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: 82Z3Y

Calculation Name: 5IFF-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IFF

Chain ID: B

ChEMBL ID:

UniProt ID: Q9V2B6

Base Structure: X-ray

Registration Date: 2023-06-20

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2551038.310939
FMO2-HF: Nuclear repulsion 2465169.820049
FMO2-HF: Total energy -85868.49089
FMO2-MP2: Total energy -86122.989637


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(B:8:GLU)


Summations of interaction energy for fragment #1(B:8: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.
-233.297-223.5581.564-4.759-6.5390.036
Interaction energy analysis for fragmet #1(B:8:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.975 / q_NPA : -0.994
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].
3B10SER0-0.046-0.0193.845-4.603-3.095-0.016-0.767-0.7240.003
4B11VAL00.0290.0156.484-0.895-0.8950.0000.0000.0000.000
5B12SER0-0.037-0.0189.335-0.899-0.8990.0000.0000.0000.000
6B13PHE00.0430.01512.815-0.104-0.1040.0000.0000.0000.000
7B14GLU-1-0.810-0.89915.21717.05817.0580.0000.0000.0000.000
8B15ASN0-0.009-0.00918.586-0.097-0.0970.0000.0000.0000.000
9B16GLY00.0410.01721.909-0.226-0.2260.0000.0000.0000.000
10B17LYS10.9200.97419.371-12.956-12.9560.0000.0000.0000.000
11B18ILE00.0110.01413.9420.3890.3890.0000.0000.0000.000
12B19VAL00.0000.02012.8050.2920.2920.0000.0000.0000.000
13B20VAL0-0.015-0.0208.9570.9970.9970.0000.0000.0000.000
14B21ARG10.8120.8908.765-21.003-21.0030.0000.0000.0000.000
15B22LEU00.0410.0095.3773.6453.6450.0000.0000.0000.000
16B23PRO00.0070.0132.986-6.468-5.4350.134-0.369-0.7980.002
17B24ILE00.0680.0285.8813.0223.0220.0000.0000.0000.000
18B25THR0-0.087-0.0367.568-2.572-2.5720.0000.0000.0000.000
19B26ARG10.9040.9514.525-47.415-47.273-0.001-0.011-0.1290.000
20B27PRO00.0130.0224.19211.39211.5440.000-0.014-0.1370.000
21B28THR00.0230.0052.881-13.429-10.5340.295-1.649-1.5410.016
22B29SER0-0.012-0.0255.608-3.457-3.465-0.0010.0010.0080.000
23B30LYS10.9370.9853.030-67.576-66.1360.119-0.636-0.9220.006
24B31ILE00.0500.0382.342-6.979-5.3740.953-1.008-1.5490.007
25B32ALA00.0080.0085.2343.3413.487-0.001-0.001-0.1440.000
26B33VAL00.0240.0267.814-2.064-2.0640.0000.0000.0000.000
27B34LYS10.8740.93410.876-24.652-24.6520.0000.0000.0000.000
28B35LYS10.9810.98614.107-14.130-14.1300.0000.0000.0000.000
29B36ILE0-0.062-0.03317.6790.1380.1380.0000.0000.0000.000
30B37GLU-1-0.890-0.94920.05012.81312.8130.0000.0000.0000.000
31B38ASN00.018-0.00423.4450.0890.0890.0000.0000.0000.000
32B39GLY00.0040.01623.015-0.156-0.1560.0000.0000.0000.000
33B40VAL00.0020.00920.8480.9270.9270.0000.0000.0000.000
34B41GLY00.0270.00616.9170.0490.0490.0000.0000.0000.000
35B42ILE0-0.0160.00216.7401.0321.0320.0000.0000.0000.000
36B43PRO0-0.028-0.01013.1671.1651.1650.0000.0000.0000.000
37B44VAL00.0290.01813.184-1.474-1.4740.0000.0000.0000.000
38B45SER0-0.045-0.02212.5421.5461.5460.0000.0000.0000.000
39B46THR00.053-0.00410.995-1.703-1.7030.0000.0000.0000.000
40B47ARG10.8880.95712.768-21.261-21.2610.0000.0000.0000.000
41B48LYS10.9420.97615.362-19.208-19.2080.0000.0000.0000.000
42B49LYS11.0080.99918.187-15.350-15.3500.0000.0000.0000.000
43B50SER00.0300.01418.6550.8060.8060.0000.0000.0000.000
44B51PHE0-0.052-0.01414.5540.2420.2420.0000.0000.0000.000
45B52PRO0-0.0090.00220.629-0.412-0.4120.0000.0000.0000.000
46B53SER00.001-0.03523.4880.5100.5100.0000.0000.0000.000
47B54ASP-1-0.861-0.90726.20910.84910.8490.0000.0000.0000.000
48B55GLU-1-0.865-0.93225.45111.32911.3290.0000.0000.0000.000
49B56ASN00.004-0.01425.2000.4780.4780.0000.0000.0000.000
50B57LEU0-0.039-0.01819.2400.6420.6420.0000.0000.0000.000
51B58ARG10.9520.96820.466-10.772-10.7720.0000.0000.0000.000
52B59ASP-1-0.872-0.91321.14213.72313.7230.0000.0000.0000.000
53B60TYR0-0.075-0.03816.2440.6530.6530.0000.0000.0000.000
54B61TYR00.0530.02914.9130.0000.0000.0000.0000.0000.000
55B62ILE0-0.036-0.0188.4661.6591.6590.0000.0000.0000.000
56B63ALA0-0.022-0.02110.268-1.514-1.5140.0000.0000.0000.000
57B64TRP0-0.014-0.0255.9172.7142.7140.0000.0000.0000.000
58B65GLN0-0.028-0.0198.259-3.231-3.2310.0000.0000.0000.000
59B66ILE0-0.0390.0018.1912.5732.5730.0000.0000.0000.000
60B67SER0-0.015-0.0218.118-2.288-2.2880.0000.0000.0000.000
61B68TYR0-0.049-0.0609.9410.0650.0650.0000.0000.0000.000
62B69ALA00.005-0.00610.877-1.278-1.2780.0000.0000.0000.000
63B70ARG10.9370.9685.426-28.133-28.1330.0000.0000.0000.000
64B71ASP-1-0.896-0.9389.94221.43221.4320.0000.0000.0000.000
65B72GLY00.0120.01212.625-1.097-1.0970.0000.0000.0000.000
66B73LYS10.9170.96011.898-18.155-18.1550.0000.0000.0000.000
67B74TYR00.0310.00812.1811.3151.3150.0000.0000.0000.000
68B75ASP-1-0.881-0.95411.75717.63517.6350.0000.0000.0000.000
69B76TYR0-0.037-0.0262.7800.5201.3090.083-0.301-0.5710.002
70B77GLU-1-0.806-0.9065.14741.19241.229-0.001-0.004-0.0320.000
71B78LEU00.0910.0467.904-1.619-1.6190.0000.0000.0000.000
72B79SER00.003-0.00111.425-1.114-1.1140.0000.0000.0000.000
73B80ARG10.9160.9668.816-20.836-20.8360.0000.0000.0000.000
74B81MET0-0.028-0.01111.040-0.237-0.2370.0000.0000.0000.000
75B82VAL00.0370.01913.223-1.017-1.0170.0000.0000.0000.000
76B83ARG10.9060.95314.984-15.642-15.6420.0000.0000.0000.000
77B84LEU00.0050.01513.068-0.544-0.5440.0000.0000.0000.000
78B85ALA00.042-0.00116.888-0.642-0.6420.0000.0000.0000.000
79B86HIS0-0.037-0.01119.076-0.300-0.3000.0000.0000.0000.000
80B87GLU-1-0.940-0.96019.08913.13813.1380.0000.0000.0000.000
81B88HIS10.7960.89819.250-13.455-13.4550.0000.0000.0000.000
82B89GLY00.0050.01322.737-0.176-0.1760.0000.0000.0000.000
83B90ILE0-0.050-0.01019.738-0.119-0.1190.0000.0000.0000.000
84B91LEU0-0.041-0.02519.8920.0200.0200.0000.0000.0000.000
85B92THR00.0670.03523.062-0.167-0.1670.0000.0000.0000.000
86B93TYR00.053-0.00125.8990.2770.2770.0000.0000.0000.000
87B94ASN0-0.001-0.00527.8140.0420.0420.0000.0000.0000.000
88B95ASP-1-0.769-0.89024.86411.07211.0720.0000.0000.0000.000
89B96ILE0-0.021-0.00822.3900.2250.2250.0000.0000.0000.000
90B97TYR0-0.006-0.00925.415-0.036-0.0360.0000.0000.0000.000
91B98GLU-1-0.899-0.94327.71310.22010.2200.0000.0000.0000.000
92B99LEU0-0.038-0.01822.2210.0790.0790.0000.0000.0000.000
93B100LEU0-0.030-0.02524.8600.1040.1040.0000.0000.0000.000
94B101LYS10.9560.99327.396-9.087-9.0870.0000.0000.0000.000
95B102PHE0-0.017-0.02025.287-0.084-0.0840.0000.0000.0000.000
96B103ALA00.020-0.00425.622-0.060-0.0600.0000.0000.0000.000
97B104ASP-1-0.989-0.99327.5239.0339.0330.0000.0000.0000.000
98B105ASP-1-0.969-0.99130.8958.8618.8610.0000.0000.0000.000
99B106VAL0-0.045-0.00327.286-0.080-0.0800.0000.0000.0000.000
100B107LYS10.9000.93930.339-8.814-8.8140.0000.0000.0000.000
101B108SER00.0120.02530.896-0.255-0.2550.0000.0000.0000.000
102B109TYR0-0.053-0.03725.7060.3340.3340.0000.0000.0000.000
103B110LEU0-0.043-0.02722.180-0.247-0.2470.0000.0000.0000.000
104B111GLU-1-0.903-0.98722.27613.61513.6150.0000.0000.0000.000
105B112ASP-1-0.822-0.88425.84410.42610.4260.0000.0000.0000.000
106B113LYS10.8480.92928.272-10.666-10.6660.0000.0000.0000.000
107B114GLY00.0310.02427.985-0.246-0.2460.0000.0000.0000.000
108B115ILE0-0.087-0.05124.6230.2380.2380.0000.0000.0000.000
109B116ARG10.8460.92529.121-9.830-9.8300.0000.0000.0000.000
110B117ARG10.8410.88931.695-9.669-9.6690.0000.0000.0000.000
111B118GLU-1-0.856-0.91734.4648.8478.8470.0000.0000.0000.000
112B119SER00.0150.00137.1210.0680.0680.0000.0000.0000.000
113B120THR0-0.002-0.02037.945-0.035-0.0350.0000.0000.0000.000
114B121ASN0-0.036-0.02740.967-0.089-0.0890.0000.0000.0000.000
115B122GLU-1-0.932-0.95639.2338.0948.0940.0000.0000.0000.000
116B123GLU-1-0.943-0.98142.0277.1197.1190.0000.0000.0000.000
117B124LEU0-0.026-0.01737.2800.0170.0170.0000.0000.0000.000
118B125TYR0-0.054-0.04441.316-0.056-0.0560.0000.0000.0000.000
119B126GLY00.0430.02444.134-0.028-0.0280.0000.0000.0000.000
120B127PHE0-0.057-0.00339.955-0.001-0.0010.0000.0000.0000.000
121B128ASN00.0250.00741.6490.0280.0280.0000.0000.0000.000
122B129ILE00.0260.02536.3140.2350.2350.0000.0000.0000.000
123B130TYR0-0.059-0.01036.009-0.200-0.2000.0000.0000.0000.000
124B131GLU-1-0.905-0.94933.2189.4659.4650.0000.0000.0000.000
125B132ASP-1-0.819-0.87129.41610.40810.4080.0000.0000.0000.000
126B133VAL0-0.015-0.01329.5540.3750.3750.0000.0000.0000.000
127B134TYR0-0.010-0.02023.7430.2550.2550.0000.0000.0000.000
128B135PRO0-0.0330.00925.5570.0330.0330.0000.0000.0000.000
129B136VAL0-0.008-0.02821.5000.7250.7250.0000.0000.0000.000
130B137ALA0-0.0150.00322.548-0.553-0.5530.0000.0000.0000.000
131B138LYS10.9260.94920.778-13.370-13.3700.0000.0000.0000.000
132B139LYS10.8660.92021.902-13.064-13.0640.0000.0000.0000.000
133B140GLU-1-0.911-0.95621.77813.53213.5320.0000.0000.0000.000
134B141LEU0-0.011-0.00219.935-0.477-0.4770.0000.0000.0000.000
135B142PRO00.0460.01523.4160.0930.0930.0000.0000.0000.000
136B143SER0-0.038-0.01621.549-0.392-0.3920.0000.0000.0000.000
137B144GLY00.0490.03921.5720.3410.3410.0000.0000.0000.000
138B145GLU-1-0.841-0.87716.67816.48016.4800.0000.0000.0000.000
139B146PHE0-0.0210.00617.709-0.637-0.6370.0000.0000.0000.000
140B147ILE0-0.014-0.01217.0931.3491.3490.0000.0000.0000.000
141B148GLY0-0.003-0.00517.043-1.028-1.0280.0000.0000.0000.000
142B149ILE0-0.034-0.01617.2830.9520.9520.0000.0000.0000.000
143B150VAL00.0120.00317.198-0.678-0.6780.0000.0000.0000.000
144B151LEU00.0430.02119.2800.5980.5980.0000.0000.0000.000
145B152LYS10.9010.95414.549-20.964-20.9640.0000.0000.0000.000
146B153HIS00.0980.03720.823-0.367-0.3670.0000.0000.0000.000
147B154LYS10.9340.98118.105-15.630-15.6300.0000.0000.0000.000
148B155GLN00.0300.01816.289-0.327-0.3270.0000.0000.0000.000
149B156ARG10.9060.93718.993-15.790-15.7900.0000.0000.0000.000
150B157ALA0-0.0040.00323.332-0.412-0.4120.0000.0000.0000.000
151B158VAL00.0630.03125.0710.1650.1650.0000.0000.0000.000
152B159GLY00.0150.02626.0110.2350.2350.0000.0000.0000.000
153B160TYR00.0330.00623.3780.2330.2330.0000.0000.0000.000
154B161GLN0-0.030-0.01516.0580.2370.2370.0000.0000.0000.000
155B162SER00.0320.02919.2910.2430.2430.0000.0000.0000.000
156B163MET0-0.098-0.05413.1881.3091.3090.0000.0000.0000.000
157B164VAL00.0340.02614.451-0.771-0.7710.0000.0000.0000.000
158B165TYR0-0.035-0.02911.3311.5461.5460.0000.0000.0000.000
159B166VAL00.0230.02411.513-1.678-1.6780.0000.0000.0000.000
160B167CYS0-0.066-0.04212.4632.4912.4910.0000.0000.0000.000
161B168ILE00.0350.02111.027-1.247-1.2470.0000.0000.0000.000
162B169PRO00.0800.05614.2951.3361.3360.0000.0000.0000.000
163B170LEU00.002-0.02613.2250.4460.4460.0000.0000.0000.000
164B171THR0-0.018-0.00716.375-0.049-0.0490.0000.0000.0000.000
165B172ASN0-0.054-0.02317.233-0.915-0.9150.0000.0000.0000.000
166B173VAL0-0.062-0.02212.7500.7150.7150.0000.0000.0000.000
167B174GLU-1-0.917-0.92115.20013.77913.7790.0000.0000.0000.000
168B175PRO0-0.044-0.05814.7201.1941.1940.0000.0000.0000.000
169B176SER00.0870.03116.7900.9230.9230.0000.0000.0000.000
170B177LEU0-0.052-0.04214.566-0.081-0.0810.0000.0000.0000.000
171B178ALA00.0140.01618.375-0.118-0.1180.0000.0000.0000.000
172B179GLY00.0330.02721.972-0.170-0.1700.0000.0000.0000.000
173B180ARG10.7850.88616.558-17.691-17.6910.0000.0000.0000.000
174B181VAL0-0.0100.00817.5830.5910.5910.0000.0000.0000.000
175B182ALA00.0230.00713.121-0.140-0.1400.0000.0000.0000.000
176B183ARG10.9430.95715.109-17.875-17.8750.0000.0000.0000.000
177B184ARG10.9550.94813.271-16.522-16.5220.0000.0000.0000.000
178B185ASN0-0.037-0.0229.0432.2852.2850.0000.0000.0000.000
179B186GLU-1-0.725-0.8189.87420.59920.5990.0000.0000.0000.000
180B187VAL0-0.006-0.0126.8123.6843.6840.0000.0000.0000.000
181B188VAL0-0.0100.0119.204-2.327-2.3270.0000.0000.0000.000
182B189LYS10.9410.96110.130-15.031-15.0310.0000.0000.0000.000
183B190TYR0-0.030-0.08011.924-0.424-0.4240.0000.0000.0000.000
184B191GLU-1-0.873-0.94313.63415.22315.2230.0000.0000.0000.000
185B192VAL0-0.023-0.02513.2090.0100.0100.0000.0000.0000.000
186B193PRO00.0440.03716.234-0.722-0.7220.0000.0000.0000.000
187B194VAL00.050-0.00919.2200.4940.4940.0000.0000.0000.000
188B195ASP-1-0.866-0.94720.94212.78112.7810.0000.0000.0000.000
189B196LEU00.0210.02014.6630.2210.2210.0000.0000.0000.000
190B197MET0-0.043-0.01115.5770.6490.6490.0000.0000.0000.000
191B198LYS10.9250.97117.803-11.382-11.3820.0000.0000.0000.000
192B199GLU-1-0.748-0.86220.57712.53412.5340.0000.0000.0000.000
193B200LEU0-0.021-0.00914.0910.2930.2930.0000.0000.0000.000
194B201LEU0-0.023-0.00917.0810.1820.1820.0000.0000.0000.000
195B202LYS10.8840.94919.049-12.162-12.1620.0000.0000.0000.000
196B203ALA00.0230.01618.411-0.379-0.3790.0000.0000.0000.000
197B204PHE0-0.019-0.03413.424-0.193-0.1930.0000.0000.0000.000
198B205ILE0-0.033-0.01219.268-0.326-0.3260.0000.0000.0000.000
199B206ILE00.0560.02422.715-0.406-0.4060.0000.0000.0000.000
200B207ALA0-0.027-0.00320.030-0.247-0.2470.0000.0000.0000.000
201B208SER00.018-0.00821.934-0.132-0.1320.0000.0000.0000.000
202B209GLU-1-0.841-0.91423.64010.61210.6120.0000.0000.0000.000
203B210THR0-0.026-0.00921.5190.0920.0920.0000.0000.0000.000
204B211HIS10.8780.92816.583-16.315-16.3150.0000.0000.0000.000
205B212LYS10.9010.97920.301-10.416-10.4160.0000.0000.0000.000
206B213ASN00.0230.00622.808-0.184-0.1840.0000.0000.0000.000
207B214ASP-1-0.830-0.87018.25114.71614.7160.0000.0000.0000.000
208B215ILE0-0.034-0.01516.7280.0850.0850.0000.0000.0000.000
209B216VAL00.0070.00219.965-0.227-0.2270.0000.0000.0000.000
210B217LYS10.9230.96621.585-11.915-11.9150.0000.0000.0000.000
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