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: 6Y22Z

Calculation Name: 4B89-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4B89

Chain ID: A

ChEMBL ID:

UniProt ID: P25655

Base Structure: X-ray

Registration Date: 2023-09-23

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2963100.924609
FMO2-HF: Nuclear repulsion 2871842.775715
FMO2-HF: Total energy -91258.148894
FMO2-MP2: Total energy -91528.192578


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:770:GLU)


Summations of interaction energy for fragment #1(A:770:GLU)
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.
-216.031-221.67634.902-16.209-13.0480.171
Interaction energy analysis for fragmet #1(A:770:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.795 / q_NPA : -0.888
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].
3A772ILE00.0140.0113.3995.5307.9310.016-1.242-1.175-0.002
4A773PRO00.014-0.0056.142-3.525-3.5250.0000.0000.0000.000
5A774LEU0-0.0020.0109.539-1.403-1.4030.0000.0000.0000.000
6A775LYS10.8610.90712.325-20.373-20.3730.0000.0000.0000.000
7A776PHE0-0.0030.00615.074-1.014-1.0140.0000.0000.0000.000
8A777PHE00.007-0.00915.289-0.901-0.9010.0000.0000.0000.000
9A778ALA00.0010.01015.9240.8310.8310.0000.0000.0000.000
10A779VAL0-0.040-0.03216.525-0.673-0.6730.0000.0000.0000.000
11A780ASP-1-0.805-0.86319.03812.39212.3920.0000.0000.0000.000
12A781GLU-1-0.749-0.84519.94013.80313.8030.0000.0000.0000.000
13A782VAL0-0.037-0.01723.347-0.370-0.3700.0000.0000.0000.000
14A783SER0-0.010-0.00326.208-0.111-0.1110.0000.0000.0000.000
15A784CYS0-0.044-0.02029.054-0.273-0.2730.0000.0000.0000.000
16A785GLN00.0260.02030.8320.0500.0500.0000.0000.0000.000
17A786ILE0-0.026-0.00133.450-0.137-0.1370.0000.0000.0000.000
18A787ASN00.0570.02431.6440.4340.4340.0000.0000.0000.000
19A788GLN0-0.051-0.03727.9500.0360.0360.0000.0000.0000.000
20A789GLU-1-0.800-0.87529.3568.6118.6110.0000.0000.0000.000
21A790GLY0-0.031-0.02427.7970.2050.2050.0000.0000.0000.000
22A791ALA00.0060.00128.422-0.252-0.2520.0000.0000.0000.000
23A792PRO00.0450.03731.0910.1450.1450.0000.0000.0000.000
24A793LYS10.9810.96032.567-8.248-8.2480.0000.0000.0000.000
25A794ASP-1-0.732-0.85534.2487.6597.6590.0000.0000.0000.000
26A795VAL0-0.046-0.00433.420-0.046-0.0460.0000.0000.0000.000
27A796VAL0-0.044-0.02330.0570.0900.0900.0000.0000.0000.000
28A797GLU-1-0.928-0.95832.5497.5747.5740.0000.0000.0000.000
29A798LYS10.8830.92835.252-7.461-7.4610.0000.0000.0000.000
30A799VAL0-0.017-0.00731.054-0.018-0.0180.0000.0000.0000.000
31A800LEU0-0.024-0.01429.1240.0830.0830.0000.0000.0000.000
32A801PHE0-0.0050.01033.018-0.034-0.0340.0000.0000.0000.000
33A802VAL00.0090.00035.460-0.095-0.0950.0000.0000.0000.000
34A803LEU0-0.026-0.02629.410-0.024-0.0240.0000.0000.0000.000
35A804ASN00.0040.00632.0330.2220.2220.0000.0000.0000.000
36A805ASN0-0.020-0.00734.450-0.223-0.2230.0000.0000.0000.000
37A806VAL0-0.049-0.00235.084-0.241-0.2410.0000.0000.0000.000
38A807THR00.009-0.01037.1680.0550.0550.0000.0000.0000.000
39A808LEU00.034-0.00637.798-0.074-0.0740.0000.0000.0000.000
40A809ALA00.0190.01940.507-0.080-0.0800.0000.0000.0000.000
41A810ASN00.0130.01241.396-0.023-0.0230.0000.0000.0000.000
42A811LEU00.0330.02637.3820.0300.0300.0000.0000.0000.000
43A812ASN00.0290.00740.7090.1810.1810.0000.0000.0000.000
44A813ASN00.0740.03642.823-0.014-0.0140.0000.0000.0000.000
45A814LYS10.8520.92638.910-7.171-7.1710.0000.0000.0000.000
46A815VAL0-0.009-0.00837.1290.1460.1460.0000.0000.0000.000
47A816ASP-1-0.838-0.91939.4986.8626.8620.0000.0000.0000.000
48A817GLU-1-0.871-0.91741.0496.6176.6170.0000.0000.0000.000
49A818LEU0-0.019-0.00934.1290.0630.0630.0000.0000.0000.000
50A819LYS10.8400.90438.134-7.056-7.0560.0000.0000.0000.000
51A820LYS10.8080.91239.908-6.565-6.5650.0000.0000.0000.000
52A821SER0-0.003-0.00837.151-0.078-0.0780.0000.0000.0000.000
53A822LEU0-0.055-0.01831.7400.1840.1840.0000.0000.0000.000
54A823THR00.0340.00135.669-0.046-0.0460.0000.0000.0000.000
55A824PRO00.033-0.01634.5550.2220.2220.0000.0000.0000.000
56A825ASN00.0180.03032.8810.1660.1660.0000.0000.0000.000
57A826TYR00.011-0.00430.5700.2180.2180.0000.0000.0000.000
58A827PHE00.0290.01829.8730.1830.1830.0000.0000.0000.000
59A828SER00.0730.04424.5540.3230.3230.0000.0000.0000.000
60A829TRP00.0180.02725.0220.3740.3740.0000.0000.0000.000
61A830PHE00.0520.01125.5850.2860.2860.0000.0000.0000.000
62A831SER00.001-0.03224.7900.0750.0750.0000.0000.0000.000
63A832THR00.000-0.01320.1710.5160.5160.0000.0000.0000.000
64A833TYR00.0120.03321.5280.3610.3610.0000.0000.0000.000
65A834LEU00.0240.00923.1780.2570.2570.0000.0000.0000.000
66A835VAL0-0.010-0.00319.7010.1160.1160.0000.0000.0000.000
67A836THR0-0.069-0.05217.7920.4020.4020.0000.0000.0000.000
68A837GLN0-0.009-0.01018.8940.2880.2880.0000.0000.0000.000
69A838ARG10.8340.90321.654-10.024-10.0240.0000.0000.0000.000
70A839ALA00.0120.01622.3620.0000.0000.0000.0000.0000.000
71A840LYS10.8830.94415.415-15.321-15.3210.0000.0000.0000.000
72A841THR0-0.003-0.00219.8920.3550.3550.0000.0000.0000.000
73A842GLU-1-0.781-0.84722.1479.7419.7410.0000.0000.0000.000
74A843PRO00.005-0.01124.224-0.212-0.2120.0000.0000.0000.000
75A844ASN0-0.033-0.02426.4390.0470.0470.0000.0000.0000.000
76A845TYR00.0530.03328.976-0.285-0.2850.0000.0000.0000.000
77A846HIS0-0.089-0.03923.888-0.304-0.3040.0000.0000.0000.000
78A847ASP-1-0.804-0.88428.9118.2398.2390.0000.0000.0000.000
79A848LEU00.0450.03332.506-0.100-0.1000.0000.0000.0000.000
80A849TYR0-0.022-0.04727.674-0.217-0.2170.0000.0000.0000.000
81A850SER0-0.052-0.03130.439-0.042-0.0420.0000.0000.0000.000
82A851LYS10.8520.90131.565-8.174-8.1740.0000.0000.0000.000
83A852VAL00.0260.01733.010-0.193-0.1930.0000.0000.0000.000
84A853ILE0-0.031-0.01128.573-0.088-0.0880.0000.0000.0000.000
85A854VAL0-0.041-0.02133.135-0.105-0.1050.0000.0000.0000.000
86A855ALA00.0170.01136.125-0.156-0.1560.0000.0000.0000.000
87A856MET0-0.013-0.00834.589-0.229-0.2290.0000.0000.0000.000
88A857GLY0-0.0210.00637.332-0.077-0.0770.0000.0000.0000.000
89A858SER0-0.0100.00434.4190.0120.0120.0000.0000.0000.000
90A859GLY00.0460.00633.6940.2470.2470.0000.0000.0000.000
91A860LEU00.0180.02030.5830.2480.2480.0000.0000.0000.000
92A861LEU00.0030.00829.3370.3320.3320.0000.0000.0000.000
93A862HIS0-0.058-0.04128.8860.2370.2370.0000.0000.0000.000
94A863GLN0-0.018-0.01827.9460.4760.4760.0000.0000.0000.000
95A864PHE00.0720.02325.0260.4690.4690.0000.0000.0000.000
96A865MET0-0.0070.02624.0810.6270.6270.0000.0000.0000.000
97A866VAL00.0140.01223.5460.4870.4870.0000.0000.0000.000
98A867ASN0-0.0200.00221.3740.8800.8800.0000.0000.0000.000
99A868VAL00.0480.01719.3090.7320.7320.0000.0000.0000.000
100A869THR0-0.033-0.03518.3500.7050.7050.0000.0000.0000.000
101A870LEU0-0.022-0.01117.9990.6350.6350.0000.0000.0000.000
102A871ARG10.8100.85615.514-13.463-13.4630.0000.0000.0000.000
103A872GLN00.0080.00313.8150.7990.7990.0000.0000.0000.000
104A873LEU0-0.002-0.00513.1420.9390.9390.0000.0000.0000.000
105A874PHE00.0260.02010.5950.9060.9060.0000.0000.0000.000
106A875VAL00.0300.0248.2941.5971.5970.0000.0000.0000.000
107A876LEU0-0.0060.0048.3371.9621.9620.0000.0000.0000.000
108A877LEU0-0.002-0.0099.2141.4071.4070.0000.0000.0000.000
109A878SER0-0.004-0.0077.6090.8180.8180.0000.0000.0000.000
110A879THR0-0.020-0.0204.0684.1754.259-0.001-0.028-0.0550.000
111A880LYS10.8100.8951.769-152.750-161.24034.888-14.914-11.4840.173
112A881ASP-1-0.802-0.9014.21628.57628.936-0.001-0.025-0.3340.000
113A882GLU-1-0.787-0.9096.07522.12622.1260.0000.0000.0000.000
114A883GLN0-0.069-0.0439.410-3.196-3.1960.0000.0000.0000.000
115A884ALA00.0010.0116.077-1.831-1.8310.0000.0000.0000.000
116A885ILE0-0.0470.0038.087-1.573-1.5730.0000.0000.0000.000
117A886ASP-1-0.781-0.8819.99914.69514.6950.0000.0000.0000.000
118A887LYS10.8770.90612.543-20.601-20.6010.0000.0000.0000.000
119A888LYS10.8550.93215.875-12.631-12.6310.0000.0000.0000.000
120A889HIS00.0330.00514.867-0.187-0.1870.0000.0000.0000.000
121A890LEU00.0100.01813.739-0.551-0.5510.0000.0000.0000.000
122A891LYS10.8530.90816.188-14.033-14.0330.0000.0000.0000.000
123A892ASN0-0.016-0.01419.773-0.922-0.9220.0000.0000.0000.000
124A893LEU00.0400.01115.925-0.521-0.5210.0000.0000.0000.000
125A894ALA00.0110.01819.375-0.309-0.3090.0000.0000.0000.000
126A895SER00.0180.00220.854-0.617-0.6170.0000.0000.0000.000
127A896TRP0-0.0100.01122.140-0.661-0.6610.0000.0000.0000.000
128A897LEU00.0390.01221.087-0.378-0.3780.0000.0000.0000.000
129A898GLY00.0230.03023.969-0.339-0.3390.0000.0000.0000.000
130A899CYS0-0.065-0.04226.806-0.484-0.4840.0000.0000.0000.000
131A900ILE00.0080.01324.694-0.415-0.4150.0000.0000.0000.000
132A901THR0-0.057-0.05226.640-0.051-0.0510.0000.0000.0000.000
133A902LEU00.0060.01527.947-0.356-0.3560.0000.0000.0000.000
134A903ALA00.0610.03430.935-0.329-0.3290.0000.0000.0000.000
135A904LEU0-0.065-0.02131.741-0.339-0.3390.0000.0000.0000.000
136A905ASN0-0.066-0.04134.237-0.142-0.1420.0000.0000.0000.000
137A906LYS10.9360.98031.489-8.782-8.7820.0000.0000.0000.000
138A907PRO00.0420.02130.7960.2280.2280.0000.0000.0000.000
139A908ILE00.0430.02224.2000.0810.0810.0000.0000.0000.000
140A909LYS10.8650.92925.834-10.711-10.7110.0000.0000.0000.000
141A910HIS00.0900.03724.7750.3460.3460.0000.0000.0000.000
142A911LYS10.8600.91723.643-11.129-11.1290.0000.0000.0000.000
143A912ASN0-0.095-0.05721.093-0.218-0.2180.0000.0000.0000.000
144A913ILE00.0420.01819.6950.7440.7440.0000.0000.0000.000
145A914ALA00.0300.03820.891-0.735-0.7350.0000.0000.0000.000
146A915PHE00.022-0.01921.9930.2850.2850.0000.0000.0000.000
147A916ARG10.9070.96022.522-10.502-10.5020.0000.0000.0000.000
148A917GLU-1-0.862-0.92321.02213.43713.4370.0000.0000.0000.000
149A918MET0-0.031-0.00615.8330.5040.5040.0000.0000.0000.000
150A919LEU0-0.021-0.00518.2930.7150.7150.0000.0000.0000.000
151A920ILE00.010-0.00320.5780.2890.2890.0000.0000.0000.000
152A921GLU-1-0.780-0.87615.71717.98917.9890.0000.0000.0000.000
153A922ALA0-0.025-0.01915.7820.9490.9490.0000.0000.0000.000
154A923TYR0-0.012-0.01316.7930.4810.4810.0000.0000.0000.000
155A924LYS10.8580.93616.989-15.748-15.7480.0000.0000.0000.000
156A925GLU-1-0.906-0.96011.89725.01425.0140.0000.0000.0000.000
157A926ASN0-0.044-0.02412.8691.0811.0810.0000.0000.0000.000
158A927ARG10.8190.9097.948-30.266-30.2660.0000.0000.0000.000
159A928LEU0-0.003-0.00413.855-0.885-0.8850.0000.0000.0000.000
160A929GLU-1-0.829-0.90715.80315.85715.8570.0000.0000.0000.000
161A930ILE0-0.0280.00811.651-0.730-0.7300.0000.0000.0000.000
162A931VAL00.011-0.01014.667-0.925-0.9250.0000.0000.0000.000
163A932VAL00.0170.01116.999-0.905-0.9050.0000.0000.0000.000
164A933PRO0-0.025-0.01918.373-0.762-0.7620.0000.0000.0000.000
165A934PHE00.0040.00917.291-0.563-0.5630.0000.0000.0000.000
166A935VAL00.0330.01319.351-0.631-0.6310.0000.0000.0000.000
167A936THR0-0.029-0.02822.375-0.478-0.4780.0000.0000.0000.000
168A937LYS10.8120.89322.154-12.186-12.1860.0000.0000.0000.000
169A938ILE00.0120.02620.843-0.415-0.4150.0000.0000.0000.000
170A939LEU00.007-0.00224.745-0.489-0.4890.0000.0000.0000.000
171A940GLN00.0710.03127.494-0.070-0.0700.0000.0000.0000.000
172A941ARG10.8200.93027.849-10.205-10.2050.0000.0000.0000.000
173A942ALA0-0.027-0.02530.316-0.186-0.1860.0000.0000.0000.000
174A943SER0-0.058-0.02932.658-0.301-0.3010.0000.0000.0000.000
175A944GLU-1-0.793-0.89333.2298.7638.7630.0000.0000.0000.000
176A945SER0-0.011-0.01034.399-0.254-0.2540.0000.0000.0000.000
177A946LYS10.9730.98736.353-7.331-7.3310.0000.0000.0000.000
178A947ILE0-0.0120.00636.318-0.109-0.1090.0000.0000.0000.000
179A948PHE00.0140.00433.0070.0590.0590.0000.0000.0000.000
180A949LYS10.9311.00334.765-7.505-7.5050.0000.0000.0000.000
181A950PRO00.0090.01335.639-0.064-0.0640.0000.0000.0000.000
182A951PRO00.0220.01638.213-0.129-0.1290.0000.0000.0000.000
183A952ASN0-0.007-0.01834.9440.2590.2590.0000.0000.0000.000
184A953PRO00.0640.00835.8700.2330.2330.0000.0000.0000.000
185A954TRP0-0.0240.00827.1740.1250.1250.0000.0000.0000.000
186A955THR00.001-0.02731.2400.4030.4030.0000.0000.0000.000
187A956VAL00.0270.00831.8650.2050.2050.0000.0000.0000.000
188A957GLY0-0.011-0.00732.1190.0830.0830.0000.0000.0000.000
189A958ILE0-0.006-0.00126.4230.2810.2810.0000.0000.0000.000
190A959LEU00.0110.00528.6180.2410.2410.0000.0000.0000.000
191A960LYS10.8290.90230.775-9.028-9.0280.0000.0000.0000.000
192A961LEU00.0270.02924.615-0.052-0.0520.0000.0000.0000.000
193A962LEU0-0.003-0.00624.2800.3130.3130.0000.0000.0000.000
194A963ILE0-0.009-0.00527.4060.1120.1120.0000.0000.0000.000
195A964GLU-1-0.708-0.81228.39310.99110.9910.0000.0000.0000.000
196A965LEU0-0.013-0.01122.8080.1240.1240.0000.0000.0000.000
197A966ASN00.0150.00926.3240.3800.3800.0000.0000.0000.000
198A967GLU-1-0.953-0.96728.2049.5129.5120.0000.0000.0000.000
199A968LYS10.8030.89027.611-10.671-10.6710.0000.0000.0000.000
200A969ALA0-0.023-0.01322.6550.3070.3070.0000.0000.0000.000
201A970ASN0-0.043-0.01123.3400.0530.0530.0000.0000.0000.000
202A971TRP00.0190.01121.9310.6370.6370.0000.0000.0000.000
203A972LYS10.9030.92318.443-16.829-16.8290.0000.0000.0000.000
204A973LEU00.0620.02523.121-0.010-0.0100.0000.0000.0000.000
205A974SER00.007-0.00721.508-0.369-0.3690.0000.0000.0000.000
206A975LEU0-0.002-0.00319.727-0.140-0.1400.0000.0000.0000.000
207A976THR00.0400.02224.012-0.129-0.1290.0000.0000.0000.000
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