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: 52LGZ

Calculation Name: 4Z8Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Z8Z

Chain ID: A

ChEMBL ID:

UniProt ID: A3DBP6

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 OptHSide
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 323
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5478192.418898
FMO2-HF: Nuclear repulsion 5345486.504815
FMO2-HF: Total energy -132705.914083
FMO2-MP2: Total energy -133088.785847


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.
-30.952-24.27520.952-10.602-17.027-0.067
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 : -0.027 / q_NPA : -0.010
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].
3A3GLU-1-0.781-0.8503.459-3.652-1.1020.023-1.335-1.2380.004
4A4ALA00.0340.0126.0700.6290.6290.0000.0000.0000.000
5A5SER0-0.052-0.0294.3311.1251.303-0.001-0.014-0.1620.000
6A6SER00.047-0.0062.674-0.1071.0061.146-0.831-1.429-0.008
7A7LYS10.8850.9454.5401.1661.240-0.001-0.018-0.0550.000
8A8PHE0-0.029-0.0088.0440.0980.0980.0000.0000.0000.000
9A9VAL0-0.029-0.0166.0130.1380.1380.0000.0000.0000.000
10A10ASP-1-0.732-0.8608.554-0.296-0.2960.0000.0000.0000.000
11A11ASN00.024-0.00510.404-0.105-0.1050.0000.0000.0000.000
12A12ILE00.0190.00711.911-0.048-0.0480.0000.0000.0000.000
13A13ALA0-0.029-0.00312.542-0.043-0.0430.0000.0000.0000.000
14A14ILE00.008-0.00614.378-0.070-0.0700.0000.0000.0000.000
15A15GLU-1-0.938-0.96016.6510.2440.2440.0000.0000.0000.000
16A16LYS10.9180.97317.167-0.494-0.4940.0000.0000.0000.000
17A17LEU00.0000.00616.655-0.033-0.0330.0000.0000.0000.000
18A18LEU00.0200.01120.059-0.026-0.0260.0000.0000.0000.000
19A19ASN0-0.040-0.02221.807-0.035-0.0350.0000.0000.0000.000
20A20GLU-1-0.920-0.97421.4340.3220.3220.0000.0000.0000.000
21A21LYS10.8340.90319.886-0.241-0.2410.0000.0000.0000.000
22A22LEU00.0310.01822.325-0.014-0.0140.0000.0000.0000.000
23A23LEU0-0.020-0.01025.358-0.020-0.0200.0000.0000.0000.000
24A24ARG10.8400.92927.163-0.168-0.1680.0000.0000.0000.000
25A25VAL00.0130.02528.725-0.002-0.0020.0000.0000.0000.000
26A26SER0-0.097-0.06431.485-0.005-0.0050.0000.0000.0000.000
27A27HIS0-0.018-0.01931.661-0.005-0.0050.0000.0000.0000.000
28A28ARG10.8760.93234.859-0.009-0.0090.0000.0000.0000.000
29A29PRO00.0370.04236.4990.0000.0000.0000.0000.0000.000
30A30LYS10.8600.90937.6030.0090.0090.0000.0000.0000.000
31A31ASN0-0.001-0.00940.2740.0020.0020.0000.0000.0000.000
32A32LEU00.0020.00837.124-0.001-0.0010.0000.0000.0000.000
33A33PHE0-0.013-0.01740.324-0.001-0.0010.0000.0000.0000.000
34A34TYR0-0.045-0.03538.4300.0050.0050.0000.0000.0000.000
35A35ASP-1-0.840-0.91940.774-0.061-0.0610.0000.0000.0000.000
36A36ASP-1-0.791-0.90937.358-0.086-0.0860.0000.0000.0000.000
37A37GLU-1-0.957-0.97539.467-0.064-0.0640.0000.0000.0000.000
38A38LYS10.8740.94141.5430.0550.0550.0000.0000.0000.000
39A39VAL0-0.0220.00835.3510.0020.0020.0000.0000.0000.000
40A40PHE00.0250.00331.8530.0010.0010.0000.0000.0000.000
41A41ASP-1-0.860-0.92436.968-0.071-0.0710.0000.0000.0000.000
42A42ASP-1-0.886-0.95138.626-0.046-0.0460.0000.0000.0000.000
43A43LEU0-0.058-0.02232.2150.0030.0030.0000.0000.0000.000
44A44CYS0-0.025-0.00436.0480.0030.0030.0000.0000.0000.000
45A45LYS10.8480.91537.6740.0560.0560.0000.0000.0000.000
46A46CYS0-0.069-0.01136.4570.0050.0050.0000.0000.0000.000
47A47GLU-1-0.845-0.90637.324-0.033-0.0330.0000.0000.0000.000
48A48THR0-0.038-0.02333.6190.0030.0030.0000.0000.0000.000
49A49ASP-1-0.789-0.84536.8400.0030.0030.0000.0000.0000.000
50A50MET00.056-0.00435.3240.0030.0030.0000.0000.0000.000
51A51SER0-0.114-0.07238.9800.0050.0050.0000.0000.0000.000
52A52LYS10.8430.90939.164-0.002-0.0020.0000.0000.0000.000
53A53VAL0-0.0230.01033.6840.0020.0020.0000.0000.0000.000
54A54LYS10.9390.97734.585-0.041-0.0410.0000.0000.0000.000
55A55LEU0-0.015-0.01130.036-0.001-0.0010.0000.0000.0000.000
56A56ALA0-0.0030.01230.9250.0020.0020.0000.0000.0000.000
57A57GLU-1-0.812-0.90629.5410.0910.0910.0000.0000.0000.000
58A58GLY00.0410.00629.6400.0040.0040.0000.0000.0000.000
59A59ASP-1-0.901-0.93629.2060.1460.1460.0000.0000.0000.000
60A60LYS10.7870.84530.370-0.088-0.0880.0000.0000.0000.000
61A61ASN0-0.0540.00724.526-0.001-0.0010.0000.0000.0000.000
62A62LEU00.0470.02321.4130.0090.0090.0000.0000.0000.000
63A63LYS10.8660.93625.194-0.098-0.0980.0000.0000.0000.000
64A64ARG10.8510.93325.453-0.090-0.0900.0000.0000.0000.000
65A65PHE00.0170.00727.550-0.001-0.0010.0000.0000.0000.000
66A66GLU-1-0.858-0.92828.9560.0650.0650.0000.0000.0000.000
67A67PHE00.0300.00028.691-0.002-0.0020.0000.0000.0000.000
68A68PRO0-0.027-0.01332.9300.0000.0000.0000.0000.0000.000
69A69SER00.0240.00132.069-0.005-0.0050.0000.0000.0000.000
70A70PHE0-0.028-0.02633.8680.0030.0030.0000.0000.0000.000
71A71LEU00.0000.01534.0940.0000.0000.0000.0000.0000.000
72A72LYS10.8630.92235.2340.0050.0050.0000.0000.0000.000
73A73THR0-0.008-0.00234.138-0.006-0.0060.0000.0000.0000.000
74A74GLU-1-0.953-0.98637.3490.0100.0100.0000.0000.0000.000
75A75GLU-1-0.905-0.92338.2160.0070.0070.0000.0000.0000.000
76A76TYR0-0.064-0.05334.1720.0050.0050.0000.0000.0000.000
77A77ILE00.0390.00135.536-0.003-0.0030.0000.0000.0000.000
78A78GLU-1-0.795-0.91332.2530.0480.0480.0000.0000.0000.000
79A79ASN00.0270.02229.9870.0050.0050.0000.0000.0000.000
80A80ASN0-0.063-0.01131.707-0.012-0.0120.0000.0000.0000.000
81A81ILE0-0.040-0.00731.223-0.005-0.0050.0000.0000.0000.000
82A82VAL00.0150.02027.5890.0030.0030.0000.0000.0000.000
83A83TYR00.018-0.00326.1790.0050.0050.0000.0000.0000.000
84A84LEU0-0.007-0.00623.847-0.005-0.0050.0000.0000.0000.000
85A85TYR0-0.064-0.05421.3800.0090.0090.0000.0000.0000.000
86A86TYR0-0.018-0.01022.261-0.008-0.0080.0000.0000.0000.000
87A87HIS00.0100.00319.5880.0230.0230.0000.0000.0000.000
88A88PRO0-0.0110.00521.425-0.014-0.0140.0000.0000.0000.000
89A89ALA00.0480.03221.5310.0150.0150.0000.0000.0000.000
90A90LYS10.8330.89823.117-0.067-0.0670.0000.0000.0000.000
91A91ASP-1-0.834-0.90625.0680.0460.0460.0000.0000.0000.000
92A92PRO00.0140.01724.860-0.006-0.0060.0000.0000.0000.000
93A93VAL00.0320.00523.639-0.003-0.0030.0000.0000.0000.000
94A94CYS0-0.060-0.01322.979-0.015-0.0150.0000.0000.0000.000
95A95ASN00.009-0.01323.5350.0240.0240.0000.0000.0000.000
96A96ILE00.001-0.00317.292-0.019-0.0190.0000.0000.0000.000
97A97LEU00.0000.01321.0200.0230.0230.0000.0000.0000.000
98A98LEU0-0.021-0.01614.427-0.026-0.0260.0000.0000.0000.000
99A99LEU00.0150.00618.1610.0320.0320.0000.0000.0000.000
100A100HIS00.007-0.00215.666-0.031-0.0310.0000.0000.0000.000
101A101GLY00.0360.01915.630-0.037-0.0370.0000.0000.0000.000
102A102LEU0-0.032-0.01916.5260.0300.0300.0000.0000.0000.000
103A103TYR0-0.042-0.03818.0610.0120.0120.0000.0000.0000.000
104A104ASP-1-0.796-0.85614.7760.1850.1850.0000.0000.0000.000
105A105ASP-1-0.854-0.91717.5280.2490.2490.0000.0000.0000.000
106A106ASN00.004-0.00414.109-0.026-0.0260.0000.0000.0000.000
107A107MET00.0350.02715.0560.0170.0170.0000.0000.0000.000
108A108LEU00.018-0.00114.378-0.012-0.0120.0000.0000.0000.000
109A109ASN0-0.050-0.00910.5710.1370.1370.0000.0000.0000.000
110A110TYR00.005-0.0259.934-0.033-0.0330.0000.0000.0000.000
111A111GLY0-0.0080.01412.091-0.058-0.0580.0000.0000.0000.000
112A112PHE0-0.029-0.0196.8070.0270.0270.0000.0000.0000.000
113A113LEU00.0630.0209.443-0.025-0.0250.0000.0000.0000.000
114A114THR0-0.017-0.02410.817-0.023-0.0230.0000.0000.0000.000
115A115ARG10.8870.95713.211-0.289-0.2890.0000.0000.0000.000
116A116MET0-0.0120.0009.816-0.009-0.0090.0000.0000.0000.000
117A117LEU0-0.0100.00213.528-0.027-0.0270.0000.0000.0000.000
118A118ASN0-0.052-0.04715.6860.0130.0130.0000.0000.0000.000
119A119GLU-1-0.886-0.94714.9690.2260.2260.0000.0000.0000.000
120A120LEU0-0.059-0.01614.557-0.008-0.0080.0000.0000.0000.000
121A121LYS10.7810.89518.694-0.051-0.0510.0000.0000.0000.000
122A122PHE00.0760.03117.978-0.016-0.0160.0000.0000.0000.000
123A123ASN0-0.028-0.01420.5140.0330.0330.0000.0000.0000.000
124A124VAL00.0080.01216.924-0.021-0.0210.0000.0000.0000.000
125A125PHE0-0.007-0.00620.1900.0230.0230.0000.0000.0000.000
126A126LEU0-0.0020.00016.516-0.018-0.0180.0000.0000.0000.000
127A127MET0-0.0130.00220.2320.0140.0140.0000.0000.0000.000
128A128GLU-1-0.761-0.85621.3260.0890.0890.0000.0000.0000.000
129A129LEU00.0050.00420.588-0.012-0.0120.0000.0000.0000.000
130A130PRO00.0580.02423.8940.0160.0160.0000.0000.0000.000
131A131PHE0-0.022-0.02126.034-0.001-0.0010.0000.0000.0000.000
132A132HIS0-0.0030.00921.0500.0120.0120.0000.0000.0000.000
133A133PHE0-0.016-0.02017.9540.0030.0030.0000.0000.0000.000
134A134ASN0-0.046-0.04324.1900.0020.0020.0000.0000.0000.000
135A135ARG10.7320.86926.474-0.015-0.0150.0000.0000.0000.000
136A136LYS10.7880.90726.881-0.105-0.1050.0000.0000.0000.000
137A137PRO00.0300.01928.8640.0040.0040.0000.0000.0000.000
138A138ALA0-0.022-0.01931.9030.0070.0070.0000.0000.0000.000
139A139GLU-1-0.860-0.92033.8180.0490.0490.0000.0000.0000.000
140A140SER0-0.064-0.03129.3750.0020.0020.0000.0000.0000.000
141A141PHE0-0.014-0.00528.0300.0130.0130.0000.0000.0000.000
142A142PHE0-0.027-0.02523.6820.0200.0200.0000.0000.0000.000
143A143SER00.005-0.01421.490-0.024-0.0240.0000.0000.0000.000
144A144GLY00.0740.00923.0430.0070.0070.0000.0000.0000.000
145A145GLU-1-0.837-0.87524.3210.0430.0430.0000.0000.0000.000
146A146TYR0-0.075-0.08026.841-0.011-0.0110.0000.0000.0000.000
147A147PHE0-0.043-0.00924.732-0.010-0.0100.0000.0000.0000.000
148A148ILE00.0190.01324.049-0.016-0.0160.0000.0000.0000.000
149A149SER00.0390.03226.7740.0130.0130.0000.0000.0000.000
150A150ALA00.0300.00229.573-0.009-0.0090.0000.0000.0000.000
151A151ASP-1-0.794-0.88332.588-0.017-0.0170.0000.0000.0000.000
152A152LEU00.019-0.00531.294-0.002-0.0020.0000.0000.0000.000
153A153LEU00.0060.02533.143-0.006-0.0060.0000.0000.0000.000
154A154ARG10.8680.94632.224-0.009-0.0090.0000.0000.0000.000
155A155ALA00.0010.00329.0080.0000.0000.0000.0000.0000.000
156A156ARG10.8210.89429.7490.0670.0670.0000.0000.0000.000
157A157ASN0-0.018-0.02831.654-0.010-0.0100.0000.0000.0000.000
158A158ALA00.0330.02928.5720.0000.0000.0000.0000.0000.000
159A159PHE00.0470.00923.976-0.001-0.0010.0000.0000.0000.000
160A160ILE00.0150.00328.255-0.006-0.0060.0000.0000.0000.000
161A161GLN00.0180.00930.4520.0000.0000.0000.0000.0000.000
162A162SER0-0.002-0.02125.4450.0050.0050.0000.0000.0000.000
163A163ILE0-0.030-0.00727.290-0.004-0.0040.0000.0000.0000.000
164A164TYR0-0.006-0.02828.859-0.002-0.0020.0000.0000.0000.000
165A165ASP-1-0.718-0.83727.932-0.014-0.0140.0000.0000.0000.000
166A166ILE0-0.0070.00924.2530.0050.0050.0000.0000.0000.000
167A167GLU-1-0.793-0.87927.397-0.071-0.0710.0000.0000.0000.000
168A168ALA00.0170.01730.8600.0040.0040.0000.0000.0000.000
169A169SER0-0.010-0.02826.6770.0100.0100.0000.0000.0000.000
170A170ARG10.8330.92127.9700.0720.0720.0000.0000.0000.000
171A171ASN0-0.014-0.02529.2790.0070.0070.0000.0000.0000.000
172A172LEU00.0060.01129.8580.0040.0040.0000.0000.0000.000
173A173ILE0-0.003-0.01525.5190.0030.0030.0000.0000.0000.000
174A174GLY0-0.057-0.03029.7860.0010.0010.0000.0000.0000.000
175A175ASN0-0.040-0.02932.5330.0030.0030.0000.0000.0000.000
176A176ILE0-0.073-0.01129.2570.0050.0050.0000.0000.0000.000
177A177ASN0-0.037-0.01828.147-0.003-0.0030.0000.0000.0000.000
178A178THR00.0680.03432.410-0.002-0.0020.0000.0000.0000.000
179A179LEU0-0.071-0.01627.289-0.006-0.0060.0000.0000.0000.000
180A180PRO00.0060.00326.977-0.004-0.0040.0000.0000.0000.000
181A181CYS0-0.0150.00225.1870.0100.0100.0000.0000.0000.000
182A182LEU00.0170.00019.614-0.011-0.0110.0000.0000.0000.000
183A183LEU0-0.0040.01921.6600.0180.0180.0000.0000.0000.000
184A184VAL00.002-0.01615.073-0.036-0.0360.0000.0000.0000.000
185A185GLY00.0510.03617.2670.0430.0430.0000.0000.0000.000
186A186PHE00.011-0.0109.718-0.066-0.0660.0000.0000.0000.000
187A187SER00.001-0.00713.5560.0850.0850.0000.0000.0000.000
188A188MET00.005-0.00515.133-0.019-0.0190.0000.0000.0000.000
189A189GLY00.0830.04617.8140.0010.0010.0000.0000.0000.000
190A190GLY0-0.037-0.01117.337-0.001-0.0010.0000.0000.0000.000
191A191CYS0-0.034-0.00718.243-0.001-0.0010.0000.0000.0000.000
192A192ILE00.011-0.00220.9460.0080.0080.0000.0000.0000.000
193A193SER0-0.009-0.02020.6560.0130.0130.0000.0000.0000.000
194A194PHE0-0.018-0.01421.5170.0000.0000.0000.0000.0000.000
195A195ARG10.8740.94623.2300.1510.1510.0000.0000.0000.000
196A196TYR00.054-0.00425.8590.0110.0110.0000.0000.0000.000
197A197HIS00.0050.01524.9690.0130.0130.0000.0000.0000.000
198A198MET0-0.116-0.02726.8300.0000.0000.0000.0000.0000.000
199A199LEU0-0.056-0.01729.3170.0080.0080.0000.0000.0000.000
200A200ARG10.8280.91330.5020.0950.0950.0000.0000.0000.000
201A201ASP-1-0.921-0.94730.076-0.115-0.1150.0000.0000.0000.000
202A202SER00.0380.01430.4280.0030.0030.0000.0000.0000.000
203A203PHE0-0.027-0.01124.6580.0110.0110.0000.0000.0000.000
204A204LYS10.8600.94325.3670.1390.1390.0000.0000.0000.000
205A205GLY00.0140.00224.092-0.010-0.0100.0000.0000.0000.000
206A206THR0-0.030-0.02621.1260.0240.0240.0000.0000.0000.000
207A207PHE0-0.0030.00113.107-0.025-0.0250.0000.0000.0000.000
208A208LEU0-0.016-0.00116.5660.0300.0300.0000.0000.0000.000
209A209ILE00.011-0.00710.357-0.087-0.0870.0000.0000.0000.000
210A210ASN0-0.0120.0107.668-0.038-0.0380.0000.0000.0000.000
211A211PRO0-0.0130.00712.2010.0920.0920.0000.0000.0000.000
212A212VAL0-0.003-0.00515.801-0.036-0.0360.0000.0000.0000.000
213A213THR00.023-0.00217.4250.0050.0050.0000.0000.0000.000
214A214ASP-1-0.911-0.97020.108-0.231-0.2310.0000.0000.0000.000
215A215MET00.0260.00523.4750.0030.0030.0000.0000.0000.000
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