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

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FMODB ID: 3Q82L

Calculation Name: 2IFT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IFT

Chain ID: A

ChEMBL ID:

UniProt ID: P44869

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1965830.807307
FMO2-HF: Nuclear repulsion 1895729.040633
FMO2-HF: Total energy -70101.766674
FMO2-MP2: Total energy -70309.089768


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:11:GLY)


Summations of interaction energy for fragment #1(A:11:GLY)
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.
1.9376.3781.36-2.856-2.946-0.008
Interaction energy analysis for fragmet #1(A:11:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.061 / q_NPA : 0.036
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].
3A13VAL00.0180.0133.8040.3462.341-0.018-1.152-0.8260.004
4A14ARG10.8720.9247.1390.7160.7160.0000.0000.0000.000
5A15ILE00.0040.02110.0320.1540.1540.0000.0000.0000.000
6A16ILE00.0200.02413.0970.0180.0180.0000.0000.0000.000
7A17ALA0-0.002-0.01415.8130.0410.0410.0000.0000.0000.000
8A18GLY00.0650.05418.661-0.036-0.0360.0000.0000.0000.000
9A19LEU0-0.001-0.00620.903-0.017-0.0170.0000.0000.0000.000
10A20TRP0-0.022-0.02216.390-0.045-0.0450.0000.0000.0000.000
11A21ARG10.8880.96516.0040.2420.2420.0000.0000.0000.000
12A22GLY0-0.022-0.01914.8420.0290.0290.0000.0000.0000.000
13A23ARG10.9490.98712.3430.6990.6990.0000.0000.0000.000
14A24LYS10.8210.8957.8231.8691.8690.0000.0000.0000.000
15A25LEU0-0.018-0.0098.1170.1390.1390.0000.0000.0000.000
16A26PRO00.0260.0265.062-0.859-0.8590.0000.0000.0000.000
17A27VAL00.0130.0202.5161.4381.8150.595-0.320-0.6520.000
18A28LEU00.0270.0252.397-3.521-1.4520.783-1.384-1.468-0.012
19A38ASP-1-0.762-0.85616.8880.0400.0400.0000.0000.0000.000
20A39ARG10.8610.89818.370-0.062-0.0620.0000.0000.0000.000
21A40VAL0-0.014-0.01122.088-0.016-0.0160.0000.0000.0000.000
22A41LYS10.9910.98214.8280.0390.0390.0000.0000.0000.000
23A42GLU-1-0.801-0.88419.557-0.203-0.2030.0000.0000.0000.000
24A43THR0-0.044-0.02222.312-0.001-0.0010.0000.0000.0000.000
25A44LEU00.0100.02821.9190.0030.0030.0000.0000.0000.000
26A45PHE00.0570.00218.483-0.005-0.0050.0000.0000.0000.000
27A46ASN0-0.052-0.02224.200-0.013-0.0130.0000.0000.0000.000
28A47TRP0-0.023-0.02627.1360.0030.0030.0000.0000.0000.000
29A48LEU00.0650.04424.4230.0020.0020.0000.0000.0000.000
30A49MET0-0.054-0.00626.181-0.005-0.0050.0000.0000.0000.000
31A50PRO0-0.035-0.01028.461-0.004-0.0040.0000.0000.0000.000
32A51TYR00.027-0.00130.5790.0030.0030.0000.0000.0000.000
33A52ILE0-0.033-0.01823.475-0.001-0.0010.0000.0000.0000.000
34A53HIS00.0630.03927.420-0.009-0.0090.0000.0000.0000.000
35A54GLN0-0.060-0.04229.1410.0050.0050.0000.0000.0000.000
36A55SER0-0.058-0.01326.6280.0070.0070.0000.0000.0000.000
37A56GLU-1-0.877-0.95026.194-0.132-0.1320.0000.0000.0000.000
38A57CYS0-0.042-0.03821.8570.0100.0100.0000.0000.0000.000
39A58LEU00.0350.02921.454-0.010-0.0100.0000.0000.0000.000
40A59ASP-1-0.873-0.94215.340-0.206-0.2060.0000.0000.0000.000
41A60GLY00.023-0.00518.256-0.006-0.0060.0000.0000.0000.000
42A61PHE00.0170.00316.1670.0170.0170.0000.0000.0000.000
43A62ALA00.0290.03213.7040.0120.0120.0000.0000.0000.000
44A63GLY00.0770.05310.718-0.003-0.0030.0000.0000.0000.000
45A64SER0-0.066-0.0566.720-0.109-0.1090.0000.0000.0000.000
46A65GLY00.0590.0338.244-0.238-0.2380.0000.0000.0000.000
47A66SER0-0.029-0.0249.849-0.030-0.0300.0000.0000.0000.000
48A67LEU0-0.0030.00911.357-0.015-0.0150.0000.0000.0000.000
49A68GLY00.1070.05014.9570.0030.0030.0000.0000.0000.000
50A69PHE0-0.015-0.03510.840-0.021-0.0210.0000.0000.0000.000
51A70GLU-1-0.799-0.87114.936-0.413-0.4130.0000.0000.0000.000
52A71ALA00.0360.00416.4610.0240.0240.0000.0000.0000.000
53A72LEU0-0.014-0.00317.1100.0080.0080.0000.0000.0000.000
54A73SER0-0.046-0.04017.4000.0130.0130.0000.0000.0000.000
55A74ARG10.7080.82218.5310.2720.2720.0000.0000.0000.000
56A75GLN0-0.053-0.03222.4010.0350.0350.0000.0000.0000.000
57A76ALA00.0180.02822.8230.0210.0210.0000.0000.0000.000
58A77LYS10.8710.96424.6360.1120.1120.0000.0000.0000.000
59A78LYS10.8920.92424.2580.1530.1530.0000.0000.0000.000
60A79VAL0-0.0460.01318.4020.0110.0110.0000.0000.0000.000
61A80THR00.002-0.01221.247-0.020-0.0200.0000.0000.0000.000
62A81PHE0-0.051-0.03814.495-0.001-0.0010.0000.0000.0000.000
63A82LEU0-0.0040.01318.195-0.002-0.0020.0000.0000.0000.000
64A83GLU-1-0.850-0.93913.3570.0240.0240.0000.0000.0000.000
65A84LEU0-0.0040.00516.740-0.013-0.0130.0000.0000.0000.000
66A85ASP-1-0.800-0.89513.6200.1750.1750.0000.0000.0000.000
67A86LYS10.9680.97714.8040.0430.0430.0000.0000.0000.000
68A87THR0-0.047-0.03611.336-0.079-0.0790.0000.0000.0000.000
69A88VAL0-0.0050.0069.517-0.127-0.1270.0000.0000.0000.000
70A89ALA00.0270.01911.323-0.152-0.1520.0000.0000.0000.000
71A90ASN0-0.041-0.03413.661-0.040-0.0400.0000.0000.0000.000
72A91GLN0-0.001-0.0067.2660.2130.2130.0000.0000.0000.000
73A92LEU00.0170.01711.126-0.140-0.1400.0000.0000.0000.000
74A93LYS10.9840.98812.6520.2060.2060.0000.0000.0000.000
75A94LYS10.9130.96910.2941.2421.2420.0000.0000.0000.000
76A95ASN0-0.019-0.0258.492-0.004-0.0040.0000.0000.0000.000
77A96LEU00.0330.02013.0050.0190.0190.0000.0000.0000.000
78A97GLN0-0.069-0.01516.1790.0070.0070.0000.0000.0000.000
79A98THR0-0.070-0.04112.907-0.045-0.0450.0000.0000.0000.000
80A99LEU0-0.069-0.02614.4130.0210.0210.0000.0000.0000.000
81A100LYS10.9200.95217.4700.3880.3880.0000.0000.0000.000
82A101CYS00.0100.01418.9250.0080.0080.0000.0000.0000.000
83A102SER0-0.0220.00021.770-0.007-0.0070.0000.0000.0000.000
84A103SER00.0360.00323.686-0.014-0.0140.0000.0000.0000.000
85A104GLU-1-0.882-0.94625.090-0.175-0.1750.0000.0000.0000.000
86A105GLN0-0.0340.00022.8120.0000.0000.0000.0000.0000.000
87A106ALA00.001-0.01319.286-0.006-0.0060.0000.0000.0000.000
88A107GLU-1-0.861-0.90321.066-0.146-0.1460.0000.0000.0000.000
89A108VAL0-0.021-0.00916.676-0.005-0.0050.0000.0000.0000.000
90A109ILE0-0.022-0.00219.4710.0110.0110.0000.0000.0000.000
91A110ASN0-0.051-0.04218.698-0.016-0.0160.0000.0000.0000.000
92A111GLN00.0160.00120.2250.0230.0230.0000.0000.0000.000
93A112SER00.0730.05120.321-0.005-0.0050.0000.0000.0000.000
94A113SER00.030-0.02620.712-0.014-0.0140.0000.0000.0000.000
95A114LEU00.0010.00822.739-0.003-0.0030.0000.0000.0000.000
96A115ASP-1-0.875-0.92725.0270.0450.0450.0000.0000.0000.000
97A116PHE00.0220.00524.612-0.007-0.0070.0000.0000.0000.000
98A117LEU0-0.011-0.01824.773-0.006-0.0060.0000.0000.0000.000
99A118LYS10.8460.91328.082-0.033-0.0330.0000.0000.0000.000
100A119GLN0-0.0270.01130.706-0.004-0.0040.0000.0000.0000.000
101A120PRO00.0510.02432.610-0.005-0.0050.0000.0000.0000.000
102A121GLN0-0.062-0.01631.686-0.010-0.0100.0000.0000.0000.000
103A122ASN00.003-0.00235.0070.0050.0050.0000.0000.0000.000
104A123GLN0-0.032-0.01735.5580.0030.0030.0000.0000.0000.000
105A124PRO00.0210.02733.406-0.004-0.0040.0000.0000.0000.000
106A125HIS10.7780.87028.9800.0640.0640.0000.0000.0000.000
107A126PHE00.0020.00225.327-0.008-0.0080.0000.0000.0000.000
108A127ASP-1-0.769-0.85027.928-0.089-0.0890.0000.0000.0000.000
109A128VAL00.000-0.01523.1760.0070.0070.0000.0000.0000.000
110A129VAL00.0120.01023.032-0.009-0.0090.0000.0000.0000.000
111A130PHE0-0.037-0.01318.2860.0060.0060.0000.0000.0000.000
112A131LEU00.001-0.00719.621-0.001-0.0010.0000.0000.0000.000
113A132ASP-1-0.882-0.95114.4930.0200.0200.0000.0000.0000.000
114A133PRO0-0.0060.01815.8730.0270.0270.0000.0000.0000.000
115A134PRO00.008-0.01115.5130.0170.0170.0000.0000.0000.000
116A135PHE00.0050.00017.559-0.032-0.0320.0000.0000.0000.000
117A136HIS0-0.054-0.05220.4790.0160.0160.0000.0000.0000.000
118A137PHE00.0310.02321.826-0.010-0.0100.0000.0000.0000.000
119A138ASN00.002-0.00424.715-0.006-0.0060.0000.0000.0000.000
120A139LEU00.0250.02220.308-0.014-0.0140.0000.0000.0000.000
121A140ALA00.0330.01222.284-0.015-0.0150.0000.0000.0000.000
122A141GLU-1-0.856-0.94123.8280.0450.0450.0000.0000.0000.000
123A142GLN0-0.030-0.02026.495-0.014-0.0140.0000.0000.0000.000
124A143ALA0-0.021-0.00924.180-0.009-0.0090.0000.0000.0000.000
125A144ILE0-0.0090.00025.839-0.013-0.0130.0000.0000.0000.000
126A145SER0-0.010-0.02728.372-0.007-0.0070.0000.0000.0000.000
127A146LEU00.0240.02027.803-0.006-0.0060.0000.0000.0000.000
128A147LEU0-0.056-0.02925.697-0.009-0.0090.0000.0000.0000.000
129A148CYS0-0.053-0.03029.949-0.007-0.0070.0000.0000.0000.000
130A149GLU-1-0.874-0.91333.3770.0160.0160.0000.0000.0000.000
131A150ASN0-0.065-0.03532.313-0.003-0.0030.0000.0000.0000.000
132A151ASN0-0.012-0.01033.886-0.006-0.0060.0000.0000.0000.000
133A152TRP00.0370.01528.208-0.014-0.0140.0000.0000.0000.000
134A153LEU0-0.034-0.00728.291-0.011-0.0110.0000.0000.0000.000
135A154LYS10.8410.90831.0210.0970.0970.0000.0000.0000.000
136A155PRO00.027-0.00533.1920.0020.0020.0000.0000.0000.000
137A156ASN0-0.039-0.02834.162-0.002-0.0020.0000.0000.0000.000
138A157ALA00.0150.03429.198-0.005-0.0050.0000.0000.0000.000
139A158LEU0-0.023-0.01527.1230.0090.0090.0000.0000.0000.000
140A159ILE0-0.004-0.01025.327-0.008-0.0080.0000.0000.0000.000
141A160TYR0-0.096-0.09118.029-0.001-0.0010.0000.0000.0000.000
142A161VAL00.0230.00821.8200.0010.0010.0000.0000.0000.000
143A162GLU-1-0.803-0.86716.5300.0710.0710.0000.0000.0000.000
144A163THR0-0.032-0.03620.3840.0080.0080.0000.0000.0000.000
145A164GLU-1-0.790-0.86521.8800.2350.2350.0000.0000.0000.000
146A165LYS10.7860.87822.917-0.202-0.2020.0000.0000.0000.000
147A166ASP-1-0.852-0.92124.7510.1340.1340.0000.0000.0000.000
148A167LYS10.8550.89128.226-0.137-0.1370.0000.0000.0000.000
149A168PRO0-0.0570.00527.063-0.005-0.0050.0000.0000.0000.000
150A169LEU0-0.0200.00825.757-0.003-0.0030.0000.0000.0000.000
151A170ILE00.0450.03730.217-0.002-0.0020.0000.0000.0000.000
152A171THR0-0.052-0.03232.5550.0010.0010.0000.0000.0000.000
153A172PRO00.0530.04931.8780.0000.0000.0000.0000.0000.000
154A173GLU-1-0.919-0.98034.8540.0060.0060.0000.0000.0000.000
155A174ASN0-0.041-0.00435.4600.0020.0020.0000.0000.0000.000
156A175TRP00.006-0.00928.412-0.004-0.0040.0000.0000.0000.000
157A176THR0-0.016-0.00734.0430.0030.0030.0000.0000.0000.000
158A177LEU0-0.0050.00229.443-0.005-0.0050.0000.0000.0000.000
159A178LEU00.0020.00830.4110.0000.0000.0000.0000.0000.000
160A179LYS10.8210.88527.4640.0150.0150.0000.0000.0000.000
161A180GLU-1-0.746-0.86427.2740.0480.0480.0000.0000.0000.000
162A181LYS10.8510.95024.5240.0020.0020.0000.0000.0000.000
163A182THR00.0790.04524.2840.0030.0030.0000.0000.0000.000
164A183THR0-0.042-0.01320.355-0.014-0.0140.0000.0000.0000.000
165A184GLY00.011-0.00120.9070.0180.0180.0000.0000.0000.000
166A185ILE00.037-0.01617.822-0.008-0.0080.0000.0000.0000.000
167A186VAL00.0240.02917.4370.0030.0030.0000.0000.0000.000
168A187SER0-0.017-0.02020.934-0.015-0.0150.0000.0000.0000.000
169A188TYR0-0.058-0.02617.5930.0020.0020.0000.0000.0000.000
170A189ARG10.8520.90522.899-0.069-0.0690.0000.0000.0000.000
171A190LEU0-0.029-0.00924.519-0.008-0.0080.0000.0000.0000.000
172A191TYR00.0430.01126.7950.0060.0060.0000.0000.0000.000
173A192GLN0-0.020-0.00829.217-0.014-0.0140.0000.0000.0000.000
174A193ASN0-0.056-0.04631.9120.0110.0110.0000.0000.0000.000
175A194LEU0-0.038-0.02033.635-0.006-0.0060.0000.0000.0000.000
176A195GLU-1-0.824-0.88236.308-0.021-0.0210.0000.0000.0000.000