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: LN419

Calculation Name: 4G54-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4G54

Chain ID: A

ChEMBL ID:

UniProt ID: A0A3Q0

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2892060.935865
FMO2-HF: Nuclear repulsion 2798683.715457
FMO2-HF: Total energy -93377.220407
FMO2-MP2: Total energy -93646.766532


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:343:TRP)


Summations of interaction energy for fragment #1(A:343:TRP)
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.
-30.053-15.26927.088-11.032-30.839-0.024
Interaction energy analysis for fragmet #1(A:343:TRP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.044
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].
3A345GLY00.0220.0223.850-0.7760.436-0.003-0.443-0.7660.001
4A346GLU-1-0.868-0.9244.037-1.257-0.8280.000-0.101-0.3270.000
5A347SER00.005-0.0132.387-1.3970.5111.326-1.428-1.8060.001
6A348ALA00.0200.0203.1151.6610.9860.0690.913-0.3070.000
7A349VAL0-0.007-0.0124.225-0.0130.191-0.001-0.020-0.1830.000
8A350ALA0-0.035-0.0172.991-1.8140.0682.114-0.917-3.0790.008
9A351ARG10.7820.9014.971-1.150-0.949-0.001-0.034-0.1660.000
10A352MET0-0.058-0.0068.046-0.448-0.4480.0000.0000.0000.000
11A353THR00.0820.0315.3440.3830.3830.0000.0000.0000.000
12A354THR0-0.028-0.0206.777-0.097-0.0970.0000.0000.0000.000
13A355ARG10.8940.9209.675-0.074-0.0740.0000.0000.0000.000
14A356ALA00.0360.01911.0410.0190.0190.0000.0000.0000.000
15A357GLN00.0310.00710.6420.0070.0070.0000.0000.0000.000
16A358GLY00.0720.01811.5180.0180.0180.0000.0000.0000.000
17A359LEU0-0.007-0.01412.394-0.004-0.0040.0000.0000.0000.000
18A360GLU-1-0.911-0.94515.509-0.055-0.0550.0000.0000.0000.000
19A361GLU-1-0.768-0.85614.7400.0240.0240.0000.0000.0000.000
20A362LEU0-0.007-0.00415.722-0.008-0.0080.0000.0000.0000.000
21A363TYR0-0.039-0.04717.538-0.008-0.0080.0000.0000.0000.000
22A364LYS10.8190.91217.8000.0020.0020.0000.0000.0000.000
23A365LEU00.0050.00817.831-0.007-0.0070.0000.0000.0000.000
24A366TRP0-0.044-0.03021.350-0.009-0.0090.0000.0000.0000.000
25A367GLY00.0060.01524.121-0.004-0.0040.0000.0000.0000.000
26A368TYR0-0.041-0.03324.482-0.008-0.0080.0000.0000.0000.000
27A369ARG10.8840.93423.5250.0360.0360.0000.0000.0000.000
28A370ALA0-0.0010.00521.093-0.001-0.0010.0000.0000.0000.000
29A371THR0-0.036-0.04823.221-0.011-0.0110.0000.0000.0000.000
30A372ARG10.9710.96119.1340.1170.1170.0000.0000.0000.000
31A373ILE00.0700.02420.6090.0010.0010.0000.0000.0000.000
32A374ASP-1-0.723-0.76522.145-0.003-0.0030.0000.0000.0000.000
33A375THR0-0.0190.00316.9530.0100.0100.0000.0000.0000.000
34A376MET0-0.0100.00716.7330.0000.0000.0000.0000.0000.000
35A377CYS0-0.091-0.04216.9980.0210.0210.0000.0000.0000.000
36A378GLU-1-0.895-0.93718.908-0.004-0.0040.0000.0000.0000.000
37A379GLN0-0.026-0.01921.512-0.003-0.0030.0000.0000.0000.000
38A380PRO00.003-0.00225.012-0.002-0.0020.0000.0000.0000.000
39A381SER00.0030.00325.811-0.002-0.0020.0000.0000.0000.000
40A382THR00.002-0.01725.147-0.001-0.0010.0000.0000.0000.000
41A383SER0-0.006-0.00125.982-0.004-0.0040.0000.0000.0000.000
42A384ILE00.0420.03428.7160.0030.0030.0000.0000.0000.000
43A385PHE0-0.0080.00323.4480.0030.0030.0000.0000.0000.000
44A386GLN0-0.0190.00423.987-0.005-0.0050.0000.0000.0000.000
45A388GLN00.0260.01918.9790.0010.0010.0000.0000.0000.000
46A389VAL00.0260.01513.4830.0090.0090.0000.0000.0000.000
47A390ARG10.8060.88015.195-0.138-0.1380.0000.0000.0000.000
48A391GLN0-0.017-0.00712.4910.0180.0180.0000.0000.0000.000
49A392LEU0-0.024-0.00714.557-0.026-0.0260.0000.0000.0000.000
50A393ASN0-0.021-0.02614.7930.0290.0290.0000.0000.0000.000
51A394TRP00.0830.00814.769-0.002-0.0020.0000.0000.0000.000
52A395GLN00.0080.03116.513-0.012-0.0120.0000.0000.0000.000
53A396GLU-1-0.802-0.90318.6280.1540.1540.0000.0000.0000.000
54A397LEU0-0.034-0.01013.046-0.011-0.0110.0000.0000.0000.000
55A398GLN0-0.030-0.03817.205-0.018-0.0180.0000.0000.0000.000
56A399GLN0-0.046-0.02019.696-0.018-0.0180.0000.0000.0000.000
57A400THR0-0.052-0.02017.606-0.005-0.0050.0000.0000.0000.000
58A401PRO0-0.0040.01320.720-0.005-0.0050.0000.0000.0000.000
59A402HIS10.7620.86920.528-0.089-0.0890.0000.0000.0000.000
60A403PRO00.0310.02617.7860.0110.0110.0000.0000.0000.000
61A404LEU0-0.0160.00714.570-0.003-0.0030.0000.0000.0000.000
62A405LEU0-0.039-0.00410.5470.0120.0120.0000.0000.0000.000
63A406LEU00.0160.0078.650-0.021-0.0210.0000.0000.0000.000
64A407THR0-0.050-0.0535.7310.1250.1250.0000.0000.0000.000
65A408LEU0-0.0090.0012.191-1.159-0.4701.884-0.757-1.8160.002
66A409GLN0-0.012-0.0382.450-4.040-2.0442.757-1.770-2.984-0.016
67A410HIS00.0230.0032.426-5.518-2.1165.138-1.827-6.7130.006
68A411GLU-1-0.927-0.9534.3583.1443.6160.007-0.024-0.4540.001
69A412GLY00.0090.0176.681-0.757-0.7570.0000.0000.0000.000
70A413GLN0-0.0260.0001.951-11.722-12.7778.178-2.773-4.350-0.021
71A414ARG10.7730.8362.438-0.1721.3350.982-0.706-1.783-0.003
72A415ALA00.0180.0252.643-1.778-0.5301.984-0.468-2.764-0.002
73A416TYR0-0.025-0.0023.779-0.629-0.4580.0020.075-0.2470.000
74A417VAL00.0360.0236.9310.0300.0300.0000.0000.0000.000
75A418VAL0-0.009-0.0049.071-0.081-0.0810.0000.0000.0000.000
76A419LEU0-0.0080.00612.661-0.013-0.0130.0000.0000.0000.000
77A420LEU0-0.021-0.01913.971-0.015-0.0150.0000.0000.0000.000
78A421GLU-1-0.815-0.91716.9840.0140.0140.0000.0000.0000.000
79A422VAL0-0.019-0.01616.8480.0070.0070.0000.0000.0000.000
80A423ASP-1-0.760-0.84418.3940.0370.0370.0000.0000.0000.000
81A424PRO00.015-0.01619.0070.0060.0060.0000.0000.0000.000
82A425GLU-1-0.960-0.95719.2350.0460.0460.0000.0000.0000.000
83A426ARG10.7460.83715.882-0.037-0.0370.0000.0000.0000.000
84A427VAL00.0070.00211.9060.0170.0170.0000.0000.0000.000
85A428VAL0-0.050-0.01614.561-0.029-0.0290.0000.0000.0000.000
86A429LEU0-0.025-0.0118.7560.0350.0350.0000.0000.0000.000
87A430LEU00.0020.00712.556-0.046-0.0460.0000.0000.0000.000
88A431THR00.0490.0109.6470.0560.0560.0000.0000.0000.000
89A432GLY00.027-0.00311.8550.0200.0200.0000.0000.0000.000
90A433GLU-1-0.856-0.91313.542-0.191-0.1910.0000.0000.0000.000
91A434GLN0-0.008-0.01311.325-0.017-0.0170.0000.0000.0000.000
92A435ARG10.8600.92413.8560.0490.0490.0000.0000.0000.000
93A436LEU0-0.012-0.0069.150-0.037-0.0370.0000.0000.0000.000
94A437THR00.009-0.00912.9660.0470.0470.0000.0000.0000.000
95A438PHE0-0.024-0.0105.9050.0020.0020.0000.0000.0000.000
96A439THR00.0700.02012.1780.0610.0610.0000.0000.0000.000
97A440VAL00.0190.00912.3180.0000.0000.0000.0000.0000.000
98A441SER0-0.005-0.00912.5030.0410.0410.0000.0000.0000.000
99A442GLN00.0080.0228.8470.1920.1920.0000.0000.0000.000
100A443LEU00.0150.0297.873-0.016-0.0160.0000.0000.0000.000
101A444MET0-0.023-0.0157.9600.0710.0710.0000.0000.0000.000
102A445SER0-0.068-0.0307.1290.0380.0380.0000.0000.0000.000
103A446LEU00.0030.0002.217-1.106-0.1032.653-0.720-2.936-0.001
104A447TRP0-0.038-0.0154.429-0.0890.101-0.001-0.032-0.1580.000
105A448ARG10.8880.9405.855-1.833-1.8330.0000.0000.0000.000
106A449GLY00.0740.0339.017-0.026-0.0260.0000.0000.0000.000
107A450GLU-1-0.724-0.7939.4130.2060.2060.0000.0000.0000.000
108A451VAL0-0.0090.00610.0580.0270.0270.0000.0000.0000.000
109A452THR0-0.002-0.00912.030-0.030-0.0300.0000.0000.0000.000
110A453ASP-1-0.758-0.83114.3420.1130.1130.0000.0000.0000.000
111A454LEU00.0610.01517.803-0.009-0.0090.0000.0000.0000.000
112A455TRP0-0.0010.00420.4090.0050.0050.0000.0000.0000.000
113A456PRO0-0.0100.01424.032-0.003-0.0030.0000.0000.0000.000
114A457MET0-0.0230.00427.4170.0040.0040.0000.0000.0000.000
115A458PRO00.0430.02029.443-0.002-0.0020.0000.0000.0000.000
116A459LEU00.0300.01732.860-0.002-0.0020.0000.0000.0000.000
117A460ARG10.8300.88127.428-0.026-0.0260.0000.0000.0000.000
118A461GLU-1-0.926-0.95633.9420.0190.0190.0000.0000.0000.000
119A462THR0-0.074-0.04537.4390.0010.0010.0000.0000.0000.000
120A463LEU00.0240.01839.605-0.002-0.0020.0000.0000.0000.000
121A464ARG10.9380.94542.054-0.021-0.0210.0000.0000.0000.000
122A465LEU00.0440.01245.234-0.001-0.0010.0000.0000.0000.000
123A466GLY0-0.016-0.00548.6830.0000.0000.0000.0000.0000.000
124A467MET0-0.0480.00843.7390.0000.0000.0000.0000.0000.000
125A468HIS0-0.059-0.02847.9160.0000.0000.0000.0000.0000.000
126A469GLY00.0680.02545.7080.0000.0000.0000.0000.0000.000
127A470GLU-1-0.819-0.91840.5050.0070.0070.0000.0000.0000.000
128A471ALA0-0.037-0.03139.7330.0010.0010.0000.0000.0000.000
129A472ILE0-0.025-0.01540.3050.0020.0020.0000.0000.0000.000
130A473GLU-1-0.798-0.86542.4810.0090.0090.0000.0000.0000.000
131A474VAL0-0.013-0.01436.3090.0010.0010.0000.0000.0000.000
132A475LEU0-0.013-0.00637.8550.0020.0020.0000.0000.0000.000
133A476ASP-1-0.750-0.87938.7960.0180.0180.0000.0000.0000.000
134A477GLN0-0.051-0.03038.1330.0000.0000.0000.0000.0000.000
135A478LEU0-0.038-0.01732.6200.0010.0010.0000.0000.0000.000
136A479LEU0-0.010-0.01335.5260.0030.0030.0000.0000.0000.000
137A480ALA00.0290.02737.9140.0010.0010.0000.0000.0000.000
138A481LYS10.8330.91031.311-0.025-0.0250.0000.0000.0000.000
139A482ALA0-0.062-0.03633.5490.0020.0020.0000.0000.0000.000
140A483LEU0-0.042-0.03134.5410.0020.0020.0000.0000.0000.000
141A484ASN0-0.106-0.03734.776-0.002-0.0020.0000.0000.0000.000
142A485ASP-1-0.783-0.85937.8390.0210.0210.0000.0000.0000.000
143A486GLU-1-0.839-0.91741.1380.0110.0110.0000.0000.0000.000
144A487PRO0-0.043-0.00641.8220.0010.0010.0000.0000.0000.000
145A488LEU0-0.011-0.02643.549-0.001-0.0010.0000.0000.0000.000
146A489LYS10.7210.85445.391-0.012-0.0120.0000.0000.0000.000
147A490THR0-0.005-0.00946.123-0.001-0.0010.0000.0000.0000.000
148A491THR0-0.003-0.02646.1880.0010.0010.0000.0000.0000.000
149A492GLN00.003-0.00247.8400.0010.0010.0000.0000.0000.000
150A493PHE00.0050.03042.7790.0010.0010.0000.0000.0000.000
151A494ASN00.0330.01247.7590.0010.0010.0000.0000.0000.000
152A495ALA00.063-0.00248.8770.0010.0010.0000.0000.0000.000
153A496GLU-1-0.897-0.93348.4050.0170.0170.0000.0000.0000.000
154A497LEU00.020-0.00142.9470.0010.0010.0000.0000.0000.000
155A498MET0-0.073-0.01044.5100.0010.0010.0000.0000.0000.000
156A499GLN0-0.011-0.01845.0260.0010.0010.0000.0000.0000.000
157A500ARG10.8150.89041.796-0.020-0.0200.0000.0000.0000.000
158A501VAL0-0.043-0.01340.0830.0020.0020.0000.0000.0000.000
159A502GLU-1-0.824-0.91140.7090.0280.0280.0000.0000.0000.000
160A503TRP0-0.0030.00340.8070.0020.0020.0000.0000.0000.000
161A504PHE00.0100.00032.9990.0030.0030.0000.0000.0000.000
162A505GLN0-0.035-0.05337.1910.0020.0020.0000.0000.0000.000
163A506ARG10.8650.91337.879-0.033-0.0330.0000.0000.0000.000
164A507TRP0-0.011-0.00233.5840.0020.0020.0000.0000.0000.000
165A508GLN00.0180.02031.7780.0070.0070.0000.0000.0000.000
166A509ALA0-0.0080.00533.8370.0040.0040.0000.0000.0000.000
167A510MET0-0.108-0.05334.1230.0050.0050.0000.0000.0000.000
168A511THR00.0210.00937.2520.0000.0000.0000.0000.0000.000
169A512GLU-1-0.820-0.88240.6670.0360.0360.0000.0000.0000.000
170A513ASP-1-0.849-0.91542.1550.0330.0330.0000.0000.0000.000
171A514GLY00.0400.01843.450-0.002-0.0020.0000.0000.0000.000
172A515ILE0-0.071-0.03941.365-0.002-0.0020.0000.0000.0000.000
173A516ALA00.0450.03138.9010.0030.0030.0000.0000.0000.000
174A517GLY00.0480.01038.199-0.001-0.0010.0000.0000.0000.000
175A518GLN00.019-0.00230.6350.0010.0010.0000.0000.0000.000
176A519ARG10.8890.94632.607-0.058-0.0580.0000.0000.0000.000
177A520THR00.018-0.00132.9290.0040.0040.0000.0000.0000.000
178A521LEU00.0510.02133.8170.0010.0010.0000.0000.0000.000
179A522ALA0-0.040-0.01128.9210.0000.0000.0000.0000.0000.000
180A523ARG10.8540.92828.858-0.058-0.0580.0000.0000.0000.000
181A524LEU00.0190.00829.5830.0020.0020.0000.0000.0000.000
182A525GLN0-0.004-0.02529.507-0.003-0.0030.0000.0000.0000.000
183A526HIS0-0.082-0.03321.415-0.004-0.0040.0000.0000.0000.000
184A527MET0-0.021-0.01425.6730.0030.0030.0000.0000.0000.000
185A528VAL0-0.0220.00727.786-0.001-0.0010.0000.0000.0000.000
186A529SER0-0.004-0.01428.0780.0010.0010.0000.0000.0000.000
187A530LEU00.0270.01330.354-0.001-0.0010.0000.0000.0000.000
188A531SER0-0.023-0.01331.106-0.002-0.0020.0000.0000.0000.000
189A532GLU-1-0.772-0.87126.7580.0350.0350.0000.0000.0000.000
190A533PRO00.0150.00826.3190.0000.0000.0000.0000.0000.000
191A534TRP00.0490.02521.927-0.002-0.0020.0000.0000.0000.000
192A535ARG10.8990.93423.628-0.036-0.0360.0000.0000.0000.000
193A536ALA00.0250.03125.901-0.002-0.0020.0000.0000.0000.000
194A537LEU00.0120.00720.815-0.004-0.0040.0000.0000.0000.000
195A538THR0-0.106-0.05621.616-0.003-0.0030.0000.0000.0000.000
196A539GLN00.0540.01523.332-0.009-0.0090.0000.0000.0000.000
197A540ALA0-0.0050.02426.560-0.002-0.0020.0000.0000.0000.000
198A541GLU-1-0.822-0.89427.948-0.012-0.0120.0000.0000.0000.000
199A542LYS10.7790.86425.3360.0040.0040.0000.0000.0000.000
200A543GLN0-0.096-0.05429.625-0.003-0.0030.0000.0000.0000.000
201A544GLY00.0120.01433.0770.0030.0030.0000.0000.0000.000
202A546GLU-1-0.898-0.92029.144-0.034-0.0340.0000.0000.0000.000
203A547GLU-1-0.897-0.95425.438-0.048-0.0480.0000.0000.0000.000
204A548GLN0-0.011-0.03724.169-0.001-0.0010.0000.0000.0000.000
205A549VAL00.0140.01627.334-0.006-0.0060.0000.0000.0000.000
206A550MET0-0.029-0.00125.791-0.004-0.0040.0000.0000.0000.000
207A551ARG10.8520.92222.5440.0660.0660.0000.0000.0000.000
208A552TYR0-0.029-0.02615.6650.0020.0020.0000.0000.0000.000
209A553PRO0-0.017-0.00717.641-0.004-0.0040.0000.0000.0000.000
210A554GLU-1-0.944-0.96319.523-0.075-0.0750.0000.0000.0000.000
211A555PHE0-0.001-0.02319.7150.0140.0140.0000.0000.0000.000
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