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: 172NZ

Calculation Name: 3OFV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OFV

Chain ID: A

ChEMBL ID:

UniProt ID: D6J9H8

Base Structure: X-ray

Registration Date: 2023-06-21

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1985936.42838
FMO2-HF: Nuclear repulsion 1914464.615552
FMO2-HF: Total energy -71471.812828
FMO2-MP2: Total energy -71683.338668


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:THR)


Summations of interaction energy for fragment #1(A:1:THR)
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.
-35.854-33.04215.665-9.074-9.403-0.027
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.008
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].
3A3LYS10.8180.8981.992-15.491-13.1985.445-3.515-4.2230.039
4A4LEU0-0.030-0.0095.5340.1750.1750.0000.0000.0000.000
5A5ILE00.0030.0118.871-0.436-0.4360.0000.0000.0000.000
6A6VAL0-0.015-0.01811.3870.1510.1510.0000.0000.0000.000
7A7GLY00.0410.01414.751-0.042-0.0420.0000.0000.0000.000
8A8LEU0-0.068-0.04517.9160.0330.0330.0000.0000.0000.000
9A9ALA00.0240.00320.5040.0300.0300.0000.0000.0000.000
10A10ASN0-0.0330.00624.145-0.030-0.0300.0000.0000.0000.000
11A11PRO00.0330.02626.6580.0110.0110.0000.0000.0000.000
12A12GLY00.0530.02128.1320.0030.0030.0000.0000.0000.000
13A13ALA00.000-0.02131.309-0.005-0.0050.0000.0000.0000.000
14A14GLU-1-0.905-0.92033.557-0.115-0.1150.0000.0000.0000.000
15A15TYR0-0.011-0.04129.815-0.009-0.0090.0000.0000.0000.000
16A16ALA0-0.0220.01328.580-0.008-0.0080.0000.0000.0000.000
17A17ALA00.0210.01428.406-0.001-0.0010.0000.0000.0000.000
18A18THR0-0.065-0.04129.723-0.002-0.0020.0000.0000.0000.000
19A19ARG10.8810.89927.7000.1240.1240.0000.0000.0000.000
20A20HIS0-0.098-0.07725.771-0.020-0.0200.0000.0000.0000.000
21A21ASN00.0180.00724.471-0.039-0.0390.0000.0000.0000.000
22A22ALA00.0210.01522.7140.0030.0030.0000.0000.0000.000
23A23GLY00.002-0.00118.971-0.002-0.0020.0000.0000.0000.000
24A24ALA0-0.014-0.01118.771-0.007-0.0070.0000.0000.0000.000
25A25TRP0-0.013-0.00220.3650.0210.0210.0000.0000.0000.000
26A26PHE00.0260.00612.6950.0210.0210.0000.0000.0000.000
27A27VAL0-0.0020.00315.0070.0320.0320.0000.0000.0000.000
28A28ASP-1-0.887-0.95717.069-0.028-0.0280.0000.0000.0000.000
29A29LEU0-0.0190.00719.3920.0400.0400.0000.0000.0000.000
30A30LEU00.000-0.00612.8860.0500.0500.0000.0000.0000.000
31A31ALA0-0.017-0.01216.6600.0710.0710.0000.0000.0000.000
32A32GLU-1-0.984-0.98718.1580.1040.1040.0000.0000.0000.000
33A33ARG10.8080.89118.078-0.076-0.0760.0000.0000.0000.000
34A34LEU0-0.058-0.03313.2100.0490.0490.0000.0000.0000.000
35A35ARG10.8860.94717.407-0.216-0.2160.0000.0000.0000.000
36A36ALA00.0160.02517.7280.0000.0000.0000.0000.0000.000
37A37PRO00.0200.02919.217-0.026-0.0260.0000.0000.0000.000
38A38LEU00.0370.01717.8600.0090.0090.0000.0000.0000.000
39A39ARG10.8680.92921.181-0.034-0.0340.0000.0000.0000.000
40A40GLU-1-0.924-0.95521.980-0.103-0.1030.0000.0000.0000.000
41A41GLU-1-0.772-0.85718.296-0.062-0.0620.0000.0000.0000.000
42A42ALA00.0450.01221.803-0.034-0.0340.0000.0000.0000.000
43A43LYS10.8100.90818.8390.0800.0800.0000.0000.0000.000
44A44PHE0-0.003-0.00716.442-0.039-0.0390.0000.0000.0000.000
45A45PHE00.022-0.01820.018-0.031-0.0310.0000.0000.0000.000
46A46GLY00.0850.03620.854-0.027-0.0270.0000.0000.0000.000
47A47TYR0-0.0280.01021.5430.0240.0240.0000.0000.0000.000
48A48THR0-0.018-0.04616.794-0.032-0.0320.0000.0000.0000.000
49A49SER00.001-0.02916.2460.0490.0490.0000.0000.0000.000
50A50ARG10.8280.89412.850-0.743-0.7430.0000.0000.0000.000
51A51VAL00.0360.03211.391-0.016-0.0160.0000.0000.0000.000
52A52THR0-0.054-0.04811.3520.0390.0390.0000.0000.0000.000
53A53LEU00.0200.0168.139-0.227-0.2270.0000.0000.0000.000
54A54GLY00.0200.0218.1890.5230.5230.0000.0000.0000.000
55A55GLY0-0.046-0.0199.6250.1400.1400.0000.0000.0000.000
56A56GLU-1-0.797-0.8654.6944.5214.659-0.001-0.007-0.1300.000
57A57ASP-1-0.800-0.8828.1240.2840.2840.0000.0000.0000.000
58A58VAL0-0.030-0.0036.5300.1970.1970.0000.0000.0000.000
59A59ARG10.8290.9008.810-0.618-0.6180.0000.0000.0000.000
60A60LEU0-0.0010.00611.165-0.129-0.1290.0000.0000.0000.000
61A61LEU0-0.009-0.01614.0240.0150.0150.0000.0000.0000.000
62A62VAL00.0500.03316.341-0.048-0.0480.0000.0000.0000.000
63A63PRO0-0.052-0.00919.1240.0280.0280.0000.0000.0000.000
64A64THR00.031-0.00621.3590.0110.0110.0000.0000.0000.000
65A65THR0-0.066-0.04122.7120.0080.0080.0000.0000.0000.000
66A66PHE00.0440.01925.4450.0020.0020.0000.0000.0000.000
67A67MET00.0630.06523.496-0.046-0.0460.0000.0000.0000.000
68A68ASN0-0.038-0.02524.251-0.038-0.0380.0000.0000.0000.000
69A69LEU0-0.031-0.01024.632-0.009-0.0090.0000.0000.0000.000
70A70SER00.0190.00220.023-0.003-0.0030.0000.0000.0000.000
71A71GLY00.0130.00118.636-0.041-0.0410.0000.0000.0000.000
72A72LYS10.8150.93218.7120.2270.2270.0000.0000.0000.000
73A73ALA00.0350.02219.057-0.003-0.0030.0000.0000.0000.000
74A74VAL00.0070.00213.438-0.010-0.0100.0000.0000.0000.000
75A75ALA00.0370.02214.318-0.079-0.0790.0000.0000.0000.000
76A76ALA0-0.0130.01315.620-0.021-0.0210.0000.0000.0000.000
77A77MET0-0.0070.00013.112-0.003-0.0030.0000.0000.0000.000
78A78ALA00.0130.00610.9450.0280.0280.0000.0000.0000.000
79A79SER0-0.001-0.01111.476-0.063-0.0630.0000.0000.0000.000
80A80PHE0-0.051-0.02214.0130.0350.0350.0000.0000.0000.000
81A81PHE0-0.026-0.03210.1880.1110.1110.0000.0000.0000.000
82A82ARG10.8530.9319.8070.5480.5480.0000.0000.0000.000
83A83ILE0-0.0060.0175.755-0.133-0.1330.0000.0000.0000.000
84A84ASN00.002-0.0015.5281.2451.2450.0000.0000.0000.000
85A85PRO00.028-0.0097.171-0.376-0.3760.0000.0000.0000.000
86A86ASP-1-0.899-0.9435.623-3.866-3.8660.0000.0000.0000.000
87A87GLU-1-0.798-0.8831.822-26.373-26.23310.224-5.529-4.835-0.066
88A88ILE0-0.017-0.0124.8391.5611.633-0.001-0.013-0.0580.000
89A89LEU00.0060.0028.189-0.174-0.1740.0000.0000.0000.000
90A90VAL0-0.022-0.0179.9470.2960.2960.0000.0000.0000.000
91A91ALA00.0100.01913.7320.0110.0110.0000.0000.0000.000
92A92HIS0-0.064-0.05515.731-0.015-0.0150.0000.0000.0000.000
93A93ASP-1-0.705-0.81619.140-0.287-0.2870.0000.0000.0000.000
94A94GLU-1-0.831-0.91020.828-0.422-0.4220.0000.0000.0000.000
95A95LEU00.0470.01422.9260.0300.0300.0000.0000.0000.000
96A96ASP-1-0.896-0.92423.272-0.275-0.2750.0000.0000.0000.000
97A97LEU0-0.0150.00019.9280.0050.0050.0000.0000.0000.000
98A98PRO00.0100.00824.5150.0000.0000.0000.0000.0000.000
99A99PRO00.0330.00425.404-0.007-0.0070.0000.0000.0000.000
100A100GLY00.0180.02825.3580.0120.0120.0000.0000.0000.000
101A101VAL0-0.067-0.02921.5730.0060.0060.0000.0000.0000.000
102A102ALA00.0550.02817.903-0.017-0.0170.0000.0000.0000.000
103A103LYS10.8750.93516.1480.2690.2690.0000.0000.0000.000
104A104PHE00.0790.04510.687-0.052-0.0520.0000.0000.0000.000
105A105LYS10.8430.92411.9450.8170.8170.0000.0000.0000.000
106A106LEU00.0640.0427.782-0.115-0.1150.0000.0000.0000.000
107A107GLY00.0210.03111.3330.1870.1870.0000.0000.0000.000
108A108GLY00.008-0.00113.9300.1020.1020.0000.0000.0000.000
109A109GLY00.009-0.00317.702-0.029-0.0290.0000.0000.0000.000
110A110HIS00.0600.02919.353-0.042-0.0420.0000.0000.0000.000
111A111GLY00.0440.02721.3660.0160.0160.0000.0000.0000.000
112A112GLY0-0.029-0.01423.8590.0310.0310.0000.0000.0000.000
113A113HIS0-0.001-0.02122.221-0.005-0.0050.0000.0000.0000.000
114A114ASN00.050-0.00723.359-0.046-0.0460.0000.0000.0000.000
115A115GLY00.0610.05022.555-0.007-0.0070.0000.0000.0000.000
116A116LEU0-0.008-0.00317.100-0.054-0.0540.0000.0000.0000.000
117A117LYS10.8960.93919.4840.2800.2800.0000.0000.0000.000
118A118ASP-1-0.774-0.87521.732-0.445-0.4450.0000.0000.0000.000
119A119ILE00.0210.01315.400-0.007-0.0070.0000.0000.0000.000
120A120ILE0-0.027-0.00717.232-0.056-0.0560.0000.0000.0000.000
121A121SER0-0.037-0.00718.291-0.017-0.0170.0000.0000.0000.000
122A122LYS10.8260.89219.2200.4120.4120.0000.0000.0000.000
123A123LEU0-0.0210.00612.669-0.002-0.0020.0000.0000.0000.000
124A124GLY0-0.0090.00315.669-0.074-0.0740.0000.0000.0000.000
125A125ASN0-0.071-0.04618.4230.0040.0040.0000.0000.0000.000
126A126ASN00.0650.04312.725-0.014-0.0140.0000.0000.0000.000
127A127PRO00.013-0.00415.038-0.076-0.0760.0000.0000.0000.000
128A128ASN0-0.066-0.02111.4650.0420.0420.0000.0000.0000.000
129A129PHE00.0650.0389.601-0.261-0.2610.0000.0000.0000.000
130A130HIS00.017-0.0154.7721.3541.415-0.001-0.005-0.0550.000
131A131ARG10.7470.8629.7061.1801.1800.0000.0000.0000.000
132A132LEU00.0050.00412.276-0.027-0.0270.0000.0000.0000.000
133A133ARG10.7410.85114.2650.4540.4540.0000.0000.0000.000
134A134ILE00.0460.01417.7670.0360.0360.0000.0000.0000.000
135A135GLY0-0.015-0.01620.1650.0010.0010.0000.0000.0000.000
136A136ILE0-0.015-0.01023.3890.0240.0240.0000.0000.0000.000
137A137GLY00.0050.01126.6710.0180.0180.0000.0000.0000.000
138A138HIS00.034-0.00528.824-0.013-0.0130.0000.0000.0000.000
139A139PRO0-0.0300.00531.6860.0100.0100.0000.0000.0000.000
140A140GLY00.0240.01934.9280.0100.0100.0000.0000.0000.000
141A141ASP-1-0.808-0.87936.163-0.125-0.1250.0000.0000.0000.000
142A142LYS10.9060.91430.8100.2030.2030.0000.0000.0000.000
143A143ASN0-0.027-0.01735.767-0.010-0.0100.0000.0000.0000.000
144A144LYS10.8780.92437.3730.1070.1070.0000.0000.0000.000
145A145VAL00.0040.00730.9350.0000.0000.0000.0000.0000.000
146A146VAL00.0350.02132.498-0.006-0.0060.0000.0000.0000.000
147A147GLY00.0360.01533.542-0.001-0.0010.0000.0000.0000.000
148A148PHE0-0.022-0.00829.7560.0060.0060.0000.0000.0000.000
149A149VAL00.0330.00928.2690.0040.0040.0000.0000.0000.000
150A150LEU0-0.026-0.01130.051-0.002-0.0020.0000.0000.0000.000
151A151GLY00.0600.04232.2900.0120.0120.0000.0000.0000.000
152A152LYS10.9300.96832.1110.0590.0590.0000.0000.0000.000
153A153PRO00.0000.01629.4920.0020.0020.0000.0000.0000.000
154A154PRO0-0.013-0.00232.6580.0100.0100.0000.0000.0000.000
155A155VAL00.042-0.00233.495-0.004-0.0040.0000.0000.0000.000
156A156SER00.0000.00333.1950.0010.0010.0000.0000.0000.000
157A157GLU-1-0.794-0.88130.574-0.117-0.1170.0000.0000.0000.000
158A158GLN0-0.075-0.05527.803-0.007-0.0070.0000.0000.0000.000
159A159LYS10.8410.90228.2310.0240.0240.0000.0000.0000.000
160A160LEU0-0.003-0.00127.7370.0050.0050.0000.0000.0000.000
161A161ILE0-0.028-0.01923.940-0.008-0.0080.0000.0000.0000.000
162A162ASP-1-0.815-0.90123.470-0.081-0.0810.0000.0000.0000.000
163A163GLU-1-0.803-0.88023.394-0.015-0.0150.0000.0000.0000.000
164A164ALA0-0.030-0.00921.3750.0080.0080.0000.0000.0000.000
165A165ILE0-0.026-0.01119.208-0.022-0.0220.0000.0000.0000.000
166A166ASP-1-0.793-0.86318.6700.0690.0690.0000.0000.0000.000
167A167GLU-1-0.837-0.91317.5480.0930.0930.0000.0000.0000.000
168A168ALA0-0.0080.00315.2990.0080.0080.0000.0000.0000.000
169A169ALA0-0.0020.00914.136-0.016-0.0160.0000.0000.0000.000
170A170ARG10.9360.94614.540-0.062-0.0620.0000.0000.0000.000
171A171CYS0-0.090-0.06012.5590.0810.0810.0000.0000.0000.000
172A172THR0-0.052-0.0369.5800.0260.0260.0000.0000.0000.000
173A173GLU-1-0.895-0.96610.1220.4160.4160.0000.0000.0000.000
174A174MET00.0110.02511.9450.1700.1700.0000.0000.0000.000
175A175TRP0-0.022-0.0017.004-0.058-0.0580.0000.0000.0000.000
176A176PHE0-0.019-0.0044.6970.1480.256-0.001-0.005-0.1020.000
177A177THR0-0.023-0.0138.379-0.012-0.0120.0000.0000.0000.000
178A178ASP-1-0.744-0.84311.5100.8400.8400.0000.0000.0000.000
179A179GLY00.0150.00112.736-0.112-0.1120.0000.0000.0000.000
180A180LEU00.0170.00416.305-0.082-0.0820.0000.0000.0000.000
181A181THR0-0.003-0.01614.332-0.065-0.0650.0000.0000.0000.000
182A182LYS10.8500.90414.782-0.565-0.5650.0000.0000.0000.000
183A183ALA0-0.054-0.01217.416-0.075-0.0750.0000.0000.0000.000
184A184THR00.009-0.01319.777-0.051-0.0510.0000.0000.0000.000
185A185ASN00.019-0.01117.106-0.053-0.0530.0000.0000.0000.000
186A186ARG10.8670.91720.459-0.400-0.4000.0000.0000.0000.000
187A187LEU0-0.034-0.00223.403-0.032-0.0320.0000.0000.0000.000
188A188HIS00.0080.00222.190-0.041-0.0410.0000.0000.0000.000
189A189ALA0-0.051-0.00823.890-0.012-0.0120.0000.0000.0000.000
190A190PHE0-0.0250.00525.738-0.023-0.0230.0000.0000.0000.000