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

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FMODB ID: 6Y3VZ

Calculation Name: 4ECC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ECC

Chain ID: A

ChEMBL ID:

UniProt ID: P08515

Base Structure: X-ray

Registration Date: 2023-09-20

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2550492.018027
FMO2-HF: Nuclear repulsion 2465556.499197
FMO2-HF: Total energy -84935.51883
FMO2-MP2: Total energy -85179.41056


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:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-15.458-8.1341.567-3.897-4.994-0.006
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.031
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].
3A4ILE0-0.0040.0053.873-2.242-1.158-0.008-0.457-0.6200.002
4A5LEU0-0.022-0.0166.1121.2171.2170.0000.0000.0000.000
5A6GLY00.0060.0129.380-0.097-0.0970.0000.0000.0000.000
6A7TYR0-0.003-0.02712.1850.2670.2670.0000.0000.0000.000
7A8TRP00.0750.05215.384-0.074-0.0740.0000.0000.0000.000
8A9LYS10.9340.98316.6360.6070.6070.0000.0000.0000.000
9A10ILE0-0.028-0.01317.7120.0660.0660.0000.0000.0000.000
10A11LYS10.8430.94818.2180.1280.1280.0000.0000.0000.000
11A12GLY00.0130.00019.028-0.030-0.0300.0000.0000.0000.000
12A13LEU0-0.050-0.05419.8970.0320.0320.0000.0000.0000.000
13A14VAL00.0220.01814.3910.0380.0380.0000.0000.0000.000
14A15GLN00.0840.07115.814-0.050-0.0500.0000.0000.0000.000
15A16PRO00.0200.00016.8270.0390.0390.0000.0000.0000.000
16A17THR0-0.007-0.00312.3720.0820.0820.0000.0000.0000.000
17A18ARG10.8270.90611.9190.6340.6340.0000.0000.0000.000
18A19LEU0-0.037-0.00913.0460.0940.0940.0000.0000.0000.000
19A20LEU00.0060.00214.2720.0750.0750.0000.0000.0000.000
20A21LEU00.015-0.0028.3440.1290.1290.0000.0000.0000.000
21A22GLU-1-0.808-0.88410.5370.3620.3620.0000.0000.0000.000
22A23TYR0-0.041-0.02112.4920.1040.1040.0000.0000.0000.000
23A24LEU0-0.056-0.03912.0470.0260.0260.0000.0000.0000.000
24A25GLU-1-0.963-0.97511.3890.9440.9440.0000.0000.0000.000
25A26GLU-1-0.884-0.9097.2282.7572.7570.0000.0000.0000.000
26A27LYS10.8200.9032.585-2.326-0.5130.897-1.051-1.6590.013
27A28TYR0-0.048-0.0542.9530.9041.8560.087-0.409-0.6300.001
28A29GLU-1-0.955-0.9632.719-15.301-11.8300.592-1.978-2.085-0.022
29A30GLU-1-0.872-0.9604.750-0.622-0.618-0.001-0.0020.0000.000
30A31HIS00.0220.0788.1810.2730.2730.0000.0000.0000.000
31A32LEU0-0.027-0.02911.0340.1980.1980.0000.0000.0000.000
32A33TYR0-0.007-0.01813.7260.0410.0410.0000.0000.0000.000
33A34GLU-1-0.843-0.95117.486-0.516-0.5160.0000.0000.0000.000
34A35ARG10.8690.93420.4600.2960.2960.0000.0000.0000.000
35A36ASP-1-0.925-0.96824.092-0.418-0.4180.0000.0000.0000.000
36A37GLU-1-0.889-0.92818.804-0.758-0.7580.0000.0000.0000.000
37A38GLY0-0.070-0.03421.568-0.034-0.0340.0000.0000.0000.000
38A39ASP-1-1.005-0.99321.572-0.411-0.4110.0000.0000.0000.000
39A62GLY00.0270.00715.008-0.015-0.0150.0000.0000.0000.000
40A63LEU0-0.025-0.03312.9990.0350.0350.0000.0000.0000.000
41A64GLU-1-0.888-0.93816.503-0.192-0.1920.0000.0000.0000.000
42A65PHE0-0.051-0.02519.2600.0270.0270.0000.0000.0000.000
43A66PRO0-0.0130.00019.135-0.027-0.0270.0000.0000.0000.000
44A67ASN00.009-0.00818.8250.0430.0430.0000.0000.0000.000
45A68LEU0-0.0010.04515.940-0.099-0.0990.0000.0000.0000.000
46A69PRO0-0.053-0.03414.9510.0850.0850.0000.0000.0000.000
47A70TYR0-0.021-0.06610.4480.2450.2450.0000.0000.0000.000
48A71TYR00.0100.0027.411-0.314-0.3140.0000.0000.0000.000
49A72ILE0-0.0130.0026.7160.4570.4570.0000.0000.0000.000
50A73ASP-1-0.844-0.9405.343-0.136-0.1360.0000.0000.0000.000
51A74GLY00.0260.0375.0890.3040.3040.0000.0000.0000.000
52A75ASP-1-0.938-0.9846.850-0.367-0.3670.0000.0000.0000.000
53A76VAL0-0.065-0.0079.353-0.053-0.0530.0000.0000.0000.000
54A77LYS10.9040.9439.5490.5180.5180.0000.0000.0000.000
55A78LEU0-0.008-0.00212.4300.1040.1040.0000.0000.0000.000
56A79THR00.0130.00714.431-0.132-0.1320.0000.0000.0000.000
57A80GLN00.019-0.00117.2020.0790.0790.0000.0000.0000.000
58A81SER00.0400.01417.7650.0170.0170.0000.0000.0000.000
59A82MET00.0410.02317.8770.0130.0130.0000.0000.0000.000
60A83ALA00.0060.00418.2380.0510.0510.0000.0000.0000.000
61A84ILE00.0050.01412.6590.0580.0580.0000.0000.0000.000
62A85ILE0-0.0180.00014.1340.0890.0890.0000.0000.0000.000
63A86ARG10.8950.92615.9990.0010.0010.0000.0000.0000.000
64A87TYR00.0310.0289.9390.0550.0550.0000.0000.0000.000
65A88ILE0-0.013-0.0059.8930.1440.1440.0000.0000.0000.000
66A89ALA00.034-0.00112.7750.1370.1370.0000.0000.0000.000
67A90ASP-1-0.921-0.97016.0370.3940.3940.0000.0000.0000.000
68A91LYS10.9250.97910.888-0.953-0.9530.0000.0000.0000.000
69A92HIS10.7500.8649.969-1.095-1.0950.0000.0000.0000.000
70A93ASN0-0.054-0.02414.982-0.080-0.0800.0000.0000.0000.000
71A94MET0-0.0050.00017.354-0.025-0.0250.0000.0000.0000.000
72A95LEU0-0.044-0.01119.196-0.050-0.0500.0000.0000.0000.000
73A96GLY00.0350.02321.665-0.039-0.0390.0000.0000.0000.000
74A97GLY00.003-0.01024.5310.0130.0130.0000.0000.0000.000
75A98CYS0-0.058-0.02026.542-0.004-0.0040.0000.0000.0000.000
76A99PRO00.019-0.01428.919-0.003-0.0030.0000.0000.0000.000
77A100LYS10.9970.99030.215-0.110-0.1100.0000.0000.0000.000
78A101GLU-1-0.812-0.91127.3840.2050.2050.0000.0000.0000.000
79A102ARG10.9590.98924.395-0.205-0.2050.0000.0000.0000.000
80A103ALA0-0.028-0.00326.999-0.011-0.0110.0000.0000.0000.000
81A104GLU-1-0.872-0.92329.7460.0750.0750.0000.0000.0000.000
82A105ILE00.0150.00923.375-0.012-0.0120.0000.0000.0000.000
83A106SER0-0.011-0.02226.200-0.015-0.0150.0000.0000.0000.000
84A107MET0-0.030-0.00527.118-0.017-0.0170.0000.0000.0000.000
85A108LEU0-0.007-0.00527.669-0.012-0.0120.0000.0000.0000.000
86A109GLU-1-0.789-0.87023.0030.0340.0340.0000.0000.0000.000
87A110GLY00.0010.00126.490-0.020-0.0200.0000.0000.0000.000
88A111ALA00.0300.01929.217-0.011-0.0110.0000.0000.0000.000
89A112VAL0-0.021-0.01125.855-0.008-0.0080.0000.0000.0000.000
90A113LEU0-0.025-0.02524.364-0.017-0.0170.0000.0000.0000.000
91A114ASP-1-0.904-0.93328.105-0.051-0.0510.0000.0000.0000.000
92A115ILE00.0090.00030.160-0.008-0.0080.0000.0000.0000.000
93A116ARG10.8480.92524.1930.1500.1500.0000.0000.0000.000
94A117TYR0-0.016-0.03824.767-0.013-0.0130.0000.0000.0000.000
95A118GLY0-0.0130.01129.508-0.006-0.0060.0000.0000.0000.000
96A119VAL00.0200.01629.695-0.003-0.0030.0000.0000.0000.000
97A120SER0-0.032-0.02527.516-0.014-0.0140.0000.0000.0000.000
98A121ARG10.9090.95629.7860.0780.0780.0000.0000.0000.000
99A122ILE00.0160.00832.7980.0000.0000.0000.0000.0000.000
100A123ALA0-0.0180.01130.6610.0000.0000.0000.0000.0000.000
101A124TYR00.0410.01926.668-0.014-0.0140.0000.0000.0000.000
102A125SER0-0.040-0.00133.4790.0000.0000.0000.0000.0000.000
103A126LYS10.9680.97637.1830.1020.1020.0000.0000.0000.000
104A127ASP-1-0.883-0.94840.170-0.090-0.0900.0000.0000.0000.000
105A128PHE00.0020.00535.3280.0060.0060.0000.0000.0000.000
106A129GLU-1-0.870-0.95838.697-0.085-0.0850.0000.0000.0000.000
107A130THR0-0.0120.00041.1140.0070.0070.0000.0000.0000.000
108A131LEU00.000-0.00738.9970.0030.0030.0000.0000.0000.000
109A132LYS10.9220.97238.0010.0820.0820.0000.0000.0000.000
110A133VAL0-0.023-0.00239.3020.0050.0050.0000.0000.0000.000
111A134ASP-1-0.885-0.95741.869-0.053-0.0530.0000.0000.0000.000
112A135PHE0-0.047-0.03033.1650.0040.0040.0000.0000.0000.000
113A136LEU00.014-0.00536.8360.0050.0050.0000.0000.0000.000
114A137SER0-0.054-0.02239.5400.0070.0070.0000.0000.0000.000
115A138LYS10.9660.97939.7530.0400.0400.0000.0000.0000.000
116A139LEU00.0180.03434.0590.0040.0040.0000.0000.0000.000
117A140PRO00.0080.00237.6090.0060.0060.0000.0000.0000.000
118A141GLU-1-0.912-0.97139.608-0.015-0.0150.0000.0000.0000.000
119A142MET0-0.049-0.01334.5470.0030.0030.0000.0000.0000.000
120A143LEU0-0.020-0.01333.3430.0070.0070.0000.0000.0000.000
121A144LYS10.9630.99035.976-0.010-0.0100.0000.0000.0000.000
122A145MET00.0380.02336.1810.0060.0060.0000.0000.0000.000
123A146PHE00.004-0.00530.2090.0110.0110.0000.0000.0000.000
124A147GLU-1-0.768-0.89834.2460.0400.0400.0000.0000.0000.000
125A148ASP-1-0.923-0.96836.5970.0390.0390.0000.0000.0000.000
126A149ARG10.7510.85131.022-0.082-0.0820.0000.0000.0000.000
127A150LEU0-0.014-0.01430.6520.0100.0100.0000.0000.0000.000
128A151CYS0-0.124-0.05234.7640.0030.0030.0000.0000.0000.000
129A152HIS0-0.039-0.01537.3160.0050.0050.0000.0000.0000.000
130A153LYS10.9030.95832.203-0.106-0.1060.0000.0000.0000.000
131A154THR0-0.0070.01629.088-0.012-0.0120.0000.0000.0000.000
132A155TYR00.000-0.01225.768-0.017-0.0170.0000.0000.0000.000
133A156LEU00.0290.01026.864-0.003-0.0030.0000.0000.0000.000
134A157ASN0-0.030-0.00626.466-0.026-0.0260.0000.0000.0000.000
135A158GLY0-0.050-0.01528.7720.0100.0100.0000.0000.0000.000
136A159ASP-1-0.884-0.94629.2380.1670.1670.0000.0000.0000.000
137A160HIS0-0.019-0.01423.7720.0180.0180.0000.0000.0000.000
138A161VAL0-0.0050.00920.454-0.021-0.0210.0000.0000.0000.000
139A162THR0-0.058-0.02921.3430.0220.0220.0000.0000.0000.000
140A163HIS00.030-0.03118.6760.0120.0120.0000.0000.0000.000
141A164PRO00.031-0.00320.385-0.031-0.0310.0000.0000.0000.000
142A165ASP-1-0.738-0.86322.9580.1190.1190.0000.0000.0000.000
143A166PHE00.0410.00818.356-0.018-0.0180.0000.0000.0000.000
144A167MET0-0.0360.00621.283-0.025-0.0250.0000.0000.0000.000
145A168LEU00.0130.00822.845-0.019-0.0190.0000.0000.0000.000
146A169TYR0-0.061-0.05022.007-0.014-0.0140.0000.0000.0000.000
147A170ASP-1-0.851-0.94021.537-0.156-0.1560.0000.0000.0000.000
148A171ALA00.0020.00723.613-0.015-0.0150.0000.0000.0000.000
149A172LEU0-0.037-0.02226.994-0.005-0.0050.0000.0000.0000.000
150A173ASP-1-0.896-0.96224.676-0.112-0.1120.0000.0000.0000.000
151A174VAL0-0.013-0.00525.575-0.009-0.0090.0000.0000.0000.000
152A175VAL0-0.003-0.02228.135-0.003-0.0030.0000.0000.0000.000
153A176LEU0-0.013-0.00630.2550.0040.0040.0000.0000.0000.000
154A177TYR0-0.021-0.01026.822-0.003-0.0030.0000.0000.0000.000
155A178MET0-0.097-0.03231.9970.0000.0000.0000.0000.0000.000
156A179ASP-1-0.874-0.95934.436-0.042-0.0420.0000.0000.0000.000
157A180PRO0-0.020-0.00335.2830.0060.0060.0000.0000.0000.000
158A181MET00.0300.01836.3520.0060.0060.0000.0000.0000.000
159A182CYS0-0.0350.01635.1240.0070.0070.0000.0000.0000.000
160A183LEU0-0.016-0.03432.1110.0060.0060.0000.0000.0000.000
161A184ASP-1-0.902-0.94136.782-0.006-0.0060.0000.0000.0000.000
162A185ALA0-0.079-0.03440.0460.0050.0050.0000.0000.0000.000
163A186PHE0-0.057-0.03236.9270.0040.0040.0000.0000.0000.000
164A187PRO00.0540.02336.6400.0020.0020.0000.0000.0000.000
165A188LYS10.9110.94035.548-0.057-0.0570.0000.0000.0000.000
166A189LEU00.0440.03031.8910.0080.0080.0000.0000.0000.000
167A190VAL00.0040.01631.6600.0020.0020.0000.0000.0000.000
168A191CYS0-0.068-0.04231.8730.0070.0070.0000.0000.0000.000
169A192PHE0-0.0160.00025.9910.0110.0110.0000.0000.0000.000
170A193LYS10.9320.96727.0490.0280.0280.0000.0000.0000.000
171A194LYS10.9250.96326.842-0.024-0.0240.0000.0000.0000.000
172A195ARG10.9160.96727.246-0.098-0.0980.0000.0000.0000.000
173A196ILE0-0.018-0.00721.9780.0210.0210.0000.0000.0000.000
174A197GLU-1-0.835-0.91422.6990.0230.0230.0000.0000.0000.000
175A198ALA0-0.028-0.00423.5590.0040.0040.0000.0000.0000.000
176A199ILE0-0.046-0.00519.7480.0240.0240.0000.0000.0000.000
177A200PRO00.0300.01520.378-0.013-0.0130.0000.0000.0000.000
178A201GLN00.0230.00415.413-0.100-0.1000.0000.0000.0000.000
179A202ILE0-0.015-0.00516.432-0.032-0.0320.0000.0000.0000.000
180A203ASP-1-0.869-0.93618.4710.0580.0580.0000.0000.0000.000
181A204LYS10.9430.97014.383-0.430-0.4300.0000.0000.0000.000
182A205TYR0-0.0060.00212.523-0.020-0.0200.0000.0000.0000.000
183A206LEU00.0060.01016.120-0.072-0.0720.0000.0000.0000.000
184A207LYS10.8730.95019.342-0.080-0.0800.0000.0000.0000.000
185A208SER0-0.104-0.05115.096-0.031-0.0310.0000.0000.0000.000
186A209SER0-0.011-0.02714.888-0.015-0.0150.0000.0000.0000.000
187A210LYS10.9280.9608.3600.1040.1040.0000.0000.0000.000
188A211TYR00.0100.03513.752-0.054-0.0540.0000.0000.0000.000
189A212ILE00.0250.01915.703-0.011-0.0110.0000.0000.0000.000
190A213ALA0-0.004-0.02118.3110.0320.0320.0000.0000.0000.000
191A214TRP0-0.0290.00621.9220.0350.0350.0000.0000.0000.000
192A215PRO00.0240.02222.254-0.026-0.0260.0000.0000.0000.000
193A216LEU0-0.023-0.02222.839-0.017-0.0170.0000.0000.0000.000
194A217GLN0-0.027-0.00723.9500.0020.0020.0000.0000.0000.000
195A218GLY00.0630.02124.569-0.021-0.0210.0000.0000.0000.000
196A219TRP00.0670.01420.7630.0440.0440.0000.0000.0000.000
197A220GLN0-0.004-0.00327.1630.0130.0130.0000.0000.0000.000
198A221ALA0-0.058-0.01529.2290.0160.0160.0000.0000.0000.000
199A222THR0-0.014-0.00731.033-0.002-0.0020.0000.0000.0000.000
200A223PHE00.004-0.00130.3800.0060.0060.0000.0000.0000.000
201A224GLY00.0320.00028.920-0.008-0.0080.0000.0000.0000.000
202A225GLY00.0170.03027.440-0.022-0.0220.0000.0000.0000.000
203A226GLY00.014-0.00529.0570.0120.0120.0000.0000.0000.000
204A227ASP-1-0.886-0.96726.670-0.295-0.2950.0000.0000.0000.000
205A228HIS0-0.074-0.04626.567-0.006-0.0060.0000.0000.0000.000
206A229PRO00.0010.02827.8380.0070.0070.0000.0000.0000.000