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: 432KN

Calculation Name: 1J1J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1J1J

Chain ID: A

ChEMBL ID:

UniProt ID: Q15631

Base Structure: X-ray

Registration Date: 2023-06-20

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2574349.891144
FMO2-HF: Nuclear repulsion 2488291.725303
FMO2-HF: Total energy -86058.165841
FMO2-MP2: Total energy -86315.680637


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.
-15.701-6.1285.575-5.396-9.752-0.028
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 : 0.003 / q_NPA : 0.010
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].
3A3VAL00.043-0.0083.322-2.1450.7870.036-1.613-1.3560.007
4A4SER00.0170.0025.8490.4550.4550.0000.0000.0000.000
5A5GLU-1-0.823-0.8712.630-6.430-3.3730.699-1.477-2.279-0.011
6A6ILE00.0040.0082.270-2.965-1.0233.202-1.321-3.822-0.001
7A7PHE0-0.001-0.0213.2170.5900.3150.0320.555-0.3120.000
8A8VAL0-0.0180.0016.0760.2760.2760.0000.0000.0000.000
9A9GLU-1-0.895-0.9532.443-6.927-5.0101.606-1.540-1.983-0.023
10A10LEU0-0.023-0.0225.4780.5730.5730.0000.0000.0000.000
11A11GLN0-0.0270.0017.7670.2220.2220.0000.0000.0000.000
12A12GLY00.0410.0289.2450.1560.1560.0000.0000.0000.000
13A13PHE0-0.024-0.0096.2430.2050.2050.0000.0000.0000.000
14A14LEU0-0.015-0.00611.0030.1070.1070.0000.0000.0000.000
15A15ALA0-0.020-0.01513.2670.0620.0620.0000.0000.0000.000
16A16ALA00.0410.02714.0190.0480.0480.0000.0000.0000.000
17A17GLU-1-0.831-0.90715.198-0.063-0.0630.0000.0000.0000.000
18A18GLN00.004-0.01817.0630.0420.0420.0000.0000.0000.000
19A19ASP-1-0.876-0.91818.830-0.173-0.1730.0000.0000.0000.000
20A20ILE0-0.043-0.01718.5330.0230.0230.0000.0000.0000.000
21A21ARG10.7890.88418.6500.1310.1310.0000.0000.0000.000
22A22GLU-1-0.767-0.86823.388-0.120-0.1200.0000.0000.0000.000
23A23GLU-1-0.843-0.91224.694-0.050-0.0500.0000.0000.0000.000
24A24ILE0-0.034-0.01624.6360.0110.0110.0000.0000.0000.000
25A25ARG10.8120.88424.3070.1040.1040.0000.0000.0000.000
26A26LYS10.9150.96928.6610.0760.0760.0000.0000.0000.000
27A27VAL0-0.014-0.00130.5290.0040.0040.0000.0000.0000.000
28A28VAL00.0260.00631.2340.0050.0050.0000.0000.0000.000
29A29GLN0-0.0210.00133.6420.0020.0020.0000.0000.0000.000
30A30SER0-0.0070.00335.6470.0020.0020.0000.0000.0000.000
31A31LEU0-0.025-0.00435.3860.0030.0030.0000.0000.0000.000
32A32GLU-1-0.844-0.94136.249-0.034-0.0340.0000.0000.0000.000
33A33GLN0-0.109-0.05239.444-0.002-0.0020.0000.0000.0000.000
34A34THR00.0070.00041.0780.0020.0020.0000.0000.0000.000
35A35ALA00.0330.01541.7580.0020.0020.0000.0000.0000.000
36A36ARG10.8680.92739.7090.0330.0330.0000.0000.0000.000
37A37GLU-1-0.812-0.87245.261-0.018-0.0180.0000.0000.0000.000
38A38ILE0-0.006-0.00144.8710.0010.0010.0000.0000.0000.000
39A39LEU0-0.006-0.00847.5470.0010.0010.0000.0000.0000.000
40A40THR0-0.049-0.03049.4160.0000.0000.0000.0000.0000.000
41A41LEU0-0.061-0.02650.7520.0010.0010.0000.0000.0000.000
42A42LEU00.0230.01250.5420.0010.0010.0000.0000.0000.000
43A43GLN0-0.027-0.02351.894-0.001-0.0010.0000.0000.0000.000
44A44GLY0-0.002-0.01455.1370.0000.0000.0000.0000.0000.000
45A45VAL0-0.018-0.01857.2240.0000.0000.0000.0000.0000.000
46A46HIS0-0.076-0.03555.2000.0010.0010.0000.0000.0000.000
47A47GLN0-0.073-0.03058.789-0.001-0.0010.0000.0000.0000.000
48A48GLY00.0020.00763.0790.0010.0010.0000.0000.0000.000
49A49ALA00.0090.00766.4200.0000.0000.0000.0000.0000.000
50A50GLY0-0.024-0.01068.3600.0000.0000.0000.0000.0000.000
51A51PHE00.0500.01862.1220.0000.0000.0000.0000.0000.000
52A52GLN0-0.014-0.01764.4580.0010.0010.0000.0000.0000.000
53A53ASP-1-0.843-0.90861.350-0.003-0.0030.0000.0000.0000.000
54A54ILE00.0510.03359.1770.0000.0000.0000.0000.0000.000
55A55PRO00.0600.03458.9520.0000.0000.0000.0000.0000.000
56A56LYS10.9660.97958.7170.0020.0020.0000.0000.0000.000
57A57ARG10.8230.90656.4630.0060.0060.0000.0000.0000.000
58A58CYS00.0170.01054.6390.0000.0000.0000.0000.0000.000
59A59LEU0-0.037-0.01253.8960.0010.0010.0000.0000.0000.000
60A60LYS10.9860.98953.7520.0060.0060.0000.0000.0000.000
61A61ALA0-0.023-0.00650.742-0.001-0.0010.0000.0000.0000.000
62A62ARG10.8660.90349.386-0.010-0.0100.0000.0000.0000.000
63A63GLU-1-0.899-0.94048.9970.0010.0010.0000.0000.0000.000
64A64HIS10.7970.88745.5090.0100.0100.0000.0000.0000.000
65A65PHE00.0700.01143.894-0.002-0.0020.0000.0000.0000.000
66A66GLY00.0140.02143.7650.0010.0010.0000.0000.0000.000
67A67THR0-0.009-0.01441.7860.0010.0010.0000.0000.0000.000
68A68VAL0-0.0010.00540.129-0.002-0.0020.0000.0000.0000.000
69A69LYS10.8940.95139.016-0.015-0.0150.0000.0000.0000.000
70A70THR0-0.034-0.00538.1550.0020.0020.0000.0000.0000.000
71A71HIS00.017-0.00136.0560.0000.0000.0000.0000.0000.000
72A72LEU00.0200.01334.349-0.002-0.0020.0000.0000.0000.000
73A73THR0-0.009-0.01033.4390.0040.0040.0000.0000.0000.000
74A74SER0-0.011-0.00932.2620.0010.0010.0000.0000.0000.000
75A75LEU0-0.015-0.01429.136-0.003-0.0030.0000.0000.0000.000
76A76LYS10.8010.89128.652-0.035-0.0350.0000.0000.0000.000
77A77THR0-0.065-0.03027.6940.0070.0070.0000.0000.0000.000
78A78LYS10.7840.88325.4920.0340.0340.0000.0000.0000.000
79A79PHE00.0180.01522.642-0.011-0.0110.0000.0000.0000.000
80A80PRO00.0570.03619.3800.0090.0090.0000.0000.0000.000
81A81ALA00.0210.01422.5790.0000.0000.0000.0000.0000.000
82A82GLU-1-0.915-0.95119.4630.1670.1670.0000.0000.0000.000
83A83GLN0-0.042-0.03917.109-0.024-0.0240.0000.0000.0000.000
84A84TYR0-0.001-0.01522.614-0.017-0.0170.0000.0000.0000.000
85A85TYR0-0.041-0.07126.079-0.008-0.0080.0000.0000.0000.000
86A86ARG10.7640.90315.1720.0010.0010.0000.0000.0000.000
87A87PHE00.0460.00919.449-0.013-0.0130.0000.0000.0000.000
88A88HIS00.0520.03325.057-0.007-0.0070.0000.0000.0000.000
89A89GLU-1-0.901-0.96725.856-0.025-0.0250.0000.0000.0000.000
90A90HIS0-0.057-0.02924.573-0.017-0.0170.0000.0000.0000.000
91A91TRP00.0510.01727.527-0.002-0.0020.0000.0000.0000.000
92A92ARG10.8800.95929.6000.0090.0090.0000.0000.0000.000
93A93PHE00.0220.00134.1080.0030.0030.0000.0000.0000.000
94A94VAL00.0370.01035.4330.0030.0030.0000.0000.0000.000
95A95LEU00.0370.03434.4480.0020.0020.0000.0000.0000.000
96A96GLN00.018-0.01537.6320.0000.0000.0000.0000.0000.000
97A97ARG10.8780.94940.1380.0160.0160.0000.0000.0000.000
98A98LEU0-0.005-0.00838.7780.0010.0010.0000.0000.0000.000
99A99VAL00.0170.02640.8150.0020.0020.0000.0000.0000.000
100A100PHE0-0.0120.00043.4030.0010.0010.0000.0000.0000.000
101A101LEU0-0.041-0.01944.4980.0000.0000.0000.0000.0000.000
102A102ALA00.0090.01345.5960.0000.0000.0000.0000.0000.000
103A103ALA00.035-0.00247.4430.0010.0010.0000.0000.0000.000
104A104PHE0-0.010-0.01249.3160.0000.0000.0000.0000.0000.000
105A105VAL0-0.029-0.01650.1480.0000.0000.0000.0000.0000.000
106A106VAL00.0090.00250.5250.0010.0010.0000.0000.0000.000
107A107TYR0-0.0080.02153.1330.0000.0000.0000.0000.0000.000
108A108LEU0-0.031-0.02355.1100.0000.0000.0000.0000.0000.000
109A109GLU-1-0.920-0.93555.8050.0090.0090.0000.0000.0000.000
110A110THR0-0.062-0.05356.0800.0010.0010.0000.0000.0000.000
111A111GLU-1-0.883-0.93358.1410.0060.0060.0000.0000.0000.000
112A112THR00.0190.01054.2830.0010.0010.0000.0000.0000.000
113A113LEU0-0.013-0.01149.598-0.001-0.0010.0000.0000.0000.000
114A114VAL0-0.0220.01447.5280.0020.0020.0000.0000.0000.000
115A115THR00.0560.02946.523-0.001-0.0010.0000.0000.0000.000
116A116ARG10.7890.86538.270-0.040-0.0400.0000.0000.0000.000
117A117GLU-1-0.802-0.92342.6140.0340.0340.0000.0000.0000.000
118A118ALA00.0530.03143.9220.0000.0000.0000.0000.0000.000
119A119VAL0-0.043-0.02742.192-0.002-0.0020.0000.0000.0000.000
120A120THR0-0.002-0.00839.022-0.003-0.0030.0000.0000.0000.000
121A121GLU-1-0.882-0.92741.2010.0280.0280.0000.0000.0000.000
122A122ILE0-0.076-0.04843.808-0.002-0.0020.0000.0000.0000.000
123A123LEU0-0.041-0.01839.675-0.003-0.0030.0000.0000.0000.000
124A124GLY0-0.058-0.02139.708-0.002-0.0020.0000.0000.0000.000
125A125ILE0-0.073-0.02235.3070.0000.0000.0000.0000.0000.000
126A126GLU-1-0.680-0.81833.9970.0410.0410.0000.0000.0000.000
127A127PRO00.0280.00537.041-0.001-0.0010.0000.0000.0000.000
128A128ASP-1-0.838-0.89836.0660.0520.0520.0000.0000.0000.000
129A129ARG10.8120.90535.669-0.075-0.0750.0000.0000.0000.000
130A130GLU-1-0.851-0.94335.4120.0500.0500.0000.0000.0000.000
131A131LYS10.8690.92928.536-0.122-0.1220.0000.0000.0000.000
132A132GLY00.0810.04830.5970.0030.0030.0000.0000.0000.000
133A133PHE0-0.024-0.01330.365-0.005-0.0050.0000.0000.0000.000
134A134HIS00.0400.04031.7930.0060.0060.0000.0000.0000.000
135A135LEU00.0250.03234.243-0.006-0.0060.0000.0000.0000.000
136A136ASP-1-0.765-0.87333.6890.0350.0350.0000.0000.0000.000
137A137VAL00.0330.01036.360-0.003-0.0030.0000.0000.0000.000
138A138GLU-1-0.884-0.95336.5550.0220.0220.0000.0000.0000.000
139A139ASP-1-0.798-0.88535.3000.0030.0030.0000.0000.0000.000
140A140TYR0-0.045-0.03138.627-0.003-0.0030.0000.0000.0000.000
141A141LEU00.0400.00841.684-0.002-0.0020.0000.0000.0000.000
142A142SER0-0.037-0.03040.325-0.003-0.0030.0000.0000.0000.000
143A143GLY00.0300.01142.596-0.002-0.0020.0000.0000.0000.000
144A144VAL00.0070.00144.191-0.002-0.0020.0000.0000.0000.000
145A145LEU0-0.029-0.00844.927-0.001-0.0010.0000.0000.0000.000
146A146ILE0-0.058-0.02443.276-0.002-0.0020.0000.0000.0000.000
147A147LEU0-0.0240.00347.738-0.001-0.0010.0000.0000.0000.000
148A148ALA00.0420.02050.246-0.001-0.0010.0000.0000.0000.000
149A149SER0-0.016-0.03150.729-0.001-0.0010.0000.0000.0000.000
150A150GLU-1-0.812-0.87151.628-0.009-0.0090.0000.0000.0000.000
151A151LEU00.008-0.00653.4620.0000.0000.0000.0000.0000.000
152A152SER00.018-0.02355.8800.0000.0000.0000.0000.0000.000
153A153ARG10.8110.89754.1940.0100.0100.0000.0000.0000.000
154A154LEU00.0100.00057.4440.0000.0000.0000.0000.0000.000
155A155SER00.0220.00859.4650.0000.0000.0000.0000.0000.000
156A156VAL00.0330.01261.6640.0000.0000.0000.0000.0000.000
157A157ASN0-0.019-0.03059.8940.0000.0000.0000.0000.0000.000
158A158SER00.0240.00263.5650.0000.0000.0000.0000.0000.000
159A159VAL0-0.0130.00465.1600.0000.0000.0000.0000.0000.000
160A160THR0-0.038-0.01066.4170.0000.0000.0000.0000.0000.000
161A161ALA0-0.031-0.00266.1760.0000.0000.0000.0000.0000.000
162A162GLY00.0010.00068.2860.0000.0000.0000.0000.0000.000
163A163ASP-1-0.858-0.92666.9690.0020.0020.0000.0000.0000.000
164A164TYR00.011-0.01468.1740.0000.0000.0000.0000.0000.000
165A165SER0-0.012-0.00268.7940.0010.0010.0000.0000.0000.000
166A166ARG10.8980.94461.943-0.002-0.0020.0000.0000.0000.000
167A167PRO0-0.0040.01463.8750.0010.0010.0000.0000.0000.000
168A168LEU00.0190.01264.1610.0000.0000.0000.0000.0000.000
169A169HIS10.8920.95362.848-0.005-0.0050.0000.0000.0000.000
170A170ILE00.0230.01258.5970.0010.0010.0000.0000.0000.000
171A171SER00.0220.00759.6430.0000.0000.0000.0000.0000.000
172A172THR0-0.028-0.01160.8130.0000.0000.0000.0000.0000.000
173A173PHE00.0320.01453.5620.0010.0010.0000.0000.0000.000
174A174ILE0-0.006-0.01755.3090.0010.0010.0000.0000.0000.000
175A175ASN0-0.031-0.02156.1830.0010.0010.0000.0000.0000.000
176A176GLU-1-0.914-0.94456.6950.0130.0130.0000.0000.0000.000
177A177LEU0-0.044-0.02551.3270.0010.0010.0000.0000.0000.000
178A178ASP-1-0.822-0.89552.5070.0080.0080.0000.0000.0000.000
179A179SER0-0.044-0.03453.6320.0010.0010.0000.0000.0000.000
180A180GLY00.0020.00052.0620.0010.0010.0000.0000.0000.000
181A181PHE0-0.003-0.02645.4760.0020.0020.0000.0000.0000.000
182A182ARG10.7900.88749.302-0.009-0.0090.0000.0000.0000.000
183A183LEU0-0.025-0.00250.4520.0010.0010.0000.0000.0000.000
184A184LEU0-0.049-0.00945.1290.0030.0030.0000.0000.0000.000
185A185ASN0-0.0010.00744.266-0.003-0.0030.0000.0000.0000.000
186A186LEU00.0140.00342.3110.0020.0020.0000.0000.0000.000
187A187LYS10.9150.94438.006-0.028-0.0280.0000.0000.0000.000
188A188ASN00.0600.04035.530-0.007-0.0070.0000.0000.0000.000
189A189ASP-1-0.753-0.89736.772-0.011-0.0110.0000.0000.0000.000
190A190SER0-0.0350.01037.063-0.004-0.0040.0000.0000.0000.000
191A191LEU0-0.0080.00239.310-0.001-0.0010.0000.0000.0000.000
192A192ARG10.9770.98841.367-0.007-0.0070.0000.0000.0000.000
193A193LYS10.8470.90740.1150.0100.0100.0000.0000.0000.000
194A194ARG10.8940.94641.0030.0060.0060.0000.0000.0000.000
195A195TYR00.0110.00345.2170.0000.0000.0000.0000.0000.000
196A196ASP-1-0.842-0.89947.254-0.001-0.0010.0000.0000.0000.000
197A197GLY0-0.033-0.00948.866-0.001-0.0010.0000.0000.0000.000
198A198LEU00.0250.02150.6440.0000.0000.0000.0000.0000.000
199A199LYS10.8600.90251.8820.0030.0030.0000.0000.0000.000
200A200TYR0-0.027-0.00554.3340.0000.0000.0000.0000.0000.000
201A201ASP-1-0.756-0.84153.004-0.005-0.0050.0000.0000.0000.000
202A202VAL0-0.022-0.01155.9560.0000.0000.0000.0000.0000.000
203A203LYS10.9090.94658.3120.0030.0030.0000.0000.0000.000
204A204LYS10.8660.94657.0090.0070.0070.0000.0000.0000.000
205A205VAL0-0.0140.00159.2160.0000.0000.0000.0000.0000.000
206A206GLU-1-0.864-0.92461.9820.0030.0030.0000.0000.0000.000
207A207GLU-1-0.890-0.94864.059-0.005-0.0050.0000.0000.0000.000
208A208VAL0-0.033-0.00464.0420.0000.0000.0000.0000.0000.000
209A209VAL0-0.015-0.00865.6480.0000.0000.0000.0000.0000.000
210A210TYR0-0.0020.00668.2160.0000.0000.0000.0000.0000.000
211A211ASP-1-0.802-0.89769.730-0.004-0.0040.0000.0000.0000.000
212A212LEU0-0.039-0.02669.0200.0000.0000.0000.0000.0000.000
213A213SER0-0.012-0.00372.2430.0000.0000.0000.0000.0000.000
214A214ILE0-0.065-0.02174.1080.0000.0000.0000.0000.0000.000
215A215ARG10.7820.87473.8750.0030.0030.0000.0000.0000.000
216A216GLY0-0.0300.00677.5310.0000.0000.0000.0000.0000.000
217A217PHE0-0.042-0.02073.6510.0000.0000.0000.0000.0000.000