FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: Z6RRN

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:


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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2839239.283765
FMO2-HF: Nuclear repulsion 2748060.324564
FMO2-HF: Total energy -91178.959202
FMO2-MP2: Total energy -91448.060219


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.
-0.1491.7340.025-0.732-1.1760
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 : 0.052 / q_NPA : 0.009
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].
3A284PRO0-0.0170.0123.670-0.5280.6700.004-0.496-0.7060.000
4A285SER00.0160.0276.1340.5310.5310.0000.0000.0000.000
5A286LYS10.9430.9547.094-0.568-0.5680.0000.0000.0000.000
6A287GLU-1-0.873-0.9448.3450.0160.0160.0000.0000.0000.000
7A288ILE0-0.025-0.00811.4910.0720.0720.0000.0000.0000.000
8A289LEU00.0210.00213.905-0.013-0.0130.0000.0000.0000.000
9A290THR0-0.008-0.01016.765-0.004-0.0040.0000.0000.0000.000
10A291LEU00.0100.01219.801-0.006-0.0060.0000.0000.0000.000
11A292LYS10.9690.97322.239-0.064-0.0640.0000.0000.0000.000
12A293GLN0-0.039-0.00815.8370.0230.0230.0000.0000.0000.000
13A294VAL00.0320.01118.952-0.008-0.0080.0000.0000.0000.000
14A295GLN0-0.053-0.03320.3190.0010.0010.0000.0000.0000.000
15A296GLU-1-0.845-0.90718.4160.0810.0810.0000.0000.0000.000
16A297PHE0-0.011-0.01714.480-0.008-0.0080.0000.0000.0000.000
17A298LEU0-0.027-0.00920.140-0.007-0.0070.0000.0000.0000.000
18A299LYS10.8330.90723.591-0.007-0.0070.0000.0000.0000.000
19A300ASP-1-0.867-0.93522.1100.0360.0360.0000.0000.0000.000
20A301GLY0-0.0060.00720.7090.0000.0000.0000.0000.0000.000
21A302ASP-1-0.890-0.94420.449-0.009-0.0090.0000.0000.0000.000
22A303ASH0-0.050-0.05518.229-0.012-0.0120.0000.0000.0000.000
23A304VAL0-0.0080.01218.6220.0020.0020.0000.0000.0000.000
24A305VAL00.0000.00517.368-0.010-0.0100.0000.0000.0000.000
25A306ILE00.005-0.00115.1930.0000.0000.0000.0000.0000.000
26A307LEU0-0.006-0.00615.037-0.027-0.0270.0000.0000.0000.000
27A308GLY00.0200.01515.3180.0100.0100.0000.0000.0000.000
28A309VAL0-0.007-0.01216.7370.0170.0170.0000.0000.0000.000
29A310PHE00.0020.00415.807-0.010-0.0100.0000.0000.0000.000
30A311GLN0-0.028-0.04919.2810.0330.0330.0000.0000.0000.000
31A312GLY00.0130.00317.4700.0270.0270.0000.0000.0000.000
32A313VAL0-0.008-0.00211.407-0.033-0.0330.0000.0000.0000.000
33A314GLY00.0290.01113.090-0.060-0.0600.0000.0000.0000.000
34A315ASP-1-0.828-0.88615.746-0.169-0.1690.0000.0000.0000.000
35A316PRO00.030-0.00516.606-0.044-0.0440.0000.0000.0000.000
36A317GLY00.0350.01817.823-0.023-0.0230.0000.0000.0000.000
37A318TYR0-0.064-0.0359.974-0.098-0.0980.0000.0000.0000.000
38A319LEU0-0.012-0.00912.452-0.094-0.0940.0000.0000.0000.000
39A320GLN00.001-0.00512.931-0.110-0.1100.0000.0000.0000.000
40A321TYR0-0.019-0.03912.815-0.025-0.0250.0000.0000.0000.000
41A322GLN00.0220.0017.809-0.209-0.2090.0000.0000.0000.000
42A323ASP-1-0.849-0.9109.749-0.625-0.6250.0000.0000.0000.000
43A324ALA00.004-0.01311.5950.0290.0290.0000.0000.0000.000
44A325ALA00.0250.01110.1670.0320.0320.0000.0000.0000.000
45A326ASN0-0.035-0.0296.592-0.046-0.0460.0000.0000.0000.000
46A327THR0-0.038-0.0268.9970.1460.1460.0000.0000.0000.000
47A328LEU00.0610.04012.0430.0700.0700.0000.0000.0000.000
48A329ARG10.8230.9123.2111.1421.8270.021-0.236-0.4700.000
49A330GLU-1-0.916-0.9699.989-0.009-0.0090.0000.0000.0000.000
50A331ASP-1-0.876-0.89712.013-0.090-0.0900.0000.0000.0000.000
51A332TYR00.0340.02913.5400.0170.0170.0000.0000.0000.000
52A333LYS10.8400.9199.7010.1570.1570.0000.0000.0000.000
53A334PHE00.0690.03710.1340.0060.0060.0000.0000.0000.000
54A335HIS00.0110.01210.291-0.064-0.0640.0000.0000.0000.000
55A336HIS00.0080.0178.6990.0340.0340.0000.0000.0000.000
56A337THR00.0190.00113.7430.0500.0500.0000.0000.0000.000
57A338PHE00.0470.03913.092-0.026-0.0260.0000.0000.0000.000
58A339SER00.0170.01818.2520.0130.0130.0000.0000.0000.000
59A340THR00.043-0.00320.653-0.005-0.0050.0000.0000.0000.000
60A341GLU-1-0.926-0.95723.4210.0230.0230.0000.0000.0000.000
61A342ILE00.0320.01319.026-0.002-0.0020.0000.0000.0000.000
62A343ALA00.0170.01722.960-0.005-0.0050.0000.0000.0000.000
63A344LYS10.9190.95824.1520.0160.0160.0000.0000.0000.000
64A345PHE0-0.032-0.01624.3330.0020.0020.0000.0000.0000.000
65A346LEU0-0.023-0.01921.3960.0010.0010.0000.0000.0000.000
66A347LYS10.9180.96426.0840.0200.0200.0000.0000.0000.000
67A348VAL00.0040.01523.859-0.003-0.0030.0000.0000.0000.000
68A349SER0-0.039-0.03026.4510.0060.0060.0000.0000.0000.000
69A350LEU0-0.007-0.01121.798-0.004-0.0040.0000.0000.0000.000
70A351GLY00.0290.01921.7950.0070.0070.0000.0000.0000.000
71A352LYS10.8010.88921.3630.1020.1020.0000.0000.0000.000
72A353LEU0-0.0110.00617.319-0.021-0.0210.0000.0000.0000.000
73A354VAL00.0100.00219.6070.0180.0180.0000.0000.0000.000
74A355LEU00.0170.01419.549-0.017-0.0170.0000.0000.0000.000
75A356MET0-0.018-0.01520.7610.0170.0170.0000.0000.0000.000
76A357GLN00.0580.03522.0320.0010.0010.0000.0000.0000.000
77A358PRO00.0300.02222.1940.0040.0040.0000.0000.0000.000
78A359GLU-1-0.859-0.91724.787-0.004-0.0040.0000.0000.0000.000
79A360LYS10.7600.87324.941-0.004-0.0040.0000.0000.0000.000
80A361PHE00.000-0.00824.9830.0010.0010.0000.0000.0000.000
81A362GLN00.0020.02426.772-0.001-0.0010.0000.0000.0000.000
82A363SER00.001-0.04930.3970.0040.0040.0000.0000.0000.000
83A364LYS10.8350.90734.1540.0170.0170.0000.0000.0000.000
84A365TYR0-0.060-0.04935.8200.0000.0000.0000.0000.0000.000
85A366GLU-1-0.763-0.83230.448-0.044-0.0440.0000.0000.0000.000
86A367PRO0-0.0240.00629.5730.0040.0040.0000.0000.0000.000
87A368ARG10.8780.91429.0070.0220.0220.0000.0000.0000.000
88A369MET0-0.025-0.00624.939-0.003-0.0030.0000.0000.0000.000
89A370HIS00.0110.02424.9950.0090.0090.0000.0000.0000.000
90A371VAL00.007-0.00924.149-0.008-0.0080.0000.0000.0000.000
91A372MET0-0.0150.01921.9330.0090.0090.0000.0000.0000.000
92A373ASP-1-0.797-0.88323.373-0.113-0.1130.0000.0000.0000.000
93A374VAL0-0.053-0.02318.420-0.010-0.0100.0000.0000.0000.000
94A375GLN00.036-0.00121.3810.0040.0040.0000.0000.0000.000
95A376GLY00.019-0.00420.076-0.012-0.0120.0000.0000.0000.000
96A377SER00.0220.01821.161-0.006-0.0060.0000.0000.0000.000
97A378THR0-0.044-0.01121.4310.0120.0120.0000.0000.0000.000
98A379GLU-1-0.841-0.89120.419-0.203-0.2030.0000.0000.0000.000
99A380ALA00.0360.00315.7240.0080.0080.0000.0000.0000.000
100A381SER0-0.043-0.02917.820-0.008-0.0080.0000.0000.0000.000
101A382ALA00.0960.04520.1550.0040.0040.0000.0000.0000.000
102A383ILE0-0.052-0.02717.0730.0090.0090.0000.0000.0000.000
103A384LYS10.8210.90314.7170.3480.3480.0000.0000.0000.000
104A385ASP-1-0.870-0.93218.682-0.148-0.1480.0000.0000.0000.000
105A386TYR0-0.072-0.06322.1530.0200.0200.0000.0000.0000.000
106A387VAL0-0.011-0.01117.0300.0110.0110.0000.0000.0000.000
107A388VAL00.0350.01519.9400.0160.0160.0000.0000.0000.000
108A389LYS10.8600.93521.9000.1040.1040.0000.0000.0000.000
109A390HIS0-0.049-0.02923.8030.0210.0210.0000.0000.0000.000
110A391ALA00.0170.01621.1410.0040.0040.0000.0000.0000.000
111A392LEU0-0.0270.00322.5090.0070.0070.0000.0000.0000.000
112A393PRO0-0.0120.00725.663-0.002-0.0020.0000.0000.0000.000
113A394LEU0-0.036-0.02828.3600.0000.0000.0000.0000.0000.000
114A395VAL00.0170.00731.5260.0020.0020.0000.0000.0000.000
115A396GLY00.0150.00828.1340.0010.0010.0000.0000.0000.000
116A397HIS0-0.006-0.00227.1890.0010.0010.0000.0000.0000.000
117A398ARG10.7830.88026.5700.0200.0200.0000.0000.0000.000
118A399LYS10.8810.93623.1650.0110.0110.0000.0000.0000.000
119A400THR00.014-0.01925.730-0.004-0.0040.0000.0000.0000.000
120A401SER0-0.056-0.02121.472-0.003-0.0030.0000.0000.0000.000
121A402ASN0-0.034-0.04220.890-0.002-0.0020.0000.0000.0000.000
122A403ASP-1-0.772-0.86822.365-0.034-0.0340.0000.0000.0000.000
123A404ALA00.0350.02322.775-0.006-0.0060.0000.0000.0000.000
124A405LYS10.8180.89115.2530.0710.0710.0000.0000.0000.000
125A406ARG0-0.0280.01116.815-0.005-0.0050.0000.0000.0000.000
126A407TYR00.0030.00122.989-0.001-0.0010.0000.0000.0000.000
127A408SER00.0410.01424.7330.0070.0070.0000.0000.0000.000
128A409LYS10.8510.94227.1220.0580.0580.0000.0000.0000.000
129A410ARG10.8300.91929.1760.0450.0450.0000.0000.0000.000
130A411PRO00.0440.01132.949-0.003-0.0030.0000.0000.0000.000
131A412LEU0-0.066-0.02230.416-0.003-0.0030.0000.0000.0000.000
132A413VAL00.0150.01834.2250.0030.0030.0000.0000.0000.000
133A414VAL0-0.044-0.02233.234-0.002-0.0020.0000.0000.0000.000
134A415VAL00.0050.00335.6430.0010.0010.0000.0000.0000.000
135A416TYR0-0.045-0.05634.858-0.001-0.0010.0000.0000.0000.000
136A417TYR00.0640.02236.251-0.001-0.0010.0000.0000.0000.000
137A418SER00.0510.04436.4770.0000.0000.0000.0000.0000.000
138A419VAL0-0.082-0.03531.659-0.001-0.0010.0000.0000.0000.000
139A420ASP-1-0.723-0.83432.2460.0190.0190.0000.0000.0000.000
140A421PHE0-0.035-0.03229.366-0.003-0.0030.0000.0000.0000.000
141A422SER0-0.053-0.05231.1480.0020.0020.0000.0000.0000.000
142A423PHE0-0.045-0.04532.496-0.003-0.0030.0000.0000.0000.000
143A424ASP-1-0.871-0.93734.6700.0190.0190.0000.0000.0000.000
144A425TYR00.0260.02136.212-0.002-0.0020.0000.0000.0000.000
145A426ARG10.8660.95432.798-0.016-0.0160.0000.0000.0000.000
146A427THR0-0.009-0.01335.200-0.003-0.0030.0000.0000.0000.000
147A428ALA00.0340.02338.497-0.002-0.0020.0000.0000.0000.000
148A429THR00.013-0.00533.349-0.002-0.0020.0000.0000.0000.000
149A430GLN00.016-0.00332.134-0.005-0.0050.0000.0000.0000.000
150A431PHE00.0010.01936.835-0.003-0.0030.0000.0000.0000.000
151A432TRP00.1060.06138.913-0.002-0.0020.0000.0000.0000.000
152A433ARG10.8430.91731.3520.0210.0210.0000.0000.0000.000
153A434ASN0-0.078-0.06736.860-0.004-0.0040.0000.0000.0000.000
154A435LYS10.8310.93338.9860.0060.0060.0000.0000.0000.000
155A436VAL00.0610.04036.304-0.001-0.0010.0000.0000.0000.000
156A437LEU0-0.026-0.01833.725-0.002-0.0020.0000.0000.0000.000
157A438GLU-1-0.804-0.88037.630-0.022-0.0220.0000.0000.0000.000
158A439VAL00.0210.02740.486-0.001-0.0010.0000.0000.0000.000
159A440ALA00.0160.00335.445-0.002-0.0020.0000.0000.0000.000
160A441LYS10.7330.86537.2860.0210.0210.0000.0000.0000.000
161A442ASP-1-0.814-0.87838.367-0.026-0.0260.0000.0000.0000.000
162A443PHE0-0.055-0.01939.4560.0010.0010.0000.0000.0000.000
163A444PRO00.0470.02535.688-0.001-0.0010.0000.0000.0000.000
164A445GLU-1-0.824-0.89934.793-0.042-0.0420.0000.0000.0000.000
165A446TYR0-0.017-0.00935.244-0.002-0.0020.0000.0000.0000.000
166A447THR0-0.013-0.00329.625-0.003-0.0030.0000.0000.0000.000
167A448PHE00.0310.01232.4360.0040.0040.0000.0000.0000.000
168A449ALA0-0.043-0.01830.591-0.003-0.0030.0000.0000.0000.000
169A450ILE0-0.0090.00631.7890.0020.0020.0000.0000.0000.000
170A451ALA00.010-0.00931.272-0.002-0.0020.0000.0000.0000.000
171A452ASP-1-0.774-0.89331.8210.0050.0050.0000.0000.0000.000
172A453GLU-1-0.892-0.96633.555-0.001-0.0010.0000.0000.0000.000
173A454GLU-1-0.948-0.96635.0620.0110.0110.0000.0000.0000.000
174A455ASP-1-0.867-0.90829.038-0.001-0.0010.0000.0000.0000.000
175A456TYR0-0.050-0.04528.644-0.002-0.0020.0000.0000.0000.000
176A457ALA00.0480.04233.959-0.002-0.0020.0000.0000.0000.000
177A458THR0-0.056-0.04234.7960.0000.0000.0000.0000.0000.000
178A459GLU-1-0.754-0.83834.319-0.020-0.0200.0000.0000.0000.000
179A460VAL00.0510.01737.028-0.001-0.0010.0000.0000.0000.000
180A461LYS10.8460.90739.6060.0040.0040.0000.0000.0000.000
181A462ASP-1-0.882-0.93038.991-0.007-0.0070.0000.0000.0000.000
182A463LEU0-0.073-0.04038.305-0.002-0.0020.0000.0000.0000.000
183A464GLY0-0.068-0.02442.050-0.001-0.0010.0000.0000.0000.000
184A465LEU00.0290.01641.7350.0000.0000.0000.0000.0000.000
185A466SER0-0.059-0.01042.9400.0010.0010.0000.0000.0000.000
186A467GLU-1-0.915-0.96744.527-0.004-0.0040.0000.0000.0000.000
187A468SER0-0.017-0.01045.4890.0010.0010.0000.0000.0000.000
188A469GLY0-0.016-0.00648.0080.0010.0010.0000.0000.0000.000
189A470GLY00.002-0.00747.6590.0000.0000.0000.0000.0000.000
190A471ASP-1-0.947-0.96444.1480.0000.0000.0000.0000.0000.000
191A472VAL0-0.051-0.03640.6740.0000.0000.0000.0000.0000.000
192A473ASN00.0220.03041.316-0.001-0.0010.0000.0000.0000.000
193A474ALA00.000-0.01339.916-0.001-0.0010.0000.0000.0000.000
194A475ALA00.0260.01838.4940.0010.0010.0000.0000.0000.000
195A476ILE0-0.041-0.01937.994-0.002-0.0020.0000.0000.0000.000
196A477LEU00.0040.00933.2470.0010.0010.0000.0000.0000.000
197A478ASP-1-0.731-0.87136.145-0.032-0.0320.0000.0000.0000.000
198A479GLU-1-0.897-0.97734.940-0.044-0.0440.0000.0000.0000.000
199A480SER0-0.120-0.05236.041-0.001-0.0010.0000.0000.0000.000
200A481GLY00.0010.01135.6440.0010.0010.0000.0000.0000.000
201A482LYS10.8050.89136.5460.0300.0300.0000.0000.0000.000
202A483LYS10.9050.93534.9390.0190.0190.0000.0000.0000.000
203A484PHE0-0.029-0.01240.1360.0010.0010.0000.0000.0000.000
204A485ALA00.0830.03641.723-0.001-0.0010.0000.0000.0000.000
205A486MET0-0.074-0.02943.762-0.001-0.0010.0000.0000.0000.000
206A487GLU-1-0.892-0.95645.566-0.009-0.0090.0000.0000.0000.000
207A488PRO0-0.024-0.01547.6220.0000.0000.0000.0000.0000.000
208A489GLU-1-0.939-0.96048.503-0.010-0.0100.0000.0000.0000.000
209A490GLU-1-0.971-0.99048.674-0.004-0.0040.0000.0000.0000.000
210A491PHE0-0.015-0.00541.182-0.001-0.0010.0000.0000.0000.000
211A492ASP-1-0.823-0.92545.875-0.011-0.0110.0000.0000.0000.000
212A493SER0-0.036-0.04843.234-0.001-0.0010.0000.0000.0000.000
213A494ASP-1-0.922-0.96045.225-0.017-0.0170.0000.0000.0000.000
214A495ALA00.0450.03847.689-0.001-0.0010.0000.0000.0000.000
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