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: MNZYZ

Calculation Name: 5I61-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5I61

Chain ID: A

ChEMBL ID:

UniProt ID: Q50LE4

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 534
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -11815936.384376
FMO2-HF: Nuclear repulsion 11599381.450107
FMO2-HF: Total energy -216554.934269
FMO2-MP2: Total energy -217177.887179


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:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-0.8333.5591.27-2.76-2.902-0.012
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / 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].
3A3VAL0-0.059-0.0133.8081.5152.481-0.011-0.539-0.4150.003
4A4ALA00.0570.0406.6030.1140.1140.0000.0000.0000.000
5A5PRO00.0610.01110.201-0.136-0.1360.0000.0000.0000.000
6A6ASN00.0220.00312.875-0.047-0.0470.0000.0000.0000.000
7A7VAL00.0070.0038.0900.0280.0280.0000.0000.0000.000
8A8TRP00.0570.0368.093-0.014-0.0140.0000.0000.0000.000
9A9SER0-0.034-0.02411.2960.0310.0310.0000.0000.0000.000
10A10LYS10.9500.98013.0570.3100.3100.0000.0000.0000.000
11A11TYR00.0320.0598.928-0.054-0.0540.0000.0000.0000.000
12A12PHE00.007-0.01410.7390.0740.0740.0000.0000.0000.000
13A13ASN0-0.026-0.01615.3870.0350.0350.0000.0000.0000.000
14A14ILE0-0.0270.00015.143-0.006-0.0060.0000.0000.0000.000
15A15PRO00.0300.00218.8070.0220.0220.0000.0000.0000.000
16A16ASN0-0.009-0.01417.4890.0210.0210.0000.0000.0000.000
17A17PRO00.0320.01418.618-0.027-0.0270.0000.0000.0000.000
18A18GLY00.0440.02220.156-0.004-0.0040.0000.0000.0000.000
19A19LEU0-0.0010.01113.5480.0040.0040.0000.0000.0000.000
20A20ARG10.9330.97315.0900.2530.2530.0000.0000.0000.000
21A21ALA00.0120.00116.537-0.005-0.0050.0000.0000.0000.000
22A22TYR0-0.059-0.04914.4650.0390.0390.0000.0000.0000.000
23A23PHE00.0420.00510.853-0.006-0.0060.0000.0000.0000.000
24A24SER00.0100.01514.1610.0090.0090.0000.0000.0000.000
25A25ASN0-0.001-0.00116.3590.0350.0350.0000.0000.0000.000
26A26VAL0-0.031-0.00212.4770.0170.0170.0000.0000.0000.000
27A27VAL0-0.041-0.02711.9970.0200.0200.0000.0000.0000.000
28A28SER0-0.024-0.01714.4890.0290.0290.0000.0000.0000.000
29A29GLY00.0070.01718.0590.0220.0220.0000.0000.0000.000
30A30GLN0-0.048-0.03719.3410.0100.0100.0000.0000.0000.000
31A31PRO00.0400.01622.9110.0020.0020.0000.0000.0000.000
32A32GLU-1-0.933-0.95525.341-0.072-0.0720.0000.0000.0000.000
33A33VAL00.009-0.00128.320-0.007-0.0070.0000.0000.0000.000
34A34TYR0-0.023-0.00927.7100.0000.0000.0000.0000.0000.000
35A35ARG10.8450.90732.4010.0520.0520.0000.0000.0000.000
36A36THR0-0.085-0.06736.0300.0000.0000.0000.0000.0000.000
37A37PRO0-0.024-0.03238.2760.0030.0030.0000.0000.0000.000
38A38PHE00.0360.03841.3080.0030.0030.0000.0000.0000.000
39A39TYR00.019-0.01842.7570.0010.0010.0000.0000.0000.000
40A40LYS10.9290.97143.7240.0450.0450.0000.0000.0000.000
41A41GLY0-0.035-0.01744.2350.0020.0020.0000.0000.0000.000
42A42MET00.0230.03845.5090.0020.0020.0000.0000.0000.000
43A43SER00.0130.00441.741-0.003-0.0030.0000.0000.0000.000
44A44LEU00.0590.01236.7190.0000.0000.0000.0000.0000.000
45A45GLU-1-0.883-0.94539.816-0.041-0.0410.0000.0000.0000.000
46A46SER00.0070.01742.6330.0010.0010.0000.0000.0000.000
47A47ILE0-0.018-0.00442.2390.0010.0010.0000.0000.0000.000
48A48CYS0-0.038-0.02641.5200.0000.0000.0000.0000.0000.000
49A49ASP-1-0.855-0.93144.393-0.030-0.0300.0000.0000.0000.000
50A50GLU-1-0.866-0.92447.225-0.027-0.0270.0000.0000.0000.000
51A51TRP0-0.046-0.02545.9290.0010.0010.0000.0000.0000.000
52A52TYR00.0230.01046.8080.0010.0010.0000.0000.0000.000
53A53LYS10.8300.89248.7640.0270.0270.0000.0000.0000.000
54A54LYS10.9250.96651.7980.0320.0320.0000.0000.0000.000
55A55LEU00.0160.01346.2990.0010.0010.0000.0000.0000.000
56A56VAL00.0470.00150.7070.0000.0000.0000.0000.0000.000
57A57SER0-0.032-0.01152.2770.0010.0010.0000.0000.0000.000
58A58ILE0-0.016-0.01848.8660.0000.0000.0000.0000.0000.000
59A59ASP-1-0.929-0.97051.673-0.025-0.0250.0000.0000.0000.000
60A60THR0-0.024-0.00953.0570.0000.0000.0000.0000.0000.000
61A61GLN00.004-0.00155.9440.0000.0000.0000.0000.0000.000
62A62TRP0-0.020-0.01851.0630.0000.0000.0000.0000.0000.000
63A63PRO00.0900.06050.603-0.002-0.0020.0000.0000.0000.000
64A64THR00.044-0.00746.949-0.001-0.0010.0000.0000.0000.000
65A65LEU0-0.056-0.01445.613-0.002-0.0020.0000.0000.0000.000
66A66MET0-0.0330.00445.875-0.003-0.0030.0000.0000.0000.000
67A67GLU-1-0.887-0.94044.605-0.030-0.0300.0000.0000.0000.000
68A68PHE0-0.026-0.01639.287-0.003-0.0030.0000.0000.0000.000
69A69GLU-1-0.730-0.82241.199-0.048-0.0480.0000.0000.0000.000
70A70ASP-1-0.874-0.95241.709-0.034-0.0340.0000.0000.0000.000
71A71ASP-1-1.010-0.99537.419-0.047-0.0470.0000.0000.0000.000
72A72LEU0-0.039-0.03535.753-0.005-0.0050.0000.0000.0000.000
73A73ARG10.9250.95237.1450.0320.0320.0000.0000.0000.000
74A74LYS10.9310.97236.7250.0330.0330.0000.0000.0000.000
75A75LYS10.8890.94031.2830.0550.0550.0000.0000.0000.000
76A76VAL0-0.0160.01033.184-0.006-0.0060.0000.0000.0000.000
77A77GLY00.0410.00533.4040.0040.0040.0000.0000.0000.000
78A78PRO0-0.047-0.00929.560-0.004-0.0040.0000.0000.0000.000
79A79MET0-0.009-0.00928.0540.0010.0010.0000.0000.0000.000
80A80SER0-0.010-0.01126.703-0.007-0.0070.0000.0000.0000.000
81A81VAL0-0.0220.01524.180-0.007-0.0070.0000.0000.0000.000
82A82MET0-0.047-0.00518.134-0.015-0.0150.0000.0000.0000.000
83A83LEU00.0180.00618.7220.0050.0050.0000.0000.0000.000
84A84PRO00.0330.00916.686-0.032-0.0320.0000.0000.0000.000
85A85LEU00.0350.0328.9610.0060.0060.0000.0000.0000.000
86A86LYS10.8860.93911.9940.0560.0560.0000.0000.0000.000
87A87GLU-1-0.897-0.96413.019-0.036-0.0360.0000.0000.0000.000
88A88ARG10.9100.96113.6030.2900.2900.0000.0000.0000.000
89A89MET0-0.035-0.0146.919-0.065-0.0650.0000.0000.0000.000
90A90SER00.0350.02811.390-0.023-0.0230.0000.0000.0000.000
91A91ASP-1-0.878-0.95213.954-0.172-0.1720.0000.0000.0000.000
92A92ILE0-0.052-0.0408.568-0.041-0.0410.0000.0000.0000.000
93A93ASP-1-0.798-0.8769.975-0.175-0.1750.0000.0000.0000.000
94A94SER0-0.0290.00012.0030.0160.0160.0000.0000.0000.000
95A95TYR0-0.059-0.05313.0150.0110.0110.0000.0000.0000.000
96A96TYR0-0.019-0.0279.025-0.079-0.0790.0000.0000.0000.000
97A97ASP-1-0.860-0.93012.821-0.044-0.0440.0000.0000.0000.000
98A98SER0-0.065-0.03715.0230.0270.0270.0000.0000.0000.000
99A99ILE0-0.036-0.01015.3300.0140.0140.0000.0000.0000.000
100A100SER0-0.023-0.01516.7750.0120.0120.0000.0000.0000.000
101A101LYS10.8890.96419.4720.0670.0670.0000.0000.0000.000
102A102ASP-1-0.865-0.92822.491-0.004-0.0040.0000.0000.0000.000
103A103GLN0-0.059-0.00921.858-0.013-0.0130.0000.0000.0000.000
104A104VAL00.0020.00527.1360.0040.0040.0000.0000.0000.000
105A105PRO00.009-0.00230.200-0.007-0.0070.0000.0000.0000.000
106A106PHE00.007-0.00728.8400.0020.0020.0000.0000.0000.000
107A107ASP-1-0.821-0.92033.492-0.030-0.0300.0000.0000.0000.000
108A108THR00.0130.00237.208-0.004-0.0040.0000.0000.0000.000
109A109LYS10.9260.95538.6750.0230.0230.0000.0000.0000.000
110A110ALA00.0490.04737.435-0.001-0.0010.0000.0000.0000.000
111A111ILE00.0070.01033.837-0.003-0.0030.0000.0000.0000.000
112A112SER0-0.070-0.03337.518-0.003-0.0030.0000.0000.0000.000
113A113ALA00.0440.01641.0090.0000.0000.0000.0000.0000.000
114A114ALA00.0250.01237.668-0.001-0.0010.0000.0000.0000.000
115A115LYS10.8420.89536.9030.0530.0530.0000.0000.0000.000
116A116SER0-0.089-0.05140.4080.0010.0010.0000.0000.0000.000
117A117GLU-1-0.797-0.85841.001-0.052-0.0520.0000.0000.0000.000
118A118TRP0-0.018-0.02136.142-0.002-0.0020.0000.0000.0000.000
119A119LYS10.9440.97543.0340.0430.0430.0000.0000.0000.000
120A120GLY0-0.023-0.01745.7040.0000.0000.0000.0000.0000.000
121A121VAL0-0.0280.00841.7270.0000.0000.0000.0000.0000.000
122A122SER0-0.020-0.01944.0940.0010.0010.0000.0000.0000.000
123A123ARG10.8290.90640.2180.0530.0530.0000.0000.0000.000
124A124LEU0-0.022-0.01335.364-0.001-0.0010.0000.0000.0000.000
125A125ARG10.8730.93535.2070.0810.0810.0000.0000.0000.000
126A126LEU0-0.020-0.01130.805-0.002-0.0020.0000.0000.0000.000
127A127ARG10.8960.96434.2500.1030.1030.0000.0000.0000.000
128A128SER00.0610.03333.660-0.008-0.0080.0000.0000.0000.000
129A129GLU-1-0.659-0.82228.933-0.141-0.1410.0000.0000.0000.000
130A130VAL00.0160.01332.249-0.005-0.0050.0000.0000.0000.000
131A131ASN00.022-0.00134.742-0.001-0.0010.0000.0000.0000.000
132A132THR0-0.036-0.03830.1950.0010.0010.0000.0000.0000.000
133A133VAL00.0210.00729.496-0.005-0.0050.0000.0000.0000.000
134A134ALA0-0.0090.00231.706-0.002-0.0020.0000.0000.0000.000
135A135VAL0-0.011-0.00633.8500.0010.0010.0000.0000.0000.000
136A136MET0-0.0430.01527.891-0.007-0.0070.0000.0000.0000.000
137A137LYS10.9010.95828.9240.1310.1310.0000.0000.0000.000
138A138LYS10.8380.90728.5760.1110.1110.0000.0000.0000.000
139A139SER0-0.026-0.03429.282-0.004-0.0040.0000.0000.0000.000
140A140THR00.0120.00524.759-0.001-0.0010.0000.0000.0000.000
141A141ASN00.0140.00719.900-0.012-0.0120.0000.0000.0000.000
142A142SER0-0.012-0.01121.0670.0050.0050.0000.0000.0000.000
143A143GLY00.0550.03417.504-0.006-0.0060.0000.0000.0000.000
144A144SER00.0110.03714.3270.0110.0110.0000.0000.0000.000
145A145PRO00.0780.02416.3990.0290.0290.0000.0000.0000.000
146A146TYR00.008-0.02717.592-0.004-0.0040.0000.0000.0000.000
147A147PHE0-0.0070.01716.8620.0100.0100.0000.0000.0000.000
148A148SER00.006-0.00119.5790.0270.0270.0000.0000.0000.000
149A149LYS10.9770.98423.3950.1530.1530.0000.0000.0000.000
150A150ARG10.9390.97223.2500.2110.2110.0000.0000.0000.000
151A151LYS10.9590.97626.7210.1340.1340.0000.0000.0000.000
152A152ALA0-0.070-0.02327.9120.0070.0070.0000.0000.0000.000
153A153VAL00.0270.00924.1580.0030.0030.0000.0000.0000.000
154A154VAL00.0340.03727.100-0.006-0.0060.0000.0000.0000.000
155A155SER00.0310.02229.117-0.006-0.0060.0000.0000.0000.000
156A156LYS10.9350.98724.8850.1900.1900.0000.0000.0000.000
157A157THR0-0.052-0.04723.959-0.021-0.0210.0000.0000.0000.000
158A158ILE0-0.0010.01026.017-0.003-0.0030.0000.0000.0000.000
159A159PRO00.0060.00128.8870.0040.0040.0000.0000.0000.000
160A160CYS0-0.158-0.10524.472-0.009-0.0090.0000.0000.0000.000
161A161ASP-1-0.849-0.91024.421-0.140-0.1400.0000.0000.0000.000
162A162VAL0-0.045-0.02020.026-0.016-0.0160.0000.0000.0000.000
163A163TYR00.0490.02719.5660.0190.0190.0000.0000.0000.000
164A164MET0-0.023-0.00313.048-0.042-0.0420.0000.0000.0000.000
165A165ASP-1-0.901-0.94115.825-0.113-0.1130.0000.0000.0000.000
166A166GLY00.0340.01514.527-0.018-0.0180.0000.0000.0000.000
167A167ARG10.9040.9325.4670.1180.1180.0000.0000.0000.000
168A168TYR00.0180.0208.626-0.166-0.1660.0000.0000.0000.000
169A169CYS00.0200.01712.1680.0810.0810.0000.0000.0000.000
170A170VAL00.0350.04414.730-0.043-0.0430.0000.0000.0000.000
171A171MET0-0.017-0.00816.8330.0120.0120.0000.0000.0000.000
172A172ARG10.9761.00319.5960.1420.1420.0000.0000.0000.000
173A173GLN0-0.029-0.03321.052-0.018-0.0180.0000.0000.0000.000
174A174ASN0-0.068-0.03124.7240.0080.0080.0000.0000.0000.000
175A175GLY00.0370.01627.3650.0050.0050.0000.0000.0000.000
176A176ARG10.9250.97320.5880.2180.2180.0000.0000.0000.000
177A177GLU-1-0.924-0.95218.349-0.212-0.2120.0000.0000.0000.000
178A178TRP0-0.101-0.05617.118-0.001-0.0010.0000.0000.0000.000
179A179SER00.002-0.00812.507-0.009-0.0090.0000.0000.0000.000
180A180GLY0-0.002-0.01814.031-0.038-0.0380.0000.0000.0000.000
181A181ALA00.009-0.0189.894-0.082-0.0820.0000.0000.0000.000
182A182ALA0-0.032-0.00411.9100.0880.0880.0000.0000.0000.000
183A183VAL0-0.036-0.01011.099-0.143-0.1430.0000.0000.0000.000
184A184LEU00.0250.02410.6180.0770.0770.0000.0000.0000.000
185A185GLY00.0220.01312.6360.0290.0290.0000.0000.0000.000
186A186TRP0-0.054-0.03016.100-0.015-0.0150.0000.0000.0000.000
187A187ARG10.8670.94318.6330.1850.1850.0000.0000.0000.000
188A188GLY00.0610.05021.930-0.003-0.0030.0000.0000.0000.000
189A189GLN0-0.057-0.03824.4160.0010.0010.0000.0000.0000.000
190A190GLU-1-0.783-0.85926.952-0.087-0.0870.0000.0000.0000.000
191A191GLY0-0.035-0.05328.9860.0000.0000.0000.0000.0000.000
192A192GLY00.0070.02329.9700.0050.0050.0000.0000.0000.000
193A193PRO00.0710.03332.216-0.005-0.0050.0000.0000.0000.000
194A194LYS10.9430.97030.9960.0320.0320.0000.0000.0000.000
195A195PRO00.0340.00828.337-0.005-0.0050.0000.0000.0000.000
196A196THR00.005-0.01225.700-0.007-0.0070.0000.0000.0000.000
197A197ASP-1-0.881-0.92526.274-0.051-0.0510.0000.0000.0000.000
198A198VAL0-0.109-0.03024.593-0.004-0.0040.0000.0000.0000.000
199A199LYS10.9350.96523.7990.0720.0720.0000.0000.0000.000
200A200GLN00.0360.01618.842-0.024-0.0240.0000.0000.0000.000
201A201ARG10.8460.92019.1440.1560.1560.0000.0000.0000.000
202A202VAL00.0160.00113.884-0.019-0.0190.0000.0000.0000.000
203A203VAL0-0.030-0.00816.6740.0150.0150.0000.0000.0000.000
204A204TRP0-0.0110.00411.391-0.079-0.0790.0000.0000.0000.000
205A205MET0-0.044-0.03115.4990.0490.0490.0000.0000.0000.000
206A206PHE00.0150.00815.901-0.062-0.0620.0000.0000.0000.000
207A207PRO0-0.0200.00315.7300.0270.0270.0000.0000.0000.000
208A208PHE00.010-0.01418.4080.0350.0350.0000.0000.0000.000
209A209ALA00.0460.01621.3590.0200.0200.0000.0000.0000.000
210A210VAL00.0600.03118.0120.0170.0170.0000.0000.0000.000
211A211ASN0-0.020-0.01121.3190.0130.0130.0000.0000.0000.000
212A212ILE0-0.033-0.02523.4250.0210.0210.0000.0000.0000.000
213A213ARG10.9730.98124.4080.1630.1630.0000.0000.0000.000
214A214GLU-1-0.768-0.87421.691-0.225-0.2250.0000.0000.0000.000
215A215LEU0-0.027-0.03025.8220.0160.0160.0000.0000.0000.000
216A216GLN0-0.027-0.01328.6050.0030.0030.0000.0000.0000.000
217A217VAL00.0360.03329.6990.0110.0110.0000.0000.0000.000
218A218TYR00.000-0.02425.6380.0030.0030.0000.0000.0000.000
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