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: 944R2

Calculation Name: 4RFS-S-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RFS

Chain ID: S

ChEMBL ID:

UniProt ID: Q03PY5

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 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973533.315751
FMO2-HF: Nuclear repulsion 1901978.986771
FMO2-HF: Total energy -71554.328979
FMO2-MP2: Total energy -71763.891095


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(S:3:ARG)


Summations of interaction energy for fragment #1(S:3:ARG)
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.
97.091100.1960.981-1.504-2.5820
Interaction energy analysis for fragmet #1(S:3:ARG)
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 : 1.005
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].
3S5LYS10.9990.9963.36922.40624.3010.008-0.850-1.0540.002
4S6THR0-0.0030.0092.5531.2682.0390.973-0.529-1.215-0.002
5S7PHE00.0520.0114.0832.2942.7330.000-0.125-0.3130.000
6S8ARG10.7580.8275.93224.11324.1130.0000.0000.0000.000
7S9LEU00.0390.0278.0741.5231.5230.0000.0000.0000.000
8S10VAL00.0190.0138.5041.6311.6310.0000.0000.0000.000
9S11VAL0-0.0010.0019.4361.5471.5470.0000.0000.0000.000
10S12ASP-1-0.855-0.93911.915-16.483-16.4830.0000.0000.0000.000
11S13ALA0-0.017-0.00813.3941.1931.1930.0000.0000.0000.000
12S14LEU00.004-0.00313.4750.9790.9790.0000.0000.0000.000
13S15LEU0-0.016-0.00715.4210.9630.9630.0000.0000.0000.000
14S16MET0-0.025-0.01016.2410.9810.9810.0000.0000.0000.000
15S17ALA00.0180.00718.9610.7250.7250.0000.0000.0000.000
16S18ILE0-0.014-0.00318.7740.6270.6270.0000.0000.0000.000
17S19VAL00.0160.01122.0760.6050.6050.0000.0000.0000.000
18S20LEU0-0.0030.00222.5120.5670.5670.0000.0000.0000.000
19S21LEU00.0070.00924.6450.4680.4680.0000.0000.0000.000
20S22GLN0-0.009-0.03125.4580.1000.1000.0000.0000.0000.000
21S23ASN0-0.061-0.03227.8680.6900.6900.0000.0000.0000.000
22S24LEU00.0140.00727.8360.3570.3570.0000.0000.0000.000
23S25VAL0-0.0020.01130.0830.2710.2710.0000.0000.0000.000
24S26PRO00.0400.01431.758-0.138-0.1380.0000.0000.0000.000
25S27PHE00.0010.00432.812-0.057-0.0570.0000.0000.0000.000
26S28LEU00.0210.01327.809-0.097-0.0970.0000.0000.0000.000
27S29GLY00.0290.02229.270-0.358-0.3580.0000.0000.0000.000
28S30TYR0-0.064-0.04431.046-0.060-0.0600.0000.0000.0000.000
29S31ILE00.0420.02934.2310.0210.0210.0000.0000.0000.000
30S32PRO0-0.030-0.03437.1390.0560.0560.0000.0000.0000.000
31S33PHE0-0.0210.01640.790-0.034-0.0340.0000.0000.0000.000
32S34GLY00.0220.01543.1770.1080.1080.0000.0000.0000.000
33S35PRO0-0.012-0.01344.487-0.084-0.0840.0000.0000.0000.000
34S36PHE00.0300.01442.420-0.027-0.0270.0000.0000.0000.000
35S37SER00.015-0.00838.0540.0340.0340.0000.0000.0000.000
36S38MET0-0.0080.03835.092-0.175-0.1750.0000.0000.0000.000
37S39THR00.004-0.02131.990-0.143-0.1430.0000.0000.0000.000
38S40LEU00.017-0.01129.137-0.110-0.1100.0000.0000.0000.000
39S41ILE0-0.0030.00826.469-0.370-0.3700.0000.0000.0000.000
40S42GLY00.0290.02026.364-0.300-0.3000.0000.0000.0000.000
41S43LEU00.027-0.00325.669-0.298-0.2980.0000.0000.0000.000
42S44THR0-0.016-0.02522.348-0.374-0.3740.0000.0000.0000.000
43S45VAL00.0170.01521.591-0.654-0.6540.0000.0000.0000.000
44S46ILE00.0500.02521.985-0.418-0.4180.0000.0000.0000.000
45S47VAL0-0.043-0.01118.379-0.421-0.4210.0000.0000.0000.000
46S48ALA00.0150.01117.458-0.637-0.6370.0000.0000.0000.000
47S49GLY00.0350.00817.443-0.618-0.6180.0000.0000.0000.000
48S50SER0-0.102-0.06019.182-0.167-0.1670.0000.0000.0000.000
49S51ALA0-0.002-0.01215.7210.0430.0430.0000.0000.0000.000
50S52LEU0-0.058-0.00811.451-1.282-1.2820.0000.0000.0000.000
51S53GLY00.0440.01614.296-0.631-0.6310.0000.0000.0000.000
52S54PRO00.0260.01916.9310.1330.1330.0000.0000.0000.000
53S55ARG10.9100.96814.18515.88415.8840.0000.0000.0000.000
54S56ASP-1-0.673-0.81313.622-18.044-18.0440.0000.0000.0000.000
55S57GLY00.0120.00816.6740.4720.4720.0000.0000.0000.000
56S58LEU0-0.040-0.01019.6020.4680.4680.0000.0000.0000.000
57S59LEU0-0.0130.00615.2770.4940.4940.0000.0000.0000.000
58S60ILE00.007-0.00717.4020.5310.5310.0000.0000.0000.000
59S61GLY00.0440.02320.8000.4790.4790.0000.0000.0000.000
60S62GLY00.018-0.01523.0130.4780.4780.0000.0000.0000.000
61S63PHE0-0.023-0.01021.4440.3570.3570.0000.0000.0000.000
62S64TRP00.0380.01323.5770.3150.3150.0000.0000.0000.000
63S65GLY00.0600.02726.4340.3510.3510.0000.0000.0000.000
64S66LEU0-0.0010.00826.2060.3760.3760.0000.0000.0000.000
65S67ILE00.0100.00425.3570.3070.3070.0000.0000.0000.000
66S68THR0-0.095-0.06529.1090.3630.3630.0000.0000.0000.000
67S69PHE00.0120.01031.5480.2440.2440.0000.0000.0000.000
68S70VAL00.0260.00930.5180.2320.2320.0000.0000.0000.000
69S71ARG10.8050.90932.2348.8338.8330.0000.0000.0000.000
70S72ALA0-0.018-0.00734.7430.2110.2110.0000.0000.0000.000
71S73PHE0-0.0100.00136.6130.2350.2350.0000.0000.0000.000
72S74THR0-0.072-0.04335.4940.0980.0980.0000.0000.0000.000
73S75TRP0-0.004-0.00632.7780.0110.0110.0000.0000.0000.000
74S76PRO00.0230.02336.972-0.213-0.2130.0000.0000.0000.000
75S77SER00.0050.00535.5900.0730.0730.0000.0000.0000.000
76S78SER00.0200.00437.6760.0900.0900.0000.0000.0000.000
77S79PRO00.0470.01941.070-0.024-0.0240.0000.0000.0000.000
78S80VAL00.0390.01441.8890.0930.0930.0000.0000.0000.000
79S81ALA0-0.023-0.00338.426-0.057-0.0570.0000.0000.0000.000
80S82PRO00.0360.00240.033-0.080-0.0800.0000.0000.0000.000
81S83LEU0-0.032-0.00341.9840.0680.0680.0000.0000.0000.000
82S84ILE0-0.0030.01338.7660.0390.0390.0000.0000.0000.000
83S85PHE00.017-0.01535.634-0.120-0.1200.0000.0000.0000.000
84S86THR00.0480.03136.115-0.236-0.2360.0000.0000.0000.000
85S87ASN00.0390.01638.078-0.091-0.0910.0000.0000.0000.000
86S88PRO00.0210.01732.976-0.107-0.1070.0000.0000.0000.000
87S89LEU0-0.010-0.01133.015-0.256-0.2560.0000.0000.0000.000
88S90ILE00.0090.00634.129-0.164-0.1640.0000.0000.0000.000
89S91SER0-0.027-0.02332.816-0.107-0.1070.0000.0000.0000.000
90S92ILE0-0.035-0.01727.895-0.279-0.2790.0000.0000.0000.000
91S93LEU00.0090.01229.107-0.330-0.3300.0000.0000.0000.000
92S94PRO00.0200.00929.803-0.258-0.2580.0000.0000.0000.000
93S95ARG10.8400.93527.6738.6668.6660.0000.0000.0000.000
94S96LEU0-0.0120.01224.032-0.431-0.4310.0000.0000.0000.000
95S97LEU00.006-0.00325.200-0.407-0.4070.0000.0000.0000.000
96S98MET0-0.0170.01827.259-0.324-0.3240.0000.0000.0000.000
97S99GLY00.0580.02723.723-0.207-0.2070.0000.0000.0000.000
98S100LEU0-0.022-0.01521.943-0.582-0.5820.0000.0000.0000.000
99S101VAL00.0150.02123.920-0.305-0.3050.0000.0000.0000.000
100S102ALA00.0030.01223.561-0.110-0.1100.0000.0000.0000.000
101S103GLY00.0250.00220.902-0.242-0.2420.0000.0000.0000.000
102S104SER0-0.070-0.06221.598-0.128-0.1280.0000.0000.0000.000
103S105LEU00.0490.01523.730-0.017-0.0170.0000.0000.0000.000
104S106TYR00.0270.01919.0890.3250.3250.0000.0000.0000.000
105S107LEU0-0.016-0.01518.441-0.016-0.0160.0000.0000.0000.000
106S108TRP00.0460.02022.4590.0810.0810.0000.0000.0000.000
107S109GLY00.019-0.00126.0640.2910.2910.0000.0000.0000.000
108S110ARG10.8480.91021.13913.25413.2540.0000.0000.0000.000
109S111HIS00.0150.01724.546-0.159-0.1590.0000.0000.0000.000
110S112ARG10.8520.94225.83410.41310.4130.0000.0000.0000.000
111S113GLN0-0.024-0.00725.7120.1090.1090.0000.0000.0000.000
112S114TRP00.0110.03028.0630.0990.0990.0000.0000.0000.000
113S115SER00.025-0.01526.581-0.604-0.6040.0000.0000.0000.000
114S116MET0-0.035-0.02818.4590.0290.0290.0000.0000.0000.000
115S117ARG10.9030.93624.3079.8869.8860.0000.0000.0000.000
116S118GLN00.1020.06627.066-0.241-0.2410.0000.0000.0000.000
117S119ALA00.0280.01925.0050.1600.1600.0000.0000.0000.000
118S120MET0-0.0260.00519.9000.0540.0540.0000.0000.0000.000
119S121GLN00.0260.02525.535-0.021-0.0210.0000.0000.0000.000
120S122VAL00.0250.01529.1910.2090.2090.0000.0000.0000.000
121S123ALA00.0060.00825.5860.2010.2010.0000.0000.0000.000
122S124ALA0-0.005-0.00227.4040.0360.0360.0000.0000.0000.000
123S125GLY00.0660.03828.3740.1330.1330.0000.0000.0000.000
124S126CYS0-0.035-0.01629.9930.2420.2420.0000.0000.0000.000
125S127ALA0-0.0080.01527.3640.1220.1220.0000.0000.0000.000
126S128ALA00.0140.01229.4310.0980.0980.0000.0000.0000.000
127S129LEU00.0670.03632.1470.1750.1750.0000.0000.0000.000
128S130THR0-0.072-0.06230.9580.0850.0850.0000.0000.0000.000
129S131ASN0-0.029-0.00831.023-0.202-0.2020.0000.0000.0000.000
130S132THR00.021-0.03232.8370.1220.1220.0000.0000.0000.000
131S133VAL0-0.016-0.01736.4690.2130.2130.0000.0000.0000.000
132S134LEU0-0.035-0.00432.9090.1650.1650.0000.0000.0000.000
133S135VAL00.0290.01635.2140.1370.1370.0000.0000.0000.000
134S136LEU0-0.026-0.00737.5190.2010.2010.0000.0000.0000.000
135S137GLY00.0290.01139.7410.1840.1840.0000.0000.0000.000
136S138LEU0-0.039-0.02335.0630.1380.1380.0000.0000.0000.000
137S139VAL00.014-0.00239.6810.1300.1300.0000.0000.0000.000
138S140PHE0-0.006-0.00442.3050.1910.1910.0000.0000.0000.000
139S141LEU0-0.036-0.02140.6070.1430.1430.0000.0000.0000.000
140S142PHE00.016-0.00539.8280.0860.0860.0000.0000.0000.000
141S143TYR0-0.062-0.01144.4650.1540.1540.0000.0000.0000.000
142S144GLN0-0.029-0.00247.7670.0840.0840.0000.0000.0000.000
143S145THR0-0.008-0.01646.9870.0750.0750.0000.0000.0000.000
144S146PRO0-0.0180.00747.573-0.088-0.0880.0000.0000.0000.000
145S147ALA0-0.009-0.02045.924-0.093-0.0930.0000.0000.0000.000
146S148VAL0-0.0160.01445.8910.0060.0060.0000.0000.0000.000
147S160LEU00.0610.01449.9960.0420.0420.0000.0000.0000.000
148S161GLY00.0630.02451.106-0.083-0.0830.0000.0000.0000.000
149S162TYR00.0230.01051.456-0.074-0.0740.0000.0000.0000.000
150S163VAL00.0390.02549.297-0.050-0.0500.0000.0000.0000.000
151S164LEU00.0310.02645.411-0.122-0.1220.0000.0000.0000.000
152S165MET00.0290.01047.106-0.171-0.1710.0000.0000.0000.000
153S166ILE0-0.002-0.00248.725-0.071-0.0710.0000.0000.0000.000
154S167SER0-0.007-0.01144.502-0.119-0.1190.0000.0000.0000.000
155S168LEU0-0.0270.00243.332-0.177-0.1770.0000.0000.0000.000
156S169PHE00.0250.00944.248-0.137-0.1370.0000.0000.0000.000
157S170THR0-0.081-0.04444.474-0.075-0.0750.0000.0000.0000.000
158S171ASN0-0.036-0.02739.390-0.321-0.3210.0000.0000.0000.000
159S172GLY00.0210.00140.516-0.167-0.1670.0000.0000.0000.000
160S173ILE00.0130.00442.2330.0780.0780.0000.0000.0000.000
161S174PRO0-0.020-0.00338.803-0.106-0.1060.0000.0000.0000.000
162S175GLU-1-0.778-0.88935.153-8.601-8.6010.0000.0000.0000.000
163S176LEU00.0010.01836.979-0.157-0.1570.0000.0000.0000.000
164S177ILE00.010-0.00237.369-0.061-0.0610.0000.0000.0000.000
165S178LEU0-0.0180.00232.301-0.189-0.1890.0000.0000.0000.000
166S179ASP-1-0.861-0.94133.222-8.821-8.8210.0000.0000.0000.000
167S180VAL0-0.012-0.01033.979-0.202-0.2020.0000.0000.0000.000
168S181LEU0-0.0340.00430.855-0.110-0.1100.0000.0000.0000.000
169S182VAL0-0.028-0.03728.912-0.281-0.2810.0000.0000.0000.000
170S183ALA00.0490.02829.650-0.305-0.3050.0000.0000.0000.000
171S184PRO0-0.051-0.02030.839-0.238-0.2380.0000.0000.0000.000
172S185LEU00.0040.00328.393-0.340-0.3400.0000.0000.0000.000
173S186ILE00.0570.02324.003-0.384-0.3840.0000.0000.0000.000
174S187ALA00.0350.01224.736-0.521-0.5210.0000.0000.0000.000
175S188MET0-0.049-0.01024.727-0.464-0.4640.0000.0000.0000.000
176S189PRO0-0.0030.00822.568-0.429-0.4290.0000.0000.0000.000
177S190LEU00.0570.04019.295-0.670-0.6700.0000.0000.0000.000
178S191ARG10.8730.92519.16411.10211.1020.0000.0000.0000.000
179S192ARG10.9310.94319.05811.94511.9450.0000.0000.0000.000
180S193GLN00.0190.03015.562-1.635-1.6350.0000.0000.0000.000
181S194TRP00.0720.03113.611-0.738-0.7380.0000.0000.0000.000
182S195GLU-1-0.850-0.90114.708-17.499-17.4990.0000.0000.0000.000
183S196ARG10.8310.90012.66417.16817.1680.0000.0000.0000.000
184S197LEU00.0190.0208.480-2.049-2.0490.0000.0000.0000.000
185S198LYS10.8490.90210.10016.26316.2630.0000.0000.0000.000
186S199PRO0-0.0170.02010.634-0.289-0.2890.0000.0000.0000.000
187S200GLN0-0.079-0.0345.968-6.874-6.8740.0000.0000.0000.000