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: 76ZZK

Calculation Name: 1YB2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YB2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HJW1

Base Structure: X-ray

Registration Date: 2023-09-23

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2679484.700639
FMO2-HF: Nuclear repulsion 2587845.111365
FMO2-HF: Total energy -91639.589275
FMO2-MP2: Total energy -91901.947991


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:6:PRO)


Summations of interaction energy for fragment #1(A:6:PRO)
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.
-24.996-11.01313.378-10.697-16.662-0.078
Interaction energy analysis for fragmet #1(A:6:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.005
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].
3A8ILE0-0.065-0.0263.683-2.593-0.053-0.033-1.342-1.1650.003
4A9LEU0-0.0260.0035.4040.5000.5000.0000.0000.0000.000
5A10VAL00.0220.0077.800-0.207-0.2070.0000.0000.0000.000
6A11SER0-0.031-0.04110.389-0.085-0.0850.0000.0000.0000.000
7A12GLU-1-0.858-0.92513.6840.2970.2970.0000.0000.0000.000
8A13ASP-1-0.882-0.93716.8060.2110.2110.0000.0000.0000.000
9A14GLU-1-0.874-0.91515.8940.2090.2090.0000.0000.0000.000
10A15TYR00.0020.00410.9430.0930.0930.0000.0000.0000.000
11A16GLY0-0.026-0.02310.586-0.108-0.1080.0000.0000.0000.000
12A17LYS10.8990.9527.9330.1040.1040.0000.0000.0000.000
13A18PHE0-0.023-0.0132.476-0.5360.5010.423-0.376-1.084-0.002
14A19ASP-1-0.881-0.9365.363-2.392-2.3920.0000.0000.0000.000
15A20GLU-1-0.837-0.9442.285-21.686-16.3394.329-4.258-5.417-0.059
16A21SER0-0.044-0.0094.8620.5210.647-0.001-0.006-0.1180.000
17A22THR0-0.054-0.0328.2080.3710.3710.0000.0000.0000.000
18A23ASN00.0060.0126.851-0.050-0.0500.0000.0000.0000.000
19A24SER0-0.026-0.0018.5110.3660.3660.0000.0000.0000.000
20A25ILE00.0420.0078.083-0.071-0.0710.0000.0000.0000.000
21A26LEU0-0.018-0.0109.9310.0410.0410.0000.0000.0000.000
22A27VAL00.0600.02411.6930.0790.0790.0000.0000.0000.000
23A28LYS10.8570.92213.847-0.201-0.2010.0000.0000.0000.000
24A29GLY0-0.004-0.00415.6190.0060.0060.0000.0000.0000.000
25A30LYS10.9090.95517.310-0.028-0.0280.0000.0000.0000.000
26A31MET0-0.006-0.01312.1760.0270.0270.0000.0000.0000.000
27A32HIS0-0.022-0.00713.2010.0140.0140.0000.0000.0000.000
28A33HIS00.0600.02612.037-0.109-0.1090.0000.0000.0000.000
29A34LEU0-0.0100.0038.2320.1060.1060.0000.0000.0000.000
30A35GLY00.008-0.01312.141-0.045-0.0450.0000.0000.0000.000
31A36ILE0-0.053-0.02212.662-0.090-0.0900.0000.0000.0000.000
32A37SER00.0370.00711.691-0.030-0.0300.0000.0000.0000.000
33A38ARG10.9020.9779.6990.3890.3890.0000.0000.0000.000
34A39VAL00.0410.0255.4900.0420.0420.0000.0000.0000.000
35A40ILE0-0.064-0.0293.9280.0610.3550.002-0.057-0.2390.000
36A41GLU-1-0.870-0.9412.799-4.785-3.2300.359-0.718-1.195-0.006
37A42PRO00.0140.0012.304-0.3920.8920.994-0.346-1.9330.002
38A43GLY00.013-0.0153.957-0.768-0.6680.003-0.023-0.0800.000
39A44ASP-1-0.796-0.8566.033-0.368-0.3680.0000.0000.0000.000
40A45GLU-1-0.886-0.9257.6430.4580.4580.0000.0000.0000.000
41A46LEU0-0.026-0.0246.339-0.166-0.1660.0000.0000.0000.000
42A47ILE0-0.026-0.01610.5780.0350.0350.0000.0000.0000.000
43A48VAL00.0190.00312.341-0.056-0.0560.0000.0000.0000.000
44A49SER0-0.036-0.03115.1390.0200.0200.0000.0000.0000.000
45A50GLY0-0.019-0.00518.3600.0080.0080.0000.0000.0000.000
46A51LYS10.8700.95315.080-0.250-0.2500.0000.0000.0000.000
47A52SER0-0.034-0.04414.104-0.031-0.0310.0000.0000.0000.000
48A53PHE0-0.027-0.0139.667-0.009-0.0090.0000.0000.0000.000
49A54ILE0-0.0010.0077.599-0.094-0.0940.0000.0000.0000.000
50A55VAL00.0120.0122.1221.136-1.0095.053-1.056-1.8520.005
51A56SER00.0240.0044.388-0.661-0.3940.001-0.077-0.1910.000
52A57ASP-1-0.814-0.9012.4978.49212.2052.231-2.666-3.278-0.021
53A58PHE0-0.036-0.0293.322-1.976-2.1110.0170.228-0.1100.000
54A59SER00.0550.0216.305-0.076-0.0760.0000.0000.0000.000
55A60PRO00.0100.0049.561-0.102-0.1020.0000.0000.0000.000
56A61MET0-0.0190.00012.032-0.070-0.0700.0000.0000.0000.000
57A62TYR00.0550.0148.091-0.053-0.0530.0000.0000.0000.000
58A63PHE0-0.014-0.00311.864-0.084-0.0840.0000.0000.0000.000
59A64GLY00.023-0.00313.303-0.065-0.0650.0000.0000.0000.000
60A65ARG10.8550.93013.487-0.457-0.4570.0000.0000.0000.000
61A66VAL0-0.0120.0009.797-0.047-0.0470.0000.0000.0000.000
62A67ILE0-0.097-0.02413.106-0.108-0.1080.0000.0000.0000.000
63A86CYS00.0490.02315.688-0.007-0.0070.0000.0000.0000.000
64A87GLY0-0.065-0.03813.803-0.034-0.0340.0000.0000.0000.000
65A88LEU00.0130.01314.3770.0650.0650.0000.0000.0000.000
66A89ARG10.9330.96310.908-1.039-1.0390.0000.0000.0000.000
67A90PRO00.012-0.00516.6930.0080.0080.0000.0000.0000.000
68A91GLY0-0.073-0.04516.2730.0620.0620.0000.0000.0000.000
69A92MET0-0.0510.00013.4080.0070.0070.0000.0000.0000.000
70A93ASP-1-0.827-0.88715.6270.2670.2670.0000.0000.0000.000
71A94ILE0-0.026-0.01316.9330.0450.0450.0000.0000.0000.000
72A95LEU00.0060.00719.173-0.046-0.0460.0000.0000.0000.000
73A96GLU-1-0.814-0.89621.4070.2750.2750.0000.0000.0000.000
74A97VAL0-0.035-0.02323.803-0.025-0.0250.0000.0000.0000.000
75A98GLY00.0230.01626.2770.0050.0050.0000.0000.0000.000
76A99VAL00.0110.00728.3210.0120.0120.0000.0000.0000.000
77A100GLY00.0350.01830.4210.0040.0040.0000.0000.0000.000
78A101SER0-0.058-0.04632.879-0.004-0.0040.0000.0000.0000.000
79A102GLY00.0960.04831.083-0.007-0.0070.0000.0000.0000.000
80A103ASN0-0.041-0.02330.5940.0060.0060.0000.0000.0000.000
81A104MET00.0150.01122.2620.0050.0050.0000.0000.0000.000
82A105SER00.023-0.03325.8260.0110.0110.0000.0000.0000.000
83A106SER00.0000.03126.8760.0080.0080.0000.0000.0000.000
84A107TYR0-0.010-0.01224.5580.0010.0010.0000.0000.0000.000
85A108ILE0-0.015-0.00221.6600.0240.0240.0000.0000.0000.000
86A109LEU00.0110.00223.0090.0190.0190.0000.0000.0000.000
87A110TYR0-0.034-0.00825.4380.0000.0000.0000.0000.0000.000
88A111ALA0-0.034-0.01620.4830.0030.0030.0000.0000.0000.000
89A112LEU0-0.026-0.01519.2940.0210.0210.0000.0000.0000.000
90A113ASN0-0.033-0.00721.774-0.017-0.0170.0000.0000.0000.000
91A114GLY00.0100.00724.563-0.013-0.0130.0000.0000.0000.000
92A115LYS10.9090.95019.965-0.249-0.2490.0000.0000.0000.000
93A116GLY00.0580.04719.3110.0410.0410.0000.0000.0000.000
94A117THR0-0.071-0.07219.935-0.039-0.0390.0000.0000.0000.000
95A118LEU00.0150.01620.9190.0370.0370.0000.0000.0000.000
96A119THR0-0.036-0.01322.949-0.036-0.0360.0000.0000.0000.000
97A120VAL00.0310.01924.6410.0160.0160.0000.0000.0000.000
98A121VAL0-0.013-0.00326.190-0.017-0.0170.0000.0000.0000.000
99A122GLU-1-0.814-0.92128.7820.1600.1600.0000.0000.0000.000
100A123ARG10.9620.97631.582-0.149-0.1490.0000.0000.0000.000
101A124ASP-1-0.881-0.93634.9460.0980.0980.0000.0000.0000.000
102A125GLU-1-0.939-0.98837.1260.0920.0920.0000.0000.0000.000
103A126ASP-1-0.866-0.92238.9920.0910.0910.0000.0000.0000.000
104A127ASN0-0.089-0.06436.250-0.002-0.0020.0000.0000.0000.000
105A128LEU00.0240.01132.4700.0060.0060.0000.0000.0000.000
106A129LYS10.8830.93335.741-0.089-0.0890.0000.0000.0000.000
107A130LYS10.9300.96438.344-0.114-0.1140.0000.0000.0000.000
108A131ALA0-0.0030.01633.2410.0010.0010.0000.0000.0000.000
109A132MET0-0.022-0.01730.6790.0070.0070.0000.0000.0000.000
110A133ASP-1-0.829-0.90034.9690.1020.1020.0000.0000.0000.000
111A134ASN0-0.018-0.01436.266-0.006-0.0060.0000.0000.0000.000
112A135LEU0-0.036-0.01630.1180.0030.0030.0000.0000.0000.000
113A136SER0-0.060-0.03734.0510.0000.0000.0000.0000.0000.000
114A137GLU-1-0.978-0.96935.8410.1020.1020.0000.0000.0000.000
115A138PHE0-0.076-0.04434.357-0.003-0.0030.0000.0000.0000.000
116A139TYR0-0.056-0.05228.9840.0110.0110.0000.0000.0000.000
117A140ASP-1-0.894-0.93930.8310.1290.1290.0000.0000.0000.000
118A141ILE00.009-0.01430.1040.0120.0120.0000.0000.0000.000
119A142GLY00.0050.01330.318-0.001-0.0010.0000.0000.0000.000
120A143ASN0-0.079-0.03423.818-0.020-0.0200.0000.0000.0000.000
121A144VAL00.0230.00525.2950.0230.0230.0000.0000.0000.000
122A145ARG10.9250.96725.673-0.155-0.1550.0000.0000.0000.000
123A146THR00.0300.01327.8850.0110.0110.0000.0000.0000.000
124A147SER0-0.031-0.00929.472-0.010-0.0100.0000.0000.0000.000
125A148ARG10.9330.97531.099-0.096-0.0960.0000.0000.0000.000
126A149SER0-0.050-0.03631.313-0.008-0.0080.0000.0000.0000.000
127A150ASP-1-0.846-0.91931.8720.1440.1440.0000.0000.0000.000
128A151ILE00.009-0.00724.843-0.002-0.0020.0000.0000.0000.000
129A152ALA0-0.080-0.05428.1500.0030.0030.0000.0000.0000.000
130A153ASP-1-0.898-0.95229.9750.1000.1000.0000.0000.0000.000
131A154PHE0-0.044-0.00123.963-0.006-0.0060.0000.0000.0000.000
132A155ILE0-0.023-0.01626.8740.0040.0040.0000.0000.0000.000
133A156SER0-0.017-0.02422.355-0.004-0.0040.0000.0000.0000.000
134A157ASP-1-0.896-0.95022.7550.1080.1080.0000.0000.0000.000
135A158GLN0-0.075-0.02118.280-0.019-0.0190.0000.0000.0000.000
136A159MET0-0.050-0.01514.740-0.002-0.0020.0000.0000.0000.000
137A160TYR00.0340.01315.5080.0080.0080.0000.0000.0000.000
138A161ASP-1-0.812-0.89712.0110.7350.7350.0000.0000.0000.000
139A162ALA0-0.021-0.01213.0140.1270.1270.0000.0000.0000.000
140A163VAL00.0000.00615.639-0.070-0.0700.0000.0000.0000.000
141A164ILE0-0.019-0.00718.7850.0290.0290.0000.0000.0000.000
142A165ALA0-0.014-0.01321.401-0.026-0.0260.0000.0000.0000.000
143A166ASP-1-0.921-0.95124.2650.2080.2080.0000.0000.0000.000
144A167ILE0-0.018-0.01527.028-0.017-0.0170.0000.0000.0000.000
145A168PRO0-0.003-0.01229.8240.0040.0040.0000.0000.0000.000
146A169ASP-1-0.828-0.92030.9500.1440.1440.0000.0000.0000.000
147A170PRO00.0400.02825.290-0.002-0.0020.0000.0000.0000.000
148A171TRP00.0360.02126.0710.0030.0030.0000.0000.0000.000
149A172ASN0-0.083-0.04827.277-0.006-0.0060.0000.0000.0000.000
150A173HIS10.8320.90926.351-0.165-0.1650.0000.0000.0000.000
151A174VAL00.0710.05221.8030.0110.0110.0000.0000.0000.000
152A175GLN00.0560.01821.2640.0280.0280.0000.0000.0000.000
153A176LYS10.8660.93821.600-0.144-0.1440.0000.0000.0000.000
154A177ILE00.0500.03419.4750.0030.0030.0000.0000.0000.000
155A178ALA00.0490.01917.5120.0270.0270.0000.0000.0000.000
156A179SER0-0.125-0.07117.0610.0190.0190.0000.0000.0000.000
157A180MET00.0380.02018.281-0.022-0.0220.0000.0000.0000.000
158A181MET0-0.0230.01313.893-0.002-0.0020.0000.0000.0000.000
159A182LYS10.8720.92110.230-0.606-0.6060.0000.0000.0000.000
160A183PRO0-0.005-0.0078.3440.0790.0790.0000.0000.0000.000
161A184GLY00.0460.0166.8280.1630.1630.0000.0000.0000.000
162A185SER0-0.080-0.0277.7810.1760.1760.0000.0000.0000.000
163A186VAL00.016-0.01210.798-0.076-0.0760.0000.0000.0000.000
164A187ALA0-0.022-0.01013.297-0.047-0.0470.0000.0000.0000.000
165A188THR0-0.021-0.02217.0620.0150.0150.0000.0000.0000.000
166A189PHE0-0.022-0.01619.515-0.028-0.0280.0000.0000.0000.000
167A190TYR00.0230.01123.0250.0000.0000.0000.0000.0000.000
168A191LEU00.010-0.00126.148-0.014-0.0140.0000.0000.0000.000
169A192PRO0-0.0090.00129.0880.0020.0020.0000.0000.0000.000
170A193ASN0-0.025-0.03632.094-0.007-0.0070.0000.0000.0000.000
171A194PHE00.0610.03130.4270.0110.0110.0000.0000.0000.000
172A195ASP-1-0.832-0.91831.1530.1290.1290.0000.0000.0000.000
173A196GLN0-0.039-0.02431.1640.0080.0080.0000.0000.0000.000
174A197SER00.0220.02227.1650.0140.0140.0000.0000.0000.000
175A198GLU-1-0.877-0.93626.8040.1540.1540.0000.0000.0000.000
176A199LYS10.9200.96327.724-0.129-0.1290.0000.0000.0000.000
177A200THR0-0.009-0.02723.7460.0000.0000.0000.0000.0000.000
178A201VAL00.0270.03322.3760.0120.0120.0000.0000.0000.000
179A202LEU0-0.037-0.02123.1730.0060.0060.0000.0000.0000.000
180A203SER0-0.094-0.05024.571-0.005-0.0050.0000.0000.0000.000
181A204LEU00.0360.02319.0910.0040.0040.0000.0000.0000.000
182A205SER00.0040.01519.1710.0090.0090.0000.0000.0000.000
183A206ALA0-0.009-0.01219.848-0.001-0.0010.0000.0000.0000.000
184A207SER0-0.041-0.02319.814-0.002-0.0020.0000.0000.0000.000
185A208GLY0-0.014-0.00716.7640.0020.0020.0000.0000.0000.000
186A209MET0-0.024-0.00414.8730.0650.0650.0000.0000.0000.000
187A210HIS0-0.044-0.03213.161-0.046-0.0460.0000.0000.0000.000
188A211HIS00.0390.03915.0130.0750.0750.0000.0000.0000.000
189A212LEU0-0.051-0.01312.1430.0240.0240.0000.0000.0000.000
190A213GLU-1-0.911-0.96916.1860.3640.3640.0000.0000.0000.000
191A214THR00.0230.00019.3810.0150.0150.0000.0000.0000.000
192A215VAL0-0.037-0.00122.070-0.017-0.0170.0000.0000.0000.000
193A216GLU-1-0.888-0.94824.6940.1590.1590.0000.0000.0000.000
194A217LEU0-0.021-0.01525.659-0.001-0.0010.0000.0000.0000.000
195A218MET0-0.0020.01228.785-0.011-0.0110.0000.0000.0000.000
196A219LYS10.9620.98231.975-0.148-0.1480.0000.0000.0000.000
197A220ARG10.9920.97833.733-0.117-0.1170.0000.0000.0000.000
198A221ARG10.9140.97437.253-0.108-0.1080.0000.0000.0000.000
199A222ILE00.0050.00138.732-0.006-0.0060.0000.0000.0000.000
200A223LEU0-0.006-0.01340.9440.0010.0010.0000.0000.0000.000
201A224VAL00.0050.02043.5210.0000.0000.0000.0000.0000.000
202A225ARG10.9800.98445.584-0.073-0.0730.0000.0000.0000.000
203A226GLU-1-0.856-0.94449.0450.0750.0750.0000.0000.0000.000
204A227GLY0-0.031-0.01451.230-0.002-0.0020.0000.0000.0000.000
205A228ALA0-0.072-0.01950.195-0.002-0.0020.0000.0000.0000.000
206A229THR00.0300.00451.4350.0010.0010.0000.0000.0000.000
207A230ARG10.7980.91246.561-0.083-0.0830.0000.0000.0000.000
208A231PRO00.0340.01544.688-0.003-0.0030.0000.0000.0000.000
209A232ALA00.0650.02346.0170.0020.0020.0000.0000.0000.000
210A233SER00.016-0.00141.0280.0000.0000.0000.0000.0000.000
211A234ASP-1-0.923-0.96741.5870.1120.1120.0000.0000.0000.000
212A235ASP-1-0.858-0.92442.0680.0920.0920.0000.0000.0000.000
213A236LEU0-0.046-0.02140.509-0.002-0.0020.0000.0000.0000.000
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