FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 2J77R

Calculation Name: 3EC3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EC3

Chain ID: A

ChEMBL ID:

UniProt ID: P38659

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:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2836707.879234
FMO2-HF: Nuclear repulsion 2745531.323981
FMO2-HF: Total energy -91176.555253
FMO2-MP2: Total energy -91445.823054


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:282:SER)


Summations of interaction energy for fragment #1(A:282: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.
0.8762.4120.002-0.432-1.1040
Interaction energy analysis for fragmet #1(A:282:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : -0.002
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].
3A284PRO00.0140.0163.7810.0691.070-0.009-0.278-0.7130.000
4A285SER0-0.0220.0026.1480.4360.4360.0000.0000.0000.000
5A286LYS10.9400.9527.4680.2660.2660.0000.0000.0000.000
6A287GLU-1-0.915-0.9608.6410.0250.0250.0000.0000.0000.000
7A288ILE0-0.045-0.01611.5320.0170.0170.0000.0000.0000.000
8A289LEU00.0170.00513.8380.0100.0100.0000.0000.0000.000
9A290THR00.016-0.00116.9230.0040.0040.0000.0000.0000.000
10A291LEU00.0600.01019.973-0.011-0.0110.0000.0000.0000.000
11A292LYS10.9570.97122.4800.0210.0210.0000.0000.0000.000
12A293GLN00.0610.05514.2550.0120.0120.0000.0000.0000.000
13A294VAL00.0190.01019.076-0.008-0.0080.0000.0000.0000.000
14A295GLN0-0.079-0.06620.4870.0020.0020.0000.0000.0000.000
15A296GLU-1-0.849-0.93019.015-0.073-0.0730.0000.0000.0000.000
16A297PHE00.0010.00314.601-0.006-0.0060.0000.0000.0000.000
17A298LEU0-0.071-0.03420.3450.0030.0030.0000.0000.0000.000
18A299LYS10.8830.95823.6860.0610.0610.0000.0000.0000.000
19A300ASP-1-0.863-0.91921.884-0.056-0.0560.0000.0000.0000.000
20A301GLY0-0.075-0.02120.765-0.001-0.0010.0000.0000.0000.000
21A302ASP-1-0.888-0.94820.083-0.075-0.0750.0000.0000.0000.000
22A303ASH0-0.153-0.17518.0590.0000.0000.0000.0000.0000.000
23A304VAL0-0.003-0.00418.530-0.002-0.0020.0000.0000.0000.000
24A305VAL0-0.015-0.00717.772-0.014-0.0140.0000.0000.0000.000
25A306ILE00.0020.00315.3570.0120.0120.0000.0000.0000.000
26A307LEU0-0.019-0.01115.322-0.029-0.0290.0000.0000.0000.000
27A308GLY00.0250.01315.4250.0160.0160.0000.0000.0000.000
28A309VAL0-0.023-0.01316.6730.0050.0050.0000.0000.0000.000
29A310PHE0-0.0030.00616.266-0.002-0.0020.0000.0000.0000.000
30A311GLN00.016-0.01819.2530.0220.0220.0000.0000.0000.000
31A312GLY00.0120.00317.5220.0200.0200.0000.0000.0000.000
32A313VAL00.0080.00411.720-0.027-0.0270.0000.0000.0000.000
33A314GLY00.0160.01213.558-0.029-0.0290.0000.0000.0000.000
34A315ASP-1-0.859-0.92016.102-0.126-0.1260.0000.0000.0000.000
35A316PRO00.0610.01616.650-0.033-0.0330.0000.0000.0000.000
36A317GLY00.0260.01917.310-0.025-0.0250.0000.0000.0000.000
37A318TYR0-0.0050.00310.114-0.070-0.0700.0000.0000.0000.000
38A319LEU0-0.020-0.00812.012-0.078-0.0780.0000.0000.0000.000
39A320GLN00.0060.00012.773-0.094-0.0940.0000.0000.0000.000
40A321TYR0-0.063-0.05512.732-0.023-0.0230.0000.0000.0000.000
41A322GLN00.000-0.0117.876-0.225-0.2250.0000.0000.0000.000
42A323ASP-1-0.932-0.9489.328-0.588-0.5880.0000.0000.0000.000
43A324ALA00.013-0.01011.1560.0150.0150.0000.0000.0000.000
44A325ALA0-0.011-0.00910.0950.0320.0320.0000.0000.0000.000
45A326ASN0-0.024-0.0226.003-0.054-0.0540.0000.0000.0000.000
46A327THR0-0.048-0.0168.2770.1800.1800.0000.0000.0000.000
47A328LEU00.0090.01011.3350.0680.0680.0000.0000.0000.000
48A329ARG10.8720.9453.5950.8031.3380.011-0.154-0.3910.000
49A330GLU-1-0.977-0.98110.2010.1160.1160.0000.0000.0000.000
50A331ASP-1-0.905-0.96012.327-0.077-0.0770.0000.0000.0000.000
51A332TYR00.0210.01213.6130.0050.0050.0000.0000.0000.000
52A333LYS10.9170.9629.1770.2150.2150.0000.0000.0000.000
53A334PHE00.0870.03910.2700.0100.0100.0000.0000.0000.000
54A335HIS00.0050.00510.403-0.078-0.0780.0000.0000.0000.000
55A336HIS0-0.009-0.0049.1560.0610.0610.0000.0000.0000.000
56A337THR00.0240.00613.9030.0320.0320.0000.0000.0000.000
57A338PHE00.0780.03713.156-0.012-0.0120.0000.0000.0000.000
58A339SER00.0020.02618.5330.0160.0160.0000.0000.0000.000
59A340THR00.041-0.00521.163-0.005-0.0050.0000.0000.0000.000
60A341GLU-1-0.942-0.96124.427-0.030-0.0300.0000.0000.0000.000
61A342ILE00.0140.00019.461-0.001-0.0010.0000.0000.0000.000
62A343ALA00.0170.01923.386-0.003-0.0030.0000.0000.0000.000
63A344LYS10.9390.95524.5180.0330.0330.0000.0000.0000.000
64A345PHE0-0.033-0.00924.9460.0020.0020.0000.0000.0000.000
65A346LEU0-0.038-0.02421.7140.0010.0010.0000.0000.0000.000
66A347LYS10.9180.96226.3560.0400.0400.0000.0000.0000.000
67A348VAL00.0160.02923.8400.0000.0000.0000.0000.0000.000
68A349SER0-0.021-0.01726.8690.0020.0020.0000.0000.0000.000
69A350LEU0-0.012-0.02221.977-0.005-0.0050.0000.0000.0000.000
70A351GLY0-0.014-0.01221.6040.0060.0060.0000.0000.0000.000
71A352LYS10.8630.92021.5200.0920.0920.0000.0000.0000.000
72A353LEU0-0.0020.01917.690-0.018-0.0180.0000.0000.0000.000
73A354VAL0-0.007-0.01019.8540.0180.0180.0000.0000.0000.000
74A355LEU00.0270.01619.755-0.016-0.0160.0000.0000.0000.000
75A356MET0-0.033-0.01421.0380.0170.0170.0000.0000.0000.000
76A357GLN00.0510.02322.229-0.007-0.0070.0000.0000.0000.000
77A358PRO00.0280.01022.5150.0040.0040.0000.0000.0000.000
78A359GLU-1-0.958-0.98324.836-0.044-0.0440.0000.0000.0000.000
79A360LYS10.8340.92725.2850.0620.0620.0000.0000.0000.000
80A361PHE00.0200.00324.7730.0030.0030.0000.0000.0000.000
81A362GLN0-0.0530.00027.2250.0030.0030.0000.0000.0000.000
82A363SER00.009-0.04830.5850.0040.0040.0000.0000.0000.000
83A364LYS10.9060.94034.1800.0310.0310.0000.0000.0000.000
84A365TYR0-0.087-0.06736.0870.0010.0010.0000.0000.0000.000
85A366GLU-1-0.795-0.83830.496-0.059-0.0590.0000.0000.0000.000
86A367PRO0-0.0060.01030.0770.0020.0020.0000.0000.0000.000
87A368ARG10.9400.95928.7650.0480.0480.0000.0000.0000.000
88A369MET0-0.049-0.03025.384-0.006-0.0060.0000.0000.0000.000
89A370HIS00.0090.02425.2440.0080.0080.0000.0000.0000.000
90A371VAL00.0190.00024.366-0.010-0.0100.0000.0000.0000.000
91A372MET0-0.046-0.00621.6100.0090.0090.0000.0000.0000.000
92A373ASP-1-0.849-0.91123.629-0.094-0.0940.0000.0000.0000.000
93A374VAL0-0.048-0.02818.509-0.008-0.0080.0000.0000.0000.000
94A375GLN00.006-0.02121.6230.0030.0030.0000.0000.0000.000
95A376GLY00.009-0.01219.966-0.013-0.0130.0000.0000.0000.000
96A377SER00.004-0.00820.724-0.008-0.0080.0000.0000.0000.000
97A378THR0-0.0030.02820.7100.0070.0070.0000.0000.0000.000
98A379GLU-1-0.848-0.91120.008-0.140-0.1400.0000.0000.0000.000
99A380ALA00.0520.01315.3120.0020.0020.0000.0000.0000.000
100A381SER0-0.027-0.02117.378-0.009-0.0090.0000.0000.0000.000
101A382ALA00.0980.05819.4260.0070.0070.0000.0000.0000.000
102A383ILE0-0.039-0.02016.5470.0060.0060.0000.0000.0000.000
103A384LYS10.9390.96715.4060.2030.2030.0000.0000.0000.000
104A385ASP-1-0.878-0.94018.034-0.110-0.1100.0000.0000.0000.000
105A386TYR0-0.040-0.02621.6900.0120.0120.0000.0000.0000.000
106A387VAL0-0.022-0.02017.2080.0070.0070.0000.0000.0000.000
107A388VAL00.0120.00919.3860.0090.0090.0000.0000.0000.000
108A389LYS10.8920.95621.6250.0880.0880.0000.0000.0000.000
109A390HIS0-0.053-0.04123.9740.0160.0160.0000.0000.0000.000
110A391ALA00.0250.02220.7250.0010.0010.0000.0000.0000.000
111A392LEU0-0.0150.00422.6180.0010.0010.0000.0000.0000.000
112A393PRO0-0.037-0.00325.3800.0010.0010.0000.0000.0000.000
113A394LEU0-0.015-0.01128.1010.0020.0020.0000.0000.0000.000
114A395VAL0-0.009-0.00231.4760.0030.0030.0000.0000.0000.000
115A396GLY00.0050.00828.001-0.001-0.0010.0000.0000.0000.000
116A397HIS00.0180.00027.2580.0010.0010.0000.0000.0000.000
117A398ARG10.7870.87226.7640.0300.0300.0000.0000.0000.000
118A399LYS10.8570.91922.9810.0620.0620.0000.0000.0000.000
119A400THR00.0700.02226.267-0.002-0.0020.0000.0000.0000.000
120A401SER0-0.076-0.03421.8630.0010.0010.0000.0000.0000.000
121A402ASN0-0.033-0.03221.5900.0010.0010.0000.0000.0000.000
122A403ASP-1-0.776-0.86422.905-0.038-0.0380.0000.0000.0000.000
123A404ALA0-0.0040.00323.019-0.002-0.0020.0000.0000.0000.000
124A405LYS10.9100.94715.6520.0360.0360.0000.0000.0000.000
125A406ARG00.0820.17117.671-0.014-0.0140.0000.0000.0000.000
126A407TYR0-0.0040.00223.442-0.002-0.0020.0000.0000.0000.000
127A408SER00.0620.03525.1410.0060.0060.0000.0000.0000.000
128A409LYS10.9120.97127.2830.0610.0610.0000.0000.0000.000
129A410ARG10.8350.92529.2630.0400.0400.0000.0000.0000.000
130A411PRO00.0280.00333.035-0.001-0.0010.0000.0000.0000.000
131A412LEU0-0.045-0.01431.113-0.003-0.0030.0000.0000.0000.000
132A413VAL0-0.018-0.00934.5120.0030.0030.0000.0000.0000.000
133A414VAL0-0.029-0.01933.686-0.003-0.0030.0000.0000.0000.000
134A415VAL00.003-0.00335.8500.0020.0020.0000.0000.0000.000
135A416TYR0-0.054-0.07635.391-0.002-0.0020.0000.0000.0000.000
136A417TYR00.0600.00536.1750.0000.0000.0000.0000.0000.000
137A418SER00.0590.06036.780-0.001-0.0010.0000.0000.0000.000
138A419VAL0-0.073-0.03131.499-0.001-0.0010.0000.0000.0000.000
139A420ASP-1-0.769-0.88232.496-0.031-0.0310.0000.0000.0000.000
140A421PHE0-0.031-0.04129.4420.0000.0000.0000.0000.0000.000
141A422SER0-0.039-0.02231.359-0.001-0.0010.0000.0000.0000.000
142A423PHE0-0.073-0.06032.3980.0000.0000.0000.0000.0000.000
143A424ASP-1-0.863-0.93634.745-0.021-0.0210.0000.0000.0000.000
144A425TYR00.0110.01735.9460.0020.0020.0000.0000.0000.000
145A426ARG10.9380.98432.2620.0330.0330.0000.0000.0000.000
146A427THR0-0.030-0.02435.421-0.001-0.0010.0000.0000.0000.000
147A428ALA00.0510.02638.6300.0000.0000.0000.0000.0000.000
148A429THR00.0410.02333.4950.0000.0000.0000.0000.0000.000
149A430GLN00.001-0.01232.092-0.001-0.0010.0000.0000.0000.000
150A431PHE0-0.064-0.01636.8310.0000.0000.0000.0000.0000.000
151A432TRP00.1030.03738.9110.0000.0000.0000.0000.0000.000
152A433ARG10.8550.93931.6380.0470.0470.0000.0000.0000.000
153A434ASN0-0.053-0.04036.896-0.003-0.0030.0000.0000.0000.000
154A435LYS10.9060.98639.0720.0240.0240.0000.0000.0000.000
155A436VAL00.0460.03436.4090.0000.0000.0000.0000.0000.000
156A437LEU0-0.047-0.02633.884-0.001-0.0010.0000.0000.0000.000
157A438GLU-1-0.867-0.91737.705-0.032-0.0320.0000.0000.0000.000
158A439VAL00.0060.02140.6850.0000.0000.0000.0000.0000.000
159A440ALA00.0340.00635.7180.0000.0000.0000.0000.0000.000
160A441LYS10.8380.92137.5230.0310.0310.0000.0000.0000.000
161A442ASP-1-0.906-0.95438.495-0.032-0.0320.0000.0000.0000.000
162A443PHE0-0.112-0.05039.4810.0020.0020.0000.0000.0000.000
163A444PRO00.0260.02235.942-0.001-0.0010.0000.0000.0000.000
164A445GLU-1-0.846-0.92434.959-0.039-0.0390.0000.0000.0000.000
165A446TYR0-0.045-0.02735.5300.0010.0010.0000.0000.0000.000
166A447THR00.0050.01029.700-0.003-0.0030.0000.0000.0000.000
167A448PHE00.0420.03332.8250.0030.0030.0000.0000.0000.000
168A449ALA0-0.032-0.01730.646-0.004-0.0040.0000.0000.0000.000
169A450ILE0-0.0110.01032.0280.0030.0030.0000.0000.0000.000
170A451ALA0-0.008-0.02531.634-0.003-0.0030.0000.0000.0000.000
171A452ASP-1-0.785-0.90432.289-0.027-0.0270.0000.0000.0000.000
172A453GLU-1-0.905-0.97534.004-0.022-0.0220.0000.0000.0000.000
173A454GLU-1-0.955-0.97035.641-0.019-0.0190.0000.0000.0000.000
174A455ASP-1-0.871-0.92229.588-0.032-0.0320.0000.0000.0000.000
175A456TYR0-0.105-0.09229.0080.0000.0000.0000.0000.0000.000
176A457ALA00.0790.04834.5940.0010.0010.0000.0000.0000.000
177A458THR0-0.112-0.06835.4620.0010.0010.0000.0000.0000.000
178A459GLU-1-0.734-0.80534.201-0.028-0.0280.0000.0000.0000.000
179A460VAL00.0450.01237.2560.0000.0000.0000.0000.0000.000
180A461LYS10.9050.95040.0490.0160.0160.0000.0000.0000.000
181A462ASP-1-0.932-0.96439.345-0.016-0.0160.0000.0000.0000.000
182A463LEU0-0.115-0.05538.6890.0000.0000.0000.0000.0000.000
183A464GLY0-0.050-0.03142.6950.0000.0000.0000.0000.0000.000
184A465LEU00.0180.01042.2820.0000.0000.0000.0000.0000.000
185A466SER0-0.074-0.03043.9510.0000.0000.0000.0000.0000.000
186A467GLU-1-0.933-0.97845.109-0.015-0.0150.0000.0000.0000.000
187A468SER0-0.0100.00646.2860.0000.0000.0000.0000.0000.000
188A469GLY0-0.013-0.00548.1840.0000.0000.0000.0000.0000.000
189A470GLY0-0.019-0.00347.7780.0000.0000.0000.0000.0000.000
190A471ASP-1-0.899-0.95243.975-0.019-0.0190.0000.0000.0000.000
191A472VAL0-0.063-0.03440.843-0.001-0.0010.0000.0000.0000.000
192A473ASN00.0230.03041.4560.0010.0010.0000.0000.0000.000
193A474ALA00.018-0.00140.273-0.002-0.0020.0000.0000.0000.000
194A475ALA00.0350.02338.8810.0010.0010.0000.0000.0000.000
195A476ILE0-0.040-0.01038.515-0.002-0.0020.0000.0000.0000.000
196A477LEU0-0.020-0.01433.3580.0020.0020.0000.0000.0000.000
197A478ASP-1-0.786-0.92036.430-0.028-0.0280.0000.0000.0000.000
198A479GLU-1-0.910-0.98234.267-0.038-0.0380.0000.0000.0000.000
199A480SER0-0.094-0.03535.4960.0000.0000.0000.0000.0000.000
200A481GLY0-0.0210.00236.2810.0010.0010.0000.0000.0000.000
201A482LYS10.8840.95037.2030.0210.0210.0000.0000.0000.000
202A483LYS10.9850.99235.1620.0230.0230.0000.0000.0000.000
203A484PHE0-0.018-0.01140.7680.0020.0020.0000.0000.0000.000
204A485ALA00.0840.04442.448-0.001-0.0010.0000.0000.0000.000
205A486MET0-0.080-0.04244.0610.0000.0000.0000.0000.0000.000
206A487GLU-1-0.918-0.96745.910-0.016-0.0160.0000.0000.0000.000
207A488PRO0-0.026-0.01147.7390.0000.0000.0000.0000.0000.000
208A489GLU-1-0.913-0.95248.736-0.018-0.0180.0000.0000.0000.000
209A490GLU-1-0.985-0.99848.783-0.017-0.0170.0000.0000.0000.000
210A491PHE00.0140.01641.620-0.001-0.0010.0000.0000.0000.000
211A492ASP-1-0.842-0.94546.140-0.021-0.0210.0000.0000.0000.000
212A493SER0-0.051-0.05943.2450.0000.0000.0000.0000.0000.000
213A494ASP-1-0.893-0.93245.421-0.023-0.0230.0000.0000.0000.000
214A495ALA00.1030.07447.6990.0000.0000.0000.0000.0000.000
215A496LEU0-0.040-0.02440.162-0.001-0.0010.0000.0000.0000.000
216A497ARG10.8710.91444.5750.0270.0270.0000.0000.0000.000
217A498GLU-1-0.967-0.98245.734-0.020-0.0200.0000.0000.0000.000
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