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: K3NL3

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 OptHSide
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 -2088289.740771
FMO2-HF: Nuclear repulsion 2002135.929595
FMO2-HF: Total energy -86153.811176
FMO2-MP2: Total energy -86409.518745


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.
-11.971-5.9012.493-3.132-5.4310.026
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 : 0.021 / 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].
3A307ILE00.0070.0222.494-4.258-0.3691.767-2.111-3.5450.018
4A308TRP00.0730.0392.496-4.000-2.2600.726-0.902-1.5640.008
5A309PHE0-0.055-0.0444.359-2.418-2.0180.001-0.118-0.2830.000
6A310GLU-1-0.910-0.9536.6240.6760.6760.0000.0000.0000.000
7A311GLU-1-0.905-0.9496.4542.0142.0140.0000.0000.0000.000
8A312LYS10.7670.8658.513-2.005-2.0050.0000.0000.0000.000
9A313LEU0-0.0090.00410.407-0.273-0.2730.0000.0000.0000.000
10A314GLN00.0570.03311.296-0.259-0.2590.0000.0000.0000.000
11A315GLU-1-0.824-0.90112.4950.8910.8910.0000.0000.0000.000
12A316VAL0-0.033-0.01614.485-0.131-0.1310.0000.0000.0000.000
13A317GLU-1-0.850-0.91516.4090.4360.4360.0000.0000.0000.000
14A318CYS0-0.0570.00017.984-0.091-0.0910.0000.0000.0000.000
15A319GLU-1-0.748-0.87719.1480.3650.3650.0000.0000.0000.000
16A320GLU-1-0.779-0.86120.5940.3100.3100.0000.0000.0000.000
17A321GLN0-0.018-0.00922.476-0.045-0.0450.0000.0000.0000.000
18A322ARG10.8300.88421.008-0.430-0.4300.0000.0000.0000.000
19A323LEU0-0.006-0.01823.787-0.030-0.0300.0000.0000.0000.000
20A324ARG10.8980.95225.355-0.306-0.3060.0000.0000.0000.000
21A325LYS10.9400.97228.455-0.233-0.2330.0000.0000.0000.000
22A326LEU0-0.0050.00429.071-0.015-0.0150.0000.0000.0000.000
23A327HIS00.0590.02330.368-0.006-0.0060.0000.0000.0000.000
24A328ALA00.0130.01632.121-0.013-0.0130.0000.0000.0000.000
25A329VAL0-0.0240.00034.339-0.011-0.0110.0000.0000.0000.000
26A330VAL00.017-0.00633.449-0.010-0.0100.0000.0000.0000.000
27A331GLU-1-0.856-0.93835.7210.1380.1380.0000.0000.0000.000
28A332THR0-0.073-0.02437.655-0.010-0.0100.0000.0000.0000.000
29A333LEU0-0.023-0.01038.250-0.007-0.0070.0000.0000.0000.000
30A334VAL00.003-0.00537.900-0.007-0.0070.0000.0000.0000.000
31A335ASN0-0.050-0.04940.019-0.011-0.0110.0000.0000.0000.000
32A336HIS00.0440.04343.211-0.005-0.0050.0000.0000.0000.000
33A337ARG10.8930.94644.705-0.103-0.1030.0000.0000.0000.000
34A338LYS10.9120.97241.731-0.120-0.1200.0000.0000.0000.000
35A339GLU-1-0.878-0.94346.2880.0810.0810.0000.0000.0000.000
36A340LEU0-0.026-0.00549.061-0.004-0.0040.0000.0000.0000.000
37A341ALA00.0590.04649.523-0.004-0.0040.0000.0000.0000.000
38A342LEU0-0.050-0.00749.829-0.003-0.0030.0000.0000.0000.000
39A343ASN0-0.043-0.05652.064-0.005-0.0050.0000.0000.0000.000
40A344THR00.007-0.00754.085-0.003-0.0030.0000.0000.0000.000
41A345ALA00.0630.04154.860-0.003-0.0030.0000.0000.0000.000
42A346GLN0-0.102-0.04256.477-0.004-0.0040.0000.0000.0000.000
43A347PHE00.0210.00658.180-0.003-0.0030.0000.0000.0000.000
44A348ALA00.0750.03559.975-0.003-0.0030.0000.0000.0000.000
45A349LYS10.9510.97660.166-0.057-0.0570.0000.0000.0000.000
46A350SER0-0.050-0.03062.389-0.003-0.0030.0000.0000.0000.000
47A351LEU00.0110.00663.628-0.002-0.0020.0000.0000.0000.000
48A352ALA00.0300.01665.534-0.002-0.0020.0000.0000.0000.000
49A353MET0-0.077-0.02566.717-0.001-0.0010.0000.0000.0000.000
50A354LEU00.024-0.00767.724-0.002-0.0020.0000.0000.0000.000
51A355GLY00.0220.00569.994-0.001-0.0010.0000.0000.0000.000
52A356SER0-0.066-0.02271.043-0.001-0.0010.0000.0000.0000.000
53A357SER0-0.074-0.04072.757-0.001-0.0010.0000.0000.0000.000
54A358GLU-1-0.896-0.92574.6800.0360.0360.0000.0000.0000.000
55A359ASP-1-0.871-0.93276.5760.0320.0320.0000.0000.0000.000
56A360ASN0-0.096-0.04779.3040.0000.0000.0000.0000.0000.000
57A361THR00.0490.00178.5880.0010.0010.0000.0000.0000.000
58A362ALA0-0.030-0.00978.0090.0010.0010.0000.0000.0000.000
59A363LEU0-0.019-0.01274.0820.0010.0010.0000.0000.0000.000
60A364SER00.0390.01874.1740.0010.0010.0000.0000.0000.000
61A365ARG10.9560.97773.209-0.036-0.0360.0000.0000.0000.000
62A366ALA0-0.0210.00272.2070.0010.0010.0000.0000.0000.000
63A367LEU00.0030.00869.4630.0020.0020.0000.0000.0000.000
64A368SER00.016-0.01068.3180.0010.0010.0000.0000.0000.000
65A369GLN0-0.026-0.02067.8730.0000.0000.0000.0000.0000.000
66A370LEU0-0.011-0.00364.3130.0010.0010.0000.0000.0000.000
67A371ALA0-0.0020.00763.9420.0020.0020.0000.0000.0000.000
68A372GLU-1-0.844-0.92362.8640.0500.0500.0000.0000.0000.000
69A373VAL0-0.083-0.03662.3000.0020.0020.0000.0000.0000.000
70A374GLU-1-0.873-0.96459.2270.0640.0640.0000.0000.0000.000
71A375GLU-1-0.876-0.91758.2940.0580.0580.0000.0000.0000.000
72A376LYS10.7760.86857.454-0.052-0.0520.0000.0000.0000.000
73A377ILE0-0.032-0.01655.7950.0030.0030.0000.0000.0000.000
74A378GLU-1-0.886-0.92253.4310.0770.0770.0000.0000.0000.000
75A379GLN00.0420.01152.6190.0040.0040.0000.0000.0000.000
76A380LEU00.0070.01451.9780.0030.0030.0000.0000.0000.000
77A381HIS0-0.017-0.01049.7800.0080.0080.0000.0000.0000.000
78A382GLN0-0.053-0.05048.1160.0090.0090.0000.0000.0000.000
79A383GLU-1-0.960-0.97347.4250.0860.0860.0000.0000.0000.000
80A384GLN0-0.015-0.01645.3280.0080.0080.0000.0000.0000.000
81A385ALA00.0360.02544.1180.0060.0060.0000.0000.0000.000
82A386ASN0-0.124-0.04742.5370.0100.0100.0000.0000.0000.000
83A387ASN00.0160.00841.348-0.001-0.0010.0000.0000.0000.000
84A388ASP-1-0.942-0.97437.5210.1370.1370.0000.0000.0000.000
85A389PHE0-0.053-0.04136.3640.0120.0120.0000.0000.0000.000
86A390PHE00.0290.00736.7190.0100.0100.0000.0000.0000.000
87A391LEU00.0640.04634.0870.0050.0050.0000.0000.0000.000
88A392LEU0-0.018-0.02330.9740.0130.0130.0000.0000.0000.000
89A393ALA00.009-0.00532.1130.0160.0160.0000.0000.0000.000
90A394GLU-1-0.903-0.95233.0500.1710.1710.0000.0000.0000.000
91A395LEU0-0.054-0.02029.2580.0150.0150.0000.0000.0000.000
92A396LEU0-0.039-0.01427.6940.0230.0230.0000.0000.0000.000
93A397SER00.008-0.00628.3820.0180.0180.0000.0000.0000.000
94A398ASP-1-0.937-0.95527.9820.2500.2500.0000.0000.0000.000
95A399TYR00.0050.00419.7980.0290.0290.0000.0000.0000.000
96A400ILE0-0.042-0.02723.8140.0320.0320.0000.0000.0000.000
97A401ARG10.9520.97624.808-0.191-0.1910.0000.0000.0000.000
98A402LEU00.0240.01820.4250.0100.0100.0000.0000.0000.000
99A403LEU0-0.020-0.01819.1360.0410.0410.0000.0000.0000.000
100A404ALA00.0050.00720.2070.0290.0290.0000.0000.0000.000
101A405ILE0-0.024-0.00820.4190.0000.0000.0000.0000.0000.000
102A406VAL0-0.024-0.01916.0690.0110.0110.0000.0000.0000.000
103A407ARG10.8410.90116.521-0.379-0.3790.0000.0000.0000.000
104A408ALA00.0050.01618.029-0.005-0.0050.0000.0000.0000.000
105A409ALA00.0000.01416.212-0.028-0.0280.0000.0000.0000.000
106A410PHE00.008-0.0209.901-0.011-0.0110.0000.0000.0000.000
107A411ASP-1-0.814-0.89014.5840.2510.2510.0000.0000.0000.000
108A412GLN0-0.016-0.02317.191-0.021-0.0210.0000.0000.0000.000
109A413ARG10.8030.8726.769-0.519-0.5190.0000.0000.0000.000
110A414MET00.0140.02111.917-0.104-0.1040.0000.0000.0000.000
111A415LYS10.8580.91014.598-0.295-0.2950.0000.0000.0000.000
112A416THR0-0.073-0.04015.449-0.050-0.0500.0000.0000.0000.000
113A417TRP00.0040.0049.0490.0140.0140.0000.0000.0000.000
114A418GLN00.007-0.00913.684-0.071-0.0710.0000.0000.0000.000
115A419ARG10.9120.97616.364-0.014-0.0140.0000.0000.0000.000
116A420TRP0-0.037-0.0169.5230.0150.0150.0000.0000.0000.000
117A421GLN00.0330.01411.722-0.044-0.0440.0000.0000.0000.000
118A422ASP-1-0.835-0.91115.802-0.075-0.0750.0000.0000.0000.000
119A423ALA0-0.059-0.03419.346-0.003-0.0030.0000.0000.0000.000
120A424GLN0-0.003-0.00613.079-0.007-0.0070.0000.0000.0000.000
121A425ALA00.0300.02118.476-0.010-0.0100.0000.0000.0000.000
122A426THR0-0.092-0.04820.3350.0120.0120.0000.0000.0000.000
123A427LEU00.0130.00420.3130.0050.0050.0000.0000.0000.000
124A428GLN0-0.029-0.02420.510-0.013-0.0130.0000.0000.0000.000
125A429LYS10.9760.98822.5850.1110.1110.0000.0000.0000.000
126A430LYS10.7660.86725.7660.1150.1150.0000.0000.0000.000
127A431ARG10.9140.94420.5310.2600.2600.0000.0000.0000.000
128A432GLU-1-0.909-0.93424.750-0.180-0.1800.0000.0000.0000.000
129A433ALA0-0.062-0.03728.2210.0090.0090.0000.0000.0000.000
130A434GLU-1-0.896-0.94630.336-0.128-0.1280.0000.0000.0000.000
131A435ALA0-0.007-0.00630.0020.0060.0060.0000.0000.0000.000
132A436ARG10.8990.95830.7050.1260.1260.0000.0000.0000.000
133A437LEU0-0.011-0.02234.7350.0060.0060.0000.0000.0000.000
134A438LEU0-0.0040.00933.6680.0060.0060.0000.0000.0000.000
135A439TRP00.0070.00436.1510.0080.0080.0000.0000.0000.000
136A440ALA00.0000.00138.7750.0060.0060.0000.0000.0000.000
137A441ASN0-0.0190.00840.4590.0080.0080.0000.0000.0000.000
138A442LYS10.9390.94341.8520.0740.0740.0000.0000.0000.000
139A443PRO00.026-0.00140.829-0.001-0.0010.0000.0000.0000.000
140A444ASP-1-0.803-0.87641.231-0.063-0.0630.0000.0000.0000.000
141A445LYS10.8770.91538.7990.0620.0620.0000.0000.0000.000
142A446LEU0-0.0100.00335.548-0.003-0.0030.0000.0000.0000.000
143A447GLN0-0.060-0.03036.008-0.002-0.0020.0000.0000.0000.000
144A448GLN0-0.024-0.02234.669-0.004-0.0040.0000.0000.0000.000
145A449ALA00.0280.00832.816-0.002-0.0020.0000.0000.0000.000
146A450LYS10.9340.97831.4150.0910.0910.0000.0000.0000.000
147A451ASP-1-0.851-0.93531.188-0.095-0.0950.0000.0000.0000.000
148A452GLU-1-0.844-0.88230.177-0.084-0.0840.0000.0000.0000.000
149A453ILE0-0.026-0.01526.100-0.004-0.0040.0000.0000.0000.000
150A454LEU00.0230.01626.360-0.009-0.0090.0000.0000.0000.000
151A455GLU-1-0.833-0.88827.381-0.077-0.0770.0000.0000.0000.000
152A456TRP0-0.013-0.03923.5280.0010.0010.0000.0000.0000.000
153A457GLU-1-0.791-0.87122.308-0.209-0.2090.0000.0000.0000.000
154A458SER0-0.022-0.00421.975-0.013-0.0130.0000.0000.0000.000
155A459ARG10.7870.88422.9660.0750.0750.0000.0000.0000.000
156A460VAL00.0270.00417.3150.0070.0070.0000.0000.0000.000
157A461THR00.0000.00417.638-0.012-0.0120.0000.0000.0000.000
158A462GLN0-0.045-0.02017.951-0.016-0.0160.0000.0000.0000.000
159A463TYR0-0.019-0.03217.9920.0260.0260.0000.0000.0000.000
160A464GLU-1-0.815-0.89712.122-0.487-0.4870.0000.0000.0000.000
161A465ARG10.9270.96913.9040.1480.1480.0000.0000.0000.000
162A466ASP-1-0.829-0.90315.3440.0190.0190.0000.0000.0000.000
163A467PHE00.020-0.0058.1320.1060.1060.0000.0000.0000.000
164A468GLU-1-0.918-0.95410.352-0.320-0.3200.0000.0000.0000.000
165A469ARG10.8100.88911.8670.0640.0640.0000.0000.0000.000
166A470ILE0-0.0020.00513.2830.0630.0630.0000.0000.0000.000
167A471SER00.0420.0248.4890.1400.1400.0000.0000.0000.000
168A472THR0-0.064-0.03010.2100.2130.2130.0000.0000.0000.000
169A473VAL0-0.016-0.01011.8840.0760.0760.0000.0000.0000.000
170A474VAL00.0190.02010.7780.0390.0390.0000.0000.0000.000
171A475ARG10.9630.9824.672-0.655-0.614-0.001-0.001-0.0390.000
172A476LYS10.9230.97311.133-0.348-0.3480.0000.0000.0000.000
173A477GLU-1-0.752-0.86814.7860.3860.3860.0000.0000.0000.000
174A478VAL0-0.0080.00410.489-0.024-0.0240.0000.0000.0000.000
175A479ILE00.0100.00113.023-0.053-0.0530.0000.0000.0000.000
176A480ARG10.7520.84215.320-0.428-0.4280.0000.0000.0000.000
177A481PHE00.0460.01614.031-0.055-0.0550.0000.0000.0000.000
178A482GLU-1-0.829-0.91012.8741.0891.0890.0000.0000.0000.000
179A483LYS10.9260.95917.440-0.455-0.4550.0000.0000.0000.000
180A484GLU-1-0.834-0.90920.6730.2680.2680.0000.0000.0000.000
181A485LYS10.8530.95815.371-0.800-0.8000.0000.0000.0000.000
182A486SER0-0.072-0.04620.576-0.018-0.0180.0000.0000.0000.000
183A487LYS10.8690.91922.242-0.311-0.3110.0000.0000.0000.000
184A488ASP-1-0.892-0.93825.0580.2420.2420.0000.0000.0000.000
185A489PHE00.0310.01225.252-0.018-0.0180.0000.0000.0000.000
186A490LYS10.8730.92323.352-0.378-0.3780.0000.0000.0000.000
187A491ASN00.014-0.01228.853-0.028-0.0280.0000.0000.0000.000
188A492HIS00.0210.03329.876-0.027-0.0270.0000.0000.0000.000
189A493VAL00.0170.01032.786-0.012-0.0120.0000.0000.0000.000
190A494ILE0-0.024-0.00132.734-0.009-0.0090.0000.0000.0000.000
191A495LYS10.9420.97432.254-0.195-0.1950.0000.0000.0000.000
192A496TYR00.0060.00537.455-0.008-0.0080.0000.0000.0000.000
193A497LEU00.0400.00937.426-0.009-0.0090.0000.0000.0000.000
194A498GLU-1-0.942-0.96639.1850.1270.1270.0000.0000.0000.000
195A499THR0-0.063-0.03441.932-0.008-0.0080.0000.0000.0000.000
196A500LEU0-0.0040.00243.021-0.007-0.0070.0000.0000.0000.000
197A501LEU00.0110.00344.494-0.007-0.0070.0000.0000.0000.000
198A502TYR00.001-0.00646.079-0.006-0.0060.0000.0000.0000.000
199A503SER00.0360.00947.855-0.005-0.0050.0000.0000.0000.000
200A504GLN0-0.041-0.02448.907-0.004-0.0040.0000.0000.0000.000
201A505GLN0-0.004-0.00148.740-0.006-0.0060.0000.0000.0000.000
202A506GLN00.001-0.00251.938-0.003-0.0030.0000.0000.0000.000
203A507LEU00.0140.02253.886-0.003-0.0030.0000.0000.0000.000
204A508ALA0-0.016-0.01455.078-0.003-0.0030.0000.0000.0000.000
205A509LYS10.8700.93252.364-0.076-0.0760.0000.0000.0000.000
206A510TYR0-0.042-0.00858.204-0.002-0.0020.0000.0000.0000.000
207A511TRP00.003-0.01759.739-0.002-0.0020.0000.0000.0000.000
208A512GLU-1-0.970-0.96860.4500.0570.0570.0000.0000.0000.000
209A513ALA0-0.085-0.02663.417-0.002-0.0020.0000.0000.0000.000