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

tag_button

FMODB ID: 7G9JK

Calculation Name: 4EQ6-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EQ6

Chain ID: B

ChEMBL ID:

UniProt ID: P40465

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2632865.426744
FMO2-HF: Nuclear repulsion 2545553.898264
FMO2-HF: Total energy -87311.52848
FMO2-MP2: Total energy -87565.615752


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:1:MET)


Summations of interaction energy for fragment #1(B: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.
-4.4651.3293.044-2.727-6.11-0.003
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.003
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].
3B3VAL00.004-0.0052.260-2.3380.5471.622-1.278-3.229-0.001
4B4LEU00.0190.0032.035-0.7950.7391.322-0.967-1.889-0.004
5B5LYS10.8600.9192.996-2.985-1.6100.100-0.482-0.9920.002
6B6ASN0-0.026-0.0185.9120.6890.6890.0000.0000.0000.000
7B7ILE00.0160.0236.6100.2290.2290.0000.0000.0000.000
8B8ARG10.8750.9478.7910.5830.5830.0000.0000.0000.000
9B9ILE00.0170.00912.2330.0170.0170.0000.0000.0000.000
10B10TYR0-0.013-0.01015.0090.0180.0180.0000.0000.0000.000
11B11PRO00.0410.02418.6460.0050.0050.0000.0000.0000.000
12B12LEU00.0460.01221.702-0.002-0.0020.0000.0000.0000.000
13B13SER00.0660.02024.4390.0000.0000.0000.0000.0000.000
14B14ASN0-0.008-0.01221.3730.0150.0150.0000.0000.0000.000
15B15PHE0-0.031-0.01420.976-0.001-0.0010.0000.0000.0000.000
16B16ILE0-0.041-0.01226.5420.0040.0040.0000.0000.0000.000
17B17THR0-0.0190.01328.5970.0100.0100.0000.0000.0000.000
18B18SER0-0.016-0.02129.512-0.006-0.0060.0000.0000.0000.000
19B19THR00.0090.01531.7460.0050.0050.0000.0000.0000.000
20B20LYS10.7980.88332.4970.0800.0800.0000.0000.0000.000
21B21ASN00.0260.02035.6750.0020.0020.0000.0000.0000.000
22B22TYR00.002-0.01532.968-0.003-0.0030.0000.0000.0000.000
23B23ILE0-0.026-0.00839.4490.0030.0030.0000.0000.0000.000
24B24ASN00.0210.01342.163-0.001-0.0010.0000.0000.0000.000
25B25LEU0-0.0060.00344.0820.0030.0030.0000.0000.0000.000
26B26PRO00.0320.02946.2950.0000.0000.0000.0000.0000.000
27B27ASN00.035-0.00949.3900.0000.0000.0000.0000.0000.000
28B28GLU-1-0.882-0.92350.572-0.035-0.0350.0000.0000.0000.000
29B29LEU0-0.063-0.03948.3950.0000.0000.0000.0000.0000.000
30B30ARG10.7940.84541.2670.0580.0580.0000.0000.0000.000
31B31ASN0-0.057-0.03045.772-0.001-0.0010.0000.0000.0000.000
32B32LEU0-0.0170.01345.6110.0000.0000.0000.0000.0000.000
33B33ILE0-0.047-0.00140.585-0.003-0.0030.0000.0000.0000.000
34B34SER00.002-0.00536.4250.0020.0020.0000.0000.0000.000
35B35GLU-1-0.750-0.84736.983-0.065-0.0650.0000.0000.0000.000
36B36GLU-1-0.821-0.92531.407-0.102-0.1020.0000.0000.0000.000
37B37GLN0-0.021-0.02135.0430.0030.0030.0000.0000.0000.000
38B38GLU-1-0.785-0.89536.764-0.056-0.0560.0000.0000.0000.000
39B39SER0-0.0230.00235.0830.0010.0010.0000.0000.0000.000
40B40LYS10.8010.90030.8590.0960.0960.0000.0000.0000.000
41B41LEU0-0.0040.00335.5610.0000.0000.0000.0000.0000.000
42B42GLY00.003-0.01438.3960.0030.0030.0000.0000.0000.000
43B43PHE0-0.040-0.01837.5490.0050.0050.0000.0000.0000.000
44B44LEU00.0280.01841.894-0.002-0.0020.0000.0000.0000.000
45B45HIS00.0180.00444.9410.0020.0020.0000.0000.0000.000
46B46ILE0-0.0030.00647.939-0.001-0.0010.0000.0000.0000.000
47B47ILE0-0.019-0.00351.1790.0010.0010.0000.0000.0000.000
48B48GLU-1-0.701-0.83354.068-0.034-0.0340.0000.0000.0000.000
49B49SER00.0530.00257.3780.0000.0000.0000.0000.0000.000
50B50ASP-1-0.885-0.90760.817-0.027-0.0270.0000.0000.0000.000
51B51PHE00.0110.00560.915-0.001-0.0010.0000.0000.0000.000
52B52LYS10.9530.96861.4970.0220.0220.0000.0000.0000.000
53B53PRO00.0120.01757.615-0.001-0.0010.0000.0000.0000.000
54B54SER00.007-0.04056.3580.0010.0010.0000.0000.0000.000
55B55VAL00.0420.00557.1110.0000.0000.0000.0000.0000.000
56B56ALA00.0150.01552.8660.0000.0000.0000.0000.0000.000
57B57LEU00.0320.01752.289-0.001-0.0010.0000.0000.0000.000
58B58GLN0-0.026-0.02453.2960.0000.0000.0000.0000.0000.000
59B59LYS10.8450.90152.7380.0340.0340.0000.0000.0000.000
60B60LEU0-0.0260.00847.552-0.001-0.0010.0000.0000.0000.000
61B61VAL00.0000.00249.343-0.001-0.0010.0000.0000.0000.000
62B62ASN0-0.047-0.01051.1000.0010.0010.0000.0000.0000.000
63B63CYS0-0.080-0.01647.4160.0000.0000.0000.0000.0000.000
64B64THR0-0.0330.00247.947-0.001-0.0010.0000.0000.0000.000
65B65THR00.016-0.00647.0550.0010.0010.0000.0000.0000.000
66B66GLY00.008-0.00548.7460.0000.0000.0000.0000.0000.000
67B67ASP-1-0.881-0.93746.422-0.028-0.0280.0000.0000.0000.000
68B68GLU-1-0.864-0.91643.732-0.040-0.0400.0000.0000.0000.000
69B69LYS10.8870.93947.6400.0260.0260.0000.0000.0000.000
70B70ILE0-0.033-0.00547.884-0.002-0.0020.0000.0000.0000.000
71B71LEU00.0050.01049.0550.0020.0020.0000.0000.0000.000
72B72ILE0-0.002-0.00750.667-0.001-0.0010.0000.0000.0000.000
73B73ILE0-0.008-0.01950.4510.0020.0020.0000.0000.0000.000
74B74ASP-1-0.726-0.84054.394-0.025-0.0250.0000.0000.0000.000
75B75ILE0-0.020-0.01355.1230.0010.0010.0000.0000.0000.000
76B76VAL0-0.015-0.01558.9900.0010.0010.0000.0000.0000.000
77B77SER00.0130.03461.2320.0010.0010.0000.0000.0000.000
78B78ILE0-0.061-0.01761.2060.0010.0010.0000.0000.0000.000
79B79TRP0-0.048-0.05755.4680.0010.0010.0000.0000.0000.000
80B80SER0-0.049-0.04959.9310.0010.0010.0000.0000.0000.000
81B81GLN0-0.040-0.04061.4050.0020.0020.0000.0000.0000.000
82B82GLN00.0620.01364.408-0.001-0.0010.0000.0000.0000.000
83B83LYS10.8910.96065.9120.0190.0190.0000.0000.0000.000
84B84GLN0-0.063-0.03562.2490.0000.0000.0000.0000.0000.000
85B85ARG10.9000.97060.5390.0190.0190.0000.0000.0000.000
86B86GLN00.0440.01554.5350.0000.0000.0000.0000.0000.000
87B87HIS00.0520.01654.1360.0010.0010.0000.0000.0000.000
88B88GLY0-0.0070.00253.2340.0000.0000.0000.0000.0000.000
89B89ALA0-0.019-0.00352.200-0.002-0.0020.0000.0000.0000.000
90B90ILE00.0020.01851.1560.0010.0010.0000.0000.0000.000
91B91TYR00.0360.00754.231-0.001-0.0010.0000.0000.0000.000
92B92MET0-0.013-0.00554.7730.0010.0010.0000.0000.0000.000
93B93ASN0-0.061-0.05256.6520.0000.0000.0000.0000.0000.000
94B94SER00.0780.03659.3920.0010.0010.0000.0000.0000.000
95B95LEU00.0550.02361.044-0.001-0.0010.0000.0000.0000.000
96B96SER0-0.071-0.03159.0630.0000.0000.0000.0000.0000.000
97B97CYS0-0.035-0.01755.407-0.001-0.0010.0000.0000.0000.000
98B98ILE00.0650.04357.872-0.001-0.0010.0000.0000.0000.000
99B99ASN00.0090.01858.431-0.001-0.0010.0000.0000.0000.000
100B100ILE00.0170.00051.4760.0000.0000.0000.0000.0000.000
101B101THR00.007-0.01053.678-0.001-0.0010.0000.0000.0000.000
102B102GLY00.0420.02554.2950.0000.0000.0000.0000.0000.000
103B103LEU00.0080.00151.4380.0000.0000.0000.0000.0000.000
104B104ILE0-0.058-0.03848.669-0.001-0.0010.0000.0000.0000.000
105B105VAL00.0270.02249.8360.0000.0000.0000.0000.0000.000
106B106PHE0-0.037-0.01851.0340.0000.0000.0000.0000.0000.000
107B107LEU00.005-0.01147.0300.0000.0000.0000.0000.0000.000
108B108GLU-1-0.918-0.97846.251-0.028-0.0280.0000.0000.0000.000
109B109LEU00.0310.02746.4880.0000.0000.0000.0000.0000.000
110B110LEU0-0.060-0.02446.0710.0000.0000.0000.0000.0000.000
111B111TYR0-0.045-0.04137.451-0.001-0.0010.0000.0000.0000.000
112B112ASP-1-0.915-0.95442.885-0.025-0.0250.0000.0000.0000.000
113B113SER0-0.073-0.09444.3540.0010.0010.0000.0000.0000.000
114B114PRO00.0500.01843.9510.0010.0010.0000.0000.0000.000
115B115MET00.014-0.00447.0720.0000.0000.0000.0000.0000.000
116B116ASP-1-0.839-0.86049.570-0.014-0.0140.0000.0000.0000.000
117B117ALA0-0.040-0.02349.8180.0000.0000.0000.0000.0000.000
118B118LEU00.032-0.00448.2090.0000.0000.0000.0000.0000.000
119B119ARG10.9380.97352.4150.0150.0150.0000.0000.0000.000
120B120ARG10.9020.95354.7870.0190.0190.0000.0000.0000.000
121B121CYS0-0.110-0.03854.2710.0000.0000.0000.0000.0000.000
122B122GLN0-0.068-0.03156.7630.0000.0000.0000.0000.0000.000
123B123VAL00.0320.05352.3770.0000.0000.0000.0000.0000.000
124B124ASP-1-0.881-0.94755.662-0.013-0.0130.0000.0000.0000.000
125B125ASN0-0.052-0.03452.7230.0000.0000.0000.0000.0000.000
126B126PHE00.042-0.00548.429-0.001-0.0010.0000.0000.0000.000
127B127ASN0-0.047-0.00647.981-0.001-0.0010.0000.0000.0000.000
128B128PHE0-0.021-0.02347.8180.0000.0000.0000.0000.0000.000
129B129GLN00.0380.05540.9110.0010.0010.0000.0000.0000.000
130B130LEU0-0.035-0.03244.3520.0010.0010.0000.0000.0000.000
131B131ARG10.8840.92143.3280.0400.0400.0000.0000.0000.000
132B132GLY00.008-0.01843.295-0.003-0.0030.0000.0000.0000.000
133B133ILE0-0.031-0.01145.2310.0030.0030.0000.0000.0000.000
134B134VAL00.0250.00547.524-0.002-0.0020.0000.0000.0000.000
135B135ILE0-0.034-0.01448.9430.0020.0020.0000.0000.0000.000
136B136ASP-1-0.784-0.87852.195-0.031-0.0310.0000.0000.0000.000
137B137ASN00.0450.02655.4450.0010.0010.0000.0000.0000.000
138B138LEU00.006-0.01949.9360.0010.0010.0000.0000.0000.000
139B139SER0-0.022-0.02054.6590.0000.0000.0000.0000.0000.000
140B140PHE0-0.0050.00757.5100.0010.0010.0000.0000.0000.000
141B141LEU0-0.0360.00253.5740.0010.0010.0000.0000.0000.000
142B142ASN0-0.010-0.01454.587-0.001-0.0010.0000.0000.0000.000
143B153ASN00.014-0.01553.7210.0010.0010.0000.0000.0000.000
144B154LEU00.0940.03347.3610.0000.0000.0000.0000.0000.000
145B155SER00.0230.02948.247-0.002-0.0020.0000.0000.0000.000
146B156LYS10.9380.97448.3220.0270.0270.0000.0000.0000.000
147B157PHE00.0580.01648.7900.0000.0000.0000.0000.0000.000
148B158GLU-1-0.891-0.92741.926-0.051-0.0510.0000.0000.0000.000
149B159LYS10.9100.95844.2380.0260.0260.0000.0000.0000.000
150B160LEU00.0150.00445.2980.0000.0000.0000.0000.0000.000
151B161PHE00.0550.03639.1210.0000.0000.0000.0000.0000.000
152B162LYS10.9510.97839.1220.0410.0410.0000.0000.0000.000
153B163ILE0-0.031-0.01740.831-0.002-0.0020.0000.0000.0000.000
154B164LEU00.0470.02242.5300.0000.0000.0000.0000.0000.000
155B165ARG10.9590.98434.8840.0620.0620.0000.0000.0000.000
156B166LYS10.8760.95337.8340.0340.0340.0000.0000.0000.000
157B167LEU00.0230.01138.5960.0000.0000.0000.0000.0000.000
158B168ARG10.8530.94436.2550.0630.0630.0000.0000.0000.000
159B169GLU-1-0.934-0.95432.559-0.077-0.0770.0000.0000.0000.000
160B170PHE0-0.050-0.01534.992-0.001-0.0010.0000.0000.0000.000
161B171LEU00.0210.00137.2940.0010.0010.0000.0000.0000.000
162B172GLY00.0320.03437.2840.0000.0000.0000.0000.0000.000
163B173CYS0-0.0420.01238.135-0.002-0.0020.0000.0000.0000.000
164B174TRP00.0320.02040.561-0.002-0.0020.0000.0000.0000.000
165B175ILE0-0.015-0.02341.9300.0030.0030.0000.0000.0000.000
166B176ILE00.0120.01144.444-0.002-0.0020.0000.0000.0000.000
167B177THR0-0.034-0.02347.3950.0020.0020.0000.0000.0000.000
168B178LYS10.8380.91049.9010.0300.0300.0000.0000.0000.000
169B179SER0-0.052-0.02653.0750.0000.0000.0000.0000.0000.000
170B180PHE00.0130.01055.1070.0000.0000.0000.0000.0000.000
171B181PRO00.0560.02157.116-0.001-0.0010.0000.0000.0000.000
172B182THR0-0.020-0.03257.9100.0010.0010.0000.0000.0000.000
173B183ASP-1-0.916-0.94259.597-0.026-0.0260.0000.0000.0000.000
174B184PHE00.0320.01560.5950.0010.0010.0000.0000.0000.000
175B185TYR0-0.044-0.02456.4500.0000.0000.0000.0000.0000.000
176B186ASN00.0270.02262.0790.0000.0000.0000.0000.0000.000
177B187GLY00.0140.01764.9270.0010.0010.0000.0000.0000.000
178B188ILE00.0310.00467.2040.0000.0000.0000.0000.0000.000
179B189GLU-1-0.920-0.96270.874-0.018-0.0180.0000.0000.0000.000
180B190ASN0-0.031-0.01868.5640.0000.0000.0000.0000.0000.000
181B191THR0-0.030-0.00668.951-0.001-0.0010.0000.0000.0000.000
182B192LEU0-0.051-0.01564.3510.0000.0000.0000.0000.0000.000
183B193VAL0-0.091-0.03364.215-0.001-0.0010.0000.0000.0000.000
184B208PRO00.0170.01251.7610.0000.0000.0000.0000.0000.000
185B209THR00.023-0.01352.1680.0010.0010.0000.0000.0000.000
186B210LYS10.9400.98953.8050.0290.0290.0000.0000.0000.000
187B211LEU00.0010.00150.3450.0010.0010.0000.0000.0000.000
188B212PRO0-0.010-0.01948.404-0.001-0.0010.0000.0000.0000.000
189B213ASP-1-0.774-0.89544.555-0.056-0.0560.0000.0000.0000.000
190B214SER0-0.077-0.01343.368-0.002-0.0020.0000.0000.0000.000
191B215TYR00.038-0.01443.102-0.002-0.0020.0000.0000.0000.000
192B216MET0-0.0050.00044.209-0.001-0.0010.0000.0000.0000.000
193B217LYS10.8260.91039.3730.0580.0580.0000.0000.0000.000
194B218GLY0-0.019-0.01539.812-0.004-0.0040.0000.0000.0000.000
195B219MET0-0.078-0.02340.0500.0000.0000.0000.0000.0000.000
196B220ASP-1-0.775-0.86337.766-0.074-0.0740.0000.0000.0000.000
197B221LEU0-0.061-0.04140.066-0.002-0.0020.0000.0000.0000.000
198B222ILE0-0.006-0.00143.2400.0030.0030.0000.0000.0000.000
199B223ILE0-0.009-0.01646.615-0.001-0.0010.0000.0000.0000.000
200B224TYR0-0.039-0.01749.5630.0020.0020.0000.0000.0000.000
201B225ARG10.8810.93552.9300.0310.0310.0000.0000.0000.000
202B226GLU-1-0.836-0.89956.039-0.037-0.0370.0000.0000.0000.000
203B227VAL0-0.032-0.03658.889-0.001-0.0010.0000.0000.0000.000
204B228VAL0-0.0110.01160.6700.0010.0010.0000.0000.0000.000
205B229ASP-1-0.772-0.86763.341-0.030-0.0300.0000.0000.0000.000
206B230GLY00.0010.00364.9830.0010.0010.0000.0000.0000.000
207B231ARG10.7740.87660.2590.0330.0330.0000.0000.0000.000
208B232PRO0-0.014-0.00959.090-0.001-0.0010.0000.0000.0000.000
209B233GLN00.0250.01256.1210.0000.0000.0000.0000.0000.000
210B234TYR00.0500.00952.1430.0010.0010.0000.0000.0000.000
211B235ARG10.8710.92851.0910.0410.0410.0000.0000.0000.000
212B236ARG11.0001.00040.2710.0670.0670.0000.0000.0000.000
213B237ILE0-0.035-0.01144.7430.0000.0000.0000.0000.0000.000