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: J3NK9

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2028262.537107
FMO2-HF: Nuclear repulsion 1952534.836135
FMO2-HF: Total energy -75727.700972
FMO2-MP2: Total energy -75951.413774


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.
-8.547-0.9536.879-3.25-11.223-0.02
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 : 0.020 / 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].
3A179GLN0-0.048-0.0343.823-0.5250.975-0.013-0.615-0.8720.002
4A180GLU-1-0.815-0.9122.804-2.570-1.3810.203-0.306-1.086-0.001
5A181LYS10.7940.8822.399-5.467-2.6793.774-2.613-3.949-0.009
6A182GLU-1-0.816-0.9043.1842.1680.6290.1321.909-0.502-0.001
7A183ARG10.8250.9334.7900.8690.962-0.001-0.004-0.0870.000
8A184PHE0-0.026-0.0222.538-0.5100.5440.622-0.309-1.3670.000
9A185GLN00.0220.0112.823-1.2690.1840.851-0.906-1.398-0.009
10A186VAL00.0200.0152.339-1.332-0.5601.310-0.361-1.722-0.002
11A187LEU0-0.059-0.0294.4140.1910.265-0.001-0.013-0.0600.000
12A188PRO00.0110.0068.083-0.062-0.0620.0000.0000.0000.000
13A189GLY00.0600.03011.186-0.005-0.0050.0000.0000.0000.000
14A190ARG10.7870.85814.210-0.004-0.0040.0000.0000.0000.000
15A191ASP-1-0.784-0.88715.989-0.055-0.0550.0000.0000.0000.000
16A192LYS10.8940.94016.084-0.045-0.0450.0000.0000.0000.000
17A193MET0-0.0150.03113.451-0.003-0.0030.0000.0000.0000.000
18A194LEU0-0.015-0.0048.1700.0360.0360.0000.0000.0000.000
19A195TYR0-0.026-0.0419.088-0.052-0.0520.0000.0000.0000.000
20A196VAL0-0.0030.0003.883-0.1900.0200.002-0.032-0.1800.000
21A197ALA0-0.018-0.0086.0500.0260.0260.0000.0000.0000.000
22A198ALA00.0310.0136.511-0.182-0.1820.0000.0000.0000.000
23A199GLN00.0430.0168.1130.0940.0940.0000.0000.0000.000
24A200ASN0-0.060-0.03810.9290.0740.0740.0000.0000.0000.000
25A201GLU-1-0.778-0.87712.690-0.296-0.2960.0000.0000.0000.000
26A202ARG10.9050.94312.2590.4700.4700.0000.0000.0000.000
27A203ASP-1-0.768-0.8788.615-0.718-0.7180.0000.0000.0000.000
28A204THR00.018-0.0039.321-0.074-0.0740.0000.0000.0000.000
29A205LEU00.002-0.00711.2270.0000.0000.0000.0000.0000.000
30A206TRP00.0130.0165.4560.0210.0210.0000.0000.0000.000
31A207ALA00.0160.0017.102-0.026-0.0260.0000.0000.0000.000
32A208ARG10.7850.8308.4720.3440.3440.0000.0000.0000.000
33A209GLN0-0.0020.01011.5560.0530.0530.0000.0000.0000.000
34A210VAL0-0.041-0.0217.1690.0450.0450.0000.0000.0000.000
35A211LEU0-0.024-0.0177.1230.0250.0250.0000.0000.0000.000
36A212ALA00.0260.01510.7370.0370.0370.0000.0000.0000.000
37A213ARG10.8660.94412.6050.4980.4980.0000.0000.0000.000
38A214GLY0-0.0080.00112.0370.0280.0280.0000.0000.0000.000
39A215ASP-1-0.820-0.88013.045-0.177-0.1770.0000.0000.0000.000
40A216TYR0-0.006-0.0118.924-0.007-0.0070.0000.0000.0000.000
41A217ASP-1-0.818-0.90012.669-0.265-0.2650.0000.0000.0000.000
42A218LYS10.7630.85614.4420.2180.2180.0000.0000.0000.000
43A219ASN0-0.058-0.04013.2930.0140.0140.0000.0000.0000.000
44A220ALA0-0.0040.0018.8270.0210.0210.0000.0000.0000.000
45A221ARG10.9200.96910.4130.1210.1210.0000.0000.0000.000
46A222VAL00.0010.0198.388-0.018-0.0180.0000.0000.0000.000
47A223ILE0-0.0100.0039.8270.0520.0520.0000.0000.0000.000
48A224ASN00.024-0.00410.897-0.019-0.0190.0000.0000.0000.000
49A225GLU-1-0.702-0.84713.295-0.075-0.0750.0000.0000.0000.000
50A226ASN0-0.009-0.00915.9320.0430.0430.0000.0000.0000.000
51A227GLU-1-0.830-0.88316.326-0.229-0.2290.0000.0000.0000.000
52A228GLU-1-0.733-0.79915.072-0.109-0.1090.0000.0000.0000.000
53A229ASN0-0.021-0.02818.2040.0300.0300.0000.0000.0000.000
54A230LYS10.9120.97720.3510.1750.1750.0000.0000.0000.000
55A231ARG10.7840.86117.6540.1130.1130.0000.0000.0000.000
56A232ILE00.018-0.01019.5950.0100.0100.0000.0000.0000.000
57A233SER0-0.008-0.01423.5990.0110.0110.0000.0000.0000.000
58A234ILE00.0360.03726.1440.0050.0050.0000.0000.0000.000
59A235TRP00.0050.00626.1570.0070.0070.0000.0000.0000.000
60A236LEU0-0.021-0.02426.6200.0070.0070.0000.0000.0000.000
61A237ASP-1-0.849-0.92029.600-0.052-0.0520.0000.0000.0000.000
62A238THR0-0.051-0.01631.3290.0030.0030.0000.0000.0000.000
63A239TYR0-0.045-0.02830.5390.0060.0060.0000.0000.0000.000
64A240TYR0-0.057-0.03330.9650.0060.0060.0000.0000.0000.000
65A241PRO00.0750.04333.373-0.001-0.0010.0000.0000.0000.000
66A242GLN0-0.031-0.01435.358-0.003-0.0030.0000.0000.0000.000
67A243LEU0-0.0330.00229.9150.0020.0020.0000.0000.0000.000
68A244ALA00.0000.00633.511-0.003-0.0030.0000.0000.0000.000
69A245TYR0-0.019-0.03926.6460.0050.0050.0000.0000.0000.000
70A246TYR0-0.054-0.05027.651-0.003-0.0030.0000.0000.0000.000
71A247ARG10.8060.88719.5920.0990.0990.0000.0000.0000.000
72A248ILE0-0.0010.00819.0320.0110.0110.0000.0000.0000.000
73A249HIS10.8290.91418.5750.0470.0470.0000.0000.0000.000
74A250PHE00.003-0.02413.5780.0110.0110.0000.0000.0000.000
75A251ASP-1-0.886-0.94013.243-0.042-0.0420.0000.0000.0000.000
76A252GLU-1-0.802-0.88512.8690.1710.1710.0000.0000.0000.000
77A253PRO00.0010.0029.218-0.002-0.0020.0000.0000.0000.000
78A254ARG10.9830.9908.118-0.333-0.3330.0000.0000.0000.000
79A255LYS10.8100.89613.491-0.138-0.1380.0000.0000.0000.000
80A256PRO00.0200.02515.788-0.003-0.0030.0000.0000.0000.000
81A257VAL0-0.009-0.00317.7560.0100.0100.0000.0000.0000.000
82A258PHE0-0.014-0.01521.088-0.013-0.0130.0000.0000.0000.000
83A259TRP00.0160.00923.6480.0040.0040.0000.0000.0000.000
84A260LEU00.0420.00426.398-0.006-0.0060.0000.0000.0000.000
85A261SER0-0.038-0.03829.8690.0030.0030.0000.0000.0000.000
86A262ARG10.8890.93332.117-0.001-0.0010.0000.0000.0000.000
87A263GLN0-0.021-0.02635.2050.0000.0000.0000.0000.0000.000
88A264ARG10.8560.90034.4400.0250.0250.0000.0000.0000.000
89A265ASN0-0.0020.00734.893-0.003-0.0030.0000.0000.0000.000
90A266THR00.0200.00736.7180.0000.0000.0000.0000.0000.000
91A267MET0-0.091-0.02032.8570.0000.0000.0000.0000.0000.000
92A268SER00.013-0.02736.8570.0020.0020.0000.0000.0000.000
93A269LYS10.9330.93033.213-0.027-0.0270.0000.0000.0000.000
94A270LYS11.0041.00633.633-0.013-0.0130.0000.0000.0000.000
95A271GLU-1-0.820-0.88234.074-0.001-0.0010.0000.0000.0000.000
96A272LEU00.0000.00431.090-0.002-0.0020.0000.0000.0000.000
97A273GLU-1-0.839-0.91229.6730.0220.0220.0000.0000.0000.000
98A274VAL0-0.025-0.01329.3010.0000.0000.0000.0000.0000.000
99A275LEU0-0.0070.00928.164-0.002-0.0020.0000.0000.0000.000
100A276SER0-0.002-0.01224.966-0.003-0.0030.0000.0000.0000.000
101A277GLN0-0.012-0.01424.636-0.003-0.0030.0000.0000.0000.000
102A278LYS10.8970.94125.3430.0110.0110.0000.0000.0000.000
103A279LEU00.0190.00922.859-0.006-0.0060.0000.0000.0000.000
104A280ARG10.9120.94420.542-0.048-0.0480.0000.0000.0000.000
105A281ALA0-0.060-0.02020.359-0.002-0.0020.0000.0000.0000.000
106A282LEU00.0170.02421.660-0.006-0.0060.0000.0000.0000.000
107A283MET0-0.0150.01316.794-0.019-0.0190.0000.0000.0000.000
108A284PRO0-0.006-0.00216.1530.0170.0170.0000.0000.0000.000
109A285TYR0-0.032-0.03611.6890.0180.0180.0000.0000.0000.000
110A286ALA0-0.0170.00613.4140.0240.0240.0000.0000.0000.000
111A287ASP-1-0.894-0.94215.6380.1320.1320.0000.0000.0000.000
112A288SER0-0.083-0.04217.734-0.006-0.0060.0000.0000.0000.000
113A289VAL00.0710.03919.206-0.002-0.0020.0000.0000.0000.000
114A290ASN00.0110.02821.479-0.003-0.0030.0000.0000.0000.000
115A291ILE00.0190.01223.589-0.007-0.0070.0000.0000.0000.000
116A292THR0-0.004-0.00325.8040.0060.0060.0000.0000.0000.000
117A293LEU0-0.021-0.00327.728-0.006-0.0060.0000.0000.0000.000
118A294MET0-0.015-0.01227.5880.0050.0050.0000.0000.0000.000
119A295ASP-1-0.777-0.86931.195-0.008-0.0080.0000.0000.0000.000
120A296ASP-1-0.684-0.78334.081-0.021-0.0210.0000.0000.0000.000
121A297VAL0-0.026-0.00935.887-0.003-0.0030.0000.0000.0000.000
122A298THR0-0.026-0.02932.5150.0000.0000.0000.0000.0000.000
123A299ALA00.0040.01232.171-0.002-0.0020.0000.0000.0000.000
124A300ALA0-0.024-0.00233.158-0.004-0.0040.0000.0000.0000.000
125A301GLY00.0300.01836.032-0.001-0.0010.0000.0000.0000.000
126A302GLN00.0280.00629.503-0.004-0.0040.0000.0000.0000.000
127A303ALA0-0.0060.01132.944-0.003-0.0030.0000.0000.0000.000
128A304GLU-1-0.804-0.89233.864-0.022-0.0220.0000.0000.0000.000
129A305ALA0-0.025-0.00334.5000.0000.0000.0000.0000.0000.000
130A306GLY00.0590.02332.8280.0000.0000.0000.0000.0000.000
131A307LEU00.0080.00333.659-0.003-0.0030.0000.0000.0000.000
132A308LYS10.8650.92836.5450.0200.0200.0000.0000.0000.000
133A309GLN0-0.049-0.02832.509-0.002-0.0020.0000.0000.0000.000
134A310GLN0-0.052-0.03132.533-0.003-0.0030.0000.0000.0000.000
135A311ALA0-0.0130.00137.030-0.001-0.0010.0000.0000.0000.000
136A312LEU00.0230.02735.696-0.001-0.0010.0000.0000.0000.000
137A313PRO00.0000.01240.2740.0020.0020.0000.0000.0000.000
138A314TYR0-0.015-0.04140.330-0.002-0.0020.0000.0000.0000.000
139A315SER0-0.021-0.00642.3650.0030.0030.0000.0000.0000.000
140A316ARG10.8610.91940.5010.0190.0190.0000.0000.0000.000
141A317ARG10.8940.94542.2340.0290.0290.0000.0000.0000.000
142A318ASN00.0450.02842.426-0.002-0.0020.0000.0000.0000.000
143A319HIS00.0420.02941.0790.0000.0000.0000.0000.0000.000
144A320LYS10.9240.95143.1750.0220.0220.0000.0000.0000.000
145A321GLY00.0570.02740.108-0.001-0.0010.0000.0000.0000.000
146A322GLY00.0350.01638.107-0.002-0.0020.0000.0000.0000.000
147A323VAL0-0.086-0.02537.8620.0030.0030.0000.0000.0000.000
148A324THR00.0540.02137.613-0.004-0.0040.0000.0000.0000.000
149A325PHE0-0.042-0.02436.2740.0040.0040.0000.0000.0000.000
150A326VAL0-0.010-0.01338.345-0.003-0.0030.0000.0000.0000.000
151A327ILE00.0440.01435.6110.0030.0030.0000.0000.0000.000
152A328GLN0-0.061-0.04240.2130.0000.0000.0000.0000.0000.000
153A329GLY00.0160.01442.8380.0000.0000.0000.0000.0000.000
154A330ALA0-0.030-0.00843.126-0.002-0.0020.0000.0000.0000.000
155A331LEU00.000-0.00938.0720.0010.0010.0000.0000.0000.000
156A332ASP-1-0.808-0.89638.525-0.053-0.0530.0000.0000.0000.000
157A333ASP-1-0.875-0.95136.120-0.066-0.0660.0000.0000.0000.000
158A334VAL0-0.043-0.02933.893-0.006-0.0060.0000.0000.0000.000
159A335GLU-1-0.883-0.94633.978-0.046-0.0460.0000.0000.0000.000
160A336ILE0-0.039-0.01634.175-0.002-0.0020.0000.0000.0000.000
161A337LEU0-0.038-0.01928.588-0.004-0.0040.0000.0000.0000.000
162A338ARG10.9470.97430.2020.0520.0520.0000.0000.0000.000
163A339ALA00.0620.03330.9120.0000.0000.0000.0000.0000.000
164A340ARG10.9300.96429.4240.0850.0850.0000.0000.0000.000
165A341GLN00.0230.01525.9430.0020.0020.0000.0000.0000.000
166A342PHE0-0.0320.00426.549-0.001-0.0010.0000.0000.0000.000
167A343VAL00.0110.00528.2260.0010.0010.0000.0000.0000.000
168A344ASP-1-0.915-0.95724.339-0.110-0.1100.0000.0000.0000.000
169A345SER0-0.033-0.04623.617-0.009-0.0090.0000.0000.0000.000
170A346TYR0-0.030-0.01924.4860.0020.0020.0000.0000.0000.000
171A347TYR00.0280.01026.1310.0060.0060.0000.0000.0000.000
172A348ARG10.9060.97319.5080.1190.1190.0000.0000.0000.000
173A349THR0-0.034-0.00521.9270.0020.0020.0000.0000.0000.000
174A350TRP00.010-0.01323.8090.0060.0060.0000.0000.0000.000
175A351GLY00.0030.01625.6600.0030.0030.0000.0000.0000.000
176A352GLY00.022-0.00426.7270.0020.0020.0000.0000.0000.000
177A353ARG10.8680.93829.0760.0530.0530.0000.0000.0000.000
178A354TYR0-0.035-0.00231.8910.0030.0030.0000.0000.0000.000
179A355VAL0-0.0100.00032.9650.0020.0020.0000.0000.0000.000
180A356GLN0-0.038-0.02232.824-0.004-0.0040.0000.0000.0000.000
181A357PHE00.0300.00431.2790.0040.0040.0000.0000.0000.000
182A358ALA0-0.009-0.00135.425-0.003-0.0030.0000.0000.0000.000
183A359ILE00.0040.01337.8140.0010.0010.0000.0000.0000.000
184A360GLU-1-0.790-0.88139.622-0.034-0.0340.0000.0000.0000.000
185A361LEU00.0150.01443.390-0.002-0.0020.0000.0000.0000.000
186A362LYS10.8450.91445.4010.0350.0350.0000.0000.0000.000