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: 3QM4L

Calculation Name: 3HVE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HVE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H2C0

Base Structure: X-ray

Registration Date: 2023-03-14

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2449922.791009
FMO2-HF: Nuclear repulsion 2358939.838222
FMO2-HF: Total energy -90982.952787
FMO2-MP2: Total energy -91245.096855


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:8:SER)


Summations of interaction energy for fragment #1(A:8:SER)
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.
4.4736.87-0.02-1.301-1.0760.002
Interaction energy analysis for fragmet #1(A:8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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].
3A10PRO00.0290.0193.8620.1142.511-0.020-1.301-1.0760.002
4A11GLN00.0100.0116.6551.0701.0700.0000.0000.0000.000
5A12HIS00.0390.0126.7610.3110.3110.0000.0000.0000.000
6A13ALA00.0420.0188.7990.3340.3340.0000.0000.0000.000
7A14ALA00.0720.04011.3080.1700.1700.0000.0000.0000.000
8A15ARG10.7720.8887.1662.5442.5440.0000.0000.0000.000
9A16LEU0-0.012-0.00312.8990.1320.1320.0000.0000.0000.000
10A17LEU00.0180.01714.6000.0800.0800.0000.0000.0000.000
11A18ARG10.9180.92914.4550.9990.9990.0000.0000.0000.000
12A19ALA0-0.023-0.00117.0240.0540.0540.0000.0000.0000.000
13A20LEU00.0190.02017.9620.0500.0500.0000.0000.0000.000
14A21SER00.0310.02220.8620.0460.0460.0000.0000.0000.000
15A22SER0-0.092-0.05222.2120.0260.0260.0000.0000.0000.000
16A23PHE0-0.051-0.01421.5670.0210.0210.0000.0000.0000.000
17A24ARG10.7800.85325.0580.3020.3020.0000.0000.0000.000
18A25GLU-1-0.800-0.92928.347-0.179-0.1790.0000.0000.0000.000
19A26GLU-1-0.813-0.90830.894-0.138-0.1380.0000.0000.0000.000
20A27SER0-0.090-0.03733.1840.0110.0110.0000.0000.0000.000
21A28ARG10.7940.90728.6020.1480.1480.0000.0000.0000.000
22A29PHE0-0.014-0.01225.3100.0050.0050.0000.0000.0000.000
23A30CYS0-0.077-0.00428.303-0.007-0.0070.0000.0000.0000.000
24A31ASP-1-0.774-0.86229.254-0.119-0.1190.0000.0000.0000.000
25A32ALA0-0.046-0.03231.7150.0140.0140.0000.0000.0000.000
26A33HIS00.0570.03333.564-0.010-0.0100.0000.0000.0000.000
27A34LEU0-0.002-0.00132.5250.0050.0050.0000.0000.0000.000
28A35VAL0-0.0180.00135.994-0.003-0.0030.0000.0000.0000.000
29A36LEU00.0240.01236.1340.0000.0000.0000.0000.0000.000
30A37ASP-1-0.818-0.90940.456-0.107-0.1070.0000.0000.0000.000
31A38GLY0-0.026-0.00943.7110.0060.0060.0000.0000.0000.000
32A39GLU-1-0.890-0.91840.331-0.122-0.1220.0000.0000.0000.000
33A40GLU-1-0.830-0.91639.285-0.087-0.0870.0000.0000.0000.000
34A41ILE0-0.024-0.00933.431-0.005-0.0050.0000.0000.0000.000
35A42PRO00.0170.01133.2830.0020.0020.0000.0000.0000.000
36A43VAL00.000-0.02629.684-0.015-0.0150.0000.0000.0000.000
37A44GLN0-0.016-0.01923.7640.0030.0030.0000.0000.0000.000
38A45LYS10.8120.88927.0820.0960.0960.0000.0000.0000.000
39A46ASN00.006-0.01022.2500.0020.0020.0000.0000.0000.000
40A47ILE00.0120.01321.5440.0000.0000.0000.0000.0000.000
41A48LEU00.0830.03723.620-0.005-0.0050.0000.0000.0000.000
42A49ALA00.0040.01726.2360.0070.0070.0000.0000.0000.000
43A50ALA0-0.051-0.02220.8240.0120.0120.0000.0000.0000.000
44A51ALA00.000-0.00122.6660.0010.0010.0000.0000.0000.000
45A52SER00.013-0.00923.8510.0110.0110.0000.0000.0000.000
46A53PRO0-0.006-0.01426.6410.0110.0110.0000.0000.0000.000
47A54TYR00.0880.06028.8910.0110.0110.0000.0000.0000.000
48A55ILE00.009-0.00129.4950.0080.0080.0000.0000.0000.000
49A56ARG10.8410.91423.8020.1250.1250.0000.0000.0000.000
50A57THR0-0.045-0.03029.7470.0100.0100.0000.0000.0000.000
51A58LYS10.8500.95832.9210.0910.0910.0000.0000.0000.000
52A59LEU0-0.053-0.01629.6240.0050.0050.0000.0000.0000.000
53A71TYR0-0.013-0.02834.7250.0030.0030.0000.0000.0000.000
54A72LYS10.7910.88436.4210.0740.0740.0000.0000.0000.000
55A73ILE0-0.042-0.00633.3050.0060.0060.0000.0000.0000.000
56A74GLU-1-0.852-0.94036.644-0.082-0.0820.0000.0000.0000.000
57A75LEU0-0.064-0.04634.4210.0020.0020.0000.0000.0000.000
58A76GLU-1-0.936-0.96439.040-0.067-0.0670.0000.0000.0000.000
59A77GLY0-0.0040.00140.543-0.002-0.0020.0000.0000.0000.000
60A78ILE0-0.005-0.00435.417-0.004-0.0040.0000.0000.0000.000
61A79SER00.0600.03139.314-0.001-0.0010.0000.0000.0000.000
62A80VAL0-0.010-0.02637.750-0.009-0.0090.0000.0000.0000.000
63A81MET0-0.024-0.01736.466-0.012-0.0120.0000.0000.0000.000
64A82VAL00.0540.03134.872-0.013-0.0130.0000.0000.0000.000
65A83MET00.0210.02132.367-0.015-0.0150.0000.0000.0000.000
66A84ARG10.8230.88831.7230.1360.1360.0000.0000.0000.000
67A85GLU-1-0.799-0.88330.551-0.229-0.2290.0000.0000.0000.000
68A86ILE00.0270.01028.828-0.020-0.0200.0000.0000.0000.000
69A87LEU0-0.024-0.01427.385-0.016-0.0160.0000.0000.0000.000
70A88ASP-1-0.798-0.87525.918-0.305-0.3050.0000.0000.0000.000
71A89TYR0-0.050-0.01723.876-0.040-0.0400.0000.0000.0000.000
72A90ILE0-0.020-0.00822.919-0.035-0.0350.0000.0000.0000.000
73A91PHE0-0.057-0.04121.385-0.029-0.0290.0000.0000.0000.000
74A92SER0-0.088-0.07120.367-0.052-0.0520.0000.0000.0000.000
75A93GLY0-0.032-0.00720.038-0.052-0.0520.0000.0000.0000.000
76A94GLN0-0.048-0.02721.0060.0360.0360.0000.0000.0000.000
77A95ILE00.0320.01624.2300.0040.0040.0000.0000.0000.000
78A96ARG10.7950.89527.9120.2120.2120.0000.0000.0000.000
79A97LEU00.0170.01031.0830.0090.0090.0000.0000.0000.000
80A98ASN0-0.069-0.04733.249-0.013-0.0130.0000.0000.0000.000
81A99GLU-1-0.763-0.89236.483-0.113-0.1130.0000.0000.0000.000
82A100ASP-1-0.920-0.93839.766-0.113-0.1130.0000.0000.0000.000
83A101THR0-0.075-0.04837.070-0.002-0.0020.0000.0000.0000.000
84A102ILE00.0070.00635.048-0.003-0.0030.0000.0000.0000.000
85A103GLN0-0.027-0.02336.3950.0010.0010.0000.0000.0000.000
86A104ASP-1-0.847-0.90838.256-0.113-0.1130.0000.0000.0000.000
87A105VAL00.003-0.01131.835-0.001-0.0010.0000.0000.0000.000
88A106VAL00.0040.00733.688-0.003-0.0030.0000.0000.0000.000
89A107GLN0-0.0110.00335.1930.0010.0010.0000.0000.0000.000
90A108ALA00.005-0.00934.3020.0040.0040.0000.0000.0000.000
91A109ALA0-0.001-0.01030.7780.0000.0000.0000.0000.0000.000
92A110ASP-1-0.897-0.93031.837-0.093-0.0930.0000.0000.0000.000
93A111LEU00.0140.02234.2260.0030.0030.0000.0000.0000.000
94A112LEU0-0.027-0.02130.7150.0040.0040.0000.0000.0000.000
95A113LEU0-0.044-0.01430.290-0.004-0.0040.0000.0000.0000.000
96A114LEU00.0050.01826.237-0.003-0.0030.0000.0000.0000.000
97A115THR00.004-0.01226.348-0.001-0.0010.0000.0000.0000.000
98A116ASP-1-0.826-0.87423.186-0.222-0.2220.0000.0000.0000.000
99A117LEU00.0620.02525.0490.0000.0000.0000.0000.0000.000
100A118LYS10.8840.92927.5070.1120.1120.0000.0000.0000.000
101A119THR0-0.030-0.01926.1000.0130.0130.0000.0000.0000.000
102A120LEU00.0150.00923.8620.0020.0020.0000.0000.0000.000
103A121CYS0-0.047-0.02727.9790.0040.0040.0000.0000.0000.000
104A122CYS0-0.082-0.03131.0110.0140.0140.0000.0000.0000.000
105A123GLU-1-0.893-0.95026.296-0.218-0.2180.0000.0000.0000.000
106A124PHE0-0.019-0.01130.8340.0040.0040.0000.0000.0000.000
107A125LEU00.019-0.00232.8820.0080.0080.0000.0000.0000.000
108A126GLU-1-0.838-0.92832.972-0.114-0.1140.0000.0000.0000.000
109A127GLY0-0.048-0.01934.2220.0050.0050.0000.0000.0000.000
110A128CYS0-0.063-0.02535.183-0.001-0.0010.0000.0000.0000.000
111A129ILE0-0.037-0.00538.2790.0070.0070.0000.0000.0000.000
112A130ALA00.0010.00840.710-0.001-0.0010.0000.0000.0000.000
113A131ALA0-0.051-0.02843.9350.0030.0030.0000.0000.0000.000
114A132GLU-1-0.823-0.92846.297-0.079-0.0790.0000.0000.0000.000
115A133ASN0-0.0150.00541.8850.0060.0060.0000.0000.0000.000
116A134CYS0-0.074-0.03843.289-0.001-0.0010.0000.0000.0000.000
117A135ILE00.002-0.00945.0970.0010.0010.0000.0000.0000.000
118A136GLY00.0680.04046.3690.0010.0010.0000.0000.0000.000
119A137ILE00.0030.00339.804-0.001-0.0010.0000.0000.0000.000
120A138ARG10.8940.93541.7780.0550.0550.0000.0000.0000.000
121A139ASP-1-0.823-0.90843.463-0.058-0.0580.0000.0000.0000.000
122A140PHE0-0.010-0.00238.1930.0010.0010.0000.0000.0000.000
123A141ALA00.008-0.00439.255-0.002-0.0020.0000.0000.0000.000
124A142LEU0-0.049-0.01340.0350.0010.0010.0000.0000.0000.000
125A143HIS0-0.045-0.01441.8350.0040.0040.0000.0000.0000.000
126A144TYR0-0.016-0.00737.5030.0010.0010.0000.0000.0000.000
127A145CYS0-0.045-0.02937.235-0.002-0.0020.0000.0000.0000.000
128A146LEU00.0060.01134.351-0.002-0.0020.0000.0000.0000.000
129A147HIS0-0.008-0.02335.6520.0010.0010.0000.0000.0000.000
130A148HIS0-0.073-0.04032.6880.0110.0110.0000.0000.0000.000
131A149VAL00.0880.04834.9350.0030.0030.0000.0000.0000.000
132A150HIS0-0.049-0.03337.0020.0070.0070.0000.0000.0000.000
133A151TYR0-0.090-0.04837.9590.0060.0060.0000.0000.0000.000
134A152LEU00.0400.01934.8410.0030.0030.0000.0000.0000.000
135A153ALA00.0120.01539.2940.0020.0020.0000.0000.0000.000
136A154THR0-0.020-0.03241.9930.0040.0040.0000.0000.0000.000
137A155GLU-1-0.844-0.89440.007-0.063-0.0630.0000.0000.0000.000
138A156TYR0-0.0100.01141.8820.0020.0020.0000.0000.0000.000
139A157LEU00.0580.01644.0560.0020.0020.0000.0000.0000.000
140A158GLU-1-0.875-0.93246.814-0.044-0.0440.0000.0000.0000.000
141A159THR0-0.046-0.05144.6340.0010.0010.0000.0000.0000.000
142A160HIS10.8240.91944.2270.0690.0690.0000.0000.0000.000
143A161PHE00.0590.04849.1430.0000.0000.0000.0000.0000.000
144A162ARG10.7870.89650.7010.0480.0480.0000.0000.0000.000
145A163ASP-1-0.869-0.93650.530-0.058-0.0580.0000.0000.0000.000
146A164VAL00.0530.01949.0380.0000.0000.0000.0000.0000.000
147A165SER0-0.085-0.06051.9770.0010.0010.0000.0000.0000.000
148A166SER0-0.110-0.06554.8220.0030.0030.0000.0000.0000.000
149A167THR00.0020.00950.753-0.001-0.0010.0000.0000.0000.000
150A168GLU-1-0.865-0.94654.119-0.055-0.0550.0000.0000.0000.000
151A169GLU-1-0.791-0.89148.503-0.070-0.0700.0000.0000.0000.000
152A170PHE0-0.023-0.01852.5480.0020.0020.0000.0000.0000.000
153A171LEU0-0.042-0.01054.4290.0030.0030.0000.0000.0000.000
154A172GLU-1-0.941-0.96455.211-0.056-0.0560.0000.0000.0000.000
155A173LEU0-0.0190.01153.0030.0010.0010.0000.0000.0000.000
156A174SER00.0370.00656.3550.0020.0020.0000.0000.0000.000
157A175PRO00.0540.03257.7500.0000.0000.0000.0000.0000.000
158A176GLN0-0.010-0.02157.5220.0000.0000.0000.0000.0000.000
159A177LYS10.7920.87549.8860.0550.0550.0000.0000.0000.000
160A178LEU00.0550.03754.6180.0000.0000.0000.0000.0000.000
161A179LYS10.8800.92955.6650.0380.0380.0000.0000.0000.000
162A180GLU-1-0.856-0.90250.453-0.048-0.0480.0000.0000.0000.000
163A181VAL00.0300.01251.1050.0000.0000.0000.0000.0000.000
164A182ILE0-0.032-0.02452.9450.0000.0000.0000.0000.0000.000
165A183SER0-0.089-0.03153.8790.0020.0020.0000.0000.0000.000
166A184LEU0-0.0210.01348.5530.0010.0010.0000.0000.0000.000
167A185GLU-1-1.039-1.01650.737-0.032-0.0320.0000.0000.0000.000
168A193ARG10.8560.87461.7260.0340.0340.0000.0000.0000.000
169A194TYR00.0280.00454.7980.0000.0000.0000.0000.0000.000
170A195VAL00.0830.05857.258-0.001-0.0010.0000.0000.0000.000
171A196PHE00.0430.00559.527-0.001-0.0010.0000.0000.0000.000
172A197GLU-1-0.852-0.90261.736-0.036-0.0360.0000.0000.0000.000
173A198ALA00.0320.03858.227-0.001-0.0010.0000.0000.0000.000
174A199VAL00.003-0.00960.305-0.001-0.0010.0000.0000.0000.000
175A200ILE0-0.025-0.03362.3130.0000.0000.0000.0000.0000.000
176A201ARG10.8660.93758.0220.0450.0450.0000.0000.0000.000
177A202TRP00.0290.01658.8120.0010.0010.0000.0000.0000.000
178A203ILE0-0.088-0.02061.7660.0000.0000.0000.0000.0000.000
179A204ALA00.0700.02362.8370.0010.0010.0000.0000.0000.000
180A205HIS00.0010.00564.3450.0000.0000.0000.0000.0000.000
181A206ASP-1-0.779-0.83467.856-0.035-0.0350.0000.0000.0000.000
182A207THR00.000-0.02070.0570.0010.0010.0000.0000.0000.000
183A208GLU-1-0.964-0.99671.267-0.034-0.0340.0000.0000.0000.000
184A209ILE0-0.0240.00366.6130.0010.0010.0000.0000.0000.000
185A210ARG10.8210.89859.8980.0440.0440.0000.0000.0000.000
186A211LYS10.7670.90467.7540.0300.0300.0000.0000.0000.000
187A212VAL0-0.009-0.00969.8620.0010.0010.0000.0000.0000.000
188A213HIS00.0400.01066.5480.0000.0000.0000.0000.0000.000
189A214MET00.0000.01968.7620.0000.0000.0000.0000.0000.000
190A215LYS10.8620.90970.0780.0250.0250.0000.0000.0000.000
191A216ASP-1-0.859-0.93868.193-0.026-0.0260.0000.0000.0000.000
192A217VAL0-0.0060.00065.7500.0010.0010.0000.0000.0000.000
193A218MET0-0.009-0.00568.3100.0000.0000.0000.0000.0000.000
194A219SER0-0.031-0.00471.3480.0010.0010.0000.0000.0000.000
195A220ALA00.0350.00966.5000.0010.0010.0000.0000.0000.000
196A221LEU00.0260.02267.0380.0000.0000.0000.0000.0000.000
197A222TRP0-0.058-0.01669.4250.0010.0010.0000.0000.0000.000
198A223VAL00.0190.00868.6810.0010.0010.0000.0000.0000.000
199A224SER00.027-0.00166.3070.0000.0000.0000.0000.0000.000
200A225GLY0-0.054-0.02267.9850.0000.0000.0000.0000.0000.000
201A226LEU0-0.100-0.04870.7650.0010.0010.0000.0000.0000.000
202A227ASP-1-0.902-0.94867.342-0.018-0.0180.0000.0000.0000.000
203A228SER0-0.014-0.00465.9390.0000.0000.0000.0000.0000.000
204A229SER00.019-0.00168.059-0.001-0.0010.0000.0000.0000.000
205A230TYR0-0.041-0.04368.407-0.001-0.0010.0000.0000.0000.000
206A231LEU0-0.0060.00965.370-0.001-0.0010.0000.0000.0000.000
207A232ARG10.8620.90868.5950.0200.0200.0000.0000.0000.000
208A233GLU-1-0.845-0.89671.714-0.024-0.0240.0000.0000.0000.000
209A234GLN00.0160.01865.470-0.002-0.0020.0000.0000.0000.000
210A235MET0-0.017-0.00265.648-0.001-0.0010.0000.0000.0000.000
211A236LEU0-0.052-0.02769.0830.0000.0000.0000.0000.0000.000
212A237ASN0-0.076-0.04470.0990.0000.0000.0000.0000.0000.000
213A238GLU-1-0.841-0.91165.468-0.038-0.0380.0000.0000.0000.000
214A239PRO0-0.022-0.01667.6080.0010.0010.0000.0000.0000.000
215A240LEU00.0260.01565.5500.0000.0000.0000.0000.0000.000
216A241VAL00.0170.00669.5520.0010.0010.0000.0000.0000.000
217A242ARG10.7700.84569.9310.0360.0360.0000.0000.0000.000
218A243GLH00.009-0.04068.4630.0010.0010.0000.0000.0000.000
219A244ILE0-0.004-0.01271.2470.0010.0010.0000.0000.0000.000
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