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: G67K1

Calculation Name: 3ZXX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZXX

Chain ID: A

ChEMBL ID:

UniProt ID: Q52QI9

Base Structure: X-ray

Registration Date: 2023-06-26

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 269
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3439211.54532
FMO2-HF: Nuclear repulsion 3339438.119563
FMO2-HF: Total energy -99773.425757
FMO2-MP2: Total energy -100062.83538


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:11:LEU)


Summations of interaction energy for fragment #1(A:11:LEU)
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.
-2.291.122-0.028-1.415-1.97-0.002
Interaction energy analysis for fragmet #1(A:11:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.022
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].
3A13GLY00.0630.0343.619-2.972-0.260-0.032-1.333-1.347-0.002
4A14ASP-1-0.833-0.9225.6862.6712.6710.0000.0000.0000.000
5A15HIS00.006-0.0138.353-0.219-0.2190.0000.0000.0000.000
6A16ASN0-0.126-0.06711.621-0.283-0.2830.0000.0000.0000.000
7A17ILE0-0.061-0.0289.816-0.120-0.1200.0000.0000.0000.000
8A18ARG10.8860.94312.294-0.221-0.2210.0000.0000.0000.000
9A19VAL00.0280.01812.315-0.046-0.0460.0000.0000.0000.000
10A20ALA00.010-0.00215.4430.0130.0130.0000.0000.0000.000
11A21ILE0-0.020-0.00917.186-0.023-0.0230.0000.0000.0000.000
12A22LEU0-0.013-0.00420.5470.0110.0110.0000.0000.0000.000
13A23ASP-1-0.761-0.85824.128-0.029-0.0290.0000.0000.0000.000
14A24GLY00.021-0.01226.1740.0070.0070.0000.0000.0000.000
15A25PRO0-0.040-0.02826.9950.0050.0050.0000.0000.0000.000
16A26VAL00.0120.01321.953-0.007-0.0070.0000.0000.0000.000
17A27ASP-1-0.848-0.93325.1660.0380.0380.0000.0000.0000.000
18A28ILE0-0.006-0.02322.083-0.002-0.0020.0000.0000.0000.000
19A29ALA0-0.0010.01122.9210.0120.0120.0000.0000.0000.000
20A30HIS0-0.045-0.00821.3130.0050.0050.0000.0000.0000.000
21A31PRO00.024-0.00921.6240.0110.0110.0000.0000.0000.000
22A32CYS0-0.053-0.01517.1070.0130.0130.0000.0000.0000.000
23A33PHE00.0330.01516.5390.0090.0090.0000.0000.0000.000
24A34GLN00.0050.01518.1830.0270.0270.0000.0000.0000.000
25A35GLY0-0.020-0.01415.624-0.001-0.0010.0000.0000.0000.000
26A36ALA0-0.019-0.00214.2500.0650.0650.0000.0000.0000.000
27A37ASP-1-0.879-0.91414.1980.4010.4010.0000.0000.0000.000
28A38LEU00.0020.00516.029-0.015-0.0150.0000.0000.0000.000
29A39THR0-0.032-0.01218.846-0.007-0.0070.0000.0000.0000.000
30A40VAL00.0110.01121.908-0.009-0.0090.0000.0000.0000.000
31A41LEU0-0.034-0.01924.0000.0010.0010.0000.0000.0000.000
32A42PRO00.0030.00726.993-0.007-0.0070.0000.0000.0000.000
33A43THR00.0490.02230.6490.0000.0000.0000.0000.0000.000
34A44LEU0-0.049-0.01432.5940.0010.0010.0000.0000.0000.000
35A45ALA00.0320.00735.222-0.003-0.0030.0000.0000.0000.000
36A46PRO00.0390.02537.9010.0000.0000.0000.0000.0000.000
37A47THR0-0.058-0.02739.045-0.001-0.0010.0000.0000.0000.000
38A48ALA00.010-0.01340.2210.0000.0000.0000.0000.0000.000
39A49ALA00.016-0.01540.9590.0000.0000.0000.0000.0000.000
40A50ARG10.7730.83637.1720.0120.0120.0000.0000.0000.000
41A51SER00.0010.00737.8120.0000.0000.0000.0000.0000.000
42A52ASP-1-0.781-0.90635.543-0.010-0.0100.0000.0000.0000.000
43A53GLY00.0630.02132.394-0.002-0.0020.0000.0000.0000.000
44A54PHE0-0.072-0.03430.110-0.003-0.0030.0000.0000.0000.000
45A55MET0-0.052-0.00128.5280.0030.0030.0000.0000.0000.000
46A56SER00.009-0.02125.203-0.004-0.0040.0000.0000.0000.000
47A57ALA0-0.020-0.01227.587-0.002-0.0020.0000.0000.0000.000
48A58HIS0-0.0050.00424.5370.0000.0000.0000.0000.0000.000
49A59GLY00.0500.02623.642-0.006-0.0060.0000.0000.0000.000
50A60THR00.027-0.00622.1750.0050.0050.0000.0000.0000.000
51A61HIS00.0160.04220.2480.0030.0030.0000.0000.0000.000
52A62VAL00.0460.03019.290-0.015-0.0150.0000.0000.0000.000
53A63ALA00.0140.00717.760-0.012-0.0120.0000.0000.0000.000
54A64SER0-0.037-0.03916.3160.0020.0020.0000.0000.0000.000
55A65ILE00.0360.03214.183-0.013-0.0130.0000.0000.0000.000
56A66ILE0-0.040-0.00711.741-0.074-0.0740.0000.0000.0000.000
57A67PHE0-0.005-0.01811.348-0.024-0.0240.0000.0000.0000.000
58A68GLY00.0390.03513.4260.0570.0570.0000.0000.0000.000
59A69GLN0-0.048-0.03012.0580.0290.0290.0000.0000.0000.000
60A70PRO0-0.005-0.0058.764-0.080-0.0800.0000.0000.0000.000
61A71GLU-1-0.940-0.97111.527-0.025-0.0250.0000.0000.0000.000
62A72THR0-0.035-0.00814.6080.0060.0060.0000.0000.0000.000
63A73SER0-0.052-0.04116.417-0.024-0.0240.0000.0000.0000.000
64A74VAL0-0.007-0.01915.572-0.016-0.0160.0000.0000.0000.000
65A75PRO0-0.0240.00011.3580.0210.0210.0000.0000.0000.000
66A76GLY00.0270.03111.621-0.044-0.0440.0000.0000.0000.000
67A77ILE0-0.093-0.0467.645-0.111-0.1110.0000.0000.0000.000
68A78ALA0-0.052-0.0376.840-0.430-0.4300.0000.0000.0000.000
69A79PRO0-0.019-0.0016.9080.2270.2270.0000.0000.0000.000
70A80GLN0-0.020-0.0125.663-0.249-0.2490.0000.0000.0000.000
71A81CYS0-0.0630.0008.8760.0560.0560.0000.0000.0000.000
72A82ARG10.9771.01110.587-0.364-0.3640.0000.0000.0000.000
73A83GLY00.014-0.01014.308-0.049-0.0490.0000.0000.0000.000
74A84LEU0-0.053-0.03316.4500.0040.0040.0000.0000.0000.000
75A85ILE00.0290.01019.800-0.020-0.0200.0000.0000.0000.000
76A86VAL0-0.026-0.02222.3880.0060.0060.0000.0000.0000.000
77A87PRO0-0.0030.02025.163-0.009-0.0090.0000.0000.0000.000
78A88ILE0-0.008-0.02027.3050.0020.0020.0000.0000.0000.000
79A89PHE00.0150.01129.283-0.004-0.0040.0000.0000.0000.000
80A90SER00.000-0.00733.0940.0040.0040.0000.0000.0000.000
81A91ASP-1-0.834-0.91535.8650.0140.0140.0000.0000.0000.000
82A92ASP-1-0.869-0.94133.5540.0110.0110.0000.0000.0000.000
83A93ARG10.8250.89535.198-0.013-0.0130.0000.0000.0000.000
84A94ARG10.8500.94037.922-0.013-0.0130.0000.0000.0000.000
85A95ARG10.8660.98537.0160.0080.0080.0000.0000.0000.000
86A96ILE00.0090.01231.9130.0020.0020.0000.0000.0000.000
87A97THR0-0.054-0.02135.300-0.003-0.0030.0000.0000.0000.000
88A98GLN00.028-0.00534.325-0.001-0.0010.0000.0000.0000.000
89A99LEU0-0.024-0.00434.0120.0020.0020.0000.0000.0000.000
90A100ASP-1-0.830-0.90333.6470.0160.0160.0000.0000.0000.000
91A101LEU00.0060.00427.6420.0040.0040.0000.0000.0000.000
92A102ALA00.000-0.00429.6150.0030.0030.0000.0000.0000.000
93A103ARG10.9730.98830.545-0.021-0.0210.0000.0000.0000.000
94A104GLY00.0190.01628.5790.0070.0070.0000.0000.0000.000
95A105ILE00.014-0.00425.5700.0080.0080.0000.0000.0000.000
96A106GLU-1-0.924-0.96426.0930.0380.0380.0000.0000.0000.000
97A107ARG10.8300.91227.748-0.049-0.0490.0000.0000.0000.000
98A108ALA00.0200.01322.4330.0120.0120.0000.0000.0000.000
99A109VAL00.007-0.00222.9090.0140.0140.0000.0000.0000.000
100A110ASN0-0.026-0.01824.2090.0110.0110.0000.0000.0000.000
101A111ALA0-0.053-0.00723.1970.0080.0080.0000.0000.0000.000
102A112GLY0-0.027-0.01921.1530.0240.0240.0000.0000.0000.000
103A113ALA0-0.034-0.01218.4460.0230.0230.0000.0000.0000.000
104A114HIS00.0470.03314.846-0.003-0.0030.0000.0000.0000.000
105A115ILE0-0.010-0.00612.738-0.029-0.0290.0000.0000.0000.000
106A116ILE0-0.011-0.00516.8620.0200.0200.0000.0000.0000.000
107A117ASN00.0240.03017.800-0.036-0.0360.0000.0000.0000.000
108A118ILE0-0.006-0.01219.7830.0130.0130.0000.0000.0000.000
109A119SER00.017-0.01221.419-0.009-0.0090.0000.0000.0000.000
110A120GLY00.0190.03023.655-0.005-0.0050.0000.0000.0000.000
111A121GLY0-0.018-0.02127.147-0.003-0.0030.0000.0000.0000.000
112A122GLU-1-0.785-0.87029.847-0.013-0.0130.0000.0000.0000.000
113A123LEU0-0.038-0.01833.458-0.002-0.0020.0000.0000.0000.000
114A124THR0-0.105-0.04334.7960.0030.0030.0000.0000.0000.000
115A125ASP-1-0.971-0.97837.127-0.028-0.0280.0000.0000.0000.000
116A126PHE0-0.058-0.06035.760-0.004-0.0040.0000.0000.0000.000
117A127GLY0-0.011-0.00634.018-0.001-0.0010.0000.0000.0000.000
118A128GLU-1-0.770-0.87334.414-0.021-0.0210.0000.0000.0000.000
119A129ALA00.013-0.01034.2370.0000.0000.0000.0000.0000.000
120A130ASP-1-0.914-0.95036.330-0.004-0.0040.0000.0000.0000.000
121A131GLY0-0.002-0.01736.5700.0010.0010.0000.0000.0000.000
122A132TRP0-0.003-0.00635.8770.0020.0020.0000.0000.0000.000
123A133LEU00.0100.00130.1120.0030.0030.0000.0000.0000.000
124A134GLU-1-0.871-0.93531.746-0.011-0.0110.0000.0000.0000.000
125A135ASN0-0.015-0.01432.206-0.001-0.0010.0000.0000.0000.000
126A136ALA00.0200.01529.6970.0030.0030.0000.0000.0000.000
127A137VAL00.003-0.00626.7610.0040.0040.0000.0000.0000.000
128A138SER0-0.019-0.01427.481-0.001-0.0010.0000.0000.0000.000
129A139LEU00.0040.01427.8720.0020.0020.0000.0000.0000.000
130A140CYS0-0.0020.00423.5720.0080.0080.0000.0000.0000.000
131A141ARG10.9600.99324.1290.0140.0140.0000.0000.0000.000
132A142GLN0-0.058-0.04025.573-0.002-0.0020.0000.0000.0000.000
133A143ASN0-0.066-0.03824.5680.0080.0080.0000.0000.0000.000
134A144ASN0-0.046-0.00919.7050.0020.0020.0000.0000.0000.000
135A145VAL00.0410.02619.6700.0110.0110.0000.0000.0000.000
136A146LEU0-0.059-0.02315.764-0.013-0.0130.0000.0000.0000.000
137A147LEU00.0250.01218.9490.0050.0050.0000.0000.0000.000
138A148VAL00.0190.00316.667-0.011-0.0110.0000.0000.0000.000
139A149ALA00.009-0.00920.1080.0100.0100.0000.0000.0000.000
140A150ALA00.0230.02423.051-0.011-0.0110.0000.0000.0000.000
141A151ALA0-0.0070.00024.1900.0080.0080.0000.0000.0000.000
142A152GLY00.0610.04626.4310.0070.0070.0000.0000.0000.000
143A153ASN0-0.005-0.01727.548-0.011-0.0110.0000.0000.0000.000
144A154ASN00.0640.03030.1590.0010.0010.0000.0000.0000.000
145A155GLY00.0670.04832.0540.0030.0030.0000.0000.0000.000
146A156CYS0-0.089-0.03633.2660.0060.0060.0000.0000.0000.000
147A157ASP-1-0.873-0.93433.402-0.054-0.0540.0000.0000.0000.000
148A159LEU00.0490.02730.974-0.006-0.0060.0000.0000.0000.000
149A160HIS0-0.014-0.01529.5280.0040.0040.0000.0000.0000.000
150A161VAL0-0.0090.03230.436-0.002-0.0020.0000.0000.0000.000
151A162PRO00.050-0.02026.5370.0010.0010.0000.0000.0000.000
152A163ALA0-0.0040.00025.9050.0000.0000.0000.0000.0000.000
153A164ALA00.009-0.00226.761-0.005-0.0050.0000.0000.0000.000
154A165LEU00.0270.02928.8060.0020.0020.0000.0000.0000.000
155A166PRO00.031-0.00327.824-0.005-0.0050.0000.0000.0000.000
156A167ALA0-0.074-0.04124.5170.0050.0050.0000.0000.0000.000
157A168VAL00.0020.02223.2240.0010.0010.0000.0000.0000.000
158A169LEU0-0.054-0.01917.204-0.006-0.0060.0000.0000.0000.000
159A170ALA00.0030.00721.5320.0010.0010.0000.0000.0000.000
160A171VAL0-0.032-0.01418.612-0.016-0.0160.0000.0000.0000.000
161A172GLY00.0530.01521.5120.0140.0140.0000.0000.0000.000
162A173ALA0-0.033-0.02421.231-0.017-0.0170.0000.0000.0000.000
163A174MET0-0.042-0.01317.6640.0140.0140.0000.0000.0000.000
164A175ASP-1-0.783-0.90721.410-0.144-0.1440.0000.0000.0000.000
165A176ASP-1-0.907-0.94819.970-0.191-0.1910.0000.0000.0000.000
166A177HIS0-0.124-0.05920.061-0.019-0.0190.0000.0000.0000.000
167A178GLY0-0.057-0.02520.7870.0000.0000.0000.0000.0000.000
168A179HIS0-0.028-0.02621.4910.0060.0060.0000.0000.0000.000
169A180PRO0-0.026-0.01324.691-0.003-0.0030.0000.0000.0000.000
170A181LEU00.0370.02323.9370.0080.0080.0000.0000.0000.000
171A182ASP-1-0.916-0.96027.300-0.072-0.0720.0000.0000.0000.000
172A183PHE0-0.020-0.01625.5770.0050.0050.0000.0000.0000.000
173A184SER00.0090.01626.0160.0020.0020.0000.0000.0000.000
174A185ASN0-0.077-0.03528.2520.0010.0010.0000.0000.0000.000
175A186TRP0-0.015-0.02028.519-0.006-0.0060.0000.0000.0000.000
176A187GLY00.0680.04230.4630.0010.0010.0000.0000.0000.000
177A188SER00.009-0.01530.924-0.004-0.0040.0000.0000.0000.000
178A189THR00.0680.03929.471-0.004-0.0040.0000.0000.0000.000
179A190TYR0-0.011-0.03526.804-0.001-0.0010.0000.0000.0000.000
180A191GLU-1-0.974-0.97726.084-0.082-0.0820.0000.0000.0000.000
181A192GLN0-0.046-0.02326.486-0.003-0.0030.0000.0000.0000.000
182A193GLN0-0.103-0.06023.769-0.001-0.0010.0000.0000.0000.000
183A194GLY00.0350.02022.9740.0000.0000.0000.0000.0000.000
184A195ILE0-0.011-0.00116.630-0.006-0.0060.0000.0000.0000.000
185A196LEU0-0.0180.00020.6910.0060.0060.0000.0000.0000.000
186A197ALA00.007-0.00416.320-0.029-0.0290.0000.0000.0000.000
187A198PRO00.004-0.00114.9280.0230.0230.0000.0000.0000.000
188A199GLY00.036-0.00518.049-0.001-0.0010.0000.0000.0000.000
189A200GLU-1-0.851-0.93220.929-0.107-0.1070.0000.0000.0000.000
190A201ASP-1-0.884-0.94421.174-0.118-0.1180.0000.0000.0000.000
191A202ILE0-0.005-0.00516.973-0.018-0.0180.0000.0000.0000.000
192A203LEU0-0.079-0.04616.6760.0200.0200.0000.0000.0000.000
193A204GLY00.0560.00917.877-0.015-0.0150.0000.0000.0000.000
194A205ALA0-0.013-0.01319.8590.0060.0060.0000.0000.0000.000
195A206LYS10.8890.95821.9080.0290.0290.0000.0000.0000.000
196A207PRO0-0.002-0.01425.6990.0070.0070.0000.0000.0000.000
197A208GLY0-0.0090.00427.524-0.004-0.0040.0000.0000.0000.000
198A209GLY0-0.0120.00026.0630.0020.0020.0000.0000.0000.000
199A210GLY0-0.015-0.01225.318-0.005-0.0050.0000.0000.0000.000
200A211THR0-0.039-0.02520.5900.0050.0050.0000.0000.0000.000
201A212GLU-1-0.899-0.96222.990-0.046-0.0460.0000.0000.0000.000
202A213ARG10.8810.95017.6630.1530.1530.0000.0000.0000.000
203A214LEU00.0240.02922.5910.0090.0090.0000.0000.0000.000
204A215SER00.0770.05322.796-0.017-0.0170.0000.0000.0000.000
205A216GLY0-0.023-0.01823.8270.0120.0120.0000.0000.0000.000
206A217THR0-0.010-0.01122.822-0.009-0.0090.0000.0000.0000.000
207A218SER0-0.017-0.00722.151-0.004-0.0040.0000.0000.0000.000
208A219PHE00.0070.00819.9790.0040.0040.0000.0000.0000.000
209A220ALA00.0530.03418.015-0.018-0.0180.0000.0000.0000.000
210A221THR0-0.020-0.03717.129-0.025-0.0250.0000.0000.0000.000
211A222PRO00.0250.01416.045-0.010-0.0100.0000.0000.0000.000
212A223ILE00.0070.01012.277-0.036-0.0360.0000.0000.0000.000
213A224VAL0-0.0020.00512.196-0.074-0.0740.0000.0000.0000.000
214A225SER0-0.011-0.02013.214-0.015-0.0150.0000.0000.0000.000
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