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: G51M1

Calculation Name: 3LJB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LJB

Chain ID: A

ChEMBL ID:

UniProt ID: P20591

Base Structure: X-ray

Registration Date: 2023-09-24

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2668271.49916
FMO2-HF: Nuclear repulsion 2575373.008979
FMO2-HF: Total energy -92898.490181
FMO2-MP2: Total energy -93168.842512


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:366:GLU)


Summations of interaction energy for fragment #1(A:366:GLU)
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.
-17.592-14.09513.321-7.243-9.5750.079
Interaction energy analysis for fragmet #1(A:366:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.891 / q_NPA : -0.959
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].
3A368GLU-1-0.822-0.8951.85917.96518.56210.046-5.302-5.3410.062
4A369ASN0-0.048-0.0262.087-24.767-22.4803.270-1.813-3.7450.017
5A370GLU-1-0.930-0.9513.71423.85724.4700.005-0.128-0.4890.000
6A371LYS10.7700.8796.006-43.619-43.6190.0000.0000.0000.000
7A372MET0-0.024-0.0136.501-4.729-4.7290.0000.0000.0000.000
8A373PHE0-0.008-0.0185.534-2.800-2.8000.0000.0000.0000.000
9A374PHE00.0410.0319.800-2.632-2.6320.0000.0000.0000.000
10A375LEU0-0.020-0.01111.646-2.051-2.0510.0000.0000.0000.000
11A376ILE0-0.011-0.00810.754-1.727-1.7270.0000.0000.0000.000
12A377ASP-1-0.849-0.92613.83917.25717.2570.0000.0000.0000.000
13A378LYS10.7810.89715.800-16.114-16.1140.0000.0000.0000.000
14A379VAL0-0.029-0.01417.173-1.079-1.0790.0000.0000.0000.000
15A380ASN0-0.041-0.02616.367-1.235-1.2350.0000.0000.0000.000
16A381ALA0-0.0090.00519.794-0.754-0.7540.0000.0000.0000.000
17A382PHE00.0510.02521.966-0.671-0.6710.0000.0000.0000.000
18A383ASN00.034-0.00221.904-0.820-0.8200.0000.0000.0000.000
19A384GLN00.0400.04123.988-0.379-0.3790.0000.0000.0000.000
20A385ASP-1-0.855-0.92325.79310.88510.8850.0000.0000.0000.000
21A386ILE0-0.055-0.03227.500-0.498-0.4980.0000.0000.0000.000
22A387THR00.006-0.01727.250-0.371-0.3710.0000.0000.0000.000
23A388ALA00.0160.01029.877-0.372-0.3720.0000.0000.0000.000
24A389LEU0-0.030-0.00831.960-0.391-0.3910.0000.0000.0000.000
25A390MET0-0.082-0.02231.106-0.205-0.2050.0000.0000.0000.000
26A391GLN0-0.062-0.03632.464-0.185-0.1850.0000.0000.0000.000
27A392GLY0-0.0210.00435.749-0.221-0.2210.0000.0000.0000.000
28A393GLU-1-0.932-0.96933.7948.8318.8310.0000.0000.0000.000
29A394GLU-1-0.812-0.90533.0828.5508.5500.0000.0000.0000.000
30A395THR0-0.011-0.00631.807-0.389-0.3890.0000.0000.0000.000
31A396VAL0-0.036-0.02334.4860.0950.0950.0000.0000.0000.000
32A397GLY00.0480.02737.3480.0240.0240.0000.0000.0000.000
33A398GLU-1-0.993-1.00639.3837.1377.1370.0000.0000.0000.000
34A399GLU-1-0.967-0.97842.2246.4136.4130.0000.0000.0000.000
35A400ASP-1-0.893-0.93340.2007.6057.6050.0000.0000.0000.000
36A401ILE0-0.082-0.04842.855-0.093-0.0930.0000.0000.0000.000
37A402ARG10.8530.92236.561-8.117-8.1170.0000.0000.0000.000
38A403LEU00.0140.00536.432-0.238-0.2380.0000.0000.0000.000
39A404PHE00.0410.02638.435-0.239-0.2390.0000.0000.0000.000
40A405THR0-0.010-0.01240.857-0.135-0.1350.0000.0000.0000.000
41A406ARG10.9080.95440.064-7.851-7.8510.0000.0000.0000.000
42A407LEU00.0290.01941.046-0.165-0.1650.0000.0000.0000.000
43A408ARG10.8850.94744.627-6.426-6.4260.0000.0000.0000.000
44A409HIS00.007-0.00946.968-0.225-0.2250.0000.0000.0000.000
45A410GLU-1-0.801-0.88246.8746.3246.3240.0000.0000.0000.000
46A411PHE00.041-0.00144.602-0.149-0.1490.0000.0000.0000.000
47A412HIS00.0430.04550.250-0.040-0.0400.0000.0000.0000.000
48A413LYS10.8080.88750.192-6.460-6.4600.0000.0000.0000.000
49A414TRP00.002-0.00652.196-0.120-0.1200.0000.0000.0000.000
50A415SER00.0240.00154.257-0.076-0.0760.0000.0000.0000.000
51A416THR0-0.068-0.03656.504-0.139-0.1390.0000.0000.0000.000
52A417ILE0-0.028-0.01555.418-0.118-0.1180.0000.0000.0000.000
53A418ILE00.0210.01655.958-0.109-0.1090.0000.0000.0000.000
54A419GLU-1-0.848-0.91259.8614.9574.9570.0000.0000.0000.000
55A420ASN0-0.017-0.01262.066-0.156-0.1560.0000.0000.0000.000
56A421ASN0-0.006-0.00862.158-0.083-0.0830.0000.0000.0000.000
57A422PHE00.0210.01663.885-0.089-0.0890.0000.0000.0000.000
58A423GLN0-0.047-0.03565.562-0.145-0.1450.0000.0000.0000.000
59A424GLU-1-0.928-0.94867.0014.7074.7070.0000.0000.0000.000
60A425GLY00.0390.01367.980-0.086-0.0860.0000.0000.0000.000
61A426HIS00.0340.01369.472-0.045-0.0450.0000.0000.0000.000
62A427LYS10.9560.98671.660-4.417-4.4170.0000.0000.0000.000
63A428ILE0-0.035-0.02170.627-0.097-0.0970.0000.0000.0000.000
64A429LEU00.0080.00172.681-0.080-0.0800.0000.0000.0000.000
65A430SER00.016-0.00475.018-0.073-0.0730.0000.0000.0000.000
66A431ARG10.9180.95977.208-4.145-4.1450.0000.0000.0000.000
67A432LYS10.8780.95777.026-4.214-4.2140.0000.0000.0000.000
68A433ILE00.0290.01977.762-0.045-0.0450.0000.0000.0000.000
69A434GLN00.0420.02080.973-0.036-0.0360.0000.0000.0000.000
70A435LYS10.9110.95982.737-3.935-3.9350.0000.0000.0000.000
71A436PHE0-0.034-0.02680.462-0.025-0.0250.0000.0000.0000.000
72A437GLU-1-0.931-0.95184.4533.7743.7740.0000.0000.0000.000
73A438ASN0-0.128-0.06087.131-0.103-0.1030.0000.0000.0000.000
74A448PHE00.0700.02380.792-0.008-0.0080.0000.0000.0000.000
75A449VAL00.0090.00281.0270.0550.0550.0000.0000.0000.000
76A450ASN00.0240.01880.5740.0590.0590.0000.0000.0000.000
77A451TYR0-0.0070.00273.1340.0430.0430.0000.0000.0000.000
78A452ARG11.0010.99474.424-4.245-4.2450.0000.0000.0000.000
79A453THR0-0.018-0.00974.5080.0690.0690.0000.0000.0000.000
80A454PHE0-0.006-0.01075.4510.0160.0160.0000.0000.0000.000
81A455GLU-1-0.839-0.92770.1114.6294.6290.0000.0000.0000.000
82A456THR0-0.030-0.02870.2500.0820.0820.0000.0000.0000.000
83A457ILE0-0.011-0.00569.6430.0530.0530.0000.0000.0000.000
84A458VAL00.0210.02066.7870.0560.0560.0000.0000.0000.000
85A459LYS10.8250.92865.657-4.757-4.7570.0000.0000.0000.000
86A460GLN00.006-0.00464.7040.0340.0340.0000.0000.0000.000
87A461GLN0-0.020-0.02364.6250.1320.1320.0000.0000.0000.000
88A462ILE00.0140.01960.5800.0850.0850.0000.0000.0000.000
89A463LYS10.8010.87858.114-5.456-5.4560.0000.0000.0000.000
90A464ALA0-0.036-0.01960.0420.0860.0860.0000.0000.0000.000
91A465LEU00.0000.00557.5380.0600.0600.0000.0000.0000.000
92A466GLU-1-0.811-0.88255.0335.8475.8470.0000.0000.0000.000
93A467GLU-1-0.780-0.87254.2315.9315.9310.0000.0000.0000.000
94A468PRO00.0410.01953.6950.1180.1180.0000.0000.0000.000
95A469ALA0-0.0160.00451.9400.1030.1030.0000.0000.0000.000
96A470VAL0-0.024-0.00849.5080.1720.1720.0000.0000.0000.000
97A471ASP-1-0.896-0.94549.0296.2586.2580.0000.0000.0000.000
98A472MET0-0.046-0.00248.3640.1260.1260.0000.0000.0000.000
99A473LEU0-0.024-0.01543.5300.1640.1640.0000.0000.0000.000
100A474HIS10.8000.86344.735-6.762-6.7620.0000.0000.0000.000
101A475THR0-0.0200.00145.0340.0700.0700.0000.0000.0000.000
102A476VAL0-0.029-0.02341.9760.1330.1330.0000.0000.0000.000
103A477THR0-0.023-0.04040.4170.1910.1910.0000.0000.0000.000
104A478ASP-1-0.744-0.85839.4017.9897.9890.0000.0000.0000.000
105A479MET0-0.052-0.00839.9080.1750.1750.0000.0000.0000.000
106A480VAL0-0.0080.00335.5350.1580.1580.0000.0000.0000.000
107A481ARG10.8560.94235.279-8.421-8.4210.0000.0000.0000.000
108A482LEU0-0.065-0.01635.0330.2530.2530.0000.0000.0000.000
109A483ALA00.0500.02335.0990.2250.2250.0000.0000.0000.000
110A484PHE00.024-0.00831.2880.2980.2980.0000.0000.0000.000
111A485THR0-0.034-0.02930.4540.4320.4320.0000.0000.0000.000
112A486ASP-1-0.864-0.93531.0949.2329.2320.0000.0000.0000.000
113A487VAL0-0.007-0.00127.5690.2450.2450.0000.0000.0000.000
114A488SER0-0.010-0.02726.7300.5760.5760.0000.0000.0000.000
115A489ILE0-0.030-0.02226.6650.4270.4270.0000.0000.0000.000
116A490LYS10.8540.92026.980-10.740-10.7400.0000.0000.0000.000
117A491ASN0-0.042-0.01123.1800.8150.8150.0000.0000.0000.000
118A492PHE00.010-0.01320.4120.7890.7890.0000.0000.0000.000
119A493GLU-1-0.869-0.91423.83310.98110.9810.0000.0000.0000.000
120A494GLU-1-0.899-0.94222.74112.26512.2650.0000.0000.0000.000
121A495PHE0-0.041-0.02417.5050.4360.4360.0000.0000.0000.000
122A496PHE00.021-0.00521.4050.1020.1020.0000.0000.0000.000
123A497ASN0-0.045-0.02019.413-1.274-1.2740.0000.0000.0000.000
124A498LEU00.0760.06117.842-0.275-0.2750.0000.0000.0000.000
125A499HIS00.0390.04920.984-0.213-0.2130.0000.0000.0000.000
126A500ARG10.8720.93023.735-13.019-13.0190.0000.0000.0000.000
127A501THR0-0.047-0.04221.158-0.287-0.2870.0000.0000.0000.000
128A502ALA00.0430.01524.152-0.142-0.1420.0000.0000.0000.000
129A503LYS10.8500.90025.500-10.214-10.2140.0000.0000.0000.000
130A504SER0-0.0270.00526.923-0.380-0.3800.0000.0000.0000.000
131A505LYS10.9290.97123.075-13.629-13.6290.0000.0000.0000.000
132A506ILE0-0.0060.00728.953-0.299-0.2990.0000.0000.0000.000
133A507GLU-1-0.792-0.88931.3448.6928.6920.0000.0000.0000.000
134A508ASP-1-0.919-0.95330.4239.9849.9840.0000.0000.0000.000
135A509ILE0-0.038-0.02529.123-0.265-0.2650.0000.0000.0000.000
136A510ARG10.7770.86033.625-8.157-8.1570.0000.0000.0000.000
137A511ALA00.022-0.00336.558-0.271-0.2710.0000.0000.0000.000
138A512GLU-1-0.860-0.89035.5008.2898.2890.0000.0000.0000.000
139A513GLN0-0.011-0.02435.851-0.228-0.2280.0000.0000.0000.000
140A514GLU-1-0.718-0.81438.6677.3507.3500.0000.0000.0000.000
141A515ARG10.7970.87238.752-8.277-8.2770.0000.0000.0000.000
142A516GLU-1-0.812-0.88241.1087.2687.2680.0000.0000.0000.000
143A517GLY00.0390.01242.623-0.158-0.1580.0000.0000.0000.000
144A518GLU-1-0.766-0.88244.2346.4026.4020.0000.0000.0000.000
145A519LYS10.7790.87744.012-7.435-7.4350.0000.0000.0000.000
146A520LEU00.013-0.00845.190-0.168-0.1680.0000.0000.0000.000
147A521ILE0-0.0060.01147.674-0.153-0.1530.0000.0000.0000.000
148A522ARG10.7540.82450.236-6.251-6.2510.0000.0000.0000.000
149A523LEU0-0.0100.00249.731-0.137-0.1370.0000.0000.0000.000
150A524HIS0-0.019-0.01451.889-0.021-0.0210.0000.0000.0000.000
151A525PHE00.025-0.00153.665-0.120-0.1200.0000.0000.0000.000
152A526GLN0-0.036-0.01755.105-0.044-0.0440.0000.0000.0000.000
153A527MET0-0.037-0.00752.952-0.102-0.1020.0000.0000.0000.000
154A528GLU-1-0.732-0.85957.3235.3905.3900.0000.0000.0000.000
155A529GLN0-0.044-0.00959.820-0.188-0.1880.0000.0000.0000.000
156A530ILE0-0.046-0.01561.005-0.124-0.1240.0000.0000.0000.000
157A531VAL0-0.017-0.00363.8600.0190.0190.0000.0000.0000.000
158A532TYR0-0.081-0.04862.5180.0410.0410.0000.0000.0000.000
159A573SER0-0.020-0.02782.890-0.030-0.0300.0000.0000.0000.000
160A574MET0-0.036-0.02379.9040.0400.0400.0000.0000.0000.000
161A575GLU-1-0.807-0.91078.8244.1754.1750.0000.0000.0000.000
162A576GLU-1-0.827-0.89378.2674.0114.0110.0000.0000.0000.000
163A577ILE0-0.037-0.02176.7360.0640.0640.0000.0000.0000.000
164A578PHE0-0.020-0.00874.6500.0750.0750.0000.0000.0000.000
165A579GLN0-0.004-0.02573.9080.1350.1350.0000.0000.0000.000
166A580HIS0-0.0080.01371.5210.0500.0500.0000.0000.0000.000
167A581LEU0-0.013-0.01170.8230.0820.0820.0000.0000.0000.000
168A582MET00.0000.01469.0680.0880.0880.0000.0000.0000.000
169A583ALA00.0060.01268.3310.0780.0780.0000.0000.0000.000
170A584TYR0-0.001-0.02663.6030.0340.0340.0000.0000.0000.000
171A585HIS00.0290.00464.5120.0380.0380.0000.0000.0000.000
172A586GLN0-0.0120.01663.9770.1330.1330.0000.0000.0000.000
173A587GLU-1-0.813-0.88861.2755.2455.2450.0000.0000.0000.000
174A588ALA00.0360.02260.2090.1040.1040.0000.0000.0000.000
175A589SER0-0.034-0.03159.0560.1060.1060.0000.0000.0000.000
176A590LYS10.8560.91658.426-5.064-5.0640.0000.0000.0000.000
177A591ARG10.7970.88755.926-5.271-5.2710.0000.0000.0000.000
178A592ILE00.0160.01354.4460.1550.1550.0000.0000.0000.000
179A593SER0-0.009-0.01353.8310.0930.0930.0000.0000.0000.000
180A594SER0-0.063-0.01251.4900.0880.0880.0000.0000.0000.000
181A595HIS0-0.005-0.03448.7600.2520.2520.0000.0000.0000.000
182A596ILE00.0190.02048.6880.1480.1480.0000.0000.0000.000
183A597PRO00.0210.00447.5070.1470.1470.0000.0000.0000.000
184A598LEU0-0.0200.01144.0060.1820.1820.0000.0000.0000.000
185A599ILE00.0130.00743.9010.2220.2220.0000.0000.0000.000
186A600ILE00.0170.00843.1270.2190.2190.0000.0000.0000.000
187A601GLN00.007-0.00140.7280.1840.1840.0000.0000.0000.000
188A602PHE0-0.0120.00238.6750.2630.2630.0000.0000.0000.000
189A603PHE00.0110.00838.2650.2530.2530.0000.0000.0000.000
190A604MET0-0.039-0.01137.4590.2600.2600.0000.0000.0000.000
191A605LEU00.0090.01235.4100.0250.0250.0000.0000.0000.000
192A606GLN0-0.032-0.01934.8010.4540.4540.0000.0000.0000.000
193A607THR0-0.008-0.00733.5780.3600.3600.0000.0000.0000.000
194A608TYR0-0.062-0.05832.9060.3220.3220.0000.0000.0000.000
195A609GLY00.0650.02231.1170.3110.3110.0000.0000.0000.000
196A610GLN00.0180.01029.1410.5010.5010.0000.0000.0000.000
197A611GLN0-0.025-0.01128.0500.6670.6670.0000.0000.0000.000
198A612LEU00.0170.01927.3380.4290.4290.0000.0000.0000.000
199A613GLN0-0.004-0.00824.9170.3820.3820.0000.0000.0000.000
200A614LYS10.8830.92923.365-10.192-10.1920.0000.0000.0000.000
201A615ALA0-0.013-0.00223.1990.5980.5980.0000.0000.0000.000
202A616MET00.0140.02521.1620.3120.3120.0000.0000.0000.000
203A617LEU00.0230.00618.5980.8220.8220.0000.0000.0000.000
204A618GLN0-0.026-0.01318.3370.7220.7220.0000.0000.0000.000
205A619LEU0-0.032-0.02017.6170.4320.4320.0000.0000.0000.000
206A620LEU00.0240.01513.2301.0971.0970.0000.0000.0000.000
207A621GLN0-0.056-0.00313.8121.0491.0490.0000.0000.0000.000
208A622ASP-1-0.838-0.89914.05922.14922.1490.0000.0000.0000.000
209A623LYS10.8780.8996.233-42.745-42.7450.0000.0000.0000.000
210A624ASP-1-0.857-0.9129.81733.42933.4290.0000.0000.0000.000
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