000.0000.0000.000
46A222VAL0-0.0040.0158.033-0.039-0.0390.0000.0000.0000.000
47A223ILE0-0.0160.0069.7120.0870.0870.0000.0000.0000.000
48A224ASN00.039-0.00110.753-0.028-0.0280.0000.0000.0000.000
49A225GLU-1-0.809-0.91713.307-0.111-0.1110.0000.0000.0000.000
50A226ASN00.002-0.01415.9510.0540.0540.0000.0000.0000.000
51A227GLU-1-0.806-0.87216.057-0.325-0.3250.0000.0000.0000.000
52A228GLU-1-0.734-0.81315.174-0.168-0.1680.0000.0000.0000.000
53A229ASN0-0.035-0.03318.2080.0440.0440.0000.0000.0000.000
54A230LYS10.9280.96521.1330.2200.2200.0000.0000.0000.000
55A231ARG10.7890.87117.7580.1630.1630.0000.0000.0000.000
56A232ILE00.009-0.00519.6690.0140.0140.0000.0000.0000.000
57A233SER0-0.0020.00923.5990.0160.0160.0000.0000.0000.000
58A234ILE00.0310.04325.8180.0070.0070.0000.0000.0000.000
59A235TRP00.0150.00426.0640.0100.0100.0000.0000.0000.000
60A236LEU0-0.037-0.03526.5820.0100.0100.0000.0000.0000.000
61A237ASP-1-0.891-0.93529.599-0.074-0.0740.0000.0000.0000.000
62A238THR0-0.072-0.03031.4490.0050.0050.0000.0000.0000.000
63A239TYR0-0.046-0.02630.2950.0070.0070.0000.0000.0000.000
64A240TYR0-0.073-0.05030.9330.0070.0070.0000.0000.0000.000
65A241PRO00.0730.04433.377-0.001-0.0010.0000.0000.0000.000
66A242GLN0-0.018-0.01135.361-0.004-0.0040.0000.0000.0000.000
67A243LEU0-0.047-0.00129.8460.0030.0030.0000.0000.0000.000
68A244ALA00.0030.00333.523-0.005-0.0050.0000.0000.0000.000
69A245TYR0-0.027-0.05926.6480.0070.0070.0000.0000.0000.000
70A246TYR0-0.061-0.04927.624-0.004-0.0040.0000.0000.0000.000
71A247ARG10.9000.95320.5800.1300.1300.0000.0000.0000.000
72A248ILE00.0090.00819.1010.0150.0150.0000.0000.0000.000
73A249HIS10.8530.94118.6110.0580.0580.0000.0000.0000.000
74A250PHE00.008-0.01413.5240.0170.0170.0000.0000.0000.000
75A251ASP-1-0.885-0.93913.273-0.057-0.0570.0000.0000.0000.000
76A252GLU-1-0.912-0.95112.9170.2160.2160.0000.0000.0000.000
77A253PRO00.004-0.0019.467-0.005-0.0050.0000.0000.0000.000
78A254ARG10.9730.9878.334-0.494-0.4940.0000.0000.0000.000
79A255LYS10.9110.96213.496-0.171-0.1710.0000.0000.0000.000
80A256PRO00.0360.03416.118-0.003-0.0030.0000.0000.0000.000
81A257VAL0-0.0050.00217.7710.0120.0120.0000.0000.0000.000
82A258PHE0-0.014-0.01821.108-0.018-0.0180.0000.0000.0000.000
83A259TRP00.0280.01223.6460.0050.0050.0000.0000.0000.000
84A260LEU00.037-0.00226.421-0.008-0.0080.0000.0000.0000.000
85A261SER0-0.058-0.04529.8890.0040.0040.0000.0000.0000.000
86A262ARG10.9410.95732.575-0.002-0.0020.0000.0000.0000.000
87A263GLN00.0300.01735.2290.0010.0010.0000.0000.0000.000
88A264ARG10.8500.91134.0630.0340.0340.0000.0000.0000.000
89A265ASN0-0.0100.00134.907-0.004-0.0040.0000.0000.0000.000
90A266THR0-0.010-0.00536.7350.0020.0020.0000.0000.0000.000
91A267MET0-0.0140.01833.3880.0000.0000.0000.0000.0000.000
92A268SER00.0270.02236.8680.0030.0030.0000.0000.0000.000
93A269LYS11.0160.98633.315-0.036-0.0360.0000.0000.0000.000
94A270LYS11.0141.00833.638-0.014-0.0140.0000.0000.0000.000
95A271GLU-1-0.873-0.94634.074-0.004-0.0040.0000.0000.0000.000
96A272LEU0-0.008-0.00531.097-0.003-0.0030.0000.0000.0000.000
97A273GLU-1-0.909-0.96129.6670.0280.0280.0000.0000.0000.000
98A274VAL0-0.031-0.01029.2990.0000.0000.0000.0000.0000.000
99A275LEU0-0.0150.00927.975-0.003-0.0030.0000.0000.0000.000
100A276SER00.000-0.00125.095-0.004-0.0040.0000.0000.0000.000
101A277GLN00.028-0.00124.633-0.004-0.0040.0000.0000.0000.000
102A278LYS10.8890.94725.3320.0180.0180.0000.0000.0000.000
103A279LEU00.0250.01322.811-0.008-0.0080.0000.0000.0000.000
104A280ARG10.9330.96520.395-0.060-0.0600.0000.0000.0000.000
105A281ALA0-0.059-0.02420.346-0.003-0.0030.0000.0000.0000.000
106A282LEU00.0130.01721.645-0.008-0.0080.0000.0000.0000.000
107A283MET0-0.0280.00716.770-0.027-0.0270.0000.0000.0000.000
108A284PRO00.0000.00416.0620.0260.0260.0000.0000.0000.000
109A285TYR0-0.010-0.02311.6880.0260.0260.0000.0000.0000.000
110A286ALA0-0.0200.00413.4050.0340.0340.0000.0000.0000.000
111A287ASP-1-0.913-0.94615.9090.1810.1810.0000.0000.0000.000
112A288SER0-0.103-0.05717.728-0.008-0.0080.0000.0000.0000.000
113A289VAL00.0710.03519.210-0.003-0.0030.0000.0000.0000.000
114A290ASN0-0.0040.00521.485-0.003-0.0030.0000.0000.0000.000
115A291ILE00.0160.01223.602-0.010-0.0100.0000.0000.0000.000
116A292THR0-0.009-0.00225.8900.0090.0090.0000.0000.0000.000
117A293LEU0-0.026-0.00927.750-0.008-0.0080.0000.0000.0000.000
118A294MET0-0.026-0.01427.6910.0060.0060.0000.0000.0000.000
119A295ASP-1-0.830-0.93031.224-0.011-0.0110.0000.0000.0000.000
120A296ASP-1-0.673-0.79334.114-0.029-0.0290.0000.0000.0000.000
121A297VAL0-0.036-0.01135.918-0.004-0.0040.0000.0000.0000.000
122A298THR0-0.022-0.01132.3790.0000.0000.0000.0000.0000.000
123A299ALA00.0170.01632.197-0.002-0.0020.0000.0000.0000.000
124A300ALA0-0.0250.00933.190-0.005-0.0050.0000.0000.0000.000
125A301GLY00.0270.01736.080-0.002-0.0020.0000.0000.0000.000
126A302GLN00.017-0.00429.531-0.005-0.0050.0000.0000.0000.000
127A303ALA0-0.0040.01232.992-0.003-0.0030.0000.0000.0000.000
128A304GLU-1-0.833-0.88933.927-0.031-0.0310.0000.0000.0000.000
129A305ALA0-0.032-0.00634.5300.0000.0000.0000.0000.0000.000
130A306GLY00.0530.01332.8950.0010.0010.0000.0000.0000.000
131A307LEU00.002-0.00333.719-0.003-0.0030.0000.0000.0000.000
132A308LYS10.9350.96736.6230.0250.0250.0000.0000.0000.000
133A309GLN0-0.064-0.03532.645-0.003-0.0030.0000.0000.0000.000
134A310GLN0-0.044-0.01831.783-0.002-0.0020.0000.0000.0000.000
135A311ALA0-0.0170.00237.109-0.001-0.0010.0000.0000.0000.000
136A312LEU00.0220.02335.935-0.001-0.0010.0000.0000.0000.000
137A313PRO00.0010.01840.3720.0030.0030.0000.0000.0000.000
138A314TYR0-0.021-0.07740.414-0.003-0.0030.0000.0000.0000.000
139A315SER0-0.031-0.01242.4680.0040.0040.0000.0000.0000.000
140A316ARG10.8700.93040.2090.0270.0270.0000.0000.0000.000
141A317ARG10.9170.95442.3250.0390.0390.0000.0000.0000.000
142A318ASN00.0600.04342.519-0.004-0.0040.0000.0000.0000.000
143A319HIS00.0570.07340.8280.0000.0000.0000.0000.0000.000
144A320LYS10.9020.94643.2010.0300.0300.0000.0000.0000.000
145A321GLY00.0510.02140.129-0.002-0.0020.0000.0000.0000.000
146A322GLY00.0320.01738.133-0.003-0.0030.0000.0000.0000.000
147A323VAL0-0.084-0.02437.9340.0040.0040.0000.0000.0000.000
148A324THR00.049-0.02537.709-0.005-0.0050.0000.0000.0000.000
149A325PHE0-0.046-0.02336.7050.0050.0050.0000.0000.0000.000
150A326VAL0-0.015-0.01338.463-0.004-0.0040.0000.0000.0000.000
151A327ILE00.0310.00835.7760.0040.0040.0000.0000.0000.000
152A328GLN0-0.046-0.02840.3380.0000.0000.0000.0000.0000.000
153A329GLY00.0050.01042.9670.0000.0000.0000.0000.0000.000
154A330ALA0-0.034-0.01243.269-0.003-0.0030.0000.0000.0000.000
155A331LEU00.007-0.00838.3190.0020.0020.0000.0000.0000.000
156A332ASP-1-0.809-0.88738.880-0.067-0.0670.0000.0000.0000.000
157A333ASP-1-0.863-0.94936.065-0.084-0.0840.0000.0000.0000.000
158A334VAL0-0.052-0.02934.215-0.007-0.0070.0000.0000.0000.000
159A335GLU-1-0.886-0.95734.111-0.060-0.0600.0000.0000.0000.000
160A336ILE0-0.047-0.01534.136-0.003-0.0030.0000.0000.0000.000
161A337LEU0-0.043-0.02729.472-0.006-0.0060.0000.0000.0000.000
162A338ARG10.9610.97830.3410.0680.0680.0000.0000.0000.000
163A339ALA00.0660.03731.0240.0000.0000.0000.0000.0000.000
164A340ARG10.9320.96429.5690.1090.1090.0000.0000.0000.000
165A341GLN00.0280.01425.6400.0040.0040.0000.0000.0000.000
166A342PHE0-0.0320.01126.660-0.002-0.0020.0000.0000.0000.000
167A343VAL00.0140.00628.3240.0010.0010.0000.0000.0000.000
168A344ASP-1-0.922-0.96224.469-0.146-0.1460.0000.0000.0000.000
169A345SER0-0.063-0.04623.691-0.011-0.0110.0000.0000.0000.000
170A346TYR0-0.031-0.04024.5670.0020.0020.0000.0000.0000.000
171A347TYR00.0180.00626.2200.0070.0070.0000.0000.0000.000
172A348ARG10.9190.97319.6150.1590.1590.0000.0000.0000.000
173A349THR00.0010.01422.0020.0010.0010.0000.0000.0000.000
174A350TRP0-0.005-0.02023.8660.0080.0080.0000.0000.0000.000
175A351GLY0-0.0050.00625.7770.0040.0040.0000.0000.0000.000
176A352GLY00.018-0.00626.7860.0030.0030.0000.0000.0000.000
177A353ARG10.9220.96728.7890.0720.0720.0000.0000.0000.000
178A354TYR0-0.0310.00031.9120.0050.0050.0000.0000.0000.000
179A355VAL0-0.004-0.00133.1630.0020.0020.0000.0000.0000.000
180A356GLN0-0.022-0.00832.924-0.006-0.0060.0000.0000.0000.000
181A357PHE00.0200.00331.2120.0050.0050.0000.0000.0000.000
182A358ALA0-0.010-0.00335.548-0.004-0.0040.0000.0000.0000.000
183A359ILE00.0020.01137.9550.0020.0020.0000.0000.0000.000
184A360GLU-1-0.886-0.95739.772-0.046-0.0460.0000.0000.0000.000
185A361LEU00.0010.00743.539-0.002-0.0020.0000.0000.0000.000
186A362LYS10.9470.98345.4330.0450.0450.0000.0000.0000.000