FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: G5921

Calculation Name: 4N7R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N7R

Chain ID: A

ChEMBL ID:

UniProt ID: Q9LU39

Base Structure: X-ray

Registration Date: 2023-09-24

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 405
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6383539.360019
FMO2-HF: Nuclear repulsion 6224210.031838
FMO2-HF: Total energy -159329.328181
FMO2-MP2: Total energy -159783.948982


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:94:ARG)


Summations of interaction energy for fragment #1(A:94: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.
-18.866-15.7710.02-1.5-1.615-0.002
Interaction energy analysis for fragmet #1(A:94:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.985 / q_NPA : 0.991
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].
3A96SER0-0.011-0.0103.868-0.0141.634-0.013-0.823-0.8130.004
4A97ILE00.0250.0236.3651.6651.6650.0000.0000.0000.000
5A98VAL0-0.055-0.0359.479-0.505-0.5050.0000.0000.0000.000
6A99VAL0-0.0090.01512.4790.5610.5610.0000.0000.0000.000
7A100ILE00.015-0.00314.897-0.154-0.1540.0000.0000.0000.000
8A101GLY00.0260.01318.6050.2900.2900.0000.0000.0000.000
9A102LEU0-0.032-0.00122.3800.0450.0450.0000.0000.0000.000
10A103SER00.0220.00426.0120.1360.1360.0000.0000.0000.000
11A104ILE00.0420.01627.9050.0860.0860.0000.0000.0000.000
12A105HIS10.8300.88727.12110.27710.2770.0000.0000.0000.000
13A106THR0-0.013-0.00125.8660.1150.1150.0000.0000.0000.000
14A107ALA00.007-0.00329.056-0.045-0.0450.0000.0000.0000.000
15A108PRO00.0350.04730.9640.0200.0200.0000.0000.0000.000
16A109VAL00.0950.04733.622-0.255-0.2550.0000.0000.0000.000
17A110GLU-1-0.784-0.87735.023-7.956-7.9560.0000.0000.0000.000
18A111MET0-0.131-0.04828.591-0.090-0.0900.0000.0000.0000.000
19A112ARG10.7570.82829.8058.8448.8440.0000.0000.0000.000
20A113GLU-1-0.777-0.89131.038-8.166-8.1660.0000.0000.0000.000
21A114LYS10.9030.96731.9998.9128.9120.0000.0000.0000.000
22A115LEU0-0.014-0.01225.183-0.203-0.2030.0000.0000.0000.000
23A116ALA00.0160.02328.215-0.339-0.3390.0000.0000.0000.000
24A117ILE00.0230.00925.327-0.062-0.0620.0000.0000.0000.000
25A118PRO00.0780.05929.488-0.137-0.1370.0000.0000.0000.000
26A119GLU-1-0.838-0.92829.599-9.401-9.4010.0000.0000.0000.000
27A120ALA0-0.012-0.01529.386-0.259-0.2590.0000.0000.0000.000
28A121GLU-1-0.838-0.90129.038-9.673-9.6730.0000.0000.0000.000
29A122TRP0-0.013-0.00924.864-0.429-0.4290.0000.0000.0000.000
30A123PRO00.014-0.00524.126-0.515-0.5150.0000.0000.0000.000
31A124ARG10.8140.89924.09510.12010.1200.0000.0000.0000.000
32A125ALA00.0350.00923.390-0.299-0.2990.0000.0000.0000.000
33A126ILE0-0.030-0.01418.803-0.523-0.5230.0000.0000.0000.000
34A127ALA0-0.009-0.00419.420-0.681-0.6810.0000.0000.0000.000
35A128GLU-1-0.782-0.87520.529-11.918-11.9180.0000.0000.0000.000
36A129LEU0-0.040-0.01417.323-0.564-0.5640.0000.0000.0000.000
37A130CYS0-0.053-0.01714.736-0.690-0.6900.0000.0000.0000.000
38A131GLY00.0100.02116.313-0.277-0.2770.0000.0000.0000.000
39A132LEU0-0.080-0.03115.4020.1720.1720.0000.0000.0000.000
40A133ASN0-0.048-0.04413.954-0.471-0.4710.0000.0000.0000.000
41A134HIS0-0.072-0.0529.098-2.984-2.9840.0000.0000.0000.000
42A135ILE0-0.051-0.0259.597-2.069-2.0690.0000.0000.0000.000
43A136GLU-1-0.862-0.9257.701-25.772-25.7720.0000.0000.0000.000
44A137GLU-1-0.829-0.90810.980-19.710-19.7100.0000.0000.0000.000
45A138ALA00.010-0.00613.389-0.531-0.5310.0000.0000.0000.000
46A139ALA0-0.012-0.01016.4150.5920.5920.0000.0000.0000.000
47A140VAL0-0.004-0.00419.420-0.310-0.3100.0000.0000.0000.000
48A141LEU0-0.0100.00722.1910.3570.3570.0000.0000.0000.000
49A142SER0-0.032-0.02324.125-0.017-0.0170.0000.0000.0000.000
50A143THR0-0.014-0.00627.5510.3530.3530.0000.0000.0000.000
51A144CYS00.0760.03430.310-0.081-0.0810.0000.0000.0000.000
52A145ASN00.0220.00930.0860.2280.2280.0000.0000.0000.000
53A146ARG10.7520.85323.99110.83410.8340.0000.0000.0000.000
54A147MET00.0040.03225.189-0.059-0.0590.0000.0000.0000.000
55A148GLU-1-0.768-0.85420.895-12.701-12.7010.0000.0000.0000.000
56A149ILE00.0270.01217.9420.1190.1190.0000.0000.0000.000
57A150TYR0-0.031-0.04115.794-0.509-0.5090.0000.0000.0000.000
58A151VAL00.013-0.00412.4910.3420.3420.0000.0000.0000.000
59A152LEU0-0.0170.0017.006-0.831-0.8310.0000.0000.0000.000
60A153ALA00.0320.0028.2710.8150.8150.0000.0000.0000.000
61A154LEU00.0060.0164.682-4.115-4.064-0.001-0.006-0.0440.000
62A155SER0-0.049-0.0294.626-4.323-4.219-0.001-0.008-0.0950.000
63A156GLN00.0550.0467.2451.5751.5750.0000.0000.0000.000
64A157HIS00.0450.0149.4911.3501.3500.0000.0000.0000.000
65A158ARG10.9290.9769.65427.51527.5150.0000.0000.0000.000
66A159GLY00.0750.03911.1221.2671.2670.0000.0000.0000.000
67A160VAL00.0240.01012.4371.3951.3950.0000.0000.0000.000
68A161LYS10.7850.89115.10017.05417.0540.0000.0000.0000.000
69A162GLU-1-0.766-0.86814.032-18.887-18.8870.0000.0000.0000.000
70A163VAL00.0470.02215.5530.9050.9050.0000.0000.0000.000
71A164THR0-0.021-0.02418.0820.9550.9550.0000.0000.0000.000
72A165GLU-1-0.829-0.90019.749-14.163-14.1630.0000.0000.0000.000
73A166TRP0-0.019-0.01920.4840.5240.5240.0000.0000.0000.000
74A167MET00.0240.01821.7920.3330.3330.0000.0000.0000.000
75A168SER0-0.066-0.02724.0330.5340.5340.0000.0000.0000.000
76A169LYS10.8340.91224.88711.97411.9740.0000.0000.0000.000
77A170THR0-0.065-0.05225.3060.2760.2760.0000.0000.0000.000
78A171SER00.0050.00027.8250.2940.2940.0000.0000.0000.000
79A172GLY0-0.0020.00530.0280.3370.3370.0000.0000.0000.000
80A173ILE0-0.050-0.01328.7710.2040.2040.0000.0000.0000.000
81A174PRO00.0500.04428.806-0.444-0.4440.0000.0000.0000.000
82A175VAL00.0700.02323.568-0.128-0.1280.0000.0000.0000.000
83A176SER00.0120.00825.826-0.321-0.3210.0000.0000.0000.000
84A177GLU-1-0.848-0.93828.179-9.257-9.2570.0000.0000.0000.000
85A178ILE00.0060.00123.809-0.091-0.0910.0000.0000.0000.000
86A179CYS0-0.081-0.06023.549-0.452-0.4520.0000.0000.0000.000
87A180GLN0-0.0180.00624.813-0.003-0.0030.0000.0000.0000.000
88A181HIS10.8470.91726.57410.15710.1570.0000.0000.0000.000
89A182ARG10.9010.95619.46014.34814.3480.0000.0000.0000.000
90A183PHE00.0010.01419.819-0.155-0.1550.0000.0000.0000.000
91A184LEU0-0.015-0.03115.833-0.347-0.3470.0000.0000.0000.000
92A185LEU0-0.0030.02115.5290.1570.1570.0000.0000.0000.000
93A186TYR00.031-0.00610.089-0.447-0.4470.0000.0000.0000.000
94A187ASN00.0260.0006.3490.3740.3740.0000.0000.0000.000
95A188LYS10.9290.9559.67918.40218.4020.0000.0000.0000.000
96A189ASP-1-0.828-0.89312.071-16.300-16.3000.0000.0000.0000.000
97A190ALA00.000-0.00512.9041.0071.0070.0000.0000.0000.000
98A191THR0-0.077-0.05612.2041.0471.0470.0000.0000.0000.000
99A192GLN00.0220.01215.0140.3920.3920.0000.0000.0000.000
100A193HIS00.002-0.01217.5870.7160.7160.0000.0000.0000.000
101A194ILE00.0040.00317.3820.6820.6820.0000.0000.0000.000
102A195PHE0-0.0090.00616.7500.6300.6300.0000.0000.0000.000
103A196GLU-1-0.778-0.87121.036-11.290-11.2900.0000.0000.0000.000
104A197VAL0-0.057-0.03322.8880.5980.5980.0000.0000.0000.000
105A198SER0-0.077-0.05922.6120.4780.4780.0000.0000.0000.000
106A199ALA0-0.027-0.00525.1480.3710.3710.0000.0000.0000.000
107A200GLY0-0.046-0.01527.0500.3560.3560.0000.0000.0000.000
108A201LEU00.0110.00326.5500.3100.3100.0000.0000.0000.000
109A202ASP-1-0.808-0.84626.000-10.307-10.3070.0000.0000.0000.000
110A203SER0-0.061-0.03828.1200.1400.1400.0000.0000.0000.000
111A204LEU00.002-0.00431.788-0.113-0.1130.0000.0000.0000.000
112A205VAL00.0170.01532.231-0.223-0.2230.0000.0000.0000.000
113A206LEU00.020-0.00330.3040.2390.2390.0000.0000.0000.000
114A207GLY00.0410.00434.0990.1770.1770.0000.0000.0000.000
115A208GLU-1-0.768-0.85335.269-8.002-8.0020.0000.0000.0000.000
116A209GLY00.0020.01633.5570.0000.0000.0000.0000.0000.000
117A210GLN0-0.049-0.04032.122-0.307-0.3070.0000.0000.0000.000
118A211ILE00.0860.05026.557-0.101-0.1010.0000.0000.0000.000
119A212LEU00.0540.04726.988-0.253-0.2530.0000.0000.0000.000
120A213ALA0-0.086-0.06128.234-0.157-0.1570.0000.0000.0000.000
121A214GLN0-0.005-0.00327.8580.1460.1460.0000.0000.0000.000
122A215VAL00.0410.02422.617-0.208-0.2080.0000.0000.0000.000
123A216LYS10.9130.95024.7158.8698.8690.0000.0000.0000.000
124A217GLN0-0.044-0.02726.870-0.162-0.1620.0000.0000.0000.000
125A218VAL00.0020.01022.103-0.054-0.0540.0000.0000.0000.000
126A219VAL0-0.003-0.00121.657-0.300-0.3000.0000.0000.0000.000
127A220LYS10.8740.93623.8339.2139.2130.0000.0000.0000.000
128A221VAL00.0200.00526.2320.1130.1130.0000.0000.0000.000
129A222GLY00.0620.01922.603-0.064-0.0640.0000.0000.0000.000
130A223GLN0-0.060-0.03522.552-0.659-0.6590.0000.0000.0000.000
131A224GLY0-0.0030.01724.2130.0190.0190.0000.0000.0000.000
132A225VAL0-0.053-0.01421.121-0.006-0.0060.0000.0000.0000.000
133A226ASN0-0.023-0.02018.850-0.878-0.8780.0000.0000.0000.000
134A227GLY00.1190.05516.760-0.566-0.5660.0000.0000.0000.000
135A228PHE0-0.0040.01316.338-0.766-0.7660.0000.0000.0000.000
136A229GLY00.0220.00514.0940.2980.2980.0000.0000.0000.000
137A230ARG10.9460.96912.03418.14718.1470.0000.0000.0000.000
138A231ASN00.014-0.0138.051-0.221-0.2210.0000.0000.0000.000
139A232ILE00.0330.01111.6200.8210.8210.0000.0000.0000.000
140A233SER0-0.0020.00714.6161.1371.1370.0000.0000.0000.000
141A234GLY0-0.018-0.01215.1960.7470.7470.0000.0000.0000.000
142A235LEU00.0090.01913.7380.6490.6490.0000.0000.0000.000
143A236PHE00.028-0.00215.8970.8390.8390.0000.0000.0000.000
144A237LYS10.8250.90419.25113.63813.6380.0000.0000.0000.000
145A238HIS00.0140.00417.6260.1460.1460.0000.0000.0000.000
146A239ALA00.0180.01319.6530.4460.4460.0000.0000.0000.000
147A240ILE0-0.058-0.03721.1640.6710.6710.0000.0000.0000.000
148A241THR0-0.056-0.02722.4710.6050.6050.0000.0000.0000.000
149A242VAL00.0850.05021.1940.4060.4060.0000.0000.0000.000
150A243GLY00.0290.01324.1940.3620.3620.0000.0000.0000.000
151A244LYS10.8250.90327.02710.29610.2960.0000.0000.0000.000
152A245ARG10.7720.85724.47910.66710.6670.0000.0000.0000.000
153A246VAL00.0210.00726.8380.3190.3190.0000.0000.0000.000
154A247ARG10.7410.83929.5548.3638.3630.0000.0000.0000.000
155A248THR0-0.030-0.02332.1720.2370.2370.0000.0000.0000.000
156A249GLU-1-0.862-0.90229.610-9.214-9.2140.0000.0000.0000.000
157A250THR0-0.035-0.02631.483-0.134-0.1340.0000.0000.0000.000
158A251ASN0-0.0100.00233.6780.1680.1680.0000.0000.0000.000
159A252ILE00.0280.01231.3760.1870.1870.0000.0000.0000.000
160A253ALA0-0.002-0.00634.7480.0780.0780.0000.0000.0000.000
161A254SER0-0.029-0.01236.1590.1750.1750.0000.0000.0000.000
162A255GLY00.0110.01838.1820.2030.2030.0000.0000.0000.000
163A256ALA0-0.036-0.00935.745-0.127-0.1270.0000.0000.0000.000
164A257VAL00.0200.01437.1940.1180.1180.0000.0000.0000.000
165A258SER0-0.027-0.02336.663-0.215-0.2150.0000.0000.0000.000
166A259VAL00.0600.00935.1540.1660.1660.0000.0000.0000.000
167A260SER0-0.001-0.02238.1410.0700.0700.0000.0000.0000.000
168A261SER00.0040.01840.9440.1140.1140.0000.0000.0000.000
169A262ALA00.0060.00440.2890.1430.1430.0000.0000.0000.000
170A263ALA00.0430.02042.2580.1000.1000.0000.0000.0000.000
171A264VAL0-0.017-0.00243.8500.1320.1320.0000.0000.0000.000
172A265GLU-1-0.780-0.86445.257-6.185-6.1850.0000.0000.0000.000
173A266LEU00.007-0.00343.7430.1040.1040.0000.0000.0000.000
174A267ALA00.0220.00846.7900.0950.0950.0000.0000.0000.000
175A268LEU0-0.023-0.02049.7380.1230.1230.0000.0000.0000.000
176A269MET0-0.100-0.04046.1320.0680.0680.0000.0000.0000.000
177A270LYS10.7740.88148.0926.3216.3210.0000.0000.0000.000
178A271LEU0-0.0240.01152.5150.0800.0800.0000.0000.0000.000
179A272PRO0-0.009-0.00255.806-0.006-0.0060.0000.0000.0000.000
180A273GLN0-0.0140.00056.095-0.020-0.0200.0000.0000.0000.000
181A274SER00.012-0.01159.0810.1350.1350.0000.0000.0000.000
182A275SER0-0.017-0.00558.594-0.108-0.1080.0000.0000.0000.000
183A276ASN0-0.011-0.00556.3660.0790.0790.0000.0000.0000.000
184A277VAL00.0220.01457.105-0.084-0.0840.0000.0000.0000.000
185A278SER0-0.021-0.00259.5470.0110.0110.0000.0000.0000.000
186A279ALA0-0.0020.01256.4680.0260.0260.0000.0000.0000.000
187A280ARG10.8090.88757.5275.0295.0290.0000.0000.0000.000
188A281MET00.0470.02253.253-0.123-0.1230.0000.0000.0000.000
189A282CYS0-0.037-0.00853.1460.0360.0360.0000.0000.0000.000
190A283VAL0-0.030-0.01147.154-0.119-0.1190.0000.0000.0000.000
191A284ILE00.0440.02647.5060.0400.0400.0000.0000.0000.000
192A285GLY00.0650.02444.676-0.166-0.1660.0000.0000.0000.000
193A286ALA00.0210.03144.728-0.077-0.0770.0000.0000.0000.000
194A287GLY0-0.013-0.00941.748-0.023-0.0230.0000.0000.0000.000
195A288LYS10.8850.92135.1398.1908.1900.0000.0000.0000.000
196A289MET00.0530.04836.653-0.012-0.0120.0000.0000.0000.000
197A290GLY00.1480.08240.3110.0690.0690.0000.0000.0000.000
198A291LYS10.7760.86043.1946.7646.7640.0000.0000.0000.000
199A292LEU0-0.040-0.02039.2920.0840.0840.0000.0000.0000.000
200A293VAL00.0160.02243.4790.0430.0430.0000.0000.0000.000
201A294ILE00.0360.01945.5820.1000.1000.0000.0000.0000.000
202A295LYS10.9480.97542.5916.8766.8760.0000.0000.0000.000
203A296HIS0-0.037-0.04345.2320.0110.0110.0000.0000.0000.000
204A297LEU00.0310.00947.3190.0810.0810.0000.0000.0000.000
205A298MET0-0.0110.01250.6130.1160.1160.0000.0000.0000.000
206A299ALA0-0.063-0.03148.7030.0850.0850.0000.0000.0000.000
207A300LYS10.7750.87348.4446.1416.1410.0000.0000.0000.000
208A301GLY00.0020.01252.4880.0750.0750.0000.0000.0000.000
209A302CYS0-0.0270.00453.9400.1030.1030.0000.0000.0000.000
210A303THR00.0510.01155.801-0.045-0.0450.0000.0000.0000.000
211A304LYS10.8100.88857.6595.0335.0330.0000.0000.0000.000
212A305VAL0-0.023-0.00752.060-0.056-0.0560.0000.0000.0000.000
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