FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 16MZZ

Calculation Name: 2RH3-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2RH3

Chain ID: A

ChEMBL ID:

UniProt ID: P07166

Base Structure: X-ray

Registration Date: 2025-07-09

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -984584.876562
FMO2-HF: Nuclear repulsion 937836.444326
FMO2-HF: Total energy -46748.432237
FMO2-MP2: Total energy -46884.680797


3D Structure Molmil
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:82:ILE)


Summations of interaction energy for fragment #1(A:82:ILE)
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.
-5.69-2.4645.893-4.47-4.645-0.006
Interaction energy analysis for fragmet #1(A:82:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.146 / q_NPA : 0.024
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].
4A83GLN0-0.0750.1074.6350.2020.5670.000-0.140-0.2240.000
5A84VAL0-0.005-0.1373.845-3.418-1.121-0.011-1.324-0.9620.007
6A84VAL0-0.0740.1204.6040.0300.082-0.001-0.008-0.0430.000
7A85PHE00.119-0.0886.4300.4310.4310.0000.0000.0000.000
8A85PHE0-0.0810.0908.5820.0040.0040.0000.0000.0000.000
9A86LEU00.047-0.12810.040-0.102-0.1020.0000.0000.0000.000
10A86LEU0-0.1010.10110.1060.0340.0340.0000.0000.0000.000
11A87SER00.051-0.06912.8300.0780.0780.0000.0000.0000.000
12A87SER0-0.0450.06516.377-0.006-0.0060.0000.0000.0000.000
13A88ALA00.083-0.10316.578-0.025-0.0250.0000.0000.0000.000
14A88ALA0-0.0230.13218.3850.0000.0000.0000.0000.0000.000
15A89ARG00.038-0.13119.6520.0130.0130.0000.0000.0000.000
16A89ARG10.8361.05523.4570.2940.2940.0000.0000.0000.000
17A90PRO0-0.020-0.08823.482-0.014-0.0140.0000.0000.0000.000
18A91PRO00.0020.00424.912-0.003-0.0030.0000.0000.0000.000
19A92ALA00.096-0.00527.3160.0030.0030.0000.0000.0000.000
20A92ALA0-0.0770.10331.7040.0010.0010.0000.0000.0000.000
21A93PRO0-0.008-0.10630.820-0.005-0.0050.0000.0000.0000.000
22A94GLU00.035-0.01033.281-0.003-0.0030.0000.0000.0000.000
23A94GLU-1-1.000-0.85535.268-0.124-0.1240.0000.0000.0000.000
24A95VAL00.030-0.12229.6480.0070.0070.0000.0000.0000.000
25A95VAL0-0.1340.07327.720-0.004-0.0040.0000.0000.0000.000
26A96SER00.051-0.08727.722-0.003-0.0030.0000.0000.0000.000
27A96SER0-0.1210.00227.159-0.008-0.0080.0000.0000.0000.000
28A97LYS00.132-0.05229.183-0.005-0.0050.0000.0000.0000.000
29A97LYS10.8591.04232.0240.1290.1290.0000.0000.0000.000
30A98ILE00.066-0.07527.4470.0110.0110.0000.0000.0000.000
31A98ILE0-0.1090.07725.585-0.002-0.0020.0000.0000.0000.000
32A99TYR00.092-0.08927.0710.0030.0030.0000.0000.0000.000
33A99TYR0-0.0690.07525.825-0.015-0.0150.0000.0000.0000.000
34A100ASP00.094-0.12027.774-0.002-0.0020.0000.0000.0000.000
35A100ASP-1-0.899-0.80032.021-0.165-0.1650.0000.0000.0000.000
36A101ASN00.140-0.06031.3510.0070.0070.0000.0000.0000.000
37A101ASN0-0.1280.05330.8040.0070.0070.0000.0000.0000.000
38A102LEU00.002-0.08827.9200.0130.0130.0000.0000.0000.000
39A102LEU0-0.0920.06325.250-0.004-0.0040.0000.0000.0000.000
40A103ILE00.067-0.08829.4430.0060.0060.0000.0000.0000.000
41A103ILE0-0.0970.09228.924-0.003-0.0030.0000.0000.0000.000
42A104LEU00.038-0.12931.0140.0020.0020.0000.0000.0000.000
43A104LEU0-0.0530.11834.2450.0020.0020.0000.0000.0000.000
44A105GLN00.027-0.08632.1900.0090.0090.0000.0000.0000.000
45A105GLN0-0.0730.09330.6710.0010.0010.0000.0000.0000.000
46A106TYR00.012-0.10328.2860.0070.0070.0000.0000.0000.000
47A106TYR0-0.0190.07427.338-0.003-0.0030.0000.0000.0000.000
48A107SER00.150-0.01727.6580.0020.0020.0000.0000.0000.000
49A107SER0-0.0360.06526.167-0.007-0.0070.0000.0000.0000.000
50A108PRO00.093-0.05926.709-0.011-0.0110.0000.0000.0000.000
51A109SER00.0810.04222.965-0.020-0.0200.0000.0000.0000.000
52A109SER0-0.0480.05721.713-0.004-0.0040.0000.0000.0000.000
53A110LYS00.084-0.07622.073-0.035-0.0350.0000.0000.0000.000
54A110LYS10.7701.02823.3760.1630.1630.0000.0000.0000.000
55A111SER00.009-0.12122.698-0.015-0.0150.0000.0000.0000.000
56A111SER0-0.0120.09126.0090.0080.0080.0000.0000.0000.000
57A112LEU00.120-0.08722.0840.0050.0050.0000.0000.0000.000
58A112LEU0-0.0830.11920.589-0.001-0.0010.0000.0000.0000.000
59A113GLN00.081-0.09718.381-0.041-0.0410.0000.0000.0000.000
60A113GLN0-0.0760.08817.7430.0410.0410.0000.0000.0000.000
61A114MET0-0.011-0.13318.181-0.042-0.0420.0000.0000.0000.000
62A114MET0-0.0970.09621.9470.0100.0100.0000.0000.0000.000
63A115ILE00.093-0.08419.565-0.004-0.0040.0000.0000.0000.000
64A115ILE0-0.0650.12120.588-0.001-0.0010.0000.0000.0000.000
65A116LEU00.129-0.09517.0660.0070.0070.0000.0000.0000.000
66A116LEU0-0.1090.10314.924-0.009-0.0090.0000.0000.0000.000
67A117ARG00.106-0.08514.511-0.090-0.0900.0000.0000.0000.000
68A117ARG10.8401.05814.5080.3550.3550.0000.0000.0000.000
69A118ARG00.035-0.09714.810-0.030-0.0300.0000.0000.0000.000
70A118ARG10.7650.97218.3100.2210.2210.0000.0000.0000.000
71A119ALA00.122-0.10516.4090.0070.0070.0000.0000.0000.000
72A119ALA0-0.0920.11917.2400.0000.0000.0000.0000.0000.000
73A120LEU00.067-0.11212.4370.0400.0400.0000.0000.0000.000
74A120LEU0-0.0630.10511.239-0.038-0.0380.0000.0000.0000.000
75A121GLY0-0.035-0.10612.181-0.064-0.0640.0000.0000.0000.000
76A122ASP00.0870.02513.6650.0330.0330.0000.0000.0000.000
77A122ASP-1-0.880-0.78417.558-0.249-0.2490.0000.0000.0000.000
78A123PHE00.106-0.08414.2340.0620.0620.0000.0000.0000.000
79A123PHE0-0.0770.09412.855-0.005-0.0050.0000.0000.0000.000
80A124GLU00.072-0.13110.751-0.022-0.0220.0000.0000.0000.000
81A124GLU-1-0.882-0.7797.601-0.968-0.9680.0000.0000.0000.000
82A125ASN00.132-0.03011.5410.0390.0390.0000.0000.0000.000
83A125ASN0-0.1460.03014.7090.0530.0530.0000.0000.0000.000
84A126MET00.093-0.09214.6170.0500.0500.0000.0000.0000.000
85A126MET0-0.0960.09216.138-0.008-0.0080.0000.0000.0000.000
86A127LEU00.048-0.08711.8030.0460.0460.0000.0000.0000.000
87A127LEU0-0.1110.0649.706-0.045-0.0450.0000.0000.0000.000
88A128ALA00.091-0.10112.9590.0070.0070.0000.0000.0000.000
89A128ALA0-0.1100.09712.5480.0120.0120.0000.0000.0000.000
90A129ASP00.012-0.10813.6280.0520.0520.0000.0000.0000.000
91A129ASP-1-0.811-0.74918.070-0.186-0.1860.0000.0000.0000.000
92A130GLY0-0.043-0.12216.1820.0160.0160.0000.0000.0000.000
93A131SER00.069-0.01717.281-0.017-0.0170.0000.0000.0000.000
94A131SER0-0.0540.05818.811-0.007-0.0070.0000.0000.0000.000
95A132PHE0-0.002-0.12916.4870.0270.0270.0000.0000.0000.000
96A132PHE0-0.0910.10014.932-0.024-0.0240.0000.0000.0000.000
97A133ARG00.073-0.09517.990-0.030-0.0300.0000.0000.0000.000
98A133ARG10.8521.07716.5010.2780.2780.0000.0000.0000.000
99A134ALA00.105-0.09119.967-0.007-0.0070.0000.0000.0000.000
100A134ALA0-0.0540.11423.2970.0060.0060.0000.0000.0000.000
101A135ALA00.011-0.10620.6170.0280.0280.0000.0000.0000.000
102A135ALA0-0.0510.11019.838-0.006-0.0060.0000.0000.0000.000
103A136PRO0-0.006-0.11321.960-0.013-0.0130.0000.0000.0000.000
104A137LYS00.087-0.00520.771-0.032-0.0320.0000.0000.0000.000
105A137LYS10.7381.01919.4380.3580.3580.0000.0000.0000.000
106A138SER00.049-0.05621.411-0.044-0.0440.0000.0000.0000.000
107A138SER0-0.0430.05023.8010.0070.0070.0000.0000.0000.000
108A139TYR00.044-0.09723.7790.0150.0150.0000.0000.0000.000
109A139TYR0-0.1230.06121.352-0.013-0.0130.0000.0000.0000.000
110A140PRO00.025-0.08926.354-0.009-0.0090.0000.0000.0000.000
111A141ILE00.0650.03028.264-0.004-0.0040.0000.0000.0000.000
112A141ILE0-0.0710.07726.127-0.006-0.0060.0000.0000.0000.000
113A142PRO00.023-0.09929.2110.0110.0110.0000.0000.0000.000
114A143HIS00.020-0.00132.039-0.010-0.0100.0000.0000.0000.000
115A143HIS0-0.0840.10031.5190.0060.0060.0000.0000.0000.000
116A144THR00.114-0.06134.8880.0080.0080.0000.0000.0000.000
117A144THR0-0.0450.07035.8010.0030.0030.0000.0000.0000.000
118A145ALA00.126-0.07036.438-0.009-0.0090.0000.0000.0000.000
119A145ALA0-0.0530.10740.3760.0020.0020.0000.0000.0000.000
120A146PHE00.005-0.10938.0030.0000.0000.0000.0000.0000.000
121A146PHE0-0.0690.08838.1170.0010.0010.0000.0000.0000.000
122A147GLU00.008-0.14533.7690.0020.0020.0000.0000.0000.000
123A147GLU-1-0.938-0.82032.679-0.176-0.1760.0000.0000.0000.000
124A148LYS00.140-0.07332.952-0.006-0.0060.0000.0000.0000.000
125A148LYS10.8711.05432.6930.1610.1610.0000.0000.0000.000
126A149SER00.090-0.06529.423-0.007-0.0070.0000.0000.0000.000
127A149SER0-0.0340.09228.096-0.007-0.0070.0000.0000.0000.000
128A150ILE00.052-0.10326.5660.0050.0050.0000.0000.0000.000
129A150ILE0-0.0530.11624.698-0.001-0.0010.0000.0000.0000.000
130A151ILE00.075-0.10522.6540.0040.0040.0000.0000.0000.000
131A151ILE0-0.1120.09520.1960.0000.0000.0000.0000.0000.000
132A152VAL00.125-0.09820.6240.0040.0040.0000.0000.0000.000
133A152VAL0-0.0810.11719.0580.0020.0020.0000.0000.0000.000
134A153GLN00.054-0.12316.778-0.043-0.0430.0000.0000.0000.000
135A153GLN0-0.0580.10716.549-0.059-0.0590.0000.0000.0000.000
136A154THR00.008-0.06014.1890.0930.0930.0000.0000.0000.000
137A154THR0-0.0640.04912.9040.0500.0500.0000.0000.0000.000
138A155SER00.030-0.0799.799-0.079-0.0790.0000.0000.0000.000
139A155SER0-0.0360.0598.7350.0540.0540.0000.0000.0000.000
140A156ARG00.117-0.1008.2170.3450.3450.0000.0000.0000.000
141A156ARG10.7160.9787.7391.0951.0950.0000.0000.0000.000
142A157MET00.078-0.0954.424-0.936-0.909-0.001-0.0540.0290.000
143A157MET0-0.0530.1264.076-0.2950.0600.030-0.130-0.2550.000
144A158PHE00.037-0.1183.0590.8861.4850.017-0.262-0.3540.001
145A158PHE0-0.0140.1163.9380.2100.314-0.001-0.032-0.0710.000
146A159PRO00.046-0.0622.057-3.161-4.8615.289-1.836-1.754-0.021
147A160VAL00.080-0.0143.563-1.951-1.6320.010-0.118-0.2110.000
148A160VAL0-0.0210.1292.885-0.5500.2030.562-0.537-0.7770.007
149A161SER00.098-0.0494.253-0.900-0.8910.000-0.0200.0120.000
150A161SER00.0010.0978.5120.0240.0240.0000.0000.0000.000
151A162LEU00.058-0.1086.832-0.046-0.0460.0000.0000.0000.000
152A162LEU0-0.0710.1147.035-0.023-0.0230.0000.0000.0000.000
153A163ILE00.064-0.0835.9690.2510.2510.0000.0000.0000.000
154A163ILE0-0.0940.0884.611-0.235-0.189-0.001-0.009-0.0350.000
155A164GLU00.120-0.1187.190-0.121-0.1210.0000.0000.0000.000
156A164GLU-1-1.000-0.8348.8670.0380.0380.0000.0000.0000.000
157A165ALA00.074-0.1089.5440.0270.0270.0000.0000.0000.000
158A165ALA0-0.0460.12711.2050.0170.0170.0000.0000.0000.000
159A166ALA00.133-0.07210.4710.1470.1470.0000.0000.0000.000
160A166ALA0-0.1010.07010.035-0.051-0.0510.0000.0000.0000.000
161A167ARG00.031-0.11610.9640.0990.0990.0000.0000.0000.000
162A167ARG10.7370.9768.9341.1731.1730.0000.0000.0000.000
163A168ASN00.062-0.07412.3610.0450.0450.0000.0000.0000.000
164A168ASN0-0.1320.04913.1070.0570.0570.0000.0000.0000.000
165A169HIS00.020-0.10215.1550.0820.0820.0000.0000.0000.000
166A169HIS0-0.0510.07916.1020.0090.0090.0000.0000.0000.000
167A170PHE00.060-0.09415.2560.0750.0750.0000.0000.0000.000
168A170PHE0-0.1010.06713.365-0.002-0.0020.0000.0000.0000.000
169A171ASP00.083-0.09114.6260.0360.0360.0000.0000.0000.000
170A171ASP-1-0.846-0.77713.760-0.734-0.7340.0000.0000.0000.000
171A172PRO00.029-0.08515.963-0.003-0.0030.0000.0000.0000.000
172A173LEU00.022-0.01817.8910.0460.0460.0000.0000.0000.000
173A173LEU0-0.0500.10519.8310.0030.0030.0000.0000.0000.000
174A174GLY00.006-0.08814.9930.0320.0320.0000.0000.0000.000
175A175LEU00.027-0.02816.027-0.001-0.0010.0000.0000.0000.000
176A175LEU0-0.0510.11319.1070.0090.0090.0000.0000.0000.000
177A176GLU00.056-0.11915.4060.0400.0400.0000.0000.0000.000
178A176GLU-1-0.935-0.79814.583-0.572-0.5720.0000.0000.0000.000
179A177THR00.075-0.06713.973-0.107-0.1070.0000.0000.0000.000
180A177THR0-0.0310.07515.334-0.013-0.0130.0000.0000.0000.000
181A178ALA00.139-0.07410.556-0.006-0.0060.0000.0000.0000.000
182A178ALA0-0.0650.1129.660-0.019-0.0190.0000.0000.0000.000
183A179ARG00.123-0.08611.337-0.170-0.1700.0000.0000.0000.000
184A179ARG10.8511.06514.5130.6130.6130.0000.0000.0000.000
185A180ALA00.050-0.12013.699-0.009-0.0090.0000.0000.0000.000
186A180ALA0-0.0680.12316.2200.0190.0190.0000.0000.0000.000
187A181PHE00.089-0.08312.0720.1080.1080.0000.0000.0000.000
188A181PHE0-0.0790.0957.937-0.004-0.0040.0000.0000.0000.000
189A182GLY00.055-0.08511.309-0.018-0.0180.0000.0000.0000.000
190A183HIS00.0850.02411.9960.0290.0290.0000.0000.0000.000
191A183HIS0-0.0840.07516.511-0.004-0.0040.0000.0000.0000.000
192A184LYS00.057-0.09215.6240.0690.0690.0000.0000.0000.000
193A184LYS10.7581.00315.4560.5520.5520.0000.0000.0000.000
194A185LEU00.147-0.05612.3420.1430.1430.0000.0000.0000.000
195A185LEU0-0.1190.0939.340-0.042-0.0420.0000.0000.0000.000
196A186ALA00.102-0.10813.8390.0520.0520.0000.0000.0000.000
197A186ALA0-0.0910.09414.4330.0000.0000.0000.0000.0000.000
198A187THR0-0.039-0.10815.2630.0630.0630.0000.0000.0000.000
199A187THR0-0.0750.04218.4950.0240.0240.0000.0000.0000.000
200A188ALA00.136-0.07017.5450.0690.0690.0000.0000.0000.000
201A188ALA0-0.0270.11416.729-0.004-0.0040.0000.0000.0000.000
202A189ALA00.085-0.09315.6790.0780.0780.0000.0000.0000.000
203A189ALA0-0.0830.10214.826-0.016-0.0160.0000.0000.0000.000
204A190LEU00.079-0.11016.9740.0540.0540.0000.0000.0000.000
205A190LEU0-0.1170.09018.3470.0010.0010.0000.0000.0000.000
206A191ALA00.102-0.10819.9600.0440.0440.0000.0000.0000.000
207A191ALA0-0.0830.10821.443-0.001-0.0010.0000.0000.0000.000
208A192CYS00.060-0.09220.1170.0440.0440.0000.0000.0000.000
209A192CYS0-0.1240.09319.1630.0130.0130.0000.0000.0000.000
210A193PHE00.091-0.07420.7580.0360.0360.0000.0000.0000.000
211A193PHE0-0.0860.07720.252-0.004-0.0040.0000.0000.0000.000
212A194PHE00.044-0.11022.0740.0280.0280.0000.0000.0000.000
213A194PHE0-0.0280.09423.582-0.004-0.0040.0000.0000.0000.000
214A195ALA00.122-0.07424.9120.0240.0240.0000.0000.0000.000
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