FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JL8M9

Calculation Name: 4E3Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E3Z

Chain ID: A

ChEMBL ID:

UniProt ID: Q2K3F6

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 OptAll
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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2542604.43428
FMO2-HF: Nuclear repulsion 2457910.47
FMO2-HF: Total energy -84693.96428
FMO2-MP2: Total energy -84938.284885


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.
0.2913.8250.181-1.465-2.2510.001
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 : -0.002 / q_NPA : -0.013
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].
3A4THR0-0.016-0.0032.673-0.6711.6120.116-1.010-1.3900.000
4A5PRO00.0230.0294.4191.7291.808-0.001-0.013-0.0660.000
5A6VAL00.0050.0036.5460.5990.5990.0000.0000.0000.000
6A7VAL0-0.003-0.0019.142-0.387-0.3870.0000.0000.0000.000
7A8LEU0-0.0130.01112.9100.1130.1130.0000.0000.0000.000
8A9VAL0-0.001-0.01415.543-0.101-0.1010.0000.0000.0000.000
9A10THR00.0470.02218.6010.0060.0060.0000.0000.0000.000
10A11GLY00.0380.01621.632-0.029-0.0290.0000.0000.0000.000
11A12GLY0-0.008-0.00820.416-0.025-0.0250.0000.0000.0000.000
12A13SER00.0350.00621.4790.0000.0000.0000.0000.0000.000
13A14ARG10.8810.92023.795-0.235-0.2350.0000.0000.0000.000
14A15GLY00.0220.01525.8780.0050.0050.0000.0000.0000.000
15A16ILE00.0550.01924.8470.0150.0150.0000.0000.0000.000
16A17GLY00.0680.04222.4330.0150.0150.0000.0000.0000.000
17A18ALA00.0450.03421.1350.0410.0410.0000.0000.0000.000
18A19ALA0-0.042-0.02321.4550.0220.0220.0000.0000.0000.000
19A20VAL00.012-0.00718.3920.0090.0090.0000.0000.0000.000
20A21CYS0-0.052-0.00516.9570.0500.0500.0000.0000.0000.000
21A22ARG10.8540.91616.562-0.272-0.2720.0000.0000.0000.000
22A23LEU0-0.058-0.00218.339-0.031-0.0310.0000.0000.0000.000
23A24ALA00.0330.00214.164-0.012-0.0120.0000.0000.0000.000
24A25ALA00.0550.03512.1200.0180.0180.0000.0000.0000.000
25A26ARG10.8580.93512.796-0.322-0.3220.0000.0000.0000.000
26A27GLN0-0.037-0.02714.338-0.078-0.0780.0000.0000.0000.000
27A28GLY00.0050.01110.185-0.095-0.0950.0000.0000.0000.000
28A29TRP0-0.044-0.0248.4970.1510.1510.0000.0000.0000.000
29A30ARG10.8670.9403.678-7.585-6.7930.068-0.300-0.5600.001
30A31VAL0-0.020-0.0188.840-0.244-0.2440.0000.0000.0000.000
31A32GLY00.0460.01712.3140.0340.0340.0000.0000.0000.000
32A33VAL00.009-0.00814.289-0.141-0.1410.0000.0000.0000.000
33A34ASN0-0.002-0.01117.506-0.055-0.0550.0000.0000.0000.000
34A35TYR0-0.020-0.00819.981-0.026-0.0260.0000.0000.0000.000
35A36ALA00.0410.01923.4880.0070.0070.0000.0000.0000.000
36A37ALA00.006-0.00126.614-0.017-0.0170.0000.0000.0000.000
37A38ASN0-0.068-0.03827.9050.0260.0260.0000.0000.0000.000
38A39ARG10.8370.89418.404-0.563-0.5630.0000.0000.0000.000
39A40GLU-1-0.862-0.91823.6540.3010.3010.0000.0000.0000.000
40A41ALA00.000-0.00324.7280.0140.0140.0000.0000.0000.000
41A42ALA00.000-0.00520.8270.0110.0110.0000.0000.0000.000
42A43ASP-1-0.748-0.86119.7670.6120.6120.0000.0000.0000.000
43A44ALA0-0.0150.00520.5520.0190.0190.0000.0000.0000.000
44A45VAL0-0.069-0.03418.873-0.006-0.0060.0000.0000.0000.000
45A46VAL0-0.021-0.01915.2530.0270.0270.0000.0000.0000.000
46A47ALA00.0380.03417.0110.0380.0380.0000.0000.0000.000
47A48ALA0-0.023-0.01019.104-0.009-0.0090.0000.0000.0000.000
48A49ILE0-0.063-0.01413.826-0.034-0.0340.0000.0000.0000.000
49A50THR00.001-0.02513.4320.0250.0250.0000.0000.0000.000
50A51GLU-1-0.884-0.92815.4460.4700.4700.0000.0000.0000.000
51A52SER0-0.126-0.06516.918-0.077-0.0770.0000.0000.0000.000
52A53GLY0-0.041-0.01514.327-0.040-0.0400.0000.0000.0000.000
53A54GLY0-0.028-0.01411.3410.0280.0280.0000.0000.0000.000
54A55GLU-1-0.908-0.9636.6773.2333.2330.0000.0000.0000.000
55A56ALA0-0.005-0.01310.241-0.031-0.0310.0000.0000.0000.000
56A57VAL00.0200.01111.283-0.026-0.0260.0000.0000.0000.000
57A58ALA00.0000.02014.080-0.050-0.0500.0000.0000.0000.000
58A59ILE0-0.059-0.03314.390-0.002-0.0020.0000.0000.0000.000
59A60PRO00.0030.00618.527-0.046-0.0460.0000.0000.0000.000
60A61GLY00.017-0.00721.3180.0200.0200.0000.0000.0000.000
61A62ASP-1-0.858-0.93723.7030.2410.2410.0000.0000.0000.000
62A63VAL0-0.002-0.01624.101-0.001-0.0010.0000.0000.0000.000
63A64GLY0-0.0120.00026.560-0.017-0.0170.0000.0000.0000.000
64A65ASN0-0.044-0.03028.312-0.032-0.0320.0000.0000.0000.000
65A66ALA00.0530.02126.8570.0190.0190.0000.0000.0000.000
66A67ALA0-0.014-0.00325.5730.0130.0130.0000.0000.0000.000
67A68ASP-1-0.781-0.87224.3610.3130.3130.0000.0000.0000.000
68A69ILE00.0000.00821.7710.0430.0430.0000.0000.0000.000
69A70ALA00.0410.02220.6390.0390.0390.0000.0000.0000.000
70A71ALA0-0.0130.00419.7910.0370.0370.0000.0000.0000.000
71A72MET0-0.0120.00218.2060.0660.0660.0000.0000.0000.000
72A73PHE00.016-0.00715.8710.0990.0990.0000.0000.0000.000
73A74SER00.0370.01514.7130.0720.0720.0000.0000.0000.000
74A75ALA0-0.099-0.03515.1160.0470.0470.0000.0000.0000.000
75A76VAL00.0210.00511.2320.1510.1510.0000.0000.0000.000
76A77ASP-1-0.801-0.87110.2480.8970.8970.0000.0000.0000.000
77A78ARG10.8540.9099.526-0.500-0.5000.0000.0000.0000.000
78A79GLN0-0.0260.00010.0370.2040.2040.0000.0000.0000.000
79A80PHE0-0.006-0.0126.4430.4110.4110.0000.0000.0000.000
80A81GLY00.0080.0104.8811.1411.218-0.001-0.001-0.0750.000
81A82ARG10.7450.8514.3240.2770.580-0.001-0.141-0.1600.000
82A83LEU0-0.030-0.0207.7310.3130.3130.0000.0000.0000.000
83A84ASP-1-0.769-0.8428.4830.1870.1870.0000.0000.0000.000
84A85GLY00.0440.00111.677-0.124-0.1240.0000.0000.0000.000
85A86LEU0-0.072-0.02114.7520.1060.1060.0000.0000.0000.000
86A87VAL00.0240.00517.590-0.060-0.0600.0000.0000.0000.000
87A88ASN0-0.012-0.01020.3200.0500.0500.0000.0000.0000.000
88A89ASN0-0.028-0.04723.020-0.051-0.0510.0000.0000.0000.000
89A90ALA0-0.036-0.00324.517-0.017-0.0170.0000.0000.0000.000
90A91GLY00.0140.00026.374-0.014-0.0140.0000.0000.0000.000
91A92ILE0-0.077-0.03130.1100.0070.0070.0000.0000.0000.000
92A93VAL00.0490.01933.609-0.008-0.0080.0000.0000.0000.000
93A94ASP-1-0.792-0.89537.0280.1290.1290.0000.0000.0000.000
94A95TYR0-0.0150.00140.332-0.004-0.0040.0000.0000.0000.000
95A96PRO0-0.043-0.03143.612-0.002-0.0020.0000.0000.0000.000
96A97GLN00.0460.03746.0360.0030.0030.0000.0000.0000.000
97A98ARG10.7980.86247.754-0.059-0.0590.0000.0000.0000.000
98A99VAL00.015-0.01647.2930.0020.0020.0000.0000.0000.000
99A100ASP-1-0.822-0.87749.1690.0620.0620.0000.0000.0000.000
100A101GLU-1-0.860-0.92350.4130.0710.0710.0000.0000.0000.000
101A102MET0-0.116-0.02645.2280.0040.0040.0000.0000.0000.000
102A103SER00.003-0.01545.980-0.001-0.0010.0000.0000.0000.000
103A104VAL00.0360.00444.3210.0030.0030.0000.0000.0000.000
104A105GLU-1-0.827-0.90342.3470.0960.0960.0000.0000.0000.000
105A106ARG10.7470.84940.820-0.094-0.0940.0000.0000.0000.000
106A107ILE00.0200.00740.0150.0070.0070.0000.0000.0000.000
107A108GLU-1-0.812-0.86637.0510.1380.1380.0000.0000.0000.000
108A109ARG10.9050.94535.729-0.136-0.1360.0000.0000.0000.000
109A110MET0-0.0490.00135.2130.0140.0140.0000.0000.0000.000
110A111LEU00.010-0.01135.1250.0060.0060.0000.0000.0000.000
111A112ARG10.7590.83732.452-0.150-0.1500.0000.0000.0000.000
112A113VAL00.005-0.00730.3140.0110.0110.0000.0000.0000.000
113A114ASN0-0.038-0.02229.7280.0230.0230.0000.0000.0000.000
114A115VAL0-0.0030.00930.0750.0040.0040.0000.0000.0000.000
115A116THR00.0180.00529.4490.0030.0030.0000.0000.0000.000
116A117GLY00.0860.05127.2090.0050.0050.0000.0000.0000.000
117A118SER0-0.020-0.01325.1200.0260.0260.0000.0000.0000.000
118A119ILE0-0.0050.00024.6810.0070.0070.0000.0000.0000.000
119A120LEU0-0.010-0.00224.973-0.001-0.0010.0000.0000.0000.000
120A121CYS0-0.026-0.01521.0420.0220.0220.0000.0000.0000.000
121A122ALA00.017-0.00220.2420.0180.0180.0000.0000.0000.000
122A123ALA00.0170.01020.985-0.009-0.0090.0000.0000.0000.000
123A124GLU-1-0.825-0.87718.4230.2590.2590.0000.0000.0000.000
124A125ALA00.0210.01416.3900.0140.0140.0000.0000.0000.000
125A126VAL00.0140.00316.583-0.019-0.0190.0000.0000.0000.000
126A127ARG10.7910.86518.367-0.232-0.2320.0000.0000.0000.000
127A128ARG10.7360.83313.015-0.434-0.4340.0000.0000.0000.000
128A129MET0-0.0150.00513.616-0.036-0.0360.0000.0000.0000.000
129A130SER0-0.036-0.03514.857-0.085-0.0850.0000.0000.0000.000
130A131ARG10.8580.91716.4080.2100.2100.0000.0000.0000.000
131A132LEU0-0.046-0.01018.297-0.025-0.0250.0000.0000.0000.000
132A133TYR0-0.055-0.03617.9210.0040.0040.0000.0000.0000.000
133A134SER0-0.042-0.01714.2360.0120.0120.0000.0000.0000.000
134A135GLY00.0730.06512.890-0.053-0.0530.0000.0000.0000.000
135A136GLN00.017-0.01911.385-0.069-0.0690.0000.0000.0000.000
136A137GLY0-0.0230.00313.648-0.031-0.0310.0000.0000.0000.000
137A138GLY00.024-0.00314.0610.0310.0310.0000.0000.0000.000
138A139ALA0-0.061-0.01815.629-0.036-0.0360.0000.0000.0000.000
139A140ILE00.0180.01617.6080.0630.0630.0000.0000.0000.000
140A141VAL0-0.028-0.01420.309-0.036-0.0360.0000.0000.0000.000
141A142ASN00.000-0.00722.8790.0470.0470.0000.0000.0000.000
142A143VAL00.0230.01825.304-0.017-0.0170.0000.0000.0000.000
143A144SER00.014-0.01127.775-0.001-0.0010.0000.0000.0000.000
144A145SER0-0.008-0.02531.3540.0060.0060.0000.0000.0000.000
145A146MET0-0.028-0.01134.153-0.006-0.0060.0000.0000.0000.000
146A147ALA00.0030.00837.334-0.007-0.0070.0000.0000.0000.000
147A148ALA0-0.007-0.00336.118-0.005-0.0050.0000.0000.0000.000
148A149ILE0-0.053-0.02537.869-0.005-0.0050.0000.0000.0000.000
149A150LEU0-0.039-0.02040.619-0.005-0.0050.0000.0000.0000.000
150A151GLY00.0210.02342.254-0.002-0.0020.0000.0000.0000.000
151A152SER0-0.010-0.01940.6290.0010.0010.0000.0000.0000.000
152A153ALA00.0830.03143.7930.0020.0020.0000.0000.0000.000
153A154THR0-0.083-0.04647.5070.0000.0000.0000.0000.0000.000
154A155GLN0-0.0280.01543.417-0.002-0.0020.0000.0000.0000.000
155A156TYR00.0600.00040.1480.0030.0030.0000.0000.0000.000
156A157VAL00.0400.02541.6110.0030.0030.0000.0000.0000.000
157A158ASP-1-0.713-0.83341.0860.1050.1050.0000.0000.0000.000
158A159TYR00.0170.00433.8060.0050.0050.0000.0000.0000.000
159A160ALA0-0.0050.00837.2670.0040.0040.0000.0000.0000.000
160A161ALA00.0140.00438.3250.0000.0000.0000.0000.0000.000
161A162SER0-0.062-0.03835.0520.0030.0030.0000.0000.0000.000
162A163LYS10.8900.94030.183-0.168-0.1680.0000.0000.0000.000
163A164ALA00.0420.02134.062-0.001-0.0010.0000.0000.0000.000
164A165ALA0-0.0060.00634.851-0.005-0.0050.0000.0000.0000.000
165A166ILE0-0.0030.00628.547-0.002-0.0020.0000.0000.0000.000
166A167ASP-1-0.750-0.83230.6430.0960.0960.0000.0000.0000.000
167A168THR0-0.020-0.02032.273-0.008-0.0080.0000.0000.0000.000
168A169PHE00.0080.00526.052-0.007-0.0070.0000.0000.0000.000
169A170THR0-0.008-0.00627.2610.0030.0030.0000.0000.0000.000
170A171ILE0-0.057-0.03128.733-0.009-0.0090.0000.0000.0000.000
171A172GLY0-0.016-0.00731.162-0.010-0.0100.0000.0000.0000.000
172A173LEU00.0420.01923.613-0.007-0.0070.0000.0000.0000.000
173A174ALA0-0.0250.00025.872-0.008-0.0080.0000.0000.0000.000
174A175ARG10.8860.93326.902-0.039-0.0390.0000.0000.0000.000
175A176GLU-1-0.966-0.96227.2670.0420.0420.0000.0000.0000.000
176A177VAL00.0420.01322.415-0.009-0.0090.0000.0000.0000.000
177A178ALA00.0050.01122.933-0.013-0.0130.0000.0000.0000.000
178A179ALA0-0.031-0.02123.464-0.019-0.0190.0000.0000.0000.000
179A180GLU-1-0.857-0.88921.054-0.020-0.0200.0000.0000.0000.000
180A181GLY0-0.030-0.02718.999-0.021-0.0210.0000.0000.0000.000
181A182ILE0-0.038-0.00117.8640.0030.0030.0000.0000.0000.000
182A183ARG10.7970.90418.839-0.048-0.0480.0000.0000.0000.000
183A184VAL00.0170.00221.1210.0310.0310.0000.0000.0000.000
184A185ASN0-0.013-0.02223.425-0.030-0.0300.0000.0000.0000.000
185A186ALA00.0190.00625.6050.0190.0190.0000.0000.0000.000
186A187VAL00.0220.02126.380-0.013-0.0130.0000.0000.0000.000
187A188ARG10.8120.87028.963-0.078-0.0780.0000.0000.0000.000
188A189PRO00.0510.02529.983-0.010-0.0100.0000.0000.0000.000
189A190GLY0-0.006-0.00632.689-0.007-0.0070.0000.0000.0000.000
190A191ILE0-0.028-0.00535.8940.0050.0050.0000.0000.0000.000
191A192ILE0-0.034-0.01230.979-0.003-0.0030.0000.0000.0000.000
192A193GLU-1-0.863-0.91031.8850.1850.1850.0000.0000.0000.000
193A212SER00.0500.02245.1740.0030.0030.0000.0000.0000.000
194A213VAL00.0000.00839.487-0.002-0.0020.0000.0000.0000.000
195A214PRO00.0080.01041.741-0.001-0.0010.0000.0000.0000.000
196A215MET0-0.0040.01036.407-0.002-0.0020.0000.0000.0000.000
197A216GLN0-0.060-0.03741.3340.0030.0030.0000.0000.0000.000
198A217ARG10.7610.85734.083-0.101-0.1010.0000.0000.0000.000
199A218ALA00.0030.00936.709-0.001-0.0010.0000.0000.0000.000
200A219GLY00.010-0.00233.422-0.003-0.0030.0000.0000.0000.000
201A220MET00.007-0.00729.8260.0050.0050.0000.0000.0000.000
202A221PRO00.002-0.00727.247-0.001-0.0010.0000.0000.0000.000
203A222GLU-1-0.751-0.88324.8160.2500.2500.0000.0000.0000.000
204A223GLU-1-0.717-0.80225.6570.1170.1170.0000.0000.0000.000
205A224VAL0-0.040-0.02026.468-0.009-0.0090.0000.0000.0000.000
206A225ALA00.0080.00522.0250.0020.0020.0000.0000.0000.000
207A226ASP-1-0.854-0.93522.1400.1930.1930.0000.0000.0000.000
208A227ALA0-0.043-0.01723.233-0.012-0.0120.0000.0000.0000.000
209A228ILE0-0.030-0.02220.240-0.012-0.0120.0000.0000.0000.000
210A229LEU00.0280.00616.0890.0020.0020.0000.0000.0000.000
211A230TYR0-0.039-0.01719.278-0.017-0.0170.0000.0000.0000.000
212A231LEU0-0.0050.00621.343-0.023-0.0230.0000.0000.0000.000
213A232LEU00.0200.01816.316-0.023-0.0230.0000.0000.0000.000
214A233SER0-0.060-0.03416.927-0.032-0.0320.0000.0000.0000.000
215A234PRO00.0660.01015.735-0.014-0.0140.0000.0000.0000.000
216A235SER0-0.0040.00418.521-0.025-0.0250.0000.0000.0000.000
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