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: YV5Y2

Calculation Name: 4QLP-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4QLP

Chain ID: B

ChEMBL ID:

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2240911.184242
FMO2-HF: Nuclear repulsion 2161102.372234
FMO2-HF: Total energy -79808.812009
FMO2-MP2: Total energy -80042.964954


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.
-1.1761.307-0.015-1.296-1.1720.005
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 : -0.009 / q_NPA : -0.005
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].
3B650MET00.0190.0003.800-0.8591.550-0.014-1.289-1.1060.005
4B651ARG10.9460.9836.4440.3750.3750.0000.0000.0000.000
5B652LEU0-0.035-0.0148.0790.0470.0470.0000.0000.0000.000
6B653SER0-0.0160.00211.3340.0070.0070.0000.0000.0000.000
7B654ASP-1-0.848-0.91114.382-0.263-0.2630.0000.0000.0000.000
8B655GLU-1-0.926-0.97717.223-0.192-0.1920.0000.0000.0000.000
9B656ALA0-0.040-0.01720.3090.0020.0020.0000.0000.0000.000
10B657VAL0-0.053-0.03222.5680.0080.0080.0000.0000.0000.000
11B658ASP-1-0.903-0.93522.733-0.149-0.1490.0000.0000.0000.000
12B659PRO0-0.016-0.00524.3390.0080.0080.0000.0000.0000.000
13B660GLN0-0.004-0.00127.3870.0020.0020.0000.0000.0000.000
14B661TYR00.016-0.00927.2810.0020.0020.0000.0000.0000.000
15B662GLY00.007-0.00229.0510.0060.0060.0000.0000.0000.000
16B663GLU-1-0.982-0.99029.462-0.068-0.0680.0000.0000.0000.000
17B664PRO0-0.068-0.04627.399-0.003-0.0030.0000.0000.0000.000
18B665LEU0-0.0030.01021.965-0.005-0.0050.0000.0000.0000.000
19B666SER0-0.037-0.01319.6530.0000.0000.0000.0000.0000.000
20B667ARG10.8390.89415.0000.2750.2750.0000.0000.0000.000
21B668HIS0-0.034-0.02019.403-0.003-0.0030.0000.0000.0000.000
22B669TRP0-0.073-0.03018.055-0.003-0.0030.0000.0000.0000.000
23B670ASP-1-0.803-0.89819.964-0.078-0.0780.0000.0000.0000.000
24B671PHE0-0.061-0.03422.1990.0050.0050.0000.0000.0000.000
25B672THR00.0300.01021.6220.0000.0000.0000.0000.0000.000
26B673ASP-1-0.887-0.94024.628-0.003-0.0030.0000.0000.0000.000
27B674ASN00.0680.02528.316-0.007-0.0070.0000.0000.0000.000
28B675PRO0-0.029-0.00728.5310.0050.0050.0000.0000.0000.000
29B676ALA00.0390.00930.5120.0020.0020.0000.0000.0000.000
30B677ASP-1-0.903-0.92233.685-0.004-0.0040.0000.0000.0000.000
31B678ARG10.9920.97435.5980.0150.0150.0000.0000.0000.000
32B679SER0-0.099-0.05737.4430.0020.0020.0000.0000.0000.000
33B680ARG10.8720.92529.030-0.002-0.0020.0000.0000.0000.000
34B681ILE0-0.0380.01134.2070.0000.0000.0000.0000.0000.000
35B682ASN00.015-0.01835.0460.0040.0040.0000.0000.0000.000
36B683PRO0-0.007-0.01536.664-0.002-0.0020.0000.0000.0000.000
37B684VAL0-0.007-0.00939.516-0.001-0.0010.0000.0000.0000.000
38B685VAL00.0460.02335.590-0.001-0.0010.0000.0000.0000.000
39B686ALA0-0.021-0.01838.864-0.002-0.0020.0000.0000.0000.000
40B687GLN0-0.072-0.03440.641-0.001-0.0010.0000.0000.0000.000
41B688LEU0-0.0140.00839.6690.0000.0000.0000.0000.0000.000
42B689MET0-0.082-0.02637.805-0.001-0.0010.0000.0000.0000.000
43B690GLU-1-0.911-0.96441.963-0.018-0.0180.0000.0000.0000.000
44B691ASP-1-0.841-0.89641.598-0.027-0.0270.0000.0000.0000.000
45B692PRO0-0.011-0.00841.191-0.001-0.0010.0000.0000.0000.000
46B693ASN0-0.052-0.03441.1210.0010.0010.0000.0000.0000.000
47B694ALA0-0.030-0.00839.382-0.001-0.0010.0000.0000.0000.000
48B695PRO0-0.0030.01335.817-0.002-0.0020.0000.0000.0000.000
49B696PHE0-0.038-0.02130.424-0.001-0.0010.0000.0000.0000.000
50B697GLY00.0560.02334.250-0.004-0.0040.0000.0000.0000.000
51B698ARG10.7460.82536.5570.0310.0310.0000.0000.0000.000
52B699ASP-1-0.741-0.85636.528-0.047-0.0470.0000.0000.0000.000
53B700PRO0-0.005-0.01836.2540.0030.0030.0000.0000.0000.000
54B701GLN0-0.038-0.01338.8410.0010.0010.0000.0000.0000.000
55B702GLY00.0020.01041.1820.0020.0020.0000.0000.0000.000
56B703GLN0-0.080-0.03239.7500.0040.0040.0000.0000.0000.000
57B704PRO0-0.007-0.00939.167-0.002-0.0020.0000.0000.0000.000
58B705TYR0-0.017-0.00133.662-0.002-0.0020.0000.0000.0000.000
59B706THR00.0240.00634.1010.0020.0020.0000.0000.0000.000
60B707GLN00.0580.01128.5250.0000.0000.0000.0000.0000.000
61B708GLU-1-0.938-0.96129.072-0.060-0.0600.0000.0000.0000.000
62B709ARG10.8940.92428.9160.0470.0470.0000.0000.0000.000
63B710TYR00.0570.03627.974-0.005-0.0050.0000.0000.0000.000
64B711GLN00.0140.01324.8490.0000.0000.0000.0000.0000.000
65B712GLU-1-0.916-0.96624.705-0.092-0.0920.0000.0000.0000.000
66B713ARG10.8710.95325.6960.0660.0660.0000.0000.0000.000
67B714PHE0-0.003-0.01825.908-0.004-0.0040.0000.0000.0000.000
68B715ASN0-0.0160.00522.0230.0070.0070.0000.0000.0000.000
69B716SER00.0790.03219.914-0.007-0.0070.0000.0000.0000.000
70B717VAL00.0160.01014.1980.0050.0050.0000.0000.0000.000
71B718GLY0-0.0180.00114.198-0.007-0.0070.0000.0000.0000.000
72B719PRO00.029-0.00210.702-0.031-0.0310.0000.0000.0000.000
73B720TRP0-0.069-0.0374.567-0.195-0.121-0.001-0.007-0.0660.000
74B721GLY00.0190.0138.9850.0240.0240.0000.0000.0000.000
75B722GLN0-0.0090.00411.5590.0200.0200.0000.0000.0000.000
76B723GLN00.0290.01913.803-0.020-0.0200.0000.0000.0000.000
77B724TYR0-0.024-0.01414.7990.0200.0200.0000.0000.0000.000
78B725SER00.0450.03019.4630.0030.0030.0000.0000.0000.000
79B726ASN0-0.046-0.01422.749-0.010-0.0100.0000.0000.0000.000
80B727PHE00.0050.00222.8750.0080.0080.0000.0000.0000.000
81B728PRO00.0480.03225.942-0.007-0.0070.0000.0000.0000.000
82B729PRO00.0520.01427.168-0.002-0.0020.0000.0000.0000.000
83B730ASN0-0.0160.00228.1360.0030.0030.0000.0000.0000.000
84B731ASN0-0.002-0.00927.6520.0030.0030.0000.0000.0000.000
85B732GLY00.0200.01628.6000.0050.0050.0000.0000.0000.000
86B733ALA00.0320.04430.9920.0040.0040.0000.0000.0000.000
87B734VAL00.0300.01733.900-0.005-0.0050.0000.0000.0000.000
88B735PRO0-0.034-0.02734.2540.0010.0010.0000.0000.0000.000
89B736GLY0-0.020-0.01336.4760.0020.0020.0000.0000.0000.000
90B737THR00.0150.00438.2230.0030.0030.0000.0000.0000.000
91B738ARG10.7950.89331.7440.0590.0590.0000.0000.0000.000
92B739ILE0-0.0010.02138.9540.0000.0000.0000.0000.0000.000
93B740ALA0-0.006-0.00740.3770.0000.0000.0000.0000.0000.000
94B741TYR0-0.062-0.04141.8090.0010.0010.0000.0000.0000.000
95B742THR00.026-0.00542.9210.0000.0000.0000.0000.0000.000
96B743ASN0-0.018-0.00144.7140.0020.0020.0000.0000.0000.000
97B744LEU00.0820.03844.751-0.001-0.0010.0000.0000.0000.000
98B745GLU-1-0.875-0.94247.066-0.012-0.0120.0000.0000.0000.000
99B746LYS10.9220.96248.9060.0180.0180.0000.0000.0000.000
100B747PHE00.0330.02242.6850.0000.0000.0000.0000.0000.000
101B748LEU0-0.015-0.00947.1650.0000.0000.0000.0000.0000.000
102B749SER0-0.066-0.03449.2230.0010.0010.0000.0000.0000.000
103B750ASP-1-0.897-0.91448.347-0.020-0.0200.0000.0000.0000.000
104B751TYR0-0.034-0.03245.246-0.001-0.0010.0000.0000.0000.000
105B752GLY0-0.0270.00348.0860.0010.0010.0000.0000.0000.000
106B753PRO00.012-0.02146.573-0.001-0.0010.0000.0000.0000.000
107B754GLN0-0.033-0.01144.9230.0010.0010.0000.0000.0000.000
108B755LEU00.0280.01639.330-0.002-0.0020.0000.0000.0000.000
109B756ASP-1-0.719-0.83939.292-0.014-0.0140.0000.0000.0000.000
110B757ARG10.8190.91128.6960.0190.0190.0000.0000.0000.000
111B758ILE00.0300.03332.7840.0030.0030.0000.0000.0000.000
112B759GLY00.0440.02330.399-0.004-0.0040.0000.0000.0000.000
113B760GLY0-0.016-0.01329.2130.0030.0030.0000.0000.0000.000
114B761ASP-1-0.867-0.93829.9460.0010.0010.0000.0000.0000.000
115B762GLN00.034-0.00824.336-0.006-0.0060.0000.0000.0000.000
116B763GLY0-0.0220.00226.535-0.006-0.0060.0000.0000.0000.000
117B764LYS10.8980.93925.7110.0400.0400.0000.0000.0000.000
118B765TYR00.0130.01729.507-0.001-0.0010.0000.0000.0000.000
119B766LEU0-0.027-0.00932.5000.0030.0030.0000.0000.0000.000
120B767ALA00.0270.02135.604-0.003-0.0030.0000.0000.0000.000
121B768ILE00.0430.01238.3060.0030.0030.0000.0000.0000.000
122B769MET0-0.071-0.01141.9090.0000.0000.0000.0000.0000.000
123B770GLU-1-0.849-0.92744.429-0.022-0.0220.0000.0000.0000.000
124B771HIS0-0.057-0.04246.9770.0020.0020.0000.0000.0000.000
125B772GLY00.0200.01348.1970.0010.0010.0000.0000.0000.000
126B773ARG10.8820.94247.6380.0150.0150.0000.0000.0000.000
127B774PRO0-0.0210.00542.924-0.001-0.0010.0000.0000.0000.000
128B775ALA00.0670.03640.5410.0000.0000.0000.0000.0000.000
129B776SER00.0850.04441.6380.0010.0010.0000.0000.0000.000
130B777TRP0-0.008-0.02732.4300.0000.0000.0000.0000.0000.000
131B778GLU-1-0.764-0.88737.299-0.026-0.0260.0000.0000.0000.000
132B779GLN00.0540.02238.184-0.002-0.0020.0000.0000.0000.000
133B780ARG10.7290.86635.3570.0200.0200.0000.0000.0000.000
134B781ALA0-0.0280.00433.555-0.002-0.0020.0000.0000.0000.000
135B782LEU0-0.017-0.00431.023-0.004-0.0040.0000.0000.0000.000
136B783HIS00.0540.02025.3690.0060.0060.0000.0000.0000.000
137B784VAL00.0180.00728.7210.0050.0050.0000.0000.0000.000
138B785THR0-0.027-0.03924.8330.0050.0050.0000.0000.0000.000
139B786SER0-0.0020.01128.0750.0040.0040.0000.0000.0000.000
140B787LEU0-0.021-0.00530.3390.0040.0040.0000.0000.0000.000
141B788ARG10.8030.91028.6110.0120.0120.0000.0000.0000.000
142B789ASP-1-0.871-0.91828.914-0.011-0.0110.0000.0000.0000.000
143B790PRO0-0.062-0.02331.0190.0000.0000.0000.0000.0000.000
144B791TYR0-0.024-0.04434.248-0.002-0.0020.0000.0000.0000.000
145B792HIS0-0.036-0.01333.8380.0030.0030.0000.0000.0000.000
146B793ALA00.0290.00838.277-0.003-0.0030.0000.0000.0000.000
147B794TYR0-0.040-0.03735.7710.0020.0020.0000.0000.0000.000
148B795THR0-0.044-0.02641.722-0.001-0.0010.0000.0000.0000.000
149B796ILE0-0.058-0.02141.1080.0010.0010.0000.0000.0000.000
150B797ASP-1-0.830-0.92043.535-0.005-0.0050.0000.0000.0000.000
151B798TRP0-0.065-0.03941.8180.0000.0000.0000.0000.0000.000
152B799LEU00.0120.00440.8780.0000.0000.0000.0000.0000.000
153B800PRO0-0.049-0.02139.7940.0000.0000.0000.0000.0000.000
154B801GLU-1-0.880-0.94642.705-0.015-0.0150.0000.0000.0000.000
155B802GLY0-0.017-0.01442.0170.0000.0000.0000.0000.0000.000
156B803TRP0-0.043-0.01736.389-0.002-0.0020.0000.0000.0000.000
157B804PHE0-0.026-0.01735.8270.0010.0010.0000.0000.0000.000
158B805ILE0-0.022-0.00538.352-0.001-0.0010.0000.0000.0000.000
159B806GLU-1-0.790-0.88434.354-0.047-0.0470.0000.0000.0000.000
160B807VAL00.0250.01037.7840.0000.0000.0000.0000.0000.000
161B808SER00.008-0.00635.944-0.002-0.0020.0000.0000.0000.000
162B809GLU-1-0.902-0.94538.585-0.035-0.0350.0000.0000.0000.000
163B810VAL0-0.050-0.00834.499-0.004-0.0040.0000.0000.0000.000
164B811ALA00.015-0.00233.8780.0020.0020.0000.0000.0000.000
165B812PRO00.0200.00535.0380.0000.0000.0000.0000.0000.000
166B813GLY00.014-0.00631.774-0.005-0.0050.0000.0000.0000.000
167B814CYS0-0.063-0.03128.7280.0030.0030.0000.0000.0000.000
168B815GLY00.0120.00731.0580.0030.0030.0000.0000.0000.000
169B816GLN00.0120.01234.3980.0040.0040.0000.0000.0000.000
170B817PRO00.008-0.00136.290-0.003-0.0030.0000.0000.0000.000
171B818GLY0-0.0100.01237.478-0.001-0.0010.0000.0000.0000.000
172B819GLY00.0200.00038.0150.0020.0020.0000.0000.0000.000
173B820SER0-0.043-0.02638.2610.0020.0020.0000.0000.0000.000
174B821ILE00.0570.04339.632-0.002-0.0020.0000.0000.0000.000
175B822GLN0-0.049-0.02932.5150.0000.0000.0000.0000.0000.000
176B823VAL00.0170.00136.8140.0000.0000.0000.0000.0000.000
177B824ARG10.7900.86229.2160.0520.0520.0000.0000.0000.000
178B825ILE00.0170.01234.2520.0010.0010.0000.0000.0000.000
179B826PHE0-0.0010.00431.028-0.002-0.0020.0000.0000.0000.000
180B827ASP-1-0.707-0.84333.473-0.027-0.0270.0000.0000.0000.000
181B828HIS00.0390.00936.087-0.002-0.0020.0000.0000.0000.000
182B829GLN0-0.096-0.04633.3070.0010.0010.0000.0000.0000.000
183B830ASN0-0.029-0.01132.228-0.002-0.0020.0000.0000.0000.000
184B831GLU-1-0.944-0.95929.676-0.039-0.0390.0000.0000.0000.000
185B832MET0-0.033-0.00328.1490.0040.0040.0000.0000.0000.000
186B833ARG10.7630.84429.2750.0200.0200.0000.0000.0000.000
187B834LYS10.8740.95726.1730.0010.0010.0000.0000.0000.000
188B835VAL00.0760.02629.9990.0030.0030.0000.0000.0000.000
189B836GLU-1-0.764-0.86130.3240.0100.0100.0000.0000.0000.000
190B837GLU-1-0.918-0.94430.337-0.009-0.0090.0000.0000.0000.000
191B838LEU00.017-0.00332.8770.0010.0010.0000.0000.0000.000
192B839ILE0-0.0050.00534.8080.0010.0010.0000.0000.0000.000
193B840ARG10.7540.85229.775-0.011-0.0110.0000.0000.0000.000
194B841ARG10.8940.94134.0970.0040.0040.0000.0000.0000.000
195B842GLY00.0470.03038.6600.0000.0000.0000.0000.0000.000
196B843VAL0-0.055-0.00638.776-0.001-0.0010.0000.0000.0000.000
197B844LEU0-0.011-0.00736.573-0.001-0.0010.0000.0000.0000.000
198B845ARG10.9310.98740.4280.0020.0020.0000.0000.0000.000
199B846GLN00.0410.00537.460-0.001-0.0010.0000.0000.0000.000