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: G64G1

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 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 485
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -9218591.010303
FMO2-HF: Nuclear repulsion 9026014.161503
FMO2-HF: Total energy -192576.848799
FMO2-MP2: Total energy -193149.376746


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.
11.315.2566.605-3.607-6.955-0.035
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 : 0.899 / q_NPA : 0.937
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-1-0.904-0.9493.805-29.410-27.236-0.028-0.877-1.269-0.001
4A104PHE0-0.068-0.0456.287-2.680-2.6800.0000.0000.0000.000
5A105PRO00.0480.0339.1222.0632.0630.0000.0000.0000.000
6A106GLU-1-0.816-0.90811.732-23.499-23.4990.0000.0000.0000.000
7A107ASP-1-0.815-0.90713.471-17.289-17.2890.0000.0000.0000.000
8A108PRO00.0600.02513.550-0.697-0.6970.0000.0000.0000.000
9A109GLU-1-0.936-0.96414.615-15.618-15.6180.0000.0000.0000.000
10A110PHE00.0330.00810.743-0.373-0.3730.0000.0000.0000.000
11A111GLU-1-0.813-0.9058.654-25.911-25.9110.0000.0000.0000.000
12A112ALA00.0130.01211.045-0.253-0.2530.0000.0000.0000.000
13A113VAL00.0180.00613.6440.3820.3820.0000.0000.0000.000
14A114VAL0-0.029-0.0148.0210.0090.0090.0000.0000.0000.000
15A115ARG10.7870.8735.62026.68526.6850.0000.0000.0000.000
16A116GLN0-0.014-0.01411.0581.0841.0840.0000.0000.0000.000
17A117ALA00.0040.00111.7350.5970.5970.0000.0000.0000.000
18A118GLU-1-0.834-0.9146.517-25.977-25.9770.0000.0000.0000.000
19A119LEU00.0110.02211.0000.8000.8000.0000.0000.0000.000
20A120ALA00.000-0.00413.8230.8250.8250.0000.0000.0000.000
21A121ILE0-0.015-0.00611.9890.6210.6210.0000.0000.0000.000
22A122GLU-1-0.879-0.92612.392-16.466-16.4660.0000.0000.0000.000
23A123ARG10.7860.89115.08114.91014.9100.0000.0000.0000.000
24A124CYS0-0.073-0.04117.6490.6630.6630.0000.0000.0000.000
25A125ILE0-0.0160.00718.4680.6370.6370.0000.0000.0000.000
26A126PHE0-0.005-0.01316.050-0.648-0.6480.0000.0000.0000.000
27A127PRO00.0380.01314.5720.5190.5190.0000.0000.0000.000
28A128GLU-1-0.881-0.89817.915-11.758-11.7580.0000.0000.0000.000
29A129ARG10.8660.92220.57313.47613.4760.0000.0000.0000.000
30A130ILE0-0.0030.01121.5080.5590.5590.0000.0000.0000.000
31A131TYR00.007-0.01324.346-0.191-0.1910.0000.0000.0000.000
32A132GLN0-0.0020.01127.148-0.104-0.1040.0000.0000.0000.000
33A133GLY00.0620.05424.396-0.003-0.0030.0000.0000.0000.000
34A134SER0-0.029-0.03824.8670.4790.4790.0000.0000.0000.000
35A135SER0-0.082-0.06020.432-0.111-0.1110.0000.0000.0000.000
36A136GLY00.0390.03918.3480.4160.4160.0000.0000.0000.000
37A137SER0-0.018-0.00317.438-0.855-0.8550.0000.0000.0000.000
38A138TYR0-0.073-0.07416.7120.9270.9270.0000.0000.0000.000
39A139PHE00.0600.02718.380-0.442-0.4420.0000.0000.0000.000
40A140VAL0-0.033-0.02514.1480.0870.0870.0000.0000.0000.000
41A141LYS10.8970.93917.03012.67112.6710.0000.0000.0000.000
42A142ASP-1-0.716-0.84217.245-13.483-13.4830.0000.0000.0000.000
43A143PRO00.004-0.01417.7350.5110.5110.0000.0000.0000.000
44A144GLN0-0.050-0.00920.3010.4160.4160.0000.0000.0000.000
45A145GLY0-0.016-0.00222.1400.4450.4450.0000.0000.0000.000
46A146ARG10.8450.90722.06312.01312.0130.0000.0000.0000.000
47A147ILE0-0.016-0.01421.013-0.580-0.5800.0000.0000.0000.000
48A148ILE00.0330.02915.9000.1960.1960.0000.0000.0000.000
49A149ALA00.010-0.00515.809-0.394-0.3940.0000.0000.0000.000
50A150VAL00.0010.01617.7340.4720.4720.0000.0000.0000.000
51A151PHE0-0.039-0.0219.941-0.462-0.4620.0000.0000.0000.000
52A152LYS10.8290.89214.11616.68016.6800.0000.0000.0000.000
53A153PRO00.0060.00711.802-1.314-1.3140.0000.0000.0000.000
54A154LYS10.8660.9129.69526.15626.1560.0000.0000.0000.000
55A155ASN00.006-0.00611.8592.4652.4650.0000.0000.0000.000
56A156GLU-1-0.746-0.81813.934-16.022-16.0220.0000.0000.0000.000
57A157GLU-1-0.727-0.86214.542-18.473-18.4730.0000.0000.0000.000
58A158PRO0-0.0140.01617.7980.2800.2800.0000.0000.0000.000
59A159TYR00.017-0.02319.1870.8330.8330.0000.0000.0000.000
60A160GLY0-0.022-0.01316.959-0.315-0.3150.0000.0000.0000.000
61A161HIS00.000-0.01216.1920.9330.9330.0000.0000.0000.000
62A162LEU0-0.043-0.02914.7830.5870.5870.0000.0000.0000.000
63A163ASN00.0180.03018.2480.7820.7820.0000.0000.0000.000
64A164PRO00.0680.01620.5190.5200.5200.0000.0000.0000.000
65A165LYS10.9430.99223.35111.76911.7690.0000.0000.0000.000
66A166TRP00.0450.00123.7780.4740.4740.0000.0000.0000.000
67A167THR00.0170.00922.0830.1690.1690.0000.0000.0000.000
68A168LYS10.9600.98524.62510.49410.4940.0000.0000.0000.000
69A169TRP0-0.026-0.01227.1460.3740.3740.0000.0000.0000.000
70A170LEU00.0090.00022.0470.2800.2800.0000.0000.0000.000
71A171GLN0-0.029-0.00426.3440.1890.1890.0000.0000.0000.000
72A172LYS10.9310.98228.6199.2869.2860.0000.0000.0000.000
73A1001GLY00.0250.02729.3500.2560.2560.0000.0000.0000.000
74A1002THR00.002-0.04030.3790.0130.0130.0000.0000.0000.000
75A1003GLY00.0300.02233.0590.1590.1590.0000.0000.0000.000
76A1004ASN0-0.051-0.03129.6140.3350.3350.0000.0000.0000.000
77A1005ILE0-0.013-0.00833.394-0.002-0.0020.0000.0000.0000.000
78A1006PHE0-0.0050.00635.7340.0640.0640.0000.0000.0000.000
79A1007GLU-1-0.832-0.92534.235-8.450-8.4500.0000.0000.0000.000
80A1008MET0-0.085-0.01431.3550.0330.0330.0000.0000.0000.000
81A1009LEU00.004-0.00534.449-0.017-0.0170.0000.0000.0000.000
82A1010ARG10.7820.86337.9497.8877.8870.0000.0000.0000.000
83A1011ILE0-0.041-0.00932.6030.0960.0960.0000.0000.0000.000
84A1012ASP-1-0.827-0.88535.260-8.859-8.8590.0000.0000.0000.000
85A1013GLU-1-0.872-0.92737.744-7.393-7.3930.0000.0000.0000.000
86A1014GLY0-0.0230.01340.4340.1840.1840.0000.0000.0000.000
87A1015LEU0-0.001-0.01541.9980.0850.0850.0000.0000.0000.000
88A1016ARG10.8810.95145.2146.7136.7130.0000.0000.0000.000
89A1017LEU00.0240.01348.7290.0160.0160.0000.0000.0000.000
90A1018LYS10.9740.99451.9485.6025.6020.0000.0000.0000.000
91A1019ILE0-0.052-0.01652.865-0.101-0.1010.0000.0000.0000.000
92A1020TYR00.0030.00546.2350.0690.0690.0000.0000.0000.000
93A1021LYS10.9070.95752.1665.6975.6970.0000.0000.0000.000
94A1022ASP-1-0.818-0.91547.303-6.524-6.5240.0000.0000.0000.000
95A1023THR0-0.011-0.02744.3470.0390.0390.0000.0000.0000.000
96A1024GLU-1-0.909-0.92947.147-6.378-6.3780.0000.0000.0000.000
97A1025GLY00.0150.02549.5940.1360.1360.0000.0000.0000.000
98A1026TYR0-0.101-0.07450.5850.2500.2500.0000.0000.0000.000
99A1027TYR0-0.046-0.03151.953-0.105-0.1050.0000.0000.0000.000
100A1028THR0-0.001-0.00847.946-0.031-0.0310.0000.0000.0000.000
101A1029ILE0-0.028-0.02350.5930.0920.0920.0000.0000.0000.000
102A1030GLY00.0410.01449.048-0.062-0.0620.0000.0000.0000.000
103A1031ILE0-0.010-0.00142.703-0.051-0.0510.0000.0000.0000.000
104A1032GLY00.0470.02244.577-0.011-0.0110.0000.0000.0000.000
105A1033HIS10.8650.95145.5376.3006.3000.0000.0000.0000.000
106A1034LEU00.013-0.00648.7650.1210.1210.0000.0000.0000.000
107A1035LEU0-0.066-0.02250.8510.0570.0570.0000.0000.0000.000
108A1036THR00.011-0.01054.5610.0790.0790.0000.0000.0000.000
109A1037LYS10.9820.99852.2015.9135.9130.0000.0000.0000.000
110A1038SER0-0.015-0.00755.9110.0430.0430.0000.0000.0000.000
111A1039PRO00.0870.03058.555-0.061-0.0610.0000.0000.0000.000
112A1040SER00.0030.02860.247-0.026-0.0260.0000.0000.0000.000
113A1041LEU00.0610.02058.741-0.049-0.0490.0000.0000.0000.000
114A1042ASN00.037-0.00560.885-0.078-0.0780.0000.0000.0000.000
115A1043ALA00.0570.05961.3560.0170.0170.0000.0000.0000.000
116A1044ALA00.0070.00257.099-0.030-0.0300.0000.0000.0000.000
117A1045LYS10.7560.88358.7715.0055.0050.0000.0000.0000.000
118A1046SER0-0.029-0.03260.840-0.001-0.0010.0000.0000.0000.000
119A1047GLU-1-0.811-0.89057.507-5.377-5.3770.0000.0000.0000.000
120A1048LEU0-0.029-0.01455.550-0.072-0.0720.0000.0000.0000.000
121A1049ASP-1-0.730-0.84558.393-5.134-5.1340.0000.0000.0000.000
122A1050LYS10.7960.88759.5405.3115.3110.0000.0000.0000.000
123A1051ALA0-0.0170.00655.452-0.015-0.0150.0000.0000.0000.000
124A1052ILE0-0.058-0.04054.560-0.049-0.0490.0000.0000.0000.000
125A1053GLY00.0110.01657.974-0.006-0.0060.0000.0000.0000.000
126A1054ARG10.8050.88457.8425.4605.4600.0000.0000.0000.000
127A1055ASN00.0350.00762.821-0.091-0.0910.0000.0000.0000.000
128A1056THR00.005-0.02558.585-0.003-0.0030.0000.0000.0000.000
129A1057ASN0-0.008-0.00761.0050.0030.0030.0000.0000.0000.000
130A1058GLY0-0.008-0.00558.854-0.013-0.0130.0000.0000.0000.000
131A1059VAL0-0.025-0.01556.253-0.120-0.1200.0000.0000.0000.000
132A1060ILE00.003-0.00151.7890.0760.0760.0000.0000.0000.000
133A1061THR00.0320.00453.712-0.064-0.0640.0000.0000.0000.000
134A1062LYS11.0130.98944.1726.9436.9430.0000.0000.0000.000
135A1063ASP-1-0.864-0.93749.049-6.341-6.3410.0000.0000.0000.000
136A1064GLU-1-0.754-0.84350.628-5.647-5.6470.0000.0000.0000.000
137A1065ALA0-0.007-0.00348.664-0.017-0.0170.0000.0000.0000.000
138A1066GLU-1-0.793-0.88244.107-7.327-7.3270.0000.0000.0000.000
139A1067LYS10.9000.96747.2065.6665.6660.0000.0000.0000.000
140A1068LEU0-0.070-0.03649.652-0.001-0.0010.0000.0000.0000.000
141A1069PHE0-0.0200.00740.080-0.076-0.0760.0000.0000.0000.000
142A1070ASN00.0410.00944.492-0.236-0.2360.0000.0000.0000.000
143A1071GLN00.0320.02745.701-0.005-0.0050.0000.0000.0000.000
144A1072ASP-1-0.821-0.90446.131-6.475-6.4750.0000.0000.0000.000
145A1073VAL0-0.026-0.01040.785-0.114-0.1140.0000.0000.0000.000
146A1074ASP-1-0.899-0.94943.258-6.994-6.9940.0000.0000.0000.000
147A1075ALA0-0.073-0.03845.4040.0110.0110.0000.0000.0000.000
148A1076ALA00.0010.00842.1670.0240.0240.0000.0000.0000.000
149A1077VAL00.012-0.00640.173-0.060-0.0600.0000.0000.0000.000
150A1078ARG10.9550.96442.5786.3066.3060.0000.0000.0000.000
151A1079GLY0-0.022-0.01245.8640.0540.0540.0000.0000.0000.000
152A1080ILE0-0.018-0.01538.9310.0150.0150.0000.0000.0000.000
153A1081LEU0-0.002-0.01140.599-0.010-0.0100.0000.0000.0000.000
154A1082ARG10.8320.89344.0006.4266.4260.0000.0000.0000.000
155A1083ASN0-0.027-0.02244.8490.0430.0430.0000.0000.0000.000
156A1084ALA00.0480.02044.690-0.143-0.1430.0000.0000.0000.000
157A1085LYS10.9090.95243.4876.9026.9020.0000.0000.0000.000
158A1086LEU0-0.047-0.01140.807-0.200-0.2000.0000.0000.0000.000
159A1087LYS10.8640.94239.6247.3967.3960.0000.0000.0000.000
160A1088PRO00.0320.01939.093-0.206-0.2060.0000.0000.0000.000
161A1089VAL00.0190.00034.598-0.249-0.2490.0000.0000.0000.000
162A1090TYR00.0170.00934.640-0.337-0.3370.0000.0000.0000.000
163A1091ASP-1-0.792-0.89134.766-8.253-8.2530.0000.0000.0000.000
164A1092SER0-0.0190.00132.263-0.188-0.1880.0000.0000.0000.000
165A1093LEU0-0.096-0.03430.092-0.474-0.4740.0000.0000.0000.000
166A1094ASP-1-0.788-0.87726.720-11.345-11.3450.0000.0000.0000.000
167A1095ALA00.034-0.00528.6920.2240.2240.0000.0000.0000.000
168A1096VAL00.0380.03625.5200.3780.3780.0000.0000.0000.000
169A1097ARG10.8780.92423.00012.54712.5470.0000.0000.0000.000
170A1098ARG10.8430.93229.7679.5379.5370.0000.0000.0000.000
171A1099ALA00.0180.01031.7660.3270.3270.0000.0000.0000.000
172A1100ALA00.0350.01830.8920.2280.2280.0000.0000.0000.000
173A1101LEU0-0.016-0.01333.0320.2160.2160.0000.0000.0000.000
174A1102ILE00.006-0.00435.7700.2560.2560.0000.0000.0000.000
175A1103ASN00.005-0.00535.1730.3920.3920.0000.0000.0000.000
176A1104MET0-0.0110.00836.2830.0990.0990.0000.0000.0000.000
177A1105VAL0-0.049-0.02138.9190.2180.2180.0000.0000.0000.000
178A1106PHE0-0.0100.00140.8450.1860.1860.0000.0000.0000.000
179A1107GLN00.0220.02940.290-0.023-0.0230.0000.0000.0000.000
180A1108MET0-0.056-0.03539.8730.1840.1840.0000.0000.0000.000
181A1109GLY00.0440.03644.4150.1740.1740.0000.0000.0000.000
182A1110GLU-1-0.783-0.87444.966-6.585-6.5850.0000.0000.0000.000
183A1111THR00.003-0.01745.335-0.070-0.0700.0000.0000.0000.000
184A1112GLY00.0180.02746.028-0.001-0.0010.0000.0000.0000.000
185A1113VAL00.0480.01639.864-0.089-0.0890.0000.0000.0000.000
186A1114ALA0-0.012-0.00141.805-0.164-0.1640.0000.0000.0000.000
187A1115GLY00.0110.00644.1030.0650.0650.0000.0000.0000.000
188A1116PHE0-0.039-0.03738.683-0.010-0.0100.0000.0000.0000.000
189A1117THR0-0.003-0.01739.603-0.161-0.1610.0000.0000.0000.000
190A1118ASN00.0110.01238.3600.0180.0180.0000.0000.0000.000
191A1119SER00.0890.02235.028-0.138-0.1380.0000.0000.0000.000
192A1120LEU0-0.0170.01134.794-0.260-0.2600.0000.0000.0000.000
193A1121ARG10.9961.00835.8847.9657.9650.0000.0000.0000.000
194A1122MET0-0.031-0.01632.196-0.067-0.0670.0000.0000.0000.000
195A1123LEU00.0240.00030.382-0.285-0.2850.0000.0000.0000.000
196A1124GLN0-0.030-0.00230.902-0.160-0.1600.0000.0000.0000.000
197A1125GLN0-0.041-0.01931.060-0.205-0.2050.0000.0000.0000.000
198A1126LYS10.9040.95726.22910.75910.7590.0000.0000.0000.000
199A1127ARG10.8740.93826.1009.3889.3880.0000.0000.0000.000
200A1128TRP00.0480.01622.7630.7100.7100.0000.0000.0000.000
201A1129ASP-1-0.813-0.89623.044-12.838-12.8380.0000.0000.0000.000
202A1130GLU-1-0.857-0.91126.120-9.701-9.7010.0000.0000.0000.000
203A1131ALA00.0120.00129.4820.3350.3350.0000.0000.0000.000
204A1132ALA0-0.006-0.01428.1080.3140.3140.0000.0000.0000.000
205A1133VAL00.0380.02929.7070.1700.1700.0000.0000.0000.000
206A1134ASN0-0.018-0.01332.0070.5570.5570.0000.0000.0000.000
207A1135LEU0-0.011-0.00632.1650.2780.2780.0000.0000.0000.000
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