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: 229VR

Calculation Name: 3KF8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KF8

Chain ID: A

ChEMBL ID:

UniProt ID: C5M4J8

Base Structure: X-ray

Registration Date: 2023-06-19

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2522085.682187
FMO2-HF: Nuclear repulsion 2438102.197801
FMO2-HF: Total energy -83983.484386
FMO2-MP2: Total energy -84235.404224


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:7:LEU)


Summations of interaction energy for fragment #1(A:7:LEU)
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.
-6.256-2.2920.393-1.886-2.4710.009
Interaction energy analysis for fragmet #1(A:7:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / 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].
3A9PRO00.013-0.0073.401-1.2241.3560.024-1.422-1.1820.004
4A10LYS10.9390.9712.570-5.051-3.6670.369-0.464-1.2890.005
5A11THR00.0280.0167.3840.0050.0050.0000.0000.0000.000
6A12LYS10.8680.93011.192-0.200-0.2000.0000.0000.0000.000
7A13ILE00.0300.01413.236-0.052-0.0520.0000.0000.0000.000
8A14ASP-1-0.926-0.94717.0760.0340.0340.0000.0000.0000.000
9A15TRP00.0340.01817.340-0.018-0.0180.0000.0000.0000.000
10A16GLY00.0280.01721.8200.0040.0040.0000.0000.0000.000
11A17PRO0-0.022-0.01222.2940.0140.0140.0000.0000.0000.000
12A18GLY00.031-0.00122.615-0.002-0.0020.0000.0000.0000.000
13A19GLU-1-0.845-0.94323.3360.1390.1390.0000.0000.0000.000
14A20ASN0-0.026-0.00925.339-0.009-0.0090.0000.0000.0000.000
15A21HIS0-0.004-0.00521.235-0.011-0.0110.0000.0000.0000.000
16A22ILE0-0.033-0.01423.550-0.001-0.0010.0000.0000.0000.000
17A23CYS00.0090.03026.968-0.004-0.0040.0000.0000.0000.000
18A24LEU00.0080.01030.331-0.002-0.0020.0000.0000.0000.000
19A25LYS10.8340.92027.512-0.088-0.0880.0000.0000.0000.000
20A26THR00.013-0.00930.196-0.011-0.0110.0000.0000.0000.000
21A27PRO0-0.021-0.00630.3900.0080.0080.0000.0000.0000.000
22A28PHE0-0.046-0.02830.1570.0010.0010.0000.0000.0000.000
23A29LYS10.8610.93927.087-0.075-0.0750.0000.0000.0000.000
24A30ASN00.0550.03624.746-0.015-0.0150.0000.0000.0000.000
25A31PHE00.0240.01126.9910.0010.0010.0000.0000.0000.000
26A32TYR00.0220.01621.450-0.001-0.0010.0000.0000.0000.000
27A33VAL00.0310.02425.629-0.007-0.0070.0000.0000.0000.000
28A34ILE00.0550.02026.6860.0010.0010.0000.0000.0000.000
29A35GLU-1-0.869-0.94124.7450.0180.0180.0000.0000.0000.000
30A36LEU0-0.022-0.01220.442-0.008-0.0080.0000.0000.0000.000
31A37PHE0-0.010-0.00323.1070.0060.0060.0000.0000.0000.000
32A38HIS0-0.015-0.00420.774-0.006-0.0060.0000.0000.0000.000
33A39GLN0-0.047-0.02517.1180.0110.0110.0000.0000.0000.000
34A40ALA00.0120.02419.7800.0220.0220.0000.0000.0000.000
35A41PRO00.0080.00719.989-0.017-0.0170.0000.0000.0000.000
36A42THR0-0.080-0.06221.769-0.005-0.0050.0000.0000.0000.000
37A43PHE00.0290.01725.008-0.003-0.0030.0000.0000.0000.000
38A44ASP-1-0.877-0.92525.699-0.038-0.0380.0000.0000.0000.000
39A45LYS10.8900.95323.822-0.024-0.0240.0000.0000.0000.000
40A46THR00.000-0.00227.9120.0070.0070.0000.0000.0000.000
41A47ILE0-0.0160.00627.9560.0010.0010.0000.0000.0000.000
42A48PRO0-0.043-0.01530.547-0.001-0.0010.0000.0000.0000.000
43A49LEU00.0260.01032.2940.0070.0070.0000.0000.0000.000
44A50PHE0-0.005-0.00135.077-0.003-0.0030.0000.0000.0000.000
45A51ILE0-0.008-0.00838.1730.0010.0010.0000.0000.0000.000
46A52SER0-0.019-0.00840.7970.0020.0020.0000.0000.0000.000
47A53ASP-1-0.820-0.90535.6600.0470.0470.0000.0000.0000.000
48A54ILE0-0.0140.00236.9820.0010.0010.0000.0000.0000.000
49A55ASN0-0.029-0.03538.464-0.001-0.0010.0000.0000.0000.000
50A56ASN0-0.062-0.05839.6110.0010.0010.0000.0000.0000.000
51A57SER0-0.037-0.01535.6040.0020.0020.0000.0000.0000.000
52A58PRO0-0.022-0.01635.504-0.003-0.0030.0000.0000.0000.000
53A59ASN0-0.014-0.01838.570-0.004-0.0040.0000.0000.0000.000
54A60LEU00.0360.01734.7340.0030.0030.0000.0000.0000.000
55A61TYR0-0.009-0.03537.5510.0020.0020.0000.0000.0000.000
56A62GLY0-0.029-0.00639.8280.0010.0010.0000.0000.0000.000
57A63ILE0-0.076-0.03633.1660.0040.0040.0000.0000.0000.000
58A64TYR00.000-0.02729.5070.0030.0030.0000.0000.0000.000
59A65ASN0-0.016-0.00135.745-0.004-0.0040.0000.0000.0000.000
60A66TYR00.0690.02236.1500.0000.0000.0000.0000.0000.000
61A67ILE00.0160.01533.123-0.004-0.0040.0000.0000.0000.000
62A68ALA0-0.006-0.00936.450-0.002-0.0020.0000.0000.0000.000
63A69ASP-1-0.869-0.90338.0420.0060.0060.0000.0000.0000.000
64A70HIS0-0.044-0.01735.857-0.005-0.0050.0000.0000.0000.000
65A71LEU0-0.010-0.00232.491-0.001-0.0010.0000.0000.0000.000
66A72ARG10.8740.94136.380-0.005-0.0050.0000.0000.0000.000
67A73HIS00.0330.02633.6490.0040.0040.0000.0000.0000.000
68A74VAL0-0.0130.01432.1750.0000.0000.0000.0000.0000.000
69A75VAL0-0.0050.01133.9890.0020.0020.0000.0000.0000.000
70A76LEU00.0100.01430.4770.0010.0010.0000.0000.0000.000
71A77VAL00.0490.03131.2540.0000.0000.0000.0000.0000.000
72A78ASN00.0270.00329.1700.0040.0040.0000.0000.0000.000
73A79ASN0-0.062-0.05625.566-0.002-0.0020.0000.0000.0000.000
74A80TYR00.0120.01023.0440.0000.0000.0000.0000.0000.000
75A81PRO0-0.0210.01426.219-0.005-0.0050.0000.0000.0000.000
76A82VAL0-0.028-0.02328.235-0.001-0.0010.0000.0000.0000.000
77A83ASN0-0.003-0.02630.1320.0030.0030.0000.0000.0000.000
78A84GLN00.0170.01530.451-0.006-0.0060.0000.0000.0000.000
79A85ILE00.0000.00032.4780.0050.0050.0000.0000.0000.000
80A86ASN00.0320.00434.5230.0000.0000.0000.0000.0000.000
81A87ILE0-0.002-0.00436.3420.0050.0050.0000.0000.0000.000
82A88PHE00.025-0.00839.239-0.003-0.0030.0000.0000.0000.000
83A89GLY00.0440.01342.0000.0030.0030.0000.0000.0000.000
84A90LYS10.8230.90745.351-0.014-0.0140.0000.0000.0000.000
85A91ILE00.0130.01249.1230.0010.0010.0000.0000.0000.000
86A92VAL0-0.043-0.02550.7560.0010.0010.0000.0000.0000.000
87A93TYR00.0030.00153.0600.0000.0000.0000.0000.0000.000
88A94GLU-1-0.724-0.84453.655-0.003-0.0030.0000.0000.0000.000
89A95GLN0-0.020-0.01155.3860.0000.0000.0000.0000.0000.000
90A96TYR00.0310.00355.8970.0000.0000.0000.0000.0000.000
91A97LYS10.8840.93355.9980.0040.0040.0000.0000.0000.000
92A98GLU-1-0.793-0.86357.029-0.012-0.0120.0000.0000.0000.000
93A99LYS10.7640.88954.0730.0140.0140.0000.0000.0000.000
94A100GLU-1-0.872-0.91859.049-0.011-0.0110.0000.0000.0000.000
95A101PHE0-0.032-0.02455.6340.0000.0000.0000.0000.0000.000
96A102ASN0-0.023-0.02360.1310.0010.0010.0000.0000.0000.000
97A103GLY00.0030.01260.452-0.001-0.0010.0000.0000.0000.000
98A104VAL0-0.068-0.03155.622-0.001-0.0010.0000.0000.0000.000
99A105GLU-1-0.833-0.92058.840-0.013-0.0130.0000.0000.0000.000
100A106GLU-1-0.818-0.88153.229-0.018-0.0180.0000.0000.0000.000
101A107SER0-0.041-0.04655.5840.0010.0010.0000.0000.0000.000
102A108TYR0-0.087-0.07049.799-0.001-0.0010.0000.0000.0000.000
103A109VAL0-0.043-0.02652.3270.0010.0010.0000.0000.0000.000
104A110ILE0-0.018-0.00151.2010.0000.0000.0000.0000.0000.000
105A111LEU0-0.017-0.01649.2420.0000.0000.0000.0000.0000.000
106A112VAL0-0.014-0.00349.3060.0010.0010.0000.0000.0000.000
107A113ILE00.0120.02145.0190.0000.0000.0000.0000.0000.000
108A114SER0-0.021-0.05646.2090.0020.0020.0000.0000.0000.000
109A115ASP-1-0.731-0.86041.1850.0210.0210.0000.0000.0000.000
110A116PHE0-0.087-0.04244.4060.0020.0020.0000.0000.0000.000
111A117ILE00.0040.01640.5740.0010.0010.0000.0000.0000.000
112A118GLY00.0350.01742.4420.0010.0010.0000.0000.0000.000
113A119ILE0-0.002-0.01643.353-0.003-0.0030.0000.0000.0000.000
114A120ASP-1-0.826-0.90344.2140.0220.0220.0000.0000.0000.000
115A121SER00.0030.03743.978-0.001-0.0010.0000.0000.0000.000
116A122LYS10.9020.95145.057-0.020-0.0200.0000.0000.0000.000
117A123ILE00.0560.04742.3170.0010.0010.0000.0000.0000.000
118A124ARG10.7830.85846.107-0.005-0.0050.0000.0000.0000.000
119A125VAL00.0000.00244.7160.0000.0000.0000.0000.0000.000
120A126ARG10.8450.89146.4570.0100.0100.0000.0000.0000.000
121A127LEU0-0.0070.01346.218-0.001-0.0010.0000.0000.0000.000
122A128SER00.047-0.01448.5150.0010.0010.0000.0000.0000.000
123A129GLN0-0.003-0.04450.6400.0020.0020.0000.0000.0000.000
124A130GLU-1-0.880-0.90050.677-0.020-0.0200.0000.0000.0000.000
125A131GLN00.0690.03244.5280.0020.0020.0000.0000.0000.000
126A132PHE0-0.019-0.01748.9440.0010.0010.0000.0000.0000.000
127A133LYS10.9460.97051.2890.0180.0180.0000.0000.0000.000
128A134GLU-1-0.943-0.96648.989-0.024-0.0240.0000.0000.0000.000
129A135VAL0-0.045-0.00546.485-0.001-0.0010.0000.0000.0000.000
130A136GLY00.010-0.00349.2670.0020.0020.0000.0000.0000.000
131A137LEU0-0.093-0.04249.7530.0020.0020.0000.0000.0000.000
132A138THR0-0.018-0.02353.866-0.001-0.0010.0000.0000.0000.000
133A139LEU00.0040.01256.4260.0010.0010.0000.0000.0000.000
134A140ASP-1-0.787-0.88659.391-0.004-0.0040.0000.0000.0000.000
135A141LYS10.8250.90959.5350.0020.0020.0000.0000.0000.000
136A142LYS10.8160.91059.6240.0040.0040.0000.0000.0000.000
137A143ASN00.017-0.02853.946-0.001-0.0010.0000.0000.0000.000
138A144TYR00.0080.01254.1780.0010.0010.0000.0000.0000.000
139A145GLY0-0.017-0.01053.5420.0000.0000.0000.0000.0000.000
140A146LYS10.8370.92951.4320.0050.0050.0000.0000.0000.000
141A147ILE0-0.0120.00645.6600.0010.0010.0000.0000.0000.000
142A148VAL0-0.023-0.01645.535-0.002-0.0020.0000.0000.0000.000
143A149GLU-1-0.738-0.84137.6370.0040.0040.0000.0000.0000.000
144A150LEU0-0.027-0.01540.807-0.003-0.0030.0000.0000.0000.000
145A151GLU-1-0.790-0.89935.758-0.017-0.0170.0000.0000.0000.000
146A152GLY00.0110.01137.674-0.002-0.0020.0000.0000.0000.000
147A153GLU-1-0.877-0.91136.413-0.022-0.0220.0000.0000.0000.000
148A154ILE0-0.045-0.02737.3880.0020.0020.0000.0000.0000.000
149A155TYR00.0190.01139.810-0.001-0.0010.0000.0000.0000.000
150A156ASN00.0090.01038.8800.0040.0040.0000.0000.0000.000
151A157TRP00.007-0.01042.682-0.001-0.0010.0000.0000.0000.000
152A158TYR0-0.048-0.05237.6720.0030.0030.0000.0000.0000.000
153A159ASP-1-0.790-0.87943.8400.0140.0140.0000.0000.0000.000
154A160SER00.0680.02644.6040.0020.0020.0000.0000.0000.000
155A161ILE00.0050.01745.6060.0010.0010.0000.0000.0000.000
156A162ASN0-0.080-0.05648.6840.0020.0020.0000.0000.0000.000
157A163VAL00.0200.00442.5150.0010.0010.0000.0000.0000.000
158A164SER00.0080.00743.0620.0010.0010.0000.0000.0000.000
159A165LYS10.8170.91144.300-0.015-0.0150.0000.0000.0000.000
160A166LYS10.8900.95341.185-0.035-0.0350.0000.0000.0000.000
161A167PRO0-0.0270.00842.095-0.001-0.0010.0000.0000.0000.000
162A168ASP-1-0.782-0.86345.3990.0080.0080.0000.0000.0000.000
163A169ARG10.8140.88339.422-0.022-0.0220.0000.0000.0000.000
164A170GLU-1-0.809-0.87144.124-0.003-0.0030.0000.0000.0000.000
165A171LEU0-0.010-0.00239.220-0.001-0.0010.0000.0000.0000.000
166A172LYN0-0.0090.00041.681-0.001-0.0010.0000.0000.0000.000
167A173VAL0-0.037-0.01541.579-0.002-0.0020.0000.0000.0000.000
168A174SER00.0610.02738.007-0.001-0.0010.0000.0000.0000.000
169A175LYS10.8390.90536.3310.0200.0200.0000.0000.0000.000
170A176ILE00.0340.01841.2670.0030.0030.0000.0000.0000.000
171A177THR0-0.038-0.02941.851-0.003-0.0030.0000.0000.0000.000
172A178VAL0-0.0070.00043.9110.0030.0030.0000.0000.0000.000
173A179LEU0-0.0080.00941.747-0.001-0.0010.0000.0000.0000.000
174A180SER0-0.008-0.01445.8170.0000.0000.0000.0000.0000.000
175A181HIS00.0290.01449.5060.0020.0020.0000.0000.0000.000
176A182ARG10.8600.91752.5190.0030.0030.0000.0000.0000.000
177A183PRO00.0370.02053.0690.0000.0000.0000.0000.0000.000
178A184ASP-1-0.822-0.90752.0000.0100.0100.0000.0000.0000.000
179A185GLY00.000-0.01949.133-0.002-0.0020.0000.0000.0000.000
180A186LEU00.0330.03047.3650.0010.0010.0000.0000.0000.000
181A187HIS0-0.0070.00545.5400.0040.0040.0000.0000.0000.000
182A188PHE00.0640.02843.2980.0010.0010.0000.0000.0000.000
183A189GLU-1-0.835-0.89942.6840.0140.0140.0000.0000.0000.000
184A190PHE00.003-0.00642.4380.0030.0030.0000.0000.0000.000
185A191GLU-1-0.916-0.95138.6230.0090.0090.0000.0000.0000.000
186A192GLN0-0.017-0.02038.0850.0030.0030.0000.0000.0000.000
187A193TRP0-0.025-0.03637.8930.0030.0030.0000.0000.0000.000
188A194LYS10.8580.91635.418-0.035-0.0350.0000.0000.0000.000
189A195LYS10.8200.90333.5230.0000.0000.0000.0000.0000.000
190A196ARG10.7760.88932.857-0.011-0.0110.0000.0000.0000.000
191A197MET0-0.015-0.00233.3330.0080.0080.0000.0000.0000.000
192A198GLU-1-0.873-0.92730.7750.0530.0530.0000.0000.0000.000
193A199PHE00.0250.02126.7500.0080.0080.0000.0000.0000.000
194A200ARG10.8950.93328.430-0.048-0.0480.0000.0000.0000.000
195A201LYS10.8880.92429.266-0.061-0.0610.0000.0000.0000.000
196A202ASN0-0.0010.00024.9100.0150.0150.0000.0000.0000.000
197A203ASN0-0.056-0.02324.0650.0060.0060.0000.0000.0000.000
198A204LEU0-0.0160.00325.576-0.002-0.0020.0000.0000.0000.000
199A205VAL0-0.043-0.01228.149-0.001-0.0010.0000.0000.0000.000
200A206GLU-1-0.908-0.94623.5400.1730.1730.0000.0000.0000.000
201A207PRO0-0.034-0.01125.381-0.007-0.0070.0000.0000.0000.000
202A208TRP00.0110.01020.2350.0100.0100.0000.0000.0000.000
203A209VAL00.015-0.00219.340-0.003-0.0030.0000.0000.0000.000
204A210PHE0-0.016-0.00217.0450.0180.0180.0000.0000.0000.000
205A211ILE00.0550.01514.159-0.003-0.0030.0000.0000.0000.000
206A212PRO00.0160.01213.9920.0460.0460.0000.0000.0000.000
207A213THR0-0.0320.0029.0710.1640.1640.0000.0000.0000.000