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: KKNR3

Calculation Name: 2BDV-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BDV

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2025-10-03

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 217
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2647177.679602
FMO2-HF: Nuclear repulsion 2562968.655111
FMO2-HF: Total energy -84209.024492
FMO2-MP2: Total energy -84458.311617


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:2:CYS)


Summations of interaction energy for fragment #1(A:2:CYS)
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.
-79.771-65.74729.905-20.201-23.726-0.109
Interaction energy analysis for fragmet #1(A:2:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.109 / q_NPA : -0.051
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].
3A4ARG10.7680.8633.551-12.716-7.0170.201-3.160-2.7410.021
4A5ILE00.0350.0253.3295.8026.8160.585-0.417-1.1820.001
5A6ALA0-0.0090.0025.684-3.601-3.618-0.001-0.0080.0260.000
59A60TRP0-0.043-0.0053.680-1.084-0.0620.241-0.485-0.7790.006
71A72ILE00.0810.0374.5850.6000.761-0.001-0.027-0.1330.000
72A73ASN0-0.052-0.0342.276-12.683-10.1151.580-1.739-2.408-0.020
73A74ALA00.0220.0175.3210.7350.825-0.001-0.006-0.0820.000
101A102TRP0-0.042-0.0362.9673.3893.8912.935-1.174-2.2620.007
102A103TYR0-0.048-0.0404.720-6.577-6.3290.001-0.131-0.1180.001
103A104GLU-1-0.760-0.8454.023-5.541-5.1880.001-0.074-0.2800.000
128A129PHE0-0.008-0.0054.6140.5960.9620.027-0.092-0.3010.000
148A149ILE00.0210.0153.257-1.981-0.8100.175-0.404-0.9410.004
150A151THR0-0.015-0.0192.539-0.3080.4680.708-0.410-1.074-0.001
162A163ASP-1-0.801-0.8871.797-55.133-57.72311.158-5.086-3.481-0.067
163A164ARG10.8150.9142.60227.02928.4440.293-0.620-1.088-0.002
164A165ARG10.8750.9261.807-24.597-25.1619.631-5.302-3.766-0.064
165A166PRO0-0.0070.0032.233-6.856-5.5272.355-0.941-2.7430.005
166A167VAL00.001-0.0093.767-0.378-0.2170.011-0.045-0.1270.000
212A213LYS10.8520.9343.30517.60717.9270.006-0.080-0.2460.000
6A7GLN0-0.040-0.0289.227-0.109-0.1090.0000.0000.0000.000
7A8LYS10.8280.90411.844-4.691-4.6910.0000.0000.0000.000
8A9SER00.003-0.01314.727-0.518-0.5180.0000.0000.0000.000
9A10ALA0-0.0090.01916.7650.1270.1270.0000.0000.0000.000
10A11PRO0-0.073-0.03617.6050.2270.2270.0000.0000.0000.000
11A12GLU-1-0.784-0.91218.6831.9841.9840.0000.0000.0000.000
12A13ASP-1-0.863-0.93218.1912.1712.1710.0000.0000.0000.000
13A14TYR0-0.075-0.07113.1270.1840.1840.0000.0000.0000.000
14A15VAL00.0270.00716.739-0.040-0.0400.0000.0000.0000.000
15A16GLU-1-0.800-0.86519.7171.2521.2520.0000.0000.0000.000
16A17ILE0-0.011-0.00416.499-0.122-0.1220.0000.0000.0000.000
17A18LEU0-0.009-0.01116.406-0.114-0.1140.0000.0000.0000.000
18A19TRP0-0.019-0.02218.674-0.144-0.1440.0000.0000.0000.000
19A20PRO00.0280.02022.116-0.039-0.0390.0000.0000.0000.000
20A21ASN0-0.074-0.04124.508-0.100-0.1000.0000.0000.0000.000
21A22ALA00.0130.03623.867-0.080-0.0800.0000.0000.0000.000
22A23ARG10.8480.87825.068-1.235-1.2350.0000.0000.0000.000
23A24LEU0-0.049-0.02427.120-0.007-0.0070.0000.0000.0000.000
24A25ILE00.0130.03121.404-0.021-0.0210.0000.0000.0000.000
25A26PHE0-0.037-0.02121.762-0.089-0.0890.0000.0000.0000.000
26A27ASP-1-0.829-0.92421.4921.9731.9730.0000.0000.0000.000
27A28ASP-1-0.809-0.89618.6022.4162.4160.0000.0000.0000.000
28A29VAL00.0430.01420.763-0.031-0.0310.0000.0000.0000.000
29A30ALA0-0.033-0.00518.637-0.099-0.0990.0000.0000.0000.000
30A31GLY00.0370.03420.107-0.031-0.0310.0000.0000.0000.000
31A32PRO00.0200.02216.5250.2200.2200.0000.0000.0000.000
32A33ARG10.8300.89013.127-2.703-2.7030.0000.0000.0000.000
33A34TYR00.0680.03212.1080.6710.6710.0000.0000.0000.000
34A35ASN00.0570.04010.2251.2011.2010.0000.0000.0000.000
35A36ILE00.0030.0198.411-1.110-1.1100.0000.0000.0000.000
36A37PRO00.0310.0167.5782.5872.5870.0000.0000.0000.000
37A38PRO0-0.003-0.0036.981-0.131-0.1310.0000.0000.0000.000
38A39GLY0-0.0080.0019.578-0.450-0.4500.0000.0000.0000.000
39A40THR0-0.034-0.02010.996-0.060-0.0600.0000.0000.0000.000
40A41ARG10.9110.94013.089-1.556-1.5560.0000.0000.0000.000
41A42PRO00.0010.0099.122-0.191-0.1910.0000.0000.0000.000
42A43LEU0-0.013-0.00511.856-0.583-0.5830.0000.0000.0000.000
43A44THR0-0.044-0.03211.5590.7860.7860.0000.0000.0000.000
44A45MET0-0.0020.01213.584-0.472-0.4720.0000.0000.0000.000
45A46HIS0-0.018-0.02215.595-0.052-0.0520.0000.0000.0000.000
46A47ARG10.9520.97818.017-1.037-1.0370.0000.0000.0000.000
47A48LEU0-0.059-0.02617.065-0.154-0.1540.0000.0000.0000.000
48A49VAL0-0.055-0.03921.381-0.120-0.1200.0000.0000.0000.000
49A50ASP-1-0.909-0.95724.8780.6460.6460.0000.0000.0000.000
50A51GLN0-0.035-0.02025.146-0.007-0.0070.0000.0000.0000.000
51A52ALA00.0220.03225.6640.0360.0360.0000.0000.0000.000
52A53GLU-1-0.915-0.96122.5251.1311.1310.0000.0000.0000.000
53A54ALA0-0.0130.00020.999-0.030-0.0300.0000.0000.0000.000
54A55LEU00.0240.00216.3930.2640.2640.0000.0000.0000.000
55A56ALA0-0.004-0.00817.354-0.224-0.2240.0000.0000.0000.000
56A57ARG10.7930.87414.253-2.796-2.7960.0000.0000.0000.000
57A58LEU00.0040.01414.470-0.415-0.4150.0000.0000.0000.000
58A59PRO0-0.025-0.01213.6730.4860.4860.0000.0000.0000.000
60A61GLY00.000-0.0149.776-0.363-0.3630.0000.0000.0000.000
61A62TYR0-0.032-0.01010.572-0.021-0.0210.0000.0000.0000.000
62A63LYS10.8950.93412.903-0.312-0.3120.0000.0000.0000.000
63A64PRO0-0.049-0.01615.0370.1780.1780.0000.0000.0000.000
64A65HIS00.0410.00117.999-0.042-0.0420.0000.0000.0000.000
65A66GLY00.0200.02421.3490.0230.0230.0000.0000.0000.000
66A67SER0-0.058-0.04318.475-0.150-0.1500.0000.0000.0000.000
67A68SER00.0200.02618.6720.0820.0820.0000.0000.0000.000
68A69PHE0-0.018-0.01113.419-0.180-0.1800.0000.0000.0000.000
69A70PHE00.0210.00311.1550.3000.3000.0000.0000.0000.000
70A71MET0-0.040-0.0169.324-0.721-0.7210.0000.0000.0000.000
74A75LYS10.8720.9297.9856.2606.2600.0000.0000.0000.000
75A76LEU00.0860.0368.8441.0671.0670.0000.0000.0000.000
76A77GLU-1-0.820-0.90111.055-1.851-1.8510.0000.0000.0000.000
77A78THR0-0.028-0.02012.6040.1780.1780.0000.0000.0000.000
78A79ILE00.0120.01310.5380.3970.3970.0000.0000.0000.000
79A80GLU-1-0.808-0.88114.959-0.633-0.6330.0000.0000.0000.000
80A81ARG10.8320.89117.2561.8051.8050.0000.0000.0000.000
81A82HIS00.0200.02418.5300.0250.0250.0000.0000.0000.000
82A83GLY00.0300.02117.4730.0920.0920.0000.0000.0000.000
83A84TRP0-0.025-0.01016.7110.1150.1150.0000.0000.0000.000
84A85PRO00.0380.00913.919-0.280-0.2800.0000.0000.0000.000
85A86TRP00.0900.00810.4610.3600.3600.0000.0000.0000.000
86A87LYS10.9580.98915.2801.1141.1140.0000.0000.0000.000
87A88LEU0-0.038-0.01918.5250.1220.1220.0000.0000.0000.000
88A89MET0-0.077-0.02314.5830.1770.1770.0000.0000.0000.000
89A90ILE00.0160.01515.1920.1790.1790.0000.0000.0000.000
90A91GLY0-0.0090.00317.1800.0950.0950.0000.0000.0000.000
91A92THR00.0380.01020.5490.0820.0820.0000.0000.0000.000
92A93GLY00.0320.00917.0510.0610.0610.0000.0000.0000.000
93A94ARG10.7960.89514.695-0.499-0.4990.0000.0000.0000.000
94A95ILE0-0.013-0.00310.903-0.021-0.0210.0000.0000.0000.000
95A96LEU00.0240.02411.712-0.002-0.0020.0000.0000.0000.000
96A97VAL0-0.021-0.0167.714-0.222-0.2220.0000.0000.0000.000
97A98PRO00.0080.0268.8801.2561.2560.0000.0000.0000.000
98A99ALA00.0120.0077.1831.0321.0320.0000.0000.0000.000
99A100ASP-1-0.719-0.8149.0724.0364.0360.0000.0000.0000.000
100A101GLY0-0.006-0.0057.839-1.492-1.4920.0000.0000.0000.000
104A105TRP0-0.014-0.0145.6760.6550.6550.0000.0000.0000.000
105A106LYS10.9120.9709.1080.8940.8940.0000.0000.0000.000
106A107ALA0-0.013-0.01411.6180.3500.3500.0000.0000.0000.000
107A108LEU0-0.027-0.01213.9100.1020.1020.0000.0000.0000.000
108A109ASP-1-0.817-0.90517.558-1.094-1.0940.0000.0000.0000.000
109A110SER0-0.040-0.02517.510-0.278-0.2780.0000.0000.0000.000
110A111GLY00.0320.02219.4120.1360.1360.0000.0000.0000.000
111A112PRO0-0.026-0.02418.514-0.204-0.2040.0000.0000.0000.000
112A113LYS10.9230.94917.1381.1411.1410.0000.0000.0000.000
113A114PRO00.0180.04515.3020.1320.1320.0000.0000.0000.000
114A115ALA00.0280.01016.458-0.040-0.0400.0000.0000.0000.000
115A116LYS10.8920.9339.7553.7153.7150.0000.0000.0000.000
116A117GLN0-0.030-0.00714.0640.1830.1830.0000.0000.0000.000
117A118PRO00.0090.01610.343-0.338-0.3380.0000.0000.0000.000
118A119TYR00.023-0.0019.5980.0510.0510.0000.0000.0000.000
119A120TYR0-0.022-0.0158.7210.1410.1410.0000.0000.0000.000
120A121ILE0-0.020-0.0166.391-1.501-1.5010.0000.0000.0000.000
121A122HIS10.8920.9388.555-1.127-1.1270.0000.0000.0000.000
122A123GLY00.0940.04510.959-0.676-0.6760.0000.0000.0000.000
123A124ASP-1-0.935-0.95413.3361.9501.9500.0000.0000.0000.000
124A125ALA0-0.012-0.00415.293-0.237-0.2370.0000.0000.0000.000
125A126PRO0-0.037-0.01312.8200.5020.5020.0000.0000.0000.000
126A127LEU0-0.0220.0017.982-0.360-0.3600.0000.0000.0000.000
127A128LEU00.0430.01110.8650.4680.4680.0000.0000.0000.000
129A130ALA00.0640.0408.548-0.590-0.5900.0000.0000.0000.000
130A131GLY00.0030.0007.8760.7080.7080.0000.0000.0000.000
131A132LEU0-0.051-0.0189.547-0.562-0.5620.0000.0000.0000.000
132A133SER00.0430.01011.448-0.070-0.0700.0000.0000.0000.000
133A134ALA00.0170.01814.034-0.191-0.1910.0000.0000.0000.000
134A135TRP0-0.025-0.00916.694-0.047-0.0470.0000.0000.0000.000
135A136ARG10.8540.91017.922-0.528-0.5280.0000.0000.0000.000
136A137ARG11.0341.01821.979-0.508-0.5080.0000.0000.0000.000
137A138GLY0-0.028-0.01525.030-0.077-0.0770.0000.0000.0000.000
138A139ALA0-0.0290.00322.085-0.067-0.0670.0000.0000.0000.000
139A140GLU-1-0.887-0.93123.3080.5770.5770.0000.0000.0000.000
140A141LEU0-0.018-0.01318.6990.0190.0190.0000.0000.0000.000
141A142ASP-1-0.769-0.88019.0750.5180.5180.0000.0000.0000.000
142A143GLU-1-0.771-0.90315.5260.3090.3090.0000.0000.0000.000
143A144ALA0-0.055-0.00715.955-0.130-0.1300.0000.0000.0000.000
144A145HIS10.8020.88017.843-0.462-0.4620.0000.0000.0000.000
145A146GLY00.0480.03413.7470.2350.2350.0000.0000.0000.000
146A147PHE0-0.019-0.0237.667-0.435-0.4350.0000.0000.0000.000
147A148ALA0-0.012-0.0047.433-0.019-0.0190.0000.0000.0000.000
149A150VAL00.001-0.0055.251-4.260-4.2600.0000.0000.0000.000
151A152ASN00.0170.0015.6780.5180.5180.0000.0000.0000.000
152A153ASP-1-0.775-0.8966.592-11.408-11.4080.0000.0000.0000.000
153A154ALA0-0.0270.0007.7010.1790.1790.0000.0000.0000.000
154A155LEU0-0.011-0.0029.4910.6350.6350.0000.0000.0000.000
155A156GLY00.0320.0317.4820.5160.5160.0000.0000.0000.000
156A157GLY0-0.007-0.0045.366-1.757-1.7570.0000.0000.0000.000
157A158MET0-0.027-0.0116.2701.4411.4410.0000.0000.0000.000
158A159VAL0-0.048-0.0248.5230.5450.5450.0000.0000.0000.000
159A160ASP-1-0.902-0.9657.060-6.625-6.6250.0000.0000.0000.000
160A161VAL00.0240.0107.565-1.971-1.9710.0000.0000.0000.000
161A162HIS0-0.053-0.0238.2510.5750.5750.0000.0000.0000.000
167A168ALA0-0.0050.0107.5720.9950.9950.0000.0000.0000.000
168A169LEU00.0020.0009.399-0.983-0.9830.0000.0000.0000.000
169A170PRO00.0430.02212.9970.3210.3210.0000.0000.0000.000
170A171PRO00.0470.01716.386-0.039-0.0390.0000.0000.0000.000
171A172GLU-1-0.920-0.95718.1931.2091.2090.0000.0000.0000.000
172A173LEU00.0220.00217.040-0.094-0.0940.0000.0000.0000.000
173A174ALA0-0.0040.00315.377-0.034-0.0340.0000.0000.0000.000
174A175ARG10.8710.92616.659-1.477-1.4770.0000.0000.0000.000
175A176GLU-1-0.798-0.86120.1650.4890.4890.0000.0000.0000.000
176A177TRP0-0.042-0.03012.528-0.382-0.3820.0000.0000.0000.000
177A178VAL0-0.027-0.01017.080-0.076-0.0760.0000.0000.0000.000
178A179ASP-1-0.826-0.89718.3770.6890.6890.0000.0000.0000.000
179A180PRO0-0.022-0.00821.833-0.080-0.0800.0000.0000.0000.000
180A181ALA0-0.015-0.00323.168-0.102-0.1020.0000.0000.0000.000
181A182THR0-0.042-0.01821.294-0.109-0.1090.0000.0000.0000.000
182A183PRO00.0150.01122.898-0.021-0.0210.0000.0000.0000.000
183A184VAL00.018-0.01020.080-0.005-0.0050.0000.0000.0000.000
184A185ALA0-0.022-0.01120.459-0.061-0.0610.0000.0000.0000.000
185A186ARG10.8420.87421.440-0.392-0.3920.0000.0000.0000.000
186A187ALA00.0290.01517.5270.0400.0400.0000.0000.0000.000
187A188LYS10.8390.91216.7650.7070.7070.0000.0000.0000.000
188A189GLU-1-0.921-0.94317.176-0.107-0.1070.0000.0000.0000.000
189A190ILE0-0.0020.00015.541-0.037-0.0370.0000.0000.0000.000
190A191LEU0-0.037-0.00811.3940.0990.0990.0000.0000.0000.000
191A192ARG10.8020.87212.3680.5840.5840.0000.0000.0000.000
192A193ALA0-0.035-0.00414.500-0.087-0.0870.0000.0000.0000.000
193A194GLY0-0.001-0.00411.5860.3010.3010.0000.0000.0000.000
194A195LEU0-0.016-0.01211.558-0.302-0.3020.0000.0000.0000.000
195A196PRO00.0080.01311.684-0.178-0.1780.0000.0000.0000.000
196A197GLU-1-0.826-0.92712.061-0.785-0.7850.0000.0000.0000.000
197A198THR0-0.010-0.01613.0620.1890.1890.0000.0000.0000.000
198A199ALA0-0.0340.00514.027-0.006-0.0060.0000.0000.0000.000
199A200PHE0-0.036-0.0259.8030.6630.6630.0000.0000.0000.000
200A201SER00.0160.01213.440-0.446-0.4460.0000.0000.0000.000
201A202TRP00.009-0.01311.5070.6840.6840.0000.0000.0000.000
202A203TYR0-0.029-0.00913.209-0.320-0.3200.0000.0000.0000.000
203A204PRO0-0.0060.01113.2860.2910.2910.0000.0000.0000.000
204A205VAL0-0.024-0.02512.2920.0730.0730.0000.0000.0000.000
205A206ARG10.9480.95314.967-0.968-0.9680.0000.0000.0000.000
206A207GLN00.0080.02416.3230.1580.1580.0000.0000.0000.000
207A208GLU-1-0.844-0.92716.2590.7670.7670.0000.0000.0000.000
208A209VAL0-0.0010.00011.3930.2370.2370.0000.0000.0000.000
209A210GLY00.0690.04612.1310.2050.2050.0000.0000.0000.000
210A211SER00.0130.00213.058-0.007-0.0070.0000.0000.0000.000
211A212SER0-0.001-0.02510.255-0.545-0.5450.0000.0000.0000.000
213A214TYR0-0.009-0.0107.4911.1611.1610.0000.0000.0000.000
214A215GLN0-0.033-0.0029.841-0.031-0.0310.0000.0000.0000.000
215A216LEU00.0110.00611.9290.3450.3450.0000.0000.0000.000
216A217PRO0-0.067-0.03513.727-0.236-0.2360.0000.0000.0000.000
217A218ASP-2-1.861-1.91316.4220.9480.9480.0000.0000.0000.000