FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: P8NRY

Calculation Name: 4B9I-A-Xray34

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4B9I

Chain ID: A

ChEMBL ID:

UniProt ID: P53508

Base Structure: X-ray

Registration Date: 2018-09-07

Reference:

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1466213.01685
FMO2-HF: Nuclear repulsion 1406015.172502
FMO2-HF: Total energy -60197.844348
FMO2-MP2: Total energy -60373.114674


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:12:ACE)


Summations of interaction energy for fragment #1(A:12:ACE)
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.
-0.2570.9710.004-0.586-0.645-0.002
Interaction energy analysis for fragmet #1(A:12:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.014
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].
3A14PHE00.0020.0093.8140.8001.804-0.015-0.481-0.507-0.002
4A15ALA00.0320.0196.900-0.026-0.0260.0000.0000.0000.000
5A16PRO00.0040.01810.3690.1160.1160.0000.0000.0000.000
6A17GLU-1-0.857-0.92613.334-0.206-0.2060.0000.0000.0000.000
7A18PRO00.0140.07016.0750.0210.0210.0000.0000.0000.000
8A19GLN0-0.046-0.02418.5060.0450.0450.0000.0000.0000.000
9A20ILE00.0310.01821.966-0.004-0.0040.0000.0000.0000.000
10A21GLN0-0.020-0.00423.7320.0080.0080.0000.0000.0000.000
11A22PRO00.0930.05328.200-0.002-0.0020.0000.0000.0000.000
12A23SER0-0.030-0.00831.6730.0020.0020.0000.0000.0000.000
13A24PHE00.0300.00034.0950.0030.0030.0000.0000.0000.000
14A25GLY00.0170.02337.8780.0020.0020.0000.0000.0000.000
15A26LYS10.8830.92739.5740.0580.0580.0000.0000.0000.000
16A27ASN0-0.020-0.02639.7420.0050.0050.0000.0000.0000.000
17A28VAL0-0.0040.02336.843-0.001-0.0010.0000.0000.0000.000
18A29GLY00.0720.03539.170-0.003-0.0030.0000.0000.0000.000
19A30LYS10.8690.95541.4160.0560.0560.0000.0000.0000.000
20A31GLU-1-0.810-0.89340.072-0.059-0.0590.0000.0000.0000.000
21A32GLY0-0.028-0.02336.9120.0010.0010.0000.0000.0000.000
22A33GLY0-0.0050.00436.669-0.003-0.0030.0000.0000.0000.000
23A34LEU0-0.071-0.03030.727-0.002-0.0020.0000.0000.0000.000
24A35LEU00.0320.01232.6300.0050.0050.0000.0000.0000.000
25A36PHE00.0140.00426.2210.0030.0030.0000.0000.0000.000
26A37SER00.0150.01726.732-0.002-0.0020.0000.0000.0000.000
27A38VAL00.0310.02520.8010.0020.0020.0000.0000.0000.000
28A39SER0-0.0150.01021.580-0.005-0.0050.0000.0000.0000.000
29A40LEU0-0.0070.00115.022-0.003-0.0030.0000.0000.0000.000
30A41THR00.0290.02413.4520.0350.0350.0000.0000.0000.000
31A42VAL0-0.032-0.00512.086-0.068-0.0680.0000.0000.0000.000
32A43PRO00.0050.0148.0770.0450.0450.0000.0000.0000.000
33A44GLU-1-0.862-0.9485.853-0.363-0.3630.0000.0000.0000.000
34A45ASN0-0.093-0.0573.3410.1340.3580.019-0.105-0.1380.000
35A46VAL0-0.0160.0087.1750.0190.0190.0000.0000.0000.000
36A47SER00.0170.0169.9430.1310.1310.0000.0000.0000.000
37A48GLN00.0660.04213.3450.0960.0960.0000.0000.0000.000
38A49VAL00.0050.00713.995-0.080-0.0800.0000.0000.0000.000
39A50THR0-0.021-0.01416.2850.0540.0540.0000.0000.0000.000
40A51VAL00.0000.00318.378-0.028-0.0280.0000.0000.0000.000
41A52TYR0-0.041-0.02419.3230.0090.0090.0000.0000.0000.000
42A53PRO00.0100.01823.555-0.006-0.0060.0000.0000.0000.000
43A54VAL00.030-0.02323.947-0.003-0.0030.0000.0000.0000.000
44A55TYR0-0.0120.04327.0500.0100.0100.0000.0000.0000.000
45A56ASP-1-0.874-0.95230.676-0.082-0.0820.0000.0000.0000.000
46A57GLU-1-0.807-0.90724.401-0.148-0.1480.0000.0000.0000.000
47A58ASP-1-0.868-0.91327.440-0.109-0.1090.0000.0000.0000.000
48A59TYR0-0.067-0.03529.358-0.001-0.0010.0000.0000.0000.000
49A60GLY00.0130.01827.8960.0010.0010.0000.0000.0000.000
50A61LEU0-0.041-0.02028.8190.0010.0010.0000.0000.0000.000
51A62GLY00.0490.01130.278-0.004-0.0040.0000.0000.0000.000
52A63ARG10.8430.89430.9100.0710.0710.0000.0000.0000.000
53A64LEU0-0.0220.00331.011-0.001-0.0010.0000.0000.0000.000
54A65VAL00.0140.00733.8800.0050.0050.0000.0000.0000.000
55A66ASN00.0180.02135.874-0.002-0.0020.0000.0000.0000.000
56A67THR00.009-0.00934.8950.0030.0030.0000.0000.0000.000
57A68ALA0-0.032-0.01037.6570.0020.0020.0000.0000.0000.000
58A69ASP-1-0.821-0.90840.872-0.040-0.0400.0000.0000.0000.000
59A70ASP-1-0.798-0.90140.490-0.050-0.0500.0000.0000.0000.000
60A71SER0-0.151-0.06641.320-0.002-0.0020.0000.0000.0000.000
61A72GLN0-0.0220.00341.991-0.002-0.0020.0000.0000.0000.000
62A73SER00.0280.00238.046-0.003-0.0030.0000.0000.0000.000
63A74ILE0-0.045-0.01636.1790.0030.0030.0000.0000.0000.000
64A75ILE0-0.0050.00435.215-0.004-0.0040.0000.0000.0000.000
65A76TYR0-0.068-0.05828.340-0.002-0.0020.0000.0000.0000.000
66A77GLN00.0540.04830.412-0.006-0.0060.0000.0000.0000.000
67A78ILE00.020-0.00224.5510.0040.0040.0000.0000.0000.000
68A79VAL0-0.0290.00227.202-0.002-0.0020.0000.0000.0000.000
69A80ASP-1-0.637-0.83824.026-0.166-0.1660.0000.0000.0000.000
70A81ASP-1-0.884-0.94824.535-0.151-0.1510.0000.0000.0000.000
71A82LYS10.8810.93627.0890.1270.1270.0000.0000.0000.000
72A83GLY0-0.058-0.02128.8680.0090.0090.0000.0000.0000.000
73A84ARG10.8300.91524.8370.1600.1600.0000.0000.0000.000
74A85LYS10.8590.91227.2980.0930.0930.0000.0000.0000.000
75A86MET0-0.099-0.00322.911-0.014-0.0140.0000.0000.0000.000
76A87LEU00.0320.01223.7690.0130.0130.0000.0000.0000.000
77A88LYS10.9240.99019.3240.1810.1810.0000.0000.0000.000
78A89ASP-1-0.843-0.90518.526-0.230-0.2300.0000.0000.0000.000
79A90HIS0-0.072-0.02319.9850.0070.0070.0000.0000.0000.000
80A91GLY00.0370.01619.9460.0120.0120.0000.0000.0000.000
81A92ALA00.0160.00719.9430.0240.0240.0000.0000.0000.000
82A93GLU-1-0.922-0.96017.638-0.304-0.3040.0000.0000.0000.000
83A94VAL0-0.054-0.03014.6610.0190.0190.0000.0000.0000.000
84A95THR00.0070.00315.025-0.009-0.0090.0000.0000.0000.000
85A96PRO00.0390.01810.5980.0090.0090.0000.0000.0000.000
86A97ASN0-0.028-0.03211.9270.0650.0650.0000.0000.0000.000
87A98GLN0-0.0190.02514.1910.0460.0460.0000.0000.0000.000
88A99GLN0-0.041-0.04016.724-0.023-0.0230.0000.0000.0000.000
89A100ILE0-0.024-0.00317.2160.0160.0160.0000.0000.0000.000
90A101THR00.021-0.01120.580-0.005-0.0050.0000.0000.0000.000
91A102PHE0-0.0090.00019.0880.0050.0050.0000.0000.0000.000
92A103ARG10.8910.93124.4640.1250.1250.0000.0000.0000.000
93A104ALA00.0340.03828.037-0.001-0.0010.0000.0000.0000.000
94A105LEU0-0.035-0.02429.7930.0070.0070.0000.0000.0000.000
95A106ASN00.030-0.00233.206-0.002-0.0020.0000.0000.0000.000
96A107TYR0-0.0060.01535.3140.0010.0010.0000.0000.0000.000
97A108THR0-0.0080.01037.2780.0020.0020.0000.0000.0000.000
98A109SER00.0020.02040.1730.0010.0010.0000.0000.0000.000
99A110GLY00.033-0.00243.5260.0000.0000.0000.0000.0000.000
100A111ASP-1-0.913-0.95146.201-0.042-0.0420.0000.0000.0000.000
101A112LYS10.8510.94842.3900.0550.0550.0000.0000.0000.000
102A113GLU-1-0.834-0.91244.249-0.054-0.0540.0000.0000.0000.000
103A114ILE0-0.049-0.02839.4180.0010.0010.0000.0000.0000.000
104A115PRO0-0.0140.00843.3360.0010.0010.0000.0000.0000.000
105A116PRO00.0710.04541.894-0.003-0.0030.0000.0000.0000.000
106A117GLY0-0.0020.01040.2860.0030.0030.0000.0000.0000.000
107A118ILE0-0.006-0.00434.492-0.003-0.0030.0000.0000.0000.000
108A119TYR0-0.030-0.03834.8100.0020.0020.0000.0000.0000.000
109A120ASN00.0590.01029.385-0.002-0.0020.0000.0000.0000.000
110A121ASP-1-0.719-0.83829.189-0.104-0.1040.0000.0000.0000.000
111A122GLN0-0.035-0.00323.693-0.007-0.0070.0000.0000.0000.000
112A123VAL0-0.031-0.00822.2140.0030.0030.0000.0000.0000.000
113A124MET0-0.040-0.01318.030-0.001-0.0010.0000.0000.0000.000
114A125VAL0-0.014-0.00115.4490.0060.0060.0000.0000.0000.000
115A126GLY00.0080.00515.054-0.017-0.0170.0000.0000.0000.000
116A127TYR00.020-0.01210.7100.0150.0150.0000.0000.0000.000
117A128TYR00.0080.00511.613-0.048-0.0480.0000.0000.0000.000
118A129VAL00.0120.0095.565-0.064-0.0640.0000.0000.0000.000
119A130ASN0-0.060-0.0547.3440.1160.1160.0000.0000.0000.000
120A131ASP-1-0.849-0.8917.161-0.262-0.2620.0000.0000.0000.000
121A132ASN0-0.042-0.0178.5250.0060.0060.0000.0000.0000.000
122A133LYS10.8570.91910.350-0.040-0.0400.0000.0000.0000.000
123A134GLN00.0140.01312.259-0.013-0.0130.0000.0000.0000.000
124A135GLY00.1040.06111.110-0.039-0.0390.0000.0000.0000.000
125A136ASN0-0.078-0.0679.067-0.071-0.0710.0000.0000.0000.000
126A137TRP00.0380.01911.119-0.154-0.1540.0000.0000.0000.000
127A138GLN0-0.068-0.0178.0440.0410.0410.0000.0000.0000.000
128A139TYR0-0.036-0.05211.470-0.003-0.0030.0000.0000.0000.000
129A140LYS10.8810.94813.7330.2500.2500.0000.0000.0000.000
130A141SER00.0200.01215.5850.0060.0060.0000.0000.0000.000
131A142LEU0-0.034-0.01918.892-0.014-0.0140.0000.0000.0000.000
132A143ASP-1-0.805-0.87821.222-0.113-0.1130.0000.0000.0000.000
133A144VAL0-0.002-0.00724.680-0.005-0.0050.0000.0000.0000.000
134A145ASN0-0.016-0.01427.2120.0130.0130.0000.0000.0000.000
135A146VAL0-0.0050.00129.656-0.001-0.0010.0000.0000.0000.000
136A147ASN0-0.080-0.02432.2460.0010.0010.0000.0000.0000.000
137A148ILE0-0.0080.00834.192-0.004-0.0040.0000.0000.0000.000
138A149GLU-2-1.683-1.83537.610-0.114-0.1140.0000.0000.0000.000
139A2003HOH0-0.018-0.0118.8560.0770.0770.0000.0000.0000.000
140A2004HOH00.0250.0159.213-0.043-0.0430.0000.0000.0000.000
141A2005HOH0-0.049-0.03713.2160.0170.0170.0000.0000.0000.000
142A2006HOH00.0040.00413.576-0.015-0.0150.0000.0000.0000.000
143A2007HOH0-0.086-0.10917.508-0.002-0.0020.0000.0000.0000.000
144A2010HOH00.0220.01621.5110.0070.0070.0000.0000.0000.000
145A2012HOH00.0170.00823.6130.0010.0010.0000.0000.0000.000
146A2013HOH0-0.033-0.02025.8510.0020.0020.0000.0000.0000.000
147A2014HOH0-0.010-0.00230.299-0.001-0.0010.0000.0000.0000.000
148A2017HOH0-0.034-0.01932.4580.0000.0000.0000.0000.0000.000
149A2018HOH00.001-0.00333.547-0.002-0.0020.0000.0000.0000.000
150A2019HOH0-0.041-0.03436.194-0.002-0.0020.0000.0000.0000.000
151A2020HOH0-0.020-0.02636.6300.0010.0010.0000.0000.0000.000
152A2026HOH0-0.047-0.02343.670-0.001-0.0010.0000.0000.0000.000
153A2027HOH00.0690.08142.432-0.001-0.0010.0000.0000.0000.000
154A2028HOH0-0.033-0.01942.4670.0010.0010.0000.0000.0000.000
155A2029HOH0-0.038-0.02540.600-0.001-0.0010.0000.0000.0000.000
156A2030HOH0-0.016-0.03043.2400.0010.0010.0000.0000.0000.000
157A2031HOH0-0.023-0.01036.631-0.001-0.0010.0000.0000.0000.000
158A2033HOH0-0.041-0.04128.7410.0020.0020.0000.0000.0000.000
159A2035HOH00.0170.00517.989-0.006-0.0060.0000.0000.0000.000
160A2043HOH00.0110.0098.229-0.045-0.0450.0000.0000.0000.000
161A2048HOH0-0.024-0.01715.2890.0030.0030.0000.0000.0000.000
162A2050HOH0-0.006-0.01120.5730.0080.0080.0000.0000.0000.000
163A2051HOH00.0120.00121.950-0.010-0.0100.0000.0000.0000.000
164A2053HOH0-0.019-0.02225.828-0.004-0.0040.0000.0000.0000.000
165A2054HOH0-0.022-0.01727.373-0.001-0.0010.0000.0000.0000.000
166A2055HOH00.0200.01629.667-0.003-0.0030.0000.0000.0000.000
167A2056HOH0-0.037-0.02131.3170.0030.0030.0000.0000.0000.000
168A2057HOH0-0.028-0.03537.8360.0020.0020.0000.0000.0000.000
169A2058HOH0-0.011-0.00130.686-0.002-0.0020.0000.0000.0000.000
170A2059HOH0-0.019-0.03825.631-0.005-0.0050.0000.0000.0000.000
171A2060HOH0-0.0100.00225.559-0.004-0.0040.0000.0000.0000.000
172A2061HOH00.0050.00837.461-0.001-0.0010.0000.0000.0000.000
173A2062HOH0-0.035-0.02627.0340.0000.0000.0000.0000.0000.000
174A2063HOH00.0110.03931.5980.0020.0020.0000.0000.0000.000
175A2064HOH00.0320.02938.789-0.001-0.0010.0000.0000.0000.000
176A2065HOH0-0.0010.00341.076-0.001-0.0010.0000.0000.0000.000
177A2067HOH0-0.037-0.02238.712-0.001-0.0010.0000.0000.0000.000
178A2068HOH00.0090.00240.150-0.001-0.0010.0000.0000.0000.000
179A2069HOH0-0.017-0.01443.153-0.001-0.0010.0000.0000.0000.000
180A2071HOH0-0.037-0.01737.332-0.001-0.0010.0000.0000.0000.000
181A2073HOH0-0.047-0.03046.3290.0000.0000.0000.0000.0000.000
182A2074HOH0-0.024-0.01445.0130.0010.0010.0000.0000.0000.000
183A2078HOH0-0.018-0.02146.5600.0000.0000.0000.0000.0000.000
184A2079HOH00.0220.01840.7890.0010.0010.0000.0000.0000.000
185A2080HOH0-0.0100.00132.677-0.001-0.0010.0000.0000.0000.000
186A2081HOH0-0.003-0.01036.222-0.001-0.0010.0000.0000.0000.000
187A2083HOH00.0180.00926.0720.0050.0050.0000.0000.0000.000
188A2084HOH00.0130.01223.4710.0070.0070.0000.0000.0000.000
189A2085HOH0-0.0090.06024.7930.0030.0030.0000.0000.0000.000
190A2086HOH0-0.071-0.09226.0800.0010.0010.0000.0000.0000.000
191A2087HOH0-0.089-0.07623.4150.0060.0060.0000.0000.0000.000
192A2088HOH00.0020.00323.389-0.002-0.0020.0000.0000.0000.000
193A2089HOH0-0.013-0.01023.922-0.003-0.0030.0000.0000.0000.000
194A2090HOH0-0.045-0.03429.7400.0010.0010.0000.0000.0000.000
195A2091HOH00.0300.02229.595-0.001-0.0010.0000.0000.0000.000
196A2092HOH0-0.004-0.01231.638-0.002-0.0020.0000.0000.0000.000
197A2094HOH0-0.043-0.04124.3490.0040.0040.0000.0000.0000.000
198A2095HOH00.0310.03034.449-0.002-0.0020.0000.0000.0000.000
199A2097HOH00.0100.00918.039-0.002-0.0020.0000.0000.0000.000
200A2098HOH0-0.014-0.01617.3160.0070.0070.0000.0000.0000.000
201A2099HOH0-0.020-0.01919.279-0.009-0.0090.0000.0000.0000.000
202A2100HOH0-0.010-0.00822.5230.0080.0080.0000.0000.0000.000
203A2101HOH00.0630.05322.0340.0000.0000.0000.0000.0000.000
204A2102HOH0-0.038-0.03714.902-0.006-0.0060.0000.0000.0000.000
205A2103HOH0-0.023-0.01416.2370.0150.0150.0000.0000.0000.000
206A2107HOH0-0.014-0.01322.8140.0010.0010.0000.0000.0000.000
207A2109HOH0-0.073-0.09140.893-0.001-0.0010.0000.0000.0000.000
208A2110HOH0-0.026-0.03438.721-0.001-0.0010.0000.0000.0000.000
209A2111HOH0-0.028-0.01744.7140.0000.0000.0000.0000.0000.000
210A2113HOH0-0.039-0.03042.5020.0000.0000.0000.0000.0000.000
211A2115HOH00.0040.00639.3190.0010.0010.0000.0000.0000.000
212A2116HOH0-0.075-0.07232.2990.0020.0020.0000.0000.0000.000
213A2117HOH0-0.033-0.01729.217-0.003-0.0030.0000.0000.0000.000
214A2120HOH0-0.035-0.02329.7150.0030.0030.0000.0000.0000.000
215A2122HOH00.0300.00514.3550.0000.0000.0000.0000.0000.000
216A2123HOH00.0300.02314.874-0.024-0.0240.0000.0000.0000.000
217A2125HOH0-0.040-0.02311.370-0.008-0.0080.0000.0000.0000.000
218A2127HOH00.0580.03015.846-0.007-0.0070.0000.0000.0000.000
219A2132HOH00.0280.02021.465-0.007-0.0070.0000.0000.0000.000
220A2133HOH00.0340.03325.9530.0050.0050.0000.0000.0000.000
221A2134HOH0-0.035-0.02723.1190.0020.0020.0000.0000.0000.000
222A2135HOH0-0.058-0.04723.460-0.004-0.0040.0000.0000.0000.000
223A2136HOH0-0.012-0.00828.912-0.004-0.0040.0000.0000.0000.000
224A2137HOH0-0.011-0.01926.3000.0040.0040.0000.0000.0000.000
225A2139HOH00.0210.00233.135-0.003-0.0030.0000.0000.0000.000