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: LZZV9

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 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1976844.216439
FMO2-HF: Nuclear repulsion 1905291.297748
FMO2-HF: Total energy -71552.918691
FMO2-MP2: Total energy -71762.735176


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.
99.929102.0824.341-2.833-3.660.001
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 : 0.998
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].
3S5LYS10.9991.0013.31222.61925.0890.009-1.130-1.3490.003
4S6THR0-0.0100.0062.2291.6530.8244.332-1.526-1.977-0.002
5S7PHE00.0450.0114.1652.4762.9880.000-0.177-0.3340.000
6S8ARG10.7840.8425.82023.82923.8290.0000.0000.0000.000
7S9LEU00.0010.0027.6921.6991.6990.0000.0000.0000.000
8S10VAL0-0.0030.0048.4531.6491.6490.0000.0000.0000.000
9S11VAL00.0250.0039.5261.4751.4750.0000.0000.0000.000
10S12ASP-1-0.848-0.91811.968-16.300-16.3000.0000.0000.0000.000
11S13ALA00.001-0.00913.4381.0961.0960.0000.0000.0000.000
12S14LEU00.0130.00413.6420.7640.7640.0000.0000.0000.000
13S15LEU0-0.028-0.01615.5660.9200.9200.0000.0000.0000.000
14S16MET0-0.049-0.02615.8500.9390.9390.0000.0000.0000.000
15S17ALA00.0080.01118.9810.6710.6710.0000.0000.0000.000
16S18ILE0-0.001-0.00619.0270.6340.6340.0000.0000.0000.000
17S19VAL00.0260.02622.1590.5910.5910.0000.0000.0000.000
18S20LEU00.0140.01022.5230.5400.5400.0000.0000.0000.000
19S21LEU0-0.0140.00424.5650.4600.4600.0000.0000.0000.000
20S22GLN0-0.021-0.04525.9130.0970.0970.0000.0000.0000.000
21S23ASN0-0.074-0.03127.9160.6640.6640.0000.0000.0000.000
22S24LEU0-0.002-0.00427.7150.3300.3300.0000.0000.0000.000
23S25VAL00.0040.01830.1620.3010.3010.0000.0000.0000.000
24S26PRO00.0370.00231.792-0.136-0.1360.0000.0000.0000.000
25S27PHE0-0.025-0.01232.5790.0000.0000.0000.0000.0000.000
26S28LEU00.0160.01027.638-0.086-0.0860.0000.0000.0000.000
27S29GLY00.0490.03630.162-0.197-0.1970.0000.0000.0000.000
28S30TYR0-0.036-0.04031.262-0.075-0.0750.0000.0000.0000.000
29S31ILE00.0490.02534.2790.0030.0030.0000.0000.0000.000
30S32PRO0-0.034-0.03937.1100.0670.0670.0000.0000.0000.000
31S33PHE0-0.0160.02040.740-0.016-0.0160.0000.0000.0000.000
32S34GLY00.0190.02343.4920.0900.0900.0000.0000.0000.000
33S35PRO00.001-0.00244.632-0.069-0.0690.0000.0000.0000.000
34S36PHE00.0260.01242.443-0.076-0.0760.0000.0000.0000.000
35S37SER00.016-0.02238.3130.0330.0330.0000.0000.0000.000
36S38MET0-0.0190.03135.450-0.150-0.1500.0000.0000.0000.000
37S39THR0-0.001-0.01631.774-0.181-0.1810.0000.0000.0000.000
38S40LEU00.0270.00629.450-0.061-0.0610.0000.0000.0000.000
39S41ILE0-0.027-0.01226.731-0.332-0.3320.0000.0000.0000.000
40S42GLY00.0270.02826.721-0.250-0.2500.0000.0000.0000.000
41S43LEU00.019-0.01226.143-0.322-0.3220.0000.0000.0000.000
42S44THR0-0.003-0.00122.473-0.391-0.3910.0000.0000.0000.000
43S45VAL00.0310.01321.760-0.652-0.6520.0000.0000.0000.000
44S46ILE00.0610.04222.147-0.422-0.4220.0000.0000.0000.000
45S47VAL0-0.015-0.00618.667-0.355-0.3550.0000.0000.0000.000
46S48ALA00.003-0.00517.694-0.534-0.5340.0000.0000.0000.000
47S49GLY00.0400.01417.768-0.557-0.5570.0000.0000.0000.000
48S50SER0-0.095-0.04419.361-0.167-0.1670.0000.0000.0000.000
49S51ALA00.015-0.01216.2900.0230.0230.0000.0000.0000.000
50S52LEU0-0.085-0.02511.794-1.201-1.2010.0000.0000.0000.000
51S53GLY00.0340.01314.619-0.557-0.5570.0000.0000.0000.000
52S54PRO00.0270.01017.2100.0270.0270.0000.0000.0000.000
53S55ARG10.8970.95413.65615.94115.9410.0000.0000.0000.000
54S56ASP-1-0.654-0.79913.391-18.160-18.1600.0000.0000.0000.000
55S57GLY00.0210.02216.5490.4680.4680.0000.0000.0000.000
56S58LEU0-0.040-0.00318.9260.5410.5410.0000.0000.0000.000
57S59LEU00.0150.00915.0830.5050.5050.0000.0000.0000.000
58S60ILE0-0.013-0.01617.4780.4830.4830.0000.0000.0000.000
59S61GLY00.0370.02220.6730.4700.4700.0000.0000.0000.000
60S62GLY00.008-0.02022.5350.4970.4970.0000.0000.0000.000
61S63PHE0-0.020-0.02221.2960.3670.3670.0000.0000.0000.000
62S64TRP00.0280.01423.4150.2920.2920.0000.0000.0000.000
63S65GLY00.0500.02426.4440.2950.2950.0000.0000.0000.000
64S66LEU0-0.0010.01125.8560.3350.3350.0000.0000.0000.000
65S67ILE0-0.002-0.00725.4430.2820.2820.0000.0000.0000.000
66S68THR0-0.038-0.03629.2250.2550.2550.0000.0000.0000.000
67S69PHE0-0.0090.01031.2290.2420.2420.0000.0000.0000.000
68S70VAL00.0550.02230.7250.2420.2420.0000.0000.0000.000
69S71ARG10.7950.90232.3038.7468.7460.0000.0000.0000.000
70S72ALA0-0.024-0.00134.7430.1960.1960.0000.0000.0000.000
71S73PHE0-0.047-0.01236.5000.2170.2170.0000.0000.0000.000
72S74THR0-0.037-0.03235.4790.0990.0990.0000.0000.0000.000
73S75TRP00.0060.00732.4950.0380.0380.0000.0000.0000.000
74S76PRO00.0410.03036.787-0.218-0.2180.0000.0000.0000.000
75S77SER0-0.009-0.00235.6700.0300.0300.0000.0000.0000.000
76S78SER00.0310.01737.7040.1400.1400.0000.0000.0000.000
77S79PRO00.0780.02440.866-0.019-0.0190.0000.0000.0000.000
78S80VAL0-0.005-0.01041.8390.0850.0850.0000.0000.0000.000
79S81ALA0-0.050-0.02238.524-0.084-0.0840.0000.0000.0000.000
80S82PRO00.016-0.00340.249-0.064-0.0640.0000.0000.0000.000
81S83LEU0-0.0250.00242.1030.0830.0830.0000.0000.0000.000
82S84ILE00.0390.02838.641-0.012-0.0120.0000.0000.0000.000
83S85PHE0-0.026-0.03435.511-0.107-0.1070.0000.0000.0000.000
84S86THR00.0710.03036.254-0.193-0.1930.0000.0000.0000.000
85S87ASN00.0180.00937.876-0.051-0.0510.0000.0000.0000.000
86S88PRO00.001-0.00232.431-0.064-0.0640.0000.0000.0000.000
87S89LEU00.0170.01032.561-0.251-0.2510.0000.0000.0000.000
88S90ILE00.0270.00733.757-0.205-0.2050.0000.0000.0000.000
89S91SER0-0.019-0.00533.132-0.110-0.1100.0000.0000.0000.000
90S92ILE0-0.006-0.00627.829-0.244-0.2440.0000.0000.0000.000
91S93LEU0-0.0050.00429.100-0.320-0.3200.0000.0000.0000.000
92S94PRO0-0.002-0.00129.874-0.247-0.2470.0000.0000.0000.000
93S95ARG10.8990.96427.3998.7028.7020.0000.0000.0000.000
94S96LEU00.0190.02223.824-0.400-0.4000.0000.0000.0000.000
95S97LEU0-0.032-0.02325.023-0.419-0.4190.0000.0000.0000.000
96S98MET0-0.0290.01427.354-0.041-0.0410.0000.0000.0000.000
97S99GLY00.0510.01623.446-0.179-0.1790.0000.0000.0000.000
98S100LEU0-0.034-0.02622.014-0.591-0.5910.0000.0000.0000.000
99S101VAL00.0240.01424.093-0.282-0.2820.0000.0000.0000.000
100S102ALA0-0.0070.02123.769-0.104-0.1040.0000.0000.0000.000
101S103GLY00.0270.00321.226-0.231-0.2310.0000.0000.0000.000
102S104SER0-0.025-0.03121.913-0.107-0.1070.0000.0000.0000.000
103S105LEU00.0300.02523.688-0.036-0.0360.0000.0000.0000.000
104S106TYR00.0240.01419.7010.3070.3070.0000.0000.0000.000
105S107LEU0-0.018-0.02418.694-0.080-0.0800.0000.0000.0000.000
106S108TRP00.0300.00022.6090.0650.0650.0000.0000.0000.000
107S109GLY00.0190.00226.1350.2440.2440.0000.0000.0000.000
108S110ARG10.8790.92421.38413.13713.1370.0000.0000.0000.000
109S111HIS00.0120.02624.521-0.217-0.2170.0000.0000.0000.000
110S112ARG10.8540.95025.87610.30410.3040.0000.0000.0000.000
111S113GLN0-0.035-0.02025.7760.1210.1210.0000.0000.0000.000
112S114TRP00.0300.04328.1490.2170.2170.0000.0000.0000.000
113S115SER00.007-0.02426.821-0.553-0.5530.0000.0000.0000.000
114S116MET0-0.033-0.02318.8490.0970.0970.0000.0000.0000.000
115S117ARG10.9080.93124.5779.9059.9050.0000.0000.0000.000
116S118GLN00.0920.05527.229-0.221-0.2210.0000.0000.0000.000
117S119ALA00.0220.02425.2010.1870.1870.0000.0000.0000.000
118S120MET0-0.0310.00220.0880.1170.1170.0000.0000.0000.000
119S121GLN00.0120.01525.7160.0710.0710.0000.0000.0000.000
120S122VAL00.0410.02229.3450.1540.1540.0000.0000.0000.000
121S123ALA0-0.002-0.00325.7390.2270.2270.0000.0000.0000.000
122S124ALA00.0080.00127.293-0.151-0.1510.0000.0000.0000.000
123S125GLY00.0450.01728.6380.1460.1460.0000.0000.0000.000
124S126CYS0-0.046-0.00530.3270.2830.2830.0000.0000.0000.000
125S127ALA0-0.0040.00827.5890.1440.1440.0000.0000.0000.000
126S128ALA00.0510.02429.6540.0350.0350.0000.0000.0000.000
127S129LEU00.1880.08832.1240.1430.1430.0000.0000.0000.000
128S130THR0-0.102-0.04930.6690.1100.1100.0000.0000.0000.000
129S131ASN0-0.144-0.09031.015-0.310-0.3100.0000.0000.0000.000
130S132THR00.018-0.02132.8110.1210.1210.0000.0000.0000.000
131S133VAL0-0.012-0.01336.3750.2060.2060.0000.0000.0000.000
132S134LEU00.0060.01732.8220.1890.1890.0000.0000.0000.000
133S135VAL00.0640.04535.3280.1420.1420.0000.0000.0000.000
134S136LEU0-0.003-0.00837.6330.1980.1980.0000.0000.0000.000
135S137GLY00.0060.00339.4290.1830.1830.0000.0000.0000.000
136S138LEU0-0.077-0.04634.9730.1050.1050.0000.0000.0000.000
137S139VAL0-0.010-0.00939.4430.1070.1070.0000.0000.0000.000
138S140PHE00.015-0.00242.2200.1910.1910.0000.0000.0000.000
139S141LEU0-0.042-0.02240.3670.1360.1360.0000.0000.0000.000
140S142PHE00.0170.00539.7240.0730.0730.0000.0000.0000.000
141S143TYR0-0.022-0.00944.3400.1480.1480.0000.0000.0000.000
142S144GLN0-0.057-0.02147.2780.0890.0890.0000.0000.0000.000
143S145THR00.002-0.00146.5840.0750.0750.0000.0000.0000.000
144S146PRO0-0.028-0.00347.606-0.064-0.0640.0000.0000.0000.000
145S147ALA0-0.010-0.01546.229-0.104-0.1040.0000.0000.0000.000
146S148VAL0-0.0010.01845.659-0.069-0.0690.0000.0000.0000.000
147S160LEU00.0460.00250.2680.0440.0440.0000.0000.0000.000
148S161GLY00.0990.03050.835-0.102-0.1020.0000.0000.0000.000
149S162TYR00.0150.00551.352-0.070-0.0700.0000.0000.0000.000
150S163VAL00.0200.02148.946-0.049-0.0490.0000.0000.0000.000
151S164LEU00.0040.03045.429-0.120-0.1200.0000.0000.0000.000
152S165MET00.0190.00747.065-0.164-0.1640.0000.0000.0000.000
153S166ILE00.004-0.00248.579-0.078-0.0780.0000.0000.0000.000
154S167SER0-0.021-0.01344.307-0.110-0.1100.0000.0000.0000.000
155S168LEU0-0.043-0.00543.342-0.170-0.1700.0000.0000.0000.000
156S169PHE00.0260.00244.511-0.115-0.1150.0000.0000.0000.000
157S170THR0-0.050-0.02044.129-0.021-0.0210.0000.0000.0000.000
158S171ASN0-0.043-0.04539.527-0.319-0.3190.0000.0000.0000.000
159S172GLY00.0060.00440.709-0.149-0.1490.0000.0000.0000.000
160S173ILE00.0220.00942.5380.0490.0490.0000.0000.0000.000
161S174PRO0-0.016-0.00238.789-0.094-0.0940.0000.0000.0000.000
162S175GLU-1-0.822-0.90035.587-8.630-8.6300.0000.0000.0000.000
163S176LEU00.0110.02137.081-0.162-0.1620.0000.0000.0000.000
164S177ILE00.0080.00137.275-0.029-0.0290.0000.0000.0000.000
165S178LEU0-0.009-0.00632.480-0.177-0.1770.0000.0000.0000.000
166S179ASP-1-0.883-0.94133.176-8.754-8.7540.0000.0000.0000.000
167S180VAL0-0.003-0.01034.404-0.160-0.1600.0000.0000.0000.000
168S181LEU0-0.080-0.01731.105-0.148-0.1480.0000.0000.0000.000
169S182VAL0-0.001-0.04028.951-0.231-0.2310.0000.0000.0000.000
170S183ALA00.0670.04129.616-0.283-0.2830.0000.0000.0000.000
171S184PRO0-0.037-0.00730.789-0.237-0.2370.0000.0000.0000.000
172S185LEU0-0.005-0.01128.550-0.375-0.3750.0000.0000.0000.000
173S186ILE00.0420.03024.206-0.340-0.3400.0000.0000.0000.000
174S187ALA0-0.0100.00525.135-0.505-0.5050.0000.0000.0000.000
175S188MET0-0.031-0.00624.455-0.539-0.5390.0000.0000.0000.000
176S189PRO0-0.0390.00322.761-0.514-0.5140.0000.0000.0000.000
177S190LEU00.0700.03219.115-0.352-0.3520.0000.0000.0000.000
178S191ARG10.8940.94019.36710.89010.8900.0000.0000.0000.000
179S192ARG10.9450.95119.45911.76411.7640.0000.0000.0000.000
180S193GLN00.0140.02415.915-1.513-1.5130.0000.0000.0000.000
181S194TRP00.0710.03314.032-0.571-0.5710.0000.0000.0000.000
182S195GLU-1-0.863-0.91114.999-17.183-17.1830.0000.0000.0000.000
183S196ARG10.8820.92612.87316.56916.5690.0000.0000.0000.000
184S197LEU00.0080.0029.129-1.885-1.8850.0000.0000.0000.000
185S198LYS10.8400.91010.49716.19416.1940.0000.0000.0000.000
186S199PRO0-0.083-0.00711.222-0.342-0.3420.0000.0000.0000.000
187S200GLN0-0.0210.0016.552-4.673-4.6730.0000.0000.0000.000