Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: G6631

Calculation Name: 5FMS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FMS

Chain ID: A

ChEMBL ID:

UniProt ID: Q62559

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2928662.357254
FMO2-HF: Nuclear repulsion 2839325.221748
FMO2-HF: Total energy -89337.135506
FMO2-MP2: Total energy -89598.808131


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:SER)


Summations of interaction energy for fragment #1(A:7: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.
-10.5-10.85220.2-11.734-8.115-0.061
Interaction energy analysis for fragmet #1(A:7:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.085
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].
3A9ILE00.0080.0283.784-1.8350.371-0.023-1.071-1.1110.005
4A10LEU0-0.017-0.0116.3270.3160.3160.0000.0000.0000.000
5A11PHE0-0.025-0.0069.4560.0940.0940.0000.0000.0000.000
6A12ASN0-0.050-0.03712.9570.0000.0000.0000.0000.0000.000
7A13ALA0-0.025-0.04915.4810.0410.0410.0000.0000.0000.000
8A14TYR0-0.0010.01217.1280.0220.0220.0000.0000.0000.000
9A15LYS10.8720.96320.3670.2660.2660.0000.0000.0000.000
10A16LYS10.8640.92622.3060.1770.1770.0000.0000.0000.000
11A17GLU-1-0.764-0.89118.802-0.305-0.3050.0000.0000.0000.000
12A18VAL0-0.060-0.01222.0530.0230.0230.0000.0000.0000.000
13A19PHE0-0.068-0.03619.5700.0230.0230.0000.0000.0000.000
14A20THR00.0590.02417.598-0.027-0.0270.0000.0000.0000.000
15A21THR00.018-0.00613.4070.0060.0060.0000.0000.0000.000
16A22ASN0-0.057-0.02616.5570.0460.0460.0000.0000.0000.000
17A23THR0-0.005-0.00619.7410.0190.0190.0000.0000.0000.000
18A24GLY00.0260.01120.125-0.014-0.0140.0000.0000.0000.000
19A25THR00.0680.07316.7660.0080.0080.0000.0000.0000.000
20A26LYS10.9390.96517.1440.0170.0170.0000.0000.0000.000
21A27SER0-0.029-0.02917.7920.0190.0190.0000.0000.0000.000
22A28LEU00.0340.02714.1190.0190.0190.0000.0000.0000.000
23A29GLN0-0.035-0.03713.158-0.003-0.0030.0000.0000.0000.000
24A30LYS10.9200.97112.855-0.030-0.0300.0000.0000.0000.000
25A31ARG10.8490.90613.8040.1250.1250.0000.0000.0000.000
26A32LEU00.0320.0289.0070.0100.0100.0000.0000.0000.000
27A33ARG10.8970.9408.420-0.033-0.0330.0000.0000.0000.000
28A34SER0-0.031-0.0069.4840.1560.1560.0000.0000.0000.000
29A35ASN00.0200.0166.4750.2260.2260.0000.0000.0000.000
30A36TRP00.0570.0471.7341.230-3.52215.734-7.498-3.484-0.026
31A37LYS10.9260.9683.5940.1210.5070.008-0.091-0.3030.000
32A38ILE00.0290.0045.117-0.672-0.718-0.001-0.0060.0530.000
33A39GLN0-0.043-0.0138.2740.3140.3140.0000.0000.0000.000
34A40SER0-0.0090.01010.025-0.106-0.1060.0000.0000.0000.000
35A41LEU00.0550.01812.594-0.016-0.0160.0000.0000.0000.000
36A42LYS10.8810.92614.4140.2300.2300.0000.0000.0000.000
37A43ASP-1-0.875-0.93417.034-0.147-0.1470.0000.0000.0000.000
38A44GLU-1-0.881-0.95317.063-0.270-0.2700.0000.0000.0000.000
39A45ILE0-0.019-0.00913.633-0.019-0.0190.0000.0000.0000.000
40A46THR00.0420.01914.8050.0260.0260.0000.0000.0000.000
41A47SER00.0400.02213.082-0.054-0.0540.0000.0000.0000.000
42A48GLU-1-0.864-0.94011.646-0.434-0.4340.0000.0000.0000.000
43A49LYS10.8890.95210.3640.2470.2470.0000.0000.0000.000
44A50LEU0-0.055-0.0258.415-0.083-0.0830.0000.0000.0000.000
45A51ILE0-0.0190.0077.232-0.342-0.3420.0000.0000.0000.000
46A52GLY00.0130.0053.817-0.0700.2120.001-0.106-0.1780.000
47A53VAL0-0.057-0.0242.053-9.738-9.1584.240-2.529-2.292-0.037
48A54LYS10.8500.9582.6971.2332.1460.242-0.423-0.732-0.003
49A55LEU00.0360.0184.6840.6390.718-0.001-0.010-0.0680.000
50A56TRP00.0280.0277.675-0.097-0.0970.0000.0000.0000.000
51A57ILE00.004-0.01010.6170.1090.1090.0000.0000.0000.000
52A58THR00.0020.00313.3290.0290.0290.0000.0000.0000.000
53A59ALA0-0.009-0.00616.9620.0220.0220.0000.0000.0000.000
54A60GLY00.032-0.00918.9820.0270.0270.0000.0000.0000.000
55A61PRO0-0.021-0.01020.9520.0110.0110.0000.0000.0000.000
56A62ARG10.9110.94622.8170.1650.1650.0000.0000.0000.000
57A63GLU-1-0.861-0.90424.766-0.154-0.1540.0000.0000.0000.000
58A64LYS10.8830.94324.9700.1270.1270.0000.0000.0000.000
59A65PHE00.016-0.00118.768-0.010-0.0100.0000.0000.0000.000
60A66THR0-0.007-0.01023.1290.0270.0270.0000.0000.0000.000
61A67ALA00.0230.00423.116-0.021-0.0210.0000.0000.0000.000
62A68ALA00.0280.01222.919-0.009-0.0090.0000.0000.0000.000
63A69GLU-1-0.741-0.87619.395-0.287-0.2870.0000.0000.0000.000
64A70PHE00.0060.00018.530-0.044-0.0440.0000.0000.0000.000
65A71GLU-1-0.865-0.92019.171-0.304-0.3040.0000.0000.0000.000
66A72VAL0-0.089-0.04414.611-0.032-0.0320.0000.0000.0000.000
67A73LEU0-0.024-0.01013.917-0.084-0.0840.0000.0000.0000.000
68A74LYS10.8850.94315.1600.2230.2230.0000.0000.0000.000
69A75LYS10.9300.97314.5120.4130.4130.0000.0000.0000.000
70A76TYR0-0.0350.0036.6440.1060.1060.0000.0000.0000.000
71A77LEU0-0.025-0.00611.701-0.112-0.1120.0000.0000.0000.000
72A78ASP-1-0.811-0.91413.880-0.407-0.4070.0000.0000.0000.000
73A79SER0-0.073-0.08511.2700.0500.0500.0000.0000.0000.000
74A80GLY0-0.0050.01610.959-0.057-0.0570.0000.0000.0000.000
75A81GLY0-0.041-0.0228.397-0.230-0.2300.0000.0000.0000.000
76A82ASP-1-0.821-0.9198.798-0.966-0.9660.0000.0000.0000.000
77A83ILE0-0.039-0.02910.588-0.086-0.0860.0000.0000.0000.000
78A84LEU00.012-0.00412.9710.0630.0630.0000.0000.0000.000
79A85VAL00.0160.01414.8430.0000.0000.0000.0000.0000.000
80A86MET0-0.034-0.00617.8570.0220.0220.0000.0000.0000.000
81A87LEU00.0350.02920.4800.0030.0030.0000.0000.0000.000
82A88GLY00.0250.01023.9030.0040.0040.0000.0000.0000.000
83A89GLU-1-0.836-0.91826.981-0.103-0.1030.0000.0000.0000.000
84A90GLY0-0.039-0.01030.7020.0000.0000.0000.0000.0000.000
85A91GLY00.0630.02528.8940.0020.0020.0000.0000.0000.000
86A92GLU-1-0.754-0.90227.604-0.186-0.1860.0000.0000.0000.000
87A93SER0-0.086-0.02630.1020.0070.0070.0000.0000.0000.000
88A94ARG10.8910.94731.7740.1100.1100.0000.0000.0000.000
89A95PHE0-0.079-0.05025.1730.0010.0010.0000.0000.0000.000
90A96ASP-1-0.904-0.92528.958-0.138-0.1380.0000.0000.0000.000
91A97THR0-0.024-0.02925.070-0.010-0.0100.0000.0000.0000.000
92A98ASN0-0.0170.01225.778-0.009-0.0090.0000.0000.0000.000
93A99ILE00.0790.02220.388-0.011-0.0110.0000.0000.0000.000
94A100ASN00.005-0.01823.917-0.027-0.0270.0000.0000.0000.000
95A101PHE0-0.053-0.01026.328-0.001-0.0010.0000.0000.0000.000
96A102LEU00.0110.03218.611-0.007-0.0070.0000.0000.0000.000
97A103LEU0-0.044-0.03520.585-0.014-0.0140.0000.0000.0000.000
98A104GLU-1-0.899-0.95823.631-0.180-0.1800.0000.0000.0000.000
99A105GLU-1-0.860-0.92023.674-0.263-0.2630.0000.0000.0000.000
100A106TYR0-0.055-0.04419.338-0.010-0.0100.0000.0000.0000.000
101A107GLY0-0.010-0.00224.0180.0010.0010.0000.0000.0000.000
102A108ILE0-0.046-0.03121.9910.0120.0120.0000.0000.0000.000
103A109MET00.0520.01825.864-0.001-0.0010.0000.0000.0000.000
104A110VAL0-0.051-0.02224.9330.0080.0080.0000.0000.0000.000
105A111ASN0-0.0250.00127.8210.0060.0060.0000.0000.0000.000
106A112ASN00.017-0.00430.826-0.006-0.0060.0000.0000.0000.000
107A113ASP-1-0.861-0.92932.912-0.113-0.1130.0000.0000.0000.000
108A114ALA0-0.033-0.03832.825-0.006-0.0060.0000.0000.0000.000
109A115VAL00.0060.02431.5050.0050.0050.0000.0000.0000.000
110A116VAL0-0.047-0.01834.0330.0020.0020.0000.0000.0000.000
111A117ARG10.8510.91936.6790.0620.0620.0000.0000.0000.000
112A118ASN00.0370.01737.9900.0010.0010.0000.0000.0000.000
113A119VAL00.0260.00640.8740.0030.0030.0000.0000.0000.000
114A120TYR0-0.054-0.02040.695-0.003-0.0030.0000.0000.0000.000
115A121TYR00.0770.01437.1170.0030.0030.0000.0000.0000.000
116A122LYS10.8890.97534.3690.0430.0430.0000.0000.0000.000
117A123TYR0-0.017-0.01130.9400.0000.0000.0000.0000.0000.000
118A124PHE00.0260.03536.6250.0000.0000.0000.0000.0000.000
119A125HIS00.0480.02235.6330.0000.0000.0000.0000.0000.000
120A126PRO0-0.001-0.01836.970-0.002-0.0020.0000.0000.0000.000
121A127LYS10.9260.94433.3280.0880.0880.0000.0000.0000.000
122A128GLU-1-0.846-0.82531.692-0.080-0.0800.0000.0000.0000.000
123A129ALA0-0.0070.00432.1620.0060.0060.0000.0000.0000.000
124A130LEU0-0.0050.00431.556-0.005-0.0050.0000.0000.0000.000
125A131VAL00.013-0.01030.2910.0040.0040.0000.0000.0000.000
126A132SER0-0.021-0.00831.272-0.002-0.0020.0000.0000.0000.000
127A133ASP-1-0.793-0.87132.582-0.082-0.0820.0000.0000.0000.000
128A134GLY00.0740.03729.960-0.002-0.0020.0000.0000.0000.000
129A135VAL0-0.016-0.00925.883-0.012-0.0120.0000.0000.0000.000
130A136LEU0-0.0270.00627.3200.0070.0070.0000.0000.0000.000
131A137ASN0-0.010-0.00825.0140.0130.0130.0000.0000.0000.000
132A138ARG10.9730.96926.9170.0930.0930.0000.0000.0000.000
133A139GLU-1-0.816-0.90123.464-0.111-0.1110.0000.0000.0000.000
134A140ILE0-0.024-0.00521.683-0.005-0.0050.0000.0000.0000.000
135A141SER0-0.068-0.02123.6210.0040.0040.0000.0000.0000.000
136A142ARG10.8070.89419.8340.1410.1410.0000.0000.0000.000
137A143ALA0-0.0030.00122.4310.0090.0090.0000.0000.0000.000
138A144ALA0-0.021-0.02124.2880.0010.0010.0000.0000.0000.000
139A145GLY00.0410.03227.883-0.005-0.0050.0000.0000.0000.000
140A146LYS10.9380.95630.3000.0420.0420.0000.0000.0000.000
141A147ALA00.0280.02332.3810.0030.0030.0000.0000.0000.000
142A162GLN0-0.014-0.02332.9940.0000.0000.0000.0000.0000.000
143A163ALA0-0.028-0.00732.621-0.005-0.0050.0000.0000.0000.000
144A164LEU0-0.020-0.01125.3060.0020.0020.0000.0000.0000.000
145A165THR0-0.0090.01329.958-0.004-0.0040.0000.0000.0000.000
146A166PHE0-0.0120.00326.163-0.004-0.0040.0000.0000.0000.000
147A167VAL0-0.008-0.03027.4570.0030.0030.0000.0000.0000.000
148A168TYR0-0.030-0.03725.500-0.014-0.0140.0000.0000.0000.000
149A169PRO0-0.019-0.00526.3650.0040.0040.0000.0000.0000.000
150A170PHE0-0.019-0.02128.054-0.009-0.0090.0000.0000.0000.000
151A171GLY00.0140.00328.357-0.010-0.0100.0000.0000.0000.000
152A172ALA00.0240.02628.2330.0110.0110.0000.0000.0000.000
153A173THR0-0.006-0.00928.768-0.007-0.0070.0000.0000.0000.000
154A174LEU0-0.041-0.01524.237-0.002-0.0020.0000.0000.0000.000
155A175SER0-0.010-0.00928.5600.0130.0130.0000.0000.0000.000
156A176VAL0-0.034-0.02126.391-0.012-0.0120.0000.0000.0000.000
157A177MET0-0.0160.00628.4390.0170.0170.0000.0000.0000.000
158A178LYS10.9420.97427.8380.1580.1580.0000.0000.0000.000
159A179PRO00.0170.00224.5170.0060.0060.0000.0000.0000.000
160A180ALA00.0150.02223.459-0.009-0.0090.0000.0000.0000.000
161A181VAL0-0.032-0.02623.6070.0240.0240.0000.0000.0000.000
162A182ALA0-0.010-0.00224.047-0.015-0.0150.0000.0000.0000.000
163A183VAL00.003-0.01221.7730.0100.0100.0000.0000.0000.000
164A184LEU0-0.0130.00523.1820.0070.0070.0000.0000.0000.000
165A185SER0-0.016-0.01526.468-0.002-0.0020.0000.0000.0000.000
166A186THR0-0.003-0.04829.8930.0010.0010.0000.0000.0000.000
167A187GLY00.0490.03531.9090.0050.0050.0000.0000.0000.000
168A188SER0-0.060-0.06234.0240.0010.0010.0000.0000.0000.000
169A189VAL0-0.029-0.02336.8020.0050.0050.0000.0000.0000.000
170A190CYS0-0.0430.00134.6720.0010.0010.0000.0000.0000.000
171A191PHE0-0.020-0.01136.6980.0000.0000.0000.0000.0000.000
172A192PRO00.0460.01334.8710.0000.0000.0000.0000.0000.000
173A193LEU00.0200.04035.742-0.004-0.0040.0000.0000.0000.000
174A194ASN0-0.029-0.01734.427-0.004-0.0040.0000.0000.0000.000
175A195ARG10.9320.97832.9790.1000.1000.0000.0000.0000.000
176A196PRO00.006-0.00728.284-0.001-0.0010.0000.0000.0000.000
177A197ILE00.0270.00825.6790.0020.0020.0000.0000.0000.000
178A198LEU00.0060.00619.545-0.009-0.0090.0000.0000.0000.000
179A199ALA0-0.0230.00422.1410.0140.0140.0000.0000.0000.000
180A200PHE00.0160.00218.166-0.028-0.0280.0000.0000.0000.000
181A201TYR00.0630.01318.3810.0540.0540.0000.0000.0000.000
182A202HIS00.000-0.00515.375-0.047-0.0470.0000.0000.0000.000
183A203SER0-0.044-0.01818.319-0.009-0.0090.0000.0000.0000.000
184A204LYS10.8800.95519.6180.3140.3140.0000.0000.0000.000
185A205ASN0-0.010-0.01418.384-0.047-0.0470.0000.0000.0000.000
186A206GLN0-0.069-0.01316.1320.0050.0050.0000.0000.0000.000
187A207GLY00.0530.03215.1350.0180.0180.0000.0000.0000.000
188A208PHE0-0.061-0.06113.560-0.058-0.0580.0000.0000.0000.000
189A209GLY00.1000.08013.043-0.085-0.0850.0000.0000.0000.000
190A210LYS10.8350.92912.2560.6510.6510.0000.0000.0000.000
191A211LEU00.0020.00913.618-0.068-0.0680.0000.0000.0000.000
192A212ALA0-0.017-0.02215.7530.0510.0510.0000.0000.0000.000
193A213VAL00.0020.01817.451-0.017-0.0170.0000.0000.0000.000
194A214LEU0-0.001-0.01819.5650.0220.0220.0000.0000.0000.000
195A215GLY00.0290.01821.643-0.002-0.0020.0000.0000.0000.000
196A216SER00.029-0.00523.5500.0110.0110.0000.0000.0000.000
197A217CYS00.0240.01021.364-0.003-0.0030.0000.0000.0000.000
198A218HIS00.023-0.00321.709-0.002-0.0020.0000.0000.0000.000
199A219MET00.0040.02222.3620.0100.0100.0000.0000.0000.000
200A220PHE00.0290.00117.6330.0090.0090.0000.0000.0000.000
201A221SER0-0.058-0.01019.8570.0050.0050.0000.0000.0000.000
202A222ASP-1-0.725-0.88621.372-0.088-0.0880.0000.0000.0000.000
203A223GLN0-0.017-0.00223.3420.0190.0190.0000.0000.0000.000
204A224TYR0-0.069-0.13325.0220.0090.0090.0000.0000.0000.000
205A225LEU0-0.0620.01118.6290.0020.0020.0000.0000.0000.000
206A226ASP-1-0.871-0.95223.076-0.042-0.0420.0000.0000.0000.000
207A227LYS10.8200.92024.8530.0660.0660.0000.0000.0000.000
208A228GLU-1-0.812-0.93627.345-0.055-0.0550.0000.0000.0000.000
209A229GLU-1-0.854-0.91725.646-0.069-0.0690.0000.0000.0000.000
210A230ASN00.0490.03223.103-0.005-0.0050.0000.0000.0000.000
211A231SER0-0.004-0.01020.764-0.018-0.0180.0000.0000.0000.000
212A232LYS10.9520.98019.9070.0540.0540.0000.0000.0000.000
213A233ILE00.0400.03220.309-0.014-0.0140.0000.0000.0000.000
214A234MET0-0.020-0.00915.217-0.024-0.0240.0000.0000.0000.000
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