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: 1YJ3Z

Calculation Name: 2RPZ-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2RPZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WV35

Base Structure: SolutionNMR

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 192
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2119879.024895
FMO2-HF: Nuclear repulsion 2043402.139937
FMO2-HF: Total energy -76476.884958
FMO2-MP2: Total energy -76700.358141


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:39:GLY)


Summations of interaction energy for fragment #1(A:39:GLY)
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.
-161.349-156.63616.739-10.966-10.485-0.119
Interaction energy analysis for fragmet #1(A:39:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.911
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].
3A41SER00.0290.0233.7098.79910.731-0.009-0.913-1.009-0.003
34A72TYR00.0640.0144.4335.1325.228-0.001-0.006-0.0890.000
52A90LEU0-0.054-0.0211.908-15.137-16.6615.300-1.778-1.998-0.022
53A91GLU-1-0.819-0.9502.014-104.329-103.1208.912-5.473-4.648-0.071
54A92ASP-1-0.872-0.9445.150-32.941-32.862-0.001-0.001-0.0770.000
64A102ALA00.0010.0032.594-0.638-0.2770.280-0.247-0.393-0.002
65A103PHE00.0640.0222.983-15.150-13.0650.057-1.224-0.918-0.012
68A106THR0-0.058-0.0372.286-4.937-4.8552.085-1.131-1.036-0.007
69A107ILE0-0.0690.0002.8241.5671.9600.116-0.193-0.317-0.002
4A42GLY00.0540.0205.6291.4931.4930.0000.0000.0000.000
5A43SER0-0.033-0.0129.3372.9152.9150.0000.0000.0000.000
6A44SER0-0.004-0.01110.9222.1622.1620.0000.0000.0000.000
7A45GLY00.0060.0198.425-2.089-2.0890.0000.0000.0000.000
8A46ARG10.8790.9249.38419.56119.5610.0000.0000.0000.000
9A47LEU00.0100.00210.609-0.148-0.1480.0000.0000.0000.000
10A48PRO00.0650.04413.7631.0181.0180.0000.0000.0000.000
11A49VAL00.0220.00417.482-0.110-0.1100.0000.0000.0000.000
12A50ASN0-0.035-0.02020.034-0.292-0.2920.0000.0000.0000.000
13A51PHE00.0430.03112.9450.2470.2470.0000.0000.0000.000
14A52PHE00.0410.01115.3250.1320.1320.0000.0000.0000.000
15A53LYS10.9500.96317.46613.04313.0430.0000.0000.0000.000
16A54PHE0-0.044-0.01919.9560.7450.7450.0000.0000.0000.000
17A55GLN0-0.011-0.00313.1891.2341.2340.0000.0000.0000.000
18A56PHE0-0.039-0.03313.747-0.475-0.4750.0000.0000.0000.000
19A57ARG10.9110.97616.98513.36013.3600.0000.0000.0000.000
20A58ASN00.0230.01316.8201.3841.3840.0000.0000.0000.000
21A59VAL0-0.041-0.00819.550-0.356-0.3560.0000.0000.0000.000
22A60GLU-1-0.842-0.92922.511-11.551-11.5510.0000.0000.0000.000
23A61TYR00.0440.02825.1400.0010.0010.0000.0000.0000.000
24A62SER0-0.020-0.01223.6190.4070.4070.0000.0000.0000.000
25A63SER0-0.018-0.00924.426-0.343-0.3430.0000.0000.0000.000
26A64GLY00.015-0.00323.1360.2950.2950.0000.0000.0000.000
27A65ARG10.8690.94017.98214.82414.8240.0000.0000.0000.000
28A66ASN0-0.015-0.00114.636-0.873-0.8730.0000.0000.0000.000
29A67LYS10.9260.9817.49735.74635.7460.0000.0000.0000.000
30A68THR00.0070.00911.5620.4340.4340.0000.0000.0000.000
31A69PHE00.0080.0076.955-1.614-1.6140.0000.0000.0000.000
32A70LEU0-0.0360.0007.1373.2323.2320.0000.0000.0000.000
33A71CYS0-0.0140.0067.179-5.246-5.2460.0000.0000.0000.000
35A73VAL00.0290.0109.760-0.351-0.3510.0000.0000.0000.000
36A74VAL0-0.035-0.02210.4860.3980.3980.0000.0000.0000.000
37A75GLU-1-0.866-0.92613.173-15.590-15.5900.0000.0000.0000.000
38A76VAL0-0.036-0.00815.2150.4000.4000.0000.0000.0000.000
39A77GLN00.010-0.00317.8510.8730.8730.0000.0000.0000.000
40A78SER00.031-0.00421.6380.1790.1790.0000.0000.0000.000
41A79LYS0-0.026-0.03124.2550.1020.1020.0000.0000.0000.000
42A80GLY0-0.0080.03126.5510.3820.3820.0000.0000.0000.000
43A81GLY00.0440.00226.4180.3870.3870.0000.0000.0000.000
44A82GLN0-0.0030.01519.5760.2060.2060.0000.0000.0000.000
45A83ALA00.009-0.00820.287-0.009-0.0090.0000.0000.0000.000
46A84GLN0-0.035-0.00312.4330.9180.9180.0000.0000.0000.000
47A85ALA00.0540.03115.028-0.355-0.3550.0000.0000.0000.000
48A86THR0-0.046-0.0238.803-0.551-0.5510.0000.0000.0000.000
49A87GLN00.002-0.0169.8791.6481.6480.0000.0000.0000.000
50A88GLY00.0000.0116.864-0.854-0.8540.0000.0000.0000.000
51A89TYR00.0020.0165.5892.7552.7550.0000.0000.0000.000
55A93GLU-1-0.913-0.9516.027-39.113-39.1130.0000.0000.0000.000
56A94HIS0-0.011-0.0168.5671.2051.2050.0000.0000.0000.000
57A95ALA0-0.020-0.01711.9521.8811.8810.0000.0000.0000.000
58A96GLY00.0100.00210.3660.5190.5190.0000.0000.0000.000
59A97ALA0-0.0140.0206.8081.5741.5740.0000.0000.0000.000
60A98HIS10.9370.9647.35723.20223.2020.0000.0000.0000.000
61A99ALA00.0390.0176.009-3.404-3.4040.0000.0000.0000.000
62A100GLU-1-0.799-0.9166.120-32.804-32.8040.0000.0000.0000.000
63A101GLU-1-0.857-0.9347.866-27.312-27.3120.0000.0000.0000.000
66A104PHE00.007-0.0135.5260.8070.8070.0000.0000.0000.000
67A105ASN0-0.062-0.0334.9564.0144.0140.0000.0000.0000.000
70A108LEU0-0.038-0.0236.1344.8464.8460.0000.0000.0000.000
71A109PRO00.0160.0228.4560.8810.8810.0000.0000.0000.000
72A110ALA0-0.018-0.01710.5832.0222.0220.0000.0000.0000.000
73A111PHE00.001-0.02213.022-0.839-0.8390.0000.0000.0000.000
74A112ASP-1-0.857-0.90816.596-14.717-14.7170.0000.0000.0000.000
75A113PRO0-0.041-0.04920.0270.0380.0380.0000.0000.0000.000
76A114ALA0-0.018-0.00122.9620.4110.4110.0000.0000.0000.000
77A115LEU0-0.0140.01520.1120.3540.3540.0000.0000.0000.000
78A116LYS10.8780.94421.17712.34912.3490.0000.0000.0000.000
79A117TYR00.0510.03114.742-0.017-0.0170.0000.0000.0000.000
80A118ASN0-0.011-0.01917.8190.2480.2480.0000.0000.0000.000
81A119VAL0-0.006-0.00312.232-0.847-0.8470.0000.0000.0000.000
82A120THR00.009-0.00313.9171.4651.4650.0000.0000.0000.000
83A121TRP0-0.006-0.0099.586-1.569-1.5690.0000.0000.0000.000
84A122TYR0-0.003-0.00512.1721.7971.7970.0000.0000.0000.000
85A123VAL00.0070.00711.532-1.737-1.7370.0000.0000.0000.000
86A124SER00.0580.02514.1411.5771.5770.0000.0000.0000.000
87A125SER00.0340.01714.9881.2951.2950.0000.0000.0000.000
88A126SER00.004-0.00515.287-0.893-0.8930.0000.0000.0000.000
89A127PRO00.0130.00714.035-0.401-0.4010.0000.0000.0000.000
90A128CYS00.0110.01915.3150.9800.9800.0000.0000.0000.000
91A129ALA00.0890.02416.882-0.625-0.6250.0000.0000.0000.000
92A130ALA00.0320.01215.918-0.051-0.0510.0000.0000.0000.000
93A131CYS0-0.066-0.05412.013-0.739-0.7390.0000.0000.0000.000
94A132ALA00.0270.00913.687-0.724-0.7240.0000.0000.0000.000
95A133ASP-1-0.874-0.93916.284-16.095-16.0950.0000.0000.0000.000
96A134ARG10.8560.90311.31224.26124.2610.0000.0000.0000.000
97A135ILE00.0170.02912.343-0.264-0.2640.0000.0000.0000.000
98A136LEU00.0350.02414.6220.8150.8150.0000.0000.0000.000
99A137LYS10.8940.95416.54616.22816.2280.0000.0000.0000.000
100A138THR0-0.0100.01113.8130.4470.4470.0000.0000.0000.000
101A139LEU00.0380.01016.6290.4930.4930.0000.0000.0000.000
102A140SER00.0250.01219.2010.8450.8450.0000.0000.0000.000
103A141LYS10.7870.90217.10517.81117.8110.0000.0000.0000.000
104A142THR0-0.001-0.00317.9640.6980.6980.0000.0000.0000.000
105A143LYS10.9310.96820.55612.63812.6380.0000.0000.0000.000
106A144ASN0-0.024-0.01420.9250.3890.3890.0000.0000.0000.000
107A145LEU00.0010.02015.082-0.264-0.2640.0000.0000.0000.000
108A146ARG10.8280.89718.67614.32414.3240.0000.0000.0000.000
109A147LEU00.0350.03413.480-0.312-0.3120.0000.0000.0000.000
110A148LEU0-0.071-0.02216.3901.3031.3030.0000.0000.0000.000
111A149ILE00.0280.00314.208-1.456-1.4560.0000.0000.0000.000
112A150LEU0-0.060-0.01215.9831.3961.3960.0000.0000.0000.000
113A151VAL00.0100.00316.314-1.165-1.1650.0000.0000.0000.000
114A152SER0-0.0220.00018.4390.5470.5470.0000.0000.0000.000
115A153ARG10.8540.91619.95313.82113.8210.0000.0000.0000.000
116A154LEU0-0.045-0.00520.262-0.787-0.7870.0000.0000.0000.000
117A155PHE0-0.005-0.01517.8390.3040.3040.0000.0000.0000.000
118A156MET0-0.029-0.00819.491-0.403-0.4030.0000.0000.0000.000
119A157TRP00.0470.00122.951-0.143-0.1430.0000.0000.0000.000
120A158GLU-1-0.886-0.94324.916-10.969-10.9690.0000.0000.0000.000
121A159GLU-1-0.884-0.94324.293-12.049-12.0490.0000.0000.0000.000
122A160PRO00.012-0.00826.928-0.190-0.1900.0000.0000.0000.000
123A161GLU-1-0.961-0.98222.537-14.009-14.0090.0000.0000.0000.000
124A162VAL00.016-0.00421.116-0.412-0.4120.0000.0000.0000.000
125A163GLN00.0110.02123.424-0.077-0.0770.0000.0000.0000.000
126A164ALA0-0.011-0.00725.785-0.050-0.0500.0000.0000.0000.000
127A165ALA0-0.057-0.02320.481-0.129-0.1290.0000.0000.0000.000
128A166LEU00.0360.00518.930-0.616-0.6160.0000.0000.0000.000
129A167LYS10.8850.94421.76511.07311.0730.0000.0000.0000.000
130A168LYS10.9440.97021.95113.79813.7980.0000.0000.0000.000
131A169LEU0-0.029-0.00117.247-0.040-0.0400.0000.0000.0000.000
132A170LYS10.9320.97021.23411.10111.1010.0000.0000.0000.000
133A171GLU-1-0.903-0.94724.526-10.865-10.8650.0000.0000.0000.000
134A172ALA0-0.0150.00321.7340.3010.3010.0000.0000.0000.000
135A173GLY0-0.0010.00623.109-0.149-0.1490.0000.0000.0000.000
136A174CYS0-0.068-0.02318.041-0.437-0.4370.0000.0000.0000.000
137A175LYS10.8710.94419.86414.27914.2790.0000.0000.0000.000
138A176LEU00.0760.04018.881-0.915-0.9150.0000.0000.0000.000
139A177ARG10.9190.94420.71915.35015.3500.0000.0000.0000.000
140A178ILE00.0550.04220.928-0.836-0.8360.0000.0000.0000.000
141A179MET0-0.091-0.04817.0490.5100.5100.0000.0000.0000.000
142A180LYS10.9370.98720.82313.04713.0470.0000.0000.0000.000
143A181PRO00.0440.01322.815-0.545-0.5450.0000.0000.0000.000
144A182GLN00.0330.00724.734-0.061-0.0610.0000.0000.0000.000
145A183ASP-1-0.824-0.92819.902-15.244-15.2440.0000.0000.0000.000
146A184PHE0-0.001-0.02117.995-0.856-0.8560.0000.0000.0000.000
147A185GLU-1-0.947-0.95220.045-12.845-12.8450.0000.0000.0000.000
148A186TYR00.0560.02716.214-0.446-0.4460.0000.0000.0000.000
149A187ILE0-0.056-0.04614.324-0.975-0.9750.0000.0000.0000.000
150A188TRP0-0.052-0.03716.588-0.937-0.9370.0000.0000.0000.000
151A189GLN0-0.037-0.01219.3690.2140.2140.0000.0000.0000.000
152A190ASN0-0.0160.00416.6640.5750.5750.0000.0000.0000.000
153A191PHE0-0.043-0.03310.239-0.860-0.8600.0000.0000.0000.000
154A192VAL0-0.036-0.00913.695-1.411-1.4110.0000.0000.0000.000
155A193GLU-1-0.856-0.90416.488-17.393-17.3930.0000.0000.0000.000
156A194GLN00.037-0.00118.8310.4210.4210.0000.0000.0000.000
157A195GLU-1-0.914-0.95922.504-12.983-12.9830.0000.0000.0000.000
158A196GLU-1-0.932-0.95725.113-11.389-11.3890.0000.0000.0000.000
159A197GLY0-0.030-0.00927.0340.3600.3600.0000.0000.0000.000
160A198GLU-1-0.950-0.97027.998-9.937-9.9370.0000.0000.0000.000
161A199SER0-0.031-0.01327.005-0.378-0.3780.0000.0000.0000.000
162A200LYS10.8410.90026.16011.34011.3400.0000.0000.0000.000
163A201ALA00.1010.04925.604-0.370-0.3700.0000.0000.0000.000
164A202PHE0-0.045-0.01823.0050.1020.1020.0000.0000.0000.000
165A203GLU-1-0.896-0.94525.113-10.173-10.1730.0000.0000.0000.000
166A204PRO0-0.054-0.02826.4720.1670.1670.0000.0000.0000.000
167A205TRP0-0.042-0.04028.5420.3170.3170.0000.0000.0000.000
168A206GLU-1-0.995-0.97029.248-10.510-10.5100.0000.0000.0000.000
169A207ASP-1-0.796-0.91430.584-9.288-9.2880.0000.0000.0000.000
170A208ILE0-0.064-0.02929.047-0.504-0.5040.0000.0000.0000.000
171A209GLN0-0.021-0.01729.272-0.437-0.4370.0000.0000.0000.000
172A210GLU-1-0.841-0.91131.334-9.400-9.4000.0000.0000.0000.000
173A211ASN0-0.032-0.03326.415-0.446-0.4460.0000.0000.0000.000
174A212PHE00.0030.00925.607-0.447-0.4470.0000.0000.0000.000
175A213LEU00.0460.00328.070-0.191-0.1910.0000.0000.0000.000
176A214TYR00.0070.01927.811-0.048-0.0480.0000.0000.0000.000
177A215TYR00.0840.03324.927-0.145-0.1450.0000.0000.0000.000
178A216GLU-1-0.950-0.97726.591-10.889-10.8890.0000.0000.0000.000
179A217GLU-1-0.880-0.92528.027-9.716-9.7160.0000.0000.0000.000
180A218LYS10.7810.88626.44910.37110.3710.0000.0000.0000.000
181A219LEU0-0.022-0.00822.541-0.299-0.2990.0000.0000.0000.000
182A220ALA0-0.040-0.03325.578-0.003-0.0030.0000.0000.0000.000
183A221ASP-1-0.872-0.94328.847-10.368-10.3680.0000.0000.0000.000
184A222ILE0-0.0050.02024.5980.1040.1040.0000.0000.0000.000
185A223LEU0-0.118-0.06925.1650.0370.0370.0000.0000.0000.000
186A224LYS10.8280.91929.0419.8549.8540.0000.0000.0000.000
187A225SER00.0750.05232.2890.0490.0490.0000.0000.0000.000
188A226GLY00.0170.00633.8470.1930.1930.0000.0000.0000.000
189A227PRO0-0.033-0.01537.582-0.083-0.0830.0000.0000.0000.000
190A228SER0-0.008-0.01338.8000.0380.0380.0000.0000.0000.000
191A229SER0-0.074-0.05741.2130.1030.1030.0000.0000.0000.000
192A230GLY-1-0.907-0.92144.217-6.877-6.8770.0000.0000.0000.000