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: 89G4Y

Calculation Name: 3UMF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UMF

Chain ID: A

ChEMBL ID:

UniProt ID: G4V9S0

Base Structure: X-ray

Registration Date: 2023-09-22

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2106190.057421
FMO2-HF: Nuclear repulsion 2028719.402381
FMO2-HF: Total energy -77470.65504
FMO2-MP2: Total energy -77694.448309


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:4:GLN)


Summations of interaction energy for fragment #1(A:4:GLN)
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.
-18.512-10.6854.402-4.31-7.9180.035
Interaction energy analysis for fragmet #1(A:4:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.111 / q_NPA : 0.049
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].
3A6LEU0-0.048-0.0292.090-13.421-7.8744.091-3.817-5.8210.034
4A7ALA00.0220.0183.350-3.342-2.7920.0300.028-0.6090.000
5A8LYS10.8800.9304.866-2.218-2.104-0.001-0.008-0.1040.000
6A9ALA0-0.042-0.0126.639-0.054-0.0540.0000.0000.0000.000
7A10LYS10.9280.9878.305-0.708-0.7080.0000.0000.0000.000
8A11VAL00.011-0.0019.8660.0640.0640.0000.0000.0000.000
9A12ILE00.0260.01212.656-0.122-0.1220.0000.0000.0000.000
10A13PHE00.0210.01713.4080.0280.0280.0000.0000.0000.000
11A14VAL00.0180.01618.014-0.027-0.0270.0000.0000.0000.000
12A15LEU00.0110.00321.541-0.008-0.0080.0000.0000.0000.000
13A16GLY00.0500.00224.2650.0020.0020.0000.0000.0000.000
14A17GLY00.0160.03027.8660.0020.0020.0000.0000.0000.000
15A18PRO00.002-0.00430.5240.0090.0090.0000.0000.0000.000
16A19GLY00.0480.02333.810-0.004-0.0040.0000.0000.0000.000
17A20SER0-0.023-0.01630.4850.0050.0050.0000.0000.0000.000
18A21GLY00.0240.01232.1290.0030.0030.0000.0000.0000.000
19A22LYS10.8750.91924.875-0.155-0.1550.0000.0000.0000.000
20A23GLY00.0060.00926.9340.0160.0160.0000.0000.0000.000
21A24THR00.0550.02427.5040.0100.0100.0000.0000.0000.000
22A25GLN0-0.019-0.01827.5830.0190.0190.0000.0000.0000.000
23A26CYS0-0.043-0.02523.2830.0150.0150.0000.0000.0000.000
24A27GLU-1-0.891-0.93823.9700.2180.2180.0000.0000.0000.000
25A28LYS10.8950.95426.106-0.141-0.1410.0000.0000.0000.000
26A29LEU0-0.025-0.01322.7020.0060.0060.0000.0000.0000.000
27A30VAL0-0.0040.01020.4160.0200.0200.0000.0000.0000.000
28A31GLN0-0.031-0.00622.6570.0110.0110.0000.0000.0000.000
29A32LYS10.8700.95025.789-0.205-0.2050.0000.0000.0000.000
30A33PHE0-0.033-0.03720.999-0.013-0.0130.0000.0000.0000.000
31A34HIS0-0.0130.01020.5440.0590.0590.0000.0000.0000.000
32A35PHE0-0.024-0.01217.5120.0700.0700.0000.0000.0000.000
33A36ASN00.0170.01912.911-0.134-0.1340.0000.0000.0000.000
34A37HIS0-0.054-0.03716.129-0.006-0.0060.0000.0000.0000.000
35A38LEU0-0.008-0.00212.0360.0150.0150.0000.0000.0000.000
36A39SER00.014-0.02316.653-0.051-0.0510.0000.0000.0000.000
37A40SER00.0440.01117.8340.0170.0170.0000.0000.0000.000
38A41GLY00.0340.01718.865-0.017-0.0170.0000.0000.0000.000
39A42ASP-1-0.841-0.89919.9620.2310.2310.0000.0000.0000.000
40A43LEU0-0.034-0.01914.0250.0080.0080.0000.0000.0000.000
41A44LEU00.0070.00017.619-0.029-0.0290.0000.0000.0000.000
42A45ARG10.9400.97619.782-0.168-0.1680.0000.0000.0000.000
43A46ALA0-0.024-0.01618.110-0.012-0.0120.0000.0000.0000.000
44A47GLU-1-0.765-0.84616.220-0.022-0.0220.0000.0000.0000.000
45A48VAL0-0.0020.00018.964-0.021-0.0210.0000.0000.0000.000
46A49GLN0-0.060-0.02922.392-0.014-0.0140.0000.0000.0000.000
47A50SER0-0.0130.00118.955-0.001-0.0010.0000.0000.0000.000
48A51GLY00.0150.01520.968-0.004-0.0040.0000.0000.0000.000
49A52SER0-0.029-0.02818.832-0.030-0.0300.0000.0000.0000.000
50A53PRO00.029-0.00920.4790.0050.0050.0000.0000.0000.000
51A54LYS10.9260.95413.9850.1440.1440.0000.0000.0000.000
52A55GLY00.0540.03220.3560.0060.0060.0000.0000.0000.000
53A56LYS10.8500.91621.4870.0210.0210.0000.0000.0000.000
54A57GLU-1-0.818-0.89323.210-0.066-0.0660.0000.0000.0000.000
55A58LEU0-0.008-0.00818.7980.0030.0030.0000.0000.0000.000
56A59LYS10.8450.91423.400-0.007-0.0070.0000.0000.0000.000
57A60ALA00.0180.01426.4070.0040.0040.0000.0000.0000.000
58A61MET0-0.039-0.00523.814-0.004-0.0040.0000.0000.0000.000
59A62MET0-0.028-0.02422.6690.0090.0090.0000.0000.0000.000
60A63GLU-1-0.886-0.92428.0020.0110.0110.0000.0000.0000.000
61A64ARG10.7540.84628.3130.0550.0550.0000.0000.0000.000
62A65GLY0-0.0230.00530.988-0.001-0.0010.0000.0000.0000.000
63A66GLU-1-0.874-0.92527.864-0.065-0.0650.0000.0000.0000.000
64A67LEU0-0.031-0.01824.8420.0090.0090.0000.0000.0000.000
65A68VAL00.004-0.00219.873-0.014-0.0140.0000.0000.0000.000
66A69PRO00.0200.00919.0390.0030.0030.0000.0000.0000.000
67A70LEU00.0280.01815.8280.0130.0130.0000.0000.0000.000
68A71GLU-1-0.825-0.92914.472-0.254-0.2540.0000.0000.0000.000
69A72VAL0-0.0090.00213.744-0.044-0.0440.0000.0000.0000.000
70A73VAL00.0160.00214.4590.0360.0360.0000.0000.0000.000
71A74LEU0-0.0050.00010.4990.0970.0970.0000.0000.0000.000
72A75ALA0-0.006-0.0039.6750.0710.0710.0000.0000.0000.000
73A76LEU00.0030.0079.7040.0950.0950.0000.0000.0000.000
74A77LEU0-0.005-0.00411.3130.1860.1860.0000.0000.0000.000
75A78LYS10.8960.9434.3402.9183.097-0.001-0.019-0.1600.000
76A79GLU-1-0.973-0.9806.5581.0891.0890.0000.0000.0000.000
77A80ALA00.002-0.0078.0780.3300.3300.0000.0000.0000.000
78A81MET0-0.022-0.0177.274-0.004-0.0040.0000.0000.0000.000
79A82ILE0-0.026-0.0182.735-0.7570.5080.284-0.483-1.0650.001
80A83LYS10.9250.9706.063-1.009-1.0090.0000.0000.0000.000
81A84LEU0-0.011-0.0139.535-0.282-0.2820.0000.0000.0000.000
82A85VAL0-0.0210.0036.050-0.346-0.3460.0000.0000.0000.000
83A86ASP-1-0.842-0.9159.2432.1022.1020.0000.0000.0000.000
84A87LYS10.9320.98611.556-0.963-0.9630.0000.0000.0000.000
85A88ASN00.0600.02113.227-0.122-0.1220.0000.0000.0000.000
86A89CYS00.0050.01910.9900.1430.1430.0000.0000.0000.000
87A90HIS0-0.022-0.01611.2320.0220.0220.0000.0000.0000.000
88A91PHE00.010-0.0019.4100.0850.0850.0000.0000.0000.000
89A92LEU00.0130.02414.064-0.080-0.0800.0000.0000.0000.000
90A93ILE0-0.011-0.01712.9360.0330.0330.0000.0000.0000.000
91A94ASP-1-0.784-0.87317.0760.1710.1710.0000.0000.0000.000
92A95GLY0-0.051-0.02020.700-0.016-0.0160.0000.0000.0000.000
93A96TYR0-0.058-0.01714.445-0.024-0.0240.0000.0000.0000.000
94A97PRO00.0010.00417.1360.0300.0300.0000.0000.0000.000
95A98ARG10.9670.95819.037-0.056-0.0560.0000.0000.0000.000
96A99GLU-1-0.824-0.92721.101-0.021-0.0210.0000.0000.0000.000
97A100LEU00.014-0.00719.9040.0040.0040.0000.0000.0000.000
98A101ASP-1-0.803-0.91918.593-0.143-0.1430.0000.0000.0000.000
99A102GLN00.0120.00816.527-0.005-0.0050.0000.0000.0000.000
100A103GLY00.0180.02014.9080.0100.0100.0000.0000.0000.000
101A104ILE00.0440.01913.975-0.010-0.0100.0000.0000.0000.000
102A105LYS10.8430.91512.8110.1740.1740.0000.0000.0000.000
103A106PHE00.0190.00910.185-0.118-0.1180.0000.0000.0000.000
104A107GLU-1-0.758-0.8518.974-0.061-0.0610.0000.0000.0000.000
105A108LYS10.8180.9188.8020.6680.6680.0000.0000.0000.000
106A109GLU-1-0.874-0.9267.268-1.663-1.6630.0000.0000.0000.000
107A110VAL0-0.069-0.0344.991-0.698-0.6980.0000.0000.0000.000
108A111CYS00.0070.0034.535-0.309-0.137-0.001-0.011-0.1590.000
109A112PRO00.0250.0047.1040.0890.0890.0000.0000.0000.000
110A113CYS0-0.114-0.03410.4750.1310.1310.0000.0000.0000.000
111A114LEU0-0.024-0.01812.996-0.058-0.0580.0000.0000.0000.000
112A115CYS0-0.047-0.02614.745-0.038-0.0380.0000.0000.0000.000
113A116VAL00.0250.01117.6810.0380.0380.0000.0000.0000.000
114A117ILE00.0020.01520.274-0.018-0.0180.0000.0000.0000.000
115A118ASN0-0.034-0.02123.1840.0070.0070.0000.0000.0000.000
116A119PHE0-0.022-0.02225.167-0.005-0.0050.0000.0000.0000.000
117A120ASP-1-0.905-0.94628.8880.0530.0530.0000.0000.0000.000
118A121VAL0-0.022-0.01631.7320.0020.0020.0000.0000.0000.000
119A122SER00.034-0.00635.225-0.002-0.0020.0000.0000.0000.000
120A123GLU-1-0.717-0.82038.0560.0290.0290.0000.0000.0000.000
121A124GLU-1-0.803-0.90139.7140.0370.0370.0000.0000.0000.000
122A125VAL0-0.041-0.01738.2450.0020.0020.0000.0000.0000.000
123A126MET0-0.0270.00337.1590.0030.0030.0000.0000.0000.000
124A127ARG10.9270.94039.261-0.027-0.0270.0000.0000.0000.000
125A128LYS10.9350.98242.777-0.050-0.0500.0000.0000.0000.000
126A129ARG10.7630.87435.758-0.079-0.0790.0000.0000.0000.000
127A130LEU0-0.063-0.04136.9590.0030.0030.0000.0000.0000.000
128A131LEU0-0.0100.01841.505-0.001-0.0010.0000.0000.0000.000
129A132LYS10.9040.95644.707-0.031-0.0310.0000.0000.0000.000
130A133ARG10.8660.92245.576-0.049-0.0490.0000.0000.0000.000
131A134ALA0-0.039-0.03150.346-0.001-0.0010.0000.0000.0000.000
132A135GLU-1-0.891-0.93452.5210.0210.0210.0000.0000.0000.000
133A136THR00.0220.02449.4140.0000.0000.0000.0000.0000.000
134A137SER0-0.003-0.01551.1160.0000.0000.0000.0000.0000.000
135A138ASN0-0.004-0.01851.6880.0010.0010.0000.0000.0000.000
136A139ARG10.9110.97149.044-0.036-0.0360.0000.0000.0000.000
137A140VAL0-0.057-0.04447.4890.0020.0020.0000.0000.0000.000
138A141ASP-1-0.743-0.86247.4980.0230.0230.0000.0000.0000.000
139A142ASP-1-0.909-0.94346.4450.0200.0200.0000.0000.0000.000
140A143ASN00.004-0.00343.791-0.001-0.0010.0000.0000.0000.000
141A144GLU-1-0.844-0.93942.5820.0390.0390.0000.0000.0000.000
142A145GLU-1-0.762-0.87842.6570.0220.0220.0000.0000.0000.000
143A146THR0-0.020-0.00639.089-0.001-0.0010.0000.0000.0000.000
144A147ILE0-0.042-0.02937.6620.0010.0010.0000.0000.0000.000
145A148VAL0-0.0020.01137.9470.0020.0020.0000.0000.0000.000
146A149LYS10.8870.93038.632-0.015-0.0150.0000.0000.0000.000
147A150ARG10.9410.99233.412-0.049-0.0490.0000.0000.0000.000
148A151PHE0-0.023-0.01733.7990.0020.0020.0000.0000.0000.000
149A152ARG10.8810.89934.195-0.020-0.0200.0000.0000.0000.000
150A153THR0-0.012-0.01432.006-0.005-0.0050.0000.0000.0000.000
151A154PHE0-0.032-0.01426.548-0.003-0.0030.0000.0000.0000.000
152A155ASN0-0.005-0.00629.734-0.005-0.0050.0000.0000.0000.000
153A156GLU-1-0.830-0.90331.044-0.002-0.0020.0000.0000.0000.000
154A157LEU0-0.033-0.01126.694-0.004-0.0040.0000.0000.0000.000
155A158THR0-0.026-0.02925.218-0.004-0.0040.0000.0000.0000.000
156A159LYS10.8660.93326.281-0.003-0.0030.0000.0000.0000.000
157A160PRO00.0020.00425.5330.0000.0000.0000.0000.0000.000
158A161VAL0-0.024-0.00820.447-0.007-0.0070.0000.0000.0000.000
159A162ILE00.0210.00622.4870.0060.0060.0000.0000.0000.000
160A163GLU-1-0.828-0.90224.8430.0030.0030.0000.0000.0000.000
161A164HIS0-0.0080.00017.683-0.019-0.0190.0000.0000.0000.000
162A165TYR0-0.039-0.05615.5510.0050.0050.0000.0000.0000.000
163A166LYS10.8720.91921.547-0.012-0.0120.0000.0000.0000.000
164A167GLN0-0.034-0.02024.503-0.006-0.0060.0000.0000.0000.000
165A168GLN0-0.040-0.00517.8310.0020.0020.0000.0000.0000.000
166A169ASN0-0.060-0.02421.4140.0020.0020.0000.0000.0000.000
167A170LYS10.8740.94014.542-0.020-0.0200.0000.0000.0000.000
168A171VAL0-0.032-0.00820.7560.0250.0250.0000.0000.0000.000
169A172ILE0-0.021-0.01522.219-0.008-0.0080.0000.0000.0000.000
170A173THR00.000-0.00825.1550.0060.0060.0000.0000.0000.000
171A174ILE0-0.054-0.02327.390-0.002-0.0020.0000.0000.0000.000
172A175ASP-1-0.784-0.85230.0690.0630.0630.0000.0000.0000.000
173A176ALA0-0.002-0.01731.8400.0050.0050.0000.0000.0000.000
174A177SER0-0.061-0.05633.9030.0000.0000.0000.0000.0000.000
175A178GLY00.0010.01136.796-0.003-0.0030.0000.0000.0000.000
176A179THR00.019-0.00837.6190.0030.0030.0000.0000.0000.000
177A180VAL00.0630.01633.3340.0030.0030.0000.0000.0000.000
178A181ASP-1-0.841-0.93333.6630.1290.1290.0000.0000.0000.000
179A182ALA00.0170.02234.4700.0040.0040.0000.0000.0000.000
180A183ILE0-0.041-0.00930.6570.0030.0030.0000.0000.0000.000
181A184PHE0-0.004-0.00727.1400.0060.0060.0000.0000.0000.000
182A185ASP-1-0.875-0.93929.5990.1370.1370.0000.0000.0000.000
183A186LYS10.8440.91730.680-0.088-0.0880.0000.0000.0000.000
184A187VAL00.032-0.00125.2330.0010.0010.0000.0000.0000.000
185A188ASN00.009-0.00625.9920.0270.0270.0000.0000.0000.000
186A189HIS0-0.081-0.03526.5680.0000.0000.0000.0000.0000.000
187A190GLU-1-0.775-0.86426.1550.0880.0880.0000.0000.0000.000
188A191LEU00.0500.02020.496-0.001-0.0010.0000.0000.0000.000
189A192GLN00.0140.02522.0520.0130.0130.0000.0000.0000.000
190A193LYS10.8260.90323.551-0.090-0.0900.0000.0000.0000.000
191A194PHE00.0060.01018.722-0.011-0.0110.0000.0000.0000.000
192A195GLY00.0110.00518.5580.0230.0230.0000.0000.0000.000
193A196VAL0-0.086-0.04417.7270.0370.0370.0000.0000.0000.000
194A197LYS10.9420.96820.386-0.162-0.1620.0000.0000.0000.000