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: 7677K

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2956998.642669
FMO2-HF: Nuclear repulsion 2865741.405343
FMO2-HF: Total energy -91257.237326
FMO2-MP2: Total energy -91527.298743


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.
-152.932-144.432.895-5.301-6.0960.041
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 : -0.913 / q_NPA : -0.965
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].
3A772ILE0-0.019-0.0023.6003.8746.476-0.009-1.310-1.2840.002
4A773PRO00.014-0.0055.927-2.763-2.7630.0000.0000.0000.000
5A774LEU0-0.011-0.0039.508-0.849-0.8490.0000.0000.0000.000
6A775LYS10.9180.96112.461-18.552-18.5520.0000.0000.0000.000
7A776PHE0-0.0040.00015.491-0.821-0.8210.0000.0000.0000.000
8A777PHE00.013-0.00515.359-0.849-0.8490.0000.0000.0000.000
9A778ALA00.0100.01216.2480.8160.8160.0000.0000.0000.000
10A779VAL0-0.041-0.01816.521-0.676-0.6760.0000.0000.0000.000
11A780ASP-1-0.843-0.90418.98712.26312.2630.0000.0000.0000.000
12A781GLU-1-0.875-0.95020.01213.95913.9590.0000.0000.0000.000
13A782VAL0-0.036-0.02323.244-0.355-0.3550.0000.0000.0000.000
14A783SER0-0.025-0.00226.113-0.033-0.0330.0000.0000.0000.000
15A784CYS0-0.029-0.02229.259-0.236-0.2360.0000.0000.0000.000
16A785GLN00.0410.02631.0300.1270.1270.0000.0000.0000.000
17A786ILE0-0.023-0.00133.391-0.129-0.1290.0000.0000.0000.000
18A787ASN00.0500.01231.2880.4770.4770.0000.0000.0000.000
19A788GLN0-0.036-0.02627.8760.0360.0360.0000.0000.0000.000
20A789GLU-1-0.855-0.90829.1908.6528.6520.0000.0000.0000.000
21A790GLY0-0.036-0.02227.8340.1590.1590.0000.0000.0000.000
22A791ALA0-0.004-0.00328.514-0.277-0.2770.0000.0000.0000.000
23A792PRO00.0340.03330.7220.1830.1830.0000.0000.0000.000
24A793LYS10.9820.95932.409-8.412-8.4120.0000.0000.0000.000
25A794ASP-1-0.799-0.89733.8767.6897.6890.0000.0000.0000.000
26A795VAL0-0.041-0.01633.372-0.089-0.0890.0000.0000.0000.000
27A796VAL0-0.027-0.01829.7470.0540.0540.0000.0000.0000.000
28A797GLU-1-0.925-0.95632.3987.6607.6600.0000.0000.0000.000
29A798LYS10.9600.98435.001-7.487-7.4870.0000.0000.0000.000
30A799VAL0-0.013-0.00731.118-0.032-0.0320.0000.0000.0000.000
31A800LEU0-0.034-0.02129.0790.0700.0700.0000.0000.0000.000
32A801PHE00.0070.01632.805-0.043-0.0430.0000.0000.0000.000
33A802VAL00.004-0.00435.420-0.113-0.1130.0000.0000.0000.000
34A803LEU0-0.036-0.03029.272-0.024-0.0240.0000.0000.0000.000
35A804ASN00.0140.01432.0350.2550.2550.0000.0000.0000.000
36A805ASN0-0.033-0.00934.449-0.216-0.2160.0000.0000.0000.000
37A806VAL0-0.0490.00134.826-0.229-0.2290.0000.0000.0000.000
38A807THR00.0130.00037.0280.0560.0560.0000.0000.0000.000
39A808LEU00.036-0.01137.944-0.031-0.0310.0000.0000.0000.000
40A809ALA00.0100.01540.535-0.080-0.0800.0000.0000.0000.000
41A810ASN0-0.019-0.00740.901-0.015-0.0150.0000.0000.0000.000
42A811LEU00.0410.02137.4680.0220.0220.0000.0000.0000.000
43A812ASN00.021-0.00440.7010.1940.1940.0000.0000.0000.000
44A813ASN00.0680.03643.0510.0340.0340.0000.0000.0000.000
45A814LYS10.9050.96338.907-7.025-7.0250.0000.0000.0000.000
46A815VAL00.0100.00037.3160.1370.1370.0000.0000.0000.000
47A816ASP-1-0.902-0.94739.5236.7136.7130.0000.0000.0000.000
48A817GLU-1-0.962-0.98540.8696.7176.7170.0000.0000.0000.000
49A818LEU0-0.013-0.01533.8520.0850.0850.0000.0000.0000.000
50A819LYS10.9070.95937.757-7.061-7.0610.0000.0000.0000.000
51A820LYS10.9040.97639.443-6.472-6.4720.0000.0000.0000.000
52A821SER0-0.018-0.00836.638-0.075-0.0750.0000.0000.0000.000
53A822LEU0-0.054-0.02931.5150.1430.1430.0000.0000.0000.000
54A823THR00.0450.00235.527-0.049-0.0490.0000.0000.0000.000
55A824PRO00.047-0.01134.1120.2230.2230.0000.0000.0000.000
56A825ASN0-0.0080.01932.5770.1900.1900.0000.0000.0000.000
57A826TYR00.0610.03730.5530.2620.2620.0000.0000.0000.000
58A827PHE00.0340.01129.6740.1920.1920.0000.0000.0000.000
59A828SER00.0100.01724.6450.3560.3560.0000.0000.0000.000
60A829TRP00.0590.02724.8210.3080.3080.0000.0000.0000.000
61A830PHE00.0420.00425.3980.2610.2610.0000.0000.0000.000
62A831SER00.005-0.02124.5010.0650.0650.0000.0000.0000.000
63A832THR00.0250.01019.7180.5150.5150.0000.0000.0000.000
64A833TYR00.0180.02921.3620.3240.3240.0000.0000.0000.000
65A834LEU00.0160.00423.3170.1780.1780.0000.0000.0000.000
66A835VAL0-0.004-0.00519.4120.1100.1100.0000.0000.0000.000
67A836THR0-0.094-0.07017.5830.3360.3360.0000.0000.0000.000
68A837GLN0-0.025-0.02219.2480.1060.1060.0000.0000.0000.000
69A838ARG10.8690.95621.916-9.943-9.9430.0000.0000.0000.000
70A839ALA00.0050.00922.4660.0140.0140.0000.0000.0000.000
71A840LYS10.9100.97014.252-15.931-15.9310.0000.0000.0000.000
72A841THR00.0230.00119.6430.4610.4610.0000.0000.0000.000
73A842GLU-1-0.861-0.90721.8259.9719.9710.0000.0000.0000.000
74A843PRO00.004-0.01123.985-0.236-0.2360.0000.0000.0000.000
75A844ASN0-0.024-0.01826.291-0.121-0.1210.0000.0000.0000.000
76A845TYR00.0350.02328.742-0.286-0.2860.0000.0000.0000.000
77A846HIS0-0.091-0.03723.825-0.259-0.2590.0000.0000.0000.000
78A847ASP-1-0.805-0.89928.7908.2178.2170.0000.0000.0000.000
79A848LEU00.0390.03332.297-0.119-0.1190.0000.0000.0000.000
80A849TYR0-0.010-0.03727.131-0.213-0.2130.0000.0000.0000.000
81A850SER0-0.053-0.03630.289-0.060-0.0600.0000.0000.0000.000
82A851LYS10.8750.92231.465-8.086-8.0860.0000.0000.0000.000
83A852VAL00.0330.02532.980-0.189-0.1890.0000.0000.0000.000
84A853ILE0-0.039-0.01928.455-0.088-0.0880.0000.0000.0000.000
85A854VAL0-0.041-0.02532.971-0.099-0.0990.0000.0000.0000.000
86A855ALA00.0090.01335.746-0.150-0.1500.0000.0000.0000.000
87A856MET0-0.040-0.02534.301-0.227-0.2270.0000.0000.0000.000
88A857GLY0-0.0200.00837.099-0.103-0.1030.0000.0000.0000.000
89A858SER0-0.0050.01234.209-0.052-0.0520.0000.0000.0000.000
90A859GLY00.024-0.00433.7250.2010.2010.0000.0000.0000.000
91A860LEU00.0430.02530.3770.2640.2640.0000.0000.0000.000
92A861LEU00.0010.00629.2430.3320.3320.0000.0000.0000.000
93A862HIS0-0.056-0.04028.7080.3160.3160.0000.0000.0000.000
94A863GLN0-0.001-0.01127.7350.4520.4520.0000.0000.0000.000
95A864PHE00.0530.01724.8140.4650.4650.0000.0000.0000.000
96A865MET0-0.0110.02423.8490.6240.6240.0000.0000.0000.000
97A866VAL00.0080.01223.2750.4850.4850.0000.0000.0000.000
98A867ASN00.0080.02821.1500.7720.7720.0000.0000.0000.000
99A868VAL00.0410.02018.9370.7480.7480.0000.0000.0000.000
100A869THR0-0.031-0.03218.1110.6920.6920.0000.0000.0000.000
101A870LEU0-0.017-0.00917.8050.6240.6240.0000.0000.0000.000
102A871ARG10.8850.93215.414-13.822-13.8220.0000.0000.0000.000
103A872GLN00.016-0.00413.5971.0821.0820.0000.0000.0000.000
104A873LEU0-0.012-0.01113.0450.8700.8700.0000.0000.0000.000
105A874PHE00.0090.01410.4100.7180.7180.0000.0000.0000.000
106A875VAL00.0200.0147.9611.5471.5470.0000.0000.0000.000
107A876LEU0-0.0070.0058.0921.8061.8060.0000.0000.0000.000
108A877LEU0-0.013-0.0139.2971.2241.2240.0000.0000.0000.000
109A878SER00.0050.0107.8090.3950.3950.0000.0000.0000.000
110A879THR00.0100.0014.1583.9764.041-0.001-0.023-0.0410.000
111A880LYS10.9400.9762.312-95.663-90.2142.906-3.943-4.4120.039
112A881ASP-1-0.839-0.9184.28430.10130.487-0.001-0.025-0.3590.000
113A882GLU-1-0.826-0.9465.94620.33020.3300.0000.0000.0000.000
114A883GLN0-0.059-0.0349.318-3.187-3.1870.0000.0000.0000.000
115A884ALA0-0.0080.0106.265-1.527-1.5270.0000.0000.0000.000
116A885ILE0-0.056-0.0068.335-1.206-1.2060.0000.0000.0000.000
117A886ASP-1-0.791-0.89210.17514.72914.7290.0000.0000.0000.000
118A887LYS10.9020.92612.754-20.448-20.4480.0000.0000.0000.000
119A888LYS10.8930.96315.938-12.561-12.5610.0000.0000.0000.000
120A889HIS00.0540.01714.907-0.051-0.0510.0000.0000.0000.000
121A890LEU00.0150.02213.932-0.489-0.4890.0000.0000.0000.000
122A891LYS10.9240.95616.146-14.082-14.0820.0000.0000.0000.000
123A892ASN0-0.045-0.03119.647-0.897-0.8970.0000.0000.0000.000
124A893LEU00.0540.01615.785-0.554-0.5540.0000.0000.0000.000
125A894ALA00.0090.02019.429-0.317-0.3170.0000.0000.0000.000
126A895SER00.0180.00220.767-0.616-0.6160.0000.0000.0000.000
127A896TRP00.0230.01022.119-0.615-0.6150.0000.0000.0000.000
128A897LEU00.0480.01920.972-0.354-0.3540.0000.0000.0000.000
129A898GLY00.0140.01723.785-0.351-0.3510.0000.0000.0000.000
130A899CYS0-0.066-0.03426.595-0.506-0.5060.0000.0000.0000.000
131A900ILE00.0370.02724.802-0.418-0.4180.0000.0000.0000.000
132A901THR0-0.049-0.03326.355-0.082-0.0820.0000.0000.0000.000
133A902LEU00.0260.01127.829-0.363-0.3630.0000.0000.0000.000
134A903ALA00.0510.02830.657-0.306-0.3060.0000.0000.0000.000
135A904LEU0-0.066-0.01931.753-0.314-0.3140.0000.0000.0000.000
136A905ASN0-0.045-0.02734.156-0.135-0.1350.0000.0000.0000.000
137A906LYS10.9240.97531.447-8.707-8.7070.0000.0000.0000.000
138A907PRO00.0600.02730.5900.2010.2010.0000.0000.0000.000
139A908ILE00.0420.02323.9910.0900.0900.0000.0000.0000.000
140A909LYS10.8620.92326.190-10.638-10.6380.0000.0000.0000.000
141A910HIS00.0990.04225.0730.3540.3540.0000.0000.0000.000
142A911LYS10.9250.96824.032-10.636-10.6360.0000.0000.0000.000
143A912ASN0-0.114-0.06521.441-0.168-0.1680.0000.0000.0000.000
144A913ILE00.0370.01319.7040.7340.7340.0000.0000.0000.000
145A914ALA00.0180.03320.956-0.712-0.7120.0000.0000.0000.000
146A915PHE00.039-0.00721.4660.3780.3780.0000.0000.0000.000
147A916ARG10.9620.97422.165-10.235-10.2350.0000.0000.0000.000
148A917GLU-1-0.867-0.93320.91213.10613.1060.0000.0000.0000.000
149A918MET0-0.043-0.00516.7970.5970.5970.0000.0000.0000.000
150A919LEU0-0.017-0.00617.8200.6540.6540.0000.0000.0000.000
151A920ILE00.0100.00619.7040.2720.2720.0000.0000.0000.000
152A921GLU-1-0.864-0.94714.72318.59418.5940.0000.0000.0000.000
153A922ALA00.002-0.00414.9510.8810.8810.0000.0000.0000.000
154A923TYR0-0.018-0.01815.9760.5170.5170.0000.0000.0000.000
155A924LYS10.9290.96917.096-14.712-14.7120.0000.0000.0000.000
156A925GLU-1-0.916-0.95311.73023.74823.7480.0000.0000.0000.000
157A926ASN0-0.064-0.01512.3570.3210.3210.0000.0000.0000.000
158A927ARG10.8800.9387.794-27.511-27.5110.0000.0000.0000.000
159A928LEU0-0.006-0.01013.660-0.617-0.6170.0000.0000.0000.000
160A929GLU-1-0.811-0.89115.59916.42116.4210.0000.0000.0000.000
161A930ILE0-0.0310.00311.701-0.572-0.5720.0000.0000.0000.000
162A931VAL00.012-0.01514.606-0.885-0.8850.0000.0000.0000.000
163A932VAL00.0070.01117.009-0.831-0.8310.0000.0000.0000.000
164A933PRO0-0.003-0.00418.341-0.719-0.7190.0000.0000.0000.000
165A934PHE00.0090.00717.201-0.516-0.5160.0000.0000.0000.000
166A935VAL00.0270.00519.312-0.616-0.6160.0000.0000.0000.000
167A936THR0-0.001-0.01222.327-0.421-0.4210.0000.0000.0000.000
168A937LYS10.9350.96222.125-11.953-11.9530.0000.0000.0000.000
169A938ILE0-0.0160.00920.765-0.415-0.4150.0000.0000.0000.000
170A939LEU00.005-0.00824.664-0.474-0.4740.0000.0000.0000.000
171A940GLN00.0600.03127.482-0.145-0.1450.0000.0000.0000.000
172A941ARG10.8210.93127.477-10.310-10.3100.0000.0000.0000.000
173A942ALA0-0.015-0.01330.170-0.215-0.2150.0000.0000.0000.000
174A943SER0-0.054-0.03432.411-0.340-0.3400.0000.0000.0000.000
175A944GLU-1-0.875-0.94534.0688.4288.4280.0000.0000.0000.000
176A945SER0-0.071-0.02134.439-0.163-0.1630.0000.0000.0000.000
177A946LYS10.9620.96936.303-7.313-7.3130.0000.0000.0000.000
178A947ILE0-0.038-0.00736.266-0.140-0.1400.0000.0000.0000.000
179A948PHE0-0.008-0.01733.1110.0510.0510.0000.0000.0000.000
180A949LYS10.9931.03934.692-7.334-7.3340.0000.0000.0000.000
181A950PRO00.0110.03035.438-0.076-0.0760.0000.0000.0000.000
182A951PRO00.0100.00237.943-0.116-0.1160.0000.0000.0000.000
183A952ASN00.014-0.00534.6530.2290.2290.0000.0000.0000.000
184A953PRO00.0680.01135.5590.2070.2070.0000.0000.0000.000
185A954TRP0-0.0260.00527.0050.1070.1070.0000.0000.0000.000
186A955THR00.007-0.02730.8440.3680.3680.0000.0000.0000.000
187A956VAL00.0270.00831.4340.1960.1960.0000.0000.0000.000
188A957GLY0-0.028-0.01431.3680.0750.0750.0000.0000.0000.000
189A958ILE0-0.016-0.00825.9850.2430.2430.0000.0000.0000.000
190A959LEU00.0090.00828.0400.2290.2290.0000.0000.0000.000
191A960LYS10.8620.91930.379-8.728-8.7280.0000.0000.0000.000
192A961LEU00.0190.02924.021-0.038-0.0380.0000.0000.0000.000
193A962LEU0-0.016-0.01224.0370.2630.2630.0000.0000.0000.000
194A963ILE0-0.002-0.00427.0310.0900.0900.0000.0000.0000.000
195A964GLU-1-0.697-0.81828.07710.70810.7080.0000.0000.0000.000
196A965LEU0-0.020-0.01722.4530.1030.1030.0000.0000.0000.000
197A966ASN0-0.003-0.01425.9030.2870.2870.0000.0000.0000.000
198A967GLU-1-0.964-0.96827.7549.2989.2980.0000.0000.0000.000
199A968LYS10.8290.90426.976-10.399-10.3990.0000.0000.0000.000
200A969ALA0-0.039-0.01822.1890.2310.2310.0000.0000.0000.000
201A970ASN0-0.0240.00522.9970.1400.1400.0000.0000.0000.000
202A971TRP00.0240.01321.6830.7190.7190.0000.0000.0000.000
203A972LYS10.8920.91718.109-16.690-16.6900.0000.0000.0000.000
204A973LEU00.0860.03323.240-0.092-0.0920.0000.0000.0000.000
205A974SER00.006-0.01021.974-0.192-0.1920.0000.0000.0000.000
206A975LEU0-0.013-0.00219.727-0.099-0.0990.0000.0000.0000.000
207A976THR00.0340.03723.998-0.084-0.0840.0000.0000.0000.000
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