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: 22KRR

Calculation Name: 4OR8-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OR8

Chain ID: A

ChEMBL ID:

UniProt ID: P35256

Base Structure: X-ray

Registration Date: 2021-09-07

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 231
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2735384.039873
FMO2-HF: Nuclear repulsion 2645424.729724
FMO2-HF: Total energy -89959.310149
FMO2-MP2: Total energy -90222.832403


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:-3:ACE )


Summations of interaction energy for fragment #1(A:-3:ACE )
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.
0.1031.6050.039-0.732-0.809-0.004
Interaction energy analysis for fragmet #1(A:-3:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.032
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].
3A-1ASP -1-0.926-0.9523.385-0.2751.2270.039-0.732-0.809-0.004
4A0LYS 10.8300.9026.0240.3950.3950.0000.0000.0000.000
5A1MET 00.0310.0138.6900.0850.0850.0000.0000.0000.000
6A2ALA 0-0.049-0.03211.2870.0020.0020.0000.0000.0000.000
7A3GLU -1-0.825-0.89214.509-0.234-0.2340.0000.0000.0000.000
8A4LEU 0-0.019-0.01117.5550.0090.0090.0000.0000.0000.000
9A5SER 00.0260.01220.782-0.007-0.0070.0000.0000.0000.000
10A6THR 00.0160.00822.6060.0070.0070.0000.0000.0000.000
11A7ARG 10.9330.96020.9770.1220.1220.0000.0000.0000.000
12A8TYR 0-0.012-0.00823.609-0.004-0.0040.0000.0000.0000.000
13A9ASN 00.0290.02027.9680.0080.0080.0000.0000.0000.000
14A10LEU 0-0.024-0.01430.829-0.001-0.0010.0000.0000.0000.000
15A11PRO 00.0170.00934.3730.0000.0000.0000.0000.0000.000
16A12NME 0-0.0090.00736.6340.0020.0020.0000.0000.0000.000
17A19ACE 00.0270.00253.0220.0000.0000.0000.0000.0000.000
18A20ASN 0-0.076-0.05153.7860.0000.0000.0000.0000.0000.000
19A21LEU 0-0.0230.00453.7380.0000.0000.0000.0000.0000.000
20A22ASP -1-0.798-0.91457.677-0.010-0.0100.0000.0000.0000.000
21A23LEU 00.0580.02160.0410.0000.0000.0000.0000.0000.000
22A24ASN 0-0.035-0.01961.6820.0000.0000.0000.0000.0000.000
23A25SER 0-0.0080.00256.4510.0000.0000.0000.0000.0000.000
24A26THR 0-0.020-0.00656.4640.0000.0000.0000.0000.0000.000
25A27ALA 0-0.0020.01658.1240.0010.0010.0000.0000.0000.000
26A28ARG 10.9550.96658.2010.0070.0070.0000.0000.0000.000
27A29TRP 00.0150.00151.074-0.001-0.0010.0000.0000.0000.000
28A30ILE 00.018-0.00755.4860.0010.0010.0000.0000.0000.000
29A31LYS 10.9050.97350.7980.0000.0000.0000.0000.0000.000
30A32GLU -1-0.898-0.95550.499-0.008-0.0080.0000.0000.0000.000
31A33PRO 0-0.034-0.00849.3230.0000.0000.0000.0000.0000.000
32A34SER 00.0110.00145.157-0.002-0.0020.0000.0000.0000.000
33A35VAL 00.0450.01040.9240.0020.0020.0000.0000.0000.000
34A36GLY 00.0270.01740.443-0.001-0.0010.0000.0000.0000.000
35A37GLY 0-0.018-0.01641.3150.0020.0020.0000.0000.0000.000
36A38TRP 0-0.045-0.02744.4270.0000.0000.0000.0000.0000.000
37A39THR 00.0190.01945.858-0.001-0.0010.0000.0000.0000.000
38A40VAL 0-0.014-0.00547.6970.0010.0010.0000.0000.0000.000
39A41LYS 10.9140.96749.4220.0110.0110.0000.0000.0000.000
40A42TRP 00.0140.00951.3740.0010.0010.0000.0000.0000.000
41A43GLY 00.0490.01251.9840.0000.0000.0000.0000.0000.000
42A44ASN 0-0.041-0.03450.1790.0000.0000.0000.0000.0000.000
43A45PHE 0-0.043-0.00746.719-0.001-0.0010.0000.0000.0000.000
44A46VAL 0-0.009-0.01445.6510.0000.0000.0000.0000.0000.000
45A47PHE 0-0.0100.00744.9340.0000.0000.0000.0000.0000.000
46A48HIS 00.0170.00741.5240.0000.0000.0000.0000.0000.000
47A49ILE 0-0.024-0.01642.3690.0010.0010.0000.0000.0000.000
48A50PRO 00.0310.03339.8040.0000.0000.0000.0000.0000.000
49A51ASN 0-0.010-0.01541.8790.0010.0010.0000.0000.0000.000
50A52THR 0-0.007-0.01338.5440.0020.0020.0000.0000.0000.000
51A53GLY 00.0280.01640.5340.0000.0000.0000.0000.0000.000
52A54MET 0-0.0180.00741.0820.0000.0000.0000.0000.0000.000
53A55THR 00.0270.00342.2220.0000.0000.0000.0000.0000.000
54A56LEU 00.0460.03439.6440.0010.0010.0000.0000.0000.000
55A57LEU 00.0380.01843.3590.0010.0010.0000.0000.0000.000
56A58HIS 00.0570.02246.2570.0010.0010.0000.0000.0000.000
57A59HIS 0-0.035-0.01645.0650.0010.0010.0000.0000.0000.000
58A60LEU 00.0130.00543.1560.0010.0010.0000.0000.0000.000
59A61LYS 10.8580.96347.086-0.012-0.0120.0000.0000.0000.000
60A62SER 0-0.031-0.02250.5340.0000.0000.0000.0000.0000.000
61A63ASN 0-0.038-0.02149.0160.0010.0010.0000.0000.0000.000
62A64PHE 00.0130.03147.3640.0010.0010.0000.0000.0000.000
63A65VAL 0-0.030-0.02243.4930.0000.0000.0000.0000.0000.000
64A66VAL 00.0590.03839.1910.0000.0000.0000.0000.0000.000
65A67PRO 00.036-0.01641.668-0.001-0.0010.0000.0000.0000.000
66A68GLU -1-0.887-0.93836.3960.0410.0410.0000.0000.0000.000
67A69TRP 00.011-0.00137.861-0.002-0.0020.0000.0000.0000.000
68A70GLN 0-0.010-0.01942.356-0.003-0.0030.0000.0000.0000.000
69A71GLN 00.0430.02139.570-0.003-0.0030.0000.0000.0000.000
70A72THR 00.0190.01941.332-0.001-0.0010.0000.0000.0000.000
71A73ARG 10.8250.89944.291-0.023-0.0230.0000.0000.0000.000
72A74ASN 0-0.020-0.02047.431-0.002-0.0020.0000.0000.0000.000
73A75LEU 00.0120.02644.229-0.001-0.0010.0000.0000.0000.000
74A76PHE 00.0160.00644.063-0.001-0.0010.0000.0000.0000.000
75A77SER 00.0400.02549.270-0.001-0.0010.0000.0000.0000.000
76A78HIS 0-0.017-0.00652.1860.0000.0000.0000.0000.0000.000
77A79LEU 0-0.009-0.01049.431-0.001-0.0010.0000.0000.0000.000
78A80PHE 0-0.011-0.00746.3440.0000.0000.0000.0000.0000.000
79A81LYS 10.8610.94451.035-0.019-0.0190.0000.0000.0000.000
80A82ASN 00.0750.02653.8500.0000.0000.0000.0000.0000.000
81A83PRO 00.0160.01056.8840.0000.0000.0000.0000.0000.000
82A84LYS 10.8390.92859.466-0.010-0.0100.0000.0000.0000.000
83A85SER 0-0.026-0.02154.496-0.001-0.0010.0000.0000.0000.000
84A86THR 0-0.034-0.02756.1510.0000.0000.0000.0000.0000.000
85A87ILE 0-0.0120.00349.8470.0000.0000.0000.0000.0000.000
86A88ILE 0-0.0090.00352.1190.0000.0000.0000.0000.0000.000
87A89GLU -1-0.870-0.95450.1270.0030.0030.0000.0000.0000.000
88A90PRO 00.0610.00446.0030.0000.0000.0000.0000.0000.000
89A91PHE 0-0.015-0.00648.295-0.001-0.0010.0000.0000.0000.000
90A92LEU 00.0250.00050.563-0.001-0.0010.0000.0000.0000.000
91A93ALA 00.0130.01149.1590.0000.0000.0000.0000.0000.000
92A94LEU 00.0090.00647.1240.0000.0000.0000.0000.0000.000
93A95ARG 10.8000.92349.9100.0000.0000.0000.0000.0000.000
94A96ILE 00.0200.01053.2450.0000.0000.0000.0000.0000.000
95A97LEU 0-0.006-0.00546.7860.0000.0000.0000.0000.0000.000
96A98LEU 00.011-0.00150.6450.0000.0000.0000.0000.0000.000
97A99GLY 00.0420.00952.521-0.001-0.0010.0000.0000.0000.000
98A100VAL 0-0.034-0.02153.1120.0000.0000.0000.0000.0000.000
99A101ALA 00.0150.02151.4070.0000.0000.0000.0000.0000.000
100A102LEU 0-0.027-0.01153.121-0.001-0.0010.0000.0000.0000.000
101A103LYS 10.8660.93456.3330.0010.0010.0000.0000.0000.000
102A104ASP -1-0.825-0.88352.833-0.004-0.0040.0000.0000.0000.000
103A105GLN 00.024-0.00855.451-0.001-0.0010.0000.0000.0000.000
104A106GLU -1-0.843-0.92951.247-0.006-0.0060.0000.0000.0000.000
105A107LEU 0-0.0150.02154.275-0.001-0.0010.0000.0000.0000.000
106A108GLN 0-0.0170.00755.911-0.001-0.0010.0000.0000.0000.000
107A109GLN 0-0.036-0.02457.7500.0000.0000.0000.0000.0000.000
108A110SER 0-0.056-0.03856.965-0.001-0.0010.0000.0000.0000.000
109A111LEU 0-0.029-0.00758.5960.0000.0000.0000.0000.0000.000
110A112ILE 00.0540.01761.7370.0000.0000.0000.0000.0000.000
111A113PRO 00.0600.01365.5120.0000.0000.0000.0000.0000.000
112A114GLY 00.0290.01668.0240.0000.0000.0000.0000.0000.000
113A115PHE 00.023-0.00259.7440.0000.0000.0000.0000.0000.000
114A116ARG 10.8690.94562.8830.0050.0050.0000.0000.0000.000
115A117SER 00.0130.01164.5310.0000.0000.0000.0000.0000.000
116A118ILE 00.0260.00263.8490.0000.0000.0000.0000.0000.000
117A119VAL 00.0300.00859.4320.0000.0000.0000.0000.0000.000
118A120HIS 0-0.0150.00261.5530.0000.0000.0000.0000.0000.000
119A121MET 00.0000.00763.6030.0000.0000.0000.0000.0000.000
120A122LEU 0-0.0140.00359.8930.0000.0000.0000.0000.0000.000
121A123SER 0-0.041-0.01958.7090.0010.0010.0000.0000.0000.000
122A124GLU -1-0.916-0.97660.2280.0000.0000.0000.0000.0000.000
123A125TRP 0-0.0120.00559.1910.0000.0000.0000.0000.0000.000
124A126LEU 0-0.034-0.02055.8550.0000.0000.0000.0000.0000.000
125A127LEU 0-0.063-0.03356.5840.0010.0010.0000.0000.0000.000
126A128LEU 0-0.050-0.02559.3860.0010.0010.0000.0000.0000.000
127A129GLU -1-0.922-0.93861.7130.0000.0000.0000.0000.0000.000
128A130VAL 0-0.032-0.02758.7850.0000.0000.0000.0000.0000.000
129A131THR 00.0340.03160.7070.0000.0000.0000.0000.0000.000
130A132SER 00.0270.00659.5990.0000.0000.0000.0000.0000.000
131A133ALA 0-0.009-0.00560.157-0.001-0.0010.0000.0000.0000.000
132A134ILE 00.0140.02462.5190.0000.0000.0000.0000.0000.000
133A135HIS 00.001-0.00864.949-0.001-0.0010.0000.0000.0000.000
134A136ILE 00.0250.01365.6220.0000.0000.0000.0000.0000.000
135A137SER 0-0.016-0.01569.3630.0000.0000.0000.0000.0000.000
136A138PRO 00.0510.00872.3380.0000.0000.0000.0000.0000.000
137A139ASN 00.0000.00273.3380.0000.0000.0000.0000.0000.000
138A140LEU 00.000-0.00571.2150.0000.0000.0000.0000.0000.000
139A141LEU 0-0.057-0.01368.0600.0000.0000.0000.0000.0000.000
140A142GLY 00.0230.03171.3960.0000.0000.0000.0000.0000.000
141A143ILE 0-0.036-0.01867.2120.0000.0000.0000.0000.0000.000
142A144TYR 00.0220.00968.7860.0000.0000.0000.0000.0000.000
143A145LEU 0-0.011-0.00864.0180.0000.0000.0000.0000.0000.000
144A146THR 00.0520.01862.8640.0000.0000.0000.0000.0000.000
145A147SER 00.0440.00458.1270.0000.0000.0000.0000.0000.000
146A148ASP -1-0.891-0.95357.688-0.014-0.0140.0000.0000.0000.000
147A149MET 0-0.0130.00457.6720.0000.0000.0000.0000.0000.000
148A150PHE 00.0710.02957.2340.0000.0000.0000.0000.0000.000
149A151LYS 10.9260.97253.4620.0150.0150.0000.0000.0000.000
150A152ILE 00.0040.00453.1700.0000.0000.0000.0000.0000.000
151A153LEU 00.0130.01654.2840.0000.0000.0000.0000.0000.000
152A154MET 0-0.059-0.02350.8680.0010.0010.0000.0000.0000.000
153A155ALA 00.0040.00049.5050.0000.0000.0000.0000.0000.000
154A156GLY 00.0420.01549.6510.0000.0000.0000.0000.0000.000
155A157VAL 0-0.0100.00048.9390.0010.0010.0000.0000.0000.000
156A158LYS 10.9160.96444.0010.0160.0160.0000.0000.0000.000
157A159ASN 00.0230.02045.689-0.001-0.0010.0000.0000.0000.000
158A160PHE 00.0090.00347.0180.0010.0010.0000.0000.0000.000
159A161PHE 0-0.028-0.03644.0070.0010.0010.0000.0000.0000.000
160A162ASN 0-0.037-0.02140.9000.0020.0020.0000.0000.0000.000
161A163LYS 10.8830.93342.7470.0050.0050.0000.0000.0000.000
162A164MET 0-0.0120.04144.2560.0020.0020.0000.0000.0000.000
163A165PHE 0-0.089-0.04237.6750.0020.0020.0000.0000.0000.000
164A166THR 0-0.067-0.05039.3580.0010.0010.0000.0000.0000.000
165A167LEU 0-0.0330.00541.4700.0010.0010.0000.0000.0000.000
166A168HIS 0-0.0010.00337.7490.0000.0000.0000.0000.0000.000
167A169VAL 00.0070.00036.267-0.001-0.0010.0000.0000.0000.000
168A170VAL 0-0.009-0.00439.3290.0000.0000.0000.0000.0000.000
169A171ASN 0-0.034-0.02339.1440.0020.0020.0000.0000.0000.000
170A172ASP -1-0.899-0.94639.5370.0280.0280.0000.0000.0000.000
171A173HIS 0-0.024-0.02536.261-0.002-0.0020.0000.0000.0000.000
172A174GLY 0-0.0050.00041.935-0.001-0.0010.0000.0000.0000.000
173A175LYS 10.9070.97037.261-0.017-0.0170.0000.0000.0000.000
174A176PRO 00.0410.01343.5410.0010.0010.0000.0000.0000.000
175A177SER 00.0410.02543.1800.0000.0000.0000.0000.0000.000
176A178SER 00.0060.00644.4890.0000.0000.0000.0000.0000.000
177A179ILE 0-0.0040.02047.6870.0000.0000.0000.0000.0000.000
178A180GLU -1-0.928-0.96350.1550.0080.0080.0000.0000.0000.000
179A181ILE 00.0150.00753.736-0.001-0.0010.0000.0000.0000.000
180A182LYS 10.8860.95256.760-0.004-0.0040.0000.0000.0000.000
181A183LEU 00.0220.00659.483-0.001-0.0010.0000.0000.0000.000
182A184THR 00.032-0.00562.8200.0000.0000.0000.0000.0000.000
183A185GLY 0-0.0200.00565.8510.0000.0000.0000.0000.0000.000
184A186GLN 00.007-0.01260.4570.0000.0000.0000.0000.0000.000
185A187GLN 0-0.034-0.00957.3050.0000.0000.0000.0000.0000.000
186A188ILE 00.0050.01153.6670.0000.0000.0000.0000.0000.000
187A189ILE 00.0210.01650.4610.0000.0000.0000.0000.0000.000
188A190ILE 0-0.0020.00046.7050.0000.0000.0000.0000.0000.000
189A191THR 00.011-0.02644.6610.0000.0000.0000.0000.0000.000
190A192ARG 10.8290.93536.423-0.005-0.0050.0000.0000.0000.000
191A193VAL 0-0.012-0.01840.3920.0020.0020.0000.0000.0000.000
192A194ASN 00.042-0.00335.082-0.002-0.0020.0000.0000.0000.000
193A195MET 0-0.017-0.00535.997-0.001-0.0010.0000.0000.0000.000
194A196GLY 00.0110.00737.921-0.002-0.0020.0000.0000.0000.000
195A197PHE 00.0000.00840.2510.0010.0010.0000.0000.0000.000
196A198LEU 0-0.011-0.01543.7970.0000.0000.0000.0000.0000.000
197A199VAL 00.0080.02046.4670.0000.0000.0000.0000.0000.000
198A200GLU -1-0.828-0.93649.8380.0100.0100.0000.0000.0000.000
199A201VAL 00.012-0.00252.885-0.001-0.0010.0000.0000.0000.000
200A202ARG 10.8720.93753.988-0.009-0.0090.0000.0000.0000.000
201A203ARG 10.9550.97059.250-0.005-0.0050.0000.0000.0000.000
202A204ILE 00.0340.01162.9850.0010.0010.0000.0000.0000.000
203A205NME 0-0.0060.00966.2640.0000.0000.0000.0000.0000.000
204A215ACE 00.0470.01770.5080.0000.0000.0000.0000.0000.000
205A216SER 0-0.026-0.03067.4340.0000.0000.0000.0000.0000.000
206A217GLU -1-0.876-0.93661.4060.0090.0090.0000.0000.0000.000
207A218SER 0-0.0370.01361.5000.0000.0000.0000.0000.0000.000
208A219VAL 00.0010.00055.4150.0000.0000.0000.0000.0000.000
209A220VAL 00.0160.01355.3620.0000.0000.0000.0000.0000.000
210A221PHE 00.0120.00048.8690.0000.0000.0000.0000.0000.000
211A222GLY 00.0490.02749.3580.0000.0000.0000.0000.0000.000
212A223LEU 0-0.024-0.00841.4470.0000.0000.0000.0000.0000.000
213A224VAL 0-0.0040.00543.864-0.001-0.0010.0000.0000.0000.000
214A225ALA 00.0260.00839.4440.0010.0010.0000.0000.0000.000
215A226GLU -1-0.747-0.88835.7990.0020.0020.0000.0000.0000.000
216A227ALA 00.001-0.00936.582-0.002-0.0020.0000.0000.0000.000
217A228VAL 0-0.0070.00638.099-0.002-0.0020.0000.0000.0000.000
218A229LEU 00.018-0.00341.369-0.001-0.0010.0000.0000.0000.000
219A230ARG 10.8970.94334.8050.0040.0040.0000.0000.0000.000
220A231GLU -1-0.844-0.89038.616-0.016-0.0160.0000.0000.0000.000
221A232HIS 0-0.079-0.04439.496-0.002-0.0020.0000.0000.0000.000
222A233SER 0-0.013-0.03439.3930.0010.0010.0000.0000.0000.000
223A234GLN 00.0020.00337.5370.0020.0020.0000.0000.0000.000
224A235MET 0-0.011-0.01640.9850.0010.0010.0000.0000.0000.000
225A236GLU -1-0.886-0.93539.167-0.025-0.0250.0000.0000.0000.000
226A237LYS 10.8950.95441.2550.0220.0220.0000.0000.0000.000
227A238GLY 00.0350.01737.6020.0010.0010.0000.0000.0000.000
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