FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: YVN22

Calculation Name: 3IBT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IBT

Chain ID: A

ChEMBL ID:

UniProt ID: O33472

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptH
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 263
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3876842.868055
FMO2-HF: Nuclear repulsion 3769587.486797
FMO2-HF: Total energy -107255.381257
FMO2-MP2: Total energy -107566.681121


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-23.107-16.38211.338-7.803-10.261-0.031
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : -0.003
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].
3A3SER00.0330.0192.903-3.730-1.1750.285-1.325-1.514-0.004
4A4LEU00.0190.0385.5100.6630.6630.0000.0000.0000.000
5A5ASN0-0.060-0.0368.601-0.087-0.0870.0000.0000.0000.000
6A6VAL0-0.0250.00011.0560.0780.0780.0000.0000.0000.000
7A7ASN0-0.045-0.03013.9070.0480.0480.0000.0000.0000.000
8A8GLY00.0520.02417.148-0.028-0.0280.0000.0000.0000.000
9A9THR0-0.025-0.00812.8360.0310.0310.0000.0000.0000.000
10A10LEU0-0.037-0.0096.519-0.076-0.0760.0000.0000.0000.000
11A11MET00.0250.0307.3100.3260.3260.0000.0000.0000.000
12A12THR0-0.071-0.0682.122-1.509-0.6580.945-0.729-1.0680.000
13A13TYR0-0.038-0.0232.7480.1851.7860.380-0.750-1.231-0.001
14A14SER00.0340.0102.039-8.498-7.9967.062-3.863-3.701-0.040
15A15GLU-1-0.847-0.9133.569-2.041-1.9310.0250.025-0.1600.000
16A16SER0-0.083-0.0486.4830.2910.2910.0000.0000.0000.000
17A17GLY00.0610.0328.775-0.036-0.0360.0000.0000.0000.000
18A18ASP-1-0.928-0.96112.088-0.043-0.0430.0000.0000.0000.000
19A19PRO0-0.008-0.01813.0410.0160.0160.0000.0000.0000.000
20A20HIS0-0.049-0.01714.408-0.008-0.0080.0000.0000.0000.000
21A21ALA00.0390.02117.1470.0150.0150.0000.0000.0000.000
22A22PRO0-0.014-0.00717.563-0.014-0.0140.0000.0000.0000.000
23A23THR00.0500.03213.3160.0450.0450.0000.0000.0000.000
24A24LEU0-0.036-0.02214.192-0.023-0.0230.0000.0000.0000.000
25A25PHE00.0050.00610.3870.1050.1050.0000.0000.0000.000
26A26LEU0-0.034-0.03510.697-0.027-0.0270.0000.0000.0000.000
27A27LEU00.0210.00510.9270.2050.2050.0000.0000.0000.000
28A28SER00.021-0.02511.801-0.045-0.0450.0000.0000.0000.000
29A29GLY00.0200.01313.708-0.127-0.1270.0000.0000.0000.000
30A30TRP00.0700.03314.7130.0800.0800.0000.0000.0000.000
31A31CYS0-0.051-0.01715.1380.0100.0100.0000.0000.0000.000
32A32GLN00.006-0.00113.3370.0360.0360.0000.0000.0000.000
33A33ASP-1-0.724-0.8617.7983.2343.2340.0000.0000.0000.000
34A34HIS10.9210.9762.753-13.381-12.4832.642-1.145-2.3960.014
35A35ARG10.8270.9035.746-2.237-2.2370.0000.0000.0000.000
36A36LEU0-0.0210.0057.408-0.412-0.4120.0000.0000.0000.000
37A37PHE0-0.013-0.0288.581-0.291-0.2910.0000.0000.0000.000
38A38LYS10.8890.9606.996-1.072-1.0720.0000.0000.0000.000
39A39ASN0-0.064-0.0417.917-0.073-0.0730.0000.0000.0000.000
40A40LEU00.0160.00311.249-0.083-0.0830.0000.0000.0000.000
41A41ALA00.0320.0107.896-0.118-0.1180.0000.0000.0000.000
42A42PRO0-0.013-0.0098.007-0.128-0.1280.0000.0000.0000.000
43A43LEU0-0.037-0.01010.344-0.135-0.1350.0000.0000.0000.000
44A44LEU0-0.027-0.01813.205-0.088-0.0880.0000.0000.0000.000
45A45ALA00.0310.02010.823-0.045-0.0450.0000.0000.0000.000
46A46ARG10.7670.89212.931-0.346-0.3460.0000.0000.0000.000
47A47ASP-1-0.787-0.89816.4510.2330.2330.0000.0000.0000.000
48A48PHE00.003-0.00215.330-0.042-0.0420.0000.0000.0000.000
49A49HIS0-0.064-0.01210.4560.0800.0800.0000.0000.0000.000
50A50VAL00.012-0.0239.747-0.011-0.0110.0000.0000.0000.000
51A51ILE0-0.0020.0027.2480.2780.2780.0000.0000.0000.000
52A52CYS0-0.061-0.0076.814-0.229-0.2290.0000.0000.0000.000
53A53PRO0-0.017-0.0265.7900.7870.7870.0000.0000.0000.000
54A54ASP-1-0.807-0.8794.4642.8343.042-0.001-0.016-0.1910.000
55A55TRP0-0.012-0.0237.504-0.457-0.4570.0000.0000.0000.000
56A56ARG00.1350.06210.460-0.026-0.0260.0000.0000.0000.000
57A57GLY00.0080.00911.8010.1110.1110.0000.0000.0000.000
58A58HIS0-0.049-0.04410.1160.1020.1020.0000.0000.0000.000
59A59ASP-1-0.780-0.8686.595-0.097-0.0970.0000.0000.0000.000
60A60ALA0-0.022-0.0245.9840.1400.1400.0000.0000.0000.000
61A61LYS10.8560.9197.7800.6090.6090.0000.0000.0000.000
62A62GLN00.0350.02110.221-0.049-0.0490.0000.0000.0000.000
63A63THR0-0.061-0.03010.770-0.034-0.0340.0000.0000.0000.000
64A64ASP-1-0.900-0.95313.423-0.043-0.0430.0000.0000.0000.000
65A65SER0-0.026-0.02616.205-0.059-0.0590.0000.0000.0000.000
66A66GLY0-0.0340.00218.8040.0340.0340.0000.0000.0000.000
67A67ASP-1-0.834-0.92319.7550.0120.0120.0000.0000.0000.000
68A68PHE0-0.026-0.01916.155-0.016-0.0160.0000.0000.0000.000
69A69ASP-1-0.795-0.88421.2790.0320.0320.0000.0000.0000.000
70A70SER0-0.011-0.03720.124-0.004-0.0040.0000.0000.0000.000
71A71GLN00.0340.00420.4800.0030.0030.0000.0000.0000.000
72A72THR0-0.032-0.00919.233-0.025-0.0250.0000.0000.0000.000
73A73LEU0-0.0080.02114.464-0.027-0.0270.0000.0000.0000.000
74A74ALA00.0450.01215.972-0.020-0.0200.0000.0000.0000.000
75A75GLN0-0.009-0.00518.076-0.010-0.0100.0000.0000.0000.000
76A76ASP-1-0.815-0.92213.428-0.240-0.2400.0000.0000.0000.000
77A77LEU00.007-0.01213.222-0.072-0.0720.0000.0000.0000.000
78A78LEU0-0.021-0.00314.676-0.024-0.0240.0000.0000.0000.000
79A79ALA0-0.0040.00016.092-0.015-0.0150.0000.0000.0000.000
80A80PHE0-0.033-0.0207.411-0.058-0.0580.0000.0000.0000.000
81A81ILE0-0.021-0.01713.371-0.044-0.0440.0000.0000.0000.000
82A82ASP-1-0.959-0.95315.355-0.306-0.3060.0000.0000.0000.000
83A83ALA00.0640.04013.778-0.011-0.0110.0000.0000.0000.000
84A84LYS10.8450.9219.3790.7130.7130.0000.0000.0000.000
85A85GLY0-0.042-0.00713.9840.0370.0370.0000.0000.0000.000
86A86ILE0-0.070-0.03212.7100.0340.0340.0000.0000.0000.000
87A87ARG10.9170.95117.3970.1610.1610.0000.0000.0000.000
88A88ASP-1-0.868-0.93420.451-0.016-0.0160.0000.0000.0000.000
89A89PHE0-0.040-0.02016.477-0.004-0.0040.0000.0000.0000.000
90A90GLN00.0140.02017.570-0.005-0.0050.0000.0000.0000.000
91A91MET00.0010.00816.1710.0200.0200.0000.0000.0000.000
92A92VAL0-0.0060.01215.945-0.025-0.0250.0000.0000.0000.000
93A93SER00.0390.02315.7600.0570.0570.0000.0000.0000.000
94A94THR00.019-0.00216.164-0.019-0.0190.0000.0000.0000.000
95A95SER0-0.032-0.00518.204-0.018-0.0180.0000.0000.0000.000
96A96HIS00.044-0.00120.524-0.031-0.0310.0000.0000.0000.000
97A97GLY00.0680.03417.334-0.033-0.0330.0000.0000.0000.000
98A98CYS0-0.106-0.04018.128-0.021-0.0210.0000.0000.0000.000
99A99TRP00.0360.02421.053-0.031-0.0310.0000.0000.0000.000
100A100VAL00.0040.01216.749-0.025-0.0250.0000.0000.0000.000
101A101ASN0-0.001-0.01319.268-0.061-0.0610.0000.0000.0000.000
102A102ILE0-0.010-0.02520.143-0.025-0.0250.0000.0000.0000.000
103A103ASP-1-0.822-0.91722.0550.0120.0120.0000.0000.0000.000
104A104VAL0-0.0080.00118.536-0.024-0.0240.0000.0000.0000.000
105A105CYS0-0.095-0.05521.882-0.010-0.0100.0000.0000.0000.000
106A106GLU-1-0.891-0.90524.2700.0350.0350.0000.0000.0000.000
107A107GLN0-0.083-0.02522.836-0.029-0.0290.0000.0000.0000.000
108A108LEU0-0.048-0.02920.501-0.017-0.0170.0000.0000.0000.000
109A109GLY0-0.044-0.04024.9880.0080.0080.0000.0000.0000.000
110A110ALA00.1170.07226.4890.0080.0080.0000.0000.0000.000
111A111ALA0-0.051-0.04527.8690.0040.0040.0000.0000.0000.000
112A112ARG10.8420.92221.3100.0580.0580.0000.0000.0000.000
113A113LEU00.0540.03620.6850.0020.0020.0000.0000.0000.000
114A114PRO00.0120.01724.3650.0090.0090.0000.0000.0000.000
115A115LYS10.9000.94324.673-0.135-0.1350.0000.0000.0000.000
116A116THR0-0.008-0.00921.6500.0150.0150.0000.0000.0000.000
117A117ILE0-0.031-0.00420.478-0.001-0.0010.0000.0000.0000.000
118A118ILE0-0.0030.00720.5600.0240.0240.0000.0000.0000.000
119A119ILE00.013-0.01017.323-0.010-0.0100.0000.0000.0000.000
120A120ASP-1-0.764-0.91121.1100.3520.3520.0000.0000.0000.000
121A121TRP00.0310.00123.0550.0170.0170.0000.0000.0000.000
122A122LEU0-0.013-0.01524.834-0.014-0.0140.0000.0000.0000.000
123A123LEU00.021-0.01028.103-0.014-0.0140.0000.0000.0000.000
124A124GLN00.0340.00330.496-0.015-0.0150.0000.0000.0000.000
125A125PRO0-0.0090.03032.0920.0090.0090.0000.0000.0000.000
126A126HIS00.028-0.00231.623-0.017-0.0170.0000.0000.0000.000
127A127PRO00.017-0.01034.8640.0040.0040.0000.0000.0000.000
128A128GLY00.0600.02634.816-0.001-0.0010.0000.0000.0000.000
129A129PHE00.0160.00727.0810.0040.0040.0000.0000.0000.000
130A130TRP00.013-0.00431.2260.0040.0040.0000.0000.0000.000
131A131GLN0-0.0190.01033.098-0.002-0.0020.0000.0000.0000.000
132A132GLN00.0790.06029.4170.0060.0060.0000.0000.0000.000
133A133LEU0-0.014-0.00726.7160.0080.0080.0000.0000.0000.000
134A134ALA0-0.0020.00129.333-0.005-0.0050.0000.0000.0000.000
135A135GLU-1-0.928-0.97631.0210.1450.1450.0000.0000.0000.000
136A136GLY0-0.011-0.01427.426-0.001-0.0010.0000.0000.0000.000
137A137GLN0-0.078-0.06926.828-0.005-0.0050.0000.0000.0000.000
138A138HIS00.0250.02528.583-0.011-0.0110.0000.0000.0000.000
139A139PRO00.0350.00429.2340.0080.0080.0000.0000.0000.000
140A140THR0-0.083-0.04929.6690.0000.0000.0000.0000.0000.000
141A141GLU-1-0.950-0.98330.8470.1200.1200.0000.0000.0000.000
142A142TYR0-0.0030.04623.7600.0220.0220.0000.0000.0000.000
143A143VAL0-0.035-0.01425.3940.0200.0200.0000.0000.0000.000
144A144ALA00.0640.03327.1750.0180.0180.0000.0000.0000.000
145A145GLY00.0520.02628.9500.0020.0020.0000.0000.0000.000
146A146ARG10.9080.94320.652-0.301-0.3010.0000.0000.0000.000
147A147GLN0-0.103-0.06225.2750.0350.0350.0000.0000.0000.000
148A148SER00.0240.01126.7760.0050.0050.0000.0000.0000.000
149A149PHE00.0430.01624.5440.0030.0030.0000.0000.0000.000
150A150PHE0-0.057-0.03020.4640.0260.0260.0000.0000.0000.000
151A151ASP-1-0.873-0.93524.3420.2400.2400.0000.0000.0000.000
152A152GLU-1-0.949-0.96427.4610.2220.2220.0000.0000.0000.000
153A153TRP0-0.076-0.06521.1090.0320.0320.0000.0000.0000.000
154A154ALA0-0.027-0.02723.0820.0220.0220.0000.0000.0000.000
155A155GLU-1-0.788-0.84424.0290.2260.2260.0000.0000.0000.000
156A156THR0-0.095-0.09327.261-0.004-0.0040.0000.0000.0000.000
157A157THR0-0.084-0.03723.0030.0060.0060.0000.0000.0000.000
158A158ASP-1-0.887-0.93824.4890.2900.2900.0000.0000.0000.000
159A159ASN00.023-0.01418.1300.0550.0550.0000.0000.0000.000
160A160ALA00.0420.02117.8540.0270.0270.0000.0000.0000.000
161A161ASP-1-0.820-0.90413.9460.7030.7030.0000.0000.0000.000
162A162VAL0-0.009-0.00414.9500.0880.0880.0000.0000.0000.000
163A163LEU00.004-0.00517.4020.0160.0160.0000.0000.0000.000
164A164ASN0-0.010-0.01412.474-0.060-0.0600.0000.0000.0000.000
165A165HIS00.0700.03312.565-0.040-0.0400.0000.0000.0000.000
166A166LEU0-0.043-0.02614.9660.0150.0150.0000.0000.0000.000
167A167ARG10.8890.94117.203-0.435-0.4350.0000.0000.0000.000
168A168ASN0-0.053-0.02613.969-0.081-0.0810.0000.0000.0000.000
169A169GLU-1-0.924-0.96610.1011.4701.4700.0000.0000.0000.000
170A170MET00.0010.01813.595-0.062-0.0620.0000.0000.0000.000
171A171PRO0-0.083-0.03916.539-0.061-0.0610.0000.0000.0000.000
172A172TRP0-0.058-0.01210.705-0.009-0.0090.0000.0000.0000.000
173A173PHE0-0.079-0.00410.991-0.016-0.0160.0000.0000.0000.000
174A174HIS00.0450.02616.2310.0030.0030.0000.0000.0000.000
175A175GLY00.0530.00319.0350.0100.0100.0000.0000.0000.000
176A176GLU-1-0.937-0.97721.0900.0410.0410.0000.0000.0000.000
177A177MET0-0.0410.00014.494-0.028-0.0280.0000.0000.0000.000
178A178TRP0-0.015-0.01319.0710.0210.0210.0000.0000.0000.000
179A179GLN00.0320.01221.218-0.002-0.0020.0000.0000.0000.000
180A180ARG10.8650.97517.994-0.054-0.0540.0000.0000.0000.000
181A181ALA00.0340.01319.869-0.008-0.0080.0000.0000.0000.000
182A182CYS0-0.045-0.01021.500-0.001-0.0010.0000.0000.0000.000
183A183ARG10.8280.89423.987-0.067-0.0670.0000.0000.0000.000
184A184GLU-1-0.854-0.93621.9380.0640.0640.0000.0000.0000.000
185A185ILE0-0.0140.00821.889-0.001-0.0010.0000.0000.0000.000
186A186GLU-1-0.879-0.95025.1240.0940.0940.0000.0000.0000.000
187A187ALA00.004-0.00627.161-0.008-0.0080.0000.0000.0000.000
188A188ASN0-0.032-0.01624.5380.0070.0070.0000.0000.0000.000
189A189TYR0-0.013-0.02526.9020.0000.0000.0000.0000.0000.000
190A190ARG10.8350.94830.580-0.091-0.0910.0000.0000.0000.000
191A191THR0-0.059-0.01630.441-0.011-0.0110.0000.0000.0000.000
192A192TRP00.003-0.01228.155-0.004-0.0040.0000.0000.0000.000
193A193GLY00.0300.03532.580-0.001-0.0010.0000.0000.0000.000
194A194SER0-0.031-0.03531.5430.0100.0100.0000.0000.0000.000
195A195PRO0-0.0080.00627.526-0.009-0.0090.0000.0000.0000.000
196A196LEU0-0.012-0.01029.467-0.003-0.0030.0000.0000.0000.000
197A197ASP-1-0.879-0.92332.5650.0830.0830.0000.0000.0000.000
198A198ARG10.7890.88026.148-0.079-0.0790.0000.0000.0000.000
199A199MET0-0.0120.00428.194-0.004-0.0040.0000.0000.0000.000
200A200ASP-1-0.905-0.96730.7470.0720.0720.0000.0000.0000.000
201A201SER0-0.116-0.05332.625-0.010-0.0100.0000.0000.0000.000
202A202LEU00.0100.00828.308-0.007-0.0070.0000.0000.0000.000
203A203PRO00.005-0.00731.7400.0020.0020.0000.0000.0000.000
204A204GLN0-0.058-0.03732.180-0.001-0.0010.0000.0000.0000.000
205A205LYS10.8500.95531.006-0.069-0.0690.0000.0000.0000.000
206A206PRO00.0220.02826.650-0.003-0.0030.0000.0000.0000.000
207A207GLU-1-0.878-0.94628.7680.1070.1070.0000.0000.0000.000
208A208ILE0-0.014-0.02025.7410.0140.0140.0000.0000.0000.000
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