FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-12-18

All entries: 87239

Number of unique PDB entries: 32030

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FMODB ID: 8NRMY

Calculation Name: 2PTU-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PTU

Chain ID: A

ChEMBL ID:

UniProt ID: Q07763

Base Structure: X-ray

Registration Date: 2025-07-09

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -810640.605974
FMO2-HF: Nuclear repulsion 769498.593761
FMO2-HF: Total energy -41142.012213
FMO2-MP2: Total energy -41263.703153


3D Structure Molmil
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:5:ASP)


Summations of interaction energy for fragment #1(A:5:ASP)
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.
-2.4920.1025.324-3.662-4.257-0.031
Interaction energy analysis for fragmet #1(A:5:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.093 / q_NPA : 0.009
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].
4A6SER0-0.0270.0884.051-0.526-0.2480.001-0.116-0.1630.000
5A7SER00.025-0.0643.8480.8642.518-0.020-0.953-0.6810.001
6A7SER0-0.0430.0686.8320.1500.1500.0000.0000.0000.000
7A8GLU00.026-0.1277.068-0.331-0.3310.0000.0000.0000.000
8A8GLU-1-0.980-0.8349.214-0.391-0.3910.0000.0000.0000.000
9A9GLU00.071-0.09310.3340.0940.0940.0000.0000.0000.000
10A9GLU-1-0.985-0.84513.3750.6090.6090.0000.0000.0000.000
11A10VAL00.047-0.12013.829-0.096-0.0960.0000.0000.0000.000
12A10VAL0-0.0520.12613.681-0.003-0.0030.0000.0000.0000.000
13A11VAL00.091-0.11416.2520.0550.0550.0000.0000.0000.000
14A11VAL0-0.0960.11218.996-0.001-0.0010.0000.0000.0000.000
15A12GLY00.021-0.10719.878-0.044-0.0440.0000.0000.0000.000
16A13VAL00.1100.02022.6960.0260.0260.0000.0000.0000.000
17A13VAL0-0.1100.08326.283-0.004-0.0040.0000.0000.0000.000
18A14SER00.088-0.07426.248-0.011-0.0110.0000.0000.0000.000
19A14SER0-0.0830.06128.0940.0000.0000.0000.0000.0000.000
20A15GLY0-0.063-0.12327.727-0.009-0.0090.0000.0000.0000.000
21A16LYS00.018-0.03527.222-0.013-0.0130.0000.0000.0000.000
22A16LYS10.8841.07627.045-0.018-0.0180.0000.0000.0000.000
23A17PRO0-0.019-0.08124.1770.0130.0130.0000.0000.0000.000
24A18VAL00.058-0.01320.842-0.006-0.0060.0000.0000.0000.000
25A18VAL0-0.0510.12418.8440.0040.0040.0000.0000.0000.000
26A19GLN00.075-0.09918.2810.0080.0080.0000.0000.0000.000
27A19GLN0-0.1040.08617.1920.0130.0130.0000.0000.0000.000
28A20LEU00.038-0.12013.8510.0140.0140.0000.0000.0000.000
29A20LEU0-0.0880.10312.7830.0150.0150.0000.0000.0000.000
30A21ARG00.182-0.07613.958-0.048-0.0480.0000.0000.0000.000
31A21ARG10.7451.01414.2750.6680.6680.0000.0000.0000.000
32A22PRO00.046-0.0619.382-0.030-0.0300.0000.0000.0000.000
33A23SER00.007-0.0039.7520.1520.1520.0000.0000.0000.000
34A23SER00.0080.09810.955-0.038-0.0380.0000.0000.0000.000
35A24ASN00.017-0.0648.879-0.333-0.3330.0000.0000.0000.000
36A24ASN0-0.1250.0559.0460.1310.1310.0000.0000.0000.000
37A25ILE00.091-0.1108.122-0.680-0.6800.0000.0000.0000.000
38A25ILE0-0.0290.1177.447-0.072-0.0720.0000.0000.0000.000
39A26GLN00.121-0.1009.5450.3020.3020.0000.0000.0000.000
40A26GLN0-0.1160.07310.913-0.170-0.1700.0000.0000.0000.000
41A27THR0-0.030-0.10211.798-0.101-0.1010.0000.0000.0000.000
42A27THR0-0.0250.09213.6480.0050.0050.0000.0000.0000.000
43A28LYS00.098-0.08314.6160.1020.1020.0000.0000.0000.000
44A28LYS10.8591.05617.3890.5400.5400.0000.0000.0000.000
45A29ASP00.105-0.06416.299-0.078-0.0780.0000.0000.0000.000
46A29ASP-1-0.993-0.86617.739-0.523-0.5230.0000.0000.0000.000
47A30VAL0-0.001-0.12513.887-0.009-0.0090.0000.0000.0000.000
48A30VAL0-0.0550.08212.446-0.037-0.0370.0000.0000.0000.000
49A31SER00.084-0.04114.4190.0770.0770.0000.0000.0000.000
50A31SER0-0.0330.06614.797-0.022-0.0220.0000.0000.0000.000
51A32VAL00.051-0.13312.512-0.171-0.1710.0000.0000.0000.000
52A32VAL0-0.0660.12112.1570.0010.0010.0000.0000.0000.000
53A33GLN00.056-0.08811.8070.0950.0950.0000.0000.0000.000
54A33GLN0-0.0400.09411.8520.0410.0410.0000.0000.0000.000
55A34TRP00.121-0.07911.161-0.075-0.0750.0000.0000.0000.000
56A34TRP0-0.1500.10911.2700.0340.0340.0000.0000.0000.000
57A35LYS00.059-0.09611.927-0.030-0.0300.0000.0000.0000.000
58A35LYS10.7260.96311.643-0.086-0.0860.0000.0000.0000.000
59A36LYS00.142-0.08812.4980.0750.0750.0000.0000.0000.000
60A36LYS10.7601.05215.452-0.346-0.3460.0000.0000.0000.000
61A37THR0-0.020-0.07813.789-0.073-0.0730.0000.0000.0000.000
62A37THR0-0.0860.03512.1930.0060.0060.0000.0000.0000.000
63A38GLU00.136-0.12214.856-0.034-0.0340.0000.0000.0000.000
64A38GLU-1-0.921-0.77219.1840.2880.2880.0000.0000.0000.000
65A39GLN00.032-0.11718.5300.0270.0270.0000.0000.0000.000
66A39GLN0-0.0690.09218.112-0.037-0.0370.0000.0000.0000.000
67A40GLY0-0.032-0.10919.489-0.054-0.0540.0000.0000.0000.000
68A41SER0-0.021-0.00321.053-0.010-0.0100.0000.0000.0000.000
69A41SER0-0.0330.04420.445-0.011-0.0110.0000.0000.0000.000
70A42HIS00.094-0.05718.3530.0600.0600.0000.0000.0000.000
71A42HIS0-0.1260.07018.6370.0160.0160.0000.0000.0000.000
72A43ARG00.093-0.07716.8250.0780.0780.0000.0000.0000.000
73A43ARG10.7870.99617.680-0.180-0.1800.0000.0000.0000.000
74A44LYS00.051-0.09114.493-0.007-0.0070.0000.0000.0000.000
75A44LYS10.8721.0599.541-1.122-1.1220.0000.0000.0000.000
76A45ILE00.118-0.09815.976-0.048-0.0480.0000.0000.0000.000
77A45ILE0-0.0730.12218.006-0.004-0.0040.0000.0000.0000.000
78A46GLU00.093-0.09616.2060.0340.0340.0000.0000.0000.000
79A46GLU-1-0.908-0.78215.8860.0550.0550.0000.0000.0000.000
80A47ILE00.024-0.10716.2690.0000.0000.0000.0000.0000.000
81A47ILE0-0.0840.09715.8990.0000.0000.0000.0000.0000.000
82A48LEU00.209-0.10416.6190.0050.0050.0000.0000.0000.000
83A48LEU0-0.1340.10116.350-0.005-0.0050.0000.0000.0000.000
84A49ASN00.084-0.05515.966-0.021-0.0210.0000.0000.0000.000
85A49ASN0-0.1120.06616.541-0.021-0.0210.0000.0000.0000.000
86A50TRP00.158-0.07716.6610.0380.0380.0000.0000.0000.000
87A50TRP0-0.1070.09816.890-0.014-0.0140.0000.0000.0000.000
88A51TYR00.150-0.03717.310-0.079-0.0790.0000.0000.0000.000
89A51TYR0-0.1370.06015.1460.0070.0070.0000.0000.0000.000
90A52ASN00.060-0.08619.725-0.027-0.0270.0000.0000.0000.000
91A52ASN0-0.0860.06323.519-0.005-0.0050.0000.0000.0000.000
92A53ASP0-0.015-0.11523.333-0.005-0.0050.0000.0000.0000.000
93A53ASP-1-0.950-0.83024.776-0.156-0.1560.0000.0000.0000.000
94A54GLY00.014-0.11122.9050.0150.0150.0000.0000.0000.000
95A55PRO0-0.029-0.02919.6600.0040.0040.0000.0000.0000.000
96A56SER00.0350.00020.5490.0170.0170.0000.0000.0000.000
97A56SER0-0.0350.10221.9250.0090.0090.0000.0000.0000.000
98A57TRP00.110-0.10020.778-0.002-0.0020.0000.0000.0000.000
99A57TRP0-0.1200.10019.3360.0040.0040.0000.0000.0000.000
100A58SER00.017-0.10221.202-0.009-0.0090.0000.0000.0000.000
101A58SER0-0.0610.03719.601-0.008-0.0080.0000.0000.0000.000
102A59ASN00.053-0.06422.4270.0080.0080.0000.0000.0000.000
103A59ASN0-0.1330.06023.1580.0010.0010.0000.0000.0000.000
104A60VAL00.154-0.08625.501-0.010-0.0100.0000.0000.0000.000
105A60VAL0-0.0540.11929.5290.0010.0010.0000.0000.0000.000
106A61SER00.094-0.04927.867-0.011-0.0110.0000.0000.0000.000
107A61SER0-0.0440.05827.5210.0020.0020.0000.0000.0000.000
108A62PHE00.014-0.10023.3250.0020.0020.0000.0000.0000.000
109A62PHE0-0.0980.09120.6470.0020.0020.0000.0000.0000.000
110A63SER00.063-0.08123.809-0.002-0.0020.0000.0000.0000.000
111A63SER00.0220.10426.017-0.001-0.0010.0000.0000.0000.000
112A64ASP00.065-0.10825.717-0.017-0.0170.0000.0000.0000.000
113A64ASP-1-0.991-0.84429.050-0.025-0.0250.0000.0000.0000.000
114A65ILE00.018-0.11224.895-0.004-0.0040.0000.0000.0000.000
115A65ILE0-0.1050.07923.0810.0040.0040.0000.0000.0000.000
116A66TYR00.035-0.10421.0760.0080.0080.0000.0000.0000.000
117A66TYR0-0.0600.08919.5350.0040.0040.0000.0000.0000.000
118A67GLY00.010-0.09520.818-0.004-0.0040.0000.0000.0000.000
119A68PHE00.1470.02318.8570.0070.0070.0000.0000.0000.000
120A68PHE0-0.1040.08815.1270.0000.0000.0000.0000.0000.000
121A69ASP00.045-0.12618.4010.0300.0300.0000.0000.0000.000
122A69ASP-1-0.909-0.79318.384-0.371-0.3710.0000.0000.0000.000
123A70TYR00.059-0.12518.058-0.067-0.0670.0000.0000.0000.000
124A70TYR0-0.0720.09521.5920.0060.0060.0000.0000.0000.000
125A71GLY0-0.025-0.09818.941-0.042-0.0420.0000.0000.0000.000
126A72ASP00.017-0.00215.952-0.079-0.0790.0000.0000.0000.000
127A72ASP-1-0.902-0.83715.979-0.488-0.4880.0000.0000.0000.000
128A73PHE00.041-0.07513.864-0.094-0.0940.0000.0000.0000.000
129A73PHE0-0.0790.06112.186-0.029-0.0290.0000.0000.0000.000
130A74ALA00.216-0.07014.2720.0000.0000.0000.0000.0000.000
131A74ALA0-0.0780.08616.2180.0090.0090.0000.0000.0000.000
132A75LEU00.095-0.09814.8780.0030.0030.0000.0000.0000.000
133A75LEU0-0.1130.09714.7820.0110.0110.0000.0000.0000.000
134A76SER0-0.012-0.08716.4420.0190.0190.0000.0000.0000.000
135A76SER0-0.0210.07919.7030.0020.0020.0000.0000.0000.000
136A77ILE00.105-0.12219.328-0.008-0.0080.0000.0000.0000.000
137A77ILE0-0.1000.11818.4240.0040.0040.0000.0000.0000.000
138A78LYS00.089-0.09021.589-0.001-0.0010.0000.0000.0000.000
139A78LYS10.7601.01824.6270.0640.0640.0000.0000.0000.000
140A79SER00.053-0.08325.183-0.008-0.0080.0000.0000.0000.000
141A79SER0-0.0720.06928.2680.0040.0040.0000.0000.0000.000
142A80ALA00.098-0.11523.8580.0050.0050.0000.0000.0000.000
143A80ALA0-0.0790.12623.1760.0030.0030.0000.0000.0000.000
144A81LYS00.181-0.03724.579-0.008-0.0080.0000.0000.0000.000
145A81LYS10.7841.02725.775-0.099-0.0990.0000.0000.0000.000
146A82LEU00.173-0.09324.0090.0130.0130.0000.0000.0000.000
147A82LEU0-0.0890.12425.259-0.003-0.0030.0000.0000.0000.000
148A83GLN00.064-0.08623.3160.0310.0310.0000.0000.0000.000
149A83GLN0-0.0410.10024.479-0.020-0.0200.0000.0000.0000.000
150A84ASP00.018-0.13120.8550.0320.0320.0000.0000.0000.000
151A84ASP-1-0.867-0.80020.5100.1290.1290.0000.0000.0000.000
152A85SER00.036-0.11318.8090.0140.0140.0000.0000.0000.000
153A85SER0-0.0240.09419.994-0.004-0.0040.0000.0000.0000.000
154A86GLY0-0.060-0.10616.716-0.009-0.0090.0000.0000.0000.000
155A87HIS00.1570.04512.534-0.077-0.0770.0000.0000.0000.000
156A87HIS0-0.0850.1067.943-0.352-0.3520.0000.0000.0000.000
157A88TYR00.017-0.10811.513-0.036-0.0360.0000.0000.0000.000
158A88TYR0-0.0830.04212.079-0.055-0.0550.0000.0000.0000.000
159A89LEU00.096-0.0847.9890.2010.2010.0000.0000.0000.000
160A89LEU0-0.1600.0735.7260.0890.0890.0000.0000.0000.000
161A90LEU00.219-0.0667.5160.0090.0090.0000.0000.0000.000
162A90LEU0-0.1220.1038.124-0.084-0.0840.0000.0000.0000.000
163A91GLU00.001-0.1346.620-0.447-0.4470.0000.0000.0000.000
164A91GLU-1-0.914-0.8197.4310.2930.2930.0000.0000.0000.000
165A92ILE00.122-0.0877.7700.3510.3510.0000.0000.0000.000
166A92ILE0-0.1000.1088.463-0.027-0.0270.0000.0000.0000.000
167A93THR0-0.040-0.0908.857-0.486-0.4860.0000.0000.0000.000
168A93THR0-0.0420.06610.3580.0700.0700.0000.0000.0000.000
169A94ASN00.2180.01911.3680.1060.1060.0000.0000.0000.000
170A94ASN0-0.0860.04211.2880.1020.1020.0000.0000.0000.000
171A95THR00.032-0.09313.2200.0530.0530.0000.0000.0000.000
172A95THR0-0.0180.10117.411-0.018-0.0180.0000.0000.0000.000
173A96GLY0-0.063-0.12514.9370.0790.0790.0000.0000.0000.000
174A97GLY00.0140.00214.0460.0820.0820.0000.0000.0000.000
175A98LYS00.0640.01710.1230.1460.1460.0000.0000.0000.000
176A98LYS10.8551.0419.1120.8730.8730.0000.0000.0000.000
177A99VAL00.029-0.1008.052-0.164-0.1640.0000.0000.0000.000
178A99VAL0-0.0310.1036.2660.0740.0740.0000.0000.0000.000
179A100CYS00.139-0.0844.299-0.627-0.521-0.001-0.014-0.0900.000
180A100CYS0-0.1920.0835.148-0.746-0.7120.001-0.004-0.0310.000
181A101ASN00.130-0.1073.1650.1270.2640.0310.167-0.3360.001
182A101ASN0-0.1270.0682.4940.5850.9940.623-0.480-0.5520.002
183A102LYS00.085-0.0892.090-5.341-6.1344.681-1.960-1.928-0.037
184A102LYS10.8091.0403.6937.4347.7620.003-0.145-0.1860.001
185A103ASN00.110-0.0774.649-0.0880.004-0.002-0.008-0.0820.000
186A103ASN0-0.0930.0463.733-2.093-1.7440.007-0.149-0.2080.001
187A104PHE00.074-0.0886.364-0.213-0.2130.0000.0000.0000.000
188A104PHE0-0.0680.0928.614-0.075-0.0750.0000.0000.0000.000
189A105GLN00.110-0.1089.9960.1040.1040.0000.0000.0000.000
190A105GLN0-0.0800.12012.4490.1300.1300.0000.0000.0000.000
191A106LEU00.130-0.08813.069-0.078-0.0780.0000.0000.0000.000
192A106LEU0-0.1380.08815.530-0.012-0.0120.0000.0000.0000.000
193A107LEU00.068-0.11916.1980.0310.0310.0000.0000.0000.000
194A107LEU0-0.1030.10416.510-0.007-0.0070.0000.0000.0000.000
195A108ILE00.078-0.12019.444-0.034-0.0340.0000.0000.0000.000
196A108ILE0-0.1090.11020.812-0.004-0.0040.0000.0000.0000.000
197A109LEU00.107-0.12922.6960.0190.0190.0000.0000.0000.000
198A109LEU0-0.0990.11523.509-0.001-0.0010.0000.0000.0000.000
199A110ASP0-0.091-0.17425.818-0.029-0.0290.0000.0000.0000.000
200A110ASP-1-0.790-0.86228.6910.1130.1130.0000.0000.0000.000