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: VK241

Calculation Name: 2IAD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IAD

Chain ID: A

ChEMBL ID:

UniProt ID: P04228

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptH
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 -1932988.889328
FMO2-HF: Nuclear repulsion 1859734.654781
FMO2-HF: Total energy -73254.234546
FMO2-MP2: Total energy -73472.917854


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:ILE)


Summations of interaction energy for fragment #1(A:1:ILE)
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.
-5.779-2.4360.772-1.803-2.311-0.011
Interaction energy analysis for fragmet #1(A:1:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.025
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].
3A2ALA0-0.012-0.0142.719-3.904-0.6870.772-1.773-2.215-0.011
4A3ASP-1-0.901-0.9374.261-1.402-1.2760.000-0.030-0.0960.000
5A4HIS10.7570.8477.0941.9201.9200.0000.0000.0000.000
6A5VAL00.0010.0115.897-0.558-0.5580.0000.0000.0000.000
7A6GLY00.0190.0177.7460.3210.3210.0000.0000.0000.000
8A7PHE0-0.063-0.0237.533-0.036-0.0360.0000.0000.0000.000
9A8TYR0-0.003-0.02411.1980.0350.0350.0000.0000.0000.000
10A9GLY00.0540.02713.8990.0270.0270.0000.0000.0000.000
11A10THR00.0250.00713.6720.0440.0440.0000.0000.0000.000
12A11THR0-0.062-0.03016.080-0.020-0.0200.0000.0000.0000.000
13A12VAL00.0330.02918.4930.0360.0360.0000.0000.0000.000
14A13TYR0-0.017-0.01620.916-0.027-0.0270.0000.0000.0000.000
15A14GLN00.003-0.00124.1290.0340.0340.0000.0000.0000.000
16A15SER00.031-0.00426.602-0.008-0.0080.0000.0000.0000.000
17A16PRO0-0.0250.00129.667-0.010-0.0100.0000.0000.0000.000
18A17GLY00.0430.01031.739-0.001-0.0010.0000.0000.0000.000
19A18ASP-1-0.948-0.96930.5560.0540.0540.0000.0000.0000.000
20A19ILE0-0.0030.01327.166-0.011-0.0110.0000.0000.0000.000
21A20GLY00.009-0.00725.1870.0160.0160.0000.0000.0000.000
22A21GLN00.008-0.00519.928-0.014-0.0140.0000.0000.0000.000
23A22TYR0-0.046-0.03219.1430.0230.0230.0000.0000.0000.000
24A23THR00.0250.00117.785-0.002-0.0020.0000.0000.0000.000
25A24HIS00.0120.03216.1680.0360.0360.0000.0000.0000.000
26A25GLU-1-0.844-0.93413.465-0.254-0.2540.0000.0000.0000.000
27A26PHE0-0.059-0.03711.637-0.079-0.0790.0000.0000.0000.000
28A27ASP-1-0.772-0.87710.527-1.425-1.4250.0000.0000.0000.000
29A28GLY0-0.0160.00011.6050.0510.0510.0000.0000.0000.000
30A29ASP-1-0.886-0.91412.459-0.346-0.3460.0000.0000.0000.000
31A30GLU-1-0.866-0.95916.063-0.193-0.1930.0000.0000.0000.000
32A31LEU0-0.045-0.03816.5030.0130.0130.0000.0000.0000.000
33A32PHE0-0.047-0.03419.5890.0260.0260.0000.0000.0000.000
34A33TYR00.0500.03021.096-0.001-0.0010.0000.0000.0000.000
35A34VAL0-0.044-0.02223.463-0.002-0.0020.0000.0000.0000.000
36A35ASP-1-0.828-0.92225.970-0.039-0.0390.0000.0000.0000.000
37A36LEU0-0.059-0.02025.9060.0000.0000.0000.0000.0000.000
38A37ASP-1-0.884-0.92929.862-0.007-0.0070.0000.0000.0000.000
39A38LYS10.8660.93733.0120.0490.0490.0000.0000.0000.000
40A39LYS10.9220.95230.8070.0260.0260.0000.0000.0000.000
41A40LYS10.9010.93930.5730.0840.0840.0000.0000.0000.000
42A41THR0-0.006-0.01024.4900.0090.0090.0000.0000.0000.000
43A42VAL0-0.031-0.00326.704-0.006-0.0060.0000.0000.0000.000
44A43TRP00.0410.01521.126-0.008-0.0080.0000.0000.0000.000
45A44ARG10.9461.00621.9870.2030.2030.0000.0000.0000.000
46A45LEU00.0460.02222.2250.0140.0140.0000.0000.0000.000
47A46PRO0-0.003-0.01325.538-0.008-0.0080.0000.0000.0000.000
48A47GLU-1-0.918-0.95826.464-0.218-0.2180.0000.0000.0000.000
49A48PHE00.015-0.01420.258-0.005-0.0050.0000.0000.0000.000
50A49GLY0-0.0030.00225.089-0.004-0.0040.0000.0000.0000.000
51A50GLN0-0.058-0.03526.5820.0110.0110.0000.0000.0000.000
52A51LEU0-0.061-0.02525.6160.0080.0080.0000.0000.0000.000
53A52ILE0-0.052-0.00520.812-0.011-0.0110.0000.0000.0000.000
54A53LEU0-0.005-0.01024.3740.0110.0110.0000.0000.0000.000
55A54PHE00.0140.01420.727-0.008-0.0080.0000.0000.0000.000
56A55GLU-1-0.841-0.91924.029-0.097-0.0970.0000.0000.0000.000
57A56PRO00.0140.00025.2550.0070.0070.0000.0000.0000.000
58A57GLN0-0.054-0.02626.2260.0060.0060.0000.0000.0000.000
59A58GLY00.0140.00723.3000.0130.0130.0000.0000.0000.000
60A59GLY00.0640.02822.6770.0090.0090.0000.0000.0000.000
61A60LEU0-0.008-0.01523.6990.0210.0210.0000.0000.0000.000
62A61GLN0-0.016-0.01124.8790.0050.0050.0000.0000.0000.000
63A62ASN00.0540.02718.4040.0250.0250.0000.0000.0000.000
64A63ILE0-0.036-0.00422.7700.0230.0230.0000.0000.0000.000
65A64ALA0-0.097-0.05925.0360.0170.0170.0000.0000.0000.000
66A65ALA00.0170.01822.5980.0110.0110.0000.0000.0000.000
67A66GLU-1-0.828-0.93119.8600.2010.2010.0000.0000.0000.000
68A67LYS10.9230.98323.385-0.031-0.0310.0000.0000.0000.000
69A68HIS0-0.048-0.02026.3190.0020.0020.0000.0000.0000.000
70A69ASN00.004-0.01721.2530.0030.0030.0000.0000.0000.000
71A70LEU0-0.0030.03724.7360.0180.0180.0000.0000.0000.000
72A71GLY00.0110.00225.6850.0090.0090.0000.0000.0000.000
73A72ILE0-0.030-0.02925.9330.0050.0050.0000.0000.0000.000
74A73LEU00.020-0.00721.5410.0080.0080.0000.0000.0000.000
75A74THR0-0.0020.01225.2740.0080.0080.0000.0000.0000.000
76A75LYS10.8970.95227.849-0.125-0.1250.0000.0000.0000.000
77A76ARG10.9100.96622.149-0.257-0.2570.0000.0000.0000.000
78A77SER0-0.0010.00424.9210.0200.0200.0000.0000.0000.000
79A78ASN0-0.069-0.01927.111-0.007-0.0070.0000.0000.0000.000
80A79PHE0-0.032-0.05130.011-0.009-0.0090.0000.0000.0000.000
81A80THR00.0020.02126.214-0.004-0.0040.0000.0000.0000.000
82A81PRO0-0.0050.00227.2360.0050.0050.0000.0000.0000.000
83A82ALA00.0190.00424.7550.0180.0180.0000.0000.0000.000
84A83THR0-0.016-0.01124.549-0.016-0.0160.0000.0000.0000.000
85A84ASN0-0.020-0.02324.5950.0160.0160.0000.0000.0000.000
86A85GLU-1-0.900-0.94021.5550.2880.2880.0000.0000.0000.000
87A86ALA00.0170.00324.706-0.021-0.0210.0000.0000.0000.000
88A87PRO00.0190.00923.4630.0080.0080.0000.0000.0000.000
89A88GLN0-0.007-0.00620.2970.0100.0100.0000.0000.0000.000
90A89ALA0-0.0250.00823.519-0.011-0.0110.0000.0000.0000.000
91A90THR0-0.032-0.01824.0450.0060.0060.0000.0000.0000.000
92A91VAL0-0.005-0.00326.001-0.010-0.0100.0000.0000.0000.000
93A92PHE0-0.042-0.02322.7440.0010.0010.0000.0000.0000.000
94A93PRO00.0250.02328.292-0.003-0.0030.0000.0000.0000.000
95A94LYS10.9690.98726.3300.1780.1780.0000.0000.0000.000
96A95SER00.002-0.00127.966-0.018-0.0180.0000.0000.0000.000
97A96PRO00.002-0.00730.6260.0090.0090.0000.0000.0000.000
98A97VAL00.0120.01033.1520.0000.0000.0000.0000.0000.000
99A98LEU00.0090.01335.6760.0030.0030.0000.0000.0000.000
100A99LEU00.0140.00639.023-0.001-0.0010.0000.0000.0000.000
101A100GLY00.0030.00542.078-0.001-0.0010.0000.0000.0000.000
102A101GLN0-0.047-0.02837.420-0.004-0.0040.0000.0000.0000.000
103A102PRO0-0.050-0.03737.9790.0000.0000.0000.0000.0000.000
104A103ASN00.0040.01832.485-0.015-0.0150.0000.0000.0000.000
105A104THR0-0.054-0.04429.6360.0020.0020.0000.0000.0000.000
106A105LEU00.0000.00130.676-0.007-0.0070.0000.0000.0000.000
107A106ILE0-0.034-0.02324.588-0.004-0.0040.0000.0000.0000.000
108A107CYS0-0.065-0.02826.8990.0080.0080.0000.0000.0000.000
109A108PHE00.0020.00717.440-0.008-0.0080.0000.0000.0000.000
110A109VAL00.016-0.01522.8970.0150.0150.0000.0000.0000.000
111A110ASP-1-0.798-0.90917.4710.0880.0880.0000.0000.0000.000
112A111ASN0-0.043-0.02618.7050.0290.0290.0000.0000.0000.000
113A112ILE0-0.048-0.00719.922-0.002-0.0020.0000.0000.0000.000
114A113PHE00.0490.02519.8170.0130.0130.0000.0000.0000.000
115A114PRO00.0490.01622.5330.0030.0030.0000.0000.0000.000
116A115PRO0-0.0280.00921.605-0.014-0.0140.0000.0000.0000.000
117A116VAL0-0.032-0.01923.498-0.018-0.0180.0000.0000.0000.000
118A117ILE0-0.035-0.02425.5520.0080.0080.0000.0000.0000.000
119A118ASN00.0320.02428.348-0.014-0.0140.0000.0000.0000.000
120A119ILE00.0040.00925.7250.0030.0030.0000.0000.0000.000
121A120THR00.0080.00330.340-0.006-0.0060.0000.0000.0000.000
122A121TRP00.0500.02329.6130.0040.0040.0000.0000.0000.000
123A122LEU0-0.046-0.02335.2870.0020.0020.0000.0000.0000.000
124A123ARG11.0191.01738.3300.0380.0380.0000.0000.0000.000
125A124ASN0-0.073-0.04340.6720.0030.0030.0000.0000.0000.000
126A125SER0-0.012-0.01141.8400.0030.0030.0000.0000.0000.000
127A126LYS10.8960.96042.6320.0250.0250.0000.0000.0000.000
128A127SER00.021-0.00239.842-0.002-0.0020.0000.0000.0000.000
129A128VAL0-0.079-0.02837.775-0.001-0.0010.0000.0000.0000.000
130A129THR0-0.024-0.01037.745-0.001-0.0010.0000.0000.0000.000
131A130ASP-1-0.865-0.95937.318-0.056-0.0560.0000.0000.0000.000
132A131GLY00.0520.02536.147-0.002-0.0020.0000.0000.0000.000
133A132VAL0-0.056-0.00232.141-0.004-0.0040.0000.0000.0000.000
134A133TYR0-0.064-0.03725.449-0.007-0.0070.0000.0000.0000.000
135A134GLU-1-0.890-0.96326.647-0.022-0.0220.0000.0000.0000.000
136A135THR0-0.013-0.00821.800-0.003-0.0030.0000.0000.0000.000
137A136SER0-0.0060.00321.2530.0310.0310.0000.0000.0000.000
138A137PHE0-0.061-0.03020.250-0.004-0.0040.0000.0000.0000.000
139A138LEU00.0260.02816.150-0.001-0.0010.0000.0000.0000.000
140A139VAL00.0200.00711.9460.0600.0600.0000.0000.0000.000
141A140ASN00.0130.04712.312-0.124-0.1240.0000.0000.0000.000
142A141ARG10.9340.9497.100-1.089-1.0890.0000.0000.0000.000
143A142ASP-1-0.954-0.9859.8890.7240.7240.0000.0000.0000.000
144A143HIS0-0.030-0.01410.705-0.092-0.0920.0000.0000.0000.000
145A144SER00.0350.05414.713-0.082-0.0820.0000.0000.0000.000
146A145PHE0-0.036-0.04515.8130.0010.0010.0000.0000.0000.000
147A146HIS0-0.011-0.02214.413-0.026-0.0260.0000.0000.0000.000
148A147LYS10.8220.90119.0130.0090.0090.0000.0000.0000.000
149A148LEU00.0040.01319.6710.0040.0040.0000.0000.0000.000
150A149SER00.0400.04423.637-0.003-0.0030.0000.0000.0000.000
151A150TYR0-0.027-0.03623.449-0.009-0.0090.0000.0000.0000.000
152A151LEU00.0480.02929.5480.0070.0070.0000.0000.0000.000
153A152THR0-0.0260.00833.188-0.004-0.0040.0000.0000.0000.000
154A153PHE0-0.026-0.01833.7830.0070.0070.0000.0000.0000.000
155A154ILE0-0.003-0.00337.494-0.007-0.0070.0000.0000.0000.000
156A155PRO0-0.055-0.01937.5600.0050.0050.0000.0000.0000.000
157A156SER00.0570.01639.795-0.001-0.0010.0000.0000.0000.000
158A157ASP-1-0.856-0.93042.134-0.039-0.0390.0000.0000.0000.000
159A158ASP-1-1.005-0.98343.880-0.029-0.0290.0000.0000.0000.000
160A159ASP-1-0.924-0.98741.821-0.036-0.0360.0000.0000.0000.000
161A160ILE0-0.0140.01339.361-0.001-0.0010.0000.0000.0000.000
162A161TYR00.003-0.01435.8010.0000.0000.0000.0000.0000.000
163A162ASP-1-0.894-0.95135.1960.0000.0000.0000.0000.0000.000
164A164LYS10.9300.94732.353-0.009-0.0090.0000.0000.0000.000
165A165VAL00.0210.01727.654-0.004-0.0040.0000.0000.0000.000
166A166GLU-1-0.954-0.98430.8320.0330.0330.0000.0000.0000.000
167A167HIS00.029-0.01225.879-0.003-0.0030.0000.0000.0000.000
168A168TRP00.0200.00828.9000.0000.0000.0000.0000.0000.000
169A169GLY0-0.072-0.01728.2960.0020.0020.0000.0000.0000.000
170A170LEU0-0.062-0.03529.3610.0000.0000.0000.0000.0000.000
171A171GLU-1-0.933-0.93231.6770.0900.0900.0000.0000.0000.000
172A172GLU-1-0.976-1.00534.9410.0450.0450.0000.0000.0000.000
173A173PRO0-0.042-0.03634.3420.0010.0010.0000.0000.0000.000
174A174VAL00.0730.05630.109-0.004-0.0040.0000.0000.0000.000
175A175LEU0-0.019-0.02833.103-0.006-0.0060.0000.0000.0000.000
176A176LYS10.8190.92528.977-0.022-0.0220.0000.0000.0000.000
177A177HIS00.0410.01632.401-0.005-0.0050.0000.0000.0000.000
178A178TRP00.017-0.00132.235-0.004-0.0040.0000.0000.0000.000
179A179SER0-0.109-0.05435.1430.0020.0020.0000.0000.0000.000
180A180SER00.0130.01737.537-0.005-0.0050.0000.0000.0000.000
181A181ALA00.1150.08139.222-0.002-0.0020.0000.0000.0000.000
182A182ASP-1-0.852-0.92937.728-0.031-0.0310.0000.0000.0000.000
183A183LEU0-0.086-0.05638.9700.0050.0050.0000.0000.0000.000
184A184VAL00.0550.03037.9330.0020.0020.0000.0000.0000.000
185A185PRO0-0.009-0.01236.963-0.001-0.0010.0000.0000.0000.000
186A186ARG10.9200.97439.264-0.004-0.0040.0000.0000.0000.000