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: YZG82

Calculation Name: 3K1R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K1R

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y6N9

Base Structure: X-ray

Registration Date: 2023-09-19

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2055166.075791
FMO2-HF: Nuclear repulsion 1978853.779754
FMO2-HF: Total energy -76312.296037
FMO2-MP2: Total energy -76536.835231


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-4.097-1.2180.028-1.025-1.8840.001
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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].
3A3ARG10.9880.9803.688-3.723-2.155-0.001-0.624-0.9440.001
4A4LYS10.8050.8963.522-0.7350.1670.026-0.313-0.6160.000
5A5VAL00.0590.0293.6980.0760.4850.003-0.088-0.3240.000
6A6ALA00.0770.0296.4150.3110.3110.0000.0000.0000.000
7A7ARG10.8270.9117.685-0.204-0.2040.0000.0000.0000.000
8A8GLU-1-0.794-0.8848.2090.0930.0930.0000.0000.0000.000
9A9PHE00.0170.02710.4100.0230.0230.0000.0000.0000.000
10A10ARG11.0101.01711.632-0.207-0.2070.0000.0000.0000.000
11A11HIS0-0.013-0.01613.871-0.002-0.0020.0000.0000.0000.000
12A12LYS10.8580.92112.008-0.070-0.0700.0000.0000.0000.000
13A13VAL00.0180.01815.870-0.003-0.0030.0000.0000.0000.000
14A14ASP-1-0.855-0.94218.3870.1100.1100.0000.0000.0000.000
15A15PHE0-0.090-0.03319.773-0.003-0.0030.0000.0000.0000.000
16A16LEU0-0.053-0.02819.748-0.004-0.0040.0000.0000.0000.000
17A17ILE00.0000.00521.366-0.004-0.0040.0000.0000.0000.000
18A18GLU-1-0.920-0.95623.7790.0590.0590.0000.0000.0000.000
19A19ASN0-0.004-0.01026.2420.0070.0070.0000.0000.0000.000
20A20ASP-1-0.790-0.90324.2590.0890.0890.0000.0000.0000.000
21A21ALA00.0420.03024.1670.0030.0030.0000.0000.0000.000
22A22GLU-1-0.801-0.88825.0040.0480.0480.0000.0000.0000.000
23A23LYS10.7640.88420.372-0.092-0.0920.0000.0000.0000.000
24A24ASP-1-0.916-0.95920.1790.0970.0970.0000.0000.0000.000
25A25TYR0-0.055-0.04121.1450.0000.0000.0000.0000.0000.000
26A26LEU00.0050.00517.674-0.003-0.0030.0000.0000.0000.000
27A27TYR0-0.010-0.02915.127-0.003-0.0030.0000.0000.0000.000
28A28ASP-1-0.836-0.88417.1120.0710.0710.0000.0000.0000.000
29A29VAL00.0530.02519.390-0.004-0.0040.0000.0000.0000.000
30A30LEU0-0.026-0.01114.106-0.006-0.0060.0000.0000.0000.000
31A31ARG10.7780.87315.287-0.086-0.0860.0000.0000.0000.000
32A32MET00.0200.00116.407-0.007-0.0070.0000.0000.0000.000
33A33TYR00.0200.03313.764-0.003-0.0030.0000.0000.0000.000
34A34HIS0-0.011-0.01310.452-0.009-0.0090.0000.0000.0000.000
35A35GLN0-0.048-0.03014.735-0.001-0.0010.0000.0000.0000.000
36A36THR0-0.043-0.04117.939-0.005-0.0050.0000.0000.0000.000
37A37MET0-0.101-0.04412.832-0.004-0.0040.0000.0000.0000.000
38A38ASP-1-0.823-0.90018.1320.0070.0070.0000.0000.0000.000
39A39VAL0-0.003-0.02018.3380.0050.0050.0000.0000.0000.000
40A40ALA00.0160.00820.2270.0030.0030.0000.0000.0000.000
41A41VAL0-0.0060.00023.3780.0020.0020.0000.0000.0000.000
42A42LEU0-0.0030.01516.7750.0030.0030.0000.0000.0000.000
43A43VAL0-0.046-0.03920.5900.0030.0030.0000.0000.0000.000
44A44GLY0-0.0050.00322.4790.0010.0010.0000.0000.0000.000
45A45ASP-1-0.865-0.93622.9050.0310.0310.0000.0000.0000.000
46A46LEU0-0.031-0.01918.5620.0030.0030.0000.0000.0000.000
47A47LYS10.8510.93922.975-0.020-0.0200.0000.0000.0000.000
48A48LEU0-0.0130.01626.4040.0000.0000.0000.0000.0000.000
49A49VAL00.0110.01022.5480.0010.0010.0000.0000.0000.000
50A50ILE0-0.064-0.01420.3610.0020.0020.0000.0000.0000.000
51A51ASN00.0130.00824.880-0.003-0.0030.0000.0000.0000.000
52A52GLU-1-0.799-0.87027.9990.0380.0380.0000.0000.0000.000
53A53PRO0-0.007-0.02327.7740.0020.0020.0000.0000.0000.000
54A54SER0-0.085-0.06227.2160.0020.0020.0000.0000.0000.000
55A55ARG10.8470.89224.010-0.044-0.0440.0000.0000.0000.000
56A56LEU0-0.0010.01422.7040.0020.0020.0000.0000.0000.000
57A57PRO0-0.056-0.03720.6150.0010.0010.0000.0000.0000.000
58A58LEU00.0260.02018.3240.0050.0050.0000.0000.0000.000
59A59PHE00.0620.02917.3960.0010.0010.0000.0000.0000.000
60A60ASP-1-0.811-0.86316.9210.0560.0560.0000.0000.0000.000
61A61ALA0-0.077-0.04614.2600.0140.0140.0000.0000.0000.000
62A62ILE00.0450.02312.722-0.005-0.0050.0000.0000.0000.000
63A63ARG10.8260.91212.602-0.075-0.0750.0000.0000.0000.000
64A64PRO0-0.081-0.0548.5670.0230.0230.0000.0000.0000.000
65A65LEU0-0.0210.0018.3670.0580.0580.0000.0000.0000.000
66A66ILE0-0.0160.0229.782-0.011-0.0110.0000.0000.0000.000
67A67PRO00.0360.02610.5680.0530.0530.0000.0000.0000.000
68A68LEU00.059-0.0019.541-0.027-0.0270.0000.0000.0000.000
69A69LYS10.8780.94312.9020.0170.0170.0000.0000.0000.000
70A70HIS00.0450.02315.323-0.009-0.0090.0000.0000.0000.000
71A71GLN0-0.028-0.00511.143-0.023-0.0230.0000.0000.0000.000
72A72VAL00.0070.00516.399-0.002-0.0020.0000.0000.0000.000
73A73GLU-1-0.867-0.93919.7780.0000.0000.0000.0000.0000.000
74A74TYR00.025-0.01717.2440.0000.0000.0000.0000.0000.000
75A75ASP-1-0.811-0.88219.0470.0430.0430.0000.0000.0000.000
76A76GLN0-0.114-0.05821.347-0.003-0.0030.0000.0000.0000.000
77A77LEU00.0040.02822.226-0.001-0.0010.0000.0000.0000.000
78A78THR0-0.023-0.01120.6880.0020.0020.0000.0000.0000.000
79A79PRO00.0040.01523.978-0.002-0.0020.0000.0000.0000.000
80A80ARG10.8930.92523.760-0.011-0.0110.0000.0000.0000.000
81A81ARG10.8130.88821.383-0.044-0.0440.0000.0000.0000.000
82A82SER0-0.023-0.02225.2990.0010.0010.0000.0000.0000.000
83A83ARG10.9650.97422.995-0.036-0.0360.0000.0000.0000.000
84A84LYS10.8990.96326.024-0.015-0.0150.0000.0000.0000.000
85A85LEU00.0320.01429.6660.0000.0000.0000.0000.0000.000
86A86LYS10.8620.94633.071-0.007-0.0070.0000.0000.0000.000
87A87GLU-1-0.849-0.91335.2700.0080.0080.0000.0000.0000.000
88A88VAL00.0120.01739.074-0.001-0.0010.0000.0000.0000.000
89A89ARG10.8870.92442.039-0.003-0.0030.0000.0000.0000.000
90A90LEU00.0130.01544.978-0.001-0.0010.0000.0000.0000.000
91A91ASP-1-0.817-0.91348.0730.0030.0030.0000.0000.0000.000
92A92ARG10.8500.91951.869-0.005-0.0050.0000.0000.0000.000
93A93LEU0-0.038-0.02153.9800.0000.0000.0000.0000.0000.000
94A94HIS00.0000.01752.1620.0000.0000.0000.0000.0000.000
95A95PRO0-0.004-0.00455.5650.0000.0000.0000.0000.0000.000
96A96GLU-1-0.906-0.94353.0210.0010.0010.0000.0000.0000.000
97A97GLY0-0.036-0.01052.5690.0010.0010.0000.0000.0000.000
98A98LEU0-0.014-0.02847.6120.0000.0000.0000.0000.0000.000
99A99GLY00.0380.02947.3150.0000.0000.0000.0000.0000.000
100A100LEU0-0.0060.00543.3990.0000.0000.0000.0000.0000.000
101A101SER0-0.045-0.02444.5540.0000.0000.0000.0000.0000.000
102A102VAL0-0.005-0.00342.5630.0000.0000.0000.0000.0000.000
103A103ARG10.9320.97440.460-0.016-0.0160.0000.0000.0000.000
104A104GLY00.0480.01941.3860.0010.0010.0000.0000.0000.000
105A105GLY00.0290.00542.073-0.001-0.0010.0000.0000.0000.000
106A106LEU0-0.002-0.00142.5440.0010.0010.0000.0000.0000.000
107A107GLU-1-0.776-0.89743.8490.0170.0170.0000.0000.0000.000
108A108PHE0-0.059-0.02742.3780.0000.0000.0000.0000.0000.000
109A109GLY00.0060.01740.5910.0010.0010.0000.0000.0000.000
110A110CYS0-0.104-0.04537.5040.0010.0010.0000.0000.0000.000
111A111GLY00.0360.02536.960-0.001-0.0010.0000.0000.0000.000
112A112LEU00.0060.00938.093-0.001-0.0010.0000.0000.0000.000
113A113PHE00.036-0.00133.5910.0000.0000.0000.0000.0000.000
114A114ILE0-0.006-0.00338.532-0.001-0.0010.0000.0000.0000.000
115A115SER00.023-0.00738.7810.0010.0010.0000.0000.0000.000
116A116HIS0-0.007-0.00840.9580.0000.0000.0000.0000.0000.000
117A117LEU00.0090.00539.7210.0000.0000.0000.0000.0000.000
118A118ILE00.0160.01443.6750.0000.0000.0000.0000.0000.000
119A119LYS10.9610.98042.9060.0000.0000.0000.0000.0000.000
120A120GLY0-0.045-0.02744.8100.0000.0000.0000.0000.0000.000
121A121GLY00.0470.02746.7250.0000.0000.0000.0000.0000.000
122A122GLN0-0.002-0.01046.1540.0000.0000.0000.0000.0000.000
123A123ALA00.0240.01043.1720.0000.0000.0000.0000.0000.000
124A124ASP-1-0.825-0.90141.5090.0030.0030.0000.0000.0000.000
125A125SER0-0.051-0.02941.491-0.001-0.0010.0000.0000.0000.000
126A126VAL0-0.0170.00341.771-0.001-0.0010.0000.0000.0000.000
127A127GLY00.0110.00838.1170.0000.0000.0000.0000.0000.000
128A128LEU0-0.073-0.03937.0880.0010.0010.0000.0000.0000.000
129A129GLN0-0.049-0.04232.053-0.002-0.0020.0000.0000.0000.000
130A130VAL00.0170.01537.0760.0010.0010.0000.0000.0000.000
131A131GLY00.0630.02334.0150.0000.0000.0000.0000.0000.000
132A132ASP-1-0.797-0.89233.3340.0140.0140.0000.0000.0000.000
133A133GLU-1-0.808-0.87933.2190.0240.0240.0000.0000.0000.000
134A134ILE0-0.018-0.01335.786-0.001-0.0010.0000.0000.0000.000
135A135VAL0-0.001-0.00834.3710.0010.0010.0000.0000.0000.000
136A136ARG10.7820.88937.805-0.015-0.0150.0000.0000.0000.000
137A137ILE00.0680.04240.829-0.001-0.0010.0000.0000.0000.000
138A138ASN00.0420.01544.4460.0000.0000.0000.0000.0000.000
139A139GLY00.0120.01643.5880.0000.0000.0000.0000.0000.000
140A140TYR00.0090.00043.3010.0010.0010.0000.0000.0000.000
141A141SER0-0.012-0.02440.8320.0000.0000.0000.0000.0000.000
142A142ILE00.0610.02640.9870.0000.0000.0000.0000.0000.000
143A143SER0-0.028-0.01838.8300.0000.0000.0000.0000.0000.000
144A144SER0-0.049-0.02940.5810.0010.0010.0000.0000.0000.000
145A145CYS0-0.0020.02543.753-0.001-0.0010.0000.0000.0000.000
146A146THR0-0.001-0.02245.3050.0010.0010.0000.0000.0000.000
147A147HIS0-0.027-0.03345.525-0.001-0.0010.0000.0000.0000.000
148A148GLU-1-0.881-0.93447.6560.0100.0100.0000.0000.0000.000
149A149GLU-1-0.825-0.87949.2750.0140.0140.0000.0000.0000.000
150A150VAL0-0.002-0.00444.795-0.001-0.0010.0000.0000.0000.000
151A151ILE0-0.027-0.01347.886-0.001-0.0010.0000.0000.0000.000
152A152ASN0-0.043-0.04750.119-0.001-0.0010.0000.0000.0000.000
153A153LEU0-0.0040.00746.765-0.001-0.0010.0000.0000.0000.000
154A154ILE0-0.037-0.01046.248-0.001-0.0010.0000.0000.0000.000
155A155ARG10.9010.94950.002-0.009-0.0090.0000.0000.0000.000
156A156THR0-0.054-0.03051.972-0.001-0.0010.0000.0000.0000.000
157A157GLU-1-0.804-0.86653.6240.0040.0040.0000.0000.0000.000
158A158LYS10.8460.89854.498-0.003-0.0030.0000.0000.0000.000
159A159THR0-0.039-0.02650.8480.0000.0000.0000.0000.0000.000
160A160VAL00.0280.01346.9040.0000.0000.0000.0000.0000.000
161A161SER0-0.049-0.02444.093-0.001-0.0010.0000.0000.0000.000
162A162ILE00.0310.02340.9310.0010.0010.0000.0000.0000.000
163A163LYS10.8380.90237.116-0.010-0.0100.0000.0000.0000.000
164A164VAL0-0.004-0.00334.8290.0010.0010.0000.0000.0000.000
165A165ARG10.8250.88729.816-0.025-0.0250.0000.0000.0000.000
166A166HIS0-0.033-0.01828.8820.0010.0010.0000.0000.0000.000
167A167ILE0-0.041-0.02229.1190.0030.0030.0000.0000.0000.000
168A168GLY00.0470.01728.7930.0020.0020.0000.0000.0000.000
169A169LEU0-0.042-0.01529.0730.0000.0000.0000.0000.0000.000
170A170ILE0-0.026-0.01532.542-0.001-0.0010.0000.0000.0000.000
171A171PRO00.0070.02636.2650.0010.0010.0000.0000.0000.000
172A172VAL0-0.015-0.02437.836-0.002-0.0020.0000.0000.0000.000
173A173LYS10.8140.88440.030-0.019-0.0190.0000.0000.0000.000
174A174SER0-0.084-0.05642.918-0.001-0.0010.0000.0000.0000.000
175A175SER0-0.003-0.02145.908-0.001-0.0010.0000.0000.0000.000
176A176PRO00.037-0.00347.2200.0010.0010.0000.0000.0000.000
177A177ASP-1-0.857-0.90248.1330.0180.0180.0000.0000.0000.000
178A178GLU-1-0.870-0.87843.5230.0210.0210.0000.0000.0000.000
179A179PRO00.0310.02539.3350.0000.0000.0000.0000.0000.000
180A180LEU0-0.030-0.01037.254-0.001-0.0010.0000.0000.0000.000
181A181THR0-0.024-0.01036.0090.0010.0010.0000.0000.0000.000
182A182TRP00.041-0.00832.746-0.002-0.0020.0000.0000.0000.000
183A183GLN0-0.016-0.00733.9840.0000.0000.0000.0000.0000.000
184A184TYR00.005-0.03326.3400.0000.0000.0000.0000.0000.000
185A185VAL0-0.008-0.00532.299-0.001-0.0010.0000.0000.0000.000
186A186ASP-1-0.844-0.92331.3060.0160.0160.0000.0000.0000.000
187A187GLN0-0.0160.00634.0790.0000.0000.0000.0000.0000.000
188A188PHE00.011-0.00135.789-0.001-0.0010.0000.0000.0000.000
189A189VAL0-0.014-0.01837.744-0.001-0.0010.0000.0000.0000.000
190A190SER0-0.035-0.01937.306-0.001-0.0010.0000.0000.0000.000
191A191GLU-1-0.845-0.90438.8550.0160.0160.0000.0000.0000.000
192A192SER0-0.144-0.06341.873-0.001-0.0010.0000.0000.0000.000