FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: VQ3R1

Calculation Name: 4QLP-B-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 4QLP

Chain ID: B

ChEMBL ID:
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UniProt ID: O05442

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2241498.533181
FMO2-HF: Nuclear repulsion 2161688.997324
FMO2-HF: Total energy -79809.535858
FMO2-MP2: Total energy -80043.708057


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:648:SER)


Summations of interaction energy for fragment #1(B:648:SER)
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.
-0.9961.563-0.009-1.393-1.1570.005
Interaction energy analysis for fragmet #1(B:648:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.003
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].
3B650MET00.0220.0003.624-0.2712.288-0.009-1.393-1.1570.005
4B651ARG10.8440.9186.238-0.343-0.3430.0000.0000.0000.000
5B652LEU0-0.038-0.0147.943-0.039-0.0390.0000.0000.0000.000
6B653SER0-0.014-0.01511.2240.0710.0710.0000.0000.0000.000
7B654ASP-1-0.790-0.86714.2430.0080.0080.0000.0000.0000.000
8B655GLU-1-0.850-0.90817.117-0.149-0.1490.0000.0000.0000.000
9B656ALA0-0.047-0.02120.1800.0210.0210.0000.0000.0000.000
10B657VAL0-0.053-0.03422.4120.0150.0150.0000.0000.0000.000
11B658ASP-1-0.906-0.93722.653-0.041-0.0410.0000.0000.0000.000
12B659PRO0-0.020-0.00524.2770.0040.0040.0000.0000.0000.000
13B660GLN0-0.044-0.03327.3060.0120.0120.0000.0000.0000.000
14B661TYR00.006-0.02427.209-0.007-0.0070.0000.0000.0000.000
15B662GLY0-0.004-0.00729.0360.0040.0040.0000.0000.0000.000
16B663GLU-1-0.916-0.94429.481-0.067-0.0670.0000.0000.0000.000
17B664PRO0-0.067-0.04427.371-0.002-0.0020.0000.0000.0000.000
18B665LEU0-0.0160.00221.9710.0050.0050.0000.0000.0000.000
19B666SER0-0.059-0.05719.589-0.012-0.0120.0000.0000.0000.000
20B667ARG10.8390.90915.3500.2120.2120.0000.0000.0000.000
21B668HIS0-0.035-0.02619.3630.0230.0230.0000.0000.0000.000
22B669TRP0-0.055-0.02418.071-0.036-0.0360.0000.0000.0000.000
23B670ASP-1-0.812-0.89619.976-0.182-0.1820.0000.0000.0000.000
24B671PHE0-0.054-0.02622.207-0.003-0.0030.0000.0000.0000.000
25B672THR00.0380.01621.664-0.005-0.0050.0000.0000.0000.000
26B673ASP-1-0.836-0.88924.633-0.085-0.0850.0000.0000.0000.000
27B674ASN00.0730.03328.321-0.002-0.0020.0000.0000.0000.000
28B675PRO0-0.026-0.01128.5400.0070.0070.0000.0000.0000.000
29B676ALA00.0390.01330.5210.0080.0080.0000.0000.0000.000
30B677ASP-1-0.877-0.91033.695-0.054-0.0540.0000.0000.0000.000
31B678ARG10.9530.94835.6050.0390.0390.0000.0000.0000.000
32B679SER0-0.093-0.05937.4360.0040.0040.0000.0000.0000.000
33B680ARG10.8130.88628.9640.0710.0710.0000.0000.0000.000
34B681ILE0-0.0410.01434.2150.0010.0010.0000.0000.0000.000
35B682ASN00.012-0.01935.0400.0020.0020.0000.0000.0000.000
36B683PRO00.002-0.01036.6740.0010.0010.0000.0000.0000.000
37B684VAL0-0.007-0.01039.5130.0010.0010.0000.0000.0000.000
38B685VAL00.0430.02135.5790.0010.0010.0000.0000.0000.000
39B686ALA0-0.026-0.01838.877-0.001-0.0010.0000.0000.0000.000
40B687GLN0-0.069-0.03240.6530.0000.0000.0000.0000.0000.000
41B688LEU0-0.0130.00639.8110.0010.0010.0000.0000.0000.000
42B689MET0-0.050-0.00137.885-0.001-0.0010.0000.0000.0000.000
43B690GLU-1-0.862-0.94541.978-0.011-0.0110.0000.0000.0000.000
44B691ASP-1-0.863-0.90441.766-0.032-0.0320.0000.0000.0000.000
45B692PRO0-0.009-0.00841.188-0.003-0.0030.0000.0000.0000.000
46B693ASN0-0.059-0.03241.133-0.004-0.0040.0000.0000.0000.000
47B694ALA0-0.016-0.00239.423-0.004-0.0040.0000.0000.0000.000
48B695PRO0-0.0080.00735.8720.0010.0010.0000.0000.0000.000
49B696PHE0-0.025-0.01530.473-0.001-0.0010.0000.0000.0000.000
50B697GLY00.0490.02134.265-0.002-0.0020.0000.0000.0000.000
51B698ARG10.7670.83536.6070.0310.0310.0000.0000.0000.000
52B699ASP-1-0.725-0.83336.537-0.052-0.0520.0000.0000.0000.000
53B700PRO00.003-0.01036.2890.0040.0040.0000.0000.0000.000
54B701GLN0-0.034-0.01138.7470.0010.0010.0000.0000.0000.000
55B702GLY00.0030.00941.1980.0010.0010.0000.0000.0000.000
56B703GLN0-0.073-0.04239.5380.0000.0000.0000.0000.0000.000
57B704PRO0-0.001-0.00839.173-0.001-0.0010.0000.0000.0000.000
58B705TYR0-0.0170.00033.667-0.006-0.0060.0000.0000.0000.000
59B706THR00.0220.00434.1690.0010.0010.0000.0000.0000.000
60B707GLN00.0230.00028.1140.0070.0070.0000.0000.0000.000
61B708GLU-1-0.952-0.97029.089-0.123-0.1230.0000.0000.0000.000
62B709ARG10.8920.92228.9280.0670.0670.0000.0000.0000.000
63B710TYR00.0470.02828.253-0.001-0.0010.0000.0000.0000.000
64B711GLN00.005-0.00524.8670.0110.0110.0000.0000.0000.000
65B712GLU-1-0.849-0.92524.719-0.134-0.1340.0000.0000.0000.000
66B713ARG10.8190.92425.6860.0910.0910.0000.0000.0000.000
67B714PHE0-0.004-0.01625.9500.0090.0090.0000.0000.0000.000
68B715ASN0-0.025-0.00322.0560.0290.0290.0000.0000.0000.000
69B716SER00.0820.03519.930-0.022-0.0220.0000.0000.0000.000
70B717VAL00.0110.00614.166-0.008-0.0080.0000.0000.0000.000
71B718GLY0-0.0110.00614.2500.0230.0230.0000.0000.0000.000
72B719PRO00.022-0.00610.834-0.065-0.0650.0000.0000.0000.000
73B720TRP0-0.060-0.0354.847-0.005-0.0050.0000.0000.0000.000
74B721GLY00.0200.0149.037-0.103-0.1030.0000.0000.0000.000
75B722GLN0-0.0150.00511.585-0.039-0.0390.0000.0000.0000.000
76B723GLN00.0320.01813.908-0.025-0.0250.0000.0000.0000.000
77B724TYR0-0.023-0.01415.0870.0330.0330.0000.0000.0000.000
78B725SER00.0530.03119.556-0.013-0.0130.0000.0000.0000.000
79B726ASN0-0.052-0.01822.8160.0190.0190.0000.0000.0000.000
80B727PHE00.0110.00823.2350.0020.0020.0000.0000.0000.000
81B728PRO00.0540.03625.967-0.001-0.0010.0000.0000.0000.000
82B729PRO00.0430.01227.1700.0070.0070.0000.0000.0000.000
83B730ASN0-0.011-0.00328.1230.0070.0070.0000.0000.0000.000
84B731ASN00.012-0.01327.7140.0070.0070.0000.0000.0000.000
85B732GLY00.0280.02628.6530.0000.0000.0000.0000.0000.000
86B733ALA00.0280.04231.045-0.003-0.0030.0000.0000.0000.000
87B734VAL00.0170.02333.9260.0000.0000.0000.0000.0000.000
88B735PRO0-0.028-0.02334.2370.0040.0040.0000.0000.0000.000
89B736GLY0-0.022-0.01236.481-0.002-0.0020.0000.0000.0000.000
90B737THR00.0140.00038.2350.0000.0000.0000.0000.0000.000
91B738ARG10.7550.87531.730-0.044-0.0440.0000.0000.0000.000
92B739ILE0-0.0100.00839.0010.0010.0010.0000.0000.0000.000
93B740ALA0-0.005-0.00140.3940.0010.0010.0000.0000.0000.000
94B741TYR0-0.057-0.03741.881-0.001-0.0010.0000.0000.0000.000
95B742THR00.0340.00143.0190.0010.0010.0000.0000.0000.000
96B743ASN0-0.019-0.00244.810-0.001-0.0010.0000.0000.0000.000
97B744LEU00.0750.03644.856-0.001-0.0010.0000.0000.0000.000
98B745GLU-1-0.871-0.94347.1930.0310.0310.0000.0000.0000.000
99B746LYS10.8170.89549.182-0.025-0.0250.0000.0000.0000.000
100B747PHE00.0360.01542.737-0.001-0.0010.0000.0000.0000.000
101B748LEU0-0.017-0.00847.276-0.002-0.0020.0000.0000.0000.000
102B749SER0-0.055-0.02549.349-0.002-0.0020.0000.0000.0000.000
103B750ASP-1-0.826-0.86448.4750.0200.0200.0000.0000.0000.000
104B751TYR0-0.024-0.02745.442-0.002-0.0020.0000.0000.0000.000
105B752GLY0-0.0180.01148.213-0.001-0.0010.0000.0000.0000.000
106B753PRO00.012-0.02046.7180.0010.0010.0000.0000.0000.000
107B754GLN0-0.040-0.01745.1040.0010.0010.0000.0000.0000.000
108B755LEU00.0240.01639.4610.0000.0000.0000.0000.0000.000
109B756ASP-1-0.732-0.83039.4710.0060.0060.0000.0000.0000.000
110B757ARG10.8310.91329.168-0.021-0.0210.0000.0000.0000.000
111B758ILE00.0270.02732.914-0.001-0.0010.0000.0000.0000.000
112B759GLY00.0460.02930.5200.0000.0000.0000.0000.0000.000
113B760GLY0-0.009-0.01029.3630.0030.0030.0000.0000.0000.000
114B761ASP-1-0.867-0.93830.1300.0460.0460.0000.0000.0000.000
115B762GLN00.0440.00024.1810.0110.0110.0000.0000.0000.000
116B763GLY0-0.0160.00626.7070.0060.0060.0000.0000.0000.000
117B764LYS10.8790.91625.961-0.091-0.0910.0000.0000.0000.000
118B765TYR00.0230.01829.4200.0030.0030.0000.0000.0000.000
119B766LEU0-0.032-0.00632.630-0.002-0.0020.0000.0000.0000.000
120B767ALA00.0250.01935.7420.0010.0010.0000.0000.0000.000
121B768ILE00.0400.01338.4330.0010.0010.0000.0000.0000.000
122B769MET0-0.065-0.00442.034-0.002-0.0020.0000.0000.0000.000
123B770GLU-1-0.849-0.92644.4040.0090.0090.0000.0000.0000.000
124B771HIS0-0.057-0.05047.097-0.002-0.0020.0000.0000.0000.000
125B772GLY00.0190.01448.336-0.001-0.0010.0000.0000.0000.000
126B773ARG10.8870.94847.779-0.003-0.0030.0000.0000.0000.000
127B774PRO0-0.0190.00343.0080.0010.0010.0000.0000.0000.000
128B775ALA00.0640.03740.695-0.001-0.0010.0000.0000.0000.000
129B776SER00.0450.01141.7680.0000.0000.0000.0000.0000.000
130B777TRP0-0.017-0.03332.3390.0030.0030.0000.0000.0000.000
131B778GLU-1-0.760-0.87437.406-0.021-0.0210.0000.0000.0000.000
132B779GLN00.0490.02438.2670.0020.0020.0000.0000.0000.000
133B780ARG10.7220.85635.4500.0030.0030.0000.0000.0000.000
134B781ALA0-0.036-0.00133.6840.0010.0010.0000.0000.0000.000
135B782LEU0-0.017-0.00131.0720.0010.0010.0000.0000.0000.000
136B783HIS00.0510.02925.0690.0030.0030.0000.0000.0000.000
137B784VAL00.0220.00928.6370.0030.0030.0000.0000.0000.000
138B785THR0-0.018-0.03224.7260.0030.0030.0000.0000.0000.000
139B786SER0-0.016-0.01728.0880.0030.0030.0000.0000.0000.000
140B787LEU0-0.028-0.00830.3530.0050.0050.0000.0000.0000.000
141B788ARG10.7840.88028.3480.0700.0700.0000.0000.0000.000
142B789ASP-1-0.841-0.89629.085-0.010-0.0100.0000.0000.0000.000
143B790PRO0-0.065-0.01831.117-0.001-0.0010.0000.0000.0000.000
144B791TYR0-0.027-0.04434.2600.0010.0010.0000.0000.0000.000
145B792HIS0-0.036-0.01433.6480.0020.0020.0000.0000.0000.000
146B793ALA00.0170.00338.4620.0000.0000.0000.0000.0000.000
147B794TYR0-0.032-0.03235.7190.0020.0020.0000.0000.0000.000
148B795THR0-0.064-0.04441.900-0.002-0.0020.0000.0000.0000.000
149B796ILE0-0.047-0.01641.2840.0020.0020.0000.0000.0000.000
150B797ASP-1-0.835-0.91643.6960.0270.0270.0000.0000.0000.000
151B798TRP0-0.049-0.03142.1930.0010.0010.0000.0000.0000.000
152B799LEU00.0140.00641.0360.0010.0010.0000.0000.0000.000
153B800PRO0-0.043-0.01739.921-0.001-0.0010.0000.0000.0000.000
154B801GLU-1-0.889-0.95042.8340.0530.0530.0000.0000.0000.000
155B802GLY0-0.008-0.00842.1230.0030.0030.0000.0000.0000.000
156B803TRP0-0.051-0.02036.2430.0030.0030.0000.0000.0000.000
157B804PHE0-0.019-0.01435.805-0.004-0.0040.0000.0000.0000.000
158B805ILE0-0.022-0.00738.4600.0030.0030.0000.0000.0000.000
159B806GLU-1-0.762-0.85634.5040.0470.0470.0000.0000.0000.000
160B807VAL00.0210.00737.879-0.001-0.0010.0000.0000.0000.000
161B808SER0-0.001-0.01235.9400.0030.0030.0000.0000.0000.000
162B809GLU-1-0.901-0.94538.6520.0060.0060.0000.0000.0000.000
163B810VAL0-0.042-0.00434.5210.0020.0020.0000.0000.0000.000
164B811ALA00.016-0.00333.923-0.002-0.0020.0000.0000.0000.000
165B812PRO00.0210.00635.091-0.001-0.0010.0000.0000.0000.000
166B813GLY00.016-0.00731.8230.0020.0020.0000.0000.0000.000
167B814CYS0-0.063-0.02728.719-0.003-0.0030.0000.0000.0000.000
168B815GLY00.0110.00631.111-0.002-0.0020.0000.0000.0000.000
169B816GLN00.0100.01034.4420.0030.0030.0000.0000.0000.000
170B817PRO00.0110.00436.3400.0010.0010.0000.0000.0000.000
171B818GLY0-0.0060.01037.5400.0020.0020.0000.0000.0000.000
172B819GLY00.0200.00038.082-0.001-0.0010.0000.0000.0000.000
173B820SER0-0.044-0.03438.4360.0020.0020.0000.0000.0000.000
174B821ILE00.0520.03639.7120.0010.0010.0000.0000.0000.000
175B822GLN0-0.038-0.01432.8070.0000.0000.0000.0000.0000.000
176B823VAL00.022-0.00136.9290.0020.0020.0000.0000.0000.000
177B824ARG10.7870.84829.495-0.052-0.0520.0000.0000.0000.000
178B825ILE00.0160.00934.382-0.001-0.0010.0000.0000.0000.000
179B826PHE0-0.007-0.00131.0920.0060.0060.0000.0000.0000.000
180B827ASP-1-0.724-0.84933.7220.0870.0870.0000.0000.0000.000
181B828HIS00.0340.00836.202-0.002-0.0020.0000.0000.0000.000
182B829GLN0-0.141-0.06933.108-0.004-0.0040.0000.0000.0000.000
183B830ASN0-0.043-0.02131.6710.0010.0010.0000.0000.0000.000
184B831GLU-1-0.890-0.93229.8920.1180.1180.0000.0000.0000.000
185B832MET0-0.0270.00328.104-0.009-0.0090.0000.0000.0000.000
186B833ARG10.8030.87829.407-0.087-0.0870.0000.0000.0000.000
187B834LYS10.7790.89726.566-0.089-0.0890.0000.0000.0000.000
188B835VAL00.0770.03130.1640.0000.0000.0000.0000.0000.000
189B836GLU-1-0.727-0.83430.1400.0770.0770.0000.0000.0000.000
190B837GLU-1-0.857-0.91231.1400.0930.0930.0000.0000.0000.000
191B838LEU00.0280.00533.065-0.001-0.0010.0000.0000.0000.000
192B839ILE00.0020.00635.103-0.002-0.0020.0000.0000.0000.000
193B840ARG10.7840.87329.757-0.082-0.0820.0000.0000.0000.000
194B841ARG10.8200.89733.508-0.079-0.0790.0000.0000.0000.000
195B842GLY00.0390.02638.782-0.001-0.0010.0000.0000.0000.000
196B843VAL0-0.048-0.00438.947-0.002-0.0020.0000.0000.0000.000
197B844LEU0-0.015-0.00936.674-0.003-0.0030.0000.0000.0000.000
198B845ARG10.9180.97640.607-0.024-0.0240.0000.0000.0000.000
199B846GLN00.0540.01437.861-0.002-0.0020.0000.0000.0000.000