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: 7G56K

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 OptH
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 -2186036.70413
FMO2-HF: Nuclear repulsion 2108782.180503
FMO2-HF: Total energy -77254.523627
FMO2-MP2: Total energy -77482.844527


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.
-13.63-10.5050.093-1.068-2.150
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 : 0.018 / q_NPA : -0.007
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].
3A3MET0-0.039-0.0083.023-0.8631.5300.083-0.830-1.6460.001
4A4PRO0-0.0260.0025.585-0.129-0.1290.0000.0000.0000.000
5A5LYS10.9410.9658.0253.1543.1540.0000.0000.0000.000
6A6VAL0-0.043-0.01411.8620.1050.1050.0000.0000.0000.000
7A7GLU-1-0.922-0.95715.345-1.208-1.2080.0000.0000.0000.000
8A8ILE0-0.062-0.03317.6970.0880.0880.0000.0000.0000.000
9A9ALA00.0450.01821.202-0.017-0.0170.0000.0000.0000.000
10A10PRO00.0590.01324.1660.0350.0350.0000.0000.0000.000
11A11SER00.0270.01126.1360.0180.0180.0000.0000.0000.000
12A12GLU-1-0.973-0.97125.866-0.217-0.2170.0000.0000.0000.000
13A13ILE0-0.084-0.04323.3380.0240.0240.0000.0000.0000.000
14A14LYS10.9440.98027.3100.1150.1150.0000.0000.0000.000
15A15ILE00.0380.01229.4420.0120.0120.0000.0000.0000.000
16A16PRO0-0.080-0.05031.1550.0070.0070.0000.0000.0000.000
17A17ASP-1-0.773-0.88334.406-0.118-0.1180.0000.0000.0000.000
18A18ASN0-0.034-0.03437.605-0.005-0.0050.0000.0000.0000.000
19A19VAL0-0.0370.00331.7280.0050.0050.0000.0000.0000.000
20A20LEU00.0550.02133.772-0.006-0.0060.0000.0000.0000.000
21A21LYS10.8900.94835.4230.0850.0850.0000.0000.0000.000
22A22ALA0-0.021-0.01237.1170.0010.0010.0000.0000.0000.000
23A23LYS10.8770.95931.2750.1650.1650.0000.0000.0000.000
24A24LEU0-0.062-0.03035.189-0.008-0.0080.0000.0000.0000.000
25A25GLY00.0220.01538.2230.0000.0000.0000.0000.0000.000
26A26PHE0-0.007-0.00341.0880.0070.0070.0000.0000.0000.000
27A27GLY00.013-0.00341.4230.0030.0030.0000.0000.0000.000
28A28GLY0-0.040-0.01442.2780.0050.0050.0000.0000.0000.000
29A29ALA00.0120.01644.5590.0030.0030.0000.0000.0000.000
30A30GLU-1-0.934-0.97144.905-0.060-0.0600.0000.0000.0000.000
31A31GLU-1-0.900-0.96644.621-0.101-0.1010.0000.0000.0000.000
32A32ILE0-0.087-0.02541.9300.0000.0000.0000.0000.0000.000
33A33PRO00.0120.01144.8510.0000.0000.0000.0000.0000.000
34A34GLU-1-0.916-0.97247.119-0.095-0.0950.0000.0000.0000.000
35A35GLU-1-0.968-0.98848.543-0.107-0.1070.0000.0000.0000.000
36A36PHE00.002-0.00243.925-0.008-0.0080.0000.0000.0000.000
37A37ARG10.9900.99843.4250.1220.1220.0000.0000.0000.000
38A38LYS10.9700.97142.7040.1440.1440.0000.0000.0000.000
39A39THR00.0120.01541.008-0.010-0.0100.0000.0000.0000.000
40A40VAL00.0440.03738.158-0.014-0.0140.0000.0000.0000.000
41A41ASN0-0.039-0.02537.899-0.004-0.0040.0000.0000.0000.000
42A42ARG10.9640.99837.5570.2110.2110.0000.0000.0000.000
43A43ALA00.0420.00935.544-0.016-0.0160.0000.0000.0000.000
44A44TYR0-0.016-0.01831.541-0.019-0.0190.0000.0000.0000.000
45A45GLU-1-0.910-0.97232.782-0.256-0.2560.0000.0000.0000.000
46A46GLU-1-0.920-0.97033.028-0.306-0.3060.0000.0000.0000.000
47A47LEU0-0.047-0.02727.480-0.028-0.0280.0000.0000.0000.000
48A48LEU0-0.048-0.02828.305-0.034-0.0340.0000.0000.0000.000
49A49ASP-1-0.945-0.96128.268-0.420-0.4200.0000.0000.0000.000
50A50ALA0-0.020-0.01027.198-0.032-0.0320.0000.0000.0000.000
51A51ALA0-0.070-0.03024.307-0.051-0.0510.0000.0000.0000.000
52A52LYS10.9130.94119.9310.7330.7330.0000.0000.0000.000
53A53PRO0-0.026-0.01119.441-0.069-0.0690.0000.0000.0000.000
54A54VAL00.0340.03013.710-0.026-0.0260.0000.0000.0000.000
55A55VAL0-0.047-0.02514.8150.0540.0540.0000.0000.0000.000
56A56LEU00.0390.0199.014-0.041-0.0410.0000.0000.0000.000
57A57TRP0-0.042-0.0269.8540.1670.1670.0000.0000.0000.000
58A58ARG11.0171.0033.959-3.167-2.7630.010-0.096-0.3170.000
59A59ASP-1-0.836-0.8827.5910.8110.8110.0000.0000.0000.000
60A60PHE00.005-0.0017.2970.7070.7070.0000.0000.0000.000
61A61GLU-1-0.923-0.9739.4012.0542.0540.0000.0000.0000.000
62A62VAL0-0.060-0.03911.6960.0990.0990.0000.0000.0000.000
63A63ASP-1-0.973-0.98514.5150.7840.7840.0000.0000.0000.000
64A64GLY0-0.0180.00917.892-0.035-0.0350.0000.0000.0000.000
65A65SER0-0.037-0.01616.643-0.108-0.1080.0000.0000.0000.000
66A66LEU00.0210.00217.9730.0150.0150.0000.0000.0000.000
67A67SER0-0.072-0.04416.308-0.123-0.1230.0000.0000.0000.000
68A68PHE00.014-0.00110.8710.0940.0940.0000.0000.0000.000
69A69ASP-1-0.949-0.9747.2681.6181.6180.0000.0000.0000.000
70A70ASP-1-0.852-0.90410.0050.1100.1100.0000.0000.0000.000
71A71MET0-0.058-0.02111.645-0.241-0.2410.0000.0000.0000.000
72A72ARG10.9780.96714.973-0.401-0.4010.0000.0000.0000.000
73A73LEU0-0.031-0.00916.695-0.087-0.0870.0000.0000.0000.000
74A74THR0-0.053-0.03520.0340.0150.0150.0000.0000.0000.000
75A75GLY00.0170.00723.6550.0000.0000.0000.0000.0000.000
76A76GLU-1-0.886-0.94826.2340.1830.1830.0000.0000.0000.000
77A77LEU0-0.062-0.03624.9620.0180.0180.0000.0000.0000.000
78A78ALA00.0190.00122.1000.0120.0120.0000.0000.0000.000
79A79THR00.0360.02323.3420.0430.0430.0000.0000.0000.000
80A80LYS10.9351.00325.414-0.159-0.1590.0000.0000.0000.000
81A81HIS0-0.039-0.03423.8010.0170.0170.0000.0000.0000.000
82A82LEU00.0160.00118.5480.0180.0180.0000.0000.0000.000
83A83SER0-0.059-0.02320.4230.0660.0660.0000.0000.0000.000
84A84GLY0-0.0060.00122.238-0.020-0.0200.0000.0000.0000.000
85A85SER0-0.031-0.03018.6150.0020.0020.0000.0000.0000.000
86A86LYS11.0431.02515.668-1.047-1.0470.0000.0000.0000.000
87A87ILE00.013-0.00411.8360.1510.1510.0000.0000.0000.000
88A88ILE0-0.0210.00013.100-0.183-0.1830.0000.0000.0000.000
89A89THR0-0.036-0.02311.6420.1570.1570.0000.0000.0000.000
90A90VAL00.0050.0099.820-0.061-0.0610.0000.0000.0000.000
91A91PHE0-0.009-0.03111.301-0.089-0.0890.0000.0000.0000.000
92A92LEU00.0270.01311.8770.0480.0480.0000.0000.0000.000
93A93ALA0-0.0050.00413.927-0.075-0.0750.0000.0000.0000.000
94A94THR00.016-0.01715.9260.0330.0330.0000.0000.0000.000
95A95LEU00.0270.01218.4380.0020.0020.0000.0000.0000.000
96A96GLY00.0590.04119.238-0.004-0.0040.0000.0000.0000.000
97A97LYS10.9670.96320.1900.8150.8150.0000.0000.0000.000
98A98LYN00.0420.02522.3150.0180.0180.0000.0000.0000.000
99A99VAL00.0190.02224.4790.0490.0490.0000.0000.0000.000
100A100ASP-1-0.837-0.92324.429-0.463-0.4630.0000.0000.0000.000
101A101GLU-1-0.937-0.97625.634-0.539-0.5390.0000.0000.0000.000
102A102LYS10.8990.96828.6770.3820.3820.0000.0000.0000.000
103A103ILE0-0.035-0.01728.7760.0270.0270.0000.0000.0000.000
104A104GLU-1-0.894-0.95131.076-0.276-0.2760.0000.0000.0000.000
105A105GLU-1-0.942-0.97332.670-0.304-0.3040.0000.0000.0000.000
106A106TYR0-0.050-0.04034.6480.0240.0240.0000.0000.0000.000
107A107PHE00.0250.01933.6190.0160.0160.0000.0000.0000.000
108A108ARG10.8870.95132.6770.3360.3360.0000.0000.0000.000
109A109LYS10.8450.93538.1450.2660.2660.0000.0000.0000.000
110A110GLY00.0250.02540.6900.0100.0100.0000.0000.0000.000
111A111GLU-1-0.993-0.99339.989-0.191-0.1910.0000.0000.0000.000
112A112ASP-1-0.833-0.94239.299-0.200-0.2000.0000.0000.0000.000
113A113LEU0-0.037-0.01139.153-0.002-0.0020.0000.0000.0000.000
114A114LEU00.0310.01337.185-0.001-0.0010.0000.0000.0000.000
115A115ALA00.0440.02035.170-0.010-0.0100.0000.0000.0000.000
116A116PHE0-0.0360.00034.516-0.012-0.0120.0000.0000.0000.000
117A117PHE00.010-0.01935.4310.0000.0000.0000.0000.0000.000
118A118ILE0-0.0040.00931.041-0.004-0.0040.0000.0000.0000.000
119A119ASP-1-0.814-0.90330.654-0.278-0.2780.0000.0000.0000.000
120A120GLY00.0160.00630.446-0.007-0.0070.0000.0000.0000.000
121A121ILE0-0.002-0.01830.6440.0070.0070.0000.0000.0000.000
122A122ALA00.0010.01327.117-0.008-0.0080.0000.0000.0000.000
123A123SER0-0.023-0.02826.493-0.026-0.0260.0000.0000.0000.000
124A124GLU-1-0.885-0.95126.520-0.157-0.1570.0000.0000.0000.000
125A125MET0-0.0220.00025.609-0.004-0.0040.0000.0000.0000.000
126A126VAL00.0270.01020.683-0.009-0.0090.0000.0000.0000.000
127A127GLU-1-0.804-0.87821.893-0.149-0.1490.0000.0000.0000.000
128A128TYR0-0.028-0.04523.3640.0380.0380.0000.0000.0000.000
129A129ALA00.0220.02520.7290.0130.0130.0000.0000.0000.000
130A130LEU00.0260.01617.2610.0070.0070.0000.0000.0000.000
131A131ARG10.7690.87019.9700.1440.1440.0000.0000.0000.000
132A132LYS10.9510.98521.7840.2560.2560.0000.0000.0000.000
133A133VAL00.0300.02215.8130.0340.0340.0000.0000.0000.000
134A134ASP-1-0.839-0.90418.7670.1240.1240.0000.0000.0000.000
135A135ALA00.019-0.00419.7110.0600.0600.0000.0000.0000.000
136A136GLU-1-0.916-0.95019.4490.0050.0050.0000.0000.0000.000
137A137LEU0-0.069-0.03414.5310.0800.0800.0000.0000.0000.000
138A138ARG10.7610.86118.269-0.068-0.0680.0000.0000.0000.000
139A139MET0-0.028-0.00721.2930.0320.0320.0000.0000.0000.000
140A140LYS10.9300.97115.204-0.368-0.3680.0000.0000.0000.000
141A141ARG10.7830.89412.220-0.552-0.5520.0000.0000.0000.000
142A142SER00.0870.03819.9230.0040.0040.0000.0000.0000.000
143A143ASN0-0.087-0.03118.801-0.039-0.0390.0000.0000.0000.000
144A144LEU0-0.055-0.02817.2050.0530.0530.0000.0000.0000.000
145A145GLU-1-0.884-0.93321.6930.2510.2510.0000.0000.0000.000
146A146GLY0-0.025-0.01020.6670.0390.0390.0000.0000.0000.000
147A147SER0-0.061-0.06620.954-0.025-0.0250.0000.0000.0000.000
148A148PHE00.0350.00622.764-0.029-0.0290.0000.0000.0000.000
149A149ARG10.9351.01919.9330.0690.0690.0000.0000.0000.000
150A150ILE0-0.020-0.00920.730-0.022-0.0220.0000.0000.0000.000
151A151SER00.0520.01220.0390.0150.0150.0000.0000.0000.000
152A152PRO0-0.020-0.02318.2750.0310.0310.0000.0000.0000.000
153A153GLY00.011-0.01021.313-0.037-0.0370.0000.0000.0000.000
154A154TYR0-0.047-0.00724.600-0.007-0.0070.0000.0000.0000.000
155A155GLY00.0130.00026.1950.0240.0240.0000.0000.0000.000
156A156ASP-1-0.822-0.90527.5270.0980.0980.0000.0000.0000.000
157A157LEU0-0.061-0.01620.4500.0250.0250.0000.0000.0000.000
158A158PRO00.0360.01221.870-0.034-0.0340.0000.0000.0000.000
159A159LEU00.0880.05121.5520.0020.0020.0000.0000.0000.000
160A160SER0-0.028-0.01420.962-0.028-0.0280.0000.0000.0000.000
161A161LEU0-0.015-0.01716.824-0.018-0.0180.0000.0000.0000.000
162A162ASN00.0260.01715.937-0.017-0.0170.0000.0000.0000.000
163A163LYS10.9800.98515.6330.2010.2010.0000.0000.0000.000
164A164LYS10.8610.94113.383-0.238-0.2380.0000.0000.0000.000
165A165ILE00.023-0.00111.308-0.040-0.0400.0000.0000.0000.000
166A166ALA00.0140.00510.786-0.192-0.1920.0000.0000.0000.000
167A167GLU-1-0.869-0.93110.446-1.198-1.1980.0000.0000.0000.000
168A168ILE0-0.053-0.0225.859-0.265-0.2650.0000.0000.0000.000
169A169PHE0-0.029-0.0266.038-0.730-0.7300.0000.0000.0000.000
170A170LYS10.8910.9548.1610.9220.9220.0000.0000.0000.000
171A171GLU-1-0.921-0.9545.344-3.477-3.4770.0000.0000.0000.000
172A172GLU-1-0.984-0.9903.862-9.264-8.9360.000-0.142-0.187-0.001
173A173VAL0-0.036-0.0377.7600.5680.5680.0000.0000.0000.000
174A174ASP-1-0.924-0.94711.376-1.441-1.4410.0000.0000.0000.000
175A175VAL0-0.033-0.02213.3060.2160.2160.0000.0000.0000.000
176A176ASN0-0.046-0.02314.170-0.136-0.1360.0000.0000.0000.000
177A177VAL0-0.013-0.00416.6350.0600.0600.0000.0000.0000.000
178A178ILE0-0.024-0.00619.2710.0430.0430.0000.0000.0000.000
179A179GLU-1-0.861-0.91621.426-0.392-0.3920.0000.0000.0000.000
180A180ASP-1-0.888-0.95423.148-0.286-0.2860.0000.0000.0000.000
181A181SER0-0.078-0.03925.0310.0320.0320.0000.0000.0000.000
182A182TYR0-0.052-0.04820.7960.0320.0320.0000.0000.0000.000
183A183VAL0-0.0010.00721.6970.0090.0090.0000.0000.0000.000
184A184LEU0-0.021-0.00916.817-0.032-0.0320.0000.0000.0000.000
185A185VAL00.0100.03119.3790.0310.0310.0000.0000.0000.000
186A186PRO00.057-0.01118.165-0.078-0.0780.0000.0000.0000.000
187A187ARG10.9340.97120.8360.3370.3370.0000.0000.0000.000
188A188LYS10.7560.89723.2680.3570.3570.0000.0000.0000.000
189A189THR00.0080.00117.067-0.074-0.0740.0000.0000.0000.000
190A190ILE0-0.0110.00718.5870.0600.0600.0000.0000.0000.000
191A191THR00.0610.02715.649-0.085-0.0850.0000.0000.0000.000
192A192ALA0-0.050-0.02916.0500.0500.0500.0000.0000.0000.000
193A193PHE00.0130.01814.293-0.017-0.0170.0000.0000.0000.000
194A194VAL0-0.011-0.01016.156-0.041-0.0410.0000.0000.0000.000
195A195GLY00.0240.02616.3150.0850.0850.0000.0000.0000.000
196A196TRP00.0140.00015.167-0.081-0.0810.0000.0000.0000.000
197A197ARG10.9670.98318.767-0.288-0.2880.0000.0000.0000.000