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: R9M38

Calculation Name: 3U8Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U8Z

Chain ID: A

ChEMBL ID:

UniProt ID: P35240

Base Structure: X-ray

Registration Date: 2023-06-22

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 260
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3529572.005283
FMO2-HF: Nuclear repulsion 3420783.989661
FMO2-HF: Total energy -108788.015623
FMO2-MP2: Total energy -109102.808894


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:20:LYS)


Summations of interaction energy for fragment #1(A:20:LYS)
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.
-14.927-14.80317.695-9.738-8.081-0.098
Interaction energy analysis for fragmet #1(A:20:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.926 / q_NPA : 0.964
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].
3A22PHE0-0.010-0.0093.8781.3503.798-0.016-1.386-1.0470.003
4A23THR00.0340.0216.749-1.470-1.4700.0000.0000.0000.000
5A24VAL0-0.068-0.03110.2351.0951.0950.0000.0000.0000.000
6A25ARG10.8100.88113.18515.50915.5090.0000.0000.0000.000
7A26ILE0-0.062-0.04815.5510.1420.1420.0000.0000.0000.000
8A27VAL00.0400.02618.5630.1540.1540.0000.0000.0000.000
9A28THR00.008-0.01021.913-0.023-0.0230.0000.0000.0000.000
10A29MET0-0.013-0.01324.3230.1960.1960.0000.0000.0000.000
11A30ASP-1-0.842-0.87826.014-11.116-11.1160.0000.0000.0000.000
12A31ALA00.0140.00023.7950.2140.2140.0000.0000.0000.000
13A32GLU-1-0.873-0.91520.755-13.991-13.9910.0000.0000.0000.000
14A33MET0-0.0100.00018.135-0.402-0.4020.0000.0000.0000.000
15A34GLU-1-0.837-0.90814.008-18.424-18.4240.0000.0000.0000.000
16A35PHE00.0120.00411.630-0.488-0.4880.0000.0000.0000.000
17A36ASN00.0160.0126.523-2.223-2.2230.0000.0000.0000.000
18A37CYS0-0.0010.0177.616-1.274-1.2740.0000.0000.0000.000
19A38GLU-1-0.776-0.8801.689-126.636-130.17417.641-7.968-6.135-0.100
20A39MET0-0.017-0.0172.9277.5488.7620.070-0.384-0.899-0.001
21A40LYS10.8600.9205.63638.92438.9240.0000.0000.0000.000
22A41TRP00.0160.0155.6205.0265.0260.0000.0000.0000.000
23A42LYS10.8060.8719.06121.61121.6110.0000.0000.0000.000
24A43GLY00.016-0.00912.708-0.886-0.8860.0000.0000.0000.000
25A44LYS10.8380.88015.31717.75017.7500.0000.0000.0000.000
26A45ASP-1-0.818-0.89310.183-26.646-26.6460.0000.0000.0000.000
27A46LEU00.0190.00911.590-0.495-0.4950.0000.0000.0000.000
28A47PHE0-0.002-0.00112.9280.5750.5750.0000.0000.0000.000
29A48ASP-1-0.745-0.86014.443-17.748-17.7480.0000.0000.0000.000
30A49LEU0-0.044-0.01710.0080.1060.1060.0000.0000.0000.000
31A50VAL00.0100.02213.6180.5960.5960.0000.0000.0000.000
32A51CYS0-0.046-0.02516.7081.0421.0420.0000.0000.0000.000
33A52ARG10.9400.96911.16224.42824.4280.0000.0000.0000.000
34A53THR0-0.034-0.02815.170-0.048-0.0480.0000.0000.0000.000
35A54LEU0-0.0120.00417.4330.6770.6770.0000.0000.0000.000
36A55GLY00.0230.02120.0710.7830.7830.0000.0000.0000.000
37A56LEU0-0.070-0.01421.3680.6150.6150.0000.0000.0000.000
38A57ARG10.9400.95521.31011.74911.7490.0000.0000.0000.000
39A58GLU-1-0.763-0.85423.566-10.944-10.9440.0000.0000.0000.000
40A59THR0-0.016-0.02920.6320.3660.3660.0000.0000.0000.000
41A60TRP0-0.001-0.00323.860-0.370-0.3700.0000.0000.0000.000
42A61PHE00.0500.03426.2280.1730.1730.0000.0000.0000.000
43A62PHE0-0.0100.00823.9500.1850.1850.0000.0000.0000.000
44A63GLY0-0.018-0.01722.543-0.170-0.1700.0000.0000.0000.000
45A64LEU00.0020.00716.8700.1790.1790.0000.0000.0000.000
46A65GLN0-0.016-0.01121.2150.1450.1450.0000.0000.0000.000
47A66TYR00.0450.00321.947-0.542-0.5420.0000.0000.0000.000
48A67THR00.0410.02424.0990.4370.4370.0000.0000.0000.000
49A68ILE0-0.039-0.02425.142-0.227-0.2270.0000.0000.0000.000
50A69LYS10.9340.95827.4519.6459.6450.0000.0000.0000.000
51A70ASP-1-0.707-0.81129.962-8.924-8.9240.0000.0000.0000.000
52A71THR0-0.057-0.04030.8060.3320.3320.0000.0000.0000.000
53A72VAL00.0730.04328.830-0.330-0.3300.0000.0000.0000.000
54A73ALA0-0.037-0.01725.5130.1860.1860.0000.0000.0000.000
55A74TRP00.0910.03523.959-0.230-0.2300.0000.0000.0000.000
56A75LEU0-0.0150.01216.0910.1900.1900.0000.0000.0000.000
57A76LYS10.9290.94820.67812.97512.9750.0000.0000.0000.000
58A77MET00.0450.04018.057-0.864-0.8640.0000.0000.0000.000
59A78ASP-1-0.776-0.86416.735-17.646-17.6460.0000.0000.0000.000
60A79LYS10.9020.95716.76614.85714.8570.0000.0000.0000.000
61A80LYS10.9780.98911.12023.58123.5810.0000.0000.0000.000
62A81VAL0-0.0130.01011.8681.8461.8460.0000.0000.0000.000
63A82LEU0-0.0130.0028.1150.1920.1920.0000.0000.0000.000
64A91PRO00.0280.01514.734-0.198-0.1980.0000.0000.0000.000
65A92VAL00.0160.01012.5760.8820.8820.0000.0000.0000.000
66A93THR00.007-0.00715.346-0.620-0.6200.0000.0000.0000.000
67A94PHE0-0.083-0.03915.6150.4750.4750.0000.0000.0000.000
68A95HIS00.0330.01920.285-0.057-0.0570.0000.0000.0000.000
69A96PHE0-0.026-0.01620.146-0.036-0.0360.0000.0000.0000.000
70A97LEU00.0080.00322.8110.4210.4210.0000.0000.0000.000
71A98ALA00.0300.00926.350-0.363-0.3630.0000.0000.0000.000
72A99LYS10.7760.89026.55212.13912.1390.0000.0000.0000.000
73A100PHE0-0.071-0.03128.2330.2730.2730.0000.0000.0000.000
74A101TYR00.0910.04831.764-0.209-0.2090.0000.0000.0000.000
75A102PRO0-0.0270.00033.8710.0170.0170.0000.0000.0000.000
76A103GLU-1-0.793-0.87636.075-7.892-7.8920.0000.0000.0000.000
77A104ASN00.011-0.00938.8220.1770.1770.0000.0000.0000.000
78A105ALA00.008-0.00636.960-0.241-0.2410.0000.0000.0000.000
79A106GLU-1-0.804-0.90936.851-7.859-7.8590.0000.0000.0000.000
80A107GLU-1-0.945-0.94838.344-7.939-7.9390.0000.0000.0000.000
81A108GLU-1-0.779-0.89534.077-9.297-9.2970.0000.0000.0000.000
82A109LEU0-0.086-0.02031.916-0.442-0.4420.0000.0000.0000.000
83A110VAL00.0780.04831.9570.0850.0850.0000.0000.0000.000
84A111GLN0-0.057-0.05124.923-0.144-0.1440.0000.0000.0000.000
85A112GLU-1-0.717-0.81430.259-9.906-9.9060.0000.0000.0000.000
86A113ILE0-0.018-0.00724.5280.1150.1150.0000.0000.0000.000
87A114THR0-0.025-0.04327.464-0.041-0.0410.0000.0000.0000.000
88A115GLN00.0750.04429.2850.1530.1530.0000.0000.0000.000
89A116HIS10.8060.86528.58710.81010.8100.0000.0000.0000.000
90A117LEU0-0.045-0.02825.0750.0370.0370.0000.0000.0000.000
91A118PHE0-0.007-0.01429.6750.0970.0970.0000.0000.0000.000
92A119PHE00.0520.03632.6280.2350.2350.0000.0000.0000.000
93A120LEU0-0.028-0.01929.9640.2910.2910.0000.0000.0000.000
94A121GLN0-0.011-0.00829.864-0.211-0.2110.0000.0000.0000.000
95A122VAL00.003-0.00232.8930.1740.1740.0000.0000.0000.000
96A123LYS10.9170.99035.1679.2199.2190.0000.0000.0000.000
97A124LYS10.8010.88833.2509.2419.2410.0000.0000.0000.000
98A125GLN0-0.041-0.03734.4180.2380.2380.0000.0000.0000.000
99A126ILE00.0260.02438.0800.1710.1710.0000.0000.0000.000
100A127LEU0-0.016-0.01238.8620.1610.1610.0000.0000.0000.000
101A128ASP-1-0.829-0.88236.967-8.668-8.6680.0000.0000.0000.000
102A129GLU-1-0.925-0.96640.500-6.837-6.8370.0000.0000.0000.000
103A130LYS10.7360.85836.0868.7058.7050.0000.0000.0000.000
104A131ILE0-0.037-0.01038.946-0.048-0.0480.0000.0000.0000.000
105A132TYR00.048-0.00542.7860.0530.0530.0000.0000.0000.000
106A133CYS00.0010.00045.812-0.071-0.0710.0000.0000.0000.000
107A134PRO00.0440.03647.8570.0810.0810.0000.0000.0000.000
108A135PRO00.0280.01150.698-0.096-0.0960.0000.0000.0000.000
109A136GLU-1-0.920-0.95651.902-5.976-5.9760.0000.0000.0000.000
110A137ALA00.0720.02848.547-0.070-0.0700.0000.0000.0000.000
111A138SER0-0.007-0.01347.283-0.199-0.1990.0000.0000.0000.000
112A139VAL0-0.011-0.01247.484-0.127-0.1270.0000.0000.0000.000
113A140LEU00.0250.03348.434-0.063-0.0630.0000.0000.0000.000
114A141LEU00.0320.02342.956-0.125-0.1250.0000.0000.0000.000
115A142ALA0-0.030-0.02044.224-0.181-0.1810.0000.0000.0000.000
116A143SER0-0.042-0.03845.169-0.077-0.0770.0000.0000.0000.000
117A144TYR0-0.007-0.02543.016-0.015-0.0150.0000.0000.0000.000
118A145ALA0-0.034-0.03040.810-0.197-0.1970.0000.0000.0000.000
119A146VAL0-0.061-0.02741.014-0.154-0.1540.0000.0000.0000.000
120A147GLN0-0.021-0.02142.775-0.093-0.0930.0000.0000.0000.000
121A148ALA00.0330.02238.004-0.076-0.0760.0000.0000.0000.000
122A149LYS10.8120.92737.6787.6767.6760.0000.0000.0000.000
123A150TYR0-0.040-0.03239.043-0.113-0.1130.0000.0000.0000.000
124A151GLY00.0300.02939.1420.1540.1540.0000.0000.0000.000
125A152ASP-1-0.996-0.98940.181-7.472-7.4720.0000.0000.0000.000
126A178GLN00.0150.00144.5120.0710.0710.0000.0000.0000.000
127A179MET0-0.051-0.02642.766-0.148-0.1480.0000.0000.0000.000
128A180THR0-0.021-0.03746.692-0.052-0.0520.0000.0000.0000.000
129A181PRO00.026-0.00348.983-0.115-0.1150.0000.0000.0000.000
130A182GLU-1-0.779-0.86249.864-6.170-6.1700.0000.0000.0000.000
131A183MET00.0240.03847.293-0.081-0.0810.0000.0000.0000.000
132A184TRP0-0.071-0.04341.837-0.318-0.3180.0000.0000.0000.000
133A185GLU-1-0.840-0.92745.693-6.920-6.9200.0000.0000.0000.000
134A186GLU-1-0.939-0.95647.784-6.449-6.4490.0000.0000.0000.000
135A187ARG10.8920.92640.2047.5867.5860.0000.0000.0000.000
136A188ILE0-0.0100.00242.869-0.216-0.2160.0000.0000.0000.000
137A189THR0-0.061-0.04643.746-0.076-0.0760.0000.0000.0000.000
138A190ALA0-0.0130.00244.133-0.023-0.0230.0000.0000.0000.000
139A191TRP00.0270.01634.864-0.141-0.1410.0000.0000.0000.000
140A192TYR0-0.004-0.01940.019-0.266-0.2660.0000.0000.0000.000
141A193ALA0-0.076-0.03641.604-0.048-0.0480.0000.0000.0000.000
142A194GLU-1-0.857-0.92239.087-8.193-8.1930.0000.0000.0000.000
143A195HIS10.7530.87135.6698.5258.5250.0000.0000.0000.000
144A196ARG10.9931.00536.7857.5007.5000.0000.0000.0000.000
145A197GLY0-0.0040.01434.453-0.101-0.1010.0000.0000.0000.000
146A198ARG10.8120.86731.78110.02410.0240.0000.0000.0000.000
147A199ALA00.0210.01735.391-0.065-0.0650.0000.0000.0000.000
148A200ARG10.7890.87233.8339.1269.1260.0000.0000.0000.000
149A201ASP-1-0.830-0.93235.598-8.318-8.3180.0000.0000.0000.000
150A202GLU-1-0.876-0.95637.432-8.368-8.3680.0000.0000.0000.000
151A203ALA00.0030.02040.1200.1320.1320.0000.0000.0000.000
152A204GLU-1-0.793-0.88534.164-9.715-9.7150.0000.0000.0000.000
153A205MET0-0.0170.00336.504-0.024-0.0240.0000.0000.0000.000
154A206GLU-1-0.791-0.86739.030-7.130-7.1300.0000.0000.0000.000
155A207TYR00.005-0.00339.6500.0300.0300.0000.0000.0000.000
156A208LEU0-0.057-0.04835.2010.0240.0240.0000.0000.0000.000
157A209LYS10.7920.88939.8297.4987.4980.0000.0000.0000.000
158A210ILE00.0030.01842.6980.1520.1520.0000.0000.0000.000
159A211ALA0-0.031-0.03140.7810.0760.0760.0000.0000.0000.000
160A212GLN0-0.025-0.03040.712-0.240-0.2400.0000.0000.0000.000
161A213ASP-1-0.883-0.93842.088-7.047-7.0470.0000.0000.0000.000
162A214LEU0-0.057-0.01443.9600.1880.1880.0000.0000.0000.000
163A215GLU-1-0.891-0.97045.000-6.552-6.5520.0000.0000.0000.000
164A216MET0-0.063-0.00343.2460.0270.0270.0000.0000.0000.000
165A217TYR00.0050.02637.367-0.360-0.3600.0000.0000.0000.000
166A218GLY0-0.001-0.00837.2610.0070.0070.0000.0000.0000.000
167A219VAL0-0.058-0.01337.820-0.174-0.1740.0000.0000.0000.000
168A220ASN0-0.072-0.04434.820-0.244-0.2440.0000.0000.0000.000
169A221TYR00.025-0.00638.0070.0540.0540.0000.0000.0000.000
170A222PHE0-0.044-0.04135.313-0.236-0.2360.0000.0000.0000.000
171A223ALA00.0150.01840.9900.1750.1750.0000.0000.0000.000
172A224ILE0-0.071-0.02742.865-0.148-0.1480.0000.0000.0000.000
173A225ARG10.8130.89445.3476.6626.6620.0000.0000.0000.000
174A226ASN00.0780.03348.504-0.058-0.0580.0000.0000.0000.000
175A227LYS10.8520.89249.2906.5086.5080.0000.0000.0000.000
176A228LYS10.9260.97452.7785.6535.6530.0000.0000.0000.000
177A229GLY00.0170.01852.4490.0850.0850.0000.0000.0000.000
178A230THR00.0140.00052.675-0.032-0.0320.0000.0000.0000.000
179A231GLU-1-0.834-0.88849.390-6.582-6.5820.0000.0000.0000.000
180A232LEU0-0.004-0.00948.7560.1230.1230.0000.0000.0000.000
181A233LEU0-0.033-0.00344.228-0.165-0.1650.0000.0000.0000.000
182A234LEU0-0.012-0.00440.5560.0880.0880.0000.0000.0000.000
183A235GLY00.0520.02341.922-0.089-0.0890.0000.0000.0000.000
184A236VAL0-0.073-0.04937.1300.0940.0940.0000.0000.0000.000
185A237ASP-1-0.683-0.82738.382-7.967-7.9670.0000.0000.0000.000
186A238ALA00.0320.01537.599-0.042-0.0420.0000.0000.0000.000
187A239LEU00.0330.01638.6300.0330.0330.0000.0000.0000.000
188A240GLY00.000-0.02141.9070.1430.1430.0000.0000.0000.000
189A241LEU0-0.052-0.00940.580-0.148-0.1480.0000.0000.0000.000
190A242HIS10.8480.90343.4097.4827.4820.0000.0000.0000.000
191A243ILE0-0.023-0.01245.665-0.136-0.1360.0000.0000.0000.000
192A244TYR00.0590.02945.3320.0550.0550.0000.0000.0000.000
193A245ASP-1-0.742-0.86350.065-5.979-5.9790.0000.0000.0000.000
194A246PRO0-0.062-0.03948.942-0.084-0.0840.0000.0000.0000.000
195A247GLU-1-0.867-0.94549.221-6.481-6.4810.0000.0000.0000.000
196A248ASN00.0010.00251.497-0.023-0.0230.0000.0000.0000.000
197A249ARG10.9320.96143.4457.1047.1040.0000.0000.0000.000
198A250LEU00.0210.04747.165-0.186-0.1860.0000.0000.0000.000
199A251THR00.0840.02649.447-0.025-0.0250.0000.0000.0000.000
200A252PRO0-0.087-0.02548.8840.0600.0600.0000.0000.0000.000
201A253LYS10.8000.87750.9825.9815.9810.0000.0000.0000.000
202A254ILE0-0.012-0.00850.8370.0970.0970.0000.0000.0000.000
203A255SER0-0.020-0.01048.263-0.184-0.1840.0000.0000.0000.000
204A256PHE0-0.005-0.00646.1790.1360.1360.0000.0000.0000.000
205A257PRO00.0830.05145.185-0.225-0.2250.0000.0000.0000.000
206A258TRP0-0.003-0.00539.0150.0330.0330.0000.0000.0000.000
207A259ASN0-0.023-0.01942.716-0.157-0.1570.0000.0000.0000.000
208A260GLU-1-0.891-0.94445.002-6.429-6.4290.0000.0000.0000.000
209A261ILE0-0.050-0.01442.8420.1270.1270.0000.0000.0000.000
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