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: 76LVK

Calculation Name: 4MEM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MEM

Chain ID: A

ChEMBL ID:

UniProt ID: Q5D006

Base Structure: X-ray

Registration Date: 2023-09-24

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2378097.667116
FMO2-HF: Nuclear repulsion 2292593.921009
FMO2-HF: Total energy -85503.746107
FMO2-MP2: Total energy -85755.293548


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:26:ALA)


Summations of interaction energy for fragment #1(A:26:ALA)
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.
1.2362.582-0.021-0.578-0.7460
Interaction energy analysis for fragmet #1(A:26:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.026
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].
3A28PRO0-0.045-0.0183.8080.3231.669-0.021-0.578-0.7460.000
4A29ASP-1-0.824-0.9076.4670.6980.6980.0000.0000.0000.000
5A30LEU00.0360.0299.564-0.172-0.1720.0000.0000.0000.000
6A31ASP-1-0.801-0.89312.4630.0060.0060.0000.0000.0000.000
7A32GLN0-0.026-0.0218.7070.0290.0290.0000.0000.0000.000
8A33GLN00.0640.0478.769-0.128-0.1280.0000.0000.0000.000
9A34TRP00.0350.01212.237-0.020-0.0200.0000.0000.0000.000
10A35ARG10.7860.87015.674-0.008-0.0080.0000.0000.0000.000
11A36GLN0-0.0100.01110.039-0.010-0.0100.0000.0000.0000.000
12A37ILE0-0.013-0.00613.109-0.002-0.0020.0000.0000.0000.000
13A38GLY00.0060.00016.2950.0140.0140.0000.0000.0000.000
14A39ASN0-0.016-0.01918.3440.0220.0220.0000.0000.0000.000
15A40GLY0-0.023-0.00518.3170.0000.0000.0000.0000.0000.000
16A41ARG10.9170.94019.1160.0960.0960.0000.0000.0000.000
17A42GLU-1-0.958-0.94722.164-0.069-0.0690.0000.0000.0000.000
18A43ARG10.7580.86120.1950.1730.1730.0000.0000.0000.000
19A44PRO0-0.008-0.01123.9790.0040.0040.0000.0000.0000.000
20A45LEU00.0390.02026.517-0.008-0.0080.0000.0000.0000.000
21A46ARG10.8940.93024.2670.1310.1310.0000.0000.0000.000
22A47ALA00.0590.02828.373-0.006-0.0060.0000.0000.0000.000
23A48GLY00.0400.02829.068-0.003-0.0030.0000.0000.0000.000
24A49GLU-1-0.787-0.85524.160-0.159-0.1590.0000.0000.0000.000
25A50SER0-0.048-0.05921.8170.0120.0120.0000.0000.0000.000
26A51TRP0-0.027-0.02421.999-0.018-0.0180.0000.0000.0000.000
27A52PHE00.0280.00819.4420.0000.0000.0000.0000.0000.000
28A53LEU00.0070.02121.5380.0030.0030.0000.0000.0000.000
29A54VAL0-0.028-0.00718.788-0.013-0.0130.0000.0000.0000.000
30A55GLU-1-0.748-0.84421.396-0.031-0.0310.0000.0000.0000.000
31A56LYS10.8610.91622.3320.0340.0340.0000.0000.0000.000
32A57HIS10.8230.86723.6050.0340.0340.0000.0000.0000.000
33A58TRP00.0200.02413.8670.0030.0030.0000.0000.0000.000
34A59TYR00.0660.03019.0180.0130.0130.0000.0000.0000.000
35A60LYS10.8160.88519.8870.0180.0180.0000.0000.0000.000
36A61GLN00.0140.01518.3810.0220.0220.0000.0000.0000.000
37A62TRP00.0210.01312.8480.0270.0270.0000.0000.0000.000
38A63GLU-1-0.796-0.86716.4970.0060.0060.0000.0000.0000.000
39A64ALA0-0.049-0.02919.0410.0140.0140.0000.0000.0000.000
40A65TYR0-0.077-0.05311.0640.0100.0100.0000.0000.0000.000
41A66VAL0-0.024-0.01713.4270.0320.0320.0000.0000.0000.000
42A67LYS10.7960.87715.8430.0060.0060.0000.0000.0000.000
43A68GLY0-0.0170.00818.534-0.001-0.0010.0000.0000.0000.000
44A69GLY0-0.033-0.01016.9420.0010.0010.0000.0000.0000.000
45A70ASP-1-0.868-0.94115.8330.4050.4050.0000.0000.0000.000
46A71GLN0-0.008-0.0138.093-0.184-0.1840.0000.0000.0000.000
47A72ASP-1-0.917-0.93811.9430.8460.8460.0000.0000.0000.000
48A73ALA00.0010.02014.017-0.067-0.0670.0000.0000.0000.000
49A74SER0-0.041-0.03715.6820.0110.0110.0000.0000.0000.000
50A75THR0-0.023-0.02217.957-0.011-0.0110.0000.0000.0000.000
51A76PHE00.0670.0319.301-0.052-0.0520.0000.0000.0000.000
52A77PRO0-0.045-0.01313.194-0.020-0.0200.0000.0000.0000.000
53A78GLY0-0.0050.00713.530-0.019-0.0190.0000.0000.0000.000
54A79SER0-0.038-0.02612.741-0.016-0.0160.0000.0000.0000.000
55A80ILE0-0.026-0.01113.5050.0320.0320.0000.0000.0000.000
56A81ASN0-0.001-0.00516.343-0.007-0.0070.0000.0000.0000.000
57A82ASN00.019-0.00919.9010.0130.0130.0000.0000.0000.000
58A83SER00.0180.00922.7720.0060.0060.0000.0000.0000.000
59A84GLY00.0050.00725.3220.0030.0030.0000.0000.0000.000
60A85LEU0-0.031-0.01824.3610.0020.0020.0000.0000.0000.000
61A86PHE0-0.016-0.00723.668-0.002-0.0020.0000.0000.0000.000
62A87GLU-1-0.842-0.91029.202-0.038-0.0380.0000.0000.0000.000
63A88ASP-1-0.744-0.85331.956-0.053-0.0530.0000.0000.0000.000
64A89GLN0-0.036-0.02926.428-0.005-0.0050.0000.0000.0000.000
65A90ILE0-0.046-0.01429.131-0.001-0.0010.0000.0000.0000.000
66A91SER0-0.072-0.06530.648-0.005-0.0050.0000.0000.0000.000
67A92TRP00.006-0.00424.981-0.007-0.0070.0000.0000.0000.000
68A93HIS10.8320.90828.7420.0620.0620.0000.0000.0000.000
69A94LEU0-0.019-0.00627.677-0.001-0.0010.0000.0000.0000.000
70A95ARG10.8920.94130.7950.0440.0440.0000.0000.0000.000
71A96GLU-1-0.825-0.89833.195-0.044-0.0440.0000.0000.0000.000
72A97ARG10.7830.88435.7530.0420.0420.0000.0000.0000.000
73A98LEU00.0210.03229.6410.0020.0020.0000.0000.0000.000
74A99VAL0-0.008-0.01832.744-0.003-0.0030.0000.0000.0000.000
75A100GLU-1-0.913-0.95627.624-0.081-0.0810.0000.0000.0000.000
76A101GLY0-0.019-0.00428.6290.0050.0050.0000.0000.0000.000
77A102ASP-1-0.928-0.95629.744-0.026-0.0260.0000.0000.0000.000
78A103ASP-1-0.846-0.92429.305-0.040-0.0400.0000.0000.0000.000
79A104TYR0-0.038-0.03225.280-0.006-0.0060.0000.0000.0000.000
80A105VAL0-0.042-0.01722.0680.0070.0070.0000.0000.0000.000
81A106LEU00.0290.02223.064-0.012-0.0120.0000.0000.0000.000
82A107LEU0-0.022-0.01216.7350.0000.0000.0000.0000.0000.000
83A108PRO00.0050.01219.274-0.005-0.0050.0000.0000.0000.000
84A109ALA00.0630.02418.087-0.025-0.0250.0000.0000.0000.000
85A110PRO0-0.046-0.01615.026-0.033-0.0330.0000.0000.0000.000
86A111ALA00.0260.00813.635-0.065-0.0650.0000.0000.0000.000
87A112TRP00.0490.02013.811-0.043-0.0430.0000.0000.0000.000
88A113ASN00.026-0.00212.209-0.014-0.0140.0000.0000.0000.000
89A114TYR0-0.031-0.0088.156-0.021-0.0210.0000.0000.0000.000
90A115LEU00.0520.0429.053-0.154-0.1540.0000.0000.0000.000
91A116VAL00.013-0.00110.776-0.007-0.0070.0000.0000.0000.000
92A117SER0-0.109-0.0586.352-0.123-0.1230.0000.0000.0000.000
93A118TRP0-0.026-0.0175.549-0.028-0.0280.0000.0000.0000.000
94A119TYR0-0.015-0.0317.1830.2150.2150.0000.0000.0000.000
95A120GLY00.0090.0209.9430.0900.0900.0000.0000.0000.000
96A121LEU0-0.016-0.01511.7450.0410.0410.0000.0000.0000.000
97A122LYS10.8190.88715.5310.0550.0550.0000.0000.0000.000
98A123ASP-1-0.869-0.91417.863-0.056-0.0560.0000.0000.0000.000
99A124ASP-1-0.882-0.93819.020-0.110-0.1100.0000.0000.0000.000
100A125GLN0-0.042-0.02620.234-0.004-0.0040.0000.0000.0000.000
101A126PRO00.0110.02819.719-0.022-0.0220.0000.0000.0000.000
102A127PRO0-0.007-0.01518.2120.0040.0040.0000.0000.0000.000
103A128ILE0-0.006-0.00620.1780.0120.0120.0000.0000.0000.000
104A129GLU-1-0.839-0.87721.948-0.178-0.1780.0000.0000.0000.000
105A130ARG10.8630.93523.5190.1150.1150.0000.0000.0000.000
106A131LYS10.9200.94624.7740.1310.1310.0000.0000.0000.000
107A132VAL0-0.046-0.00827.0990.0080.0080.0000.0000.0000.000
108A133ILE0-0.013-0.00429.584-0.001-0.0010.0000.0000.0000.000
109A134GLU-1-0.837-0.92433.260-0.072-0.0720.0000.0000.0000.000
110A135LEU00.0230.00836.2450.0020.0020.0000.0000.0000.000
111A136PRO00.0310.00939.5430.0000.0000.0000.0000.0000.000
112A137GLY0-0.0080.00241.5450.0020.0020.0000.0000.0000.000
113A138ILE0-0.054-0.02736.7290.0000.0000.0000.0000.0000.000
114A139ARG10.8210.91231.5220.0740.0740.0000.0000.0000.000
115A140LYS10.8760.92732.2730.0650.0650.0000.0000.0000.000
116A141VAL00.0420.02426.863-0.003-0.0030.0000.0000.0000.000
117A142GLU-1-0.770-0.86729.839-0.062-0.0620.0000.0000.0000.000
118A143VAL00.0300.00128.696-0.005-0.0050.0000.0000.0000.000
119A144TYR0-0.058-0.05630.626-0.002-0.0020.0000.0000.0000.000
120A145PRO0-0.0060.01331.3630.0040.0040.0000.0000.0000.000
121A146ILE0-0.0180.01334.4620.0020.0020.0000.0000.0000.000
122A147GLU-1-0.818-0.89734.170-0.070-0.0700.0000.0000.0000.000
123A148LEU0-0.0040.00538.0310.0040.0040.0000.0000.0000.000
124A149LEU00.0050.00840.488-0.002-0.0020.0000.0000.0000.000
125A150LEU00.0230.00940.9060.0030.0030.0000.0000.0000.000
126A151VAL00.0230.00943.9910.0000.0000.0000.0000.0000.000
127A152GLN00.0160.01346.8400.0010.0010.0000.0000.0000.000
128A153HIS0-0.010-0.02849.0520.0010.0010.0000.0000.0000.000
129A154SER0-0.041-0.04052.4700.0010.0010.0000.0000.0000.000
130A155ASP-1-0.849-0.91147.730-0.039-0.0390.0000.0000.0000.000
131A156MET0-0.028-0.01348.942-0.001-0.0010.0000.0000.0000.000
132A157GLU-1-0.984-0.97348.871-0.032-0.0320.0000.0000.0000.000
133A158THR0-0.055-0.03443.727-0.002-0.0020.0000.0000.0000.000
134A159ALA0-0.033-0.01444.1520.0000.0000.0000.0000.0000.000
135A160LEU0-0.0060.00139.169-0.002-0.0020.0000.0000.0000.000
136A161THR0-0.003-0.01037.2070.0020.0020.0000.0000.0000.000
137A162ILE0-0.024-0.00435.977-0.004-0.0040.0000.0000.0000.000
138A163GLN0-0.074-0.03431.016-0.002-0.0020.0000.0000.0000.000
139A164PHE00.0290.01234.662-0.002-0.0020.0000.0000.0000.000
140A165SER0-0.031-0.02734.324-0.001-0.0010.0000.0000.0000.000
141A166TYR0-0.014-0.02236.0310.0020.0020.0000.0000.0000.000
142A167SER0-0.059-0.04736.4450.0020.0020.0000.0000.0000.000
143A168ASP-1-0.804-0.89236.706-0.070-0.0700.0000.0000.0000.000
144A169SER00.013-0.00239.3640.0020.0020.0000.0000.0000.000
145A170VAL00.0390.00842.469-0.001-0.0010.0000.0000.0000.000
146A171ASP-1-0.870-0.91844.628-0.047-0.0470.0000.0000.0000.000
147A172LEU00.0060.01136.9340.0000.0000.0000.0000.0000.000
148A173VAL00.0180.02340.682-0.002-0.0020.0000.0000.0000.000
149A174LEU0-0.039-0.01941.9930.0000.0000.0000.0000.0000.000
150A175GLN0-0.044-0.04141.157-0.001-0.0010.0000.0000.0000.000
151A176THR00.0290.01237.160-0.002-0.0020.0000.0000.0000.000
152A177ALA00.000-0.00539.766-0.001-0.0010.0000.0000.0000.000
153A178ARG10.8060.87642.3700.0450.0450.0000.0000.0000.000
154A179GLU-1-0.953-0.96437.217-0.069-0.0690.0000.0000.0000.000
155A180GLN0-0.028-0.02035.947-0.003-0.0030.0000.0000.0000.000
156A181PHE0-0.062-0.03439.8590.0000.0000.0000.0000.0000.000
157A182LEU0-0.075-0.02640.7360.0020.0020.0000.0000.0000.000
158A183VAL0-0.0090.00043.6560.0020.0020.0000.0000.0000.000
159A184GLU-1-0.880-0.92145.642-0.041-0.0410.0000.0000.0000.000
160A185PRO0-0.017-0.02446.3460.0010.0010.0000.0000.0000.000
161A186GLN0-0.075-0.05948.025-0.001-0.0010.0000.0000.0000.000
162A187GLU-1-0.865-0.91150.896-0.034-0.0340.0000.0000.0000.000
163A188ASP-1-0.781-0.84951.080-0.035-0.0350.0000.0000.0000.000
164A189THR00.0310.01248.7770.0000.0000.0000.0000.0000.000
165A190ARG10.7610.88051.0600.0300.0300.0000.0000.0000.000
166A191LEU00.0530.03046.1890.0000.0000.0000.0000.0000.000
167A192TRP0-0.030-0.02750.5880.0020.0020.0000.0000.0000.000
168A193THR00.004-0.01048.975-0.001-0.0010.0000.0000.0000.000
169A194LYS10.9280.96751.1640.0310.0310.0000.0000.0000.000
170A195ASN00.0690.05051.1070.0000.0000.0000.0000.0000.000
171A196SER0-0.022-0.03650.3610.0010.0010.0000.0000.0000.000
172A197GLU-1-0.945-0.92652.795-0.024-0.0240.0000.0000.0000.000
173A198GLY0-0.048-0.03255.8960.0010.0010.0000.0000.0000.000
174A199SER0-0.072-0.04955.9750.0010.0010.0000.0000.0000.000
175A200LEU0-0.050-0.02154.511-0.001-0.0010.0000.0000.0000.000
176A201ASP-1-0.814-0.90155.002-0.027-0.0270.0000.0000.0000.000
177A202ARG10.8930.94354.3860.0280.0280.0000.0000.0000.000
178A203LEU00.0180.00448.3200.0010.0010.0000.0000.0000.000
179A204CYS0-0.055-0.03251.939-0.001-0.0010.0000.0000.0000.000
180A205ASN0-0.001-0.00351.568-0.001-0.0010.0000.0000.0000.000
181A206THR00.016-0.01047.9180.0000.0000.0000.0000.0000.000
182A207GLN0-0.031-0.02046.961-0.003-0.0030.0000.0000.0000.000
183A208ILE0-0.043-0.00447.0240.0000.0000.0000.0000.0000.000
184A209THR0-0.013-0.03742.311-0.002-0.0020.0000.0000.0000.000
185A210LEU00.0150.00140.2120.0030.0030.0000.0000.0000.000
186A211LEU0-0.016-0.00641.6560.0020.0020.0000.0000.0000.000
187A212ASP-1-0.855-0.90444.032-0.040-0.0400.0000.0000.0000.000
188A213ALA0-0.066-0.02746.5500.0020.0020.0000.0000.0000.000
189A214CYS0-0.108-0.04347.0330.0020.0020.0000.0000.0000.000
190A215LEU0-0.026-0.00344.0160.0010.0010.0000.0000.0000.000
191A216GLU-1-0.876-0.94543.879-0.038-0.0380.0000.0000.0000.000
192A217THR00.002-0.01338.254-0.002-0.0020.0000.0000.0000.000
193A218GLY0-0.017-0.02041.0580.0020.0020.0000.0000.0000.000
194A219GLN0-0.035-0.01442.3150.0020.0020.0000.0000.0000.000
195A220LEU0-0.0030.00444.735-0.002-0.0020.0000.0000.0000.000
196A221VAL0-0.029-0.01345.3440.0020.0020.0000.0000.0000.000
197A222ILE00.0100.00947.043-0.001-0.0010.0000.0000.0000.000
198A223MET00.0020.01446.3360.0000.0000.0000.0000.0000.000
199A224GLU-1-0.701-0.79349.394-0.029-0.0290.0000.0000.0000.000
200A225THR00.0620.01650.950-0.001-0.0010.0000.0000.0000.000
201A226ARG10.7440.85953.2740.0320.0320.0000.0000.0000.000
202A227ASN00.0160.01156.474-0.001-0.0010.0000.0000.0000.000
203A228LYS10.8890.91655.2520.0330.0330.0000.0000.0000.000
204A229ASP-1-0.836-0.87960.423-0.025-0.0250.0000.0000.0000.000
205A230GLY0-0.008-0.00361.0880.0010.0010.0000.0000.0000.000
206A231THR0-0.056-0.04761.7770.0000.0000.0000.0000.0000.000
207A232TRP00.011-0.01354.328-0.001-0.0010.0000.0000.0000.000
208A233PRO00.0640.04056.5720.0010.0010.0000.0000.0000.000
209A234SER0-0.086-0.07357.6060.0010.0010.0000.0000.0000.000
210A235ALA0-0.076-0.05459.6360.0010.0010.0000.0000.0000.000
211A236GLN0-0.037-0.02162.5670.0010.0010.0000.0000.0000.000
212A237LEU0-0.0290.00165.0940.0010.0010.0000.0000.0000.000