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: 4J32N

Calculation Name: 2B4I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B4I

Chain ID: A

ChEMBL ID:

UniProt ID: P12473

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2731670.402228
FMO2-HF: Nuclear repulsion 2640088.854931
FMO2-HF: Total energy -91581.547297
FMO2-MP2: Total energy -91849.271122


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:246:MET)


Summations of interaction energy for fragment #1(A:246:MET)
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.
-7.012-3.4370.492-1.911-2.156-0.005
Interaction energy analysis for fragmet #1(A:246:MET)
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 : -0.003
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].
3A248ALA0-0.032-0.0212.756-3.717-0.5370.492-1.820-1.852-0.005
4A249GLN0-0.038-0.0215.0110.8220.949-0.001-0.005-0.1210.000
5A250ALA00.0210.0188.762-0.252-0.2520.0000.0000.0000.000
6A251ASN00.000-0.02011.792-0.061-0.0610.0000.0000.0000.000
7A252GLU-1-0.701-0.8276.906-3.690-3.6900.0000.0000.0000.000
8A253ASP-1-0.819-0.88710.212-0.886-0.8860.0000.0000.0000.000
9A254ILE0-0.0160.0023.713-0.1010.1670.001-0.086-0.1830.000
10A255VAL0-0.018-0.0187.1970.2600.2600.0000.0000.0000.000
11A256VAL0-0.044-0.0196.302-0.215-0.2150.0000.0000.0000.000
12A257SER00.016-0.0148.1510.2810.2810.0000.0000.0000.000
13A258LYS10.9080.95511.6750.1080.1080.0000.0000.0000.000
14A259THR00.0340.02014.4570.0630.0630.0000.0000.0000.000
15A260SER00.006-0.00318.269-0.029-0.0290.0000.0000.0000.000
16A261LEU00.0310.01121.306-0.011-0.0110.0000.0000.0000.000
17A262TRP0-0.0060.01918.829-0.017-0.0170.0000.0000.0000.000
18A263LYS10.8710.93413.8140.4170.4170.0000.0000.0000.000
19A264GLU-1-0.786-0.84111.679-0.165-0.1650.0000.0000.0000.000
20A265MET00.0030.00810.176-0.012-0.0120.0000.0000.0000.000
21A266GLN00.0070.0085.394-0.186-0.1860.0000.0000.0000.000
22A267TYR0-0.019-0.0028.372-0.150-0.1500.0000.0000.0000.000
23A268ASN0-0.041-0.0176.5070.5080.5080.0000.0000.0000.000
24A269ARG10.8050.85610.8670.8890.8890.0000.0000.0000.000
25A270ASP-1-0.759-0.84514.415-0.563-0.5630.0000.0000.0000.000
26A271ILE0-0.052-0.03316.8380.0080.0080.0000.0000.0000.000
27A272THR00.0250.02120.2150.0250.0250.0000.0000.0000.000
28A273ILE0-0.0120.02222.6430.0120.0120.0000.0000.0000.000
29A274ARG10.8560.92125.7210.2150.2150.0000.0000.0000.000
30A275PHE00.0150.01429.485-0.001-0.0010.0000.0000.0000.000
31A276LYS10.8480.92731.9640.1280.1280.0000.0000.0000.000
32A277PHE00.0430.00535.494-0.002-0.0020.0000.0000.0000.000
33A278ALA0-0.0010.00738.0550.0010.0010.0000.0000.0000.000
34A279SER00.034-0.00641.086-0.001-0.0010.0000.0000.0000.000
35A280SER0-0.045-0.00344.3940.0000.0000.0000.0000.0000.000
36A281ILE00.007-0.00647.3760.0010.0010.0000.0000.0000.000
37A282VAL0-0.0120.00850.5450.0010.0010.0000.0000.0000.000
38A283LYS10.8840.94653.8950.0470.0470.0000.0000.0000.000
39A284SER0-0.012-0.01457.4740.0000.0000.0000.0000.0000.000
40A285GLY00.0420.01960.2590.0000.0000.0000.0000.0000.000
41A286GLY0-0.010-0.00763.4230.0000.0000.0000.0000.0000.000
42A287LEU00.004-0.00966.342-0.001-0.0010.0000.0000.0000.000
43A288GLY00.0420.03362.8690.0000.0000.0000.0000.0000.000
44A289TYR00.000-0.01562.304-0.001-0.0010.0000.0000.0000.000
45A290LYS10.7890.89960.7390.0350.0350.0000.0000.0000.000
46A291TRP00.0430.02954.2940.0000.0000.0000.0000.0000.000
47A292SER00.0010.00756.0520.0010.0010.0000.0000.0000.000
48A293GLU-1-0.820-0.88648.952-0.061-0.0610.0000.0000.0000.000
49A294ILE0-0.022-0.00748.2930.0000.0000.0000.0000.0000.000
50A295SER0-0.009-0.01345.777-0.001-0.0010.0000.0000.0000.000
51A296PHE00.028-0.00740.147-0.002-0.0020.0000.0000.0000.000
52A297LYS10.8520.93041.1840.0860.0860.0000.0000.0000.000
53A298PRO0-0.015-0.02036.415-0.003-0.0030.0000.0000.0000.000
54A299ALA0-0.022-0.00236.0870.0050.0050.0000.0000.0000.000
55A300ASN0-0.0070.00733.794-0.006-0.0060.0000.0000.0000.000
56A301TYR0-0.044-0.05131.9250.0050.0050.0000.0000.0000.000
57A302GLN00.0140.01430.763-0.008-0.0080.0000.0000.0000.000
58A303TYR0-0.069-0.04426.1180.0120.0120.0000.0000.0000.000
59A304THR00.008-0.01828.160-0.009-0.0090.0000.0000.0000.000
60A305TYR0-0.034-0.04621.677-0.004-0.0040.0000.0000.0000.000
61A306THR00.0340.02123.010-0.006-0.0060.0000.0000.0000.000
62A307ARG10.7760.87218.1020.4770.4770.0000.0000.0000.000
63A308ASP-1-0.852-0.92314.888-0.656-0.6560.0000.0000.0000.000
64A309GLY0-0.0140.00118.2560.0100.0100.0000.0000.0000.000
65A310GLU-1-0.953-0.96019.831-0.372-0.3720.0000.0000.0000.000
66A311GLU-1-0.912-0.94422.545-0.199-0.1990.0000.0000.0000.000
67A312VAL0-0.040-0.01321.443-0.018-0.0180.0000.0000.0000.000
68A313THR0-0.001-0.02224.5460.0270.0270.0000.0000.0000.000
69A314ALA0-0.029-0.02124.923-0.024-0.0240.0000.0000.0000.000
70A315HIS0-0.022-0.02526.4870.0310.0310.0000.0000.0000.000
71A316THR0-0.050-0.03826.864-0.012-0.0120.0000.0000.0000.000
72A317THR00.006-0.02229.1230.0170.0170.0000.0000.0000.000
73A318CYS0-0.0670.00230.935-0.002-0.0020.0000.0000.0000.000
74A319SER00.010-0.00432.7100.0090.0090.0000.0000.0000.000
75A320VAL00.0350.00734.095-0.005-0.0050.0000.0000.0000.000
76A321ASN0-0.021-0.02536.1220.0060.0060.0000.0000.0000.000
77A322GLY00.0790.04137.596-0.001-0.0010.0000.0000.0000.000
78A323MET0-0.0240.02639.8310.0000.0000.0000.0000.0000.000
79A324ASN0-0.0200.01142.1290.0060.0060.0000.0000.0000.000
80A325ASP-1-0.790-0.88545.398-0.058-0.0580.0000.0000.0000.000
81A326PHE0-0.050-0.02247.0460.0020.0020.0000.0000.0000.000
82A327ASN0-0.006-0.00651.4120.0010.0010.0000.0000.0000.000
83A328PHE0-0.002-0.01154.7710.0000.0000.0000.0000.0000.000
84A329ASN00.0590.02357.6290.0000.0000.0000.0000.0000.000
85A330GLY00.0270.01361.3100.0010.0010.0000.0000.0000.000
86A331GLY00.0240.02264.0900.0010.0010.0000.0000.0000.000
87A332SER00.010-0.00965.707-0.001-0.0010.0000.0000.0000.000
88A333LEU00.0260.02967.8540.0000.0000.0000.0000.0000.000
89A334PRO0-0.005-0.02368.018-0.001-0.0010.0000.0000.0000.000
90A335THR00.0250.00167.619-0.001-0.0010.0000.0000.0000.000
91A336ASP-1-0.858-0.90266.424-0.032-0.0320.0000.0000.0000.000
92A337PHE00.0210.01157.0850.0000.0000.0000.0000.0000.000
93A338VAL0-0.047-0.02559.5620.0010.0010.0000.0000.0000.000
94A339ILE0-0.035-0.00653.490-0.001-0.0010.0000.0000.0000.000
95A340SER0-0.022-0.03556.1780.0010.0010.0000.0000.0000.000
96A341ARG10.7830.86146.6450.0620.0620.0000.0000.0000.000
97A342TYR0-0.025-0.02249.030-0.001-0.0010.0000.0000.0000.000
98A343GLU-1-0.726-0.84244.079-0.071-0.0710.0000.0000.0000.000
99A344VAL0-0.059-0.02543.937-0.002-0.0020.0000.0000.0000.000
100A345ILE0-0.0270.01137.3770.0010.0010.0000.0000.0000.000
101A346LYS10.9370.94240.0600.0600.0600.0000.0000.0000.000
102A347GLU-1-0.780-0.89237.421-0.073-0.0730.0000.0000.0000.000
103A348ASN0-0.060-0.02137.284-0.001-0.0010.0000.0000.0000.000
104A349SER0-0.048-0.04037.7590.0020.0020.0000.0000.0000.000
105A350TYR0-0.036-0.01831.157-0.004-0.0040.0000.0000.0000.000
106A351VAL00.0110.00331.9890.0040.0040.0000.0000.0000.000
107A352TYR0-0.030-0.02429.023-0.007-0.0070.0000.0000.0000.000
108A353VAL00.011-0.00427.5740.0080.0080.0000.0000.0000.000
109A354ASP-1-0.753-0.80726.356-0.189-0.1890.0000.0000.0000.000
110A355TYR0-0.012-0.04120.7550.0150.0150.0000.0000.0000.000
111A356TRP00.0320.02322.909-0.011-0.0110.0000.0000.0000.000
112A357ASP-1-0.715-0.80820.262-0.449-0.4490.0000.0000.0000.000
113A358ASP-1-0.764-0.87122.151-0.319-0.3190.0000.0000.0000.000
114A359SER0-0.012-0.00818.262-0.030-0.0300.0000.0000.0000.000
115A360GLN00.007-0.02715.3440.0670.0670.0000.0000.0000.000
116A361ALA00.0200.01315.0960.0210.0210.0000.0000.0000.000
117A362PHE00.0210.01816.2300.0220.0220.0000.0000.0000.000
118A363ARG10.8410.93119.0700.3750.3750.0000.0000.0000.000
119A364ASN0-0.012-0.02419.114-0.011-0.0110.0000.0000.0000.000
120A365MET0-0.0030.02216.9400.0170.0170.0000.0000.0000.000
121A366VAL00.0120.00419.6420.0200.0200.0000.0000.0000.000
122A367TYR0-0.019-0.00719.1270.0270.0270.0000.0000.0000.000
123A368VAL0-0.0010.00114.873-0.037-0.0370.0000.0000.0000.000
124A369ARG10.8650.91010.8830.1750.1750.0000.0000.0000.000
125A370SER0-0.007-0.02710.464-0.049-0.0490.0000.0000.0000.000
126A371LEU00.0050.01611.957-0.086-0.0860.0000.0000.0000.000
127A372ALA0-0.0050.00912.8060.0720.0720.0000.0000.0000.000
128A373ALA00.015-0.00914.431-0.081-0.0810.0000.0000.0000.000
129A374ASN0-0.045-0.01116.6680.0200.0200.0000.0000.0000.000
130A375LEU00.0090.00718.474-0.026-0.0260.0000.0000.0000.000
131A376ASN0-0.0150.00321.8240.0110.0110.0000.0000.0000.000
132A377SER0-0.033-0.02424.7650.0050.0050.0000.0000.0000.000
133A378VAL00.003-0.00228.282-0.005-0.0050.0000.0000.0000.000
134A379ILE00.0100.00731.2560.0050.0050.0000.0000.0000.000
135A380CYS0-0.067-0.01735.058-0.004-0.0040.0000.0000.0000.000
136A381THR00.008-0.01537.2230.0040.0040.0000.0000.0000.000
137A382GLY00.0410.02040.953-0.002-0.0020.0000.0000.0000.000
138A383GLY0-0.016-0.01044.1720.0000.0000.0000.0000.0000.000
139A384ASP-1-0.857-0.90946.568-0.057-0.0570.0000.0000.0000.000
140A385TYR0-0.0010.00349.857-0.001-0.0010.0000.0000.0000.000
141A386SER0-0.008-0.00251.8040.0030.0030.0000.0000.0000.000
142A387PHE0-0.004-0.01953.168-0.001-0.0010.0000.0000.0000.000
143A388ALA00.019-0.00457.5630.0020.0020.0000.0000.0000.000
144A389LEU0-0.032-0.01060.0160.0000.0000.0000.0000.0000.000
145A390PRO0-0.0170.00863.3560.0000.0000.0000.0000.0000.000
146A391VAL00.0450.01466.3390.0010.0010.0000.0000.0000.000
147A392GLY00.0210.01667.5310.0000.0000.0000.0000.0000.000
148A393GLN0-0.006-0.01864.614-0.002-0.0020.0000.0000.0000.000
149A394TRP00.0430.02859.331-0.001-0.0010.0000.0000.0000.000
150A395PRO00.0210.03358.7270.0000.0000.0000.0000.0000.000
151A396VAL0-0.0050.00853.681-0.001-0.0010.0000.0000.0000.000
152A397MET0-0.0140.00650.0070.0000.0000.0000.0000.0000.000
153A398THR0-0.005-0.02849.913-0.002-0.0020.0000.0000.0000.000
154A399GLY00.0560.03147.3360.0020.0020.0000.0000.0000.000
155A400GLY0-0.013-0.01545.042-0.001-0.0010.0000.0000.0000.000
156A401ALA0-0.0070.00240.539-0.003-0.0030.0000.0000.0000.000
157A402VAL0-0.013-0.00536.7130.0040.0040.0000.0000.0000.000
158A403SER00.012-0.01333.480-0.006-0.0060.0000.0000.0000.000
159A404LEU0-0.017-0.00530.3900.0030.0030.0000.0000.0000.000
160A405HIS0-0.015-0.02128.445-0.013-0.0130.0000.0000.0000.000
161A406SER00.0060.00522.3670.0070.0070.0000.0000.0000.000
162A407ALA00.0300.00925.6040.0090.0090.0000.0000.0000.000
163A408GLY00.0030.00423.2500.0160.0160.0000.0000.0000.000
164A409VAL00.0000.00119.574-0.009-0.0090.0000.0000.0000.000
165A410THR0-0.0240.00021.8810.0100.0100.0000.0000.0000.000
166A411LEU00.0370.02318.986-0.019-0.0190.0000.0000.0000.000
167A412SER0-0.069-0.06122.8620.0170.0170.0000.0000.0000.000
168A413THR0-0.013-0.01825.530-0.010-0.0100.0000.0000.0000.000
169A414GLN00.0010.02226.7000.0250.0250.0000.0000.0000.000
170A415PHE0-0.007-0.01530.218-0.004-0.0040.0000.0000.0000.000
171A416THR0-0.006-0.01131.9080.0080.0080.0000.0000.0000.000
172A417ASP-1-0.918-0.96434.623-0.109-0.1090.0000.0000.0000.000
173A418PHE0-0.069-0.02234.8390.0050.0050.0000.0000.0000.000
174A419VAL00.0020.00429.653-0.001-0.0010.0000.0000.0000.000
175A420SER00.0280.02230.5410.0020.0020.0000.0000.0000.000
176A421LEU0-0.0010.01226.674-0.009-0.0090.0000.0000.0000.000
177A422ASN0-0.017-0.00722.7800.0220.0220.0000.0000.0000.000
178A423SER0-0.026-0.01823.224-0.019-0.0190.0000.0000.0000.000
179A424LEU00.0060.01317.5950.0030.0030.0000.0000.0000.000
180A425ARG10.8210.87322.1650.1640.1640.0000.0000.0000.000
181A426PHE00.0270.00719.5990.0010.0010.0000.0000.0000.000
182A427ARG10.8570.92924.7140.1360.1360.0000.0000.0000.000
183A428PHE00.0110.00226.032-0.006-0.0060.0000.0000.0000.000
184A429ARG10.9150.95529.2320.1080.1080.0000.0000.0000.000
185A430LEU00.001-0.01731.822-0.007-0.0070.0000.0000.0000.000
186A431THR0-0.0090.00234.6830.0020.0020.0000.0000.0000.000
187A432VAL0-0.053-0.01836.604-0.003-0.0030.0000.0000.0000.000
188A433GLU-1-0.817-0.87236.738-0.083-0.0830.0000.0000.0000.000
189A434GLU-1-0.779-0.84140.932-0.051-0.0510.0000.0000.0000.000
190A435PRO0-0.031-0.01342.504-0.003-0.0030.0000.0000.0000.000
191A436SER00.0160.00745.627-0.001-0.0010.0000.0000.0000.000
192A437PHE0-0.024-0.01746.7340.0000.0000.0000.0000.0000.000
193A438SER0-0.070-0.03648.9690.0030.0030.0000.0000.0000.000
194A439ILE0-0.015-0.00952.470-0.002-0.0020.0000.0000.0000.000
195A440THR00.0530.04255.2460.0030.0030.0000.0000.0000.000
196A441ARG10.8510.90057.8210.0400.0400.0000.0000.0000.000
197A442THR0-0.034-0.01958.0790.0010.0010.0000.0000.0000.000
198A443ARG10.8990.93759.9490.0350.0350.0000.0000.0000.000
199A444VAL0-0.0130.01153.7240.0000.0000.0000.0000.0000.000
200A445SER00.004-0.01753.683-0.001-0.0010.0000.0000.0000.000
201A446ARG10.8640.89648.7240.0490.0490.0000.0000.0000.000
202A447LEU00.0130.04349.4590.0000.0000.0000.0000.0000.000
203A448TYR0-0.004-0.03744.324-0.001-0.0010.0000.0000.0000.000
204A449GLY00.029-0.00542.0530.0010.0010.0000.0000.0000.000
205A450LEU0-0.0320.00338.8640.0010.0010.0000.0000.0000.000
206A451PRO00.011-0.01342.435-0.001-0.0010.0000.0000.0000.000
207A452ALA00.0290.02543.943-0.003-0.0030.0000.0000.0000.000
208A453ALA0-0.017-0.00244.993-0.001-0.0010.0000.0000.0000.000
209A454ASN0-0.044-0.03745.152-0.004-0.0040.0000.0000.0000.000
210A455PRO00.0540.03540.318-0.001-0.0010.0000.0000.0000.000
211A456ASN00.0470.02338.863-0.008-0.0080.0000.0000.0000.000
212A457ASN0-0.048-0.01940.514-0.003-0.0030.0000.0000.0000.000
213A458GLY00.0420.01542.349-0.002-0.0020.0000.0000.0000.000
214A459LYS10.8110.93037.1850.1000.1000.0000.0000.0000.000
215A460GLU-1-0.752-0.85837.217-0.119-0.1190.0000.0000.0000.000
216A461TYR0-0.046-0.02532.013-0.003-0.0030.0000.0000.0000.000
217A462TYR00.005-0.00532.8950.0060.0060.0000.0000.0000.000
218A463GLU-1-0.816-0.90927.820-0.208-0.2080.0000.0000.0000.000
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