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: NNNVQ

Calculation Name: 3OBF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OBF

Chain ID: A

ChEMBL ID:

UniProt ID: A1RB88

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptHSide
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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1802666.939801
FMO2-HF: Nuclear repulsion 1734874.477974
FMO2-HF: Total energy -67792.461827
FMO2-MP2: Total energy -67989.211457


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:126:SER)


Summations of interaction energy for fragment #1(A:126:SER)
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.
-8.778-5.5640.098-1.43-1.8790.004
Interaction energy analysis for fragmet #1(A:126:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.001
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].
3A128ALA00.0090.0053.828-0.3301.370-0.006-0.792-0.9020.002
4A129GLU-1-0.901-0.9535.3970.0290.193-0.001-0.010-0.1520.000
5A130GLU-1-0.783-0.8996.688-0.910-0.9100.0000.0000.0000.000
6A131ARG10.8850.9362.699-4.701-3.4360.106-0.622-0.7480.002
7A132ARG10.9330.9798.602-1.348-1.3480.0000.0000.0000.000
8A133VAL0-0.032-0.01210.738-0.111-0.1110.0000.0000.0000.000
9A134ALA00.0470.02111.902-0.065-0.0650.0000.0000.0000.000
10A135TYR00.0540.04712.346-0.058-0.0580.0000.0000.0000.000
11A136PRO0-0.083-0.05614.056-0.058-0.0580.0000.0000.0000.000
12A137VAL0-0.0110.00316.919-0.025-0.0250.0000.0000.0000.000
13A138LEU00.0000.00213.155-0.035-0.0350.0000.0000.0000.000
14A139ARG10.9540.97717.703-0.236-0.2360.0000.0000.0000.000
15A140GLU-1-0.837-0.91019.6240.0540.0540.0000.0000.0000.000
16A141LEU00.0390.01019.584-0.011-0.0110.0000.0000.0000.000
17A142THR0-0.0050.00320.673-0.015-0.0150.0000.0000.0000.000
18A143GLU-1-0.944-0.95522.6610.0710.0710.0000.0000.0000.000
19A144ARG10.8060.90125.422-0.042-0.0420.0000.0000.0000.000
20A145THR00.0040.00124.061-0.009-0.0090.0000.0000.0000.000
21A146GLY0-0.058-0.01526.105-0.005-0.0050.0000.0000.0000.000
22A147GLU-1-0.768-0.85623.560-0.103-0.1030.0000.0000.0000.000
23A148THR00.0240.01617.8260.0300.0300.0000.0000.0000.000
24A149SER00.0000.00917.986-0.020-0.0200.0000.0000.0000.000
25A150ALA0-0.005-0.02213.3690.0290.0290.0000.0000.0000.000
26A151LEU00.0010.0088.6590.0210.0210.0000.0000.0000.000
27A152MET0-0.051-0.01310.046-0.082-0.0820.0000.0000.0000.000
28A153VAL00.0310.0014.9150.0500.0500.0000.0000.0000.000
29A154TRP00.0260.0118.1660.0160.0160.0000.0000.0000.000
30A155ASN0-0.053-0.0538.326-0.090-0.0900.0000.0000.0000.000
31A156GLY00.0250.0209.5200.1240.1240.0000.0000.0000.000
32A157ASN0-0.031-0.02413.0990.1060.1060.0000.0000.0000.000
33A158GLU-1-0.792-0.86611.696-1.094-1.0940.0000.0000.0000.000
34A159SER0-0.017-0.00611.533-0.232-0.2320.0000.0000.0000.000
35A160MET0-0.009-0.0136.402-0.155-0.1550.0000.0000.0000.000
36A161CYS0-0.047-0.0168.733-0.071-0.0710.0000.0000.0000.000
37A162VAL0-0.038-0.0184.608-0.158-0.073-0.001-0.006-0.0770.000
38A163GLU-1-0.880-0.9717.1990.9740.9740.0000.0000.0000.000
39A164GLN0-0.038-0.02610.213-0.057-0.0570.0000.0000.0000.000
40A165ILE0-0.0420.00013.8550.0860.0860.0000.0000.0000.000
41A166PRO00.0430.02617.423-0.035-0.0350.0000.0000.0000.000
42A167SER00.0340.00219.8900.0240.0240.0000.0000.0000.000
43A168ARG10.9300.96923.3050.0260.0260.0000.0000.0000.000
44A169HIS0-0.054-0.04326.1760.0110.0110.0000.0000.0000.000
45A170GLN00.0360.03420.986-0.027-0.0270.0000.0000.0000.000
46A171VAL00.0270.01825.4870.0090.0090.0000.0000.0000.000
47A172LYS10.8390.89323.9750.1510.1510.0000.0000.0000.000
48A173HIS0-0.023-0.01019.577-0.002-0.0020.0000.0000.0000.000
49A174LEU00.0290.02419.594-0.028-0.0280.0000.0000.0000.000
50A175ALA00.0480.02114.8910.0190.0190.0000.0000.0000.000
51A176PRO00.0230.03914.6460.0180.0180.0000.0000.0000.000
52A177LEU00.031-0.0159.687-0.083-0.0830.0000.0000.0000.000
53A178GLY0-0.043-0.0258.6170.0380.0380.0000.0000.0000.000
54A179ALA0-0.0210.0069.624-0.073-0.0730.0000.0000.0000.000
55A180ARG10.8610.9068.5241.3321.3320.0000.0000.0000.000
56A181TYR0-0.001-0.00512.8740.1230.1230.0000.0000.0000.000
57A182ASN00.040-0.00515.375-0.066-0.0660.0000.0000.0000.000
58A183GLU-1-0.877-0.91717.775-0.320-0.3200.0000.0000.0000.000
59A184ALA00.0470.00220.494-0.022-0.0220.0000.0000.0000.000
60A185LEU00.0230.01622.257-0.005-0.0050.0000.0000.0000.000
61A186SER00.0130.02518.5010.0190.0190.0000.0000.0000.000
62A187SER0-0.024-0.03020.088-0.026-0.0260.0000.0000.0000.000
63A188SER00.0310.01714.542-0.044-0.0440.0000.0000.0000.000
64A189VAL00.0040.01616.032-0.057-0.0570.0000.0000.0000.000
65A190GLN0-0.028-0.02317.3860.0150.0150.0000.0000.0000.000
66A191VAL00.004-0.00316.1910.0110.0110.0000.0000.0000.000
67A192PHE00.0070.00211.015-0.026-0.0260.0000.0000.0000.000
68A193LEU00.0100.02315.8590.0060.0060.0000.0000.0000.000
69A194ALA00.0030.00618.8070.0330.0330.0000.0000.0000.000
70A195SER0-0.114-0.06915.9360.0090.0090.0000.0000.0000.000
71A196GLU-1-0.874-0.92816.073-0.638-0.6380.0000.0000.0000.000
72A197ASN0-0.013-0.02119.3320.0310.0310.0000.0000.0000.000
73A198GLU-1-0.771-0.88422.630-0.229-0.2290.0000.0000.0000.000
74A199ASP-1-0.835-0.90525.389-0.243-0.2430.0000.0000.0000.000
75A200ARG10.8960.96716.2890.5850.5850.0000.0000.0000.000
76A201VAL00.0250.01221.177-0.025-0.0250.0000.0000.0000.000
77A202ARG10.7810.85722.8250.2170.2170.0000.0000.0000.000
78A203GLN0-0.031-0.01623.425-0.019-0.0190.0000.0000.0000.000
79A204LEU0-0.0110.01018.020-0.004-0.0040.0000.0000.0000.000
80A205LEU0-0.0070.00222.174-0.001-0.0010.0000.0000.0000.000
81A206ARG10.7760.86824.9250.2240.2240.0000.0000.0000.000
82A207SER0-0.055-0.03423.3100.0000.0000.0000.0000.0000.000
83A208GLY0-0.0020.00924.6340.0020.0020.0000.0000.0000.000
84A209SER0-0.081-0.03719.173-0.028-0.0280.0000.0000.0000.000
85A210ILE0-0.0200.00717.200-0.047-0.0470.0000.0000.0000.000
86A211THR00.0000.00121.0060.0370.0370.0000.0000.0000.000
87A212LEU00.0450.00323.871-0.009-0.0090.0000.0000.0000.000
88A213THR0-0.021-0.01826.7850.0030.0030.0000.0000.0000.000
89A214GLY0-0.0060.00930.2880.0060.0060.0000.0000.0000.000
90A215VAL0-0.0030.00127.9900.0020.0020.0000.0000.0000.000
91A216ASP-1-0.814-0.91131.372-0.164-0.1640.0000.0000.0000.000
92A217GLU-1-0.813-0.91532.988-0.191-0.1910.0000.0000.0000.000
93A218ASP-1-0.909-0.94933.642-0.154-0.1540.0000.0000.0000.000
94A219ALA00.0310.03732.034-0.003-0.0030.0000.0000.0000.000
95A220VAL0-0.080-0.04828.228-0.016-0.0160.0000.0000.0000.000
96A221GLU-1-0.827-0.91429.404-0.209-0.2090.0000.0000.0000.000
97A222ALA0-0.0090.00431.285-0.001-0.0010.0000.0000.0000.000
98A223TYR0-0.048-0.04622.191-0.011-0.0110.0000.0000.0000.000
99A224LEU00.020-0.00325.454-0.016-0.0160.0000.0000.0000.000
100A225LEU0-0.043-0.01027.439-0.003-0.0030.0000.0000.0000.000
101A226ARG10.8220.86726.2740.2310.2310.0000.0000.0000.000
102A227LEU0-0.027-0.00622.174-0.006-0.0060.0000.0000.0000.000
103A228LYS10.8720.93624.8180.2010.2010.0000.0000.0000.000
104A229GLU-1-0.905-0.95626.948-0.155-0.1550.0000.0000.0000.000
105A230SER0-0.112-0.06623.4390.0000.0000.0000.0000.0000.000
106A231MET0-0.053-0.02820.194-0.004-0.0040.0000.0000.0000.000
107A232GLU-1-0.943-0.96224.413-0.130-0.1300.0000.0000.0000.000
108A233ARG10.8130.92126.0540.1960.1960.0000.0000.0000.000
109A234GLY00.0280.02424.1170.0140.0140.0000.0000.0000.000
110A235TRP0-0.032-0.00922.288-0.013-0.0130.0000.0000.0000.000
111A236ALA00.0370.03521.3930.0140.0140.0000.0000.0000.000
112A237VAL00.024-0.00623.3110.0040.0040.0000.0000.0000.000
113A238ASN00.0330.03422.4010.0110.0110.0000.0000.0000.000
114A239PHE00.064-0.00225.4020.0110.0110.0000.0000.0000.000
115A240GLY0-0.014-0.00627.4960.0130.0130.0000.0000.0000.000
116A241GLU-1-0.824-0.88027.132-0.202-0.2020.0000.0000.0000.000
117A242THR00.0250.03922.494-0.001-0.0010.0000.0000.0000.000
118A243SER00.0400.02125.2040.0090.0090.0000.0000.0000.000
119A244ILE00.001-0.00526.9740.0050.0050.0000.0000.0000.000
120A245GLU-1-0.864-0.91627.419-0.137-0.1370.0000.0000.0000.000
121A246GLU-1-0.949-0.97222.730-0.258-0.2580.0000.0000.0000.000
122A247VAL0-0.028-0.01225.345-0.001-0.0010.0000.0000.0000.000
123A248GLY00.0310.00922.130-0.011-0.0110.0000.0000.0000.000
124A249VAL0-0.0450.01122.1510.0030.0030.0000.0000.0000.000
125A250ALA00.032-0.00617.433-0.016-0.0160.0000.0000.0000.000
126A251SER00.013-0.00518.0770.0210.0210.0000.0000.0000.000
127A252PRO00.0180.01215.924-0.044-0.0440.0000.0000.0000.000
128A253VAL0-0.041-0.01013.0340.0650.0650.0000.0000.0000.000
129A254TYR00.0540.00614.141-0.090-0.0900.0000.0000.0000.000
130A255ASP-1-0.703-0.84712.646-0.188-0.1880.0000.0000.0000.000
131A256HIS00.0290.00314.271-0.019-0.0190.0000.0000.0000.000
132A257ARG10.8620.92415.1330.0640.0640.0000.0000.0000.000
133A258GLY0-0.032-0.01117.437-0.003-0.0030.0000.0000.0000.000
134A259ASN0-0.065-0.03213.826-0.026-0.0260.0000.0000.0000.000
135A260MET0-0.016-0.00413.9470.0090.0090.0000.0000.0000.000
136A261VAL0-0.045-0.0259.465-0.077-0.0770.0000.0000.0000.000
137A262ALA0-0.015-0.0108.903-0.289-0.2890.0000.0000.0000.000
138A263SER0-0.006-0.00510.7450.1440.1440.0000.0000.0000.000
139A264VAL0-0.0130.00813.045-0.042-0.0420.0000.0000.0000.000
140A265LEU00.007-0.00815.580-0.001-0.0010.0000.0000.0000.000
141A266ILE00.0150.00517.3170.0300.0300.0000.0000.0000.000
142A267PRO0-0.056-0.01218.280-0.005-0.0050.0000.0000.0000.000
143A268ALA00.0380.00121.1330.0250.0250.0000.0000.0000.000
144A269PRO0-0.0050.00324.577-0.012-0.0120.0000.0000.0000.000
145A270LYS10.8700.92327.3040.1600.1600.0000.0000.0000.000
146A271PHE0-0.018-0.01429.8590.0080.0080.0000.0000.0000.000
147A272ARG10.7280.83526.6090.0910.0910.0000.0000.0000.000
148A273VAL0-0.027-0.00427.9840.0070.0070.0000.0000.0000.000
149A274SER00.017-0.00131.361-0.007-0.0070.0000.0000.0000.000
150A275GLN00.037-0.00332.395-0.011-0.0110.0000.0000.0000.000
151A276ASP-1-0.821-0.89432.768-0.085-0.0850.0000.0000.0000.000
152A277THR00.0010.00430.0310.0020.0020.0000.0000.0000.000
153A278LEU00.0010.00027.152-0.002-0.0020.0000.0000.0000.000
154A279ASN0-0.049-0.03928.233-0.011-0.0110.0000.0000.0000.000
155A280SER00.0010.01929.3570.0020.0020.0000.0000.0000.000
156A281LEU00.018-0.00425.2540.0040.0040.0000.0000.0000.000
157A282GLY00.0210.00424.628-0.007-0.0070.0000.0000.0000.000
158A283GLU-1-0.919-0.95124.687-0.074-0.0740.0000.0000.0000.000
159A284ALA00.0130.00525.2990.0060.0060.0000.0000.0000.000
160A285CYS0-0.084-0.03120.269-0.002-0.0020.0000.0000.0000.000
161A286ALA00.0470.02620.671-0.009-0.0090.0000.0000.0000.000
162A287ALA0-0.029-0.01122.0580.0070.0070.0000.0000.0000.000
163A288ALA0-0.006-0.01019.4620.0190.0190.0000.0000.0000.000
164A289ALA00.007-0.01017.3440.0190.0190.0000.0000.0000.000
165A290ALA00.0510.03317.9900.0030.0030.0000.0000.0000.000
166A291LYS10.8520.91919.937-0.027-0.0270.0000.0000.0000.000
167A292VAL0-0.011-0.00713.4180.0470.0470.0000.0000.0000.000
168A293THR0-0.0050.00316.0520.0130.0130.0000.0000.0000.000
169A294THR0-0.039-0.02917.2850.0280.0280.0000.0000.0000.000
170A295ARG10.8260.90116.825-0.175-0.1750.0000.0000.0000.000
171A296LEU0-0.0270.00411.5470.0520.0520.0000.0000.0000.000
172A297GLY0-0.0190.00515.2720.0100.0100.0000.0000.0000.000
173A298GLY0-0.030-0.01317.362-0.018-0.0180.0000.0000.0000.000
174A299ARG10.8700.93218.0430.1350.1350.0000.0000.0000.000
175A300ALA00.0180.01720.511-0.026-0.0260.0000.0000.0000.000
176A301PRO00.0060.01720.2510.0280.0280.0000.0000.0000.000