FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 668YZ

Calculation Name: 1J6R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1J6R

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WYA6

Base Structure: X-ray

Registration Date: 2023-06-19

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2194608.484225
FMO2-HF: Nuclear repulsion 2117351.860166
FMO2-HF: Total energy -77256.624059
FMO2-MP2: Total energy -77485.157197


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:HIS)


Summations of interaction energy for fragment #1(A:1:HIS)
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.
-15.849-12.4291.42-1.602-3.237-0.006
Interaction energy analysis for fragmet #1(A:1:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.013
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].
3A3MET0-0.0030.0092.120-2.1200.5211.416-1.305-2.751-0.004
4A4PRO0-0.055-0.0045.2810.0660.145-0.001-0.003-0.0750.000
5A5LYS10.8610.8917.4013.8333.8330.0000.0000.0000.000
6A6VAL0-0.042-0.02311.2220.1580.1580.0000.0000.0000.000
7A7GLU-1-0.921-0.94514.406-1.400-1.4000.0000.0000.0000.000
8A8ILE0-0.071-0.04217.0500.1070.1070.0000.0000.0000.000
9A9ALA00.0530.02420.647-0.012-0.0120.0000.0000.0000.000
10A10PRO00.0350.00223.8380.0360.0360.0000.0000.0000.000
11A11SER0-0.009-0.01925.8480.0160.0160.0000.0000.0000.000
12A12GLU-1-0.915-0.92624.920-0.295-0.2950.0000.0000.0000.000
13A13ILE0-0.065-0.02222.7720.0190.0190.0000.0000.0000.000
14A14LYS10.8280.90326.6960.1930.1930.0000.0000.0000.000
15A15ILE00.0150.01328.8080.0180.0180.0000.0000.0000.000
16A16PRO0-0.002-0.00430.9040.0100.0100.0000.0000.0000.000
17A17ASP-1-0.758-0.86934.099-0.166-0.1660.0000.0000.0000.000
18A18ASN00.023-0.00237.191-0.005-0.0050.0000.0000.0000.000
19A19VAL0-0.0230.00732.0630.0050.0050.0000.0000.0000.000
20A20LEU00.0200.00933.548-0.005-0.0050.0000.0000.0000.000
21A21LYS10.8510.91135.1690.1220.1220.0000.0000.0000.000
22A22ALA0-0.018-0.01537.2730.0020.0020.0000.0000.0000.000
23A23LYS10.7960.90230.0130.2370.2370.0000.0000.0000.000
24A24LEU0-0.044-0.01334.629-0.008-0.0080.0000.0000.0000.000
25A25GLY00.0350.02237.8600.0020.0020.0000.0000.0000.000
26A26PHE0-0.020-0.01240.6080.0100.0100.0000.0000.0000.000
27A27GLY00.0330.01041.2910.0020.0020.0000.0000.0000.000
28A28GLY0-0.051-0.02742.1170.0050.0050.0000.0000.0000.000
29A29ALA0-0.0020.01344.3980.0060.0060.0000.0000.0000.000
30A30GLU-1-0.925-0.95844.584-0.090-0.0900.0000.0000.0000.000
31A31GLU-1-0.872-0.94843.641-0.141-0.1410.0000.0000.0000.000
32A32ILE0-0.072-0.02341.0810.0010.0010.0000.0000.0000.000
33A33PRO00.0180.01344.4870.0020.0020.0000.0000.0000.000
34A34GLU-1-0.912-0.97046.514-0.121-0.1210.0000.0000.0000.000
35A35GLU-1-0.992-0.99447.548-0.130-0.1300.0000.0000.0000.000
36A36PHE00.0290.00243.175-0.008-0.0080.0000.0000.0000.000
37A37ARG10.9250.98242.7490.1480.1480.0000.0000.0000.000
38A38LYS10.9770.96942.1100.1570.1570.0000.0000.0000.000
39A39THR00.0160.01640.828-0.011-0.0110.0000.0000.0000.000
40A40VAL00.0590.03037.219-0.014-0.0140.0000.0000.0000.000
41A41ASN0-0.017-0.00237.191-0.002-0.0020.0000.0000.0000.000
42A42ARG10.8020.88136.9640.2350.2350.0000.0000.0000.000
43A43ALA00.0300.00335.152-0.016-0.0160.0000.0000.0000.000
44A44TYR0-0.017-0.00330.611-0.019-0.0190.0000.0000.0000.000
45A45GLU-1-0.880-0.95632.083-0.302-0.3020.0000.0000.0000.000
46A46GLU-1-0.807-0.88232.311-0.335-0.3350.0000.0000.0000.000
47A47LEU0-0.023-0.01126.789-0.030-0.0300.0000.0000.0000.000
48A48LEU0-0.053-0.03127.773-0.039-0.0390.0000.0000.0000.000
49A49ASP-1-0.902-0.92727.901-0.459-0.4590.0000.0000.0000.000
50A50ALA0-0.032-0.01026.982-0.038-0.0380.0000.0000.0000.000
51A51ALA0-0.045-0.03023.881-0.053-0.0530.0000.0000.0000.000
52A52LYS10.8870.91519.7610.7460.7460.0000.0000.0000.000
53A53PRO0-0.027-0.01319.006-0.078-0.0780.0000.0000.0000.000
54A54VAL00.0260.02413.095-0.028-0.0280.0000.0000.0000.000
55A55VAL0-0.036-0.02014.9060.0630.0630.0000.0000.0000.000
56A56LEU00.0220.0128.510-0.091-0.0910.0000.0000.0000.000
57A57TRP0-0.027-0.02110.0690.1670.1670.0000.0000.0000.000
58A58ARG10.8830.9304.391-1.876-1.678-0.001-0.021-0.1750.000
59A59ASP-1-0.800-0.8547.7050.5180.5180.0000.0000.0000.000
60A60PHE0-0.007-0.0097.2420.5260.5260.0000.0000.0000.000
61A61GLU-1-0.790-0.8839.4861.1001.1000.0000.0000.0000.000
62A62VAL0-0.062-0.03811.7970.0890.0890.0000.0000.0000.000
63A63ASP-1-0.909-0.96414.5200.6820.6820.0000.0000.0000.000
64A64GLY0-0.038-0.00417.900-0.038-0.0380.0000.0000.0000.000
65A65SER0-0.050-0.01916.559-0.108-0.1080.0000.0000.0000.000
66A66LEU00.0090.00617.3080.0170.0170.0000.0000.0000.000
67A67SER0-0.076-0.04916.219-0.086-0.0860.0000.0000.0000.000
68A68PHE00.0480.01810.8720.0910.0910.0000.0000.0000.000
69A69ASP-1-0.832-0.8986.5401.4991.4990.0000.0000.0000.000
70A70ASP-1-0.793-0.87910.115-0.004-0.0040.0000.0000.0000.000
71A71MET0-0.0130.01111.367-0.197-0.1970.0000.0000.0000.000
72A72ARG10.9430.95615.131-0.304-0.3040.0000.0000.0000.000
73A73LEU0-0.0050.00916.358-0.073-0.0730.0000.0000.0000.000
74A74THR0-0.036-0.03519.8760.0320.0320.0000.0000.0000.000
75A75GLY00.0390.04323.514-0.003-0.0030.0000.0000.0000.000
76A76GLU-1-0.914-0.95825.7390.1200.1200.0000.0000.0000.000
77A77LEU0-0.029-0.01825.6090.0170.0170.0000.0000.0000.000
78A78ALA00.012-0.00621.7280.0050.0050.0000.0000.0000.000
79A79THR00.0150.00223.0430.0380.0380.0000.0000.0000.000
80A80LYS10.9060.96825.020-0.093-0.0930.0000.0000.0000.000
81A81HIS0-0.002-0.00323.5620.0140.0140.0000.0000.0000.000
82A82LEU00.0070.00518.5000.0130.0130.0000.0000.0000.000
83A83SER0-0.0300.00220.5770.0570.0570.0000.0000.0000.000
84A84GLY00.0200.01122.427-0.017-0.0170.0000.0000.0000.000
85A85SER0-0.026-0.02918.788-0.006-0.0060.0000.0000.0000.000
86A86LYS10.8630.93215.115-1.050-1.0500.0000.0000.0000.000
87A87ILE00.0240.00312.1030.1190.1190.0000.0000.0000.000
88A88ILE0-0.013-0.00113.104-0.155-0.1550.0000.0000.0000.000
89A89THR0-0.038-0.03011.5780.1510.1510.0000.0000.0000.000
90A90VAL0-0.027-0.0129.851-0.022-0.0220.0000.0000.0000.000
91A91PHE00.012-0.01711.298-0.109-0.1090.0000.0000.0000.000
92A92LEU00.0280.01211.5550.0780.0780.0000.0000.0000.000
93A93ALA00.0080.01413.708-0.116-0.1160.0000.0000.0000.000
94A94THR00.014-0.01715.4240.0560.0560.0000.0000.0000.000
95A95LEU00.0170.01117.8990.0070.0070.0000.0000.0000.000
96A96GLY00.0790.05218.6280.0040.0040.0000.0000.0000.000
97A97LYS10.8310.87019.5530.8080.8080.0000.0000.0000.000
98A98LYN00.0840.06321.8570.0390.0390.0000.0000.0000.000
99A99VAL00.0220.02423.8820.0570.0570.0000.0000.0000.000
100A100ASP-1-0.770-0.88123.819-0.490-0.4900.0000.0000.0000.000
101A101GLU-1-0.829-0.89825.069-0.602-0.6020.0000.0000.0000.000
102A102LYS10.8330.91328.0930.4210.4210.0000.0000.0000.000
103A103ILE0-0.042-0.01928.1000.0310.0310.0000.0000.0000.000
104A104GLU-1-0.791-0.87530.580-0.306-0.3060.0000.0000.0000.000
105A105GLU-1-0.919-0.94832.080-0.328-0.3280.0000.0000.0000.000
106A106TYR0-0.076-0.07134.0440.0250.0250.0000.0000.0000.000
107A107PHE00.0290.01333.4820.0170.0170.0000.0000.0000.000
108A108ARG10.7750.86632.3290.3560.3560.0000.0000.0000.000
109A109LYS10.8040.90736.7610.3040.3040.0000.0000.0000.000
110A110GLY00.0100.02440.2190.0120.0120.0000.0000.0000.000
111A111GLU-1-0.876-0.92439.231-0.222-0.2220.0000.0000.0000.000
112A112ASP-1-0.856-0.94338.535-0.224-0.2240.0000.0000.0000.000
113A113LEU0-0.021-0.01038.326-0.005-0.0050.0000.0000.0000.000
114A114LEU0-0.0070.00936.261-0.002-0.0020.0000.0000.0000.000
115A115ALA00.0460.01334.701-0.014-0.0140.0000.0000.0000.000
116A116PHE0-0.029-0.00733.765-0.017-0.0170.0000.0000.0000.000
117A117PHE0-0.006-0.01634.422-0.004-0.0040.0000.0000.0000.000
118A118ILE00.0220.02030.139-0.007-0.0070.0000.0000.0000.000
119A119ASP-1-0.742-0.85429.631-0.359-0.3590.0000.0000.0000.000
120A120GLY00.0520.03429.712-0.010-0.0100.0000.0000.0000.000
121A121ILE00.005-0.01329.8870.0010.0010.0000.0000.0000.000
122A122ALA00.0250.01026.338-0.011-0.0110.0000.0000.0000.000
123A123SER0-0.060-0.04925.746-0.028-0.0280.0000.0000.0000.000
124A124GLU-1-0.858-0.91626.336-0.230-0.2300.0000.0000.0000.000
125A125MET0-0.0190.00424.291-0.014-0.0140.0000.0000.0000.000
126A126VAL00.0430.02119.991-0.019-0.0190.0000.0000.0000.000
127A127GLU-1-0.721-0.82421.302-0.269-0.2690.0000.0000.0000.000
128A128TYR0-0.038-0.04623.3060.0380.0380.0000.0000.0000.000
129A129ALA00.0120.02120.1120.0150.0150.0000.0000.0000.000
130A130LEU00.0140.00817.166-0.001-0.0010.0000.0000.0000.000
131A131ARG10.7770.85819.9450.2380.2380.0000.0000.0000.000
132A132LYS10.8980.95521.5520.3610.3610.0000.0000.0000.000
133A133VAL00.0370.01615.6030.0330.0330.0000.0000.0000.000
134A134ASP-1-0.796-0.86018.638-0.027-0.0270.0000.0000.0000.000
135A135ALA00.0200.00519.9050.0610.0610.0000.0000.0000.000
136A136GLU-1-0.902-0.95619.569-0.091-0.0910.0000.0000.0000.000
137A137LEU0-0.053-0.02714.2590.0780.0780.0000.0000.0000.000
138A138ARG10.7370.83218.1360.0650.0650.0000.0000.0000.000
139A139MET0-0.037-0.00521.1920.0430.0430.0000.0000.0000.000
140A140LYS10.9080.94816.818-0.100-0.1000.0000.0000.0000.000
141A141ARG10.7860.88912.083-0.328-0.3280.0000.0000.0000.000
142A142SER00.0460.01819.8820.0130.0130.0000.0000.0000.000
143A143ASN0-0.056-0.01818.729-0.042-0.0420.0000.0000.0000.000
144A144LEU0-0.045-0.02617.2820.0460.0460.0000.0000.0000.000
145A145GLU-1-0.910-0.94721.6160.1790.1790.0000.0000.0000.000
146A146GLY00.0040.00520.3460.0280.0280.0000.0000.0000.000
147A147SER0-0.024-0.02720.925-0.025-0.0250.0000.0000.0000.000
148A148PHE00.0190.00722.589-0.029-0.0290.0000.0000.0000.000
149A149ARG10.8410.92819.4910.2010.2010.0000.0000.0000.000
150A150ILE0-0.026-0.00920.812-0.011-0.0110.0000.0000.0000.000
151A151SER00.051-0.00319.9520.0010.0010.0000.0000.0000.000
152A152PRO0-0.033-0.01617.9200.0380.0380.0000.0000.0000.000
153A153GLY00.0060.00521.013-0.035-0.0350.0000.0000.0000.000
154A154TYR0-0.056-0.01624.2680.0030.0030.0000.0000.0000.000
155A155GLY00.0220.00626.1370.0230.0230.0000.0000.0000.000
156A156ASP-1-0.827-0.91627.5070.0310.0310.0000.0000.0000.000
157A157LEU0-0.0190.00420.0350.0280.0280.0000.0000.0000.000
158A158PRO00.018-0.00221.792-0.034-0.0340.0000.0000.0000.000
159A159LEU00.0740.02321.140-0.006-0.0060.0000.0000.0000.000
160A160SER0-0.013-0.00520.572-0.038-0.0380.0000.0000.0000.000
161A161LEU0-0.009-0.00516.490-0.021-0.0210.0000.0000.0000.000
162A162ASN00.0550.01415.650-0.057-0.0570.0000.0000.0000.000
163A163LYS10.8450.91815.5100.2650.2650.0000.0000.0000.000
164A164LYS10.7770.88513.187-0.183-0.1830.0000.0000.0000.000
165A165ILE0-0.010-0.01211.206-0.055-0.0550.0000.0000.0000.000
166A166ALA00.0250.01010.785-0.218-0.2180.0000.0000.0000.000
167A167GLU-1-0.803-0.88510.665-1.268-1.2680.0000.0000.0000.000
168A168ILE0-0.065-0.0335.939-0.236-0.2360.0000.0000.0000.000
169A169PHE0-0.031-0.0256.006-0.722-0.7220.0000.0000.0000.000
170A170LYS10.8320.9227.7480.9530.9530.0000.0000.0000.000
171A171GLU-1-0.927-0.9635.355-3.020-3.0200.0000.0000.0000.000
172A172GLU-1-0.910-0.9403.696-11.365-10.8630.006-0.273-0.236-0.002
173A173VAL0-0.022-0.0237.3620.6170.6170.0000.0000.0000.000
174A174ASP-1-0.911-0.94011.126-1.537-1.5370.0000.0000.0000.000
175A175VAL0-0.054-0.02713.1250.2400.2400.0000.0000.0000.000
176A176ASN0-0.029-0.01813.737-0.079-0.0790.0000.0000.0000.000
177A177VAL0-0.007-0.01016.2390.0640.0640.0000.0000.0000.000
178A178ILE0-0.0130.00218.8250.0300.0300.0000.0000.0000.000
179A179GLU-1-0.852-0.93021.320-0.426-0.4260.0000.0000.0000.000
180A180ASP-1-0.834-0.92123.237-0.297-0.2970.0000.0000.0000.000
181A181SER0-0.047-0.01524.5100.0320.0320.0000.0000.0000.000
182A182TYR0-0.030-0.03220.6040.0260.0260.0000.0000.0000.000
183A183VAL0-0.0110.01021.722-0.001-0.0010.0000.0000.0000.000
184A184LEU0-0.0090.00016.746-0.029-0.0290.0000.0000.0000.000
185A185VAL00.0070.01519.1180.0430.0430.0000.0000.0000.000
186A186PRO00.0420.00417.767-0.085-0.0850.0000.0000.0000.000
187A187ARG10.8290.91120.4850.3920.3920.0000.0000.0000.000
188A188LYS10.7150.86322.7490.4100.4100.0000.0000.0000.000
189A189THR00.016-0.01216.608-0.092-0.0920.0000.0000.0000.000
190A190ILE0-0.034-0.00318.3950.0710.0710.0000.0000.0000.000
191A191THR00.0420.01914.952-0.105-0.1050.0000.0000.0000.000
192A192ALA0-0.041-0.01215.9720.0760.0760.0000.0000.0000.000
193A193PHE00.0180.00714.064-0.040-0.0400.0000.0000.0000.000
194A194VAL00.009-0.00216.251-0.028-0.0280.0000.0000.0000.000
195A195GLY00.0200.02316.2170.0590.0590.0000.0000.0000.000
196A196TRP0-0.003-0.01115.231-0.060-0.0600.0000.0000.0000.000
197A197ARG10.8910.94118.796-0.195-0.1950.0000.0000.0000.000