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: 7GQQK

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 OptHSide
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 -2666142.405566
FMO2-HF: Nuclear repulsion 2569100.422803
FMO2-HF: Total energy -97041.982763
FMO2-MP2: Total energy -97324.302863


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.
-2.813-0.9341.865-1.48-2.264-0.009
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 : -0.044 / q_NPA : -0.030
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].
3B341LYS10.9790.9892.555-1.771-0.0871.865-1.461-2.088-0.009
4B342VAL00.0310.0164.1190.3610.5560.000-0.019-0.1760.000
5B343ARG10.7580.8466.4940.1950.1950.0000.0000.0000.000
6B344SER00.021-0.0049.4810.0330.0330.0000.0000.0000.000
7B345ASP-1-0.899-0.91811.250-0.251-0.2510.0000.0000.0000.000
8B346LEU0-0.017-0.01313.5480.0440.0440.0000.0000.0000.000
9B347ASP-1-0.734-0.84816.487-0.135-0.1350.0000.0000.0000.000
10B348PHE00.0380.00520.2540.0030.0030.0000.0000.0000.000
11B349ALA00.0250.00822.7580.0070.0070.0000.0000.0000.000
12B350GLU-1-0.728-0.85717.804-0.174-0.1740.0000.0000.0000.000
13B351GLN0-0.060-0.03717.6190.0090.0090.0000.0000.0000.000
14B352LEU0-0.0170.00319.3640.0070.0070.0000.0000.0000.000
15B353TRP00.0830.04818.0180.0120.0120.0000.0000.0000.000
16B354CYS0-0.076-0.02316.3960.0060.0060.0000.0000.0000.000
17B355LYS10.9570.98618.5150.1460.1460.0000.0000.0000.000
18B356MET0-0.0010.02121.0520.0120.0120.0000.0000.0000.000
19B357SER0-0.042-0.04119.6800.0090.0090.0000.0000.0000.000
20B358SER0-0.050-0.02519.1510.0090.0090.0000.0000.0000.000
21B359SER0-0.064-0.04421.2440.0040.0040.0000.0000.0000.000
22B360VAL0-0.040-0.01224.8390.0040.0040.0000.0000.0000.000
23B361ILE00.0220.01827.3530.0060.0060.0000.0000.0000.000
24B362SER0-0.050-0.04229.9340.0040.0040.0000.0000.0000.000
25B363TYR0-0.001-0.02832.329-0.004-0.0040.0000.0000.0000.000
26B364GLN00.0720.02034.456-0.005-0.0050.0000.0000.0000.000
27B365ASP-1-0.809-0.87730.578-0.025-0.0250.0000.0000.0000.000
28B366LEU00.0410.03229.012-0.005-0.0050.0000.0000.0000.000
29B367VAL00.0090.01231.974-0.004-0.0040.0000.0000.0000.000
30B368LYS10.8870.95433.9890.0230.0230.0000.0000.0000.000
31B369CYS0-0.021-0.01929.282-0.004-0.0040.0000.0000.0000.000
32B370PHE00.030-0.00828.255-0.005-0.0050.0000.0000.0000.000
33B371THR0-0.031-0.03132.542-0.001-0.0010.0000.0000.0000.000
34B372LEU0-0.026-0.01132.455-0.001-0.0010.0000.0000.0000.000
35B373ILE00.0040.00228.355-0.003-0.0030.0000.0000.0000.000
36B374ILE00.0260.01132.187-0.002-0.0020.0000.0000.0000.000
37B375GLN00.0230.01235.242-0.002-0.0020.0000.0000.0000.000
38B376SER0-0.050-0.01432.967-0.002-0.0020.0000.0000.0000.000
39B377LEU00.004-0.01131.570-0.002-0.0020.0000.0000.0000.000
40B378GLN0-0.021-0.02335.3140.0000.0000.0000.0000.0000.000
41B379ARG10.7860.89536.9960.0530.0530.0000.0000.0000.000
42B380GLY00.0230.01336.8970.0000.0000.0000.0000.0000.000
43B381ASP-1-0.865-0.91134.763-0.063-0.0630.0000.0000.0000.000
44B382ILE0-0.070-0.03229.570-0.006-0.0060.0000.0000.0000.000
45B383GLN00.0220.00730.6660.0010.0010.0000.0000.0000.000
46B384PRO0-0.0350.00126.761-0.009-0.0090.0000.0000.0000.000
47B385TRP00.0250.00918.9710.0110.0110.0000.0000.0000.000
48B386LEU00.002-0.01023.996-0.001-0.0010.0000.0000.0000.000
49B387HIS10.7370.85617.7960.2020.2020.0000.0000.0000.000
50B388SER00.000-0.00422.8230.0090.0090.0000.0000.0000.000
51B389GLY0-0.013-0.00124.505-0.002-0.0020.0000.0000.0000.000
52B390SER00.009-0.03224.646-0.005-0.0050.0000.0000.0000.000
53B391ASN0-0.030-0.01626.8670.0000.0000.0000.0000.0000.000
54B392SER00.0320.02826.8590.0050.0050.0000.0000.0000.000
55B393LEU00.034-0.00229.335-0.004-0.0040.0000.0000.0000.000
56B394LEU00.0080.00026.934-0.002-0.0020.0000.0000.0000.000
57B395SER00.017-0.00727.875-0.003-0.0030.0000.0000.0000.000
58B396LYS10.8630.93829.7670.0300.0300.0000.0000.0000.000
59B397LEU0-0.029-0.02733.322-0.001-0.0010.0000.0000.0000.000
60B398ILE00.0300.02228.310-0.001-0.0010.0000.0000.0000.000
61B399HIS00.000-0.00729.276-0.003-0.0030.0000.0000.0000.000
62B400GLN0-0.025-0.03333.8570.0000.0000.0000.0000.0000.000
63B401SER0-0.037-0.00734.4860.0010.0010.0000.0000.0000.000
64B402TYR0-0.015-0.00131.7930.0000.0000.0000.0000.0000.000
65B403HIS0-0.033-0.01933.8490.0040.0040.0000.0000.0000.000
66B404GLY0-0.017-0.00338.1010.0030.0030.0000.0000.0000.000
67B405THR00.0230.00640.647-0.001-0.0010.0000.0000.0000.000
68B406MET0-0.075-0.01935.5860.0010.0010.0000.0000.0000.000
69B407ASP-1-0.803-0.87939.603-0.030-0.0300.0000.0000.0000.000
70B408THR0-0.046-0.02740.507-0.001-0.0010.0000.0000.0000.000
71B409VAL0-0.025-0.01536.5600.0020.0020.0000.0000.0000.000
72B410SER00.0160.01039.9330.0020.0020.0000.0000.0000.000
73B411LEU0-0.0250.00135.1190.0010.0010.0000.0000.0000.000
74B412SER00.0410.01838.5630.0010.0010.0000.0000.0000.000
75B413GLY00.0540.01839.4080.0000.0000.0000.0000.0000.000
76B414THR00.0440.01135.907-0.002-0.0020.0000.0000.0000.000
77B415ILE00.0430.03334.8600.0000.0000.0000.0000.0000.000
78B416PRO00.0240.01633.379-0.002-0.0020.0000.0000.0000.000
79B417VAL00.0110.00230.815-0.002-0.0020.0000.0000.0000.000
80B418GLN0-0.049-0.02530.0150.0010.0010.0000.0000.0000.000
81B419MET0-0.0080.00229.731-0.001-0.0010.0000.0000.0000.000
82B420LEU00.0080.00424.484-0.006-0.0060.0000.0000.0000.000
83B421LEU00.000-0.00725.389-0.003-0.0030.0000.0000.0000.000
84B422GLU-1-0.819-0.89925.330-0.027-0.0270.0000.0000.0000.000
85B423ILE0-0.009-0.01023.035-0.004-0.0040.0000.0000.0000.000
86B424GLY00.0370.00821.149-0.012-0.0120.0000.0000.0000.000
87B425LEU0-0.017-0.00720.424-0.001-0.0010.0000.0000.0000.000
88B426ASP-1-0.814-0.87421.020-0.064-0.0640.0000.0000.0000.000
89B427LYS10.8330.91313.2350.1780.1780.0000.0000.0000.000
90B428LEU00.015-0.00515.785-0.018-0.0180.0000.0000.0000.000
91B429LYS10.8760.94616.4770.0190.0190.0000.0000.0000.000
92B430LYS10.8500.91516.8850.0990.0990.0000.0000.0000.000
93B431ASP-1-0.797-0.86112.363-0.212-0.2120.0000.0000.0000.000
94B432TYR00.0270.01712.516-0.030-0.0300.0000.0000.0000.000
95B433ILE00.0090.00714.4320.0220.0220.0000.0000.0000.000
96B434SER0-0.076-0.03911.870-0.025-0.0250.0000.0000.0000.000
97B435PHE00.0190.0118.257-0.042-0.0420.0000.0000.0000.000
98B436PHE00.023-0.01011.2230.0500.0500.0000.0000.0000.000
99B437ILE0-0.023-0.01514.4030.0220.0220.0000.0000.0000.000
100B438GLY00.0010.01911.6810.0090.0090.0000.0000.0000.000
101B439GLN0-0.039-0.0207.250-0.250-0.2500.0000.0000.0000.000
102B440GLU-1-0.953-0.96611.1920.1000.1000.0000.0000.0000.000
103B441LEU0-0.044-0.02411.9940.0440.0440.0000.0000.0000.000
104B442ALA0-0.021-0.02515.847-0.002-0.0020.0000.0000.0000.000
105B443SER00.010-0.00418.393-0.030-0.0300.0000.0000.0000.000
106B444LEU00.0720.00520.9950.0090.0090.0000.0000.0000.000
107B445ASN00.0220.01622.0360.0050.0050.0000.0000.0000.000
108B446HIS00.0070.02222.3640.0040.0040.0000.0000.0000.000
109B447LEU00.0100.00318.1950.0100.0100.0000.0000.0000.000
110B448GLU-1-0.872-0.93022.820-0.007-0.0070.0000.0000.0000.000
111B449TYR0-0.0030.00025.862-0.003-0.0030.0000.0000.0000.000
112B450PHE0-0.023-0.02122.4520.0000.0000.0000.0000.0000.000
113B451ILE0-0.0040.00020.228-0.005-0.0050.0000.0000.0000.000
114B452ALA0-0.0080.00624.165-0.010-0.0100.0000.0000.0000.000
115B453PRO00.0190.00327.8960.0020.0020.0000.0000.0000.000
116B454SER0-0.034-0.01129.5500.0010.0010.0000.0000.0000.000
117B455VAL0-0.0070.00630.0110.0010.0010.0000.0000.0000.000
118B456ASP-1-0.790-0.89531.9600.0190.0190.0000.0000.0000.000
119B457ILE00.025-0.00529.2180.0030.0030.0000.0000.0000.000
120B458GLN00.014-0.00129.0920.0050.0050.0000.0000.0000.000
121B459GLU-1-0.749-0.84029.4600.0570.0570.0000.0000.0000.000
122B460GLN0-0.054-0.04126.4180.0010.0010.0000.0000.0000.000
123B461VAL0-0.005-0.00124.8820.0040.0040.0000.0000.0000.000
124B462TYR00.0310.02824.4350.0130.0130.0000.0000.0000.000
125B463ARG10.7740.85524.967-0.030-0.0300.0000.0000.0000.000
126B464VAL00.0150.00719.3440.0110.0110.0000.0000.0000.000
127B465GLN0-0.012-0.00820.2350.0120.0120.0000.0000.0000.000
128B466LYS10.8610.94221.484-0.067-0.0670.0000.0000.0000.000
129B467LEU0-0.033-0.01118.0140.0220.0220.0000.0000.0000.000
130B468HIS0-0.036-0.02715.1110.0200.0200.0000.0000.0000.000
131B469HIS0-0.025-0.01817.0470.0400.0400.0000.0000.0000.000
132B470ILE00.0180.00517.0470.0330.0330.0000.0000.0000.000
133B471LEU0-0.021-0.00410.6100.0590.0590.0000.0000.0000.000
134B472GLU-1-0.826-0.90313.7060.3740.3740.0000.0000.0000.000
135B473ILE00.0080.02915.7520.0600.0600.0000.0000.0000.000
136B474LEU0-0.003-0.01312.8240.0560.0560.0000.0000.0000.000
137B475VAL0-0.024-0.0209.9440.1340.1340.0000.0000.0000.000
138B476SER0-0.027-0.03012.2300.0650.0650.0000.0000.0000.000
139B477CYS0-0.040-0.01715.153-0.037-0.0370.0000.0000.0000.000
140B478MET0-0.0140.0058.8900.2300.2300.0000.0000.0000.000
141B479PRO0-0.092-0.04611.9920.0790.0790.0000.0000.0000.000
142B480PHE0-0.017-0.01212.896-0.064-0.0640.0000.0000.0000.000
143B481ILE0-0.0100.00614.237-0.078-0.0780.0000.0000.0000.000
144B482LYS10.9740.9887.869-1.637-1.6370.0000.0000.0000.000
145B483SER0-0.021-0.02510.177-0.031-0.0310.0000.0000.0000.000
146B484GLN0-0.0130.01011.442-0.197-0.1970.0000.0000.0000.000
147B485HIS00.0220.01511.9400.0320.0320.0000.0000.0000.000
148B486GLU-1-0.786-0.91214.0330.3060.3060.0000.0000.0000.000
149B487LEU0-0.038-0.00116.814-0.025-0.0250.0000.0000.0000.000
150B488LEU00.0270.00611.050-0.010-0.0100.0000.0000.0000.000
151B489PHE00.0190.02215.292-0.040-0.0400.0000.0000.0000.000
152B490SER0-0.043-0.04217.372-0.042-0.0420.0000.0000.0000.000
153B491LEU0-0.0060.00816.764-0.030-0.0300.0000.0000.0000.000
154B492THR00.0730.02316.421-0.015-0.0150.0000.0000.0000.000
155B493GLN0-0.049-0.02318.781-0.049-0.0490.0000.0000.0000.000
156B494ILE0-0.074-0.04322.157-0.023-0.0230.0000.0000.0000.000
157B495CYS0-0.036-0.00520.548-0.010-0.0100.0000.0000.0000.000
158B496ILE00.0190.01019.953-0.022-0.0220.0000.0000.0000.000
159B497LYS10.8950.93923.480-0.120-0.1200.0000.0000.0000.000
160B498TYR00.004-0.02025.877-0.007-0.0070.0000.0000.0000.000
161B499TYR00.0840.02522.522-0.004-0.0040.0000.0000.0000.000
162B500LYS10.8460.94826.278-0.088-0.0880.0000.0000.0000.000
163B501GLN0-0.071-0.03128.681-0.013-0.0130.0000.0000.0000.000
164B502ASN0-0.057-0.02629.665-0.007-0.0070.0000.0000.0000.000
165B503PRO0-0.024-0.00729.4080.0020.0020.0000.0000.0000.000
166B504LEU0-0.035-0.04123.7560.0070.0070.0000.0000.0000.000
167B505ASP-1-0.921-0.96027.3200.1030.1030.0000.0000.0000.000
168B506GLU-1-0.837-0.87829.8840.0990.0990.0000.0000.0000.000
169B507GLN0-0.029-0.01329.1370.0180.0180.0000.0000.0000.000
170B508HIS00.004-0.00226.693-0.017-0.0170.0000.0000.0000.000
171B509ILE0-0.030-0.00827.2160.0150.0150.0000.0000.0000.000
172B510PHE00.0230.02123.703-0.007-0.0070.0000.0000.0000.000
173B511GLN0-0.024-0.02425.5970.0100.0100.0000.0000.0000.000
174B512LEU00.0200.00619.183-0.009-0.0090.0000.0000.0000.000
175B513PRO0-0.041-0.01923.8170.0060.0060.0000.0000.0000.000
176B514VAL00.0630.03521.0510.0140.0140.0000.0000.0000.000
177B515ARG10.9610.97823.299-0.175-0.1750.0000.0000.0000.000
178B516PRO00.0740.01223.6010.0190.0190.0000.0000.0000.000
179B517THR00.012-0.00223.8960.0110.0110.0000.0000.0000.000
180B518ALA0-0.0060.00319.5500.0060.0060.0000.0000.0000.000
181B519VAL00.0370.02119.2960.0380.0380.0000.0000.0000.000
182B520LYS10.9290.98121.393-0.187-0.1870.0000.0000.0000.000
183B521ASN0-0.015-0.02818.779-0.040-0.0400.0000.0000.0000.000
184B522LEU00.0000.01318.098-0.004-0.0040.0000.0000.0000.000
185B523TYR00.0260.00322.145-0.014-0.0140.0000.0000.0000.000
186B524GLN0-0.041-0.01125.929-0.015-0.0150.0000.0000.0000.000
187B525SER0-0.039-0.00726.887-0.012-0.0120.0000.0000.0000.000
188B526GLU-1-0.906-0.94725.0450.2050.2050.0000.0000.0000.000
189B527LYS10.8160.89928.279-0.149-0.1490.0000.0000.0000.000
190B528PRO0-0.0050.00330.4300.0070.0070.0000.0000.0000.000
191B529GLN00.019-0.00128.8610.0000.0000.0000.0000.0000.000
192B530LYS10.9250.94632.216-0.145-0.1450.0000.0000.0000.000
193B531TRP00.0010.01834.1160.0040.0040.0000.0000.0000.000
194B532ARG10.8930.93436.727-0.115-0.1150.0000.0000.0000.000
195B533VAL00.0160.02539.1360.0020.0020.0000.0000.0000.000
196B534GLU-1-0.826-0.91341.9110.0770.0770.0000.0000.0000.000
197B535ILE0-0.005-0.00143.8460.0000.0000.0000.0000.0000.000
198B536TYR00.0540.01043.598-0.001-0.0010.0000.0000.0000.000
199B537SER00.0570.01848.7600.0000.0000.0000.0000.0000.000
200B538GLY00.0320.03949.786-0.002-0.0020.0000.0000.0000.000
201B539GLN00.0390.00550.1640.0020.0020.0000.0000.0000.000
202B540LYS10.8520.93742.498-0.076-0.0760.0000.0000.0000.000
203B541LYS10.9350.95846.996-0.054-0.0540.0000.0000.0000.000
204B542ILE0-0.0120.00049.0260.0010.0010.0000.0000.0000.000
205B543LYS10.8230.89544.479-0.072-0.0720.0000.0000.0000.000
206B544THR00.0260.02248.513-0.002-0.0020.0000.0000.0000.000
207B545VAL0-0.042-0.02742.7340.0020.0020.0000.0000.0000.000
208B546TRP00.0610.03441.7300.0000.0000.0000.0000.0000.000
209B547GLN00.0320.01238.5880.0040.0040.0000.0000.0000.000
210B548LEU0-0.0040.01338.782-0.003-0.0030.0000.0000.0000.000
211B549SER00.006-0.00836.6450.0080.0080.0000.0000.0000.000
212B550ASP-1-0.839-0.90732.9890.1410.1410.0000.0000.0000.000
213B551SER0-0.001-0.00434.4570.0010.0010.0000.0000.0000.000
214B552SER00.0310.00337.083-0.002-0.0020.0000.0000.0000.000
215B553PRO0-0.073-0.03137.9110.0040.0040.0000.0000.0000.000
216B554ILE0-0.039-0.01638.989-0.001-0.0010.0000.0000.0000.000
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