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: 2299R

Calculation Name: 3IF8-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IF8

Chain ID: B

ChEMBL ID:

UniProt ID: Q9H900

Base Structure: X-ray

Registration Date: 2023-06-19

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 237
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2671821.523112
FMO2-HF: Nuclear repulsion 2574778.908125
FMO2-HF: Total energy -97042.614987
FMO2-MP2: Total energy -97324.892853


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:339:LEU)


Summations of interaction energy for fragment #1(B:339:LEU)
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.
-2.751-0.30.855-1.306-2.001-0.007
Interaction energy analysis for fragmet #1(B:339:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.027
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].
3B341LYS10.9400.9742.670-2.0740.1500.855-1.283-1.796-0.007
4B342VAL00.0570.0284.1080.3510.5780.000-0.023-0.2050.000
5B343ARG10.7630.8546.2990.1610.1610.0000.0000.0000.000
6B344SER00.003-0.0119.3970.0440.0440.0000.0000.0000.000
7B345ASP-1-0.865-0.90610.883-0.209-0.2090.0000.0000.0000.000
8B346LEU0-0.0090.00013.0810.0350.0350.0000.0000.0000.000
9B347ASP-1-0.742-0.85916.258-0.123-0.1230.0000.0000.0000.000
10B348PHE00.0300.01120.0430.0010.0010.0000.0000.0000.000
11B349ALA00.0280.01222.7520.0070.0070.0000.0000.0000.000
12B350GLU-1-0.745-0.86317.785-0.150-0.1500.0000.0000.0000.000
13B351GLN0-0.052-0.03817.3840.0080.0080.0000.0000.0000.000
14B352LEU0-0.0190.00419.2390.0070.0070.0000.0000.0000.000
15B353TRP00.0720.03218.0830.0110.0110.0000.0000.0000.000
16B354CYS0-0.083-0.02216.3690.0050.0050.0000.0000.0000.000
17B355LYS10.9490.99618.5110.1320.1320.0000.0000.0000.000
18B356MET00.0190.02821.3690.0100.0100.0000.0000.0000.000
19B357SER0-0.060-0.04819.8940.0070.0070.0000.0000.0000.000
20B358SER0-0.038-0.02719.3890.0090.0090.0000.0000.0000.000
21B359SER0-0.063-0.04721.5220.0010.0010.0000.0000.0000.000
22B360VAL0-0.036-0.01425.1550.0030.0030.0000.0000.0000.000
23B361ILE00.0050.01027.5190.0050.0050.0000.0000.0000.000
24B362SER0-0.063-0.04830.2050.0040.0040.0000.0000.0000.000
25B363TYR0-0.007-0.03632.533-0.004-0.0040.0000.0000.0000.000
26B364GLN00.0790.01534.550-0.004-0.0040.0000.0000.0000.000
27B365ASP-1-0.788-0.86430.571-0.021-0.0210.0000.0000.0000.000
28B366LEU00.0340.03128.820-0.005-0.0050.0000.0000.0000.000
29B367VAL00.0210.01931.718-0.004-0.0040.0000.0000.0000.000
30B368LYS10.8650.94633.7750.0210.0210.0000.0000.0000.000
31B369CYS0-0.004-0.00829.180-0.004-0.0040.0000.0000.0000.000
32B370PHE00.0410.00028.177-0.005-0.0050.0000.0000.0000.000
33B371THR0-0.015-0.02432.429-0.001-0.0010.0000.0000.0000.000
34B372LEU0-0.030-0.01032.628-0.001-0.0010.0000.0000.0000.000
35B373ILE0-0.002-0.00128.064-0.003-0.0030.0000.0000.0000.000
36B374ILE00.000-0.00232.121-0.002-0.0020.0000.0000.0000.000
37B375GLN00.0370.00735.123-0.002-0.0020.0000.0000.0000.000
38B376SER0-0.067-0.03633.136-0.002-0.0020.0000.0000.0000.000
39B377LEU0-0.010-0.01431.181-0.002-0.0020.0000.0000.0000.000
40B378GLN0-0.014-0.02135.0470.0010.0010.0000.0000.0000.000
41B379ARG10.7800.89637.0780.0470.0470.0000.0000.0000.000
42B380GLY00.0400.02736.8330.0010.0010.0000.0000.0000.000
43B381ASP-1-0.841-0.89934.384-0.057-0.0570.0000.0000.0000.000
44B382ILE0-0.060-0.02729.710-0.006-0.0060.0000.0000.0000.000
45B383GLN00.0550.02930.6420.0000.0000.0000.0000.0000.000
46B384PRO0-0.0340.00026.602-0.008-0.0080.0000.0000.0000.000
47B385TRP00.0340.01718.8860.0080.0080.0000.0000.0000.000
48B386LEU00.008-0.01723.5560.0000.0000.0000.0000.0000.000
49B387HIS10.7540.86117.7270.1810.1810.0000.0000.0000.000
50B388SER00.0210.01122.6260.0090.0090.0000.0000.0000.000
51B389GLY00.0050.00223.901-0.002-0.0020.0000.0000.0000.000
52B390SER0-0.006-0.03024.469-0.004-0.0040.0000.0000.0000.000
53B391ASN0-0.031-0.02026.4900.0010.0010.0000.0000.0000.000
54B392SER00.0410.04126.6660.0040.0040.0000.0000.0000.000
55B393LEU00.0240.00829.446-0.004-0.0040.0000.0000.0000.000
56B394LEU00.0180.00126.747-0.002-0.0020.0000.0000.0000.000
57B395SER0-0.018-0.02327.712-0.004-0.0040.0000.0000.0000.000
58B396LYS10.8660.92829.5240.0240.0240.0000.0000.0000.000
59B397LEU0-0.004-0.00533.085-0.001-0.0010.0000.0000.0000.000
60B398ILE00.0360.01727.806-0.001-0.0010.0000.0000.0000.000
61B399HIS0-0.003-0.00628.920-0.003-0.0030.0000.0000.0000.000
62B400GLN0-0.041-0.05133.4360.0000.0000.0000.0000.0000.000
63B401SER0-0.065-0.02834.1690.0000.0000.0000.0000.0000.000
64B402TYR0-0.050-0.02531.426-0.001-0.0010.0000.0000.0000.000
65B403HIS0-0.035-0.02133.4840.0030.0030.0000.0000.0000.000
66B404GLY0-0.002-0.00337.9280.0030.0030.0000.0000.0000.000
67B405THR00.0150.01540.7030.0000.0000.0000.0000.0000.000
68B406MET0-0.074-0.01635.3350.0010.0010.0000.0000.0000.000
69B407ASP-1-0.785-0.85939.413-0.024-0.0240.0000.0000.0000.000
70B408THR0-0.043-0.02740.446-0.001-0.0010.0000.0000.0000.000
71B409VAL0-0.022-0.02236.3570.0020.0020.0000.0000.0000.000
72B410SER00.0080.01339.7810.0020.0020.0000.0000.0000.000
73B411LEU0-0.0100.00735.0490.0020.0020.0000.0000.0000.000
74B412SER00.0170.00838.4730.0010.0010.0000.0000.0000.000
75B413GLY00.0700.03139.2900.0000.0000.0000.0000.0000.000
76B414THR00.0550.01435.716-0.001-0.0010.0000.0000.0000.000
77B415ILE00.0360.04034.7690.0000.0000.0000.0000.0000.000
78B416PRO0-0.006-0.00433.529-0.002-0.0020.0000.0000.0000.000
79B417VAL00.0220.00530.786-0.002-0.0020.0000.0000.0000.000
80B418GLN0-0.059-0.03629.8740.0020.0020.0000.0000.0000.000
81B419MET00.0090.00929.621-0.001-0.0010.0000.0000.0000.000
82B420LEU00.0060.00824.237-0.006-0.0060.0000.0000.0000.000
83B421LEU00.0070.00125.267-0.002-0.0020.0000.0000.0000.000
84B422GLU-1-0.809-0.90025.268-0.019-0.0190.0000.0000.0000.000
85B423ILE0-0.011-0.00422.783-0.003-0.0030.0000.0000.0000.000
86B424GLY00.0350.01121.073-0.010-0.0100.0000.0000.0000.000
87B425LEU0-0.022-0.01420.4480.0000.0000.0000.0000.0000.000
88B426ASP-1-0.819-0.87721.220-0.056-0.0560.0000.0000.0000.000
89B427LYS10.8250.90213.2130.1640.1640.0000.0000.0000.000
90B428LEU00.0190.00515.867-0.014-0.0140.0000.0000.0000.000
91B429LYS10.8450.92116.5080.0090.0090.0000.0000.0000.000
92B430LYS10.8270.89917.0310.0850.0850.0000.0000.0000.000
93B431ASP-1-0.808-0.86212.498-0.186-0.1860.0000.0000.0000.000
94B432TYR00.0220.01212.629-0.026-0.0260.0000.0000.0000.000
95B433ILE00.0070.00814.3980.0270.0270.0000.0000.0000.000
96B434SER0-0.082-0.05711.583-0.024-0.0240.0000.0000.0000.000
97B435PHE00.0220.0138.001-0.052-0.0520.0000.0000.0000.000
98B436PHE00.013-0.01311.0070.0570.0570.0000.0000.0000.000
99B437ILE0-0.033-0.00914.2890.0290.0290.0000.0000.0000.000
100B438GLY00.0050.01211.2830.0020.0020.0000.0000.0000.000
101B439GLN0-0.051-0.0236.643-0.313-0.3130.0000.0000.0000.000
102B440GLU-1-0.933-0.96310.6570.1490.1490.0000.0000.0000.000
103B441LEU0-0.035-0.01411.4480.0390.0390.0000.0000.0000.000
104B442ALA0-0.029-0.02715.271-0.007-0.0070.0000.0000.0000.000
105B443SER00.014-0.00617.971-0.029-0.0290.0000.0000.0000.000
106B444LEU00.0500.00520.6300.0100.0100.0000.0000.0000.000
107B445ASN00.0590.03021.9920.0060.0060.0000.0000.0000.000
108B446HIS0-0.0210.01721.9820.0060.0060.0000.0000.0000.000
109B447LEU00.0230.00818.2240.0120.0120.0000.0000.0000.000
110B448GLU-1-0.841-0.92222.8370.0060.0060.0000.0000.0000.000
111B449TYR0-0.031-0.01125.722-0.003-0.0030.0000.0000.0000.000
112B450PHE00.003-0.01222.382-0.002-0.0020.0000.0000.0000.000
113B451ILE00.0020.01020.368-0.005-0.0050.0000.0000.0000.000
114B452ALA00.0080.00124.049-0.009-0.0090.0000.0000.0000.000
115B453PRO00.0150.00327.2330.0010.0010.0000.0000.0000.000
116B454SER0-0.029-0.00529.0940.0000.0000.0000.0000.0000.000
117B455VAL0-0.0230.00729.7840.0010.0010.0000.0000.0000.000
118B456ASP-1-0.768-0.88431.6590.0250.0250.0000.0000.0000.000
119B457ILE00.0180.00629.0010.0030.0030.0000.0000.0000.000
120B458GLN0-0.002-0.00828.8530.0060.0060.0000.0000.0000.000
121B459GLU-1-0.723-0.84629.0940.0650.0650.0000.0000.0000.000
122B460GLN0-0.044-0.03026.2500.0030.0030.0000.0000.0000.000
123B461VAL00.0060.00624.7740.0040.0040.0000.0000.0000.000
124B462TYR00.0050.01324.3920.0120.0120.0000.0000.0000.000
125B463ARG10.7520.84824.724-0.037-0.0370.0000.0000.0000.000
126B464VAL00.0210.00919.3190.0110.0110.0000.0000.0000.000
127B465GLN0-0.024-0.01420.0930.0150.0150.0000.0000.0000.000
128B466LYS10.8410.92321.223-0.073-0.0730.0000.0000.0000.000
129B467LEU0-0.048-0.02117.9260.0230.0230.0000.0000.0000.000
130B468HIS0-0.028-0.01815.1070.0220.0220.0000.0000.0000.000
131B469HIS0-0.015-0.01816.6190.0440.0440.0000.0000.0000.000
132B470ILE0-0.0040.00016.8970.0350.0350.0000.0000.0000.000
133B471LEU00.0020.00510.3270.0630.0630.0000.0000.0000.000
134B472GLU-1-0.829-0.89613.5520.3800.3800.0000.0000.0000.000
135B473ILE00.0190.02515.5130.0600.0600.0000.0000.0000.000
136B474LEU0-0.009-0.00612.8900.0460.0460.0000.0000.0000.000
137B475VAL00.005-0.0149.6880.1290.1290.0000.0000.0000.000
138B476SER0-0.036-0.03612.0080.0580.0580.0000.0000.0000.000
139B477CYS0-0.045-0.02414.610-0.058-0.0580.0000.0000.0000.000
140B478MET0-0.0200.0118.9240.2140.2140.0000.0000.0000.000
141B479PRO0-0.072-0.03610.8770.1440.1440.0000.0000.0000.000
142B480PHE0-0.0110.00312.667-0.053-0.0530.0000.0000.0000.000
143B481ILE00.0250.01614.092-0.057-0.0570.0000.0000.0000.000
144B482LYS10.9110.9588.274-1.348-1.3480.0000.0000.0000.000
145B483SER0-0.006-0.0199.675-0.018-0.0180.0000.0000.0000.000
146B484GLN0-0.036-0.00111.019-0.186-0.1860.0000.0000.0000.000
147B485HIS00.0120.00911.3840.0190.0190.0000.0000.0000.000
148B486GLU-1-0.788-0.90913.5680.3220.3220.0000.0000.0000.000
149B487LEU0-0.0190.00616.686-0.028-0.0280.0000.0000.0000.000
150B488LEU00.0230.01110.734-0.003-0.0030.0000.0000.0000.000
151B489PHE00.0290.02914.925-0.035-0.0350.0000.0000.0000.000
152B490SER0-0.045-0.04216.854-0.043-0.0430.0000.0000.0000.000
153B491LEU0-0.019-0.01516.362-0.031-0.0310.0000.0000.0000.000
154B492THR00.0560.01315.887-0.014-0.0140.0000.0000.0000.000
155B493GLN0-0.051-0.02418.281-0.053-0.0530.0000.0000.0000.000
156B494ILE0-0.069-0.03221.617-0.027-0.0270.0000.0000.0000.000
157B495CYS0-0.030-0.00120.230-0.013-0.0130.0000.0000.0000.000
158B496ILE00.005-0.00119.414-0.024-0.0240.0000.0000.0000.000
159B497LYS10.9070.94623.047-0.130-0.1300.0000.0000.0000.000
160B498TYR0-0.001-0.01225.688-0.009-0.0090.0000.0000.0000.000
161B499TYR00.0790.02522.324-0.006-0.0060.0000.0000.0000.000
162B500LYS10.8370.93025.678-0.101-0.1010.0000.0000.0000.000
163B501GLN0-0.091-0.04728.313-0.013-0.0130.0000.0000.0000.000
164B502ASN0-0.062-0.03129.334-0.006-0.0060.0000.0000.0000.000
165B503PRO00.0060.00629.3980.0010.0010.0000.0000.0000.000
166B504LEU0-0.056-0.04723.3130.0090.0090.0000.0000.0000.000
167B505ASP-1-0.873-0.93826.7560.1070.1070.0000.0000.0000.000
168B506GLU-1-0.816-0.86729.5320.0990.0990.0000.0000.0000.000
169B507GLN0-0.032-0.01229.0190.0180.0180.0000.0000.0000.000
170B508HIS0-0.008-0.00826.372-0.016-0.0160.0000.0000.0000.000
171B509ILE0-0.031-0.01227.1010.0130.0130.0000.0000.0000.000
172B510PHE00.0340.02123.560-0.006-0.0060.0000.0000.0000.000
173B511GLN0-0.031-0.02025.4350.0060.0060.0000.0000.0000.000
174B512LEU00.0170.00418.773-0.006-0.0060.0000.0000.0000.000
175B513PRO0-0.031-0.01623.4510.0050.0050.0000.0000.0000.000
176B514VAL00.0570.03620.9820.0140.0140.0000.0000.0000.000
177B515ARG10.9650.98323.244-0.174-0.1740.0000.0000.0000.000
178B516PRO00.0530.00723.6680.0170.0170.0000.0000.0000.000
179B517THR0-0.008-0.01523.6430.0090.0090.0000.0000.0000.000
180B518ALA00.0200.01619.3840.0030.0030.0000.0000.0000.000
181B519VAL00.0420.02619.0840.0380.0380.0000.0000.0000.000
182B520LYS10.8950.95821.208-0.168-0.1680.0000.0000.0000.000
183B521ASN0-0.007-0.03218.330-0.038-0.0380.0000.0000.0000.000
184B522LEU00.0020.01717.9030.0000.0000.0000.0000.0000.000
185B523TYR00.0180.00922.168-0.013-0.0130.0000.0000.0000.000
186B524GLN0-0.033-0.01325.910-0.017-0.0170.0000.0000.0000.000
187B525SER0-0.049-0.02526.781-0.012-0.0120.0000.0000.0000.000
188B526GLU-1-0.843-0.90425.0420.1830.1830.0000.0000.0000.000
189B527LYS10.7740.87528.340-0.146-0.1460.0000.0000.0000.000
190B528PRO00.0050.01529.9210.0050.0050.0000.0000.0000.000
191B529GLN00.026-0.00428.583-0.003-0.0030.0000.0000.0000.000
192B530LYS10.8580.92831.882-0.134-0.1340.0000.0000.0000.000
193B531TRP00.0200.02633.6870.0050.0050.0000.0000.0000.000
194B532ARG10.8780.92436.268-0.108-0.1080.0000.0000.0000.000
195B533VAL00.0260.02938.8190.0020.0020.0000.0000.0000.000
196B534GLU-1-0.821-0.90441.6310.0740.0740.0000.0000.0000.000
197B535ILE00.0170.01743.8280.0000.0000.0000.0000.0000.000
198B536TYR00.038-0.00643.570-0.001-0.0010.0000.0000.0000.000
199B537SER00.0660.02448.6630.0000.0000.0000.0000.0000.000
200B538GLY00.0380.03949.767-0.002-0.0020.0000.0000.0000.000
201B539GLN00.0260.01050.0020.0020.0020.0000.0000.0000.000
202B540LYS10.8430.91842.325-0.074-0.0740.0000.0000.0000.000
203B541LYS10.9450.96746.886-0.054-0.0540.0000.0000.0000.000
204B542ILE00.0110.00548.8940.0010.0010.0000.0000.0000.000
205B543LYS10.7920.88344.538-0.069-0.0690.0000.0000.0000.000
206B544THR00.0330.02648.459-0.002-0.0020.0000.0000.0000.000
207B545VAL0-0.041-0.01942.6560.0020.0020.0000.0000.0000.000
208B546TRP00.0450.02141.618-0.001-0.0010.0000.0000.0000.000
209B547GLN00.0640.03638.3060.0040.0040.0000.0000.0000.000
210B548LEU00.0370.04938.553-0.004-0.0040.0000.0000.0000.000
211B549SER0-0.029-0.04436.4940.0070.0070.0000.0000.0000.000
212B550ASP-1-0.773-0.85332.5640.1310.1310.0000.0000.0000.000
213B551SER00.0380.00733.934-0.001-0.0010.0000.0000.0000.000
214B552SER00.0310.00436.353-0.001-0.0010.0000.0000.0000.000
215B553PRO0-0.072-0.03437.4570.0060.0060.0000.0000.0000.000
216B554ILE0-0.020-0.00838.968-0.001-0.0010.0000.0000.0000.000
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