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: G58Z1

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 OptH
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 -2103972.239506
FMO2-HF: Nuclear repulsion 2026502.573157
FMO2-HF: Total energy -77469.666349
FMO2-MP2: Total energy -77693.354598


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.
-15.677-7.8384.07-4.231-7.6770.031
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 : 0.110 / q_NPA : 0.051
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].
3A6LEU0-0.052-0.0321.959-12.228-6.4893.957-3.878-5.8170.029
4A7ALA00.0310.0223.361-2.774-2.3780.0250.149-0.5710.000
5A8LYS10.8760.9304.914-1.646-1.532-0.001-0.007-0.1050.000
6A9ALA0-0.037-0.0136.6230.0050.0050.0000.0000.0000.000
7A10LYS10.9380.9818.278-0.639-0.6390.0000.0000.0000.000
8A11VAL00.0270.0119.9060.0770.0770.0000.0000.0000.000
9A12ILE00.0300.01712.644-0.123-0.1230.0000.0000.0000.000
10A13PHE00.0170.01713.3720.0350.0350.0000.0000.0000.000
11A14VAL00.0130.01318.005-0.034-0.0340.0000.0000.0000.000
12A15LEU00.002-0.00321.519-0.003-0.0030.0000.0000.0000.000
13A16GLY00.0520.00424.290-0.002-0.0020.0000.0000.0000.000
14A17GLY00.0090.02427.8910.0050.0050.0000.0000.0000.000
15A18PRO00.003-0.01130.5470.0080.0080.0000.0000.0000.000
16A19GLY00.0500.02233.832-0.005-0.0050.0000.0000.0000.000
17A20SER0-0.028-0.01130.4500.0040.0040.0000.0000.0000.000
18A21GLY00.0310.01732.1570.0010.0010.0000.0000.0000.000
19A22LYS10.8710.91625.200-0.190-0.1900.0000.0000.0000.000
20A23GLY00.0110.01227.0430.0170.0170.0000.0000.0000.000
21A24THR00.0640.02627.6680.0100.0100.0000.0000.0000.000
22A25GLN0-0.011-0.01327.4960.0150.0150.0000.0000.0000.000
23A26CYS0-0.0090.00023.3940.0160.0160.0000.0000.0000.000
24A27GLU-1-0.913-0.94624.1450.2380.2380.0000.0000.0000.000
25A28LYS10.9230.96426.276-0.152-0.1520.0000.0000.0000.000
26A29LEU0-0.018-0.00622.5210.0030.0030.0000.0000.0000.000
27A30VAL00.0010.01120.5950.0150.0150.0000.0000.0000.000
28A31GLN0-0.035-0.00722.8300.0060.0060.0000.0000.0000.000
29A32LYS10.8860.95425.930-0.198-0.1980.0000.0000.0000.000
30A33PHE0-0.050-0.04320.893-0.017-0.0170.0000.0000.0000.000
31A34HIS0-0.0230.00320.4890.0480.0480.0000.0000.0000.000
32A35PHE0-0.030-0.01317.6070.0630.0630.0000.0000.0000.000
33A36ASN00.0170.01613.390-0.124-0.1240.0000.0000.0000.000
34A37HIS0-0.033-0.02316.289-0.011-0.0110.0000.0000.0000.000
35A38LEU0-0.009-0.00212.0700.0220.0220.0000.0000.0000.000
36A39SER00.0520.02316.787-0.053-0.0530.0000.0000.0000.000
37A40SER00.0330.00818.1480.0200.0200.0000.0000.0000.000
38A41GLY00.0290.01419.134-0.011-0.0110.0000.0000.0000.000
39A42ASP-1-0.853-0.93120.1190.2950.2950.0000.0000.0000.000
40A43LEU0-0.048-0.02814.2370.0100.0100.0000.0000.0000.000
41A44LEU00.0150.00617.995-0.022-0.0220.0000.0000.0000.000
42A45ARG10.9610.99020.128-0.221-0.2210.0000.0000.0000.000
43A46ALA0-0.032-0.02318.441-0.018-0.0180.0000.0000.0000.000
44A47GLU-1-0.820-0.89316.3840.1540.1540.0000.0000.0000.000
45A48VAL0-0.0220.01719.250-0.030-0.0300.0000.0000.0000.000
46A49GLN0-0.090-0.05122.693-0.030-0.0300.0000.0000.0000.000
47A50SER0-0.018-0.02819.250-0.009-0.0090.0000.0000.0000.000
48A51GLY0-0.0080.00421.199-0.007-0.0070.0000.0000.0000.000
49A52SER0-0.021-0.02218.831-0.032-0.0320.0000.0000.0000.000
50A53PRO00.019-0.01520.6340.0020.0020.0000.0000.0000.000
51A54LYS11.0071.00314.5470.0720.0720.0000.0000.0000.000
52A55GLY00.0670.04320.5250.0040.0040.0000.0000.0000.000
53A56LYS10.8810.93521.711-0.035-0.0350.0000.0000.0000.000
54A57GLU-1-0.850-0.92823.287-0.008-0.0080.0000.0000.0000.000
55A58LEU00.008-0.00219.1840.0020.0020.0000.0000.0000.000
56A59LYS10.9540.97823.649-0.067-0.0670.0000.0000.0000.000
57A60ALA00.0140.01126.6730.0000.0000.0000.0000.0000.000
58A61MET0-0.032-0.00623.109-0.004-0.0040.0000.0000.0000.000
59A62MET0-0.038-0.03023.2380.0040.0040.0000.0000.0000.000
60A63GLU-1-1.003-0.98628.2960.0450.0450.0000.0000.0000.000
61A64ARG10.7980.88129.031-0.002-0.0020.0000.0000.0000.000
62A65GLY0-0.0250.00331.287-0.003-0.0030.0000.0000.0000.000
63A66GLU-1-0.882-0.91928.049-0.012-0.0120.0000.0000.0000.000
64A67LEU0-0.015-0.01424.9710.0110.0110.0000.0000.0000.000
65A68VAL0-0.017-0.00720.176-0.010-0.0100.0000.0000.0000.000
66A69PRO00.0240.01319.3390.0050.0050.0000.0000.0000.000
67A70LEU00.0470.02115.8270.0180.0180.0000.0000.0000.000
68A71GLU-1-0.874-0.95314.581-0.109-0.1090.0000.0000.0000.000
69A72VAL0-0.028-0.00614.064-0.005-0.0050.0000.0000.0000.000
70A73VAL00.0230.00614.7550.0550.0550.0000.0000.0000.000
71A74LEU0-0.006-0.00710.6980.1160.1160.0000.0000.0000.000
72A75ALA0-0.015-0.0079.9560.1380.1380.0000.0000.0000.000
73A76LEU00.0140.01510.0210.1580.1580.0000.0000.0000.000
74A77LEU0-0.007-0.00611.4370.1910.1910.0000.0000.0000.000
75A78LYS10.9540.9823.7532.0662.5590.018-0.172-0.3400.001
76A79GLU-1-0.970-0.9826.9521.5721.5720.0000.0000.0000.000
77A80ALA00.012-0.0018.4240.2900.2900.0000.0000.0000.000
78A81MET0-0.031-0.0217.309-0.017-0.0170.0000.0000.0000.000
79A82ILE0-0.026-0.0163.111-0.3430.5960.072-0.313-0.6980.001
80A83LYS10.9180.9726.123-1.218-1.2180.0000.0000.0000.000
81A84LEU0-0.016-0.0159.648-0.311-0.3110.0000.0000.0000.000
82A85VAL0-0.0210.0006.451-0.408-0.4080.0000.0000.0000.000
83A86ASP-1-0.829-0.9159.3831.6951.6950.0000.0000.0000.000
84A87LYS10.9250.98611.664-0.971-0.9710.0000.0000.0000.000
85A88ASN00.0680.01513.361-0.143-0.1430.0000.0000.0000.000
86A89CYS00.0090.01410.7980.1300.1300.0000.0000.0000.000
87A90HIS0-0.0170.00211.1800.0150.0150.0000.0000.0000.000
88A91PHE00.0160.0019.6660.1120.1120.0000.0000.0000.000
89A92LEU00.0040.01914.116-0.082-0.0820.0000.0000.0000.000
90A93ILE0-0.003-0.00913.2250.0440.0440.0000.0000.0000.000
91A94ASP-1-0.831-0.90917.2390.1980.1980.0000.0000.0000.000
92A95GLY0-0.037-0.01520.856-0.010-0.0100.0000.0000.0000.000
93A96TYR0-0.054-0.00614.564-0.020-0.0200.0000.0000.0000.000
94A97PRO00.0110.00817.3050.0270.0270.0000.0000.0000.000
95A98ARG10.9520.94519.064-0.120-0.1200.0000.0000.0000.000
96A99GLU-1-0.895-0.94321.1120.0140.0140.0000.0000.0000.000
97A100LEU00.027-0.00219.8340.0100.0100.0000.0000.0000.000
98A101ASP-1-0.838-0.91718.631-0.029-0.0290.0000.0000.0000.000
99A102GLN00.021-0.01116.5550.0040.0040.0000.0000.0000.000
100A103GLY00.0200.01314.9360.0250.0250.0000.0000.0000.000
101A104ILE00.0560.02714.008-0.002-0.0020.0000.0000.0000.000
102A105LYS10.9140.94912.8180.0710.0710.0000.0000.0000.000
103A106PHE00.0340.02110.467-0.074-0.0740.0000.0000.0000.000
104A107GLU-1-0.811-0.9019.0040.0080.0080.0000.0000.0000.000
105A108LYS10.8800.9678.8390.3550.3550.0000.0000.0000.000
106A109GLU-1-0.961-0.9877.272-1.062-1.0620.0000.0000.0000.000
107A110VAL0-0.100-0.0535.030-0.360-0.3600.0000.0000.0000.000
108A111CYS0-0.004-0.0094.570-0.328-0.170-0.001-0.010-0.1460.000
109A112PRO00.0250.0127.1390.1000.1000.0000.0000.0000.000
110A113CYS0-0.089-0.01110.5260.1120.1120.0000.0000.0000.000
111A114LEU0-0.058-0.03913.036-0.065-0.0650.0000.0000.0000.000
112A115CYS0-0.038-0.02614.785-0.040-0.0400.0000.0000.0000.000
113A116VAL00.0200.01317.6980.0420.0420.0000.0000.0000.000
114A117ILE00.0110.01620.294-0.022-0.0220.0000.0000.0000.000
115A118ASN0-0.011-0.00823.1880.0120.0120.0000.0000.0000.000
116A119PHE0-0.021-0.02125.184-0.007-0.0070.0000.0000.0000.000
117A120ASP-1-0.927-0.96128.8800.0690.0690.0000.0000.0000.000
118A121VAL0-0.028-0.01431.7350.0010.0010.0000.0000.0000.000
119A122SER00.0910.04735.230-0.001-0.0010.0000.0000.0000.000
120A123GLU-1-0.719-0.83938.0850.0450.0450.0000.0000.0000.000
121A124GLU-1-0.870-0.95439.7420.0470.0470.0000.0000.0000.000
122A125VAL0-0.029-0.01438.2530.0010.0010.0000.0000.0000.000
123A126MET0-0.0230.00437.2630.0030.0030.0000.0000.0000.000
124A127ARG10.9440.95239.285-0.041-0.0410.0000.0000.0000.000
125A128LYS10.9420.98642.801-0.058-0.0580.0000.0000.0000.000
126A129ARG10.7690.88035.863-0.092-0.0920.0000.0000.0000.000
127A130LEU0-0.062-0.04337.0130.0030.0030.0000.0000.0000.000
128A131LEU0-0.0040.02441.5530.0000.0000.0000.0000.0000.000
129A132LYS10.9130.96244.728-0.043-0.0430.0000.0000.0000.000
130A133ARG10.8670.92645.642-0.060-0.0600.0000.0000.0000.000
131A134ALA0-0.038-0.03250.368-0.001-0.0010.0000.0000.0000.000
132A135GLU-1-0.886-0.92752.5410.0310.0310.0000.0000.0000.000
133A136THR00.0320.03449.0280.0010.0010.0000.0000.0000.000
134A137SER00.0350.00650.772-0.001-0.0010.0000.0000.0000.000
135A138ASN00.019-0.00551.6520.0020.0020.0000.0000.0000.000
136A139ARG10.9310.97949.093-0.048-0.0480.0000.0000.0000.000
137A140VAL0-0.076-0.06047.5200.0020.0020.0000.0000.0000.000
138A141ASP-1-0.857-0.91947.5170.0370.0370.0000.0000.0000.000
139A142ASP-1-0.855-0.92046.3430.0390.0390.0000.0000.0000.000
140A143ASN00.000-0.00543.8020.0000.0000.0000.0000.0000.000
141A144GLU-1-0.880-0.96042.6010.0530.0530.0000.0000.0000.000
142A145GLU-1-0.821-0.91542.6780.0380.0380.0000.0000.0000.000
143A146THR0-0.018-0.00839.0250.0000.0000.0000.0000.0000.000
144A147ILE0-0.041-0.02937.7150.0030.0030.0000.0000.0000.000
145A148VAL00.0050.01037.9700.0030.0030.0000.0000.0000.000
146A149LYS10.9200.96438.656-0.032-0.0320.0000.0000.0000.000
147A150ARG10.9510.98433.199-0.076-0.0760.0000.0000.0000.000
148A151PHE0-0.036-0.02233.8220.0040.0040.0000.0000.0000.000
149A152ARG10.8560.89134.221-0.035-0.0350.0000.0000.0000.000
150A153THR00.0060.01431.895-0.004-0.0040.0000.0000.0000.000
151A154PHE0-0.037-0.02426.5240.0000.0000.0000.0000.0000.000
152A155ASN0-0.013-0.01829.762-0.005-0.0050.0000.0000.0000.000
153A156GLU-1-0.850-0.93031.0750.0180.0180.0000.0000.0000.000
154A157LEU0-0.027-0.00926.594-0.002-0.0020.0000.0000.0000.000
155A158THR0-0.046-0.02725.464-0.002-0.0020.0000.0000.0000.000
156A159LYS10.9050.96326.312-0.024-0.0240.0000.0000.0000.000
157A160PRO00.0240.01725.521-0.001-0.0010.0000.0000.0000.000
158A161VAL0-0.012-0.00320.527-0.007-0.0070.0000.0000.0000.000
159A162ILE00.003-0.00722.5210.0050.0050.0000.0000.0000.000
160A163GLU-1-0.900-0.95324.8770.0120.0120.0000.0000.0000.000
161A164HIS0-0.0070.00117.980-0.020-0.0200.0000.0000.0000.000
162A165TYR0-0.055-0.05715.6230.0050.0050.0000.0000.0000.000
163A166LYS10.9450.96121.584-0.042-0.0420.0000.0000.0000.000
164A167GLN0-0.0210.00124.346-0.009-0.0090.0000.0000.0000.000
165A168GLN0-0.054-0.01117.977-0.011-0.0110.0000.0000.0000.000
166A169ASN0-0.040-0.01321.3370.0040.0040.0000.0000.0000.000
167A170LYS10.9270.97114.515-0.017-0.0170.0000.0000.0000.000
168A171VAL0-0.034-0.00520.8020.0260.0260.0000.0000.0000.000
169A172ILE0-0.011-0.00922.468-0.010-0.0100.0000.0000.0000.000
170A173THR0-0.020-0.02125.1840.0080.0080.0000.0000.0000.000
171A174ILE0-0.042-0.01727.476-0.004-0.0040.0000.0000.0000.000
172A175ASP-1-0.784-0.86930.0770.0730.0730.0000.0000.0000.000
173A176ALA0-0.010-0.01431.8860.0040.0040.0000.0000.0000.000
174A177SER0-0.057-0.04333.8920.0010.0010.0000.0000.0000.000
175A178GLY00.0010.01036.790-0.003-0.0030.0000.0000.0000.000
176A179THR00.023-0.00537.5940.0040.0040.0000.0000.0000.000
177A180VAL00.0530.00833.2710.0030.0030.0000.0000.0000.000
178A181ASP-1-0.882-0.95133.6260.1300.1300.0000.0000.0000.000
179A182ALA00.0200.02334.4410.0030.0030.0000.0000.0000.000
180A183ILE0-0.046-0.01030.5480.0020.0020.0000.0000.0000.000
181A184PHE00.000-0.00626.9590.0060.0060.0000.0000.0000.000
182A185ASP-1-0.885-0.93929.5770.1320.1320.0000.0000.0000.000
183A186LYS10.8670.94130.651-0.087-0.0870.0000.0000.0000.000
184A187VAL00.0310.00225.218-0.001-0.0010.0000.0000.0000.000
185A188ASN00.024-0.00625.9660.0220.0220.0000.0000.0000.000
186A189HIS0-0.079-0.02026.567-0.004-0.0040.0000.0000.0000.000
187A190GLU-1-0.814-0.91826.1410.0840.0840.0000.0000.0000.000
188A191LEU00.0390.01620.521-0.002-0.0020.0000.0000.0000.000
189A192GLN00.0470.03522.0680.0130.0130.0000.0000.0000.000
190A193LYS10.8250.91623.582-0.087-0.0870.0000.0000.0000.000
191A194PHE00.0060.01118.787-0.011-0.0110.0000.0000.0000.000
192A195GLY0-0.002-0.00218.5930.0170.0170.0000.0000.0000.000
193A196VAL0-0.065-0.02717.8010.0300.0300.0000.0000.0000.000
194A197LYS10.9110.94820.387-0.144-0.1440.0000.0000.0000.000