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: NN34Q

Calculation Name: 4L11-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L11

Chain ID: A

ChEMBL ID:

UniProt ID: Q7QJX3

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2229545.175932
FMO2-HF: Nuclear repulsion 2149121.51087
FMO2-HF: Total energy -80423.665062
FMO2-MP2: Total energy -80655.362063


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(A:537:THR)


Summations of interaction energy for fragment #1(A:537:THR)
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.
-9.73-6.8460.014-1.288-1.6090.005
Interaction energy analysis for fragmet #1(A:537:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / 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].
3A539ARG10.9280.9553.657-6.963-4.2220.016-1.275-1.4810.005
4A540TYR00.0940.0485.679-0.537-0.489-0.001-0.007-0.0400.000
5A541HIS00.0690.0236.578-0.184-0.1840.0000.0000.0000.000
6A542THR0-0.008-0.0074.906-0.294-0.2940.0000.0000.0000.000
7A543GLN0-0.044-0.0306.739-0.388-0.3880.0000.0000.0000.000
8A544MET00.0390.0269.802-0.158-0.1580.0000.0000.0000.000
9A545LEU0-0.034-0.02711.378-0.125-0.1250.0000.0000.0000.000
10A546ARG10.8770.9486.606-0.532-0.5320.0000.0000.0000.000
11A547VAL00.0170.01513.087-0.092-0.0920.0000.0000.0000.000
12A548ARG10.8440.90214.786-0.502-0.5020.0000.0000.0000.000
13A549GLU-1-0.879-0.92514.3230.3330.3330.0000.0000.0000.000
14A550PHE00.0310.01316.942-0.043-0.0430.0000.0000.0000.000
15A551ILE00.009-0.00118.777-0.029-0.0290.0000.0000.0000.000
16A552ARG10.8840.94320.560-0.169-0.1690.0000.0000.0000.000
17A553PHE0-0.012-0.01617.916-0.020-0.0200.0000.0000.0000.000
18A554HIS10.8270.92921.003-0.085-0.0850.0000.0000.0000.000
19A555GLN00.0440.03024.749-0.005-0.0050.0000.0000.0000.000
20A556ILE00.0220.03122.477-0.007-0.0070.0000.0000.0000.000
21A557PRO00.0450.02126.5530.0120.0120.0000.0000.0000.000
22A558ASN00.014-0.00427.9870.0160.0160.0000.0000.0000.000
23A559PRO00.004-0.00428.1780.0110.0110.0000.0000.0000.000
24A560LEU00.0400.03625.5570.0080.0080.0000.0000.0000.000
25A561ARG10.8430.88822.948-0.223-0.2230.0000.0000.0000.000
26A562GLN00.009-0.00323.4160.0050.0050.0000.0000.0000.000
27A563ARG10.7780.86124.459-0.152-0.1520.0000.0000.0000.000
28A564LEU0-0.0130.00220.4860.0090.0090.0000.0000.0000.000
29A565GLU-1-0.760-0.86419.6360.2970.2970.0000.0000.0000.000
30A566GLU-1-0.841-0.87320.0160.2330.2330.0000.0000.0000.000
31A567TYR0-0.033-0.01618.0170.0150.0150.0000.0000.0000.000
32A568PHE0-0.002-0.01511.4600.0290.0290.0000.0000.0000.000
33A569GLN0-0.107-0.07015.8240.0760.0760.0000.0000.0000.000
34A570HIS0-0.013-0.00917.0590.0530.0530.0000.0000.0000.000
35A571ALA0-0.0110.00416.447-0.018-0.0180.0000.0000.0000.000
36A572TRP0-0.0110.0158.7750.0000.0000.0000.0000.0000.000
37A573THR00.0260.0009.953-0.038-0.0380.0000.0000.0000.000
38A574TYR0-0.0050.0014.7890.0880.183-0.001-0.006-0.0880.000
39A575THR00.0260.0095.426-0.204-0.2040.0000.0000.0000.000
40A576ASN0-0.0030.0106.463-0.289-0.2890.0000.0000.0000.000
41A577GLY00.0500.0076.0750.0960.0960.0000.0000.0000.000
42A578ILE0-0.075-0.0317.0200.1670.1670.0000.0000.0000.000
43A579ASP-1-0.822-0.9096.9560.0060.0060.0000.0000.0000.000
44A580MET00.0010.0179.5390.0520.0520.0000.0000.0000.000
45A581ASN00.0670.01113.2640.0420.0420.0000.0000.0000.000
46A582SER00.0190.00113.0230.0270.0270.0000.0000.0000.000
47A583VAL00.0350.00511.534-0.005-0.0050.0000.0000.0000.000
48A584LEU0-0.0350.00314.0970.0330.0330.0000.0000.0000.000
49A585LYS10.9680.98316.2920.0770.0770.0000.0000.0000.000
50A586GLY0-0.023-0.00216.725-0.012-0.0120.0000.0000.0000.000
51A587PHE0-0.0120.01216.3970.0380.0380.0000.0000.0000.000
52A588PRO00.0140.01720.152-0.022-0.0220.0000.0000.0000.000
53A589GLU-1-0.818-0.92823.7440.0180.0180.0000.0000.0000.000
54A590CYS0-0.043-0.02826.114-0.002-0.0020.0000.0000.0000.000
55A591LEU0-0.017-0.00523.0500.0030.0030.0000.0000.0000.000
56A592GLN00.0300.00322.2310.0170.0170.0000.0000.0000.000
57A593ALA00.0240.02724.016-0.007-0.0070.0000.0000.0000.000
58A594ASP-1-0.859-0.93927.7730.0710.0710.0000.0000.0000.000
59A595ILE0-0.035-0.02121.4390.0020.0020.0000.0000.0000.000
60A596CYS0-0.044-0.02525.236-0.007-0.0070.0000.0000.0000.000
61A597LEU00.0200.02627.205-0.004-0.0040.0000.0000.0000.000
62A598HIS0-0.066-0.04526.747-0.006-0.0060.0000.0000.0000.000
63A599LEU0-0.029-0.01623.571-0.001-0.0010.0000.0000.0000.000
64A600ASN0-0.002-0.02228.292-0.007-0.0070.0000.0000.0000.000
65A601ARG10.9550.97831.304-0.047-0.0470.0000.0000.0000.000
66A602ASN0-0.128-0.05829.6770.0020.0020.0000.0000.0000.000
67A603LEU00.0160.03332.3820.0000.0000.0000.0000.0000.000
68A604LEU0-0.011-0.00534.0340.0000.0000.0000.0000.0000.000
69A605ASN0-0.056-0.02736.366-0.002-0.0020.0000.0000.0000.000
70A606ASN0-0.086-0.05235.4190.0040.0040.0000.0000.0000.000
71A607CYS0-0.032-0.00137.021-0.002-0.0020.0000.0000.0000.000
72A608SER00.0480.01438.9710.0000.0000.0000.0000.0000.000
73A609ALA00.0240.01040.4640.0000.0000.0000.0000.0000.000
74A610PHE0-0.022-0.03337.407-0.002-0.0020.0000.0000.0000.000
75A611GLU-1-0.848-0.90542.2870.0150.0150.0000.0000.0000.000
76A612ALA0-0.051-0.04445.214-0.002-0.0020.0000.0000.0000.000
77A613ALA0-0.0260.00743.457-0.001-0.0010.0000.0000.0000.000
78A614SER00.008-0.01145.4300.0030.0030.0000.0000.0000.000
79A615PRO0-0.006-0.02343.7650.0000.0000.0000.0000.0000.000
80A616GLY0-0.084-0.03542.9720.0020.0020.0000.0000.0000.000
81A617CYS00.0430.03942.441-0.001-0.0010.0000.0000.0000.000
82A618LEU00.0480.02340.127-0.001-0.0010.0000.0000.0000.000
83A619ARG10.9190.96238.343-0.020-0.0200.0000.0000.0000.000
84A620ALA00.0400.03137.5190.0000.0000.0000.0000.0000.000
85A621LEU00.0380.02237.402-0.003-0.0030.0000.0000.0000.000
86A622SER0-0.083-0.05634.239-0.001-0.0010.0000.0000.0000.000
87A623LEU0-0.040-0.02132.9040.0030.0030.0000.0000.0000.000
88A624LYS10.7440.87533.2960.0180.0180.0000.0000.0000.000
89A625PHE00.0060.00631.738-0.007-0.0070.0000.0000.0000.000
90A626LYS10.8180.93426.8590.0390.0390.0000.0000.0000.000
91A627THR00.0560.02224.2150.0010.0010.0000.0000.0000.000
92A628THR0-0.098-0.05522.486-0.016-0.0160.0000.0000.0000.000
93A629HIS0-0.037-0.02519.0810.0240.0240.0000.0000.0000.000
94A630ALA00.0730.05019.381-0.019-0.0190.0000.0000.0000.000
95A631PRO00.008-0.00416.7710.0190.0190.0000.0000.0000.000
96A632PRO0-0.029-0.00917.4280.0040.0040.0000.0000.0000.000
97A633GLY0-0.006-0.01319.191-0.035-0.0350.0000.0000.0000.000
98A634ASP-1-0.919-0.95221.022-0.192-0.1920.0000.0000.0000.000
99A635ILE0-0.039-0.03122.4240.0170.0170.0000.0000.0000.000
100A636LEU0-0.0190.00125.1450.0000.0000.0000.0000.0000.000
101A637VAL0-0.011-0.00327.3380.0070.0070.0000.0000.0000.000
102A638HIS0-0.002-0.00527.792-0.002-0.0020.0000.0000.0000.000
103A639LYS10.8180.90332.8510.0810.0810.0000.0000.0000.000
104A640GLY0-0.002-0.00436.0050.0060.0060.0000.0000.0000.000
105A641ASP-1-0.828-0.91332.199-0.111-0.1110.0000.0000.0000.000
106A642VAL0-0.023-0.02235.7280.0060.0060.0000.0000.0000.000
107A643LEU00.0080.01935.748-0.004-0.0040.0000.0000.0000.000
108A644THR0-0.043-0.04432.5750.0040.0040.0000.0000.0000.000
109A645TYR0-0.028-0.01930.5070.0050.0050.0000.0000.0000.000
110A646LEU0-0.0230.02234.045-0.003-0.0030.0000.0000.0000.000
111A647TYR0-0.023-0.02827.9520.0000.0000.0000.0000.0000.000
112A648PHE00.0820.03331.7960.0010.0010.0000.0000.0000.000
113A649ILE0-0.013-0.00628.495-0.002-0.0020.0000.0000.0000.000
114A650ALA00.0310.02128.1880.0060.0060.0000.0000.0000.000
115A651ARG10.8240.89024.857-0.036-0.0360.0000.0000.0000.000
116A652GLY00.0490.02425.346-0.009-0.0090.0000.0000.0000.000
117A653SER0-0.039-0.04026.0210.0080.0080.0000.0000.0000.000
118A654ILE0-0.006-0.00226.545-0.012-0.0120.0000.0000.0000.000
119A655GLU-1-0.758-0.86228.994-0.116-0.1160.0000.0000.0000.000
120A656ILE0-0.010-0.00530.724-0.006-0.0060.0000.0000.0000.000
121A657LEU0-0.035-0.01830.4900.0020.0020.0000.0000.0000.000
122A658LYS10.7950.85434.5810.0680.0680.0000.0000.0000.000
123A659ASP-1-0.916-0.93936.158-0.092-0.0920.0000.0000.0000.000
124A660ASP-1-0.938-0.97535.442-0.085-0.0850.0000.0000.0000.000
125A661VAL0-0.034-0.01633.4960.0000.0000.0000.0000.0000.000
126A662VAL00.0080.01035.7160.0050.0050.0000.0000.0000.000
127A663MET0-0.0160.00236.3890.0060.0060.0000.0000.0000.000
128A664ALA0-0.013-0.01432.835-0.007-0.0070.0000.0000.0000.000
129A665ILE00.0010.00732.3630.0060.0060.0000.0000.0000.000
130A666LEU0-0.015-0.02130.610-0.005-0.0050.0000.0000.0000.000
131A667GLY00.0040.00330.1310.0020.0020.0000.0000.0000.000
132A668LYS10.7680.87330.8900.0220.0220.0000.0000.0000.000
133A669ASP-1-0.794-0.89833.245-0.005-0.0050.0000.0000.0000.000
134A670ASP-1-0.807-0.87833.964-0.027-0.0270.0000.0000.0000.000
135A671ILE0-0.013-0.01034.309-0.002-0.0020.0000.0000.0000.000
136A672PHE00.011-0.00430.122-0.002-0.0020.0000.0000.0000.000
137A673GLY00.0500.00535.270-0.002-0.0020.0000.0000.0000.000
138A674GLU-1-0.728-0.84437.390-0.046-0.0460.0000.0000.0000.000
139A675ASN00.0860.02440.2160.0010.0010.0000.0000.0000.000
140A676PRO0-0.015-0.01540.2570.0000.0000.0000.0000.0000.000
141A677CYS0-0.0190.01843.2920.0000.0000.0000.0000.0000.000
142A678ILE00.0080.02146.1510.0020.0020.0000.0000.0000.000
143A679HIS0-0.044-0.02444.3910.0010.0010.0000.0000.0000.000
144A680SER00.0010.00447.253-0.001-0.0010.0000.0000.0000.000
145A681THR0-0.020-0.00847.253-0.001-0.0010.0000.0000.0000.000
146A682LEU0-0.0100.00639.3010.0000.0000.0000.0000.0000.000
147A683GLY00.0540.03142.353-0.002-0.0020.0000.0000.0000.000
148A684LYS10.8540.91239.3770.0750.0750.0000.0000.0000.000
149A685SER00.0580.02535.3630.0050.0050.0000.0000.0000.000
150A686ASN00.0370.02437.9220.0000.0000.0000.0000.0000.000
151A687SER0-0.025-0.00936.2560.0000.0000.0000.0000.0000.000
152A688ASN00.0020.00330.3320.0030.0030.0000.0000.0000.000
153A689VAL00.0160.01829.2130.0060.0060.0000.0000.0000.000
154A690LYS10.8180.88824.9220.1300.1300.0000.0000.0000.000
155A691ALA00.0020.01023.0670.0140.0140.0000.0000.0000.000
156A692LEU0-0.013-0.01123.874-0.018-0.0180.0000.0000.0000.000
157A693THR0-0.029-0.03422.028-0.005-0.0050.0000.0000.0000.000
158A694TYR00.0270.00813.954-0.015-0.0150.0000.0000.0000.000
159A695CYS0-0.075-0.00620.5560.0200.0200.0000.0000.0000.000
160A696ASP-1-0.833-0.89023.0190.0130.0130.0000.0000.0000.000
161A697LEU0-0.009-0.01024.9080.0000.0000.0000.0000.0000.000
162A698HIS00.0250.01826.770-0.002-0.0020.0000.0000.0000.000
163A699LYS10.9230.95725.5820.0780.0780.0000.0000.0000.000
164A700ILE00.0150.01431.1630.0030.0030.0000.0000.0000.000
165A701HIS00.0030.01433.369-0.001-0.0010.0000.0000.0000.000
166A702ARG10.8730.90234.8590.0480.0480.0000.0000.0000.000
167A703ASP-1-0.762-0.88138.143-0.040-0.0400.0000.0000.0000.000
168A704ASP-1-0.848-0.92634.174-0.030-0.0300.0000.0000.0000.000
169A705LEU00.009-0.00737.8570.0040.0040.0000.0000.0000.000
170A706LEU00.0150.00539.8570.0030.0030.0000.0000.0000.000
171A707ASP-1-0.788-0.87240.068-0.021-0.0210.0000.0000.0000.000
172A708VAL0-0.080-0.04939.3980.0030.0030.0000.0000.0000.000
173A709LEU00.014-0.01442.5160.0030.0030.0000.0000.0000.000
174A710ASP-1-0.909-0.94145.663-0.017-0.0170.0000.0000.0000.000
175A711LEU0-0.132-0.06243.0830.0020.0020.0000.0000.0000.000
176A712PHE0-0.081-0.04143.6990.0040.0040.0000.0000.0000.000
177A713PRO00.0590.03547.6960.0000.0000.0000.0000.0000.000
178A714GLU-1-0.846-0.92548.8750.0000.0000.0000.0000.0000.000
179A715PHE00.0030.00142.8400.0000.0000.0000.0000.0000.000
180A716TYR0-0.011-0.01448.104-0.001-0.0010.0000.0000.0000.000
181A717ASP-1-0.881-0.94349.009-0.009-0.0090.0000.0000.0000.000
182A718SER0-0.032-0.02148.3360.0000.0000.0000.0000.0000.000
183A719PHE00.0050.01640.952-0.001-0.0010.0000.0000.0000.000
184A720VAL0-0.022-0.02445.849-0.002-0.0020.0000.0000.0000.000
185A721ASN0-0.111-0.05347.9310.0000.0000.0000.0000.0000.000
186A722SER00.0080.00145.6040.0010.0010.0000.0000.0000.000
187A723LEU0-0.060-0.01839.7070.0000.0000.0000.0000.0000.000
188A724GLU-1-0.928-0.96642.871-0.015-0.0150.0000.0000.0000.000
189A725ILE0-0.083-0.04939.267-0.001-0.0010.0000.0000.0000.000
190A726THR0-0.0070.01137.867-0.001-0.0010.0000.0000.0000.000
191A727TYR0-0.014-0.01137.321-0.001-0.0010.0000.0000.0000.000
192A728ASN00.0360.00838.768-0.003-0.0030.0000.0000.0000.000
193A729MET0-0.013-0.00134.763-0.001-0.0010.0000.0000.0000.000
194A730ARG10.7410.86039.2170.0390.0390.0000.0000.0000.000
195A731ASP-1-0.869-0.92141.878-0.064-0.0640.0000.0000.0000.000
196A732GLU-1-0.885-0.93343.547-0.039-0.0390.0000.0000.0000.000
197A733GLU-1-0.915-0.93043.964-0.062-0.0620.0000.0000.0000.000