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: 1JG8Z

Calculation Name: 1XKR-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XKR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X006

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 206
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2306199.445311
FMO2-HF: Nuclear repulsion 2226090.343637
FMO2-HF: Total energy -80109.101674
FMO2-MP2: Total energy -80338.61637


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:0:HIS )


Summations of interaction energy for fragment #1(A:0: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.
-12.91-8.8722.834-3.183-3.689-0.015
Interaction energy analysis for fragmet #1(A:0:HIS )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / 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].
3A2LYS 10.9410.9622.208-10.217-6.4142.833-3.147-3.489-0.015
4A3ILE 00.0280.0264.5071.3871.6220.001-0.036-0.2000.000
5A4SER 0-0.064-0.0317.3040.3220.3220.0000.0000.0000.000
6A5GLU -1-0.774-0.9139.849-1.570-1.5700.0000.0000.0000.000
7A6ARG 10.8990.96112.8340.9110.9110.0000.0000.0000.000
8A7GLN 00.015-0.00510.245-0.255-0.2550.0000.0000.0000.000
9A8LYS 10.9150.9549.3092.2272.2270.0000.0000.0000.000
10A9ASP -1-0.903-0.95514.175-0.640-0.6400.0000.0000.0000.000
11A10LEU 00.0140.01317.0400.0730.0730.0000.0000.0000.000
12A11LEU 0-0.015-0.01313.8990.0610.0610.0000.0000.0000.000
13A12LYS 10.9530.98717.9280.6890.6890.0000.0000.0000.000
14A13GLU -1-0.957-0.98120.002-0.508-0.5080.0000.0000.0000.000
15A14ILE 00.0040.00619.8820.0500.0500.0000.0000.0000.000
16A15GLY 00.0110.00021.8070.0450.0450.0000.0000.0000.000
17A16ASN 0-0.036-0.02923.2200.0810.0810.0000.0000.0000.000
18A17ILE 0-0.0370.00625.8920.0440.0440.0000.0000.0000.000
19A18GLY 00.0130.00126.5100.0320.0320.0000.0000.0000.000
20A19ALA 00.0200.00427.1740.0280.0280.0000.0000.0000.000
21A20GLY 00.0580.03028.9120.0280.0280.0000.0000.0000.000
22A21ASN 0-0.017-0.01830.9960.0420.0420.0000.0000.0000.000
23A22ALA 00.0010.00130.9390.0220.0220.0000.0000.0000.000
24A23ALA 0-0.009-0.00632.9390.0190.0190.0000.0000.0000.000
25A24THR 00.0010.01134.7410.0220.0220.0000.0000.0000.000
26A25ALA 00.003-0.00336.1590.0150.0150.0000.0000.0000.000
27A26ILE 00.0400.00333.9390.0140.0140.0000.0000.0000.000
28A27SER 0-0.023-0.01738.0250.0130.0130.0000.0000.0000.000
29A28TYR 0-0.069-0.03840.4440.0150.0150.0000.0000.0000.000
30A29MET 0-0.065-0.00839.8720.0050.0050.0000.0000.0000.000
31A30ILE 0-0.028-0.01639.5710.0080.0080.0000.0000.0000.000
32A31ASN 0-0.056-0.00843.1740.0060.0060.0000.0000.0000.000
33A32LYS 10.8230.88642.3940.1670.1670.0000.0000.0000.000
34A33LYS 10.8530.93838.8220.1990.1990.0000.0000.0000.000
35A34VAL 0-0.021-0.00635.5000.0000.0000.0000.0000.0000.000
36A35GLU -1-0.890-0.93034.214-0.236-0.2360.0000.0000.0000.000
37A36ILE 0-0.009-0.00729.027-0.001-0.0010.0000.0000.0000.000
38A37SER 0-0.0270.00127.956-0.009-0.0090.0000.0000.0000.000
39A38VAL 00.009-0.00321.736-0.002-0.0020.0000.0000.0000.000
40A39PRO 0-0.0020.01523.088-0.023-0.0230.0000.0000.0000.000
41A40ASN 0-0.070-0.05718.435-0.068-0.0680.0000.0000.0000.000
42A41VAL 00.0340.02614.7840.0280.0280.0000.0000.0000.000
43A42GLU -1-0.963-0.96713.460-1.010-1.0100.0000.0000.0000.000
44A43ILE 0-0.054-0.0349.126-0.021-0.0210.0000.0000.0000.000
45A44VAL 00.0190.01010.525-0.213-0.2130.0000.0000.0000.000
46A45PRO 00.0130.0119.6550.0370.0370.0000.0000.0000.000
47A46ILE 00.0850.02211.6930.1080.1080.0000.0000.0000.000
48A47SER 00.0300.02313.9860.0370.0370.0000.0000.0000.000
49A48LYS 10.8450.90513.0540.5440.5440.0000.0000.0000.000
50A49VAL 00.0550.04115.9430.0140.0140.0000.0000.0000.000
51A50ILE 0-0.0090.01218.0510.0350.0350.0000.0000.0000.000
52A51PHE 0-0.093-0.05317.8010.0420.0420.0000.0000.0000.000
53A52ILE 00.0050.02216.9620.0150.0150.0000.0000.0000.000
54A53ALA 0-0.032-0.00220.9890.0230.0230.0000.0000.0000.000
55A54LYS 10.9420.95924.4320.2910.2910.0000.0000.0000.000
56A55ASP -1-0.848-0.92927.325-0.176-0.1760.0000.0000.0000.000
57A56PRO 0-0.037-0.01825.342-0.011-0.0110.0000.0000.0000.000
58A57GLU -1-0.912-0.99427.054-0.146-0.1460.0000.0000.0000.000
59A58GLU -1-0.841-0.89630.153-0.233-0.2330.0000.0000.0000.000
60A59ILE 0-0.050-0.02230.762-0.010-0.0100.0000.0000.0000.000
61A60VAL 0-0.031-0.01728.226-0.003-0.0030.0000.0000.0000.000
62A61VAL 00.001-0.00531.6580.0120.0120.0000.0000.0000.000
63A62GLY 00.0260.01128.504-0.023-0.0230.0000.0000.0000.000
64A63VAL 0-0.049-0.01728.3330.0220.0220.0000.0000.0000.000
65A64LYS 10.9930.99823.3340.3120.3120.0000.0000.0000.000
66A65MET 0-0.0200.00225.7560.0250.0250.0000.0000.0000.000
67A66PRO 0-0.030-0.01624.340-0.039-0.0390.0000.0000.0000.000
68A67VAL 0-0.002-0.01021.6090.0160.0160.0000.0000.0000.000
69A68THR 0-0.015-0.02123.2160.0010.0010.0000.0000.0000.000
70A69GLY 00.0230.01324.1010.0040.0040.0000.0000.0000.000
71A70ASP -1-0.876-0.94421.877-0.407-0.4070.0000.0000.0000.000
72A71ILE 0-0.061-0.04117.534-0.081-0.0810.0000.0000.0000.000
73A72GLU -1-0.838-0.89018.739-0.323-0.3230.0000.0000.0000.000
74A73GLY 00.0260.00918.141-0.079-0.0790.0000.0000.0000.000
75A74SER 0-0.078-0.03119.6620.0790.0790.0000.0000.0000.000
76A75VAL 00.0110.02420.319-0.068-0.0680.0000.0000.0000.000
77A76LEU 0-0.003-0.00622.2040.0550.0550.0000.0000.0000.000
78A77LEU 00.0080.00223.685-0.035-0.0350.0000.0000.0000.000
79A78ILE 00.0160.00524.4500.0270.0270.0000.0000.0000.000
80A79MET 0-0.017-0.01827.195-0.005-0.0050.0000.0000.0000.000
81A80GLY 00.0850.04230.4630.0130.0130.0000.0000.0000.000
82A81THR 0-0.008-0.03331.6290.0140.0140.0000.0000.0000.000
83A82THR 0-0.025-0.02234.5710.0100.0100.0000.0000.0000.000
84A83VAL 00.0220.01931.9430.0100.0100.0000.0000.0000.000
85A84VAL 00.0170.01434.1460.0090.0090.0000.0000.0000.000
86A85LYS 10.8830.93836.5860.1640.1640.0000.0000.0000.000
87A86LYS 10.9210.99138.3170.1780.1780.0000.0000.0000.000
88A87ILE 0-0.002-0.00535.0440.0070.0070.0000.0000.0000.000
89A88LEU 00.013-0.00639.5740.0080.0080.0000.0000.0000.000
90A89GLU -1-0.931-0.94442.079-0.138-0.1380.0000.0000.0000.000
91A90ILE 0-0.047-0.02240.9780.0070.0070.0000.0000.0000.000
92A91LEU 0-0.043-0.01141.8510.0050.0050.0000.0000.0000.000
93A92THR 0-0.056-0.05144.6760.0080.0080.0000.0000.0000.000
94A93GLY 0-0.0030.01247.0380.0070.0070.0000.0000.0000.000
95A94ARG 10.8930.93647.3480.1230.1230.0000.0000.0000.000
96A95ALA 00.0520.03543.202-0.005-0.0050.0000.0000.0000.000
97A96PRO 0-0.066-0.01341.8030.0080.0080.0000.0000.0000.000
98A97ASP -1-0.853-0.94143.212-0.120-0.1200.0000.0000.0000.000
99A98ASN 0-0.053-0.03141.145-0.008-0.0080.0000.0000.0000.000
100A99LEU 00.0520.00835.3010.0020.0020.0000.0000.0000.000
101A100LEU 00.0480.01637.887-0.003-0.0030.0000.0000.0000.000
102A101ASN 0-0.107-0.05040.3180.0090.0090.0000.0000.0000.000
103A102LEU 0-0.0180.01038.3840.0040.0040.0000.0000.0000.000
104A103ASP -1-0.818-0.88742.667-0.134-0.1340.0000.0000.0000.000
105A104GLU -1-0.884-0.96743.288-0.131-0.1310.0000.0000.0000.000
106A105PHE 0-0.035-0.01042.977-0.007-0.0070.0000.0000.0000.000
107A106SER 00.028-0.01541.927-0.009-0.0090.0000.0000.0000.000
108A107ALA 00.0020.01538.971-0.012-0.0120.0000.0000.0000.000
109A108SER 0-0.028-0.02338.163-0.013-0.0130.0000.0000.0000.000
110A109ALA 0-0.0060.00838.873-0.009-0.0090.0000.0000.0000.000
111A110LEU 00.0320.00535.696-0.012-0.0120.0000.0000.0000.000
112A111ARG 10.8650.93334.3200.1910.1910.0000.0000.0000.000
113A112GLU -1-0.875-0.94434.192-0.237-0.2370.0000.0000.0000.000
114A113ILE 00.006-0.00733.141-0.012-0.0120.0000.0000.0000.000
115A114GLY 00.027-0.00330.979-0.020-0.0200.0000.0000.0000.000
116A115ASN 0-0.051-0.03030.367-0.035-0.0350.0000.0000.0000.000
117A116ILE 0-0.0080.01331.646-0.016-0.0160.0000.0000.0000.000
118A117MET 0-0.0120.00228.508-0.012-0.0120.0000.0000.0000.000
119A118CYS 0-0.030-0.01426.645-0.034-0.0340.0000.0000.0000.000
120A119GLY 00.0540.02926.987-0.024-0.0240.0000.0000.0000.000
121A120THR 0-0.057-0.05429.028-0.015-0.0150.0000.0000.0000.000
122A121TYR 00.0010.00919.511-0.029-0.0290.0000.0000.0000.000
123A122VAL 00.0220.00224.164-0.034-0.0340.0000.0000.0000.000
124A123SER 0-0.018-0.00425.435-0.012-0.0120.0000.0000.0000.000
125A124ALA 00.0250.01825.5560.0020.0020.0000.0000.0000.000
126A125LEU 0-0.016-0.01819.047-0.020-0.0200.0000.0000.0000.000
127A126ALA 0-0.017-0.01322.994-0.024-0.0240.0000.0000.0000.000
128A127ASP -1-0.887-0.93624.759-0.350-0.3500.0000.0000.0000.000
129A128PHE 0-0.075-0.04823.5870.0100.0100.0000.0000.0000.000
130A129LEU 0-0.043-0.00718.426-0.029-0.0290.0000.0000.0000.000
131A130GLY 0-0.0150.00122.401-0.003-0.0030.0000.0000.0000.000
132A131PHE 0-0.093-0.04818.1370.0040.0040.0000.0000.0000.000
133A132LYS 10.9160.95124.1280.3120.3120.0000.0000.0000.000
134A133ILE 0-0.037-0.01722.249-0.017-0.0170.0000.0000.0000.000
135A134ASP -1-0.894-0.92325.909-0.262-0.2620.0000.0000.0000.000
136A135THR 0-0.016-0.03126.804-0.020-0.0200.0000.0000.0000.000
137A136LEU 0-0.018-0.00727.8230.0270.0270.0000.0000.0000.000
138A137PRO 0-0.029-0.02630.257-0.007-0.0070.0000.0000.0000.000
139A138PRO 00.0290.02330.354-0.006-0.0060.0000.0000.0000.000
140A139GLN 0-0.011-0.01428.7120.0190.0190.0000.0000.0000.000
141A140LEU 0-0.0160.00130.349-0.017-0.0170.0000.0000.0000.000
142A141VAL 00.0240.01728.8880.0150.0150.0000.0000.0000.000
143A142ILE 0-0.020-0.01632.061-0.012-0.0120.0000.0000.0000.000
144A143ASP -1-0.822-0.91130.441-0.173-0.1730.0000.0000.0000.000
145A144MET 0-0.089-0.01929.581-0.011-0.0110.0000.0000.0000.000
146A145ILE 00.0130.00124.844-0.012-0.0120.0000.0000.0000.000
147A146SER 00.014-0.01124.893-0.020-0.0200.0000.0000.0000.000
148A147ALA 00.0230.01725.032-0.006-0.0060.0000.0000.0000.000
149A148ILE 00.0270.01824.402-0.008-0.0080.0000.0000.0000.000
150A149PHE 00.000-0.02719.901-0.023-0.0230.0000.0000.0000.000
151A150ALA 0-0.0280.01520.832-0.018-0.0180.0000.0000.0000.000
152A151GLU -1-0.928-0.97221.908-0.211-0.2110.0000.0000.0000.000
153A152ALA 0-0.023-0.00920.182-0.006-0.0060.0000.0000.0000.000
154A153SER 0-0.038-0.05017.377-0.052-0.0520.0000.0000.0000.000
155A154ILE 0-0.055-0.02317.4000.0090.0090.0000.0000.0000.000
156A155GLU -1-0.916-0.95419.270-0.252-0.2520.0000.0000.0000.000
157A156GLU -1-0.942-0.97214.684-0.536-0.5360.0000.0000.0000.000
158A157LEU 0-0.078-0.04211.909-0.013-0.0130.0000.0000.0000.000
159A158GLU -1-0.985-0.96215.318-0.120-0.1200.0000.0000.0000.000
160A159ASP -1-0.935-0.97617.133-0.079-0.0790.0000.0000.0000.000
161A160ASN 0-0.102-0.06012.283-0.051-0.0510.0000.0000.0000.000
162A161SER 00.000-0.0129.0630.0670.0670.0000.0000.0000.000
163A162GLU -1-0.949-0.9517.504-1.168-1.1680.0000.0000.0000.000
164A163ASP -1-0.802-0.9138.730-1.017-1.0170.0000.0000.0000.000
165A164GLN 0-0.093-0.0366.171-0.293-0.2930.0000.0000.0000.000
166A165ILE 00.0250.0249.9890.1050.1050.0000.0000.0000.000
167A166VAL 0-0.049-0.02513.103-0.200-0.2000.0000.0000.0000.000
168A167PHE 00.012-0.00415.2330.1600.1600.0000.0000.0000.000
169A168VAL 00.032-0.00117.347-0.046-0.0460.0000.0000.0000.000
170A169GLU -1-0.877-0.92620.215-0.420-0.4200.0000.0000.0000.000
171A170THR 0-0.026-0.04223.2450.0010.0010.0000.0000.0000.000
172A171LEU 00.0170.00926.4230.0250.0250.0000.0000.0000.000
173A172LEU 00.0080.00529.1810.0070.0070.0000.0000.0000.000
174A173LYS 10.9210.94832.5730.2150.2150.0000.0000.0000.000
175A174VAL 00.0190.01535.4620.0040.0040.0000.0000.0000.000
176A175GLU -1-0.897-0.97639.078-0.168-0.1680.0000.0000.0000.000
177A176GLU -1-0.950-0.94141.415-0.140-0.1400.0000.0000.0000.000
178A177GLU -1-0.893-0.96739.670-0.162-0.1620.0000.0000.0000.000
179A178GLU -1-0.958-0.98639.285-0.179-0.1790.0000.0000.0000.000
180A179GLU -1-0.905-0.94234.965-0.217-0.2170.0000.0000.0000.000
181A180PRO 0-0.078-0.04032.1360.0000.0000.0000.0000.0000.000
182A181LEU 0-0.010-0.00832.920-0.004-0.0040.0000.0000.0000.000
183A182THR 0-0.025-0.01026.923-0.017-0.0170.0000.0000.0000.000
184A183SER 0-0.037-0.01428.1330.0250.0250.0000.0000.0000.000
185A184TYR 00.0190.01922.823-0.012-0.0120.0000.0000.0000.000
186A185MET 0-0.028-0.00722.8530.0430.0430.0000.0000.0000.000
187A186MET 0-0.0130.01618.344-0.065-0.0650.0000.0000.0000.000
188A187MET 0-0.0200.00617.3430.0460.0460.0000.0000.0000.000
189A188ILE 00.022-0.00116.079-0.140-0.1400.0000.0000.0000.000
190A189PRO 0-0.035-0.01812.9430.0860.0860.0000.0000.0000.000
191A190LYS 10.9820.99414.3840.4120.4120.0000.0000.0000.000
192A191PRO 00.0420.01011.807-0.122-0.1220.0000.0000.0000.000
193A192GLY 0-0.018-0.01210.8280.0900.0900.0000.0000.0000.000
194A193TYR 0-0.015-0.02511.893-0.071-0.0710.0000.0000.0000.000
195A194LEU 00.0520.0358.999-0.054-0.0540.0000.0000.0000.000
196A195VAL 0-0.013-0.0158.036-0.153-0.1530.0000.0000.0000.000
197A196LYS 10.9540.98210.7410.7240.7240.0000.0000.0000.000
198A197ILE 00.0350.02314.3410.0860.0860.0000.0000.0000.000
199A198PHE 00.000-0.0299.9660.0280.0280.0000.0000.0000.000
200A199GLU -1-0.968-0.96913.499-0.646-0.6460.0000.0000.0000.000
201A200ARG 10.8500.93314.7300.6860.6860.0000.0000.0000.000
202A201MET 0-0.0310.01515.3160.0310.0310.0000.0000.0000.000
203A202GLY 0-0.0100.00217.3910.0580.0580.0000.0000.0000.000
204A203ILE 00.019-0.01515.421-0.097-0.0970.0000.0000.0000.000
205A204GLN 0-0.041-0.01414.837-0.006-0.0060.0000.0000.0000.000
206A205NME 0-0.0230.01011.7770.0120.0120.0000.0000.0000.000