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: 3QLGL

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 OptAll
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 -2030635.677593
FMO2-HF: Nuclear repulsion 1954907.552802
FMO2-HF: Total energy -75728.124791
FMO2-MP2: Total energy -75951.830934


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.
-6.903-0.9518.184-2.771-11.365-0.018
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 : 0.013 / q_NPA : -0.002
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].
3A179GLN0-0.021-0.0323.877-0.3510.952-0.003-0.536-0.7650.002
4A180GLU-1-0.822-0.9053.037-2.391-1.4240.084-0.189-0.8610.000
5A181LYS10.7750.8682.338-4.951-2.6515.625-3.455-4.470-0.011
6A182GLU-1-0.780-0.8773.0172.6810.3470.1612.786-0.614-0.002
7A183ARG10.8240.9314.5201.0311.136-0.001-0.007-0.0970.000
8A184PHE0-0.045-0.0292.449-0.5580.5520.816-0.390-1.5360.000
9A185GLN00.0230.0162.958-1.0380.3050.493-0.703-1.133-0.006
10A186VAL00.0190.0052.385-1.223-0.4360.990-0.205-1.572-0.001
11A187LEU0-0.029-0.0154.6830.1380.192-0.001-0.008-0.0450.000
12A188PRO00.0060.0148.428-0.051-0.0510.0000.0000.0000.000
13A189GLY00.0590.02611.547-0.008-0.0080.0000.0000.0000.000
14A190ARG10.7710.85514.374-0.025-0.0250.0000.0000.0000.000
15A191ASP-1-0.787-0.88915.951-0.022-0.0220.0000.0000.0000.000
16A192LYS10.8960.94616.006-0.068-0.0680.0000.0000.0000.000
17A193MET0-0.0080.03113.3400.0000.0000.0000.0000.0000.000
18A194LEU0-0.008-0.0077.9470.0300.0300.0000.0000.0000.000
19A195TYR0-0.036-0.0478.961-0.055-0.0550.0000.0000.0000.000
20A196VAL0-0.010-0.0013.461-0.2660.0510.020-0.064-0.2720.000
21A197ALA00.002-0.0025.893-0.025-0.0250.0000.0000.0000.000
22A198ALA00.0210.0006.187-0.190-0.1900.0000.0000.0000.000
23A199GLN00.0420.0117.7570.1000.1000.0000.0000.0000.000
24A200ASN0-0.050-0.03310.4470.0800.0800.0000.0000.0000.000
25A201GLU-1-0.696-0.82312.364-0.285-0.2850.0000.0000.0000.000
26A202ARG10.8940.93011.8300.5210.5210.0000.0000.0000.000
27A203ASP-1-0.753-0.8478.512-0.741-0.7410.0000.0000.0000.000
28A204THR0-0.006-0.0168.988-0.077-0.0770.0000.0000.0000.000
29A205LEU00.013-0.00410.8780.0050.0050.0000.0000.0000.000
30A206TRP00.0060.0145.1310.0100.0100.0000.0000.0000.000
31A207ALA00.0310.0106.600-0.013-0.0130.0000.0000.0000.000
32A208ARG10.7700.8308.1640.3390.3390.0000.0000.0000.000
33A209GLN00.0510.01911.5510.0470.0470.0000.0000.0000.000
34A210VAL0-0.048-0.0046.9920.0260.0260.0000.0000.0000.000
35A211LEU0-0.017-0.0197.2050.0410.0410.0000.0000.0000.000
36A212ALA00.0360.02510.6280.0350.0350.0000.0000.0000.000
37A213ARG10.8130.90012.6370.4540.4540.0000.0000.0000.000
38A214GLY0-0.0040.01011.7710.0090.0090.0000.0000.0000.000
39A215ASP-1-0.834-0.89712.791-0.131-0.1310.0000.0000.0000.000
40A216TYR00.000-0.0038.746-0.004-0.0040.0000.0000.0000.000
41A217ASP-1-0.805-0.90612.701-0.222-0.2220.0000.0000.0000.000
42A218LYS10.7610.86214.1570.1830.1830.0000.0000.0000.000
43A219ASN0-0.058-0.03213.4980.0110.0110.0000.0000.0000.000
44A220ALA0-0.0100.0018.8650.0260.0260.0000.0000.0000.000
45A221ARG10.9070.95710.1460.0760.0760.0000.0000.0000.000
46A222VAL00.0130.0178.065-0.008-0.0080.0000.0000.0000.000
47A223ILE0-0.0110.0169.6550.0370.0370.0000.0000.0000.000
48A224ASN00.0400.00010.550-0.020-0.0200.0000.0000.0000.000
49A225GLU-1-0.696-0.82212.955-0.081-0.0810.0000.0000.0000.000
50A226ASN0-0.008-0.00615.6440.0420.0420.0000.0000.0000.000
51A227GLU-1-0.838-0.89315.856-0.223-0.2230.0000.0000.0000.000
52A228GLU-1-0.744-0.80514.836-0.092-0.0920.0000.0000.0000.000
53A229ASN0-0.036-0.03217.9030.0290.0290.0000.0000.0000.000
54A230LYS10.8440.92519.0120.1880.1880.0000.0000.0000.000
55A231ARG10.7740.84817.2530.0990.0990.0000.0000.0000.000
56A232ILE0-0.002-0.00919.3610.0100.0100.0000.0000.0000.000
57A233SER0-0.006-0.01423.2960.0060.0060.0000.0000.0000.000
58A234ILE00.0330.02425.9720.0060.0060.0000.0000.0000.000
59A235TRP00.0300.02226.1100.0060.0060.0000.0000.0000.000
60A236LEU0-0.001-0.01125.9310.0060.0060.0000.0000.0000.000
61A237ASP-1-0.840-0.90429.256-0.048-0.0480.0000.0000.0000.000
62A238THR0-0.041-0.02930.7160.0020.0020.0000.0000.0000.000
63A239TYR0-0.056-0.02330.8040.0050.0050.0000.0000.0000.000
64A240TYR0-0.036-0.01530.7630.0050.0050.0000.0000.0000.000
65A241PRO00.0640.03933.291-0.001-0.0010.0000.0000.0000.000
66A242GLN0-0.029-0.01834.904-0.003-0.0030.0000.0000.0000.000
67A243LEU0-0.0280.00129.8150.0020.0020.0000.0000.0000.000
68A244ALA00.0120.00732.911-0.004-0.0040.0000.0000.0000.000
69A245TYR0-0.006-0.00126.6310.0010.0010.0000.0000.0000.000
70A246TYR0-0.063-0.05427.427-0.003-0.0030.0000.0000.0000.000
71A247ARG10.7950.88119.1240.1070.1070.0000.0000.0000.000
72A248ILE0-0.003-0.00218.9250.0110.0110.0000.0000.0000.000
73A249HIS10.8230.89818.0870.0560.0560.0000.0000.0000.000
74A250PHE00.008-0.02113.2490.0110.0110.0000.0000.0000.000
75A251ASP-1-0.867-0.92912.813-0.054-0.0540.0000.0000.0000.000
76A252GLU-1-0.824-0.89412.4000.1680.1680.0000.0000.0000.000
77A253PRO0-0.024-0.0128.976-0.003-0.0030.0000.0000.0000.000
78A254ARG10.9430.9687.946-0.335-0.3350.0000.0000.0000.000
79A255LYS10.8180.89413.398-0.139-0.1390.0000.0000.0000.000
80A256PRO00.0100.01715.705-0.005-0.0050.0000.0000.0000.000
81A257VAL0-0.010-0.00317.7320.0090.0090.0000.0000.0000.000
82A258PHE0-0.010-0.01220.908-0.012-0.0120.0000.0000.0000.000
83A259TRP00.0080.00223.3970.0040.0040.0000.0000.0000.000
84A260LEU00.0470.01026.335-0.005-0.0050.0000.0000.0000.000
85A261SER0-0.039-0.03929.9210.0020.0020.0000.0000.0000.000
86A262ARG10.8730.91932.3000.0040.0040.0000.0000.0000.000
87A263GLN0-0.021-0.02035.2710.0010.0010.0000.0000.0000.000
88A264ARG10.8790.91734.3190.0270.0270.0000.0000.0000.000
89A265ASN0-0.009-0.00234.375-0.002-0.0020.0000.0000.0000.000
90A266THR00.0150.00536.2570.0010.0010.0000.0000.0000.000
91A267MET0-0.073-0.00232.4150.0000.0000.0000.0000.0000.000
92A268SER00.022-0.02836.4280.0020.0020.0000.0000.0000.000
93A269LYS10.9240.92832.770-0.026-0.0260.0000.0000.0000.000
94A270LYS10.9220.96433.470-0.017-0.0170.0000.0000.0000.000
95A271GLU-1-0.787-0.86734.0810.0000.0000.0000.0000.0000.000
96A272LEU00.0020.00230.809-0.002-0.0020.0000.0000.0000.000
97A273GLU-1-0.819-0.89429.5530.0220.0220.0000.0000.0000.000
98A274VAL0-0.008-0.00829.1610.0010.0010.0000.0000.0000.000
99A275LEU0-0.0090.01027.805-0.002-0.0020.0000.0000.0000.000
100A276SER0-0.014-0.02424.655-0.002-0.0020.0000.0000.0000.000
101A277GLN0-0.018-0.01824.540-0.002-0.0020.0000.0000.0000.000
102A278LYS10.9000.95025.2940.0080.0080.0000.0000.0000.000
103A279LEU00.0370.01722.505-0.004-0.0040.0000.0000.0000.000
104A280ARG10.8830.92420.451-0.059-0.0590.0000.0000.0000.000
105A281ALA0-0.037-0.01220.4640.0030.0030.0000.0000.0000.000
106A282LEU0-0.0010.01121.368-0.004-0.0040.0000.0000.0000.000
107A283MET0-0.0010.02416.670-0.018-0.0180.0000.0000.0000.000
108A284PRO00.0040.00216.1450.0170.0170.0000.0000.0000.000
109A285TYR0-0.038-0.04311.7820.0180.0180.0000.0000.0000.000
110A286ALA0-0.0230.01313.4540.0230.0230.0000.0000.0000.000
111A287ASP-1-0.821-0.90915.3220.1500.1500.0000.0000.0000.000
112A288SER0-0.087-0.03817.552-0.007-0.0070.0000.0000.0000.000
113A289VAL00.0640.03419.025-0.002-0.0020.0000.0000.0000.000
114A290ASN00.0340.04221.259-0.005-0.0050.0000.0000.0000.000
115A291ILE00.0070.00423.297-0.008-0.0080.0000.0000.0000.000
116A292THR00.001-0.00125.5020.0060.0060.0000.0000.0000.000
117A293LEU0-0.024-0.00427.536-0.006-0.0060.0000.0000.0000.000
118A294MET00.0120.02027.1600.0050.0050.0000.0000.0000.000
119A295ASP-1-0.779-0.88030.627-0.011-0.0110.0000.0000.0000.000
120A296ASP-1-0.708-0.79733.821-0.025-0.0250.0000.0000.0000.000
121A297VAL0-0.0190.00035.753-0.003-0.0030.0000.0000.0000.000
122A298THR0-0.017-0.03332.397-0.001-0.0010.0000.0000.0000.000
123A299ALA0-0.0050.01232.061-0.002-0.0020.0000.0000.0000.000
124A300ALA00.0040.00633.070-0.004-0.0040.0000.0000.0000.000
125A301GLY00.0100.00736.055-0.001-0.0010.0000.0000.0000.000
126A302GLN00.0410.00929.171-0.005-0.0050.0000.0000.0000.000
127A303ALA0-0.0060.00932.836-0.003-0.0030.0000.0000.0000.000
128A304GLU-1-0.793-0.88233.832-0.027-0.0270.0000.0000.0000.000
129A305ALA0-0.037-0.00833.8940.0000.0000.0000.0000.0000.000
130A306GLY00.0700.03032.4470.0000.0000.0000.0000.0000.000
131A307LEU0-0.013-0.00233.284-0.003-0.0030.0000.0000.0000.000
132A308LYS10.8840.93636.3000.0260.0260.0000.0000.0000.000
133A309GLN0-0.042-0.02532.256-0.002-0.0020.0000.0000.0000.000
134A310GLN0-0.052-0.03832.349-0.004-0.0040.0000.0000.0000.000
135A311ALA0-0.0090.00236.512-0.001-0.0010.0000.0000.0000.000
136A312LEU00.0150.02435.1310.0000.0000.0000.0000.0000.000
137A313PRO00.0120.01739.6840.0020.0020.0000.0000.0000.000
138A314TYR0-0.058-0.05740.243-0.002-0.0020.0000.0000.0000.000
139A315SER00.0150.00342.2490.0030.0030.0000.0000.0000.000
140A316ARG10.8420.91940.3980.0240.0240.0000.0000.0000.000
141A317ARG10.8850.92741.8050.0310.0310.0000.0000.0000.000
142A318ASN00.0650.03842.089-0.003-0.0030.0000.0000.0000.000
143A319HIS00.0330.03641.0010.0000.0000.0000.0000.0000.000
144A320LYS10.9090.93743.1260.0250.0250.0000.0000.0000.000
145A321GLY00.0600.03239.715-0.001-0.0010.0000.0000.0000.000
146A322GLY00.0280.00937.690-0.002-0.0020.0000.0000.0000.000
147A323VAL0-0.110-0.04637.5730.0030.0030.0000.0000.0000.000
148A324THR00.0350.01437.245-0.004-0.0040.0000.0000.0000.000
149A325PHE0-0.026-0.02736.1600.0040.0040.0000.0000.0000.000
150A326VAL00.0050.01037.874-0.003-0.0030.0000.0000.0000.000
151A327ILE00.0620.02535.4050.0030.0030.0000.0000.0000.000
152A328GLN0-0.052-0.04039.9400.0000.0000.0000.0000.0000.000
153A329GLY0-0.0010.00343.0050.0000.0000.0000.0000.0000.000
154A330ALA0-0.036-0.02142.970-0.002-0.0020.0000.0000.0000.000
155A331LEU0-0.010-0.00438.0050.0020.0020.0000.0000.0000.000
156A332ASP-1-0.801-0.89137.920-0.060-0.0600.0000.0000.0000.000
157A333ASP-1-0.883-0.95635.549-0.072-0.0720.0000.0000.0000.000
158A334VAL0-0.050-0.02833.220-0.006-0.0060.0000.0000.0000.000
159A335GLU-1-0.879-0.94333.512-0.052-0.0520.0000.0000.0000.000
160A336ILE0-0.014-0.00633.919-0.002-0.0020.0000.0000.0000.000
161A337LEU0-0.050-0.02127.917-0.005-0.0050.0000.0000.0000.000
162A338ARG10.9510.98129.7960.0610.0610.0000.0000.0000.000
163A339ALA00.0530.02430.370-0.001-0.0010.0000.0000.0000.000
164A340ARG10.9190.96728.9930.0920.0920.0000.0000.0000.000
165A341GLN00.0260.01425.6040.0040.0040.0000.0000.0000.000
166A342PHE0-0.0340.00226.050-0.002-0.0020.0000.0000.0000.000
167A343VAL00.0190.01127.6510.0000.0000.0000.0000.0000.000
168A344ASP-1-0.896-0.96024.286-0.114-0.1140.0000.0000.0000.000
169A345SER0-0.030-0.03523.209-0.013-0.0130.0000.0000.0000.000
170A346TYR0-0.030-0.01124.2610.0030.0030.0000.0000.0000.000
171A347TYR00.0120.00525.9780.0050.0050.0000.0000.0000.000
172A348ARG10.9020.95819.2790.1330.1330.0000.0000.0000.000
173A349THR0-0.033-0.01321.4880.0010.0010.0000.0000.0000.000
174A350TRP0-0.001-0.02023.6840.0070.0070.0000.0000.0000.000
175A351GLY00.0000.01525.4030.0040.0040.0000.0000.0000.000
176A352GLY00.0400.00626.4810.0010.0010.0000.0000.0000.000
177A353ARG10.8170.89929.0630.0510.0510.0000.0000.0000.000
178A354TYR0-0.052-0.03231.8630.0040.0040.0000.0000.0000.000
179A355VAL0-0.0060.01832.5140.0020.0020.0000.0000.0000.000
180A356GLN0-0.036-0.02432.584-0.004-0.0040.0000.0000.0000.000
181A357PHE00.015-0.00231.1380.0040.0040.0000.0000.0000.000
182A358ALA0-0.007-0.00234.970-0.003-0.0030.0000.0000.0000.000
183A359ILE0-0.0030.00837.3600.0010.0010.0000.0000.0000.000
184A360GLU-1-0.772-0.86539.517-0.037-0.0370.0000.0000.0000.000
185A361LEU00.0120.01043.209-0.002-0.0020.0000.0000.0000.000
186A362LYS10.8490.91945.4250.0370.0370.0000.0000.0000.000