Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: ZNNLN

Calculation Name: 4I61-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4I61

Chain ID: B

ChEMBL ID:

UniProt ID: F8DQ39

Base Structure: X-ray

Registration Date: 2023-09-27

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2510973.084916
FMO2-HF: Nuclear repulsion 2426415.1668
FMO2-HF: Total energy -84557.918116
FMO2-MP2: Total energy -84800.17155


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(B:11:VAL)


Summations of interaction energy for fragment #1(B:11:VAL)
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.
-6.759-1.523.099-2.846-5.493-0.02
Interaction energy analysis for fragmet #1(B:11:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.017
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].
3B13GLU-1-0.868-0.9362.346-6.336-2.7102.392-2.271-3.748-0.016
4B14PHE0-0.042-0.0112.544-0.1511.4050.703-0.551-1.709-0.004
5B15VAL0-0.075-0.0283.9840.2490.3060.004-0.024-0.0360.000
6B16GLY00.013-0.0047.7910.2060.2060.0000.0000.0000.000
7B17ALA0-0.022-0.0179.358-0.078-0.0780.0000.0000.0000.000
8B18SER0-0.0020.00311.1130.0610.0610.0000.0000.0000.000
9B19GLU-1-0.851-0.92814.758-0.295-0.2950.0000.0000.0000.000
10B20ILE0-0.0230.00217.4650.0230.0230.0000.0000.0000.000
11B21GLY00.0630.03818.142-0.024-0.0240.0000.0000.0000.000
12B22ASP-1-0.881-0.92214.954-0.300-0.3000.0000.0000.0000.000
13B23THR0-0.028-0.02313.941-0.040-0.0400.0000.0000.0000.000
14B24ILE0-0.012-0.0186.388-0.043-0.0430.0000.0000.0000.000
15B25GLY00.0240.0089.6360.0840.0840.0000.0000.0000.000
16B26MET0-0.040-0.0325.089-0.301-0.3010.0000.0000.0000.000
17B27VAL00.002-0.0146.1040.3150.3150.0000.0000.0000.000
18B28ILE00.0200.0266.281-0.309-0.3090.0000.0000.0000.000
19B29PRO0-0.002-0.0177.3310.1850.1850.0000.0000.0000.000
20B30ARG10.9330.96810.5080.1770.1770.0000.0000.0000.000
21B31VAL00.0090.02411.733-0.012-0.0120.0000.0000.0000.000
22B32ASP-1-0.807-0.90412.741-0.102-0.1020.0000.0000.0000.000
23B33GLN0-0.033-0.03314.689-0.023-0.0230.0000.0000.0000.000
24B34GLN0-0.031-0.01717.8690.0080.0080.0000.0000.0000.000
25B35LEU00.0110.00012.1190.0020.0020.0000.0000.0000.000
26B36LEU00.0200.01216.444-0.012-0.0120.0000.0000.0000.000
27B37ASP-1-0.857-0.91717.643-0.128-0.1280.0000.0000.0000.000
28B38LYS10.7360.85418.4660.1670.1670.0000.0000.0000.000
29B39LEU0-0.0150.01514.452-0.010-0.0100.0000.0000.0000.000
30B40HIS00.0150.01518.9080.0240.0240.0000.0000.0000.000
31B41VAL0-0.040-0.01818.126-0.005-0.0050.0000.0000.0000.000
32B42THR0-0.009-0.01421.3520.0130.0130.0000.0000.0000.000
33B43LYS10.8030.88722.5970.1680.1680.0000.0000.0000.000
34B44GLN0-0.0010.00420.176-0.011-0.0110.0000.0000.0000.000
35B45TYR00.015-0.00617.7460.0180.0180.0000.0000.0000.000
36B46LYS10.7680.88316.2340.1580.1580.0000.0000.0000.000
37B47THR0-0.056-0.03312.214-0.002-0.0020.0000.0000.0000.000
38B48LEU00.0350.02011.6590.0310.0310.0000.0000.0000.000
39B49GLY00.023-0.00210.713-0.108-0.1080.0000.0000.0000.000
40B50ILE0-0.020-0.0099.3720.0780.0780.0000.0000.0000.000
41B51LEU00.0160.00810.546-0.111-0.1110.0000.0000.0000.000
42B52SER0-0.050-0.02111.7330.0570.0570.0000.0000.0000.000
43B53ASP-1-0.807-0.91313.209-0.368-0.3680.0000.0000.0000.000
44B54ARG10.8270.89515.3660.3020.3020.0000.0000.0000.000
45B55THR0-0.071-0.05717.9770.0400.0400.0000.0000.0000.000
46B56GLY00.0570.04120.759-0.008-0.0080.0000.0000.0000.000
47B57ALA00.0260.01221.392-0.005-0.0050.0000.0000.0000.000
48B58GLY00.0570.03922.396-0.010-0.0100.0000.0000.0000.000
49B59PRO00.0130.00722.424-0.002-0.0020.0000.0000.0000.000
50B60GLN00.0250.00817.5510.0230.0230.0000.0000.0000.000
51B61ILE00.004-0.00119.838-0.013-0.0130.0000.0000.0000.000
52B62MET0-0.020-0.01821.8600.0050.0050.0000.0000.0000.000
53B63ALA0-0.0200.00020.1260.0090.0090.0000.0000.0000.000
54B64MET00.0130.00515.4040.0020.0020.0000.0000.0000.000
55B65ASP-1-0.785-0.88219.736-0.163-0.1630.0000.0000.0000.000
56B66GLU-1-0.802-0.88622.629-0.150-0.1500.0000.0000.0000.000
57B67GLY00.0070.00419.0730.0050.0050.0000.0000.0000.000
58B68ILE0-0.041-0.01919.8190.0040.0040.0000.0000.0000.000
59B69LYS10.7250.85321.6620.1700.1700.0000.0000.0000.000
60B70ALA0-0.058-0.01021.3270.0170.0170.0000.0000.0000.000
61B71THR0-0.127-0.06917.901-0.009-0.0090.0000.0000.0000.000
62B72ASN0-0.083-0.06020.3320.0300.0300.0000.0000.0000.000
63B73MET0-0.0530.01914.5480.0030.0030.0000.0000.0000.000
64B74GLU-1-0.781-0.85619.396-0.148-0.1480.0000.0000.0000.000
65B75CYS0-0.049-0.02019.526-0.024-0.0240.0000.0000.0000.000
66B76ILE0-0.0180.00117.2210.0200.0200.0000.0000.0000.000
67B77ASH0-0.027-0.06018.5810.0210.0210.0000.0000.0000.000
68B78VAL00.0060.00519.274-0.026-0.0260.0000.0000.0000.000
69B79GLU-1-0.863-0.88718.768-0.242-0.2420.0000.0000.0000.000
70B80TRP00.032-0.00320.059-0.018-0.0180.0000.0000.0000.000
71B81PRO00.0300.03118.0260.0220.0220.0000.0000.0000.000
72B82ARG10.8300.93021.2360.1510.1510.0000.0000.0000.000
73B83ASP-1-0.796-0.88319.734-0.243-0.2430.0000.0000.0000.000
74B84THR0-0.048-0.01322.4330.0230.0230.0000.0000.0000.000
75B85LYS10.8210.89118.8180.2600.2600.0000.0000.0000.000
76B86GLY0-0.0170.00122.9650.0100.0100.0000.0000.0000.000
77B87GLY00.0090.02026.3750.0110.0110.0000.0000.0000.000
78B88GLY0-0.005-0.01428.2400.0000.0000.0000.0000.0000.000
79B89GLY00.0680.02327.1980.0060.0060.0000.0000.0000.000
80B90HIS0-0.031-0.01123.3810.0040.0040.0000.0000.0000.000
81B91GLY00.0260.03219.6480.0010.0010.0000.0000.0000.000
82B92CYS0-0.036-0.01218.3130.0180.0180.0000.0000.0000.000
83B93LEU00.0130.00613.374-0.051-0.0510.0000.0000.0000.000
84B94ILE00.0220.01915.8350.0370.0370.0000.0000.0000.000
85B95ILE0-0.018-0.01214.112-0.065-0.0650.0000.0000.0000.000
86B96ILE00.0150.00014.2490.0480.0480.0000.0000.0000.000
87B97GLY00.017-0.00615.120-0.047-0.0470.0000.0000.0000.000
88B98GLY00.0830.02816.9380.0180.0180.0000.0000.0000.000
89B99ASP-1-0.836-0.94417.348-0.167-0.1670.0000.0000.0000.000
90B100ASP-1-0.786-0.88016.313-0.161-0.1610.0000.0000.0000.000
91B101PRO00.0030.00011.028-0.038-0.0380.0000.0000.0000.000
92B102ALA0-0.068-0.02411.999-0.089-0.0890.0000.0000.0000.000
93B103ASP-1-0.755-0.88014.320-0.258-0.2580.0000.0000.0000.000
94B104ALA00.0580.01012.467-0.020-0.0200.0000.0000.0000.000
95B105ARG10.8810.9268.0970.5400.5400.0000.0000.0000.000
96B106GLN00.0190.02211.858-0.030-0.0300.0000.0000.0000.000
97B107ALA00.0420.02415.3870.0090.0090.0000.0000.0000.000
98B108ILE0-0.031-0.01110.2390.0120.0120.0000.0000.0000.000
99B109ARG10.8900.94411.9930.3900.3900.0000.0000.0000.000
100B110VAL00.0470.03014.6890.0200.0200.0000.0000.0000.000
101B111ALA00.0150.02416.0220.0270.0270.0000.0000.0000.000
102B112LEU00.003-0.00811.5300.0150.0150.0000.0000.0000.000
103B113ASP-1-0.912-0.95916.277-0.269-0.2690.0000.0000.0000.000
104B114ASN0-0.061-0.04219.1040.0560.0560.0000.0000.0000.000
105B115LEU00.0090.01816.3920.0170.0170.0000.0000.0000.000
106B116HIS0-0.005-0.00620.9830.0260.0260.0000.0000.0000.000
107B117ARG10.8240.90423.5300.1800.1800.0000.0000.0000.000
108B118THR0-0.072-0.03722.9470.0110.0110.0000.0000.0000.000
109B119PHE00.0520.01020.9110.0050.0050.0000.0000.0000.000
110B120GLY00.0230.03625.6930.0090.0090.0000.0000.0000.000
111B121ASP-1-0.774-0.83928.959-0.098-0.0980.0000.0000.0000.000
112B122VAL0-0.0110.00126.0720.0020.0020.0000.0000.0000.000
113B123TYR0-0.077-0.05529.3630.0040.0040.0000.0000.0000.000
114B124ASN0-0.026-0.02527.280-0.001-0.0010.0000.0000.0000.000
115B125ALA00.0460.01731.3760.0070.0070.0000.0000.0000.000
116B126LYS10.8350.89133.0870.0740.0740.0000.0000.0000.000
117B127ALA0-0.042-0.01534.5770.0000.0000.0000.0000.0000.000
118B128GLY0-0.011-0.01533.2320.0020.0020.0000.0000.0000.000
119B129HIS00.009-0.00129.0860.0020.0020.0000.0000.0000.000
120B130LEU0-0.033-0.02132.0840.0060.0060.0000.0000.0000.000
121B131GLU-1-0.806-0.89827.025-0.180-0.1800.0000.0000.0000.000
122B132LEU0-0.056-0.01630.8180.0080.0080.0000.0000.0000.000
123B133GLN0-0.019-0.01026.833-0.003-0.0030.0000.0000.0000.000
124B134PHE00.012-0.01730.9110.0100.0100.0000.0000.0000.000
125B135THR00.0400.02730.068-0.003-0.0030.0000.0000.0000.000
126B136ALA00.0170.00132.3370.0060.0060.0000.0000.0000.000
127B137ARG10.8680.92732.1210.0940.0940.0000.0000.0000.000
128B138ALA00.0510.04029.343-0.008-0.0080.0000.0000.0000.000
129B139ALA0-0.017-0.01326.0780.0100.0100.0000.0000.0000.000
130B140GLY00.0730.04025.028-0.002-0.0020.0000.0000.0000.000
131B141ALA00.0070.00321.805-0.004-0.0040.0000.0000.0000.000
132B142ALA00.022-0.00223.4870.0010.0010.0000.0000.0000.000
133B143HIS0-0.114-0.05726.6750.0090.0090.0000.0000.0000.000
134B144LEU0-0.013-0.00822.6280.0060.0060.0000.0000.0000.000
135B145GLY0-0.0060.00124.499-0.001-0.0010.0000.0000.0000.000
136B146LEU0-0.048-0.03825.2440.0040.0040.0000.0000.0000.000
137B147GLY00.0250.02428.5310.0100.0100.0000.0000.0000.000
138B148ALA0-0.0200.00130.1680.0100.0100.0000.0000.0000.000
139B149VAL00.005-0.00231.9130.0010.0010.0000.0000.0000.000
140B150GLU-1-0.819-0.92228.473-0.139-0.1390.0000.0000.0000.000
141B151GLY0-0.049-0.02731.8520.0080.0080.0000.0000.0000.000
142B152LYS10.8670.93633.8030.0880.0880.0000.0000.0000.000
143B153ALA00.0210.01934.051-0.006-0.0060.0000.0000.0000.000
144B154PHE00.0010.00929.9300.0020.0020.0000.0000.0000.000
145B155GLY00.013-0.00133.913-0.001-0.0010.0000.0000.0000.000
146B156LEU0-0.0030.00929.0230.0020.0020.0000.0000.0000.000
147B157ILE0-0.013-0.01033.1110.0000.0000.0000.0000.0000.000
148B158CYS00.0100.00630.3780.0050.0050.0000.0000.0000.000
149B159GLY00.0380.01233.7290.0010.0010.0000.0000.0000.000
150B160CYS0-0.068-0.00431.6660.0020.0020.0000.0000.0000.000
151B161PRO00.0700.01934.6230.0010.0010.0000.0000.0000.000
152B162SER0-0.007-0.00335.8790.0050.0050.0000.0000.0000.000
153B163GLY0-0.033-0.01237.1260.0010.0010.0000.0000.0000.000
154B164ILE0-0.004-0.00538.1660.0030.0030.0000.0000.0000.000
155B165GLY00.0870.03837.1790.0010.0010.0000.0000.0000.000
156B166VAL0-0.036-0.01237.9970.0010.0010.0000.0000.0000.000
157B167VAL0-0.0130.00141.0850.0020.0020.0000.0000.0000.000
158B168MET0-0.0470.00135.8790.0020.0020.0000.0000.0000.000
159B169GLY00.0430.01540.4670.0000.0000.0000.0000.0000.000
160B170ASP-1-0.831-0.90441.030-0.058-0.0580.0000.0000.0000.000
161B171LYS10.9360.96943.5990.0630.0630.0000.0000.0000.000
162B172ALA00.0040.01940.9310.0020.0020.0000.0000.0000.000
163B173LEU00.009-0.01042.4440.0020.0020.0000.0000.0000.000
164B174LYS10.7490.87445.0090.0610.0610.0000.0000.0000.000
165B175THR0-0.081-0.04344.8740.0020.0020.0000.0000.0000.000
166B176ALA0-0.046-0.02944.9650.0020.0020.0000.0000.0000.000
167B177GLY00.0030.01146.452-0.001-0.0010.0000.0000.0000.000
168B178VAL0-0.056-0.02641.639-0.001-0.0010.0000.0000.0000.000
169B179GLU-1-0.885-0.94341.361-0.064-0.0640.0000.0000.0000.000
170B180PRO0-0.042-0.02840.140-0.005-0.0050.0000.0000.0000.000
171B181LEU0-0.050-0.01234.4920.0020.0020.0000.0000.0000.000
172B182ASN00.0250.00433.7500.0060.0060.0000.0000.0000.000
173B183PHE0-0.029-0.01636.7100.0000.0000.0000.0000.0000.000
174B184THR0-0.0220.01331.7700.0020.0020.0000.0000.0000.000
175B185SER00.0330.00234.7590.0030.0030.0000.0000.0000.000
176B186PRO00.0470.03533.580-0.003-0.0030.0000.0000.0000.000
177B187SER0-0.089-0.04234.3620.0020.0020.0000.0000.0000.000
178B188HIS0-0.0190.00034.9980.0010.0010.0000.0000.0000.000
179B189GLY00.0510.02231.7600.0000.0000.0000.0000.0000.000
180B190THR0-0.035-0.02929.193-0.006-0.0060.0000.0000.0000.000
181B191SER0-0.016-0.02424.8990.0090.0090.0000.0000.0000.000
182B192PHE0-0.032-0.02328.007-0.001-0.0010.0000.0000.0000.000
183B193SER0-0.007-0.01128.3940.0020.0020.0000.0000.0000.000
184B194ASN0-0.013-0.01930.2410.0100.0100.0000.0000.0000.000
185B195GLU-1-0.749-0.87228.610-0.148-0.1480.0000.0000.0000.000
186B196GLY0-0.014-0.01033.2010.0030.0030.0000.0000.0000.000
187B197CYS0-0.028-0.01431.265-0.001-0.0010.0000.0000.0000.000
188B198LEU00.0160.02834.7000.0020.0020.0000.0000.0000.000
189B199THR0-0.007-0.00932.326-0.005-0.0050.0000.0000.0000.000
190B200ILE0-0.013-0.00635.4590.0060.0060.0000.0000.0000.000
191B201THR00.016-0.01336.235-0.004-0.0040.0000.0000.0000.000
192B202GLY00.0540.02438.3300.0040.0040.0000.0000.0000.000
193B203ASP-1-0.905-0.95540.268-0.066-0.0660.0000.0000.0000.000
194B204SER0-0.004-0.01738.4350.0000.0000.0000.0000.0000.000
195B205GLY0-0.053-0.02039.757-0.002-0.0020.0000.0000.0000.000
196B206ALA00.0860.04142.316-0.001-0.0010.0000.0000.0000.000
197B207VAL00.0290.01436.975-0.001-0.0010.0000.0000.0000.000
198B208ARG10.9410.98437.6190.0770.0770.0000.0000.0000.000
199B209GLN0-0.010-0.01639.226-0.001-0.0010.0000.0000.0000.000
200B210ALA00.0290.02240.9500.0000.0000.0000.0000.0000.000
201B211VAL00.0380.00935.0990.0000.0000.0000.0000.0000.000
202B212MET0-0.063-0.02538.349-0.001-0.0010.0000.0000.0000.000
203B213ALA00.0100.00339.9750.0010.0010.0000.0000.0000.000
204B214GLY00.0180.00339.7530.0020.0020.0000.0000.0000.000
205B215ARG10.8620.91635.4840.0930.0930.0000.0000.0000.000
206B216GLU-1-0.856-0.89938.609-0.061-0.0610.0000.0000.0000.000
207B217VAL00.001-0.01042.0260.0020.0020.0000.0000.0000.000
208B218GLY00.0550.01638.8430.0010.0010.0000.0000.0000.000
209B219LEU00.0200.01236.6710.0000.0000.0000.0000.0000.000
210B220LYS10.8030.90639.7910.0630.0630.0000.0000.0000.000
211B221LEU0-0.018-0.00441.4970.0030.0030.0000.0000.0000.000
212B222LEU00.0160.01535.0260.0020.0020.0000.0000.0000.000
213B223SER00.017-0.01639.6690.0000.0000.0000.0000.0000.000
214B224GLN0-0.119-0.05841.6830.0050.0050.0000.0000.0000.000
215B225PHE0-0.059-0.02840.0450.0020.0020.0000.0000.0000.000
216B226GLY0-0.043-0.01141.8770.0000.0000.0000.0000.0000.000
217B227GLU-1-0.861-0.92035.806-0.085-0.0850.0000.0000.0000.000
218B228GLU-1-0.931-0.96038.461-0.073-0.0730.0000.0000.0000.000
219B229PRO0-0.049-0.02735.496-0.003-0.0030.0000.0000.0000.000
220B230VAL00.0370.02531.9620.0020.0020.0000.0000.0000.000
221B231ASN0-0.002-0.00230.600-0.001-0.0010.0000.0000.0000.000
222B232ASP-1-0.910-0.95026.663-0.139-0.1390.0000.0000.0000.000
223B233PHE0-0.004-0.00922.712-0.004-0.0040.0000.0000.0000.000
224B234PRO0-0.017-0.01828.4280.0050.0050.0000.0000.0000.000
225B235SER0-0.048-0.03030.384-0.005-0.0050.0000.0000.0000.000
226B236TYR00.006-0.02828.9370.0060.0060.0000.0000.0000.000
227B237ILE0-0.111-0.04532.0730.0130.0130.0000.0000.0000.000