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: 859GY

Calculation Name: 1FS0-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1FS0

Chain ID: G

ChEMBL ID:

UniProt ID: P0A6E6

Base Structure: X-ray

Registration Date: 2023-06-22

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2616389.631433
FMO2-HF: Nuclear repulsion 2527254.172465
FMO2-HF: Total energy -89135.458968
FMO2-MP2: Total energy -89389.244745


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(G:19:LYS)


Summations of interaction energy for fragment #1(G:19:LYS)
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.
103.593107.590.674-1.872-2.80
Interaction energy analysis for fragmet #1(G:19:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.034 / q_NPA : 0.992
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].
3G21THR00.0660.0332.999-1.8920.8400.023-1.306-1.4490.001
4G22LYS10.9901.0112.52133.44934.4560.651-0.494-1.164-0.001
5G23ALA00.0010.0004.0232.6632.9210.000-0.072-0.1870.000
6G24MET0-0.002-0.0055.7923.2423.2420.0000.0000.0000.000
7G25GLU-1-0.884-0.9567.020-23.641-23.6410.0000.0000.0000.000
8G26MET0-0.060-0.0207.4682.1072.1070.0000.0000.0000.000
9G27VAL0-0.015-0.0069.8212.0962.0960.0000.0000.0000.000
10G28ALA00.0140.00411.8471.5761.5760.0000.0000.0000.000
11G29ALA00.012-0.00412.7051.2711.2710.0000.0000.0000.000
12G30SER0-0.055-0.02114.0561.3401.3400.0000.0000.0000.000
13G31LYS10.9490.97215.95216.98716.9870.0000.0000.0000.000
14G32MET0-0.0240.00617.4410.7900.7900.0000.0000.0000.000
15G33ARG11.0121.00414.57118.31318.3130.0000.0000.0000.000
16G34LYS10.9791.00320.24213.10413.1040.0000.0000.0000.000
17G35SER0-0.041-0.06422.0890.7060.7060.0000.0000.0000.000
18G36GLN00.033-0.00420.6850.1140.1140.0000.0000.0000.000
19G37ASP-1-0.865-0.91824.048-12.028-12.0280.0000.0000.0000.000
20G38ARG10.8500.93925.08211.66011.6600.0000.0000.0000.000
21G39MET0-0.0170.01125.2220.4290.4290.0000.0000.0000.000
22G40ALA00.0170.01028.6260.3980.3980.0000.0000.0000.000
23G41ALA0-0.020-0.01930.2000.3290.3290.0000.0000.0000.000
24G42SER0-0.041-0.02632.1300.3790.3790.0000.0000.0000.000
25G43ARG10.8300.88233.3898.8358.8350.0000.0000.0000.000
26G44PRO00.0260.02335.2990.2710.2710.0000.0000.0000.000
27G45TYR00.0310.01938.4210.2380.2380.0000.0000.0000.000
28G46ALA00.0680.03338.8760.2160.2160.0000.0000.0000.000
29G47GLU-1-0.804-0.88837.666-7.867-7.8670.0000.0000.0000.000
30G48THR0-0.063-0.03641.6550.2220.2220.0000.0000.0000.000
31G49MET00.0320.02743.7790.1700.1700.0000.0000.0000.000
32G50ARG10.9220.96044.0256.6206.6200.0000.0000.0000.000
33G51LYS10.9280.96844.5917.0437.0430.0000.0000.0000.000
34G52VAL00.0000.01847.9270.1320.1320.0000.0000.0000.000
35G53ILE00.0110.00947.4730.1290.1290.0000.0000.0000.000
36G54GLY0-0.038-0.02050.0930.1160.1160.0000.0000.0000.000
37G55HIS0-0.062-0.02851.6900.0230.0230.0000.0000.0000.000
38G56LEU0-0.001-0.01853.9210.1020.1020.0000.0000.0000.000
39G57ALA0-0.030-0.01153.9540.0960.0960.0000.0000.0000.000
40G58HIS0-0.086-0.02055.7830.0720.0720.0000.0000.0000.000
41G59GLY00.016-0.01057.5880.0780.0780.0000.0000.0000.000
42G60ASN0-0.044-0.00359.2890.0750.0750.0000.0000.0000.000
43G61LEU00.0280.00961.028-0.014-0.0140.0000.0000.0000.000
44G62GLU-1-0.929-0.96064.131-4.551-4.5510.0000.0000.0000.000
45G63TYR0-0.047-0.03159.681-0.003-0.0030.0000.0000.0000.000
46G64LYS10.9650.98756.5625.3095.3090.0000.0000.0000.000
47G65HIS0-0.004-0.01354.1490.0290.0290.0000.0000.0000.000
48G66PRO00.1090.04256.015-0.049-0.0490.0000.0000.0000.000
49G67TYR0-0.083-0.07550.379-0.092-0.0920.0000.0000.0000.000
50G68LEU0-0.097-0.04852.089-0.119-0.1190.0000.0000.0000.000
51G69GLU-1-0.929-0.95754.261-5.122-5.1220.0000.0000.0000.000
52G70ASP-1-0.929-0.95453.522-5.695-5.6950.0000.0000.0000.000
53G71ARG10.8210.89355.3255.5415.5410.0000.0000.0000.000
54G72ASP-1-0.891-0.94656.720-5.146-5.1460.0000.0000.0000.000
55G73VAL0-0.028-0.01752.394-0.046-0.0460.0000.0000.0000.000
56G74LYS10.8980.93955.6155.0445.0440.0000.0000.0000.000
57G75ARG10.7560.84251.8265.6975.6970.0000.0000.0000.000
58G76VAL00.0000.00347.755-0.015-0.0150.0000.0000.0000.000
59G77GLY00.0350.01746.763-0.017-0.0170.0000.0000.0000.000
60G78TYR00.014-0.00641.298-0.042-0.0420.0000.0000.0000.000
61G79LEU00.0160.02639.521-0.026-0.0260.0000.0000.0000.000
62G80VAL0-0.014-0.02635.790-0.114-0.1140.0000.0000.0000.000
63G81VAL0-0.0070.00531.354-0.081-0.0810.0000.0000.0000.000
64G82SER0-0.038-0.00431.146-0.121-0.1210.0000.0000.0000.000
65G83THR0-0.021-0.02025.6640.0460.0460.0000.0000.0000.000
66G84ASP-1-0.711-0.85927.759-9.420-9.4200.0000.0000.0000.000
67G85ARG10.7920.88623.04811.99111.9910.0000.0000.0000.000
68G86GLY00.0150.00824.3920.1440.1440.0000.0000.0000.000
69G87LEU00.0430.02017.609-0.264-0.2640.0000.0000.0000.000
70G88CYS00.0190.01919.955-0.383-0.3830.0000.0000.0000.000
71G89GLY00.0560.02221.7130.2630.2630.0000.0000.0000.000
72G90GLY00.0160.00123.0060.2450.2450.0000.0000.0000.000
73G91LEU0-0.0080.02424.2700.3210.3210.0000.0000.0000.000
74G92ASN00.028-0.00226.7340.3610.3610.0000.0000.0000.000
75G93ILE00.0360.02728.1720.2410.2410.0000.0000.0000.000
76G94ASN00.004-0.01628.2570.4430.4430.0000.0000.0000.000
77G95LEU0-0.0210.01831.4130.2260.2260.0000.0000.0000.000
78G96PHE00.010-0.00333.1220.1920.1920.0000.0000.0000.000
79G97LYS10.9730.99234.1248.1868.1860.0000.0000.0000.000
80G98LYS10.9130.96535.7907.7647.7640.0000.0000.0000.000
81G99LEU00.0370.01937.4930.1480.1480.0000.0000.0000.000
82G100LEU00.009-0.00338.4210.1750.1750.0000.0000.0000.000
83G101ALA0-0.028-0.00540.7170.1770.1770.0000.0000.0000.000
84G102GLU-1-0.869-0.95141.562-6.752-6.7520.0000.0000.0000.000
85G103MET0-0.0040.01143.1440.0930.0930.0000.0000.0000.000
86G104LYS10.9030.95845.3526.0846.0840.0000.0000.0000.000
87G105THR0-0.053-0.02846.7830.1460.1460.0000.0000.0000.000
88G106TRP00.0280.00046.9930.2020.2020.0000.0000.0000.000
89G107THR00.027-0.00449.1140.0820.0820.0000.0000.0000.000
90G108ASP-1-0.895-0.93351.084-5.689-5.6890.0000.0000.0000.000
91G109LYS10.8610.93252.6365.6935.6930.0000.0000.0000.000
92G110GLY00.0060.01554.9350.0790.0790.0000.0000.0000.000
93G111VAL0-0.0450.00051.4730.0310.0310.0000.0000.0000.000
94G112GLN00.0270.01651.847-0.145-0.1450.0000.0000.0000.000
95G113CYS0-0.032-0.00746.623-0.051-0.0510.0000.0000.0000.000
96G114ASP-1-0.776-0.85647.466-6.016-6.0160.0000.0000.0000.000
97G115LEU0-0.051-0.05041.540-0.106-0.1060.0000.0000.0000.000
98G116ALA00.0380.02642.0370.0380.0380.0000.0000.0000.000
99G117MET0-0.055-0.00936.744-0.215-0.2150.0000.0000.0000.000
100G118ILE00.0510.02533.562-0.015-0.0150.0000.0000.0000.000
101G119GLY00.0170.00732.330-0.173-0.1730.0000.0000.0000.000
102G120SER00.022-0.02431.0450.2450.2450.0000.0000.0000.000
103G121LYS10.8690.94427.36210.09910.0990.0000.0000.0000.000
104G122GLY00.0880.02031.9010.1590.1590.0000.0000.0000.000
105G123VAL00.0280.01734.8100.1990.1990.0000.0000.0000.000
106G124SER0-0.095-0.04234.0840.1120.1120.0000.0000.0000.000
107G125PHE0-0.015-0.02434.7330.1160.1160.0000.0000.0000.000
108G126PHE00.031-0.01736.5750.1260.1260.0000.0000.0000.000
109G127ASN0-0.0020.02239.6760.2400.2400.0000.0000.0000.000
110G128SER0-0.093-0.03838.8980.2060.2060.0000.0000.0000.000
111G129VAL0-0.029-0.00739.5540.1140.1140.0000.0000.0000.000
112G130GLY00.0230.03642.2680.1600.1600.0000.0000.0000.000
113G131GLY00.019-0.01243.379-0.138-0.1380.0000.0000.0000.000
114G132ASN0-0.035-0.01945.237-0.023-0.0230.0000.0000.0000.000
115G133VAL0-0.015-0.00941.632-0.047-0.0470.0000.0000.0000.000
116G134VAL00.0180.01444.5090.0420.0420.0000.0000.0000.000
117G135ALA0-0.003-0.00844.1860.0430.0430.0000.0000.0000.000
118G136GLN0-0.011-0.00839.0010.0330.0330.0000.0000.0000.000
119G137VAL00.0230.02236.0010.0690.0690.0000.0000.0000.000
120G138THR0-0.039-0.01933.827-0.054-0.0540.0000.0000.0000.000
121G139GLY0-0.035-0.01630.8560.0550.0550.0000.0000.0000.000
122G140MET00.0530.05130.821-0.057-0.0570.0000.0000.0000.000
123G141GLY0-0.032-0.01926.826-0.329-0.3290.0000.0000.0000.000
124G142ASP-1-0.860-0.95221.758-13.116-13.1160.0000.0000.0000.000
125G143ASN0-0.105-0.06025.029-0.266-0.2660.0000.0000.0000.000
126G144PRO00.0800.05528.1620.2620.2620.0000.0000.0000.000
127G145SER00.003-0.01431.096-0.001-0.0010.0000.0000.0000.000
128G146LEU00.0720.02834.2120.0730.0730.0000.0000.0000.000
129G147SER00.032-0.00537.5460.1240.1240.0000.0000.0000.000
130G148GLU-1-0.926-0.96034.663-8.516-8.5160.0000.0000.0000.000
131G149LEU0-0.023-0.01535.3110.0500.0500.0000.0000.0000.000
132G150ILE00.0000.01339.3260.1570.1570.0000.0000.0000.000
133G151GLY00.0180.01642.7730.1580.1580.0000.0000.0000.000
134G152PRO00.0420.00440.0030.1510.1510.0000.0000.0000.000
135G153VAL00.0150.01041.3280.1140.1140.0000.0000.0000.000
136G154LYS10.9490.98243.9796.2926.2920.0000.0000.0000.000
137G155VAL00.0110.01046.4950.1490.1490.0000.0000.0000.000
138G156MET0-0.022-0.00444.6310.1540.1540.0000.0000.0000.000
139G157LEU0-0.014-0.01047.0150.1110.1110.0000.0000.0000.000
140G158GLN0-0.019-0.00349.516-0.013-0.0130.0000.0000.0000.000
141G159ALA00.0030.00350.8800.1280.1280.0000.0000.0000.000
142G160TYR0-0.019-0.00550.8760.0900.0900.0000.0000.0000.000
143G161ASP-1-0.804-0.89052.977-5.673-5.6730.0000.0000.0000.000
144G162GLU-1-0.855-0.92355.482-5.381-5.3810.0000.0000.0000.000
145G163GLY0-0.0170.00856.5790.0870.0870.0000.0000.0000.000
146G164ARG10.8250.90952.9595.6365.6360.0000.0000.0000.000
147G165LEU0-0.021-0.00748.637-0.090-0.0900.0000.0000.0000.000
148G166ASP-1-0.747-0.85952.492-5.402-5.4020.0000.0000.0000.000
149G167LYS10.8840.94948.4535.9555.9550.0000.0000.0000.000
150G168LEU00.0030.01844.746-0.019-0.0190.0000.0000.0000.000
151G169TYR00.0240.00542.136-0.009-0.0090.0000.0000.0000.000
152G170ILE00.0030.01336.318-0.046-0.0460.0000.0000.0000.000
153G171VAL00.000-0.00735.899-0.011-0.0110.0000.0000.0000.000
154G172SER0-0.011-0.01632.393-0.186-0.1860.0000.0000.0000.000
155G173ASN0-0.032-0.03128.4220.1760.1760.0000.0000.0000.000
156G174LYS10.9931.00229.7698.2148.2140.0000.0000.0000.000
157G175PHE0-0.032-0.03021.465-0.284-0.2840.0000.0000.0000.000
158G176ILE0-0.0440.00225.6560.1670.1670.0000.0000.0000.000
159G177ASN00.0650.01321.595-0.405-0.4050.0000.0000.0000.000
160G178THR0-0.017-0.02616.5360.3300.3300.0000.0000.0000.000
161G179MET0-0.027-0.01217.544-0.539-0.5390.0000.0000.0000.000
162G180SER0-0.0240.00520.2990.4490.4490.0000.0000.0000.000
163G181GLN00.005-0.00421.5900.0020.0020.0000.0000.0000.000
164G182VAL00.0080.00126.3650.1260.1260.0000.0000.0000.000
165G183PRO00.0200.02929.9150.1040.1040.0000.0000.0000.000
166G184THR0-0.066-0.04832.3170.2240.2240.0000.0000.0000.000
167G185ILE00.0060.01135.326-0.103-0.1030.0000.0000.0000.000
168G186SER0-0.044-0.01638.3290.0670.0670.0000.0000.0000.000
169G187GLN00.019-0.01040.722-0.007-0.0070.0000.0000.0000.000
170G188LEU0-0.092-0.04440.794-0.060-0.0600.0000.0000.0000.000
171G189LEU0-0.0280.01644.6960.0740.0740.0000.0000.0000.000
172G190PRO00.0800.01948.404-0.065-0.0650.0000.0000.0000.000
173G191LEU0-0.021-0.01946.580-0.124-0.1240.0000.0000.0000.000
174G192PRO0-0.060-0.00144.8490.1190.1190.0000.0000.0000.000
175G200LYS10.9550.96354.7295.3395.3390.0000.0000.0000.000
176G201HIS00.0450.02554.803-0.098-0.0980.0000.0000.0000.000
177G202LYS10.8840.95451.1565.9835.9830.0000.0000.0000.000
178G203SER00.0290.01257.2500.0280.0280.0000.0000.0000.000
179G204TRP0-0.0130.01153.8490.0510.0510.0000.0000.0000.000
180G205ASP-1-0.742-0.87459.103-5.339-5.3390.0000.0000.0000.000
181G206TYR0-0.075-0.04652.087-0.045-0.0450.0000.0000.0000.000
182G207LEU00.0300.03958.7060.0800.0800.0000.0000.0000.000
183G208TYR0-0.083-0.08256.712-0.150-0.1500.0000.0000.0000.000
184G209GLU-1-0.909-0.92758.544-5.210-5.2100.0000.0000.0000.000
185G210PRO0-0.080-0.04457.961-0.113-0.1130.0000.0000.0000.000
186G211ASP-1-0.756-0.90960.289-5.050-5.0500.0000.0000.0000.000
187G212PRO00.027-0.00158.476-0.098-0.0980.0000.0000.0000.000
188G213LYS10.9551.00357.7704.8864.8860.0000.0000.0000.000
189G214ALA00.0110.00157.663-0.095-0.0950.0000.0000.0000.000
190G215LEU0-0.007-0.00854.225-0.137-0.1370.0000.0000.0000.000
191G216LEU00.0130.00352.890-0.154-0.1540.0000.0000.0000.000
192G217ASP-1-0.792-0.87352.831-5.840-5.8400.0000.0000.0000.000
193G218THR0-0.007-0.00149.979-0.130-0.1300.0000.0000.0000.000
194G219LEU0-0.039-0.03448.787-0.186-0.1860.0000.0000.0000.000
195G220LEU00.0230.01347.778-0.186-0.1860.0000.0000.0000.000
196G221ARG10.7880.88947.5715.7545.7540.0000.0000.0000.000
197G222ARG10.8960.95144.9386.4786.4780.0000.0000.0000.000
198G223TYR0-0.033-0.01842.369-0.260-0.2600.0000.0000.0000.000
199G224VAL00.0500.02942.586-0.187-0.1870.0000.0000.0000.000
200G225GLU-1-0.868-0.94041.723-7.092-7.0920.0000.0000.0000.000
201G226SER0-0.011-0.01138.855-0.255-0.2550.0000.0000.0000.000
202G227GLN00.013-0.00137.787-0.115-0.1150.0000.0000.0000.000
203G228VAL00.0330.02437.201-0.199-0.1990.0000.0000.0000.000
204G229TYR0-0.030-0.01731.782-0.318-0.3180.0000.0000.0000.000
205G230GLN0-0.048-0.03533.453-0.127-0.1270.0000.0000.0000.000
206G231GLY00.0730.03932.329-0.257-0.2570.0000.0000.0000.000
207G232VAL0-0.001-0.00331.188-0.285-0.2850.0000.0000.0000.000
208G233VAL0-0.059-0.02828.875-0.404-0.4040.0000.0000.0000.000
209G234GLU-1-0.781-0.89927.507-9.813-9.8130.0000.0000.0000.000
210G235ASN00.0610.04527.021-0.176-0.1760.0000.0000.0000.000
211G236LEU0-0.041-0.00124.176-0.371-0.3710.0000.0000.0000.000
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213G238SER0-0.016-0.02722.150-0.481-0.4810.0000.0000.0000.000
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