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

tag_button

FMODB ID: 6NLLZ

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 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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2836604.267003
FMO2-HF: Nuclear repulsion 2745426.150993
FMO2-HF: Total energy -91178.11601
FMO2-MP2: Total energy -91447.366501


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.
0.2242.0720.02-0.593-1.2750.002
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 : 0.039 / q_NPA : 0.000
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].
3A284PRO00.0050.0143.781-0.1420.927-0.010-0.331-0.7270.001
4A285SER0-0.0130.0116.0540.3270.3270.0000.0000.0000.000
5A286LYS10.9370.9517.6270.2740.2740.0000.0000.0000.000
6A287GLU-1-0.918-0.9628.7350.0830.0830.0000.0000.0000.000
7A288ILE0-0.029-0.00711.6800.0000.0000.0000.0000.0000.000
8A289LEU00.0200.00514.2980.0100.0100.0000.0000.0000.000
9A290THR00.013-0.00617.1010.0020.0020.0000.0000.0000.000
10A291LEU00.0410.01420.108-0.009-0.0090.0000.0000.0000.000
11A292LYS10.9640.97222.6770.0140.0140.0000.0000.0000.000
12A293GLN0-0.0160.01916.014-0.001-0.0010.0000.0000.0000.000
13A294VAL00.0240.00719.259-0.007-0.0070.0000.0000.0000.000
14A295GLN0-0.049-0.04020.5680.0000.0000.0000.0000.0000.000
15A296GLU-1-0.844-0.92218.853-0.068-0.0680.0000.0000.0000.000
16A297PHE0-0.004-0.00614.602-0.004-0.0040.0000.0000.0000.000
17A298LEU0-0.045-0.01620.3770.0010.0010.0000.0000.0000.000
18A299LYS10.8170.89923.7070.0390.0390.0000.0000.0000.000
19A300ASP-1-0.893-0.95022.114-0.047-0.0470.0000.0000.0000.000
20A301GLY0-0.059-0.00520.746-0.002-0.0020.0000.0000.0000.000
21A302ASP-1-0.887-0.95519.974-0.063-0.0630.0000.0000.0000.000
22A303ASH0-0.063-0.06717.809-0.002-0.0020.0000.0000.0000.000
23A304VAL00.0170.02618.394-0.001-0.0010.0000.0000.0000.000
24A305VAL0-0.013-0.00517.735-0.011-0.0110.0000.0000.0000.000
25A306ILE00.0010.00215.2650.0100.0100.0000.0000.0000.000
26A307LEU0-0.019-0.01215.314-0.021-0.0210.0000.0000.0000.000
27A308GLY00.0270.01815.4560.0110.0110.0000.0000.0000.000
28A309VAL0-0.021-0.01216.7400.0070.0070.0000.0000.0000.000
29A310PHE00.0090.01116.310-0.003-0.0030.0000.0000.0000.000
30A311GLN0-0.014-0.03319.2870.0160.0160.0000.0000.0000.000
31A312GLY00.0150.00017.5530.0150.0150.0000.0000.0000.000
32A313VAL00.0120.00711.756-0.024-0.0240.0000.0000.0000.000
33A314GLY00.0190.01113.590-0.018-0.0180.0000.0000.0000.000
34A315ASP-1-0.846-0.90716.133-0.070-0.0700.0000.0000.0000.000
35A316PRO00.0640.01516.684-0.023-0.0230.0000.0000.0000.000
36A317GLY00.0290.01917.345-0.020-0.0200.0000.0000.0000.000
37A318TYR0-0.040-0.03110.393-0.050-0.0500.0000.0000.0000.000
38A319LEU0-0.028-0.01312.131-0.058-0.0580.0000.0000.0000.000
39A320GLN0-0.0010.00112.806-0.074-0.0740.0000.0000.0000.000
40A321TYR0-0.053-0.04913.009-0.020-0.0200.0000.0000.0000.000
41A322GLN00.009-0.0058.137-0.189-0.1890.0000.0000.0000.000
42A323ASP-1-0.905-0.9409.386-0.414-0.4140.0000.0000.0000.000
43A324ALA00.019-0.01411.2150.0160.0160.0000.0000.0000.000
44A325ALA0-0.016-0.00610.2100.0270.0270.0000.0000.0000.000
45A326ASN0-0.007-0.0135.9760.0300.0300.0000.0000.0000.000
46A327THR0-0.039-0.0148.3520.1590.1590.0000.0000.0000.000
47A328LEU00.0350.03211.4070.0520.0520.0000.0000.0000.000
48A329ARG10.8540.9283.3380.1600.9390.030-0.262-0.5480.001
49A330GLU-1-0.939-0.97210.2890.1320.1320.0000.0000.0000.000
50A331ASP-1-0.872-0.90312.350-0.043-0.0430.0000.0000.0000.000
51A332TYR00.0300.02513.463-0.006-0.0060.0000.0000.0000.000
52A333LYS10.8480.9299.5350.1160.1160.0000.0000.0000.000
53A334PHE00.0880.04010.2480.0080.0080.0000.0000.0000.000
54A335HIS00.0080.01210.402-0.053-0.0530.0000.0000.0000.000
55A336HIS00.0190.0189.2400.0580.0580.0000.0000.0000.000
56A337THR00.0240.00213.9810.0250.0250.0000.0000.0000.000
57A338PHE00.0670.04013.137-0.013-0.0130.0000.0000.0000.000
58A339SER00.0060.02318.6760.0100.0100.0000.0000.0000.000
59A340THR00.0600.00621.317-0.007-0.0070.0000.0000.0000.000
60A341GLU-1-0.946-0.96524.430-0.012-0.0120.0000.0000.0000.000
61A342ILE00.0280.00719.702-0.002-0.0020.0000.0000.0000.000
62A343ALA00.0200.01923.509-0.003-0.0030.0000.0000.0000.000
63A344LYS10.9140.94524.6210.0090.0090.0000.0000.0000.000
64A345PHE0-0.034-0.01224.9470.0000.0000.0000.0000.0000.000
65A346LEU0-0.034-0.02121.764-0.001-0.0010.0000.0000.0000.000
66A347LYS10.9250.96526.4270.0220.0220.0000.0000.0000.000
67A348VAL00.0150.02323.961-0.001-0.0010.0000.0000.0000.000
68A349SER0-0.021-0.01226.9520.0030.0030.0000.0000.0000.000
69A350LEU0-0.030-0.02622.299-0.004-0.0040.0000.0000.0000.000
70A351GLY00.002-0.00821.6370.0030.0030.0000.0000.0000.000
71A352LYS10.8210.90021.5600.0510.0510.0000.0000.0000.000
72A353LEU0-0.0130.01517.661-0.011-0.0110.0000.0000.0000.000
73A354VAL00.002-0.00719.8470.0120.0120.0000.0000.0000.000
74A355LEU00.0260.02119.634-0.012-0.0120.0000.0000.0000.000
75A356MET0-0.024-0.01220.9670.0120.0120.0000.0000.0000.000
76A357GLN00.0510.02122.186-0.007-0.0070.0000.0000.0000.000
77A358PRO00.0400.02822.2680.0040.0040.0000.0000.0000.000
78A359GLU-1-0.844-0.91724.815-0.033-0.0330.0000.0000.0000.000
79A360LYS10.8180.91924.9930.0520.0520.0000.0000.0000.000
80A361PHE00.015-0.00224.5910.0020.0020.0000.0000.0000.000
81A362GLN0-0.0210.01426.9060.0040.0040.0000.0000.0000.000
82A363SER00.019-0.03730.5450.0030.0030.0000.0000.0000.000
83A364LYS10.8310.89634.1330.0220.0220.0000.0000.0000.000
84A365TYR0-0.079-0.07436.0470.0010.0010.0000.0000.0000.000
85A366GLU-1-0.776-0.82630.332-0.040-0.0400.0000.0000.0000.000
86A367PRO0-0.0150.00629.9030.0010.0010.0000.0000.0000.000
87A368ARG10.8880.92728.8020.0320.0320.0000.0000.0000.000
88A369MET0-0.049-0.03025.385-0.004-0.0040.0000.0000.0000.000
89A370HIS00.0050.02325.1260.0060.0060.0000.0000.0000.000
90A371VAL00.0270.00124.338-0.006-0.0060.0000.0000.0000.000
91A372MET0-0.046-0.00521.5970.0060.0060.0000.0000.0000.000
92A373ASP-1-0.810-0.89623.576-0.055-0.0550.0000.0000.0000.000
93A374VAL0-0.042-0.02518.570-0.006-0.0060.0000.0000.0000.000
94A375GLN0-0.003-0.01921.6620.0060.0060.0000.0000.0000.000
95A376GLY00.021-0.00319.992-0.010-0.0100.0000.0000.0000.000
96A377SER00.0230.00420.752-0.006-0.0060.0000.0000.0000.000
97A378THR0-0.0180.00820.8950.0050.0050.0000.0000.0000.000
98A379GLU-1-0.828-0.89720.051-0.092-0.0920.0000.0000.0000.000
99A380ALA00.0320.00815.3600.0020.0020.0000.0000.0000.000
100A381SER0-0.041-0.03117.431-0.006-0.0060.0000.0000.0000.000
101A382ALA00.0970.05319.4870.0050.0050.0000.0000.0000.000
102A383ILE0-0.046-0.02416.7180.0040.0040.0000.0000.0000.000
103A384LYS10.8840.93414.4830.1590.1590.0000.0000.0000.000
104A385ASP-1-0.855-0.93018.108-0.069-0.0690.0000.0000.0000.000
105A386TYR0-0.048-0.02821.8120.0080.0080.0000.0000.0000.000
106A387VAL0-0.029-0.02717.0400.0040.0040.0000.0000.0000.000
107A388VAL00.0230.01619.4740.0060.0060.0000.0000.0000.000
108A389LYS10.8890.95721.7090.0560.0560.0000.0000.0000.000
109A390HIS0-0.063-0.05223.9070.0110.0110.0000.0000.0000.000
110A391ALA00.0250.02620.6420.0000.0000.0000.0000.0000.000
111A392LEU0-0.0230.00422.5050.0000.0000.0000.0000.0000.000
112A393PRO0-0.032-0.00325.2760.0010.0010.0000.0000.0000.000
113A394LEU00.006-0.00428.0040.0010.0010.0000.0000.0000.000
114A395VAL0-0.015-0.00231.4030.0020.0020.0000.0000.0000.000
115A396GLY00.0150.01727.893-0.001-0.0010.0000.0000.0000.000
116A397HIS00.008-0.00427.2460.0010.0010.0000.0000.0000.000
117A398ARG10.7770.87826.6380.0230.0230.0000.0000.0000.000
118A399LYS10.8640.93122.6870.0520.0520.0000.0000.0000.000
119A400THR00.0510.00126.104-0.001-0.0010.0000.0000.0000.000
120A401SER0-0.063-0.02621.7200.0010.0010.0000.0000.0000.000
121A402ASN0-0.021-0.02621.4350.0020.0020.0000.0000.0000.000
122A403ASP-1-0.787-0.87722.738-0.027-0.0270.0000.0000.0000.000
123A404ALA00.0290.02423.0730.0000.0000.0000.0000.0000.000
124A405LYS10.8410.89315.5360.0080.0080.0000.0000.0000.000
125A406ARG0-0.0180.02117.040-0.005-0.0050.0000.0000.0000.000
126A407TYR00.0090.01023.268-0.001-0.0010.0000.0000.0000.000
127A408SER00.0510.01724.9920.0040.0040.0000.0000.0000.000
128A409LYS10.9160.97327.3670.0370.0370.0000.0000.0000.000
129A410ARG10.8300.92329.3480.0270.0270.0000.0000.0000.000
130A411PRO00.014-0.00733.119-0.001-0.0010.0000.0000.0000.000
131A412LEU0-0.051-0.01630.827-0.002-0.0020.0000.0000.0000.000
132A413VAL0-0.009-0.00534.3360.0020.0020.0000.0000.0000.000
133A414VAL0-0.045-0.02433.462-0.002-0.0020.0000.0000.0000.000
134A415VAL00.007-0.00135.7100.0010.0010.0000.0000.0000.000
135A416TYR0-0.040-0.05635.145-0.001-0.0010.0000.0000.0000.000
136A417TYR00.0440.00236.1490.0000.0000.0000.0000.0000.000
137A418SER00.0720.06436.666-0.001-0.0010.0000.0000.0000.000
138A419VAL0-0.087-0.04031.5680.0000.0000.0000.0000.0000.000
139A420ASP-1-0.749-0.85732.419-0.030-0.0300.0000.0000.0000.000
140A421PHE0-0.035-0.04129.2830.0010.0010.0000.0000.0000.000
141A422SER0-0.037-0.03531.336-0.001-0.0010.0000.0000.0000.000
142A423PHE0-0.062-0.06232.3760.0010.0010.0000.0000.0000.000
143A424ASP-1-0.880-0.94634.745-0.020-0.0200.0000.0000.0000.000
144A425TYR00.0180.01835.9610.0020.0020.0000.0000.0000.000
145A426ARG10.9190.98832.2950.0270.0270.0000.0000.0000.000
146A427THR0-0.031-0.02735.386-0.001-0.0010.0000.0000.0000.000
147A428ALA00.0520.02538.5990.0000.0000.0000.0000.0000.000
148A429THR00.0410.03233.4350.0000.0000.0000.0000.0000.000
149A430GLN0-0.003-0.02332.1480.0000.0000.0000.0000.0000.000
150A431PHE0-0.0350.00136.7750.0000.0000.0000.0000.0000.000
151A432TRP00.0780.03238.8630.0000.0000.0000.0000.0000.000
152A433ARG10.8380.92231.2800.0350.0350.0000.0000.0000.000
153A434ASN0-0.093-0.06636.811-0.001-0.0010.0000.0000.0000.000
154A435LYS10.9280.99438.9980.0180.0180.0000.0000.0000.000
155A436VAL00.0490.03036.2890.0000.0000.0000.0000.0000.000
156A437LEU0-0.037-0.02133.7440.0000.0000.0000.0000.0000.000
157A438GLU-1-0.779-0.85737.611-0.022-0.0220.0000.0000.0000.000
158A439VAL00.0140.03240.5880.0010.0010.0000.0000.0000.000
159A440ALA00.0270.00635.6180.0000.0000.0000.0000.0000.000
160A441LYS10.7490.86737.4210.0210.0210.0000.0000.0000.000
161A442ASP-1-0.825-0.88838.391-0.021-0.0210.0000.0000.0000.000
162A443PHE0-0.078-0.03639.3620.0010.0010.0000.0000.0000.000
163A444PRO00.0290.02435.824-0.001-0.0010.0000.0000.0000.000
164A445GLU-1-0.844-0.91034.894-0.026-0.0260.0000.0000.0000.000
165A446TYR0-0.042-0.02835.4740.0010.0010.0000.0000.0000.000
166A447THR00.0010.01129.504-0.002-0.0020.0000.0000.0000.000
167A448PHE00.0500.03232.6920.0020.0020.0000.0000.0000.000
168A449ALA0-0.022-0.01330.518-0.002-0.0020.0000.0000.0000.000
169A450ILE0-0.0140.00831.9170.0020.0020.0000.0000.0000.000
170A451ALA0-0.005-0.02431.505-0.002-0.0020.0000.0000.0000.000
171A452ASP-1-0.783-0.90132.154-0.024-0.0240.0000.0000.0000.000
172A453GLU-1-0.890-0.97133.879-0.019-0.0190.0000.0000.0000.000
173A454GLU-1-0.941-0.96235.701-0.019-0.0190.0000.0000.0000.000
174A455ASP-1-0.865-0.90929.567-0.029-0.0290.0000.0000.0000.000
175A456TYR0-0.093-0.07029.0880.0000.0000.0000.0000.0000.000
176A457ALA00.0800.05234.4450.0010.0010.0000.0000.0000.000
177A458THR0-0.036-0.02735.4240.0010.0010.0000.0000.0000.000
178A459GLU-1-0.776-0.85334.515-0.021-0.0210.0000.0000.0000.000
179A460VAL00.0430.01437.2270.0010.0010.0000.0000.0000.000
180A461LYS10.8310.90239.9210.0150.0150.0000.0000.0000.000
181A462ASP-1-0.896-0.94439.542-0.014-0.0140.0000.0000.0000.000
182A463LEU0-0.086-0.04038.6030.0000.0000.0000.0000.0000.000
183A464GLY0-0.047-0.02642.6200.0000.0000.0000.0000.0000.000
184A465LEU00.0290.01941.9860.0000.0000.0000.0000.0000.000
185A466SER0-0.066-0.02343.7160.0000.0000.0000.0000.0000.000
186A467GLU-1-0.912-0.96044.952-0.013-0.0130.0000.0000.0000.000
187A468SER0-0.027-0.01246.1330.0000.0000.0000.0000.0000.000
188A469GLY0-0.013-0.00848.0460.0000.0000.0000.0000.0000.000
189A470GLY0-0.016-0.00247.6510.0000.0000.0000.0000.0000.000
190A471ASP-1-0.918-0.95943.976-0.016-0.0160.0000.0000.0000.000
191A472VAL0-0.054-0.03540.667-0.001-0.0010.0000.0000.0000.000
192A473ASN00.0180.02541.3240.0010.0010.0000.0000.0000.000
193A474ALA00.007-0.00640.122-0.001-0.0010.0000.0000.0000.000
194A475ALA00.0350.02338.6880.0010.0010.0000.0000.0000.000
195A476ILE0-0.047-0.01438.323-0.001-0.0010.0000.0000.0000.000
196A477LEU0-0.006-0.00133.3030.0010.0010.0000.0000.0000.000
197A478ASP-1-0.767-0.91336.450-0.019-0.0190.0000.0000.0000.000
198A479GLU-1-0.919-0.98734.442-0.024-0.0240.0000.0000.0000.000
199A480SER0-0.101-0.04235.5740.0000.0000.0000.0000.0000.000
200A481GLY0-0.0200.00036.3610.0010.0010.0000.0000.0000.000
201A482LYS10.8800.95337.2810.0150.0150.0000.0000.0000.000
202A483LYS10.9160.94735.0530.0180.0180.0000.0000.0000.000
203A484PHE0-0.035-0.01640.6930.0010.0010.0000.0000.0000.000
204A485ALA00.0800.03942.267-0.001-0.0010.0000.0000.0000.000
205A486MET0-0.080-0.04043.8880.0000.0000.0000.0000.0000.000
206A487GLU-1-0.906-0.96345.744-0.012-0.0120.0000.0000.0000.000
207A488PRO0-0.026-0.00947.5330.0000.0000.0000.0000.0000.000
208A489GLU-1-0.935-0.96048.599-0.013-0.0130.0000.0000.0000.000
209A490GLU-1-0.986-0.99248.654-0.013-0.0130.0000.0000.0000.000
210A491PHE00.0070.00441.349-0.001-0.0010.0000.0000.0000.000
211A492ASP-1-0.846-0.94246.016-0.016-0.0160.0000.0000.0000.000
212A493SER0-0.054-0.05943.2690.0000.0000.0000.0000.0000.000
213A494ASP-1-0.887-0.92745.311-0.016-0.0160.0000.0000.0000.000
214A495ALA00.0910.06147.6610.0000.0000.0000.0000.0000.000
215A496LEU0-0.028-0.01840.1110.0000.0000.0000.0000.0000.000
216A497ARG10.8120.86844.4330.0180.0180.0000.0000.0000.000
217A498GLU-1-0.954-0.97745.600-0.014-0.0140.0000.0000.0000.000
218A499PHE0-0.0050.01641.5590.0000.0000.0000.0000.0000.000
219A500VAL00.0520.01941.2120.0000.0000.0000.0000.0000.000
220A501MET0-0.032-0.02043.7990.0000.0000.0000.0000.0000.000
221A502ALA0-0.043-0.01946.8360.0000.0000.0000.0000.0000.000
222A503PHE0-0.0030.00040.1170.0000.0000.0000.0000.0000.000
223A504LYS10.8250.90542.2720.0210.0210.0000.0000.0000.000
224A505LYS10.8520.92245.1470.0150.0150.0000.0000.0000.000
225A506GLY00.0050.01847.2740.0010.0010.0000.0000.0000.000
226A507LYS10.8800.92848.3480.0140.0140.0000.0000.0000.000
227A508LEU00.0130.02845.2850.0000.0000.0000.0000.0000.000
228A509LYS10.9160.94148.5510.0120.0120.0000.0000.0000.000
229A510PRO0-0.0160.00344.5030.0000.0000.0000.0000.0000.000
230A511VAL00.0140.01143.5140.0010.0010.0000.0000.0000.000
231A512ILE0-0.033-0.00944.6910.0000.0000.0000.0000.0000.000