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: 22M1R

Calculation Name: 4GHU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GHU

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VCF0

Base Structure: X-ray

Registration Date: 2023-03-14

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1977597.460823
FMO2-HF: Nuclear repulsion 1900725.880271
FMO2-HF: Total energy -76871.580552
FMO2-MP2: Total energy -77091.413995


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:376:ASN)


Summations of interaction energy for fragment #1(A:376:ASN)
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.
-18.128-10.7123.783-4.123-7.0780.032
Interaction energy analysis for fragmet #1(A:376:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.022
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].
3A378GLY00.1170.0812.925-3.658-0.4990.304-1.590-1.8740.006
4A379LEU0-0.021-0.0102.298-12.290-8.7173.471-2.293-4.7510.026
5A380LEU0-0.014-0.0103.621-2.702-2.0180.008-0.240-0.4530.000
6A381GLU-1-0.856-0.9316.1822.2012.2010.0000.0000.0000.000
7A382SER0-0.020-0.0206.658-0.754-0.7540.0000.0000.0000.000
8A383GLN0-0.030-0.0158.168-0.437-0.4370.0000.0000.0000.000
9A384LEU00.0320.02210.016-0.134-0.1340.0000.0000.0000.000
10A385SER00.0070.02211.561-0.088-0.0880.0000.0000.0000.000
11A386ARG10.9190.94612.545-0.246-0.2460.0000.0000.0000.000
12A387HIS0-0.039-0.02512.863-0.049-0.0490.0000.0000.0000.000
13A388ASP-1-0.898-0.93615.9770.2550.2550.0000.0000.0000.000
14A389GLN00.0260.00917.211-0.042-0.0420.0000.0000.0000.000
15A390MET0-0.060-0.03218.886-0.039-0.0390.0000.0000.0000.000
16A391LEU0-0.004-0.01119.309-0.027-0.0270.0000.0000.0000.000
17A392SER00.0240.02021.637-0.012-0.0120.0000.0000.0000.000
18A393VAL0-0.037-0.02023.488-0.015-0.0150.0000.0000.0000.000
19A394HIS0-0.029-0.03823.445-0.007-0.0070.0000.0000.0000.000
20A395ASP-1-0.894-0.93426.3170.0670.0670.0000.0000.0000.000
21A396ILE00.0070.01027.404-0.004-0.0040.0000.0000.0000.000
22A397ARG10.8930.94527.634-0.036-0.0360.0000.0000.0000.000
23A398LEU00.001-0.00729.104-0.008-0.0080.0000.0000.0000.000
24A399ALA00.0580.04232.407-0.005-0.0050.0000.0000.0000.000
25A400ASP-1-0.908-0.96133.8720.0540.0540.0000.0000.0000.000
26A401MET0-0.119-0.07232.909-0.007-0.0070.0000.0000.0000.000
27A402ASP-1-0.859-0.91036.7300.0240.0240.0000.0000.0000.000
28A403LEU0-0.052-0.02838.431-0.003-0.0030.0000.0000.0000.000
29A404ARG10.9170.95538.553-0.017-0.0170.0000.0000.0000.000
30A405PHE00.0200.00438.010-0.004-0.0040.0000.0000.0000.000
31A406GLN00.0280.03041.5830.0000.0000.0000.0000.0000.000
32A407VAL0-0.045-0.01444.637-0.001-0.0010.0000.0000.0000.000
33A408LEU0-0.052-0.02644.778-0.001-0.0010.0000.0000.0000.000
34A409GLU-1-0.937-0.96945.5680.0100.0100.0000.0000.0000.000
35A410THR0-0.120-0.06848.6370.0000.0000.0000.0000.0000.000
36A411ALA00.0070.02050.2680.0010.0010.0000.0000.0000.000
37A412SER0-0.040-0.03052.108-0.002-0.0020.0000.0000.0000.000
38A413TYR00.017-0.01450.7090.0010.0010.0000.0000.0000.000
39A414ASN00.0400.02057.3730.0000.0000.0000.0000.0000.000
40A415GLY00.0420.02459.8750.0000.0000.0000.0000.0000.000
41A416VAL0-0.055-0.01660.6200.0010.0010.0000.0000.0000.000
42A417LEU00.0090.02854.8930.0000.0000.0000.0000.0000.000
43A418ILE0-0.006-0.02257.4140.0000.0000.0000.0000.0000.000
44A419TRP00.0450.01551.8550.0000.0000.0000.0000.0000.000
45A420LYS10.9480.98553.821-0.019-0.0190.0000.0000.0000.000
46A421ILE0-0.0040.00352.8610.0010.0010.0000.0000.0000.000
47A422ARG11.0060.99750.092-0.027-0.0270.0000.0000.0000.000
48A423ASP-1-0.785-0.88249.2340.0380.0380.0000.0000.0000.000
49A424TYR0-0.013-0.03152.5200.0020.0020.0000.0000.0000.000
50A425LYS10.9100.94155.001-0.029-0.0290.0000.0000.0000.000
51A426ARG10.8570.90046.799-0.046-0.0460.0000.0000.0000.000
52A427ARG10.8810.93647.332-0.037-0.0370.0000.0000.0000.000
53A428LYS10.8090.89752.057-0.031-0.0310.0000.0000.0000.000
54A429GLN00.021-0.00752.9090.0020.0020.0000.0000.0000.000
55A430GLU-1-0.844-0.90947.6230.0530.0530.0000.0000.0000.000
56A431ALA0-0.0010.01450.9860.0020.0020.0000.0000.0000.000
57A432VAL0-0.057-0.03253.3620.0000.0000.0000.0000.0000.000
58A433MET0-0.071-0.03751.1220.0000.0000.0000.0000.0000.000
59A434GLY00.0040.00451.4080.0020.0020.0000.0000.0000.000
60A435LYS10.8900.96546.398-0.057-0.0570.0000.0000.0000.000
61A436THR00.006-0.00747.1710.0030.0030.0000.0000.0000.000
62A437LEU0-0.0200.00448.981-0.003-0.0030.0000.0000.0000.000
63A438SER0-0.021-0.00450.954-0.003-0.0030.0000.0000.0000.000
64A439LEU0-0.015-0.00649.1450.0020.0020.0000.0000.0000.000
65A440TYR00.0640.00149.100-0.001-0.0010.0000.0000.0000.000
66A441SER0-0.051-0.02450.1980.0010.0010.0000.0000.0000.000
67A442GLN00.0230.01449.2010.0030.0030.0000.0000.0000.000
68A443PRO00.019-0.00548.538-0.001-0.0010.0000.0000.0000.000
69A444PHE0-0.045-0.01251.561-0.001-0.0010.0000.0000.0000.000
70A445TYR00.0380.00849.5690.0010.0010.0000.0000.0000.000
71A446THR0-0.016-0.01556.4610.0000.0000.0000.0000.0000.000
72A447GLY00.0760.02958.149-0.001-0.0010.0000.0000.0000.000
73A448TYR0-0.036-0.02054.5580.0010.0010.0000.0000.0000.000
74A449PHE0-0.014-0.00552.4290.0000.0000.0000.0000.0000.000
75A450GLY00.0010.01655.6880.0000.0000.0000.0000.0000.000
76A451TYR0-0.015-0.04655.8940.0010.0010.0000.0000.0000.000
77A452LYS10.8690.93747.411-0.019-0.0190.0000.0000.0000.000
78A453MET0-0.051-0.00654.3330.0010.0010.0000.0000.0000.000
79A454CYS00.0150.01551.3050.0000.0000.0000.0000.0000.000
80A455ALA00.0010.01454.451-0.001-0.0010.0000.0000.0000.000
81A456ARG10.9340.96452.005-0.035-0.0350.0000.0000.0000.000
82A457VAL0-0.013-0.00154.675-0.001-0.0010.0000.0000.0000.000
83A458TYR00.005-0.01154.8980.0030.0030.0000.0000.0000.000
84A459LEU00.004-0.00254.012-0.001-0.0010.0000.0000.0000.000
85A460ASN00.0530.01857.208-0.002-0.0020.0000.0000.0000.000
86A461GLY00.0380.04158.8710.0000.0000.0000.0000.0000.000
87A462ASP-1-0.803-0.93858.3240.0360.0360.0000.0000.0000.000
88A463GLY00.0020.00160.245-0.001-0.0010.0000.0000.0000.000
89A464MET00.001-0.01662.6920.0010.0010.0000.0000.0000.000
90A465GLY00.0400.02664.374-0.001-0.0010.0000.0000.0000.000
91A466LYS10.7970.92057.237-0.036-0.0360.0000.0000.0000.000
92A467GLY0-0.020-0.00861.3330.0000.0000.0000.0000.0000.000
93A468THR00.0180.01262.596-0.001-0.0010.0000.0000.0000.000
94A469HIS0-0.042-0.02664.136-0.002-0.0020.0000.0000.0000.000
95A470LEU0-0.0050.02459.6570.0010.0010.0000.0000.0000.000
96A471SER0-0.048-0.04160.117-0.001-0.0010.0000.0000.0000.000
97A472LEU0-0.025-0.01459.1610.0010.0010.0000.0000.0000.000
98A473PHE0-0.033-0.01458.115-0.001-0.0010.0000.0000.0000.000
99A474PHE00.0380.00858.5470.0000.0000.0000.0000.0000.000
100A475VAL00.003-0.01353.4720.0010.0010.0000.0000.0000.000
101A476ILE00.0260.03156.013-0.001-0.0010.0000.0000.0000.000
102A477MET0-0.011-0.02448.7460.0010.0010.0000.0000.0000.000
103A478ARG10.9080.95545.275-0.027-0.0270.0000.0000.0000.000
104A479GLY00.0250.00850.3070.0010.0010.0000.0000.0000.000
105A480GLU-1-0.886-0.94947.5930.0140.0140.0000.0000.0000.000
106A481TYR00.0380.01550.653-0.001-0.0010.0000.0000.0000.000
107A482ASP-1-0.769-0.88253.9640.0140.0140.0000.0000.0000.000
108A483ALA0-0.043-0.02055.2540.0000.0000.0000.0000.0000.000
109A484LEU0-0.009-0.00356.745-0.001-0.0010.0000.0000.0000.000
110A485LEU0-0.052-0.00357.4640.0000.0000.0000.0000.0000.000
111A486PRO00.0170.01160.8540.0000.0000.0000.0000.0000.000
112A487TRP0-0.041-0.00557.2570.0020.0020.0000.0000.0000.000
113A488PRO00.0440.00262.969-0.001-0.0010.0000.0000.0000.000
114A489PHE0-0.029-0.00961.092-0.001-0.0010.0000.0000.0000.000
115A490LYS10.8650.91763.422-0.007-0.0070.0000.0000.0000.000
116A491GLN0-0.0070.00564.335-0.001-0.0010.0000.0000.0000.000
117A492LYS10.9870.99066.301-0.010-0.0100.0000.0000.0000.000
118A493VAL00.0250.02362.9490.0000.0000.0000.0000.0000.000
119A494THR0-0.046-0.02765.5950.0000.0000.0000.0000.0000.000
120A495LEU0-0.021-0.00561.9260.0000.0000.0000.0000.0000.000
121A496MET00.032-0.00963.776-0.001-0.0010.0000.0000.0000.000
122A497LEU0-0.0090.00862.1720.0010.0010.0000.0000.0000.000
123A498MET0-0.041-0.02963.020-0.001-0.0010.0000.0000.0000.000
124A499ASP-1-0.739-0.83864.8860.0160.0160.0000.0000.0000.000
125A500GLN0-0.114-0.08660.787-0.002-0.0020.0000.0000.0000.000
126A501GLY00.0470.02866.0590.0000.0000.0000.0000.0000.000
127A502SER0-0.032-0.02969.4150.0000.0000.0000.0000.0000.000
128A503SER0-0.003-0.00771.826-0.001-0.0010.0000.0000.0000.000
129A504ARG10.8440.94565.622-0.013-0.0130.0000.0000.0000.000
130A505ARG10.9730.98271.370-0.014-0.0140.0000.0000.0000.000
131A506HIS00.0190.00467.9540.0010.0010.0000.0000.0000.000
132A507LEU00.0120.02067.8070.0000.0000.0000.0000.0000.000
133A508GLY00.004-0.01867.6320.0000.0000.0000.0000.0000.000
134A509ASP-1-0.850-0.89968.2840.0150.0150.0000.0000.0000.000
135A510ALA0-0.078-0.04768.2200.0000.0000.0000.0000.0000.000
136A511PHE00.0160.01663.6240.0000.0000.0000.0000.0000.000
137A512LYS10.9020.93368.688-0.010-0.0100.0000.0000.0000.000
138A513PRO0-0.037-0.01165.2940.0000.0000.0000.0000.0000.000
139A514ASP-1-0.785-0.89067.3710.0150.0150.0000.0000.0000.000
140A515PRO0-0.018-0.02066.7970.0010.0010.0000.0000.0000.000
141A516ASN0-0.046-0.02966.8200.0000.0000.0000.0000.0000.000
142A517SER00.0270.03663.8480.0010.0010.0000.0000.0000.000
143A518SER00.026-0.00259.8350.0000.0000.0000.0000.0000.000
144A519SER0-0.061-0.03859.3900.0000.0000.0000.0000.0000.000
145A520PHE0-0.019-0.01159.5980.0000.0000.0000.0000.0000.000
146A521LYS10.9350.99355.138-0.024-0.0240.0000.0000.0000.000
147A522LYS10.8900.94253.552-0.014-0.0140.0000.0000.0000.000
148A523PRO00.0030.02053.2900.0010.0010.0000.0000.0000.000
149A524THR00.0120.01252.598-0.001-0.0010.0000.0000.0000.000
150A525GLY00.0120.00749.1640.0010.0010.0000.0000.0000.000
151A526GLU-1-0.890-0.95543.9610.0340.0340.0000.0000.0000.000
152A527MET0-0.0090.00148.129-0.002-0.0020.0000.0000.0000.000
153A528ASN0-0.056-0.03051.5170.0020.0020.0000.0000.0000.000
154A529ILE00.002-0.00154.5710.0010.0010.0000.0000.0000.000
155A530ALA0-0.0080.00455.964-0.002-0.0020.0000.0000.0000.000
156A531SER00.0050.00057.7330.0000.0000.0000.0000.0000.000
157A532GLY00.0320.01061.4520.0000.0000.0000.0000.0000.000
158A533CYS00.0040.01463.3610.0000.0000.0000.0000.0000.000
159A534PRO00.0460.00563.1700.0010.0010.0000.0000.0000.000
160A535VAL00.0270.02864.2440.0010.0010.0000.0000.0000.000
161A536PHE0-0.061-0.00564.330-0.001-0.0010.0000.0000.0000.000
162A537VAL00.0430.01864.847-0.001-0.0010.0000.0000.0000.000
163A538ALA00.0400.02765.8960.0010.0010.0000.0000.0000.000
164A539GLN00.032-0.00561.5890.0000.0000.0000.0000.0000.000
165A540THR00.0130.01865.3360.0000.0000.0000.0000.0000.000
166A541VAL00.0400.02168.1840.0000.0000.0000.0000.0000.000
167A542LEU0-0.016-0.00661.688-0.001-0.0010.0000.0000.0000.000
168A543GLU-1-0.842-0.90661.5550.0290.0290.0000.0000.0000.000
169A544ASN0-0.079-0.03865.2890.0000.0000.0000.0000.0000.000
170A545GLY00.0150.03567.985-0.001-0.0010.0000.0000.0000.000
171A546THR0-0.046-0.05367.4200.0000.0000.0000.0000.0000.000
172A547TYR0-0.014-0.00864.5920.0000.0000.0000.0000.0000.000
173A548ILE0-0.0200.00860.0530.0000.0000.0000.0000.0000.000
174A549LYS10.8690.92361.138-0.018-0.0180.0000.0000.0000.000
175A550ASP-1-0.826-0.91257.8390.0200.0200.0000.0000.0000.000
176A551ASP-1-0.817-0.89655.4190.0320.0320.0000.0000.0000.000
177A552THR0-0.049-0.02555.7510.0010.0010.0000.0000.0000.000
178A553ILE00.0180.01457.153-0.001-0.0010.0000.0000.0000.000
179A554PHE00.016-0.00757.6410.0000.0000.0000.0000.0000.000
180A555ILE00.0120.01357.6620.0000.0000.0000.0000.0000.000
181A556LYS10.9320.97059.448-0.012-0.0120.0000.0000.0000.000
182A557VAL0-0.0070.00459.7230.0000.0000.0000.0000.0000.000
183A558ILE0-0.023-0.01061.906-0.001-0.0010.0000.0000.0000.000
184A559VAL0-0.010-0.00661.1310.0010.0010.0000.0000.0000.000
185A560ASP-1-0.871-0.92564.2030.0070.0070.0000.0000.0000.000
186A561THR00.009-0.01762.9870.0000.0000.0000.0000.0000.000
187A562SER0-0.058-0.03766.107-0.001-0.0010.0000.0000.0000.000
188A563ASP-1-0.863-0.91768.3020.0060.0060.0000.0000.0000.000
189A564LEU0-0.030-0.00563.7420.0000.0000.0000.0000.0000.000
190A565PRO00.0170.01864.1190.0000.0000.0000.0000.0000.000