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: 856MY

Calculation Name: 5EUT-A-Xray372

Preferred Name: Lysozyme

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5EUT

Chain ID: A

ChEMBL ID: CHEMBL5206

UniProt ID: P00720

Base Structure: X-ray

Registration Date: 2023-06-26

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 485
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -9244495.161555
FMO2-HF: Nuclear repulsion 9051917.06716
FMO2-HF: Total energy -192578.094395
FMO2-MP2: Total energy -193150.670107


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:101:ARG)


Summations of interaction energy for fragment #1(A:101:ARG)
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.
10.50111.69611.138-4.16-8.173-0.041
Interaction energy analysis for fragmet #1(A:101:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.907 / q_NPA : 0.936
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].
3A103GLU-1-0.907-0.9543.847-31.137-29.552-0.010-0.506-1.0690.001
4A104PHE0-0.038-0.0335.946-2.891-2.8910.0000.0000.0000.000
5A105PRO00.0420.0269.0972.1852.1850.0000.0000.0000.000
6A106GLU-1-0.827-0.90411.704-23.769-23.7690.0000.0000.0000.000
7A107ASP-1-0.826-0.89813.428-18.044-18.0440.0000.0000.0000.000
8A108PRO00.0500.01713.009-0.692-0.6920.0000.0000.0000.000
9A109GLU-1-0.906-0.95414.096-16.070-16.0700.0000.0000.0000.000
10A110PHE00.0450.01610.592-0.460-0.4600.0000.0000.0000.000
11A111GLU-1-0.810-0.8978.648-26.453-26.4530.0000.0000.0000.000
12A112ALA00.0080.01211.040-0.162-0.1620.0000.0000.0000.000
13A113VAL00.0090.00313.5770.3900.3900.0000.0000.0000.000
14A114VAL0-0.033-0.0207.944-0.098-0.0980.0000.0000.0000.000
15A115ARG10.7740.8565.17327.35627.3560.0000.0000.0000.000
16A116GLN00.007-0.00310.8581.0121.0120.0000.0000.0000.000
17A117ALA00.0250.01311.6680.6420.6420.0000.0000.0000.000
18A118GLU-1-0.843-0.9086.167-26.700-26.7000.0000.0000.0000.000
19A119LEU00.0030.00910.5190.6990.6990.0000.0000.0000.000
20A120ALA0-0.0010.01013.6410.9330.9330.0000.0000.0000.000
21A121ILE0-0.036-0.01911.2370.6310.6310.0000.0000.0000.000
22A122GLU-1-0.861-0.91711.963-16.580-16.5800.0000.0000.0000.000
23A123ARG10.7500.85614.42015.35915.3590.0000.0000.0000.000
24A124CYS0-0.036-0.01917.1500.6780.6780.0000.0000.0000.000
25A125ILE0-0.0190.01018.3370.4980.4980.0000.0000.0000.000
26A126PHE00.011-0.00615.244-0.710-0.7100.0000.0000.0000.000
27A127PRO00.0300.01414.2330.5560.5560.0000.0000.0000.000
28A128GLU-1-0.879-0.90217.553-11.838-11.8380.0000.0000.0000.000
29A129ARG10.8240.90120.03413.80413.8040.0000.0000.0000.000
30A130ILE00.0110.00821.6780.5720.5720.0000.0000.0000.000
31A131TYR00.008-0.00524.214-0.054-0.0540.0000.0000.0000.000
32A132GLN00.0010.00826.820-0.084-0.0840.0000.0000.0000.000
33A133GLY00.0670.06124.4030.0540.0540.0000.0000.0000.000
34A134SER0-0.026-0.04524.4420.4840.4840.0000.0000.0000.000
35A135SER0-0.063-0.03819.768-0.153-0.1530.0000.0000.0000.000
36A136GLY00.0130.01218.0180.4680.4680.0000.0000.0000.000
37A137SER0-0.014-0.00717.406-0.872-0.8720.0000.0000.0000.000
38A138TYR0-0.046-0.05716.6740.9590.9590.0000.0000.0000.000
39A139PHE00.0700.03118.255-0.508-0.5080.0000.0000.0000.000
40A140VAL0-0.031-0.02014.0330.0430.0430.0000.0000.0000.000
41A141LYS10.9060.94316.86812.99012.9900.0000.0000.0000.000
42A142ASP-1-0.682-0.82516.653-13.838-13.8380.0000.0000.0000.000
43A143PRO00.007-0.01217.1330.5340.5340.0000.0000.0000.000
44A144GLN0-0.061-0.01919.7880.5610.5610.0000.0000.0000.000
45A145GLY0-0.024-0.00421.7130.4310.4310.0000.0000.0000.000
46A146ARG10.8270.89721.56412.24112.2410.0000.0000.0000.000
47A147ILE0-0.026-0.01620.894-0.607-0.6070.0000.0000.0000.000
48A148ILE00.0030.01015.6390.2480.2480.0000.0000.0000.000
49A149ALA00.011-0.00115.611-0.366-0.3660.0000.0000.0000.000
50A150VAL0-0.0130.00517.7200.5400.5400.0000.0000.0000.000
51A151PHE0-0.014-0.0129.915-0.568-0.5680.0000.0000.0000.000
52A152LYS10.8310.89413.71817.25017.2500.0000.0000.0000.000
53A153PRO00.0260.02411.487-1.572-1.5720.0000.0000.0000.000
54A154LYS10.8550.9139.49726.53726.5370.0000.0000.0000.000
55A155ASN00.009-0.00111.7982.4182.4180.0000.0000.0000.000
56A156GLU-1-0.789-0.85113.857-16.184-16.1840.0000.0000.0000.000
57A157GLU-1-0.712-0.84614.551-18.563-18.5630.0000.0000.0000.000
58A158PRO0-0.0040.01317.6500.3650.3650.0000.0000.0000.000
59A159TYR00.0580.02418.7750.9170.9170.0000.0000.0000.000
60A160GLY0-0.0070.01216.889-0.142-0.1420.0000.0000.0000.000
61A161HIS00.004-0.01816.3050.8670.8670.0000.0000.0000.000
62A162LEU0-0.019-0.00414.8850.5210.5210.0000.0000.0000.000
63A163ASN00.0160.01918.4340.6690.6690.0000.0000.0000.000
64A164PRO00.0530.01720.2560.6430.6430.0000.0000.0000.000
65A165LYS10.9140.97023.19611.91411.9140.0000.0000.0000.000
66A166TRP00.0500.01023.3130.5390.5390.0000.0000.0000.000
67A167THR0-0.012-0.00122.0990.3500.3500.0000.0000.0000.000
68A168LYS10.9480.96524.56410.67110.6710.0000.0000.0000.000
69A169TRP0-0.023-0.00226.9080.4270.4270.0000.0000.0000.000
70A170LEU00.0040.00021.7570.2930.2930.0000.0000.0000.000
71A171GLN0-0.005-0.00426.2760.3170.3170.0000.0000.0000.000
72A172LYS10.9420.99528.6159.5169.5160.0000.0000.0000.000
73A1001GLY00.0220.02029.2250.2760.2760.0000.0000.0000.000
74A1002THR0-0.035-0.05830.2600.0220.0220.0000.0000.0000.000
75A1003GLY00.0260.02133.0110.2120.2120.0000.0000.0000.000
76A1004ASN0-0.052-0.04329.5310.3310.3310.0000.0000.0000.000
77A1005ILE0-0.009-0.00233.2620.0200.0200.0000.0000.0000.000
78A1006PHE00.0150.01035.7370.0700.0700.0000.0000.0000.000
79A1007GLU-1-0.861-0.92533.866-8.467-8.4670.0000.0000.0000.000
80A1008MET0-0.070-0.01031.3180.0590.0590.0000.0000.0000.000
81A1009LEU00.0130.00434.4720.0150.0150.0000.0000.0000.000
82A1010ARG10.8250.88738.1127.9217.9210.0000.0000.0000.000
83A1011ILE0-0.041-0.01132.5450.0690.0690.0000.0000.0000.000
84A1012ASP-1-0.806-0.87335.148-8.951-8.9510.0000.0000.0000.000
85A1013GLU-1-0.840-0.89837.616-7.466-7.4660.0000.0000.0000.000
86A1014GLY0-0.0330.00340.3760.1880.1880.0000.0000.0000.000
87A1015LEU00.002-0.01841.8850.0430.0430.0000.0000.0000.000
88A1016ARG10.8630.93945.0226.7446.7440.0000.0000.0000.000
89A1017LEU00.0320.02048.6080.0330.0330.0000.0000.0000.000
90A1018LYS10.9680.98951.6985.6265.6260.0000.0000.0000.000
91A1019ILE0-0.032-0.00652.658-0.106-0.1060.0000.0000.0000.000
92A1020TYR0-0.014-0.00246.0310.0600.0600.0000.0000.0000.000
93A1021LYS10.8860.93952.0225.7405.7400.0000.0000.0000.000
94A1022ASP-1-0.823-0.91847.276-6.498-6.4980.0000.0000.0000.000
95A1023THR0-0.014-0.03144.0530.0930.0930.0000.0000.0000.000
96A1024GLU-1-0.887-0.90147.245-6.442-6.4420.0000.0000.0000.000
97A1025GLY00.0270.03249.5580.1280.1280.0000.0000.0000.000
98A1026TYR0-0.115-0.07750.5840.2430.2430.0000.0000.0000.000
99A1027TYR0-0.060-0.04352.359-0.076-0.0760.0000.0000.0000.000
100A1028THR00.0260.00247.9250.0300.0300.0000.0000.0000.000
101A1029ILE0-0.013-0.00950.5550.0740.0740.0000.0000.0000.000
102A1030GLY00.0420.01448.721-0.075-0.0750.0000.0000.0000.000
103A1031ILE00.0000.00742.229-0.047-0.0470.0000.0000.0000.000
104A1032GLY00.0260.01244.604-0.028-0.0280.0000.0000.0000.000
105A1033HIS10.8310.91745.5266.3206.3200.0000.0000.0000.000
106A1034LEU00.0270.00748.7410.1430.1430.0000.0000.0000.000
107A1035LEU0-0.070-0.02150.6910.0550.0550.0000.0000.0000.000
108A1036THR00.013-0.01354.4960.0780.0780.0000.0000.0000.000
109A1037LYS10.9890.99751.9665.9645.9640.0000.0000.0000.000
110A1038SER0-0.0070.00656.0170.0350.0350.0000.0000.0000.000
111A1039PRO00.0950.03358.735-0.059-0.0590.0000.0000.0000.000
112A1040SER00.0000.02360.419-0.030-0.0300.0000.0000.0000.000
113A1041LEU00.0580.02458.494-0.031-0.0310.0000.0000.0000.000
114A1042ASN00.030-0.00661.040-0.086-0.0860.0000.0000.0000.000
115A1043ALA00.0480.04361.5130.0220.0220.0000.0000.0000.000
116A1044ALA0-0.013-0.00157.118-0.042-0.0420.0000.0000.0000.000
117A1045LYS10.7530.86958.7995.0345.0340.0000.0000.0000.000
118A1046SER00.002-0.00860.958-0.006-0.0060.0000.0000.0000.000
119A1047GLU-1-0.797-0.87557.383-5.396-5.3960.0000.0000.0000.000
120A1048LEU0-0.008-0.00855.241-0.062-0.0620.0000.0000.0000.000
121A1049ASP-1-0.751-0.83958.051-5.144-5.1440.0000.0000.0000.000
122A1050LYS10.8120.89359.2565.3335.3330.0000.0000.0000.000
123A1051ALA0-0.0080.01155.349-0.020-0.0200.0000.0000.0000.000
124A1052ILE0-0.052-0.02954.435-0.068-0.0680.0000.0000.0000.000
125A1053GLY00.0200.00757.699-0.025-0.0250.0000.0000.0000.000
126A1054ARG10.7640.85557.7075.4725.4720.0000.0000.0000.000
127A1055ASN00.0490.02262.292-0.112-0.1120.0000.0000.0000.000
128A1056THR00.033-0.02358.227-0.015-0.0150.0000.0000.0000.000
129A1057ASN0-0.041-0.02260.563-0.004-0.0040.0000.0000.0000.000
130A1058GLY00.0070.00258.793-0.003-0.0030.0000.0000.0000.000
131A1059VAL0-0.042-0.03056.161-0.120-0.1200.0000.0000.0000.000
132A1060ILE00.0050.00051.6010.0810.0810.0000.0000.0000.000
133A1061THR00.020-0.01853.332-0.063-0.0630.0000.0000.0000.000
134A1062LYS10.9790.98443.3237.0807.0800.0000.0000.0000.000
135A1063ASP-1-0.810-0.89049.043-6.294-6.2940.0000.0000.0000.000
136A1064GLU-1-0.736-0.82650.685-5.639-5.6390.0000.0000.0000.000
137A1065ALA0-0.010-0.00348.424-0.022-0.0220.0000.0000.0000.000
138A1066GLU-1-0.814-0.91144.039-7.348-7.3480.0000.0000.0000.000
139A1067LYS10.8510.94847.2845.6445.6440.0000.0000.0000.000
140A1068LEU0-0.037-0.02349.490-0.030-0.0300.0000.0000.0000.000
141A1069PHE0-0.0260.00240.076-0.066-0.0660.0000.0000.0000.000
142A1070ASN0-0.018-0.02644.319-0.228-0.2280.0000.0000.0000.000
143A1071GLN00.0550.02645.799-0.011-0.0110.0000.0000.0000.000
144A1072ASP-1-0.813-0.89346.277-6.447-6.4470.0000.0000.0000.000
145A1073VAL0-0.032-0.00840.885-0.108-0.1080.0000.0000.0000.000
146A1074ASP-1-0.884-0.93843.476-6.962-6.9620.0000.0000.0000.000
147A1075ALA0-0.080-0.04445.7080.0270.0270.0000.0000.0000.000
148A1076ALA00.0060.00242.4290.0190.0190.0000.0000.0000.000
149A1077VAL00.007-0.00640.301-0.078-0.0780.0000.0000.0000.000
150A1078ARG10.9440.96342.7576.3256.3250.0000.0000.0000.000
151A1079GLY0-0.0090.00145.8850.0730.0730.0000.0000.0000.000
152A1080ILE0-0.013-0.01738.8410.0090.0090.0000.0000.0000.000
153A1081LEU0-0.008-0.01740.3970.0180.0180.0000.0000.0000.000
154A1082ARG10.8410.89943.8326.4246.4240.0000.0000.0000.000
155A1083ASN0-0.020-0.02845.2370.0610.0610.0000.0000.0000.000
156A1084ALA00.0500.01744.438-0.178-0.1780.0000.0000.0000.000
157A1085LYS10.8850.95343.4286.8306.8300.0000.0000.0000.000
158A1086LEU0-0.055-0.01140.692-0.196-0.1960.0000.0000.0000.000
159A1087LYS10.8710.93239.4987.3847.3840.0000.0000.0000.000
160A1088PRO00.0510.02738.946-0.212-0.2120.0000.0000.0000.000
161A1089VAL0-0.0060.00634.940-0.264-0.2640.0000.0000.0000.000
162A1090TYR00.0260.00234.710-0.327-0.3270.0000.0000.0000.000
163A1091ASP-1-0.819-0.90434.684-8.216-8.2160.0000.0000.0000.000
164A1092SER0-0.005-0.00532.617-0.210-0.2100.0000.0000.0000.000
165A1093LEU0-0.085-0.02530.211-0.471-0.4710.0000.0000.0000.000
166A1094ASP-1-0.782-0.86926.931-11.245-11.2450.0000.0000.0000.000
167A1095ALA00.030-0.00128.7620.2510.2510.0000.0000.0000.000
168A1096VAL00.0280.04325.5300.3520.3520.0000.0000.0000.000
169A1097ARG10.8510.89523.11112.56612.5660.0000.0000.0000.000
170A1098ARG10.8500.93129.9809.5259.5250.0000.0000.0000.000
171A1099ALA00.0330.02331.8390.3230.3230.0000.0000.0000.000
172A1100ALA00.0180.01130.9670.2530.2530.0000.0000.0000.000
173A1101LEU00.003-0.00333.0850.2310.2310.0000.0000.0000.000
174A1102ILE00.0160.00035.9170.2560.2560.0000.0000.0000.000
175A1103ASN0-0.019-0.02435.1710.3950.3950.0000.0000.0000.000
176A1104MET0-0.025-0.00536.2530.0990.0990.0000.0000.0000.000
177A1105VAL0-0.031-0.02538.8600.2150.2150.0000.0000.0000.000
178A1106PHE0-0.0130.00140.9230.1900.1900.0000.0000.0000.000
179A1107GLN00.0170.02540.069-0.024-0.0240.0000.0000.0000.000
180A1108MET0-0.049-0.02239.8870.1670.1670.0000.0000.0000.000
181A1109GLY00.0530.03544.7340.1680.1680.0000.0000.0000.000
182A1110GLU-1-0.773-0.84944.972-6.589-6.5890.0000.0000.0000.000
183A1111THR0-0.001-0.02245.471-0.073-0.0730.0000.0000.0000.000
184A1112GLY00.0220.03645.7950.0260.0260.0000.0000.0000.000
185A1113VAL00.0250.00339.817-0.095-0.0950.0000.0000.0000.000
186A1114ALA0-0.008-0.00442.066-0.126-0.1260.0000.0000.0000.000
187A1115GLY00.0170.01444.4010.0370.0370.0000.0000.0000.000
188A1116PHE0-0.004-0.00738.850-0.007-0.0070.0000.0000.0000.000
189A1117THR00.0330.00139.423-0.171-0.1710.0000.0000.0000.000
190A1118ASN00.0050.01438.2130.0120.0120.0000.0000.0000.000
191A1119SER00.1020.03035.140-0.145-0.1450.0000.0000.0000.000
192A1120LEU0-0.0150.01034.749-0.264-0.2640.0000.0000.0000.000
193A1121ARG11.0011.00135.7227.8567.8560.0000.0000.0000.000
194A1122MET0-0.040-0.01732.375-0.053-0.0530.0000.0000.0000.000
195A1123LEU00.0130.00630.359-0.354-0.3540.0000.0000.0000.000
196A1124GLN0-0.028-0.00731.015-0.166-0.1660.0000.0000.0000.000
197A1125GLN0-0.043-0.01931.469-0.217-0.2170.0000.0000.0000.000
198A1126LYS10.9070.95126.53310.62810.6280.0000.0000.0000.000
199A1127ARG10.8730.93726.3669.2459.2450.0000.0000.0000.000
200A1128TRP00.0230.00323.0430.6620.6620.0000.0000.0000.000
201A1129ASP-1-0.786-0.88523.434-12.733-12.7330.0000.0000.0000.000
202A1130GLU-1-0.827-0.90026.444-9.694-9.6940.0000.0000.0000.000
203A1131ALA0-0.006-0.00429.8650.4120.4120.0000.0000.0000.000
204A1132ALA0-0.011-0.00728.2270.3130.3130.0000.0000.0000.000
205A1133VAL00.0120.00329.5560.2070.2070.0000.0000.0000.000
206A1134ASN0-0.046-0.02632.0270.5970.5970.0000.0000.0000.000
207A1135LEU0-0.007-0.01032.2700.3000.3000.0000.0000.0000.000
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