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: 85J8Y

Calculation Name: 5H4U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H4U

Chain ID: A

ChEMBL ID:

UniProt ID: D3GDK4

Base Structure: X-ray

Registration Date: 2023-06-21

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2311666.201761
FMO2-HF: Nuclear repulsion 2230084.391175
FMO2-HF: Total energy -81581.810586
FMO2-MP2: Total energy -81806.577241


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:1:LEU)


Summations of interaction energy for fragment #1(A:1:LEU)
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.
-6.607-0.2632.658-3.506-5.495-0.017
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : 0.013
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].
3A3SER0-0.017-0.0143.322-1.8290.9200.041-1.431-1.3590.002
4A4GLY00.0340.0305.4330.1520.1520.0000.0000.0000.000
5A5SER0-0.002-0.0079.2420.0960.0960.0000.0000.0000.000
6A6GLY00.0270.00812.584-0.038-0.0380.0000.0000.0000.000
7A7VAL0-0.0060.01214.7040.0270.0270.0000.0000.0000.000
8A8THR0-0.051-0.04816.016-0.006-0.0060.0000.0000.0000.000
9A9THR00.004-0.01718.5670.0200.0200.0000.0000.0000.000
10A10ARG10.7310.85921.1000.1230.1230.0000.0000.0000.000
11A11TYR0-0.037-0.00620.9550.0060.0060.0000.0000.0000.000
12A12TRP00.025-0.01523.6140.0030.0030.0000.0000.0000.000
13A13ASP-1-0.762-0.89025.870-0.018-0.0180.0000.0000.0000.000
14A14CYS0-0.095-0.03027.2950.0070.0070.0000.0000.0000.000
15A15CYS0-0.101-0.03426.0950.0030.0030.0000.0000.0000.000
16A16LYS10.8370.92524.863-0.096-0.0960.0000.0000.0000.000
17A17PRO0-0.0260.00620.281-0.003-0.0030.0000.0000.0000.000
18A18SER00.001-0.03218.2680.0190.0190.0000.0000.0000.000
19A19CYS00.019-0.0019.766-0.015-0.0150.0000.0000.0000.000
20A20SER0-0.043-0.02018.3800.0240.0240.0000.0000.0000.000
21A21TRP00.0020.00321.493-0.002-0.0020.0000.0000.0000.000
22A22GLY00.0310.00820.9290.0220.0220.0000.0000.0000.000
23A23GLY0-0.004-0.01120.210-0.014-0.0140.0000.0000.0000.000
24A24LYS10.7930.89516.983-0.094-0.0940.0000.0000.0000.000
25A25ALA00.0160.00412.9400.0200.0200.0000.0000.0000.000
26A26SER0-0.0030.01313.536-0.051-0.0510.0000.0000.0000.000
27A27VAL0-0.020-0.02713.8170.1030.1030.0000.0000.0000.000
28A28THR00.0040.00015.938-0.027-0.0270.0000.0000.0000.000
29A29LYS10.8920.94218.381-0.224-0.2240.0000.0000.0000.000
30A30PRO00.0340.01618.5180.0230.0230.0000.0000.0000.000
31A31VAL0-0.021-0.00917.336-0.006-0.0060.0000.0000.0000.000
32A32ARG10.8070.89119.845-0.096-0.0960.0000.0000.0000.000
33A33THR00.0480.02423.129-0.012-0.0120.0000.0000.0000.000
34A34CYS0-0.117-0.04025.1230.0080.0080.0000.0000.0000.000
35A35LYS11.0161.01029.417-0.051-0.0510.0000.0000.0000.000
36A36ALA00.0640.03432.426-0.001-0.0010.0000.0000.0000.000
37A37ASN00.0390.01833.723-0.001-0.0010.0000.0000.0000.000
38A38GLY00.0720.04630.252-0.003-0.0030.0000.0000.0000.000
39A39ASN00.0240.01229.3550.0020.0020.0000.0000.0000.000
40A40THR0-0.021-0.01130.7090.0050.0050.0000.0000.0000.000
41A41THR00.0530.01527.470-0.005-0.0050.0000.0000.0000.000
42A42ILE0-0.066-0.00728.716-0.005-0.0050.0000.0000.0000.000
43A43ASP-1-0.752-0.86228.4380.1280.1280.0000.0000.0000.000
44A44SER0-0.047-0.02124.644-0.005-0.0050.0000.0000.0000.000
45A45ASN0-0.016-0.02526.1550.0040.0040.0000.0000.0000.000
46A46THR0-0.052-0.02728.608-0.009-0.0090.0000.0000.0000.000
47A47GLN00.0980.05029.4160.0000.0000.0000.0000.0000.000
48A48SER00.0640.01628.361-0.002-0.0020.0000.0000.0000.000
49A49GLY00.0340.01930.091-0.002-0.0020.0000.0000.0000.000
50A51ASN0-0.046-0.02528.519-0.009-0.0090.0000.0000.0000.000
51A52GLY00.0240.01432.9350.0030.0030.0000.0000.0000.000
52A53GLY0-0.024-0.00233.8100.0030.0030.0000.0000.0000.000
53A54SER00.002-0.00933.517-0.004-0.0040.0000.0000.0000.000
54A55SER0-0.070-0.02428.2990.0010.0010.0000.0000.0000.000
55A56TYR00.026-0.00328.670-0.003-0.0030.0000.0000.0000.000
56A57VAL00.0300.02923.6150.0120.0120.0000.0000.0000.000
57A59ASN00.000-0.04425.724-0.011-0.0110.0000.0000.0000.000
58A60ASP-1-0.861-0.92624.2400.0620.0620.0000.0000.0000.000
59A61GLN0-0.077-0.05320.574-0.004-0.0040.0000.0000.0000.000
60A62GLN0-0.003-0.00521.936-0.020-0.0200.0000.0000.0000.000
61A63PRO0-0.0110.00820.6240.0080.0080.0000.0000.0000.000
62A64PHE0-0.032-0.03118.3130.0080.0080.0000.0000.0000.000
63A65THR00.0120.00720.468-0.019-0.0190.0000.0000.0000.000
64A66GLN0-0.024-0.01117.6100.0300.0300.0000.0000.0000.000
65A67GLY00.0370.02319.833-0.012-0.0120.0000.0000.0000.000
66A68ASN00.014-0.00820.8710.0080.0080.0000.0000.0000.000
67A69VAL0-0.0200.01714.976-0.022-0.0220.0000.0000.0000.000
68A70GLY00.0600.03017.8100.0280.0280.0000.0000.0000.000
69A71TYR0-0.022-0.02514.310-0.019-0.0190.0000.0000.0000.000
70A72GLY00.0600.02316.172-0.001-0.0010.0000.0000.0000.000
71A73PHE0-0.033-0.00515.8780.0140.0140.0000.0000.0000.000
72A74ALA00.0180.01014.893-0.025-0.0250.0000.0000.0000.000
73A75ALA00.0190.02516.1500.0390.0390.0000.0000.0000.000
74A76ALA0-0.017-0.01713.026-0.040-0.0400.0000.0000.0000.000
75A77SER00.008-0.00214.7410.0500.0500.0000.0000.0000.000
76A78ILE00.0010.0048.567-0.061-0.0610.0000.0000.0000.000
77A79SER00.016-0.00610.177-0.051-0.0510.0000.0000.0000.000
78A80GLY00.0410.03612.050-0.022-0.0220.0000.0000.0000.000
79A81GLN0-0.030-0.0116.0540.3810.3810.0000.0000.0000.000
80A82PRO00.0350.02510.2620.0140.0140.0000.0000.0000.000
81A83GLU-1-0.644-0.80411.3740.1590.1590.0000.0000.0000.000
82A84SER00.0310.01812.5610.0520.0520.0000.0000.0000.000
83A85GLN0-0.069-0.0346.1550.3910.3910.0000.0000.0000.000
84A86THR00.0370.0217.6390.1820.1820.0000.0000.0000.000
85A88CYS0-0.0460.01011.7500.1430.1430.0000.0000.0000.000
86A89ALA00.0220.0266.8560.1120.1120.0000.0000.0000.000
87A90CYS0-0.067-0.0246.677-0.312-0.3120.0000.0000.0000.000
88A91TYR00.0800.0275.9810.1010.1010.0000.0000.0000.000
89A92GLU-1-0.868-0.8877.399-0.390-0.3900.0000.0000.0000.000
90A93MET00.0250.0018.948-0.213-0.2130.0000.0000.0000.000
91A94THR0-0.033-0.01411.6430.0560.0560.0000.0000.0000.000
92A95PHE00.0530.02514.421-0.041-0.0410.0000.0000.0000.000
93A96THR0-0.026-0.02616.688-0.021-0.0210.0000.0000.0000.000
94A97ASN00.0640.03519.0180.0030.0030.0000.0000.0000.000
95A98THR00.0520.03622.5280.0180.0180.0000.0000.0000.000
96A99ALA00.0630.02524.453-0.007-0.0070.0000.0000.0000.000
97A100ILE0-0.0310.00321.0690.0090.0090.0000.0000.0000.000
98A101SER0-0.040-0.01320.436-0.031-0.0310.0000.0000.0000.000
99A102GLY00.0150.00918.4210.0210.0210.0000.0000.0000.000
100A103GLN0-0.021-0.01217.8430.0010.0010.0000.0000.0000.000
101A104LYS10.8510.89910.6450.4150.4150.0000.0000.0000.000
102A105MET0-0.022-0.00514.3050.0500.0500.0000.0000.0000.000
103A106ILE0-0.016-0.00810.120-0.066-0.0660.0000.0000.0000.000
104A107VAL00.0240.00911.5090.0510.0510.0000.0000.0000.000
105A108GLN0-0.011-0.01311.017-0.049-0.0490.0000.0000.0000.000
106A109VAL00.0060.00911.135-0.028-0.0280.0000.0000.0000.000
107A110THR0-0.012-0.02413.2710.0680.0680.0000.0000.0000.000
108A111ASN00.0440.01316.5570.0350.0350.0000.0000.0000.000
109A112THR0-0.004-0.00316.448-0.017-0.0170.0000.0000.0000.000
110A113GLY00.0140.00917.3070.0070.0070.0000.0000.0000.000
111A114SER0-0.004-0.01119.2580.0190.0190.0000.0000.0000.000
112A115ASP-1-0.932-0.94818.452-0.194-0.1940.0000.0000.0000.000
113A116LEU00.0130.00218.6880.0120.0120.0000.0000.0000.000
114A117ASN00.0250.01517.940-0.062-0.0620.0000.0000.0000.000
115A118GLY00.0090.02216.0130.0090.0090.0000.0000.0000.000
116A119ASN0-0.042-0.04211.533-0.034-0.0340.0000.0000.0000.000
117A120HIS00.0140.00414.2060.0120.0120.0000.0000.0000.000
118A121PHE0-0.012-0.0169.9180.0160.0160.0000.0000.0000.000
119A122ASP-1-0.826-0.87916.199-0.168-0.1680.0000.0000.0000.000
120A123LEU0-0.008-0.01816.8510.0260.0260.0000.0000.0000.000
121A124MET0-0.022-0.01019.5780.0170.0170.0000.0000.0000.000
122A125ILE0-0.005-0.01221.7280.0030.0030.0000.0000.0000.000
123A126PRO0-0.025-0.00224.561-0.001-0.0010.0000.0000.0000.000
124A127GLY00.0440.01928.112-0.004-0.0040.0000.0000.0000.000
125A128GLY0-0.011-0.00927.085-0.004-0.0040.0000.0000.0000.000
126A129GLY00.0480.02928.170-0.009-0.0090.0000.0000.0000.000
127A130VAL0-0.081-0.04028.3890.0030.0030.0000.0000.0000.000
128A131GLY00.0430.02027.6370.0020.0020.0000.0000.0000.000
129A132ILE00.0350.02325.8710.0060.0060.0000.0000.0000.000
130A133PHE0-0.0030.00625.2630.0070.0070.0000.0000.0000.000
131A134ASN0-0.028-0.04930.180-0.003-0.0030.0000.0000.0000.000
132A135GLY00.0760.03830.9250.0040.0040.0000.0000.0000.000
133A137GLN00.0160.02933.3970.0020.0020.0000.0000.0000.000
134A138SER00.0150.00635.1410.0020.0020.0000.0000.0000.000
135A139GLN0-0.069-0.02730.272-0.001-0.0010.0000.0000.0000.000
136A140TRP0-0.048-0.05031.6460.0020.0020.0000.0000.0000.000
137A141GLY00.0290.03237.119-0.001-0.0010.0000.0000.0000.000
138A142ALA0-0.045-0.00936.033-0.002-0.0020.0000.0000.0000.000
139A143PRO00.0480.01637.6400.0020.0020.0000.0000.0000.000
140A144SER00.0490.01637.381-0.001-0.0010.0000.0000.0000.000
141A145ASN0-0.048-0.03336.5680.0030.0030.0000.0000.0000.000
142A146GLY00.0470.02033.921-0.005-0.0050.0000.0000.0000.000
143A147TRP0-0.017-0.03430.8770.0000.0000.0000.0000.0000.000
144A148GLY00.0180.01534.093-0.005-0.0050.0000.0000.0000.000
145A149GLN00.0230.01133.9300.0050.0050.0000.0000.0000.000
146A150ARG10.8750.93532.2630.0410.0410.0000.0000.0000.000
147A151TYR00.0280.01627.812-0.001-0.0010.0000.0000.0000.000
148A152GLY00.0410.02729.0130.0000.0000.0000.0000.0000.000
149A153GLY00.0380.02029.984-0.002-0.0020.0000.0000.0000.000
150A154ILE0-0.038-0.01332.0180.0010.0010.0000.0000.0000.000
151A155SER00.002-0.00133.156-0.009-0.0090.0000.0000.0000.000
152A156SER0-0.037-0.03734.594-0.006-0.0060.0000.0000.0000.000
153A157GLN0-0.004-0.01534.0980.0030.0030.0000.0000.0000.000
154A158SER00.0380.01835.1090.0030.0030.0000.0000.0000.000
155A159GLU-1-0.722-0.85336.641-0.055-0.0550.0000.0000.0000.000
156A160CYS0-0.071-0.01126.898-0.010-0.0100.0000.0000.0000.000
157A161ASN0-0.074-0.04935.4010.0070.0070.0000.0000.0000.000
158A162GLN00.0100.00338.1260.0040.0040.0000.0000.0000.000
159A163LEU0-0.0070.00931.8330.0010.0010.0000.0000.0000.000
160A164PRO00.0390.02534.0470.0020.0020.0000.0000.0000.000
161A165THR00.0430.01434.360-0.002-0.0020.0000.0000.0000.000
162A166SER0-0.021-0.00932.214-0.003-0.0030.0000.0000.0000.000
163A167LEU00.0060.01028.6010.0020.0020.0000.0000.0000.000
164A168ARG10.8820.94630.2940.0150.0150.0000.0000.0000.000
165A169ALA00.0170.03028.476-0.006-0.0060.0000.0000.0000.000
166A170GLY00.0610.01126.086-0.008-0.0080.0000.0000.0000.000
167A172ASN00.023-0.01129.676-0.009-0.0090.0000.0000.0000.000
168A173TRP0-0.019-0.00820.266-0.008-0.0080.0000.0000.0000.000
169A174ARG10.8000.88725.9870.0790.0790.0000.0000.0000.000
170A175PHE00.018-0.00326.990-0.010-0.0100.0000.0000.0000.000
171A176GLY00.0210.02428.876-0.002-0.0020.0000.0000.0000.000
172A177TRP0-0.030-0.02218.511-0.009-0.0090.0000.0000.0000.000
173A178PHE0-0.002-0.00620.570-0.015-0.0150.0000.0000.0000.000
174A179LYS10.8580.92324.5530.1470.1470.0000.0000.0000.000
175A180ASN00.0140.01827.9160.0000.0000.0000.0000.0000.000
176A181ALA0-0.0210.00923.981-0.002-0.0020.0000.0000.0000.000
177A182ASP-1-0.832-0.91225.667-0.141-0.1410.0000.0000.0000.000
178A183ASN0-0.021-0.02222.664-0.013-0.0130.0000.0000.0000.000
179A184PRO0-0.0160.02220.041-0.015-0.0150.0000.0000.0000.000
180A185SER00.0180.00918.268-0.020-0.0200.0000.0000.0000.000
181A186MET0-0.074-0.02412.428-0.017-0.0170.0000.0000.0000.000
182A187LYS10.9600.98811.4060.6620.6620.0000.0000.0000.000
183A188PHE00.006-0.0167.7440.0680.0680.0000.0000.0000.000
184A189THR0-0.014-0.0233.329-0.813-0.4360.023-0.068-0.3310.000
185A190GLN00.0300.0352.357-2.0140.1400.987-1.050-2.091-0.006
186A191VAL0-0.010-0.0112.552-1.570-0.5761.608-0.956-1.646-0.013
187A192ARG10.9480.9694.368-0.786-0.716-0.001-0.001-0.0680.000
188A194PRO00.0480.0369.8000.0310.0310.0000.0000.0000.000
189A195THR00.0700.01012.520-0.013-0.0130.0000.0000.0000.000
190A196ILE0-0.0170.00815.785-0.001-0.0010.0000.0000.0000.000
191A197LEU0-0.0050.01412.664-0.019-0.0190.0000.0000.0000.000
192A198THR00.0450.01413.432-0.015-0.0150.0000.0000.0000.000
193A199GLN00.0100.01916.241-0.007-0.0070.0000.0000.0000.000
194A200LYS10.8560.94119.192-0.058-0.0580.0000.0000.0000.000
195A201SER00.007-0.02415.977-0.001-0.0010.0000.0000.0000.000
196A202GLN0-0.037-0.01219.1700.0130.0130.0000.0000.0000.000
197A204VAL00.025-0.00212.6650.0030.0030.0000.0000.0000.000
198A205ARG10.8570.9138.251-1.017-1.0170.0000.0000.0000.000
199A206THR00.015-0.00111.6980.0900.0900.0000.0000.0000.000
200A207PRO0-0.0260.00011.336-0.022-0.0220.0000.0000.0000.000
201A208GLY0-0.0210.0107.4120.0450.0450.0000.0000.0000.000