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: 6N2VZ

Calculation Name: 1A58-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1A58

Chain ID: A

ChEMBL ID:

UniProt ID: Q27450

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1891386.406248
FMO2-HF: Nuclear repulsion 1821578.513584
FMO2-HF: Total energy -69807.892664
FMO2-MP2: Total energy -70006.364352


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.
-12.697-13.65514.452-6.292-7.199-0.056
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 : 0.005 / q_NPA : -0.003
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].
3A3LYS11.0100.9953.877-0.2671.836-0.016-1.244-0.8430.004
4A4LYS10.9200.9595.8863.2003.2000.0000.0000.0000.000
5A5ASP-1-0.790-0.8951.865-15.969-18.74111.076-4.776-3.527-0.057
6A6ARG10.7260.8514.8922.7992.916-0.001-0.004-0.1110.000
7A7ARG10.9070.9546.8450.4900.4900.0000.0000.0000.000
8A8ARG10.8760.9199.7430.7560.7560.0000.0000.0000.000
9A9VAL00.0090.00613.2650.0480.0480.0000.0000.0000.000
10A10PHE0-0.028-0.01816.099-0.014-0.0140.0000.0000.0000.000
11A11LEU00.0310.00719.8070.0280.0280.0000.0000.0000.000
12A12ASP-1-0.793-0.84922.929-0.158-0.1580.0000.0000.0000.000
13A13VAL0-0.040-0.03026.0740.0140.0140.0000.0000.0000.000
14A14THR0-0.031-0.01528.692-0.002-0.0020.0000.0000.0000.000
15A15ILE00.001-0.01132.4990.0020.0020.0000.0000.0000.000
16A16ASP-1-0.832-0.91535.159-0.049-0.0490.0000.0000.0000.000
17A17GLY0-0.0050.00536.3390.0010.0010.0000.0000.0000.000
18A18ASN0-0.043-0.02736.416-0.005-0.0050.0000.0000.0000.000
19A19LEU0-0.014-0.01629.929-0.001-0.0010.0000.0000.0000.000
20A20ALA0-0.015-0.00531.316-0.001-0.0010.0000.0000.0000.000
21A21GLY00.0220.00329.035-0.006-0.0060.0000.0000.0000.000
22A22ARG10.8380.89522.7410.1990.1990.0000.0000.0000.000
23A23ILE00.0080.02120.756-0.015-0.0150.0000.0000.0000.000
24A24VAL0-0.017-0.01217.7220.0050.0050.0000.0000.0000.000
25A25MET0-0.024-0.01215.5830.0050.0050.0000.0000.0000.000
26A26GLU-1-0.836-0.89710.501-0.990-0.9900.0000.0000.0000.000
27A27LEU0-0.002-0.0039.5460.0780.0780.0000.0000.0000.000
28A28TYR00.005-0.0187.181-0.290-0.2900.0000.0000.0000.000
29A29ASN00.007-0.0284.861-0.122-0.1220.0000.0000.0000.000
30A30ASP-1-0.794-0.8652.081-3.309-2.4023.331-1.965-2.2730.000
31A31ILE0-0.040-0.0132.7751.7140.4010.0621.697-0.445-0.003
32A32ALA00.0260.0226.5470.2210.2210.0000.0000.0000.000
33A33PRO00.0540.0435.964-0.170-0.1700.0000.0000.0000.000
34A34ARG10.8620.9177.569-0.831-0.8310.0000.0000.0000.000
35A35THR0-0.004-0.03311.343-0.136-0.1360.0000.0000.0000.000
36A36CYS0-0.051-0.0128.592-0.155-0.1550.0000.0000.0000.000
37A37ASN0-0.033-0.01510.136-0.166-0.1660.0000.0000.0000.000
38A38ASN00.008-0.00711.539-0.061-0.0610.0000.0000.0000.000
39A39PHE00.0660.02414.109-0.043-0.0430.0000.0000.0000.000
40A40LEU00.0140.01212.111-0.031-0.0310.0000.0000.0000.000
41A41MET00.0100.00714.461-0.037-0.0370.0000.0000.0000.000
42A42LEU0-0.0110.01416.733-0.015-0.0150.0000.0000.0000.000
43A43CYS0-0.039-0.02017.427-0.022-0.0220.0000.0000.0000.000
44A44THR0-0.016-0.02217.290-0.006-0.0060.0000.0000.0000.000
45A45GLY0-0.0030.02119.923-0.003-0.0030.0000.0000.0000.000
46A46MET0-0.016-0.02218.5270.0210.0210.0000.0000.0000.000
47A47ALA00.0020.00218.8620.0250.0250.0000.0000.0000.000
48A48GLY00.0070.01820.6980.0170.0170.0000.0000.0000.000
49A49THR0-0.002-0.00824.542-0.016-0.0160.0000.0000.0000.000
50A50GLY0-0.046-0.01325.1860.0190.0190.0000.0000.0000.000
51A51LYS10.8680.92221.443-0.236-0.2360.0000.0000.0000.000
52A52ILE0-0.036-0.01226.985-0.005-0.0050.0000.0000.0000.000
53A53SER0-0.068-0.06127.986-0.014-0.0140.0000.0000.0000.000
54A54GLY00.0170.01829.809-0.010-0.0100.0000.0000.0000.000
55A55LYS10.8410.92929.615-0.044-0.0440.0000.0000.0000.000
56A56PRO00.030-0.00327.1290.0120.0120.0000.0000.0000.000
57A57LEU0-0.0310.00421.531-0.005-0.0050.0000.0000.0000.000
58A58HIS0-0.052-0.04422.286-0.009-0.0090.0000.0000.0000.000
59A59TYR0-0.027-0.03218.9100.0040.0040.0000.0000.0000.000
60A60LYS10.9040.97124.2620.0540.0540.0000.0000.0000.000
61A61GLY00.0170.01226.7490.0100.0100.0000.0000.0000.000
62A62SER0-0.086-0.04526.3380.0050.0050.0000.0000.0000.000
63A63THR00.024-0.00528.862-0.007-0.0070.0000.0000.0000.000
64A64PHE00.018-0.00323.9010.0040.0040.0000.0000.0000.000
65A65HIS0-0.051-0.01127.248-0.004-0.0040.0000.0000.0000.000
66A66ARG10.8600.91630.0130.0190.0190.0000.0000.0000.000
67A67VAL00.0080.01029.840-0.006-0.0060.0000.0000.0000.000
68A68ILE0-0.029-0.01730.5320.0080.0080.0000.0000.0000.000
69A69LYS10.8160.90131.2540.0550.0550.0000.0000.0000.000
70A70ASN00.0230.02332.1450.0020.0020.0000.0000.0000.000
71A71PHE0-0.0130.01627.237-0.001-0.0010.0000.0000.0000.000
72A72MET00.0220.01725.680-0.008-0.0080.0000.0000.0000.000
73A73ILE0-0.0090.01525.3590.0090.0090.0000.0000.0000.000
74A74GLN00.0560.01625.220-0.007-0.0070.0000.0000.0000.000
75A75GLY00.0390.01825.012-0.001-0.0010.0000.0000.0000.000
76A76GLY00.0540.02823.5750.0080.0080.0000.0000.0000.000
77A77ASP-1-0.747-0.86424.5480.0470.0470.0000.0000.0000.000
78A78PHE00.0930.03523.534-0.010-0.0100.0000.0000.0000.000
79A79THR0-0.040-0.01327.957-0.002-0.0020.0000.0000.0000.000
80A80LYS10.8880.93430.479-0.041-0.0410.0000.0000.0000.000
81A81GLY00.0450.04831.129-0.004-0.0040.0000.0000.0000.000
82A82ASP-1-0.823-0.89132.1160.0140.0140.0000.0000.0000.000
83A83GLY00.0130.02229.875-0.004-0.0040.0000.0000.0000.000
84A84THR0-0.092-0.06830.2530.0090.0090.0000.0000.0000.000
85A85GLY00.0180.01029.7370.0080.0080.0000.0000.0000.000
86A86GLY0-0.011-0.00825.724-0.004-0.0040.0000.0000.0000.000
87A87GLU-1-0.760-0.84024.2340.1460.1460.0000.0000.0000.000
88A88SER0-0.011-0.00519.0770.0010.0010.0000.0000.0000.000
89A89ILE00.0280.00015.012-0.001-0.0010.0000.0000.0000.000
90A90TYR0-0.041-0.03813.4840.0490.0490.0000.0000.0000.000
91A91GLY0-0.020-0.00319.4320.0010.0010.0000.0000.0000.000
92A92GLY00.011-0.00623.2520.0110.0110.0000.0000.0000.000
93A93MET0-0.071-0.02422.372-0.018-0.0180.0000.0000.0000.000
94A94PHE0-0.019-0.01315.0290.0230.0230.0000.0000.0000.000
95A95ASP-1-0.765-0.88516.8530.3670.3670.0000.0000.0000.000
96A96ASP-1-0.830-0.90017.2100.1640.1640.0000.0000.0000.000
97A97GLU-1-0.765-0.85810.7010.7810.7810.0000.0000.0000.000
98A98GLU-1-0.883-0.94211.7230.1710.1710.0000.0000.0000.000
99A99PHE00.0240.02412.768-0.048-0.0480.0000.0000.0000.000
100A100VAL0-0.011-0.0119.845-0.058-0.0580.0000.0000.0000.000
101A101MET0-0.0240.01210.837-0.078-0.0780.0000.0000.0000.000
102A102LYS10.8440.92013.5890.2010.2010.0000.0000.0000.000
103A103HIS00.009-0.00717.358-0.026-0.0260.0000.0000.0000.000
104A104ASP-1-0.880-0.95018.453-0.242-0.2420.0000.0000.0000.000
105A105GLU-1-0.851-0.90918.458-0.347-0.3470.0000.0000.0000.000
106A106PRO0-0.0050.00421.2850.0100.0100.0000.0000.0000.000
107A107PHE00.021-0.00921.147-0.032-0.0320.0000.0000.0000.000
108A108VAL00.0070.02816.196-0.035-0.0350.0000.0000.0000.000
109A109VAL0-0.017-0.01515.8130.0360.0360.0000.0000.0000.000
110A110SER00.018-0.01115.9870.0030.0030.0000.0000.0000.000
111A111MET00.0150.02116.549-0.003-0.0030.0000.0000.0000.000
112A112ALA0-0.046-0.02219.227-0.003-0.0030.0000.0000.0000.000
113A113ASN0-0.039-0.02021.536-0.004-0.0040.0000.0000.0000.000
114A114LYS10.8420.89824.251-0.067-0.0670.0000.0000.0000.000
115A115GLY00.0460.03326.012-0.004-0.0040.0000.0000.0000.000
116A116PRO00.0100.02023.3010.0010.0010.0000.0000.0000.000
117A117ASN0-0.048-0.04520.202-0.015-0.0150.0000.0000.0000.000
118A118THR00.000-0.00322.210-0.005-0.0050.0000.0000.0000.000
119A119ASN0-0.021-0.01718.244-0.063-0.0630.0000.0000.0000.000
120A120GLY00.0580.01720.8720.0230.0230.0000.0000.0000.000
121A121SER0-0.005-0.01020.1310.0160.0160.0000.0000.0000.000
122A122GLN0-0.076-0.04821.571-0.031-0.0310.0000.0000.0000.000
123A123PHE00.0050.01319.6510.0110.0110.0000.0000.0000.000
124A124PHE0-0.044-0.02920.976-0.003-0.0030.0000.0000.0000.000
125A125ILE00.0180.01420.365-0.012-0.0120.0000.0000.0000.000
126A126THR00.0000.00221.7470.0090.0090.0000.0000.0000.000
127A127THR0-0.048-0.05823.724-0.017-0.0170.0000.0000.0000.000
128A128THR0-0.020-0.02026.362-0.004-0.0040.0000.0000.0000.000
129A129PRO0-0.0130.00323.986-0.001-0.0010.0000.0000.0000.000
130A130ALA00.006-0.00823.8020.0160.0160.0000.0000.0000.000
131A131PRO00.0300.00723.1070.0100.0100.0000.0000.0000.000
132A132HIS00.0160.00524.1440.0070.0070.0000.0000.0000.000
133A133LEU0-0.016-0.00223.0960.0160.0160.0000.0000.0000.000
134A134ASN00.0690.03220.307-0.001-0.0010.0000.0000.0000.000
135A135ASN0-0.033-0.02619.7370.0020.0020.0000.0000.0000.000
136A136ILE0-0.0070.02120.9190.0200.0200.0000.0000.0000.000
137A137HIS10.8490.93020.088-0.014-0.0140.0000.0000.0000.000
138A138VAL00.0320.02913.593-0.027-0.0270.0000.0000.0000.000
139A139VAL00.0160.01214.275-0.007-0.0070.0000.0000.0000.000
140A140PHE0-0.009-0.02111.4510.0200.0200.0000.0000.0000.000
141A141GLY00.0580.00910.938-0.082-0.0820.0000.0000.0000.000
142A142LYS10.7770.89212.9780.3860.3860.0000.0000.0000.000
143A143VAL0-0.011-0.00415.525-0.030-0.0300.0000.0000.0000.000
144A144VAL0-0.063-0.03015.462-0.019-0.0190.0000.0000.0000.000
145A145SER00.002-0.00418.6280.0000.0000.0000.0000.0000.000
146A146GLY00.0710.03821.9170.0010.0010.0000.0000.0000.000
147A147GLN0-0.010-0.01422.2960.0230.0230.0000.0000.0000.000
148A148GLU-1-0.812-0.91024.946-0.173-0.1730.0000.0000.0000.000
149A149VAL00.0060.00626.3230.0150.0150.0000.0000.0000.000
150A150VAL0-0.015-0.00623.5840.0140.0140.0000.0000.0000.000
151A151THR00.0400.01127.0220.0130.0130.0000.0000.0000.000
152A152LYS10.9210.96830.0310.1020.1020.0000.0000.0000.000
153A153ILE00.0090.00327.9140.0110.0110.0000.0000.0000.000
154A154GLU-1-0.772-0.86529.770-0.092-0.0920.0000.0000.0000.000
155A155TYR0-0.055-0.05631.6200.0090.0090.0000.0000.0000.000
156A156LEU0-0.0030.02233.8910.0050.0050.0000.0000.0000.000
157A157LYS10.9370.98236.7290.0360.0360.0000.0000.0000.000
158A158THR00.0220.02635.9510.0000.0000.0000.0000.0000.000
159A159ASN00.021-0.00639.0060.0030.0030.0000.0000.0000.000
160A160SER00.0700.02539.650-0.002-0.0020.0000.0000.0000.000
161A161LYS10.8690.94235.608-0.006-0.0060.0000.0000.0000.000
162A162ASN0-0.044-0.03434.731-0.003-0.0030.0000.0000.0000.000
163A163ARG10.9170.96534.1080.0110.0110.0000.0000.0000.000
164A164PRO00.003-0.00633.4610.0010.0010.0000.0000.0000.000
165A165LEU0-0.060-0.04336.6020.0050.0050.0000.0000.0000.000
166A166ALA00.0050.03137.1660.0020.0020.0000.0000.0000.000
167A167ASP-1-0.902-0.96335.654-0.030-0.0300.0000.0000.0000.000
168A168VAL0-0.038-0.02030.312-0.006-0.0060.0000.0000.0000.000
169A169VAL00.0290.01630.8240.0010.0010.0000.0000.0000.000
170A170ILE00.0040.00724.288-0.011-0.0110.0000.0000.0000.000
171A171LEU00.0080.01928.0290.0080.0080.0000.0000.0000.000
172A172ASN0-0.050-0.05226.0220.0190.0190.0000.0000.0000.000
173A173CYS0-0.061-0.01221.3710.0010.0010.0000.0000.0000.000
174A174GLY00.0520.03419.7950.0170.0170.0000.0000.0000.000
175A175GLU-1-0.821-0.89612.857-0.387-0.3870.0000.0000.0000.000
176A176LEU0-0.023-0.01415.7730.0280.0280.0000.0000.0000.000
177A177VAL0-0.024-0.00614.781-0.114-0.1140.0000.0000.0000.000