FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 946K2

Calculation Name: 3GRP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GRP

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-20

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2806772.51237
FMO2-HF: Nuclear repulsion 2715162.446715
FMO2-HF: Total energy -91610.065655
FMO2-MP2: Total energy -91870.483464


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-0.930.6310.633-0.829-1.3640
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.024
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].
3A2PHE0-0.037-0.0403.8710.1251.092-0.010-0.408-0.5490.002
4A3LYS10.8220.9302.583-1.129-0.5350.643-0.421-0.815-0.002
5A4LEU0-0.001-0.0065.416-0.004-0.0040.0000.0000.0000.000
6A5THR0-0.017-0.0185.8900.2340.2340.0000.0000.0000.000
7A6GLY0-0.0060.0158.601-0.094-0.0940.0000.0000.0000.000
8A7ARG10.8540.92410.8530.8560.8560.0000.0000.0000.000
9A8LYS10.8280.93013.3570.3950.3950.0000.0000.0000.000
10A9ALA0-0.008-0.01515.7320.0110.0110.0000.0000.0000.000
11A10LEU00.0080.01917.7420.0230.0230.0000.0000.0000.000
12A11VAL00.008-0.00318.6560.0090.0090.0000.0000.0000.000
13A12THR00.0490.02721.7950.0080.0080.0000.0000.0000.000
14A13GLY00.0140.00725.2150.0130.0130.0000.0000.0000.000
15A14ALA0-0.011-0.00422.7770.0150.0150.0000.0000.0000.000
16A15THR0-0.016-0.00724.4150.0040.0040.0000.0000.0000.000
17A16GLY00.0320.01226.0200.0030.0030.0000.0000.0000.000
18A17GLY0-0.027-0.01025.436-0.002-0.0020.0000.0000.0000.000
19A18ILE00.0190.00522.0580.0130.0130.0000.0000.0000.000
20A19GLY00.0700.03721.3060.0090.0090.0000.0000.0000.000
21A20GLU-1-0.833-0.90120.9660.0990.0990.0000.0000.0000.000
22A21ALA0-0.002-0.00619.1590.0070.0070.0000.0000.0000.000
23A22ILE0-0.025-0.01917.0310.0330.0330.0000.0000.0000.000
24A23ALA00.0230.01615.955-0.003-0.0030.0000.0000.0000.000
25A24ARG10.7830.86315.864-0.154-0.1540.0000.0000.0000.000
26A25CYS0-0.045-0.01112.7740.0550.0550.0000.0000.0000.000
27A26PHE00.032-0.01711.3640.0200.0200.0000.0000.0000.000
28A27HIS0-0.0150.00911.262-0.041-0.0410.0000.0000.0000.000
29A28ALA00.0310.02810.627-0.058-0.0580.0000.0000.0000.000
30A29GLN0-0.068-0.0405.8970.3960.3960.0000.0000.0000.000
31A30GLY00.0360.0137.232-0.398-0.3980.0000.0000.0000.000
32A31ALA0-0.024-0.0039.346-0.112-0.1120.0000.0000.0000.000
33A32ILE00.0210.01712.2530.0690.0690.0000.0000.0000.000
34A33VAL0-0.010-0.00715.3140.0100.0100.0000.0000.0000.000
35A34GLY00.0430.01017.8740.0040.0040.0000.0000.0000.000
36A35LEU0-0.010-0.00620.1680.0150.0150.0000.0000.0000.000
37A36HIS00.0570.01223.3870.0010.0010.0000.0000.0000.000
38A37GLY0-0.009-0.01726.5550.0140.0140.0000.0000.0000.000
39A38THR0-0.012-0.01029.397-0.004-0.0040.0000.0000.0000.000
40A39ARG10.8230.88231.491-0.020-0.0200.0000.0000.0000.000
41A40GLU-1-0.730-0.83830.851-0.031-0.0310.0000.0000.0000.000
42A41ASP-1-0.807-0.86830.8960.0130.0130.0000.0000.0000.000
43A42LYS10.8930.92128.255-0.047-0.0470.0000.0000.0000.000
44A43LEU0-0.024-0.01726.1220.0070.0070.0000.0000.0000.000
45A44LYS10.8880.93725.6790.0290.0290.0000.0000.0000.000
46A45GLU-1-0.857-0.90026.7150.0400.0400.0000.0000.0000.000
47A46ILE0-0.0050.00221.6950.0020.0020.0000.0000.0000.000
48A47ALA00.013-0.00621.9910.0010.0010.0000.0000.0000.000
49A48ALA0-0.049-0.01622.208-0.010-0.0100.0000.0000.0000.000
50A49ASP-1-0.872-0.92221.9560.1050.1050.0000.0000.0000.000
51A50LEU0-0.020-0.00916.6410.0170.0170.0000.0000.0000.000
52A51GLY00.0010.01818.078-0.016-0.0160.0000.0000.0000.000
53A52LYS10.8060.87115.0680.2730.2730.0000.0000.0000.000
54A53ASP-1-0.850-0.90115.467-0.299-0.2990.0000.0000.0000.000
55A54VAL00.0050.00417.681-0.003-0.0030.0000.0000.0000.000
56A55PHE00.0220.01920.2540.0010.0010.0000.0000.0000.000
57A56VAL0-0.025-0.01723.3620.0150.0150.0000.0000.0000.000
58A57PHE00.0100.00523.929-0.003-0.0030.0000.0000.0000.000
59A58SER00.008-0.02928.6330.0110.0110.0000.0000.0000.000
60A59ALA0-0.008-0.00631.525-0.006-0.0060.0000.0000.0000.000
61A60ASN00.0360.03233.1140.0100.0100.0000.0000.0000.000
62A61LEU00.022-0.00229.694-0.003-0.0030.0000.0000.0000.000
63A62SER00.0150.00234.1160.0030.0030.0000.0000.0000.000
64A63ASP-1-0.860-0.92337.238-0.030-0.0300.0000.0000.0000.000
65A64ARG10.9320.97036.9770.0280.0280.0000.0000.0000.000
66A65LYS10.9350.95836.9880.0260.0260.0000.0000.0000.000
67A66SER00.0400.01835.868-0.005-0.0050.0000.0000.0000.000
68A67ILE0-0.0140.00131.841-0.005-0.0050.0000.0000.0000.000
69A68LYS10.8100.87732.2090.0610.0610.0000.0000.0000.000
70A69GLN00.0090.01333.113-0.004-0.0040.0000.0000.0000.000
71A70LEU0-0.0100.00127.814-0.006-0.0060.0000.0000.0000.000
72A71ALA0-0.005-0.00628.327-0.009-0.0090.0000.0000.0000.000
73A72GLU-1-0.865-0.90728.585-0.100-0.1000.0000.0000.0000.000
74A73VAL0-0.031-0.01929.442-0.009-0.0090.0000.0000.0000.000
75A74ALA00.0410.03125.177-0.010-0.0100.0000.0000.0000.000
76A75GLU-1-0.791-0.87024.065-0.212-0.2120.0000.0000.0000.000
77A76ARG10.8140.88725.3030.0890.0890.0000.0000.0000.000
78A77GLU-1-0.913-0.96826.303-0.116-0.1160.0000.0000.0000.000
79A78MET0-0.053-0.00919.400-0.003-0.0030.0000.0000.0000.000
80A79GLU-1-0.908-0.93721.216-0.302-0.3020.0000.0000.0000.000
81A80GLY0-0.071-0.04421.647-0.030-0.0300.0000.0000.0000.000
82A81ILE0-0.001-0.01620.252-0.021-0.0210.0000.0000.0000.000
83A82ASP-1-0.841-0.89716.120-0.417-0.4170.0000.0000.0000.000
84A83ILE0-0.023-0.01813.7430.0150.0150.0000.0000.0000.000
85A84LEU0-0.0190.00418.4530.0080.0080.0000.0000.0000.000
86A85VAL0-0.010-0.01118.1820.0120.0120.0000.0000.0000.000
87A86ASN0-0.030-0.02521.4340.0020.0020.0000.0000.0000.000
88A87ASN0-0.010-0.02623.6400.0280.0280.0000.0000.0000.000
89A88ALA0-0.066-0.01925.5920.0080.0080.0000.0000.0000.000
90A89GLY00.0350.01628.829-0.003-0.0030.0000.0000.0000.000
91A90ILE0-0.063-0.03131.7150.0020.0020.0000.0000.0000.000
92A91THR0-0.006-0.02532.7220.0010.0010.0000.0000.0000.000
93A92ARG10.7900.90235.640-0.021-0.0210.0000.0000.0000.000
94A93ASP-1-0.755-0.87939.1700.0280.0280.0000.0000.0000.000
95A94GLY0-0.0140.00842.1710.0030.0030.0000.0000.0000.000
96A95LEU0-0.033-0.00645.974-0.002-0.0020.0000.0000.0000.000
97A96PHE00.0340.00548.4600.0010.0010.0000.0000.0000.000
98A97VAL00.0160.01752.9570.0000.0000.0000.0000.0000.000
99A98ARG10.7200.81644.384-0.025-0.0250.0000.0000.0000.000
100A99MET00.0330.02550.5510.0010.0010.0000.0000.0000.000
101A100GLN00.0430.00948.4650.0010.0010.0000.0000.0000.000
102A101ASP-1-0.871-0.93447.5430.0130.0130.0000.0000.0000.000
103A102GLN00.0400.00747.044-0.001-0.0010.0000.0000.0000.000
104A103ASP-1-0.808-0.87644.4580.0210.0210.0000.0000.0000.000
105A104TRP0-0.052-0.02642.9840.0040.0040.0000.0000.0000.000
106A105ASP-1-0.870-0.93842.1490.0040.0040.0000.0000.0000.000
107A106ASP-1-0.855-0.92241.1410.0130.0130.0000.0000.0000.000
108A107VAL0-0.023-0.00937.3640.0000.0000.0000.0000.0000.000
109A108LEU00.0120.00337.2750.0000.0000.0000.0000.0000.000
110A109ALA0-0.0140.01437.698-0.005-0.0050.0000.0000.0000.000
111A110VAL0-0.012-0.01034.150-0.004-0.0040.0000.0000.0000.000
112A111ASN00.0090.00032.788-0.003-0.0030.0000.0000.0000.000
113A112LEU0-0.024-0.00232.7700.0020.0020.0000.0000.0000.000
114A113THR0-0.020-0.00533.517-0.008-0.0080.0000.0000.0000.000
115A114ALA00.0170.02832.607-0.008-0.0080.0000.0000.0000.000
116A115ALA00.0380.02528.754-0.008-0.0080.0000.0000.0000.000
117A116SER0-0.031-0.01729.537-0.011-0.0110.0000.0000.0000.000
118A117THR0-0.035-0.04231.814-0.008-0.0080.0000.0000.0000.000
119A118LEU00.0300.01027.228-0.007-0.0070.0000.0000.0000.000
120A119THR0-0.015-0.02726.637-0.012-0.0120.0000.0000.0000.000
121A120ARG10.8130.87428.1640.0460.0460.0000.0000.0000.000
122A121GLU-1-0.824-0.88130.227-0.077-0.0770.0000.0000.0000.000
123A122LEU00.0280.01724.804-0.008-0.0080.0000.0000.0000.000
124A123ILE00.0200.00825.153-0.018-0.0180.0000.0000.0000.000
125A124HIS00.0110.00725.927-0.020-0.0200.0000.0000.0000.000
126A125SER0-0.029-0.05624.672-0.008-0.0080.0000.0000.0000.000
127A126MET0-0.0030.03520.856-0.017-0.0170.0000.0000.0000.000
128A127MET0-0.014-0.00822.512-0.015-0.0150.0000.0000.0000.000
129A128ARG10.8510.93125.1830.1880.1880.0000.0000.0000.000
130A129ARG10.7970.87519.2620.2930.2930.0000.0000.0000.000
131A130ARG10.7930.90320.4240.1900.1900.0000.0000.0000.000
132A131TYR0-0.021-0.04012.600-0.011-0.0110.0000.0000.0000.000
133A132GLY00.0360.01418.3980.0120.0120.0000.0000.0000.000
134A133ARG10.7760.89113.2410.3230.3230.0000.0000.0000.000
135A134ILE00.0150.00919.0020.0030.0030.0000.0000.0000.000
136A135ILE0-0.011-0.00116.9350.0170.0170.0000.0000.0000.000
137A136ASN00.007-0.00821.584-0.007-0.0070.0000.0000.0000.000
138A137ILE00.0140.00120.7990.0160.0160.0000.0000.0000.000
139A138THR0-0.028-0.03124.884-0.005-0.0050.0000.0000.0000.000
140A139SER00.0640.02728.1270.0080.0080.0000.0000.0000.000
141A140ILE0-0.035-0.00828.545-0.002-0.0020.0000.0000.0000.000
142A148GLY00.0740.02243.2150.0010.0010.0000.0000.0000.000
143A149GLN00.002-0.01239.3440.0000.0000.0000.0000.0000.000
144A150THR00.0450.02839.7020.0020.0020.0000.0000.0000.000
145A151ASN00.0420.03040.9740.0000.0000.0000.0000.0000.000
146A152TYR00.002-0.01535.639-0.002-0.0020.0000.0000.0000.000
147A153CYS0-0.074-0.03735.9730.0030.0030.0000.0000.0000.000
148A154ALA00.0330.02336.8870.0000.0000.0000.0000.0000.000
149A155ALA00.0180.01435.361-0.003-0.0030.0000.0000.0000.000
150A156LYS10.8670.93830.032-0.089-0.0890.0000.0000.0000.000
151A157ALA00.0130.00132.4580.0000.0000.0000.0000.0000.000
152A158GLY00.0380.02134.295-0.003-0.0030.0000.0000.0000.000
153A159LEU00.0060.00728.716-0.006-0.0060.0000.0000.0000.000
154A160ILE00.0180.00429.072-0.005-0.0050.0000.0000.0000.000
155A161GLY0-0.0090.00030.564-0.004-0.0040.0000.0000.0000.000
156A162PHE00.001-0.00729.183-0.007-0.0070.0000.0000.0000.000
157A163SER00.003-0.01826.748-0.010-0.0100.0000.0000.0000.000
158A164LYS10.8600.91928.042-0.047-0.0470.0000.0000.0000.000
159A165ALA00.0150.01629.736-0.004-0.0040.0000.0000.0000.000
160A166LEU00.0110.00227.270-0.007-0.0070.0000.0000.0000.000
161A167ALA0-0.031-0.01225.997-0.012-0.0120.0000.0000.0000.000
162A168GLN0-0.048-0.03426.822-0.013-0.0130.0000.0000.0000.000
163A169GLU-1-0.887-0.90329.579-0.070-0.0700.0000.0000.0000.000
164A170ILE00.003-0.01124.959-0.009-0.0090.0000.0000.0000.000
165A171ALA00.0810.05423.645-0.019-0.0190.0000.0000.0000.000
166A172SER0-0.013-0.00423.554-0.023-0.0230.0000.0000.0000.000
167A173ARG10.8390.90724.0680.1510.1510.0000.0000.0000.000
168A174ASN00.0020.00618.6630.0040.0040.0000.0000.0000.000
169A175ILE00.0020.01419.106-0.029-0.0290.0000.0000.0000.000
170A176THR0-0.025-0.00318.1620.0190.0190.0000.0000.0000.000
171A177VAL00.0210.00620.824-0.005-0.0050.0000.0000.0000.000
172A178ASN0-0.031-0.02720.0390.0270.0270.0000.0000.0000.000
173A179CYS0-0.0310.00423.226-0.007-0.0070.0000.0000.0000.000
174A180ILE00.0160.01719.2230.0150.0150.0000.0000.0000.000
175A181ALA0-0.0030.00523.775-0.016-0.0160.0000.0000.0000.000
176A182PRO00.0090.01424.9290.0150.0150.0000.0000.0000.000
177A183GLY00.0180.00726.784-0.014-0.0140.0000.0000.0000.000
178A184PHE00.009-0.00929.324-0.004-0.0040.0000.0000.0000.000
179A185ILE0-0.0180.00824.9850.0160.0160.0000.0000.0000.000
180A186LYS10.8620.91227.339-0.172-0.1720.0000.0000.0000.000
181A187SER00.0110.00328.042-0.003-0.0030.0000.0000.0000.000
182A188ALA00.0450.01930.641-0.001-0.0010.0000.0000.0000.000
183A189MET0-0.069-0.02933.541-0.008-0.0080.0000.0000.0000.000
184A190THR00.0450.00032.119-0.002-0.0020.0000.0000.0000.000
185A191ASP-1-0.811-0.88432.4750.1370.1370.0000.0000.0000.000
186A192LYS10.9280.97135.427-0.075-0.0750.0000.0000.0000.000
187A193LEU0-0.055-0.00436.338-0.006-0.0060.0000.0000.0000.000
188A194ASN00.0640.03239.9330.0030.0030.0000.0000.0000.000
189A195GLU-1-0.763-0.88241.1400.1050.1050.0000.0000.0000.000
190A196LYS10.9550.96842.337-0.065-0.0650.0000.0000.0000.000
191A197GLN0-0.025-0.01241.3800.0000.0000.0000.0000.0000.000
192A198LYS10.8190.90236.949-0.110-0.1100.0000.0000.0000.000
193A199GLU-1-0.848-0.92438.2140.1240.1240.0000.0000.0000.000
194A200ALA0-0.0020.00240.0030.0020.0020.0000.0000.0000.000
195A201ILE0-0.019-0.02135.1150.0010.0010.0000.0000.0000.000
196A202MET0-0.0110.00732.8040.0100.0100.0000.0000.0000.000
197A203ALA00.0030.01536.0140.0060.0060.0000.0000.0000.000
198A204MET0-0.035-0.01936.7040.0000.0000.0000.0000.0000.000
199A205ILE0-0.0020.01330.6310.0020.0020.0000.0000.0000.000
200A206PRO0-0.012-0.00331.5250.0030.0030.0000.0000.0000.000
201A207MET0-0.038-0.01024.6780.0070.0070.0000.0000.0000.000
202A208LYS10.8100.90030.185-0.131-0.1310.0000.0000.0000.000
203A209ARG10.8290.87722.972-0.291-0.2910.0000.0000.0000.000
204A210MET0-0.026-0.01029.397-0.007-0.0070.0000.0000.0000.000
205A211GLY00.0340.01925.2820.0190.0190.0000.0000.0000.000
206A212ILE0-0.005-0.01421.070-0.030-0.0300.0000.0000.0000.000
207A213GLY00.0240.00322.0970.0100.0100.0000.0000.0000.000
208A214GLU-1-0.860-0.94517.1060.4170.4170.0000.0000.0000.000
209A215GLU-1-0.752-0.83817.1860.3490.3490.0000.0000.0000.000
210A216ILE0-0.010-0.00718.3360.0040.0040.0000.0000.0000.000
211A217ALA00.0240.03916.202-0.020-0.0200.0000.0000.0000.000
212A218PHE00.0250.00512.708-0.012-0.0120.0000.0000.0000.000
213A219ALA0-0.0020.00813.6930.0040.0040.0000.0000.0000.000
214A220THR0-0.036-0.04716.055-0.054-0.0540.0000.0000.0000.000
215A221VAL00.0370.0119.833-0.066-0.0660.0000.0000.0000.000
216A222TYR0-0.035-0.00611.566-0.092-0.0920.0000.0000.0000.000
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