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: 5JZ8Z

Calculation Name: 2IU5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IU5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CIV9

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2073182.798846
FMO2-HF: Nuclear repulsion 1998115.845064
FMO2-HF: Total energy -75066.953782
FMO2-MP2: Total energy -75288.353707


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.
-56.06-50.75620.47-12.804-12.968-0.117
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 : -0.046 / 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].
3A3LYS10.9320.9493.783-5.255-3.119-0.030-1.081-1.0250.004
4A4SER0-0.030-0.0133.588-2.599-1.4700.195-0.499-0.8250.005
5A5ILE0-0.007-0.0072.562-1.2630.1740.947-0.458-1.9260.000
6A6ILE00.0520.0445.660-0.831-0.8310.0000.0000.0000.000
7A7THR0-0.020-0.0248.072-0.269-0.2690.0000.0000.0000.000
8A8GLN00.0430.0247.529-0.096-0.0960.0000.0000.0000.000
9A9LYS10.8610.9302.7565.1906.0160.039-0.370-0.4950.001
10A10ILE0-0.035-0.0078.8030.0480.0480.0000.0000.0000.000
11A11ILE0-0.031-0.02012.3650.0230.0230.0000.0000.0000.000
12A12ALA00.0420.01710.4820.0350.0350.0000.0000.0000.000
13A13LYS10.8120.89711.7290.5950.5950.0000.0000.0000.000
14A14ALA00.0170.01013.2540.0680.0680.0000.0000.0000.000
15A15PHE00.003-0.01315.7210.0600.0600.0000.0000.0000.000
16A16LYS10.8790.9209.7481.6951.6950.0000.0000.0000.000
17A17ASP-1-0.816-0.88816.423-0.444-0.4440.0000.0000.0000.000
18A18LEU0-0.065-0.02418.7320.0460.0460.0000.0000.0000.000
19A19MET00.0160.01319.2080.0630.0630.0000.0000.0000.000
20A20GLN0-0.0060.02220.1010.0320.0320.0000.0000.0000.000
21A21SER0-0.040-0.03022.3440.0210.0210.0000.0000.0000.000
22A22ASN0-0.039-0.01124.4900.0530.0530.0000.0000.0000.000
23A23ALA00.0130.01425.130-0.032-0.0320.0000.0000.0000.000
24A24TYR00.1280.03920.3450.0010.0010.0000.0000.0000.000
25A25HIS0-0.0030.00224.130-0.011-0.0110.0000.0000.0000.000
26A26GLN0-0.075-0.04226.3720.0150.0150.0000.0000.0000.000
27A27ILE0-0.0010.03121.4550.0140.0140.0000.0000.0000.000
28A28SER0-0.030-0.04223.506-0.007-0.0070.0000.0000.0000.000
29A29VAL00.0600.01120.030-0.011-0.0110.0000.0000.0000.000
30A30SER0-0.012-0.00821.8100.0100.0100.0000.0000.0000.000
31A31ASP-1-0.806-0.84924.031-0.179-0.1790.0000.0000.0000.000
32A32ILE00.0400.02517.2930.0050.0050.0000.0000.0000.000
33A33MET0-0.043-0.00717.570-0.018-0.0180.0000.0000.0000.000
34A34GLN0-0.062-0.04020.6190.0390.0390.0000.0000.0000.000
35A35THR0-0.041-0.02619.6780.0230.0230.0000.0000.0000.000
36A36ALA00.0140.00616.8480.0010.0010.0000.0000.0000.000
37A37LYS10.8690.95418.4110.1300.1300.0000.0000.0000.000
38A38ILE00.0130.01515.3840.0510.0510.0000.0000.0000.000
39A39ARG10.9610.97119.838-0.136-0.1360.0000.0000.0000.000
40A40ARG11.0110.98320.8240.1070.1070.0000.0000.0000.000
41A41GLN00.0420.01320.861-0.031-0.0310.0000.0000.0000.000
42A42THR0-0.025-0.01416.3180.0190.0190.0000.0000.0000.000
43A43PHE00.0590.02616.3530.0210.0210.0000.0000.0000.000
44A44TYR00.009-0.00816.039-0.022-0.0220.0000.0000.0000.000
45A45ASN0-0.095-0.02915.4900.0320.0320.0000.0000.0000.000
46A46TYR0-0.068-0.03110.7920.1120.1120.0000.0000.0000.000
47A47PHE00.0440.0269.805-0.045-0.0450.0000.0000.0000.000
48A48GLN0-0.063-0.03915.0330.0700.0700.0000.0000.0000.000
49A49ASN0-0.026-0.03217.679-0.012-0.0120.0000.0000.0000.000
50A50GLN00.039-0.01017.298-0.031-0.0310.0000.0000.0000.000
51A51GLU-1-0.914-0.93317.310-0.413-0.4130.0000.0000.0000.000
52A52GLU-1-0.783-0.88614.378-0.343-0.3430.0000.0000.0000.000
53A53LEU0-0.058-0.01912.007-0.101-0.1010.0000.0000.0000.000
54A54LEU0-0.010-0.01012.577-0.188-0.1880.0000.0000.0000.000
55A55SER00.005-0.00213.224-0.127-0.1270.0000.0000.0000.000
56A56TRP00.0390.0124.657-0.148-0.038-0.001-0.005-0.1030.000
57A57ILE0-0.036-0.0218.560-0.478-0.4780.0000.0000.0000.000
58A58PHE0-0.013-0.00610.136-0.278-0.2780.0000.0000.0000.000
59A59GLU-1-0.936-0.9757.862-1.521-1.5210.0000.0000.0000.000
60A60ASN0-0.085-0.0424.243-1.940-1.822-0.001-0.025-0.0920.000
61A61ASP-1-0.743-0.8316.276-3.267-3.2670.0000.0000.0000.000
62A62PHE00.002-0.0168.1780.1150.1150.0000.0000.0000.000
63A63ALA00.0400.0305.5950.2440.2440.0000.0000.0000.000
64A64GLU-1-0.794-0.9031.894-19.431-20.7949.091-4.463-3.265-0.051
65A65LEU0-0.063-0.0235.4541.0891.0890.0000.0000.0000.000
66A66ILE0-0.047-0.0198.8440.4830.4830.0000.0000.0000.000
67A67ASN0-0.045-0.0457.8850.3170.3170.0000.0000.0000.000
68A68ASP-1-0.902-0.9201.871-27.120-26.27810.231-5.900-5.173-0.076
69A69ASN0-0.002-0.0205.0471.0241.093-0.001-0.003-0.0640.000
70A70SER0-0.042-0.0257.3870.0910.0910.0000.0000.0000.000
71A71ASP-1-0.946-0.95910.362-0.243-0.2430.0000.0000.0000.000
72A72TYR0-0.032-0.01713.136-0.052-0.0520.0000.0000.0000.000
73A73TYR0-0.063-0.08016.299-0.016-0.0160.0000.0000.0000.000
74A74GLY00.0810.04414.1370.0410.0410.0000.0000.0000.000
75A75TRP00.0130.01615.004-0.044-0.0440.0000.0000.0000.000
76A76GLN0-0.017-0.00816.411-0.025-0.0250.0000.0000.0000.000
77A77ASN00.0140.01214.8130.0210.0210.0000.0000.0000.000
78A78GLU-1-0.725-0.83811.206-0.958-0.9580.0000.0000.0000.000
79A79LEU00.0010.00913.719-0.064-0.0640.0000.0000.0000.000
80A80LEU0-0.040-0.01216.768-0.005-0.0050.0000.0000.0000.000
81A81LEU0-0.005-0.01411.3370.0290.0290.0000.0000.0000.000
82A82LEU00.0410.03312.969-0.041-0.0410.0000.0000.0000.000
83A83LEU0-0.038-0.03014.4240.0330.0330.0000.0000.0000.000
84A84ARG10.8290.87615.9210.4520.4520.0000.0000.0000.000
85A85TYR0-0.019-0.00811.7320.0870.0870.0000.0000.0000.000
86A86LEU00.001-0.00914.6580.0400.0400.0000.0000.0000.000
87A87ASP-1-0.742-0.86317.392-0.402-0.4020.0000.0000.0000.000
88A88GLU-1-0.971-0.96214.623-0.704-0.7040.0000.0000.0000.000
89A89ASN0-0.122-0.07614.5200.0240.0240.0000.0000.0000.000
90A90GLN00.0580.04317.866-0.001-0.0010.0000.0000.0000.000
91A91ILE0-0.009-0.00521.1010.0120.0120.0000.0000.0000.000
92A92PHE00.006-0.00415.5620.0290.0290.0000.0000.0000.000
93A93TYR00.047-0.01013.6420.0330.0330.0000.0000.0000.000
94A94GLN0-0.061-0.02820.3250.0290.0290.0000.0000.0000.000
95A95LYS10.7910.87822.8020.4090.4090.0000.0000.0000.000
96A96ILE00.0120.01318.4750.0360.0360.0000.0000.0000.000
97A97PHE0-0.004-0.00921.8920.0160.0160.0000.0000.0000.000
98A98VAL0-0.082-0.02724.3130.0340.0340.0000.0000.0000.000
99A99ILE0-0.070-0.03423.0710.0270.0270.0000.0000.0000.000
100A100ASP-1-0.804-0.90120.049-0.522-0.5220.0000.0000.0000.000
101A101LYS10.9030.94423.3630.3320.3320.0000.0000.0000.000
102A102ASN0-0.054-0.03921.6300.0380.0380.0000.0000.0000.000
103A103PHE00.0620.04416.158-0.030-0.0300.0000.0000.0000.000
104A104GLU-1-0.827-0.89919.791-0.443-0.4430.0000.0000.0000.000
105A105HIS0-0.027-0.02621.407-0.021-0.0210.0000.0000.0000.000
106A106PHE00.0480.03811.8010.0280.0280.0000.0000.0000.000
107A107PHE0-0.011-0.00316.682-0.079-0.0790.0000.0000.0000.000
108A108LEU00.006-0.01418.178-0.034-0.0340.0000.0000.0000.000
109A109ILE00.0260.01915.096-0.005-0.0050.0000.0000.0000.000
110A110GLN0-0.028-0.00712.381-0.224-0.2240.0000.0000.0000.000
111A111TRP00.016-0.00815.252-0.054-0.0540.0000.0000.0000.000
112A112GLU-1-0.925-0.98218.228-0.486-0.4860.0000.0000.0000.000
113A113ASN0-0.0010.01412.7140.1390.1390.0000.0000.0000.000
114A114LEU0-0.022-0.00914.6930.0120.0120.0000.0000.0000.000
115A115LEU0-0.049-0.04316.2210.0700.0700.0000.0000.0000.000
116A116ASP-1-0.832-0.91016.804-0.501-0.5010.0000.0000.0000.000
117A117LYS10.7570.85612.0370.9530.9530.0000.0000.0000.000
118A118VAL0-0.023-0.01816.3340.0750.0750.0000.0000.0000.000
119A119ILE0-0.010-0.00319.3100.0630.0630.0000.0000.0000.000
120A120PHE00.0060.00114.7330.0490.0490.0000.0000.0000.000
121A121ASP-1-0.753-0.87416.176-0.513-0.5130.0000.0000.0000.000
122A122GLN0-0.0100.00319.0180.0360.0360.0000.0000.0000.000
123A123GLU-1-0.781-0.86622.459-0.211-0.2110.0000.0000.0000.000
124A124LYS10.7940.91915.9640.4150.4150.0000.0000.0000.000
125A125LYS10.8050.92122.4440.2290.2290.0000.0000.0000.000
126A126SER0-0.035-0.02524.4750.0270.0270.0000.0000.0000.000
127A127ASP-1-0.885-0.92327.145-0.120-0.1200.0000.0000.0000.000
128A128TYR0-0.078-0.06426.458-0.013-0.0130.0000.0000.0000.000
129A129HIS0-0.071-0.03030.5070.0040.0040.0000.0000.0000.000
130A130TRP0-0.073-0.03925.373-0.002-0.0020.0000.0000.0000.000
131A131SER0-0.002-0.04930.433-0.001-0.0010.0000.0000.0000.000
132A132ASP-1-0.861-0.95027.128-0.209-0.2090.0000.0000.0000.000
133A133LEU0-0.066-0.02827.882-0.021-0.0210.0000.0000.0000.000
134A134GLU-1-0.808-0.87729.696-0.187-0.1870.0000.0000.0000.000
135A135LYS10.8930.94124.7080.2180.2180.0000.0000.0000.000
136A136SER00.0210.02424.898-0.027-0.0270.0000.0000.0000.000
137A137PHE0-0.050-0.02425.971-0.021-0.0210.0000.0000.0000.000
138A138ILE00.0260.01225.744-0.014-0.0140.0000.0000.0000.000
139A139CYS00.0020.00921.431-0.010-0.0100.0000.0000.0000.000
140A140ARG10.9490.96423.6390.2870.2870.0000.0000.0000.000
141A141TYR0-0.065-0.01725.129-0.002-0.0020.0000.0000.0000.000
142A142ASN0-0.009-0.03524.7150.0030.0030.0000.0000.0000.000
143A143ALA00.0340.03921.379-0.015-0.0150.0000.0000.0000.000
144A144ALA0-0.001-0.00122.907-0.020-0.0200.0000.0000.0000.000
145A145ALA0-0.0080.00125.6410.0040.0040.0000.0000.0000.000
146A146ILE00.0250.00321.3460.0080.0080.0000.0000.0000.000
147A147CYS00.0010.03522.264-0.025-0.0250.0000.0000.0000.000
148A148ALA0-0.031-0.01123.3150.0020.0020.0000.0000.0000.000
149A149ILE00.0190.01025.9850.0130.0130.0000.0000.0000.000
150A150THR0-0.004-0.02221.118-0.001-0.0010.0000.0000.0000.000
151A151ARG10.8700.93323.6520.3900.3900.0000.0000.0000.000
152A152GLU-1-0.906-0.93524.511-0.276-0.2760.0000.0000.0000.000
153A153SER0-0.033-0.03024.9610.0260.0260.0000.0000.0000.000
154A154ILE00.0160.01220.2140.0190.0190.0000.0000.0000.000
155A155ILE0-0.024-0.01924.3710.0230.0230.0000.0000.0000.000
156A156ARG10.8230.90227.2630.2910.2910.0000.0000.0000.000
157A157GLY0-0.0190.01726.7580.0220.0220.0000.0000.0000.000
158A158ASN0-0.156-0.08327.3890.0300.0300.0000.0000.0000.000
159A159SER0-0.017-0.01124.077-0.013-0.0130.0000.0000.0000.000
160A160LEU00.045-0.02120.3760.0200.0200.0000.0000.0000.000
161A161GLU-1-0.775-0.84421.036-0.383-0.3830.0000.0000.0000.000
162A162LYS10.8830.94222.7020.3070.3070.0000.0000.0000.000
163A163LEU0-0.024-0.01224.8680.0270.0270.0000.0000.0000.000
164A164TYR0-0.023-0.02019.6000.0240.0240.0000.0000.0000.000
165A165SER00.0200.00423.931-0.003-0.0030.0000.0000.0000.000
166A166GLN0-0.015-0.01526.6560.0030.0030.0000.0000.0000.000
167A167ILE00.0350.02022.9360.0090.0090.0000.0000.0000.000
168A168VAL00.0470.02422.1900.0000.0000.0000.0000.0000.000
169A169ASN0-0.022-0.01524.7850.0120.0120.0000.0000.0000.000
170A170LEU0-0.014-0.00528.3140.0160.0160.0000.0000.0000.000
171A171LEU00.0020.02022.3130.0090.0090.0000.0000.0000.000
172A172LEU00.013-0.00124.7670.0140.0140.0000.0000.0000.000
173A173ALA0-0.044-0.01827.4700.0190.0190.0000.0000.0000.000
174A174GLN0-0.054-0.03428.3390.0160.0160.0000.0000.0000.000
175A175ILE00.0220.00324.1840.0110.0110.0000.0000.0000.000
176A176LYS10.8270.90128.4940.1780.1780.0000.0000.0000.000
177A177ILE0-0.041-0.01631.2820.0150.0150.0000.0000.0000.000
178A178PHE00.0080.01230.4210.0070.0070.0000.0000.0000.000
179A179GLU-1-0.835-0.87629.840-0.159-0.1590.0000.0000.0000.000