Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: K9Z23

Calculation Name: 4OF0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4OF0

Chain ID: A

ChEMBL ID:

UniProt ID: B1Q236

Base Structure: X-ray

Registration Date: 2023-06-26

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2468434.265041
FMO2-HF: Nuclear repulsion 2378418.430219
FMO2-HF: Total energy -90015.834822
FMO2-MP2: Total energy -90277.524685


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:23:GLN)


Summations of interaction energy for fragment #1(A:23:GLN)
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.
-62.172-53.51535.817-18.176-26.301-0.026
Interaction energy analysis for fragmet #1(A:23:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / 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].
3A25ILE00.0290.0133.889-0.1701.785-0.020-1.062-0.8720.002
4A26VAL0-0.065-0.0266.958-0.114-0.1140.0000.0000.0000.000
5A27GLU-1-0.841-0.8959.1480.2480.2480.0000.0000.0000.000
6A28ALA00.0340.00711.5770.0330.0330.0000.0000.0000.000
7A29PRO00.0120.01312.5070.0700.0700.0000.0000.0000.000
8A30LYS10.8980.94615.677-0.109-0.1090.0000.0000.0000.000
9A31ASP-1-0.827-0.90919.104-0.151-0.1510.0000.0000.0000.000
10A32THR0-0.075-0.03621.8670.0530.0530.0000.0000.0000.000
11A33LEU0-0.0040.00024.507-0.023-0.0230.0000.0000.0000.000
12A34ALA00.0470.02127.4040.0210.0210.0000.0000.0000.000
13A35ALA0-0.020-0.00629.310-0.019-0.0190.0000.0000.0000.000
14A36VAL0-0.047-0.03132.0040.0090.0090.0000.0000.0000.000
15A37GLY0-0.050-0.01932.7420.0010.0010.0000.0000.0000.000
16A38GLU-1-0.886-0.93130.5030.0690.0690.0000.0000.0000.000
17A39THR0-0.013-0.01825.897-0.010-0.0100.0000.0000.0000.000
18A40ALA0-0.0100.00924.4020.0050.0050.0000.0000.0000.000
19A41ILE0-0.003-0.01720.2640.0310.0310.0000.0000.0000.000
20A42LEU0-0.0110.01118.277-0.031-0.0310.0000.0000.0000.000
21A43THR0-0.032-0.03815.9740.0330.0330.0000.0000.0000.000
22A44CYS0-0.028-0.01310.3150.1290.1290.0000.0000.0000.000
23A45ARG10.8170.91110.345-0.528-0.5280.0000.0000.0000.000
24A46VAL0-0.025-0.0064.872-0.339-0.3390.0000.0000.0000.000
25A47GLU-1-0.806-0.8913.9601.4501.7090.000-0.073-0.1870.000
26A48HIS0-0.029-0.0372.335-3.356-0.9962.800-2.577-2.583-0.023
27A49GLN00.0080.0042.197-4.934-2.1155.301-4.208-3.913-0.012
28A50GLN00.0410.0141.882-12.560-16.51911.951-2.773-5.2200.029
29A51GLY00.0170.0462.141-11.406-11.7723.398-0.895-2.1370.021
30A52PRO0-0.030-0.0124.0221.5511.8270.000-0.040-0.2360.001
31A53VAL00.0210.0116.209-0.627-0.6270.0000.0000.0000.000
32A54GLN0-0.011-0.0238.024-0.056-0.0560.0000.0000.0000.000
33A55TRP00.001-0.02910.723-0.196-0.1960.0000.0000.0000.000
34A56MET0-0.049-0.00711.085-0.033-0.0330.0000.0000.0000.000
35A57LYS10.7930.87015.2230.1940.1940.0000.0000.0000.000
36A58ASP-1-0.820-0.90719.028-0.434-0.4340.0000.0000.0000.000
37A59ASP-1-0.877-0.92515.948-0.742-0.7420.0000.0000.0000.000
38A60PHE0-0.0180.00215.702-0.091-0.0910.0000.0000.0000.000
39A61GLY0-0.013-0.01213.7860.0470.0470.0000.0000.0000.000
40A62LEU0-0.046-0.03314.4550.0690.0690.0000.0000.0000.000
41A63GLY00.0300.01514.2770.0540.0540.0000.0000.0000.000
42A64THR0-0.016-0.0169.8340.0050.0050.0000.0000.0000.000
43A65ASP-1-0.819-0.89912.6040.5680.5680.0000.0000.0000.000
44A66ARG10.8050.84913.588-0.992-0.9920.0000.0000.0000.000
45A67ASP-1-0.851-0.86716.4500.7710.7710.0000.0000.0000.000
46A68LYS10.8090.89319.282-0.505-0.5050.0000.0000.0000.000
47A69PRO0-0.047-0.04120.2820.0230.0230.0000.0000.0000.000
48A70LEU00.0060.01616.7640.0170.0170.0000.0000.0000.000
49A71PRO0-0.018-0.01218.206-0.043-0.0430.0000.0000.0000.000
50A72GLY00.0180.02220.218-0.036-0.0360.0000.0000.0000.000
51A73ASN0-0.028-0.02421.657-0.014-0.0140.0000.0000.0000.000
52A74LYS10.9710.98723.673-0.059-0.0590.0000.0000.0000.000
53A75ARG10.7780.87726.084-0.018-0.0180.0000.0000.0000.000
54A76TYR0-0.045-0.03620.414-0.008-0.0080.0000.0000.0000.000
55A77ARG10.8670.91220.339-0.349-0.3490.0000.0000.0000.000
56A78MET00.0030.04013.0080.0350.0350.0000.0000.0000.000
57A79VAL0-0.024-0.01517.0300.0430.0430.0000.0000.0000.000
58A80GLY00.0610.02716.3960.0160.0160.0000.0000.0000.000
59A81SER0-0.026-0.01216.3490.0760.0760.0000.0000.0000.000
60A82ALA00.0580.02512.9720.0820.0820.0000.0000.0000.000
61A83ALA0-0.027-0.01012.1150.2580.2580.0000.0000.0000.000
62A84ASN0-0.094-0.05412.6950.1010.1010.0000.0000.0000.000
63A85GLY00.0670.0369.304-0.013-0.0130.0000.0000.0000.000
64A86GLU-1-0.860-0.9249.7170.7520.7520.0000.0000.0000.000
65A87TYR00.001-0.0168.8570.1610.1610.0000.0000.0000.000
66A88ASN00.0400.03112.523-0.166-0.1660.0000.0000.0000.000
67A89LEU00.0000.01415.5980.0410.0410.0000.0000.0000.000
68A90GLU-1-0.817-0.87717.7840.2110.2110.0000.0000.0000.000
69A91ILE00.008-0.00521.319-0.008-0.0080.0000.0000.0000.000
70A92SER00.044-0.00224.110-0.020-0.0200.0000.0000.0000.000
71A93ASN0-0.061-0.03427.552-0.007-0.0070.0000.0000.0000.000
72A94VAL00.0080.01727.219-0.013-0.0130.0000.0000.0000.000
73A95THR0-0.022-0.02829.445-0.008-0.0080.0000.0000.0000.000
74A96LEU00.0580.00630.132-0.006-0.0060.0000.0000.0000.000
75A97PHE0-0.0050.00828.816-0.013-0.0130.0000.0000.0000.000
76A98ASP-1-0.737-0.81725.832-0.012-0.0120.0000.0000.0000.000
77A99ASP-1-0.825-0.89925.685-0.117-0.1170.0000.0000.0000.000
78A100ASP-1-0.773-0.86922.364-0.255-0.2550.0000.0000.0000.000
79A101ASP-1-0.880-0.95021.101-0.253-0.2530.0000.0000.0000.000
80A102PHE00.019-0.00117.851-0.039-0.0390.0000.0000.0000.000
81A103ALA00.0150.00913.530-0.042-0.0420.0000.0000.0000.000
82A105GLN00.0600.0277.070-0.054-0.0540.0000.0000.0000.000
83A106ILE0-0.0020.0072.537-1.2490.1893.348-1.290-3.4960.013
84A107SER0-0.030-0.0354.114-3.585-3.3150.003-0.088-0.1840.000
85A108GLU-1-0.851-0.9312.229-14.720-13.5941.566-1.129-1.563-0.019
86A109SER0-0.030-0.0383.8941.5752.0340.003-0.075-0.3880.000
87A110ASP-1-0.905-0.9435.006-1.495-1.480-0.0010.000-0.0140.000
88A111HIS0-0.075-0.0417.9310.0700.0700.0000.0000.0000.000
89A112ALA0-0.030-0.0132.994-0.4830.0800.107-0.205-0.4650.001
90A113LYS10.9730.9933.3691.8923.1580.156-0.629-0.793-0.003
91A114ALA00.0090.0001.946-15.080-16.0036.454-2.688-2.843-0.036
92A115VAL0-0.091-0.0412.5640.4121.4260.752-0.441-1.3260.000
93A116VAL0-0.003-0.0074.9851.4311.516-0.001-0.003-0.0810.000
94A117SER0-0.025-0.0178.6490.0100.0100.0000.0000.0000.000
95A118SER00.0120.00811.062-0.091-0.0910.0000.0000.0000.000
96A119LYS10.7780.88114.6030.5860.5860.0000.0000.0000.000
97A120ALA0-0.0210.00017.1150.0240.0240.0000.0000.0000.000
98A121LYS10.8240.93419.5180.2020.2020.0000.0000.0000.000
99A122LEU0-0.024-0.00522.9090.0410.0410.0000.0000.0000.000
100A123THR0-0.016-0.01724.445-0.020-0.0200.0000.0000.0000.000
101A124VAL0-0.048-0.02428.2370.0190.0190.0000.0000.0000.000
102A125LEU0-0.011-0.00830.486-0.011-0.0110.0000.0000.0000.000
103A126VAL0-0.009-0.02433.6980.0070.0070.0000.0000.0000.000
104A127ARG10.8660.92637.015-0.030-0.0300.0000.0000.0000.000
105A128PRO00.0050.00739.725-0.001-0.0010.0000.0000.0000.000
106A129THR0-0.041-0.01842.9910.0040.0040.0000.0000.0000.000
107A130PRO00.0500.03446.340-0.003-0.0030.0000.0000.0000.000
108A131PRO0-0.0170.01048.444-0.003-0.0030.0000.0000.0000.000
109A132LYS10.7990.88650.916-0.002-0.0020.0000.0000.0000.000
110A133ILE00.0270.00254.410-0.003-0.0030.0000.0000.0000.000
111A134VAL0-0.044-0.02557.5060.0010.0010.0000.0000.0000.000
112A135LYS10.8200.92558.469-0.003-0.0030.0000.0000.0000.000
113A136SER0-0.002-0.01362.0830.0000.0000.0000.0000.0000.000
114A137HIS00.002-0.01760.8570.0000.0000.0000.0000.0000.000
115A138HIS0-0.0040.02264.7100.0010.0010.0000.0000.0000.000
116A139SER00.0010.00266.2600.0000.0000.0000.0000.0000.000
117A140LEU00.0240.00864.626-0.001-0.0010.0000.0000.0000.000
118A141LYS10.8850.94167.844-0.002-0.0020.0000.0000.0000.000
119A142ALA00.0280.02669.361-0.001-0.0010.0000.0000.0000.000
120A143ILE0-0.025-0.02671.4830.0010.0010.0000.0000.0000.000
121A144ALA0-0.013-0.00272.969-0.001-0.0010.0000.0000.0000.000
122A145GLY00.0120.00672.5790.0000.0000.0000.0000.0000.000
123A146ASP-1-0.893-0.94373.130-0.012-0.0120.0000.0000.0000.000
124A147PRO0-0.055-0.02968.9180.0000.0000.0000.0000.0000.000
125A148ILE0-0.031-0.01966.2320.0000.0000.0000.0000.0000.000
126A149THR0-0.002-0.01162.4000.0000.0000.0000.0000.0000.000
127A150GLN0-0.065-0.04460.9250.0030.0030.0000.0000.0000.000
128A151SER00.0260.00057.772-0.001-0.0010.0000.0000.0000.000
129A152CYS0-0.071-0.01153.5880.0000.0000.0000.0000.0000.000
130A153LEU0-0.0140.00351.794-0.003-0.0030.0000.0000.0000.000
131A154SER0-0.006-0.01746.8850.0030.0030.0000.0000.0000.000
132A155ARG10.8560.89746.6130.0240.0240.0000.0000.0000.000
133A156LYS10.9090.92442.3600.0300.0300.0000.0000.0000.000
134A157GLY00.0490.04640.7680.0040.0040.0000.0000.0000.000
135A158LYS10.8030.90831.9370.0720.0720.0000.0000.0000.000
136A159PRO00.0650.01835.5820.0050.0050.0000.0000.0000.000
137A160PRO00.0520.01338.2030.0070.0070.0000.0000.0000.000
138A161PRO0-0.0110.01241.6480.0010.0010.0000.0000.0000.000
139A162THR0-0.032-0.00543.269-0.005-0.0050.0000.0000.0000.000
140A163ILE00.013-0.00145.4390.0050.0050.0000.0000.0000.000
141A164GLY00.0130.00849.094-0.004-0.0040.0000.0000.0000.000
142A165TRP00.013-0.01052.0160.0040.0040.0000.0000.0000.000
143A166ALA00.0190.00455.5740.0000.0000.0000.0000.0000.000
144A167ILE00.0190.02157.7000.0000.0000.0000.0000.0000.000
145A168ALA00.0130.01758.7100.0010.0010.0000.0000.0000.000
146A169SER00.0330.01060.871-0.001-0.0010.0000.0000.0000.000
147A170ASP-1-0.824-0.91658.0520.0190.0190.0000.0000.0000.000
148A171GLU-1-0.852-0.92659.1140.0170.0170.0000.0000.0000.000
149A172HIS0-0.026-0.00255.012-0.001-0.0010.0000.0000.0000.000
150A173GLY00.0000.01154.5230.0010.0010.0000.0000.0000.000
151A174LYS10.8220.88651.841-0.024-0.0240.0000.0000.0000.000
152A175HIS0-0.017-0.00155.8550.0000.0000.0000.0000.0000.000
153A176ILE00.004-0.00254.264-0.001-0.0010.0000.0000.0000.000
154A177VAL00.002-0.00458.5780.0010.0010.0000.0000.0000.000
155A178SER00.0490.00060.5200.0000.0000.0000.0000.0000.000
156A179TRP00.001-0.00751.5010.0000.0000.0000.0000.0000.000
157A180LEU00.0030.00457.173-0.001-0.0010.0000.0000.0000.000
158A181GLY00.0530.03656.745-0.002-0.0020.0000.0000.0000.000
159A182GLU-1-0.885-0.94952.735-0.021-0.0210.0000.0000.0000.000
160A183SER0-0.051-0.02452.191-0.001-0.0010.0000.0000.0000.000
161A184ARG10.9140.93551.4340.0020.0020.0000.0000.0000.000
162A185SER0-0.046-0.02749.7100.0010.0010.0000.0000.0000.000
163A186LYS10.8040.89247.0750.0270.0270.0000.0000.0000.000
164A187PHE0-0.043-0.00246.3540.0050.0050.0000.0000.0000.000
165A195GLU-1-0.825-0.88857.567-0.003-0.0030.0000.0000.0000.000
166A196ILE0-0.064-0.04058.8960.0010.0010.0000.0000.0000.000
167A197SER0-0.050-0.02062.4380.0000.0000.0000.0000.0000.000
168A198GLN0-0.034-0.02363.777-0.001-0.0010.0000.0000.0000.000
169A199GLU-1-0.858-0.90366.312-0.008-0.0080.0000.0000.0000.000
170A200THR0-0.0070.00062.3760.0010.0010.0000.0000.0000.000
171A201VAL00.0310.01663.193-0.001-0.0010.0000.0000.0000.000
172A202ILE00.0300.01863.716-0.002-0.0020.0000.0000.0000.000
173A203ALA00.002-0.01461.1820.0010.0010.0000.0000.0000.000
174A204HIS0-0.0080.00457.7980.0000.0000.0000.0000.0000.000
175A205VAL00.0200.00254.4510.0020.0020.0000.0000.0000.000
176A206ASN00.0050.01555.886-0.004-0.0040.0000.0000.0000.000
177A207GLU-1-0.813-0.87749.699-0.028-0.0280.0000.0000.0000.000
178A208THR00.0050.00751.096-0.003-0.0030.0000.0000.0000.000
179A209THR00.003-0.00944.6310.0040.0040.0000.0000.0000.000
180A210GLN0-0.027-0.01547.073-0.004-0.0040.0000.0000.0000.000
181A211VAL00.0180.01541.6800.0040.0040.0000.0000.0000.000
182A212GLU-1-0.747-0.84141.459-0.029-0.0290.0000.0000.0000.000
183A222SER00.0320.00231.922-0.001-0.0010.0000.0000.0000.000
184A223SER0-0.0010.00133.9810.0050.0050.0000.0000.0000.000
185A224ILE0-0.0120.00437.5560.0030.0030.0000.0000.0000.000
186A225TYR0-0.006-0.01338.577-0.005-0.0050.0000.0000.0000.000
187A226SER0-0.059-0.01643.0340.0070.0070.0000.0000.0000.000
188A227ILE0-0.007-0.00746.484-0.005-0.0050.0000.0000.0000.000
189A228MET00.0170.01648.7200.0060.0060.0000.0000.0000.000
190A229SER0-0.013-0.02452.010-0.002-0.0020.0000.0000.0000.000
191A230ASN0-0.005-0.01553.8190.0050.0050.0000.0000.0000.000
192A231LEU00.0360.04857.577-0.002-0.0020.0000.0000.0000.000
193A232SER0-0.016-0.01759.4110.0000.0000.0000.0000.0000.000
194A233PHE00.003-0.00962.9410.0000.0000.0000.0000.0000.000
195A234ILE00.0420.04064.8820.0000.0000.0000.0000.0000.000
196A235PRO0-0.061-0.00967.7750.0010.0010.0000.0000.0000.000
197A236ARG10.8130.85265.1900.0020.0020.0000.0000.0000.000
198A237PRO00.0320.00270.9950.0010.0010.0000.0000.0000.000
199A238GLU-1-0.869-0.92869.7800.0000.0000.0000.0000.0000.000
200A239ASP-1-0.811-0.87866.5750.0000.0000.0000.0000.0000.000
201A240ASP-1-0.791-0.90668.2680.0040.0040.0000.0000.0000.000
202A241HIS0-0.096-0.04269.4870.0020.0020.0000.0000.0000.000
203A242LYS10.8450.94164.795-0.004-0.0040.0000.0000.0000.000
204A243TYR00.0020.00761.415-0.001-0.0010.0000.0000.0000.000
205A244LEU00.0230.03060.3010.0000.0000.0000.0000.0000.000
206A245ILE0-0.041-0.03355.1110.0010.0010.0000.0000.0000.000
207A247ILE00.004-0.00849.5140.0040.0040.0000.0000.0000.000
208A248SER00.0220.00846.552-0.005-0.0050.0000.0000.0000.000
209A249GLN00.0450.01043.4170.0100.0100.0000.0000.0000.000
210A250HIS00.0170.01437.4590.0010.0010.0000.0000.0000.000
211A251MET00.0190.01234.9870.0050.0050.0000.0000.0000.000
212A252THR00.007-0.01935.5930.0080.0080.0000.0000.0000.000
213A253PHE0-0.076-0.03637.2320.0080.0080.0000.0000.0000.000
214A254PRO00.0490.02035.694-0.003-0.0030.0000.0000.0000.000
215A255ASN0-0.039-0.02138.8900.0020.0020.0000.0000.0000.000
216A256LYS10.9270.97840.105-0.053-0.0530.0000.0000.0000.000
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