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

tag_button

FMODB ID: 2N53R

Calculation Name: 2BDV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BDV

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptHSide
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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2646206.843987
FMO2-HF: Nuclear repulsion 2561997.418907
FMO2-HF: Total energy -84209.42508
FMO2-MP2: Total energy -84458.778254


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: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.
-34.068-20.76819.736-13.108-19.923-0.092
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 : -0.054 / q_NPA : -0.018
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].
3A4ARG10.7790.8873.349-4.606-0.5680.003-2.110-1.9310.005
4A5ILE00.0340.0143.064-0.2470.2381.465-0.429-1.521-0.003
5A6ALA0-0.021-0.0065.584-0.396-0.394-0.001-0.0130.0120.000
6A7GLN0-0.025-0.0188.941-0.065-0.0650.0000.0000.0000.000
7A8LYS10.8590.90811.537-0.134-0.1340.0000.0000.0000.000
8A9SER0-0.021-0.01714.464-0.054-0.0540.0000.0000.0000.000
9A10ALA00.0110.02716.5300.0410.0410.0000.0000.0000.000
10A11PRO00.0240.00217.4350.0140.0140.0000.0000.0000.000
11A12GLU-1-0.882-0.95818.5100.1810.1810.0000.0000.0000.000
12A13ASP-1-0.850-0.93518.0940.1350.1350.0000.0000.0000.000
13A14TYR0-0.084-0.07012.9880.0310.0310.0000.0000.0000.000
14A15VAL00.0440.00816.759-0.005-0.0050.0000.0000.0000.000
15A16GLU-1-0.786-0.84619.6100.0780.0780.0000.0000.0000.000
16A17ILE0-0.009-0.00416.358-0.020-0.0200.0000.0000.0000.000
17A18LEU0-0.016-0.01016.315-0.017-0.0170.0000.0000.0000.000
18A19TRP0-0.032-0.03218.776-0.009-0.0090.0000.0000.0000.000
19A20PRO00.0050.01121.900-0.001-0.0010.0000.0000.0000.000
20A21ASN0-0.094-0.04424.423-0.004-0.0040.0000.0000.0000.000
21A22ALA00.0510.00925.674-0.004-0.0040.0000.0000.0000.000
22A23ARG10.7910.88625.284-0.088-0.0880.0000.0000.0000.000
23A24LEU00.0170.00921.4660.0010.0010.0000.0000.0000.000
24A25ILE0-0.022-0.00325.459-0.003-0.0030.0000.0000.0000.000
25A26PHE0-0.012-0.00822.933-0.001-0.0010.0000.0000.0000.000
26A27ASP-1-0.913-0.96221.3680.2040.2040.0000.0000.0000.000
27A28ASP-1-0.826-0.91419.2580.3670.3670.0000.0000.0000.000
28A29VAL00.0250.02721.447-0.017-0.0170.0000.0000.0000.000
29A30ALA00.0280.01719.322-0.002-0.0020.0000.0000.0000.000
30A31GLY0-0.0100.01020.0950.0030.0030.0000.0000.0000.000
31A32PRO00.0250.03216.3900.0430.0430.0000.0000.0000.000
32A33ARG10.8540.90813.110-0.351-0.3510.0000.0000.0000.000
33A34TYR00.0710.03411.6020.0840.0840.0000.0000.0000.000
34A35ASN00.0400.02510.4860.0640.0640.0000.0000.0000.000
35A36ILE00.0060.0208.329-0.087-0.0870.0000.0000.0000.000
36A37PRO00.0130.0157.5360.4950.4950.0000.0000.0000.000
37A38PRO00.005-0.0116.816-0.043-0.0430.0000.0000.0000.000
38A39GLY0-0.008-0.0059.376-0.144-0.1440.0000.0000.0000.000
39A40THR0-0.034-0.01011.137-0.099-0.0990.0000.0000.0000.000
40A41ARG10.9090.93713.054-0.370-0.3700.0000.0000.0000.000
41A42PRO0-0.0100.0079.121-0.081-0.0810.0000.0000.0000.000
42A43LEU00.0180.00911.854-0.060-0.0600.0000.0000.0000.000
43A44THR0-0.057-0.03811.4030.1310.1310.0000.0000.0000.000
44A45MET0-0.0040.00413.505-0.079-0.0790.0000.0000.0000.000
45A46HIS0-0.025-0.02815.467-0.006-0.0060.0000.0000.0000.000
46A47ARG10.9670.98718.015-0.151-0.1510.0000.0000.0000.000
47A48LEU0-0.060-0.02517.111-0.016-0.0160.0000.0000.0000.000
48A49VAL0-0.066-0.04121.369-0.011-0.0110.0000.0000.0000.000
49A50ASP-1-0.892-0.95124.7640.1360.1360.0000.0000.0000.000
50A51GLN0-0.044-0.02925.048-0.011-0.0110.0000.0000.0000.000
51A52ALA00.0280.03825.701-0.005-0.0050.0000.0000.0000.000
52A53GLU-1-0.912-0.95722.2590.1610.1610.0000.0000.0000.000
53A54ALA0-0.020-0.01220.876-0.007-0.0070.0000.0000.0000.000
54A55LEU00.0170.00016.5600.0340.0340.0000.0000.0000.000
55A56ALA00.0100.01017.468-0.024-0.0240.0000.0000.0000.000
56A57ARG10.8160.89414.676-0.405-0.4050.0000.0000.0000.000
57A58LEU00.0020.00814.325-0.053-0.0530.0000.0000.0000.000
58A59PRO0-0.011-0.00513.4740.0850.0850.0000.0000.0000.000
59A60TRP0-0.0550.0003.643-0.5720.0630.054-0.162-0.5270.000
60A61GLY00.009-0.0139.837-0.009-0.0090.0000.0000.0000.000
61A62TYR0-0.047-0.01610.657-0.128-0.1280.0000.0000.0000.000
62A63LYS10.8900.92312.793-0.294-0.2940.0000.0000.0000.000
63A64PRO0-0.048-0.02015.281-0.036-0.0360.0000.0000.0000.000
64A65HIS00.0450.01018.1710.0020.0020.0000.0000.0000.000
65A66GLY00.0200.02221.730-0.011-0.0110.0000.0000.0000.000
66A67SER0-0.079-0.04719.099-0.016-0.0160.0000.0000.0000.000
67A68SER00.0340.02919.2730.0060.0060.0000.0000.0000.000
68A69PHE0-0.017-0.00614.3590.0160.0160.0000.0000.0000.000
69A70PHE00.0300.01211.3380.0040.0040.0000.0000.0000.000
70A71MET0-0.037-0.01410.0160.1050.1050.0000.0000.0000.000
71A72ILE00.0890.0425.228-0.201-0.061-0.001-0.021-0.1170.000
72A73ASN0-0.0110.0032.4970.7662.0570.820-0.732-1.378-0.001
73A74ALA00.0050.0055.444-0.149-0.1490.0000.0000.0000.000
74A75LYS10.8720.9228.423-0.023-0.0230.0000.0000.0000.000
75A76LEU00.1040.0509.6250.0630.0630.0000.0000.0000.000
76A77GLU-1-0.806-0.89711.454-0.130-0.1300.0000.0000.0000.000
77A78THR0-0.016-0.00513.4550.0240.0240.0000.0000.0000.000
78A79ILE00.0230.02110.7430.0310.0310.0000.0000.0000.000
79A80GLU-1-0.788-0.85915.087-0.070-0.0700.0000.0000.0000.000
80A81ARG10.7860.87717.5370.1300.1300.0000.0000.0000.000
81A82HIS00.0160.01418.5990.0110.0110.0000.0000.0000.000
82A83GLY00.0100.00517.8330.0030.0030.0000.0000.0000.000
83A84TRP0-0.039-0.00217.4290.0220.0220.0000.0000.0000.000
84A85PRO00.0530.00314.199-0.013-0.0130.0000.0000.0000.000
85A86TRP00.1280.01910.6220.0020.0020.0000.0000.0000.000
86A87LYS10.9270.97915.293-0.094-0.0940.0000.0000.0000.000
87A88LEU0-0.031-0.02118.363-0.015-0.0150.0000.0000.0000.000
88A89MET0-0.053-0.01214.4390.0180.0180.0000.0000.0000.000
89A90ILE0-0.0090.01015.1470.0080.0080.0000.0000.0000.000
90A91GLY00.000-0.00817.257-0.014-0.0140.0000.0000.0000.000
91A92THR00.0370.00920.2090.0040.0040.0000.0000.0000.000
92A93GLY00.0260.00816.9010.0060.0060.0000.0000.0000.000
93A94ARG10.8030.90214.687-0.081-0.0810.0000.0000.0000.000
94A95ILE0-0.0110.00111.509-0.018-0.0180.0000.0000.0000.000
95A96LEU00.0300.02311.5500.0100.0100.0000.0000.0000.000
96A97VAL0-0.030-0.0247.6390.0160.0160.0000.0000.0000.000
97A98PRO00.0040.0218.5520.1460.1460.0000.0000.0000.000
98A99ALA00.0230.0106.9830.2290.2290.0000.0000.0000.000
99A100ASP-1-0.710-0.8098.9260.1340.1340.0000.0000.0000.000
100A101GLY0-0.012-0.0157.155-0.191-0.1910.0000.0000.0000.000
101A102TRP0-0.067-0.0462.515-2.564-0.7412.006-1.315-2.513-0.016
102A103TYR0-0.051-0.0394.446-0.449-0.328-0.001-0.019-0.1010.000
103A104GLU-1-0.745-0.8373.984-4.165-3.7830.001-0.080-0.3040.000
104A105TRP0-0.022-0.0285.6120.2930.2930.0000.0000.0000.000
105A106LYS10.8980.9478.9010.6150.6150.0000.0000.0000.000
106A107ALA0-0.015-0.02111.4220.0990.0990.0000.0000.0000.000
107A108LEU0-0.013-0.00613.429-0.017-0.0170.0000.0000.0000.000
108A109ASP-1-0.851-0.92116.906-0.171-0.1710.0000.0000.0000.000
109A110SER0-0.039-0.02517.155-0.020-0.0200.0000.0000.0000.000
110A111GLY00.0340.02419.0560.0110.0110.0000.0000.0000.000
111A112PRO0-0.008-0.02018.428-0.013-0.0130.0000.0000.0000.000
112A113LYS10.9120.95016.8360.0060.0060.0000.0000.0000.000
113A114PRO00.0380.05214.6570.0120.0120.0000.0000.0000.000
114A115ALA00.0100.01115.875-0.001-0.0010.0000.0000.0000.000
115A116LYS10.8600.9278.6790.6430.6430.0000.0000.0000.000
116A117GLN0-0.0060.00013.7650.0740.0740.0000.0000.0000.000
117A118PRO0-0.0060.00710.400-0.135-0.1350.0000.0000.0000.000
118A119TYR00.0440.0139.4940.0970.0970.0000.0000.0000.000
119A120TYR0-0.023-0.0178.612-0.057-0.0570.0000.0000.0000.000
120A121ILE0-0.013-0.0105.9670.1140.1140.0000.0000.0000.000
121A122HIS10.8760.9247.7170.3480.3480.0000.0000.0000.000
122A123GLY00.0930.0499.901-0.076-0.0760.0000.0000.0000.000
123A124ASP-1-0.914-0.94012.480-0.151-0.1510.0000.0000.0000.000
124A125ALA0-0.018-0.01414.2520.0310.0310.0000.0000.0000.000
125A126PRO0-0.038-0.01112.389-0.019-0.0190.0000.0000.0000.000
126A127LEU0-0.024-0.0047.397-0.091-0.0910.0000.0000.0000.000
127A128LEU00.0310.00510.5090.1640.1640.0000.0000.0000.000
128A129PHE0-0.020-0.0124.401-0.3170.2170.041-0.170-0.406-0.001
129A130ALA00.0820.0558.1970.0300.0300.0000.0000.0000.000
130A131GLY00.004-0.0018.1370.1580.1580.0000.0000.0000.000
131A132LEU0-0.039-0.0109.741-0.134-0.1340.0000.0000.0000.000
132A133SER00.0560.02011.5350.0820.0820.0000.0000.0000.000
133A134ALA00.0160.01914.001-0.063-0.0630.0000.0000.0000.000
134A135TRP0-0.032-0.02016.680-0.031-0.0310.0000.0000.0000.000
135A136ARG10.8430.90317.859-0.270-0.2700.0000.0000.0000.000
136A137ARG11.0581.02421.942-0.146-0.1460.0000.0000.0000.000
137A138GLY0-0.046-0.02024.943-0.012-0.0120.0000.0000.0000.000
138A139ALA0-0.0250.00622.201-0.007-0.0070.0000.0000.0000.000
139A140GLU-1-0.885-0.93223.2000.2340.2340.0000.0000.0000.000
140A141LEU0-0.017-0.01818.6650.0260.0260.0000.0000.0000.000
141A142ASP-1-0.751-0.86119.0220.3280.3280.0000.0000.0000.000
142A143GLU-1-0.769-0.89415.6500.3760.3760.0000.0000.0000.000
143A144ALA0-0.056-0.00616.0580.0230.0230.0000.0000.0000.000
144A145HIS10.7770.86117.575-0.308-0.3080.0000.0000.0000.000
145A146GLY00.0560.04013.5740.0090.0090.0000.0000.0000.000
146A147PHE0-0.030-0.0337.648-0.059-0.0590.0000.0000.0000.000
147A148ALA0-0.017-0.0087.3360.1160.1160.0000.0000.0000.000
148A149ILE0-0.003-0.0023.311-1.110-0.2740.143-0.202-0.7760.000
149A150VAL00.007-0.0045.196-0.233-0.231-0.001-0.0030.0020.000
150A151THR0-0.0030.0002.951-0.5520.2000.211-0.247-0.7150.000
151A152ASN0-0.007-0.0175.7290.5950.5950.0000.0000.0000.000
152A153ASP-1-0.784-0.9057.071-0.543-0.5430.0000.0000.0000.000
153A154ALA0-0.0140.0138.035-0.039-0.0390.0000.0000.0000.000
154A155LEU0-0.006-0.0019.7740.0890.0890.0000.0000.0000.000
155A156GLY00.0280.0267.3620.0000.0000.0000.0000.0000.000
156A157GLY0-0.012-0.0065.332-0.629-0.6290.0000.0000.0000.000
157A158MET0-0.046-0.0186.2000.6340.6340.0000.0000.0000.000
158A159VAL0-0.032-0.0168.3230.3950.3950.0000.0000.0000.000
159A160ASP-1-0.844-0.9326.852-0.799-0.7990.0000.0000.0000.000
160A161VAL00.0370.0177.474-0.404-0.4040.0000.0000.0000.000
161A162HIS0-0.053-0.0148.3630.1380.1380.0000.0000.0000.000
162A163ASP-1-0.860-0.9302.028-8.854-9.8235.759-2.436-2.354-0.033
163A164ARG10.8470.9242.694-1.505-0.2880.214-0.488-0.9430.002
164A165ARG10.8640.9231.966-10.225-9.8006.526-3.619-3.331-0.044
165A166PRO0-0.016-0.0062.435-0.7730.0762.416-0.791-2.474-0.001
166A167VAL00.000-0.0104.0010.0270.1680.005-0.051-0.0940.000
167A168ALA00.0060.0107.7530.3500.3500.0000.0000.0000.000
168A169LEU00.0080.0099.612-0.109-0.1090.0000.0000.0000.000
169A170PRO00.0380.01813.2880.0380.0380.0000.0000.0000.000
170A171PRO00.0600.02216.3040.0280.0280.0000.0000.0000.000
171A172GLU-1-0.851-0.91918.0600.0270.0270.0000.0000.0000.000
172A173LEU00.0180.00017.2080.0080.0080.0000.0000.0000.000
173A174ALA0-0.0130.00515.1680.0190.0190.0000.0000.0000.000
174A175ARG10.8310.89316.541-0.040-0.0400.0000.0000.0000.000
175A176GLU-1-0.795-0.86319.8410.0220.0220.0000.0000.0000.000
176A177TRP0-0.043-0.02912.636-0.031-0.0310.0000.0000.0000.000
177A178VAL0-0.0230.00417.2060.0160.0160.0000.0000.0000.000
178A179ASP-1-0.815-0.89018.6280.1060.1060.0000.0000.0000.000
179A180PRO0-0.024-0.01322.354-0.008-0.0080.0000.0000.0000.000
180A181ALA0-0.0190.00023.543-0.008-0.0080.0000.0000.0000.000
181A182THR0-0.057-0.03021.519-0.012-0.0120.0000.0000.0000.000
182A183PRO00.0310.02023.0370.0100.0100.0000.0000.0000.000
183A184VAL00.0410.00820.241-0.003-0.0030.0000.0000.0000.000
184A185ALA0-0.034-0.01820.651-0.007-0.0070.0000.0000.0000.000
185A186ARG10.8340.87321.9730.0030.0030.0000.0000.0000.000
186A187ALA00.0120.00517.653-0.011-0.0110.0000.0000.0000.000
187A188LYS10.8310.89717.078-0.028-0.0280.0000.0000.0000.000
188A189GLU-1-0.910-0.93417.131-0.073-0.0730.0000.0000.0000.000
189A190ILE00.0010.00415.626-0.035-0.0350.0000.0000.0000.000
190A191LEU0-0.0140.00311.835-0.027-0.0270.0000.0000.0000.000
191A192ARG10.7760.86412.6170.0820.0820.0000.0000.0000.000
192A193ALA0-0.041-0.01414.775-0.036-0.0360.0000.0000.0000.000
193A194GLY0-0.018-0.01111.5380.0320.0320.0000.0000.0000.000
194A195LEU0-0.017-0.01711.595-0.024-0.0240.0000.0000.0000.000
195A196PRO00.0120.01711.835-0.131-0.1310.0000.0000.0000.000
196A197GLU-1-0.805-0.92211.904-0.835-0.8350.0000.0000.0000.000
197A198THR0-0.032-0.01612.9140.0100.0100.0000.0000.0000.000
198A199ALA0-0.0350.00013.4910.0590.0590.0000.0000.0000.000
199A200PHE0-0.043-0.0338.814-0.019-0.0190.0000.0000.0000.000
200A201SER00.0130.02112.3430.0190.0190.0000.0000.0000.000
201A202TRP00.004-0.02310.672-0.091-0.0910.0000.0000.0000.000
202A203TYR0-0.026-0.00512.5100.0470.0470.0000.0000.0000.000
203A204PRO0-0.0040.01013.045-0.037-0.0370.0000.0000.0000.000
204A205VAL0-0.030-0.02612.3430.0490.0490.0000.0000.0000.000
205A206ARG10.9710.96414.9150.1280.1280.0000.0000.0000.000
206A207GLN00.0070.02415.9660.0070.0070.0000.0000.0000.000
207A208GLU-1-0.856-0.92216.576-0.029-0.0290.0000.0000.0000.000
208A209VAL00.000-0.01611.2010.0350.0350.0000.0000.0000.000
209A210GLY00.0430.01712.0870.0830.0830.0000.0000.0000.000
210A211SER00.0220.02713.112-0.049-0.0490.0000.0000.0000.000
211A212SER00.008-0.01610.098-0.099-0.0990.0000.0000.0000.000
212A213LYS10.8330.9262.8491.1361.7320.076-0.220-0.4520.000
213A214TYR0-0.014-0.0167.0590.2210.2210.0000.0000.0000.000
214A215GLN0-0.017-0.0029.474-0.045-0.0450.0000.0000.0000.000
215A216LEU00.0080.00911.488-0.010-0.0100.0000.0000.0000.000
216A217PRO0-0.040-0.01313.251-0.033-0.0330.0000.0000.0000.000
217A218ASP-1-0.926-0.95016.0300.0990.0990.0000.0000.0000.000