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

tag_button

FMODB ID: 4JRGN

Calculation Name: 2FD5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FD5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HZ91

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1699472.931684
FMO2-HF: Nuclear repulsion 1632113.172193
FMO2-HF: Total energy -67359.759491
FMO2-MP2: Total energy -67555.800474


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:1:MET)


Summations of interaction energy for fragment #1(A: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.
-2.224-0.453-0.018-0.895-0.8570.003
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.008
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].
3A3ASP-1-0.761-0.8433.877-1.1020.669-0.018-0.895-0.8570.003
4A4LYS10.9350.9396.663-0.697-0.6970.0000.0000.0000.000
5A5LYS10.9461.0069.7600.2600.2600.0000.0000.0000.000
6A6THR00.018-0.0318.4680.1220.1220.0000.0000.0000.000
7A7GLN00.0350.0206.463-0.174-0.1740.0000.0000.0000.000
8A8THR0-0.051-0.0439.5130.0790.0790.0000.0000.0000.000
9A9ARG10.7510.83713.1700.1580.1580.0000.0000.0000.000
10A10ALA00.0230.01311.273-0.002-0.0020.0000.0000.0000.000
11A11ARG10.8320.91512.577-0.391-0.3910.0000.0000.0000.000
12A12ILE0-0.016-0.00515.039-0.020-0.0200.0000.0000.0000.000
13A13LEU00.0330.01516.247-0.004-0.0040.0000.0000.0000.000
14A14GLY00.0260.03216.592-0.013-0.0130.0000.0000.0000.000
15A15ALA0-0.0020.00217.538-0.010-0.0100.0000.0000.0000.000
16A16ALA0-0.008-0.01220.645-0.014-0.0140.0000.0000.0000.000
17A17THR0-0.024-0.02719.201-0.005-0.0050.0000.0000.0000.000
18A18GLN0-0.040-0.01820.760-0.007-0.0070.0000.0000.0000.000
19A19ALA00.0370.01223.153-0.011-0.0110.0000.0000.0000.000
20A20LEU0-0.040-0.00324.778-0.009-0.0090.0000.0000.0000.000
21A21LEU0-0.044-0.02223.021-0.010-0.0100.0000.0000.0000.000
22A22GLU-1-0.956-0.96125.7240.0930.0930.0000.0000.0000.000
23A23ARG10.7470.84228.623-0.066-0.0660.0000.0000.0000.000
24A24GLY00.0510.04730.289-0.003-0.0030.0000.0000.0000.000
25A25ALA0-0.004-0.03729.4580.0050.0050.0000.0000.0000.000
26A26VAL0-0.049-0.02830.4590.0000.0000.0000.0000.0000.000
27A27GLU-1-0.870-0.91533.3070.0420.0420.0000.0000.0000.000
28A28PRO0-0.0050.02128.3760.0040.0040.0000.0000.0000.000
29A29SER0-0.019-0.04029.871-0.006-0.0060.0000.0000.0000.000
30A30VAL00.036-0.00625.2260.0070.0070.0000.0000.0000.000
31A31GLY0-0.005-0.00125.7000.0120.0120.0000.0000.0000.000
32A32GLU-1-0.735-0.81926.4900.0750.0750.0000.0000.0000.000
33A33VAL00.0170.02221.9750.0160.0160.0000.0000.0000.000
34A34MET0-0.052-0.01920.2950.0190.0190.0000.0000.0000.000
35A35GLY00.0220.01221.6840.0260.0260.0000.0000.0000.000
36A36ALA00.001-0.00322.7360.0220.0220.0000.0000.0000.000
37A37ALA00.0120.02117.9640.0280.0280.0000.0000.0000.000
38A38GLY0-0.0030.01617.6470.0590.0590.0000.0000.0000.000
39A39LEU0-0.082-0.05115.9140.0300.0300.0000.0000.0000.000
40A40THR00.0310.00620.026-0.016-0.0160.0000.0000.0000.000
41A41VAL00.0640.02022.505-0.010-0.0100.0000.0000.0000.000
42A42GLY00.0150.00824.632-0.012-0.0120.0000.0000.0000.000
43A43GLY0-0.010-0.00420.995-0.012-0.0120.0000.0000.0000.000
44A44PHE00.0140.00020.882-0.014-0.0140.0000.0000.0000.000
45A45TYR00.0510.00621.830-0.016-0.0160.0000.0000.0000.000
46A46ALA0-0.0480.00019.541-0.016-0.0160.0000.0000.0000.000
47A47HIS0-0.091-0.04514.901-0.061-0.0610.0000.0000.0000.000
48A48PHE00.0600.02218.512-0.026-0.0260.0000.0000.0000.000
49A49GLN00.0320.01322.7690.0050.0050.0000.0000.0000.000
50A50SER00.018-0.00126.4040.0070.0070.0000.0000.0000.000
51A51LYS10.8470.90126.545-0.016-0.0160.0000.0000.0000.000
52A52ASP-1-0.854-0.93027.272-0.019-0.0190.0000.0000.0000.000
53A53ALA0-0.020-0.00225.846-0.006-0.0060.0000.0000.0000.000
54A54LEU0-0.022-0.00321.357-0.009-0.0090.0000.0000.0000.000
55A55MET0-0.018-0.00723.380-0.001-0.0010.0000.0000.0000.000
56A56LEU00.0010.01125.8800.0010.0010.0000.0000.0000.000
57A57GLU-1-0.754-0.84418.422-0.155-0.1550.0000.0000.0000.000
58A58ALA0-0.008-0.01321.155-0.009-0.0090.0000.0000.0000.000
59A59PHE00.000-0.00822.2030.0020.0020.0000.0000.0000.000
60A60GLU-1-0.919-0.97723.347-0.136-0.1360.0000.0000.0000.000
61A61GLN0-0.035-0.01115.9750.0210.0210.0000.0000.0000.000
62A62LEU0-0.013-0.00120.515-0.004-0.0040.0000.0000.0000.000
63A63LEU0-0.021-0.01622.165-0.001-0.0010.0000.0000.0000.000
64A64GLY0-0.005-0.00821.706-0.005-0.0050.0000.0000.0000.000
65A65LYS10.8980.94716.5790.1240.1240.0000.0000.0000.000
66A66ARG10.8110.89120.8240.0280.0280.0000.0000.0000.000
67A67ARG10.9060.94524.4710.1300.1300.0000.0000.0000.000
68A68GLU-1-0.880-0.93017.771-0.200-0.2000.0000.0000.0000.000
69A69LEU0-0.010-0.01420.9450.0020.0020.0000.0000.0000.000
70A70LEU0-0.037-0.01223.2400.0060.0060.0000.0000.0000.000
71A71GLY0-0.007-0.00124.9810.0030.0030.0000.0000.0000.000
72A72GLU-1-0.960-0.97820.656-0.129-0.1290.0000.0000.0000.000
73A73LEU0-0.086-0.03824.5700.0120.0120.0000.0000.0000.000
74A74ASP-1-0.852-0.93228.351-0.096-0.0960.0000.0000.0000.000
75A75PRO0-0.031-0.02828.9400.0050.0050.0000.0000.0000.000
76A76GLY0-0.0230.00231.9940.0020.0020.0000.0000.0000.000
77A77LEU0-0.064-0.01532.4390.0070.0070.0000.0000.0000.000
78A78SER0-0.002-0.03535.835-0.003-0.0030.0000.0000.0000.000
79A79GLY00.0740.03437.2580.0010.0010.0000.0000.0000.000
80A80LYS10.8800.93037.7560.0340.0340.0000.0000.0000.000
81A81GLU-1-0.845-0.88236.901-0.047-0.0470.0000.0000.0000.000
82A82ARG10.8050.87532.0090.0830.0830.0000.0000.0000.000
83A83ARG10.7530.85333.7800.0500.0500.0000.0000.0000.000
84A84ALA0-0.0060.00335.8000.0040.0040.0000.0000.0000.000
85A85LEU00.016-0.00231.3690.0060.0060.0000.0000.0000.000
86A86ALA00.0130.01731.0190.0040.0040.0000.0000.0000.000
87A87ALA00.022-0.00431.9210.0060.0060.0000.0000.0000.000
88A88ALA0-0.049-0.03033.4220.0070.0070.0000.0000.0000.000
89A89PHE0-0.0030.00228.2720.0090.0090.0000.0000.0000.000
90A90TYR00.006-0.00930.0890.0110.0110.0000.0000.0000.000
91A91LEU0-0.0020.01231.2750.0080.0080.0000.0000.0000.000
92A92SER0-0.007-0.00830.3120.0050.0050.0000.0000.0000.000
93A93ARG10.8950.92632.415-0.031-0.0310.0000.0000.0000.000
94A94LYS10.8910.94426.096-0.083-0.0830.0000.0000.0000.000
95A95HIS00.0250.01927.3180.0060.0060.0000.0000.0000.000
96A96ARG10.7670.83529.234-0.034-0.0340.0000.0000.0000.000
97A97ASP-1-0.821-0.88930.9380.0490.0490.0000.0000.0000.000
98A98ALA00.0070.00226.9040.0090.0090.0000.0000.0000.000
99A99GLN0-0.0110.02125.4500.0140.0140.0000.0000.0000.000
100A100VAL0-0.016-0.03823.422-0.003-0.0030.0000.0000.0000.000
101A101ASP-1-0.881-0.92918.0810.1140.1140.0000.0000.0000.000
102A102ALA00.0140.01219.048-0.003-0.0030.0000.0000.0000.000
103A103GLY00.0270.02921.315-0.014-0.0140.0000.0000.0000.000
104A104CYS00.0030.01024.419-0.015-0.0150.0000.0000.0000.000
105A105PRO00.0660.03525.7760.0070.0070.0000.0000.0000.000
106A106LEU00.0200.02828.3640.0030.0030.0000.0000.0000.000
107A107PRO0-0.031-0.02430.9940.0010.0010.0000.0000.0000.000
108A108ALA0-0.0140.00830.7620.0030.0030.0000.0000.0000.000
109A109THR00.029-0.00829.827-0.002-0.0020.0000.0000.0000.000
110A110LEU0-0.0030.00733.207-0.003-0.0030.0000.0000.0000.000
111A111ALA0-0.0020.00636.022-0.002-0.0020.0000.0000.0000.000
112A112GLU-1-0.785-0.88932.9660.0020.0020.0000.0000.0000.000
113A113VAL00.0370.00933.338-0.002-0.0020.0000.0000.0000.000
114A114ALA0-0.037-0.01235.888-0.003-0.0030.0000.0000.0000.000
115A115ARG10.8450.91538.4750.0090.0090.0000.0000.0000.000
116A116LEU00.0050.02832.1430.0020.0020.0000.0000.0000.000
117A117PRO00.012-0.00332.542-0.003-0.0030.0000.0000.0000.000
118A118GLU-1-0.768-0.87533.781-0.055-0.0550.0000.0000.0000.000
119A119GLY00.0260.02631.082-0.003-0.0030.0000.0000.0000.000
120A120PHE00.0310.00028.863-0.005-0.0050.0000.0000.0000.000
121A121ARG10.8600.91531.9020.0430.0430.0000.0000.0000.000
122A122GLU-1-0.831-0.89532.283-0.101-0.1010.0000.0000.0000.000
123A123VAL0-0.035-0.00927.464-0.003-0.0030.0000.0000.0000.000
124A124LEU0-0.017-0.01030.475-0.001-0.0010.0000.0000.0000.000
125A125SER0-0.030-0.02232.5950.0020.0020.0000.0000.0000.000
126A126ARG10.9180.94429.3450.1120.1120.0000.0000.0000.000
127A127HIS0-0.0150.00627.417-0.013-0.0130.0000.0000.0000.000
128A128VAL0-0.006-0.01130.6570.0000.0000.0000.0000.0000.000
129A129GLU-1-0.890-0.94534.053-0.084-0.0840.0000.0000.0000.000
130A130ILE0-0.0140.00628.590-0.002-0.0020.0000.0000.0000.000
131A131MET0-0.042-0.01328.5170.0020.0020.0000.0000.0000.000
132A132VAL00.0210.00832.3000.0020.0020.0000.0000.0000.000
133A133THR0-0.021-0.01934.2030.0020.0020.0000.0000.0000.000
134A134SER0-0.075-0.04431.1570.0000.0000.0000.0000.0000.000
135A135LEU0-0.036-0.01432.9770.0020.0020.0000.0000.0000.000
136A136ALA00.0110.01135.6160.0070.0070.0000.0000.0000.000
137A137GLU-1-0.844-0.90937.613-0.080-0.0800.0000.0000.0000.000
138A138SER0-0.062-0.05040.514-0.001-0.0010.0000.0000.0000.000
139A139PRO00.0270.01143.1470.0000.0000.0000.0000.0000.000
140A140GLU-1-0.823-0.89044.912-0.049-0.0490.0000.0000.0000.000
141A141GLU-1-0.796-0.87341.004-0.051-0.0510.0000.0000.0000.000
142A142THR0-0.025-0.02140.981-0.002-0.0020.0000.0000.0000.000
143A143ASP-1-0.881-0.94741.388-0.043-0.0430.0000.0000.0000.000
144A144VAL0-0.059-0.02142.1690.0030.0030.0000.0000.0000.000
145A145ALA00.0390.01437.6020.0020.0020.0000.0000.0000.000
146A146LEU0-0.0090.00238.2790.0010.0010.0000.0000.0000.000
147A147ALA00.001-0.00439.8240.0030.0030.0000.0000.0000.000
148A148ASP-1-0.691-0.82838.303-0.030-0.0300.0000.0000.0000.000
149A149LEU00.000-0.00133.3450.0030.0030.0000.0000.0000.000
150A150VAL0-0.026-0.00636.5510.0040.0040.0000.0000.0000.000
151A151LEU0-0.028-0.01139.1990.0050.0050.0000.0000.0000.000
152A152MET0-0.020-0.00733.9440.0050.0050.0000.0000.0000.000
153A153ILE0-0.005-0.00433.3420.0060.0060.0000.0000.0000.000
154A154GLY00.0150.00535.4140.0050.0050.0000.0000.0000.000
155A155GLY00.0210.00938.6880.0040.0040.0000.0000.0000.000
156A156LEU0-0.046-0.02831.2300.0050.0050.0000.0000.0000.000
157A157ALA00.0120.01735.7710.0050.0050.0000.0000.0000.000
158A158LEU00.0030.00437.0430.0040.0040.0000.0000.0000.000
159A159ALA00.004-0.00637.1640.0030.0030.0000.0000.0000.000
160A160ARG10.8560.91629.447-0.028-0.0280.0000.0000.0000.000
161A161ALA0-0.024-0.00436.6280.0040.0040.0000.0000.0000.000
162A162LEU0-0.059-0.02939.6580.0010.0010.0000.0000.0000.000
163A163GLY00.0250.03738.0630.0020.0020.0000.0000.0000.000
164A164PRO0-0.041-0.03835.782-0.003-0.0030.0000.0000.0000.000
165A165GLY00.0670.03138.4790.0010.0010.0000.0000.0000.000
166A166GLU-1-0.936-0.96941.7560.0210.0210.0000.0000.0000.000
167A167LEU0-0.007-0.00744.117-0.003-0.0030.0000.0000.0000.000
168A168SER00.0350.02638.936-0.003-0.0030.0000.0000.0000.000
169A169ASP-1-0.760-0.88338.7350.0250.0250.0000.0000.0000.000
170A170ARG10.8890.95340.581-0.010-0.0100.0000.0000.0000.000
171A171VAL00.0170.01940.489-0.003-0.0030.0000.0000.0000.000
172A172LEU0-0.0050.00135.736-0.003-0.0030.0000.0000.0000.000
173A173ARG10.8820.94339.140-0.014-0.0140.0000.0000.0000.000
174A174ALA00.0150.00041.411-0.003-0.0030.0000.0000.0000.000
175A175ALA00.0290.01439.837-0.002-0.0020.0000.0000.0000.000
176A176LYS10.8660.92435.802-0.005-0.0050.0000.0000.0000.000
177A177GLN0-0.066-0.03540.0300.0000.0000.0000.0000.0000.000
178A178ALA0-0.0160.00943.431-0.001-0.0010.0000.0000.0000.000
179A179VAL0-0.042-0.00438.312-0.002-0.0020.0000.0000.0000.000
180A180ASN0-0.077-0.06241.077-0.003-0.0030.0000.0000.0000.000