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: LJ959

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1964662.837964
FMO2-HF: Nuclear repulsion 1894560.355512
FMO2-HF: Total energy -70102.482453
FMO2-MP2: Total energy -70309.690184


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.
1.4415.841.48-2.796-3.082-0.011
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 : 0.079 / q_NPA : 0.046
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].
3A13VAL00.0130.0183.8530.1512.193-0.014-1.210-0.8170.004
4A14ARG10.8450.9017.3730.6060.6060.0000.0000.0000.000
5A15ILE00.0170.02910.4800.1090.1090.0000.0000.0000.000
6A16ILE00.004-0.00113.6700.0340.0340.0000.0000.0000.000
7A17ALA0-0.012-0.01816.6500.0460.0460.0000.0000.0000.000
8A18GLY00.0740.04919.425-0.035-0.0350.0000.0000.0000.000
9A19LEU0-0.002-0.00521.186-0.019-0.0190.0000.0000.0000.000
10A20TRP0-0.012-0.01216.932-0.038-0.0380.0000.0000.0000.000
11A21ARG10.8610.94116.5620.2400.2400.0000.0000.0000.000
12A22GLY0-0.004-0.00115.2700.0400.0400.0000.0000.0000.000
13A23ARG10.9290.97712.7940.7390.7390.0000.0000.0000.000
14A24LYS10.8150.8917.8361.5371.5370.0000.0000.0000.000
15A25LEU0-0.0010.0008.2710.2340.2340.0000.0000.0000.000
16A26PRO00.0240.0274.850-0.668-0.6680.0000.0000.0000.000
17A27VAL00.0080.0143.1041.5802.1950.066-0.240-0.4400.000
18A28LEU00.0050.0092.393-3.695-1.9531.428-1.346-1.825-0.015
19A38ASP-1-0.770-0.84117.262-0.012-0.0120.0000.0000.0000.000
20A39ARG10.8720.89518.822-0.020-0.0200.0000.0000.0000.000
21A40VAL0-0.048-0.03622.301-0.009-0.0090.0000.0000.0000.000
22A41LYS10.8790.92615.4490.1150.1150.0000.0000.0000.000
23A42GLU-1-0.813-0.87720.194-0.241-0.2410.0000.0000.0000.000
24A43THR0-0.037-0.02922.2260.0010.0010.0000.0000.0000.000
25A44LEU00.0250.03222.0940.0040.0040.0000.0000.0000.000
26A45PHE00.0330.00418.571-0.003-0.0030.0000.0000.0000.000
27A46ASN0-0.017-0.01624.298-0.010-0.0100.0000.0000.0000.000
28A47TRP0-0.027-0.01827.3710.0070.0070.0000.0000.0000.000
29A48LEU00.0540.03224.4090.0030.0030.0000.0000.0000.000
30A49MET0-0.030-0.00826.322-0.005-0.0050.0000.0000.0000.000
31A50PRO0-0.047-0.01828.642-0.004-0.0040.0000.0000.0000.000
32A51TYR00.002-0.00530.7320.0050.0050.0000.0000.0000.000
33A52ILE0-0.0220.00023.8350.0000.0000.0000.0000.0000.000
34A53HIS00.0560.02727.680-0.013-0.0130.0000.0000.0000.000
35A54GLN0-0.087-0.06729.5530.0080.0080.0000.0000.0000.000
36A55SER0-0.0080.01126.4570.0060.0060.0000.0000.0000.000
37A56GLU-1-0.800-0.87426.690-0.164-0.1640.0000.0000.0000.000
38A57CYS0-0.060-0.03322.4530.0120.0120.0000.0000.0000.000
39A58LEU00.0210.01921.414-0.012-0.0120.0000.0000.0000.000
40A59ASP-1-0.848-0.93815.402-0.354-0.3540.0000.0000.0000.000
41A60GLY00.0530.02318.320-0.011-0.0110.0000.0000.0000.000
42A61PHE00.021-0.00116.2790.0340.0340.0000.0000.0000.000
43A62ALA00.0370.04613.7340.0060.0060.0000.0000.0000.000
44A63GLY00.0890.05710.557-0.052-0.0520.0000.0000.0000.000
45A64SER0-0.066-0.0546.441-0.181-0.1810.0000.0000.0000.000
46A65GLY00.0340.0048.281-0.259-0.2590.0000.0000.0000.000
47A66SER0-0.031-0.0239.7950.0040.0040.0000.0000.0000.000
48A67LEU00.0250.01911.6210.0180.0180.0000.0000.0000.000
49A68GLY00.0840.03415.2380.0270.0270.0000.0000.0000.000
50A69PHE0-0.020-0.03210.703-0.001-0.0010.0000.0000.0000.000
51A70GLU-1-0.758-0.84515.044-0.443-0.4430.0000.0000.0000.000
52A71ALA00.014-0.00116.5790.0400.0400.0000.0000.0000.000
53A72LEU0-0.007-0.00217.4370.0180.0180.0000.0000.0000.000
54A73SER0-0.037-0.03217.6700.0180.0180.0000.0000.0000.000
55A74ARG10.7260.82319.0000.3140.3140.0000.0000.0000.000
56A75GLN0-0.045-0.02922.5210.0410.0410.0000.0000.0000.000
57A76ALA00.0250.01822.5460.0230.0230.0000.0000.0000.000
58A77LYS10.7880.92324.5450.1340.1340.0000.0000.0000.000
59A78LYS10.8250.88824.4760.2090.2090.0000.0000.0000.000
60A79VAL0-0.041-0.00818.7840.0100.0100.0000.0000.0000.000
61A80THR0-0.021-0.03021.065-0.027-0.0270.0000.0000.0000.000
62A81PHE0-0.048-0.02814.7090.0020.0020.0000.0000.0000.000
63A82LEU0-0.026-0.00318.3820.0060.0060.0000.0000.0000.000
64A83GLU-1-0.823-0.91013.460-0.156-0.1560.0000.0000.0000.000
65A84LEU0-0.009-0.00516.7250.0020.0020.0000.0000.0000.000
66A85ASP-1-0.793-0.88813.0870.0180.0180.0000.0000.0000.000
67A86LYS10.9430.97014.5670.0940.0940.0000.0000.0000.000
68A87THR0-0.033-0.03710.808-0.062-0.0620.0000.0000.0000.000
69A88VAL0-0.0040.0079.551-0.181-0.1810.0000.0000.0000.000
70A89ALA00.0240.01311.181-0.154-0.1540.0000.0000.0000.000
71A90ASN0-0.042-0.03013.039-0.012-0.0120.0000.0000.0000.000
72A91GLN0-0.014-0.0176.6760.3160.3160.0000.0000.0000.000
73A92LEU00.0090.01310.587-0.147-0.1470.0000.0000.0000.000
74A93LYS10.9530.97812.6720.3050.3050.0000.0000.0000.000
75A94LYS10.8800.9409.6751.3991.3990.0000.0000.0000.000
76A95ASN00.007-0.0028.3500.0700.0700.0000.0000.0000.000
77A96LEU00.0340.02612.7800.0370.0370.0000.0000.0000.000
78A97GLN0-0.031-0.00815.7950.0200.0200.0000.0000.0000.000
79A98THR0-0.027-0.01812.525-0.034-0.0340.0000.0000.0000.000
80A99LEU0-0.048-0.02014.672-0.006-0.0060.0000.0000.0000.000
81A100LYS10.8340.90817.2850.4330.4330.0000.0000.0000.000
82A101CYS00.0270.04519.0730.0240.0240.0000.0000.0000.000
83A102SER00.0210.01621.673-0.007-0.0070.0000.0000.0000.000
84A103SER00.0490.00523.838-0.016-0.0160.0000.0000.0000.000
85A104GLU-1-0.879-0.93325.197-0.209-0.2090.0000.0000.0000.000
86A105GLN00.0070.01823.0550.0020.0020.0000.0000.0000.000
87A106ALA0-0.018-0.02419.560-0.016-0.0160.0000.0000.0000.000
88A107GLU-1-0.822-0.86820.839-0.193-0.1930.0000.0000.0000.000
89A108VAL0-0.019-0.01116.279-0.016-0.0160.0000.0000.0000.000
90A109ILE0-0.0060.00919.4500.0120.0120.0000.0000.0000.000
91A110ASN0-0.070-0.04518.586-0.031-0.0310.0000.0000.0000.000
92A111GLN00.008-0.00520.3330.0310.0310.0000.0000.0000.000
93A112SER00.0390.01820.542-0.013-0.0130.0000.0000.0000.000
94A113SER00.036-0.02220.827-0.005-0.0050.0000.0000.0000.000
95A114LEU0-0.0040.01522.5550.0020.0020.0000.0000.0000.000
96A115ASP-1-0.862-0.90925.1520.0050.0050.0000.0000.0000.000
97A116PHE00.0340.00424.817-0.003-0.0030.0000.0000.0000.000
98A117LEU00.001-0.00525.130-0.002-0.0020.0000.0000.0000.000
99A118LYS10.8360.90428.2970.0090.0090.0000.0000.0000.000
100A119GLN0-0.0130.02030.820-0.002-0.0020.0000.0000.0000.000
101A120PRO00.0500.02432.709-0.006-0.0060.0000.0000.0000.000
102A121GLN0-0.057-0.01432.004-0.010-0.0100.0000.0000.0000.000
103A122ASN0-0.002-0.01335.2890.0060.0060.0000.0000.0000.000
104A123GLN0-0.030-0.01235.5490.0050.0050.0000.0000.0000.000
105A124PRO00.0160.02733.394-0.006-0.0060.0000.0000.0000.000
106A125HIS10.7600.86229.3160.1000.1000.0000.0000.0000.000
107A126PHE00.0200.01725.533-0.011-0.0110.0000.0000.0000.000
108A127ASP-1-0.776-0.86528.336-0.117-0.1170.0000.0000.0000.000
109A128VAL00.006-0.00323.1950.0060.0060.0000.0000.0000.000
110A129VAL00.0110.00823.117-0.011-0.0110.0000.0000.0000.000
111A130PHE0-0.040-0.01818.4060.0060.0060.0000.0000.0000.000
112A131LEU00.001-0.00719.936-0.004-0.0040.0000.0000.0000.000
113A132ASP-1-0.867-0.93914.535-0.103-0.1030.0000.0000.0000.000
114A133PRO0-0.0060.01915.9780.0210.0210.0000.0000.0000.000
115A134PRO0-0.006-0.02015.5860.0190.0190.0000.0000.0000.000
116A135PHE00.0150.01717.771-0.023-0.0230.0000.0000.0000.000
117A136HIS0-0.035-0.02820.5100.0140.0140.0000.0000.0000.000
118A137PHE0-0.010-0.00821.566-0.009-0.0090.0000.0000.0000.000
119A138ASN0-0.005-0.01424.808-0.007-0.0070.0000.0000.0000.000
120A139LEU00.0180.01719.928-0.013-0.0130.0000.0000.0000.000
121A140ALA00.0370.01422.309-0.015-0.0150.0000.0000.0000.000
122A141GLU-1-0.794-0.92523.7290.0030.0030.0000.0000.0000.000
123A142GLN0-0.034-0.01626.399-0.009-0.0090.0000.0000.0000.000
124A143ALA0-0.0030.00324.260-0.008-0.0080.0000.0000.0000.000
125A144ILE0-0.024-0.01025.920-0.011-0.0110.0000.0000.0000.000
126A145SER0-0.011-0.01628.548-0.004-0.0040.0000.0000.0000.000
127A146LEU00.0090.01228.174-0.006-0.0060.0000.0000.0000.000
128A147LEU0-0.025-0.02925.972-0.008-0.0080.0000.0000.0000.000
129A148CYS0-0.047-0.01630.140-0.006-0.0060.0000.0000.0000.000
130A149GLU-1-0.869-0.92533.671-0.014-0.0140.0000.0000.0000.000
131A150ASN0-0.061-0.02732.3940.0010.0010.0000.0000.0000.000
132A151ASN0-0.013-0.01334.133-0.007-0.0070.0000.0000.0000.000
133A152TRP00.0330.01228.356-0.015-0.0150.0000.0000.0000.000
134A153LEU0-0.031-0.00628.467-0.013-0.0130.0000.0000.0000.000
135A154LYS10.8310.88531.2780.1290.1290.0000.0000.0000.000
136A155PRO00.0410.01233.6150.0020.0020.0000.0000.0000.000
137A156ASN0-0.019-0.02334.554-0.001-0.0010.0000.0000.0000.000
138A157ALA0-0.0060.02129.595-0.005-0.0050.0000.0000.0000.000
139A158LEU0-0.023-0.01527.4370.0100.0100.0000.0000.0000.000
140A159ILE0-0.007-0.00425.534-0.013-0.0130.0000.0000.0000.000
141A160TYR0-0.069-0.07118.2730.0080.0080.0000.0000.0000.000
142A161VAL00.0290.00621.690-0.005-0.0050.0000.0000.0000.000
143A162GLU-1-0.748-0.83916.538-0.032-0.0320.0000.0000.0000.000
144A163THR0-0.019-0.03320.1700.0060.0060.0000.0000.0000.000
145A164GLU-1-0.784-0.87121.7680.1720.1720.0000.0000.0000.000
146A165LYS10.7930.87623.119-0.157-0.1570.0000.0000.0000.000
147A166ASP-1-0.815-0.89724.9220.1000.1000.0000.0000.0000.000
148A167LYS10.8500.90328.560-0.106-0.1060.0000.0000.0000.000
149A168PRO0-0.0390.00026.627-0.004-0.0040.0000.0000.0000.000
150A169LEU0-0.0030.01425.319-0.002-0.0020.0000.0000.0000.000
151A170ILE00.0060.01229.852-0.001-0.0010.0000.0000.0000.000
152A171THR0-0.047-0.03432.550-0.003-0.0030.0000.0000.0000.000
153A172PRO00.0350.03132.1100.0030.0030.0000.0000.0000.000
154A173GLU-1-0.930-0.96635.155-0.014-0.0140.0000.0000.0000.000
155A174ASN0-0.024-0.01435.2150.0030.0030.0000.0000.0000.000
156A175TRP00.002-0.00728.445-0.006-0.0060.0000.0000.0000.000
157A176THR0-0.012-0.01434.1780.0050.0050.0000.0000.0000.000
158A177LEU0-0.017-0.00229.283-0.007-0.0070.0000.0000.0000.000
159A178LEU00.0180.02530.7160.0030.0030.0000.0000.0000.000
160A179LYS10.8020.87927.9580.0410.0410.0000.0000.0000.000
161A180GLU-1-0.747-0.85327.4240.0150.0150.0000.0000.0000.000
162A181LYS10.8530.93224.6650.0290.0290.0000.0000.0000.000
163A182THR00.0730.05124.425-0.001-0.0010.0000.0000.0000.000
164A183THR0-0.057-0.02520.940-0.012-0.0120.0000.0000.0000.000
165A184GLY00.0080.00421.2460.0120.0120.0000.0000.0000.000
166A185ILE00.013-0.00617.355-0.003-0.0030.0000.0000.0000.000
167A186VAL00.0090.01717.3970.0040.0040.0000.0000.0000.000
168A187SER0-0.009-0.01420.873-0.008-0.0080.0000.0000.0000.000
169A188TYR0-0.052-0.02717.6520.0000.0000.0000.0000.0000.000
170A189ARG10.8360.89422.831-0.028-0.0280.0000.0000.0000.000
171A190LEU0-0.011-0.00324.509-0.012-0.0120.0000.0000.0000.000
172A191TYR00.0290.00626.7900.0070.0070.0000.0000.0000.000
173A192GLN0-0.030-0.01529.265-0.013-0.0130.0000.0000.0000.000
174A193ASN0-0.023-0.03032.0110.0120.0120.0000.0000.0000.000
175A194LEU0-0.062-0.03433.715-0.005-0.0050.0000.0000.0000.000
176A195GLU-1-0.823-0.87736.495-0.046-0.0460.0000.0000.0000.000