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: 437VN

Calculation Name: 4FZS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FZS

Chain ID: A

ChEMBL ID:

UniProt ID: Q13596

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2096370.311253
FMO2-HF: Nuclear repulsion 2010215.583381
FMO2-HF: Total energy -86154.727872
FMO2-MP2: Total energy -86410.393571


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:305:SER)


Summations of interaction energy for fragment #1(A:305:SER)
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.
-8.44-2.9660.35-2.526-3.30.009
Interaction energy analysis for fragmet #1(A:305:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.011
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].
3A307ILE00.0600.0362.997-4.541-0.3760.251-2.085-2.3320.007
4A308TRP00.0590.0382.906-2.244-1.1520.100-0.405-0.7880.002
5A309PHE0-0.078-0.0444.735-1.429-1.212-0.001-0.036-0.1800.000
6A310GLU-1-0.890-0.9397.2950.7760.7760.0000.0000.0000.000
7A311GLU-1-0.909-0.9486.2532.1012.1010.0000.0000.0000.000
8A312LYS10.7690.8568.779-1.701-1.7010.0000.0000.0000.000
9A313LEU0-0.0040.00910.739-0.219-0.2190.0000.0000.0000.000
10A314GLN00.015-0.00511.337-0.239-0.2390.0000.0000.0000.000
11A315GLU-1-0.818-0.89412.7350.8190.8190.0000.0000.0000.000
12A316VAL0-0.022-0.00514.870-0.112-0.1120.0000.0000.0000.000
13A317GLU-1-0.813-0.90116.8250.3530.3530.0000.0000.0000.000
14A318CYS0-0.0290.01618.179-0.075-0.0750.0000.0000.0000.000
15A319GLU-1-0.748-0.86919.3020.3220.3220.0000.0000.0000.000
16A320GLU-1-0.759-0.85320.8080.2680.2680.0000.0000.0000.000
17A321GLN0-0.034-0.01222.693-0.044-0.0440.0000.0000.0000.000
18A322ARG10.8180.87721.174-0.380-0.3800.0000.0000.0000.000
19A323LEU00.002-0.00223.513-0.026-0.0260.0000.0000.0000.000
20A324ARG10.8810.92825.563-0.264-0.2640.0000.0000.0000.000
21A325LYS10.9310.96528.604-0.211-0.2110.0000.0000.0000.000
22A326LEU0-0.0110.00929.162-0.012-0.0120.0000.0000.0000.000
23A327HIS00.0650.01430.679-0.006-0.0060.0000.0000.0000.000
24A328ALA0-0.0100.00632.430-0.011-0.0110.0000.0000.0000.000
25A329VAL00.0080.01034.749-0.009-0.0090.0000.0000.0000.000
26A330VAL00.0200.01733.526-0.008-0.0080.0000.0000.0000.000
27A331GLU-1-0.772-0.89836.3320.1140.1140.0000.0000.0000.000
28A332THR0-0.090-0.03438.178-0.009-0.0090.0000.0000.0000.000
29A333LEU0-0.014-0.00738.438-0.006-0.0060.0000.0000.0000.000
30A334VAL00.0080.00438.493-0.006-0.0060.0000.0000.0000.000
31A335ASN0-0.072-0.06340.707-0.009-0.0090.0000.0000.0000.000
32A336HIS00.0360.03443.643-0.004-0.0040.0000.0000.0000.000
33A337ARG10.8740.93245.067-0.092-0.0920.0000.0000.0000.000
34A338LYS10.8690.94141.094-0.113-0.1130.0000.0000.0000.000
35A339GLU-1-0.887-0.93946.4080.0720.0720.0000.0000.0000.000
36A340LEU0-0.022-0.00749.270-0.004-0.0040.0000.0000.0000.000
37A341ALA00.0390.03449.595-0.004-0.0040.0000.0000.0000.000
38A342LEU0-0.025-0.00250.117-0.003-0.0030.0000.0000.0000.000
39A343ASN0-0.049-0.04852.397-0.005-0.0050.0000.0000.0000.000
40A344THR0-0.010-0.01254.289-0.003-0.0030.0000.0000.0000.000
41A345ALA00.0500.03054.890-0.003-0.0030.0000.0000.0000.000
42A346GLN0-0.080-0.03756.584-0.004-0.0040.0000.0000.0000.000
43A347PHE00.0210.00958.415-0.003-0.0030.0000.0000.0000.000
44A348ALA00.0670.03460.109-0.002-0.0020.0000.0000.0000.000
45A349LYS10.9460.97060.288-0.050-0.0500.0000.0000.0000.000
46A350SER0-0.055-0.02762.516-0.003-0.0030.0000.0000.0000.000
47A351LEU00.0070.00663.765-0.002-0.0020.0000.0000.0000.000
48A352ALA00.0250.00865.525-0.002-0.0020.0000.0000.0000.000
49A353MET0-0.093-0.03366.726-0.001-0.0010.0000.0000.0000.000
50A354LEU00.0390.00768.011-0.001-0.0010.0000.0000.0000.000
51A355GLY00.0440.02270.218-0.001-0.0010.0000.0000.0000.000
52A356SER0-0.083-0.02671.268-0.001-0.0010.0000.0000.0000.000
53A357SER0-0.115-0.06173.021-0.001-0.0010.0000.0000.0000.000
54A358GLU-1-0.848-0.91975.0410.0320.0320.0000.0000.0000.000
55A359ASP-1-0.876-0.93577.0970.0290.0290.0000.0000.0000.000
56A360ASN0-0.059-0.03579.3620.0000.0000.0000.0000.0000.000
57A361THR00.029-0.00278.7810.0010.0010.0000.0000.0000.000
58A362ALA0-0.027-0.00878.2840.0010.0010.0000.0000.0000.000
59A363LEU0-0.018-0.00274.3010.0010.0010.0000.0000.0000.000
60A364SER00.0300.00974.2680.0010.0010.0000.0000.0000.000
61A365ARG10.9550.98573.296-0.032-0.0320.0000.0000.0000.000
62A366ALA0-0.037-0.00772.3930.0010.0010.0000.0000.0000.000
63A367LEU00.0030.00669.7730.0010.0010.0000.0000.0000.000
64A368SER00.013-0.01468.4360.0010.0010.0000.0000.0000.000
65A369GLN0-0.009-0.01968.0220.0000.0000.0000.0000.0000.000
66A370LEU0-0.0160.00164.5800.0010.0010.0000.0000.0000.000
67A371ALA00.000-0.00364.2490.0020.0020.0000.0000.0000.000
68A372GLU-1-0.852-0.91063.1020.0450.0450.0000.0000.0000.000
69A373VAL0-0.063-0.02262.4800.0020.0020.0000.0000.0000.000
70A374GLU-1-0.867-0.95659.3870.0570.0570.0000.0000.0000.000
71A375GLU-1-0.875-0.92658.5310.0520.0520.0000.0000.0000.000
72A376LYS10.7810.86257.785-0.047-0.0470.0000.0000.0000.000
73A377ILE0-0.028-0.00756.0570.0020.0020.0000.0000.0000.000
74A378GLU-1-0.878-0.93753.6420.0680.0680.0000.0000.0000.000
75A379GLN00.0180.01552.9440.0030.0030.0000.0000.0000.000
76A380LEU00.0190.01552.4250.0030.0030.0000.0000.0000.000
77A381HIS0-0.012-0.00250.1340.0070.0070.0000.0000.0000.000
78A382GLN0-0.051-0.04648.5340.0080.0080.0000.0000.0000.000
79A383GLU-1-0.955-0.96647.7850.0770.0770.0000.0000.0000.000
80A384GLN0-0.002-0.00545.6920.0070.0070.0000.0000.0000.000
81A385ALA0-0.023-0.01844.4700.0060.0060.0000.0000.0000.000
82A386ASN0-0.095-0.05842.9770.0080.0080.0000.0000.0000.000
83A387ASN00.0210.02641.3940.0010.0010.0000.0000.0000.000
84A388ASP-1-0.875-0.94137.4250.1250.1250.0000.0000.0000.000
85A389PHE0-0.041-0.02636.6290.0110.0110.0000.0000.0000.000
86A390PHE00.0120.01336.9220.0080.0080.0000.0000.0000.000
87A391LEU00.0270.01834.0410.0060.0060.0000.0000.0000.000
88A392LEU0-0.049-0.03231.0310.0120.0120.0000.0000.0000.000
89A393ALA00.0170.00232.3440.0130.0130.0000.0000.0000.000
90A394GLU-1-0.871-0.94533.1850.1500.1500.0000.0000.0000.000
91A395LEU0-0.045-0.01929.4770.0130.0130.0000.0000.0000.000
92A396LEU0-0.043-0.01527.8320.0210.0210.0000.0000.0000.000
93A397SER0-0.021-0.01128.8330.0140.0140.0000.0000.0000.000
94A398ASP-1-0.923-0.95428.4000.2140.2140.0000.0000.0000.000
95A399TYR00.0020.00319.9970.0200.0200.0000.0000.0000.000
96A400ILE0-0.021-0.02024.1840.0290.0290.0000.0000.0000.000
97A401ARG10.9200.96525.477-0.173-0.1730.0000.0000.0000.000
98A402LEU00.0090.00920.4070.0100.0100.0000.0000.0000.000
99A403LEU0-0.005-0.01319.5910.0340.0340.0000.0000.0000.000
100A404ALA00.0100.01020.5080.0250.0250.0000.0000.0000.000
101A405ILE0-0.030-0.01120.7280.0030.0030.0000.0000.0000.000
102A406VAL0-0.021-0.01616.3170.0050.0050.0000.0000.0000.000
103A407ARG10.8030.88316.844-0.322-0.3220.0000.0000.0000.000
104A408ALA00.0040.01018.252-0.004-0.0040.0000.0000.0000.000
105A409ALA00.0010.00516.444-0.023-0.0230.0000.0000.0000.000
106A410PHE00.035-0.00310.337-0.013-0.0130.0000.0000.0000.000
107A411ASP-1-0.801-0.88114.9330.2080.2080.0000.0000.0000.000
108A412GLN0-0.025-0.02117.672-0.028-0.0280.0000.0000.0000.000
109A413ARG10.7740.8496.994-0.406-0.4060.0000.0000.0000.000
110A414MET00.0250.02412.494-0.088-0.0880.0000.0000.0000.000
111A415LYS10.8290.89215.078-0.241-0.2410.0000.0000.0000.000
112A416THR0-0.065-0.04315.683-0.043-0.0430.0000.0000.0000.000
113A417TRP00.0010.0029.6750.0030.0030.0000.0000.0000.000
114A418GLN0-0.004-0.01314.015-0.045-0.0450.0000.0000.0000.000
115A419ARG10.9160.97816.828-0.016-0.0160.0000.0000.0000.000
116A420TRP0-0.045-0.0319.4600.0080.0080.0000.0000.0000.000
117A421GLN00.0560.03512.107-0.045-0.0450.0000.0000.0000.000
118A422ASP-1-0.844-0.91816.273-0.046-0.0460.0000.0000.0000.000
119A423ALA0-0.063-0.03519.761-0.002-0.0020.0000.0000.0000.000
120A424GLN0-0.007-0.00513.319-0.017-0.0170.0000.0000.0000.000
121A425ALA00.0300.01118.728-0.010-0.0100.0000.0000.0000.000
122A426THR0-0.066-0.04120.5210.0100.0100.0000.0000.0000.000
123A427LEU00.0130.01320.0100.0060.0060.0000.0000.0000.000
124A428GLN0-0.023-0.01320.785-0.012-0.0120.0000.0000.0000.000
125A429LYS10.9240.96222.7620.0980.0980.0000.0000.0000.000
126A430LYS10.7690.87925.9020.1040.1040.0000.0000.0000.000
127A431ARG10.9170.93920.5450.2390.2390.0000.0000.0000.000
128A432GLU-1-0.809-0.89125.732-0.144-0.1440.0000.0000.0000.000
129A433ALA0-0.0320.00428.3320.0080.0080.0000.0000.0000.000
130A434GLU-1-0.886-0.95630.447-0.120-0.1200.0000.0000.0000.000
131A435ALA0-0.017-0.01229.6890.0050.0050.0000.0000.0000.000
132A436ARG10.7800.87629.5060.1190.1190.0000.0000.0000.000
133A437LEU0-0.032-0.02734.5710.0060.0060.0000.0000.0000.000
134A438LEU0-0.032-0.00733.4970.0050.0050.0000.0000.0000.000
135A439TRP00.0150.00135.8330.0060.0060.0000.0000.0000.000
136A440ALA00.0000.01138.8980.0050.0050.0000.0000.0000.000
137A441ASN0-0.0120.00340.1540.0070.0070.0000.0000.0000.000
138A442LYS10.9330.94441.6830.0680.0680.0000.0000.0000.000
139A443PRO00.0460.01140.792-0.001-0.0010.0000.0000.0000.000
140A444ASP-1-0.790-0.85940.796-0.059-0.0590.0000.0000.0000.000
141A445LYS10.8760.90438.9430.0560.0560.0000.0000.0000.000
142A446LEU0-0.0010.01535.408-0.003-0.0030.0000.0000.0000.000
143A447GLN0-0.054-0.03735.928-0.002-0.0020.0000.0000.0000.000
144A448GLN0-0.020-0.02135.018-0.005-0.0050.0000.0000.0000.000
145A449ALA00.0260.00932.966-0.002-0.0020.0000.0000.0000.000
146A450LYS10.8870.95231.5020.0840.0840.0000.0000.0000.000
147A451ASP-1-0.832-0.91930.693-0.092-0.0920.0000.0000.0000.000
148A452GLU-1-0.821-0.88030.551-0.075-0.0750.0000.0000.0000.000
149A453ILE0-0.0210.00525.753-0.004-0.0040.0000.0000.0000.000
150A454LEU00.0170.01826.238-0.007-0.0070.0000.0000.0000.000
151A455GLU-1-0.836-0.89426.846-0.075-0.0750.0000.0000.0000.000
152A456TRP0-0.013-0.02923.8420.0030.0030.0000.0000.0000.000
153A457GLU-1-0.790-0.88822.005-0.197-0.1970.0000.0000.0000.000
154A458SER0-0.031-0.00521.828-0.012-0.0120.0000.0000.0000.000
155A459ARG10.8090.88422.6690.0660.0660.0000.0000.0000.000
156A460VAL00.0130.01117.2700.0060.0060.0000.0000.0000.000
157A461THR00.0100.00117.597-0.005-0.0050.0000.0000.0000.000
158A462GLN0-0.048-0.02318.017-0.015-0.0150.0000.0000.0000.000
159A463TYR0-0.006-0.02618.1750.0210.0210.0000.0000.0000.000
160A464GLU-1-0.828-0.90312.395-0.427-0.4270.0000.0000.0000.000
161A465ARG10.9300.96913.7820.1470.1470.0000.0000.0000.000
162A466ASP-1-0.836-0.89715.8970.0090.0090.0000.0000.0000.000
163A467PHE00.0350.0058.1880.0860.0860.0000.0000.0000.000
164A468GLU-1-0.919-0.94110.491-0.335-0.3350.0000.0000.0000.000
165A469ARG10.8220.90611.9970.0670.0670.0000.0000.0000.000
166A470ILE00.0080.00813.7070.0580.0580.0000.0000.0000.000
167A471SER00.0220.0038.7320.1070.1070.0000.0000.0000.000
168A472THR0-0.033-0.02710.3700.1850.1850.0000.0000.0000.000
169A473VAL0-0.041-0.01411.8500.0610.0610.0000.0000.0000.000
170A474VAL00.0220.01511.1230.0380.0380.0000.0000.0000.000
171A475ARG10.9430.9815.050-0.163-0.1630.0000.0000.0000.000
172A476LYS10.9360.97811.046-0.271-0.2710.0000.0000.0000.000
173A477GLU-1-0.773-0.86814.6060.3280.3280.0000.0000.0000.000
174A478VAL00.0160.01110.983-0.041-0.0410.0000.0000.0000.000
175A479ILE0-0.001-0.00212.493-0.054-0.0540.0000.0000.0000.000
176A480ARG10.7700.85115.433-0.373-0.3730.0000.0000.0000.000
177A481PHE00.0660.02314.384-0.037-0.0370.0000.0000.0000.000
178A482GLU-1-0.805-0.90212.8940.9770.9770.0000.0000.0000.000
179A483LYS10.9100.95817.448-0.418-0.4180.0000.0000.0000.000
180A484GLU-1-0.837-0.90720.5110.2440.2440.0000.0000.0000.000
181A485LYS10.7900.90615.087-0.779-0.7790.0000.0000.0000.000
182A486SER0-0.043-0.02921.045-0.018-0.0180.0000.0000.0000.000
183A487LYS10.8650.93022.554-0.273-0.2730.0000.0000.0000.000
184A488ASP-1-0.868-0.93025.3710.2120.2120.0000.0000.0000.000
185A489PHE00.0470.01725.317-0.015-0.0150.0000.0000.0000.000
186A490LYS10.8390.89823.242-0.341-0.3410.0000.0000.0000.000
187A491ASN0-0.005-0.02228.846-0.024-0.0240.0000.0000.0000.000
188A492HIS00.0250.03229.840-0.024-0.0240.0000.0000.0000.000
189A493VAL00.0130.01032.932-0.011-0.0110.0000.0000.0000.000
190A494ILE0-0.037-0.00432.868-0.009-0.0090.0000.0000.0000.000
191A495LYS10.9390.96732.034-0.180-0.1800.0000.0000.0000.000
192A496TYR0-0.0070.00237.663-0.007-0.0070.0000.0000.0000.000
193A497LEU00.0300.01037.432-0.008-0.0080.0000.0000.0000.000
194A498GLU-1-0.928-0.96538.8640.1170.1170.0000.0000.0000.000
195A499THR0-0.048-0.03342.078-0.007-0.0070.0000.0000.0000.000
196A500LEU0-0.0040.00643.301-0.006-0.0060.0000.0000.0000.000
197A501LEU00.0040.00044.674-0.006-0.0060.0000.0000.0000.000
198A502TYR00.003-0.00846.193-0.005-0.0050.0000.0000.0000.000
199A503SER00.0240.00947.935-0.005-0.0050.0000.0000.0000.000
200A504GLN0-0.020-0.01749.157-0.003-0.0030.0000.0000.0000.000
201A505GLN00.0140.01548.944-0.006-0.0060.0000.0000.0000.000
202A506GLN00.0020.00151.981-0.003-0.0030.0000.0000.0000.000
203A507LEU0-0.0010.01153.908-0.003-0.0030.0000.0000.0000.000
204A508ALA0-0.003-0.01055.211-0.003-0.0030.0000.0000.0000.000
205A509LYS10.8720.92552.740-0.069-0.0690.0000.0000.0000.000
206A510TYR0-0.040-0.00658.399-0.002-0.0020.0000.0000.0000.000
207A511TRP0-0.024-0.01959.859-0.002-0.0020.0000.0000.0000.000
208A512GLU-1-0.962-0.97060.3910.0520.0520.0000.0000.0000.000
209A513ALA0-0.087-0.02963.326-0.002-0.0020.0000.0000.0000.000