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: 14GRZ

Calculation Name: 5GPD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GPD

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UUD1

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2595357.143321
FMO2-HF: Nuclear repulsion 2508112.115609
FMO2-HF: Total energy -87245.027712
FMO2-MP2: Total energy -87497.169167


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:649:ILE)


Summations of interaction energy for fragment #1(A:649:ILE)
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.
-5.336-1.5039.886-4.742-8.978-0.015
Interaction energy analysis for fragmet #1(A:649:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.056 / q_NPA : -0.028
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].
3A651ASN00.049-0.0023.804-0.4021.520-0.029-0.906-0.9880.004
4A652SER0-0.0160.0191.918-1.509-2.1195.945-1.968-3.367-0.015
5A653HIS00.006-0.0072.166-0.4480.6643.739-1.512-3.339-0.005
6A654ALA00.0410.0253.6900.2720.6060.009-0.034-0.3090.000
7A655ASP-1-0.865-0.9346.053-0.758-0.7580.0000.0000.0000.000
8A656ASP-1-0.986-0.9847.0640.1560.1560.0000.0000.0000.000
9A657VAL0-0.045-0.0067.6090.2010.2010.0000.0000.0000.000
10A658PHE00.018-0.01710.3400.1240.1240.0000.0000.0000.000
11A659SER0-0.003-0.00912.0380.1070.1070.0000.0000.0000.000
12A660PRO0-0.092-0.02313.0190.0810.0810.0000.0000.0000.000
13A661ASN0-0.070-0.04916.1130.0370.0370.0000.0000.0000.000
14A662MET00.079-0.11117.5490.0230.0230.0000.0000.0000.000
15A663VAL0-0.0200.16420.9650.0200.0200.0000.0000.0000.000
16A664GLU-1-0.874-0.91422.200-0.233-0.2330.0000.0000.0000.000
17A665ARG10.8550.91421.0350.2510.2510.0000.0000.0000.000
18A666LEU00.0500.01725.173-0.006-0.0060.0000.0000.0000.000
19A667TRP00.0590.03224.406-0.034-0.0340.0000.0000.0000.000
20A668VAL0-0.055-0.02621.4420.0170.0170.0000.0000.0000.000
21A669LEU00.0530.00320.225-0.025-0.0250.0000.0000.0000.000
22A670ALA00.0310.01319.515-0.043-0.0430.0000.0000.0000.000
23A671LYS10.8940.95718.9470.2870.2870.0000.0000.0000.000
24A672SER00.0670.02114.8800.0220.0220.0000.0000.0000.000
25A673THR00.0570.04313.849-0.096-0.0960.0000.0000.0000.000
26A674ARG10.8870.99112.6680.4170.4170.0000.0000.0000.000
27A675ASP-1-0.882-0.9558.246-1.695-1.6950.0000.0000.0000.000
28A676SER0-0.023-0.0459.059-0.076-0.0760.0000.0000.0000.000
29A677ALA0-0.049-0.02810.096-0.023-0.0230.0000.0000.0000.000
30A678GLN0-0.011-0.0138.3780.0690.0690.0000.0000.0000.000
31A679MET00.0710.2202.5320.0501.1250.222-0.322-0.9750.001
32A680SER0-0.003-0.1086.6430.2640.2640.0000.0000.0000.000
33A681ASP-1-0.846-0.9207.592-1.896-1.8960.0000.0000.0000.000
34A682SER0-0.075-0.0709.5340.3030.3030.0000.0000.0000.000
35A683ILE0-0.034-0.0537.5530.2710.2710.0000.0000.0000.000
36A684ILE0-0.044-0.02511.6930.1280.1280.0000.0000.0000.000
37A685SER0-0.029-0.02214.8830.1610.1610.0000.0000.0000.000
38A686SER00.0690.03111.7460.1240.1240.0000.0000.0000.000
39A687LEU00.0280.01714.9690.0620.0620.0000.0000.0000.000
40A688SER0-0.065-0.05016.4090.0880.0880.0000.0000.0000.000
41A689ASP-1-0.814-0.91016.607-0.496-0.4960.0000.0000.0000.000
42A690VAL0-0.075-0.03017.0760.0470.0470.0000.0000.0000.000
43A691LEU0-0.055-0.01419.5760.0440.0440.0000.0000.0000.000
44A692VAL0-0.005-0.00822.9560.0380.0380.0000.0000.0000.000
45A693LEU00.0480.02518.1740.0020.0020.0000.0000.0000.000
46A694SER0-0.024-0.00121.028-0.005-0.0050.0000.0000.0000.000
47A695PRO00.0290.00319.000-0.023-0.0230.0000.0000.0000.000
48A696LEU00.0240.01718.034-0.008-0.0080.0000.0000.0000.000
49A697GLU-1-0.825-0.93618.252-0.205-0.2050.0000.0000.0000.000
50A698VAL00.0020.01814.026-0.027-0.0270.0000.0000.0000.000
51A699LEU00.0390.01713.145-0.043-0.0430.0000.0000.0000.000
52A700ALA0-0.026-0.00914.8090.0130.0130.0000.0000.0000.000
53A701SER0-0.003-0.01315.3400.0100.0100.0000.0000.0000.000
54A702TRP00.0290.0357.038-0.024-0.0240.0000.0000.0000.000
55A703TYR0-0.041-0.01112.1050.0150.0150.0000.0000.0000.000
56A704ALA00.0330.00014.1000.0240.0240.0000.0000.0000.000
57A705ALA0-0.015-0.00711.018-0.009-0.0090.0000.0000.0000.000
58A706ASP-1-0.845-0.9258.681-0.276-0.2760.0000.0000.0000.000
59A707LEU0-0.064-0.04111.1560.0790.0790.0000.0000.0000.000
60A708LEU0-0.026-0.00314.1630.0300.0300.0000.0000.0000.000
61A709ASP-1-0.894-0.9659.652-0.797-0.7970.0000.0000.0000.000
62A710ALA0-0.041-0.02212.3360.0550.0550.0000.0000.0000.000
63A711LEU00.0230.02613.8760.0260.0260.0000.0000.0000.000
64A712LEU0-0.032-0.02414.8350.0040.0040.0000.0000.0000.000
65A713MET0-0.013-0.00512.2540.0030.0030.0000.0000.0000.000
66A714GLU-1-0.868-0.92016.4210.1100.1100.0000.0000.0000.000
67A715SER0-0.063-0.03319.3830.0040.0040.0000.0000.0000.000
68A716LEU0-0.035-0.01018.662-0.006-0.0060.0000.0000.0000.000
69A717SER0-0.050-0.01821.0730.0010.0010.0000.0000.0000.000
70A718ARG10.7770.87220.836-0.029-0.0290.0000.0000.0000.000
71A719LYS10.9160.95824.8710.0070.0070.0000.0000.0000.000
72A720VAL00.0060.01122.4900.0100.0100.0000.0000.0000.000
73A721GLU-1-0.938-0.96325.631-0.019-0.0190.0000.0000.0000.000
74A722ILE00.007-0.00625.981-0.005-0.0050.0000.0000.0000.000
75A723SER00.0320.02126.462-0.008-0.0080.0000.0000.0000.000
76A724GLU-1-0.748-0.87522.311-0.011-0.0110.0000.0000.0000.000
77A725ILE0-0.030-0.01921.050-0.015-0.0150.0000.0000.0000.000
78A726GLU-1-0.939-0.99223.042-0.098-0.0980.0000.0000.0000.000
79A727GLU-1-0.937-0.95923.187-0.020-0.0200.0000.0000.0000.000
80A728ILE0-0.016-0.00917.871-0.009-0.0090.0000.0000.0000.000
81A729ILE0-0.056-0.03520.698-0.026-0.0260.0000.0000.0000.000
82A730SER0-0.085-0.04122.952-0.006-0.0060.0000.0000.0000.000
83A731LEU0-0.0280.00118.4770.0020.0020.0000.0000.0000.000
84A732CYS0-0.054-0.01318.716-0.024-0.0240.0000.0000.0000.000
85A733PRO0-0.0070.01419.2220.0210.0210.0000.0000.0000.000
86A734LYS10.8630.90022.2590.1770.1770.0000.0000.0000.000
87A735ASN0-0.0080.00124.101-0.002-0.0020.0000.0000.0000.000
88A736SER00.0330.03618.505-0.015-0.0150.0000.0000.0000.000
89A737SER00.013-0.00715.5540.0160.0160.0000.0000.0000.000
90A738ILE00.0300.00813.1220.0100.0100.0000.0000.0000.000
91A739ILE00.0140.02216.6770.0350.0350.0000.0000.0000.000
92A740ARG10.9100.95319.5230.5090.5090.0000.0000.0000.000
93A741HIS0-0.048-0.03815.642-0.042-0.0420.0000.0000.0000.000
94A742ALA00.0840.04018.5120.0230.0230.0000.0000.0000.000
95A743LEU00.0000.00519.8310.0300.0300.0000.0000.0000.000
96A744LEU0-0.044-0.02119.9550.0180.0180.0000.0000.0000.000
97A745ALA00.0310.01819.1460.0190.0190.0000.0000.0000.000
98A746LYS10.9631.00021.1810.1660.1660.0000.0000.0000.000
99A747LEU0-0.043-0.01824.5750.0170.0170.0000.0000.0000.000
100A748VAL00.000-0.01922.4170.0140.0140.0000.0000.0000.000
101A749LEU0-0.036-0.01920.5950.0170.0170.0000.0000.0000.000
102A750PHE00.0140.02824.5700.0150.0150.0000.0000.0000.000
103A751PRO0-0.023-0.01928.407-0.006-0.0060.0000.0000.0000.000
104A752GLU-1-0.890-0.96031.275-0.082-0.0820.0000.0000.0000.000
105A753ASN0-0.0110.00530.622-0.002-0.0020.0000.0000.0000.000
106A754THR00.0250.00030.137-0.011-0.0110.0000.0000.0000.000
107A755ALA0-0.011-0.00331.877-0.010-0.0100.0000.0000.0000.000
108A756ASP-1-0.842-0.92133.616-0.105-0.1050.0000.0000.0000.000
109A757SER00.0470.03127.612-0.013-0.0130.0000.0000.0000.000
110A758LEU0-0.037-0.02529.279-0.017-0.0170.0000.0000.0000.000
111A759ASN0-0.066-0.04430.690-0.004-0.0040.0000.0000.0000.000
112A760GLU-1-0.851-0.92728.799-0.150-0.1500.0000.0000.0000.000
113A761VAL0-0.0050.00925.307-0.018-0.0180.0000.0000.0000.000
114A762LEU0-0.022-0.03127.468-0.016-0.0160.0000.0000.0000.000
115A763ALA0-0.044-0.00930.0610.0000.0000.0000.0000.0000.000
116A764ALA00.0620.03225.564-0.001-0.0010.0000.0000.0000.000
117A765TYR0-0.018-0.01322.154-0.037-0.0370.0000.0000.0000.000
118A766LYS10.9220.95127.5400.1570.1570.0000.0000.0000.000
119A767ASN0-0.028-0.00628.531-0.005-0.0050.0000.0000.0000.000
120A768THR00.023-0.00324.027-0.010-0.0100.0000.0000.0000.000
121A769LEU0-0.055-0.02427.087-0.007-0.0070.0000.0000.0000.000
122A770ASP-1-0.898-0.95429.601-0.172-0.1720.0000.0000.0000.000
123A771LEU0-0.0200.00228.9940.0080.0080.0000.0000.0000.000
124A772CYS0-0.0420.00127.436-0.022-0.0220.0000.0000.0000.000
125A773SER0-0.076-0.04729.4370.0050.0050.0000.0000.0000.000
126A774GLN0-0.060-0.01132.9370.0130.0130.0000.0000.0000.000
127A775ASP-1-0.760-0.89230.471-0.185-0.1850.0000.0000.0000.000
128A776LYS10.9330.96831.1870.1900.1900.0000.0000.0000.000
129A777ARG10.8040.90832.2010.1650.1650.0000.0000.0000.000
130A778LYS10.7980.86326.3770.2390.2390.0000.0000.0000.000
131A779GLN00.012-0.00725.923-0.012-0.0120.0000.0000.0000.000
132A780SER00.0100.01126.7990.0100.0100.0000.0000.0000.000
133A781SER0-0.002-0.01627.466-0.014-0.0140.0000.0000.0000.000
134A782VAL0-0.0290.00126.3210.0160.0160.0000.0000.0000.000
135A783LEU00.0270.01624.887-0.022-0.0220.0000.0000.0000.000
136A784LYS10.9400.96619.8410.4640.4640.0000.0000.0000.000
137A785ILE00.0200.02119.658-0.039-0.0390.0000.0000.0000.000
138A786ASN00.0930.04814.7170.0610.0610.0000.0000.0000.000
139A787LEU00.0580.01718.4820.0220.0220.0000.0000.0000.000
140A788SER00.0600.04214.9920.0160.0160.0000.0000.0000.000
141A789LYS10.9200.98514.6360.7900.7900.0000.0000.0000.000
142A790LEU00.0110.00518.2270.0490.0490.0000.0000.0000.000
143A791PHE00.0450.02018.8000.0370.0370.0000.0000.0000.000
144A792THR0-0.021-0.03217.8660.0150.0150.0000.0000.0000.000
145A793LEU0-0.023-0.02220.2860.0370.0370.0000.0000.0000.000
146A794HIS0-0.071-0.02623.2410.0280.0280.0000.0000.0000.000
147A795SER00.0450.00923.0480.0340.0340.0000.0000.0000.000
148A796CYS0-0.0340.00323.0160.0320.0320.0000.0000.0000.000
149A797LEU00.0250.02925.0420.0220.0220.0000.0000.0000.000
150A798SER00.0480.01328.3800.0210.0210.0000.0000.0000.000
151A799LEU00.0120.01825.7720.0180.0180.0000.0000.0000.000
152A800ALA00.0070.00428.9450.0160.0160.0000.0000.0000.000
153A801LEU0-0.035-0.02930.4880.0130.0130.0000.0000.0000.000
154A802GLN0-0.021-0.01032.4500.0040.0040.0000.0000.0000.000
155A803ARG10.8130.90227.2810.1530.1530.0000.0000.0000.000
156A804LEU0-0.0230.00234.3610.0070.0070.0000.0000.0000.000
157A805GLY00.0010.01436.9420.0040.0040.0000.0000.0000.000
158A806TYR00.0280.01637.6510.0040.0040.0000.0000.0000.000
159A807GLY0-0.0110.00036.890-0.005-0.0050.0000.0000.0000.000
160A808ASP-1-0.922-0.96737.903-0.097-0.0970.0000.0000.0000.000
161A809VAL0-0.030-0.02437.090-0.002-0.0020.0000.0000.0000.000
162A810SER0-0.051-0.04432.766-0.007-0.0070.0000.0000.0000.000
163A811LYS10.9870.99233.4140.0920.0920.0000.0000.0000.000
164A812ARG10.8890.94234.1550.1030.1030.0000.0000.0000.000
165A813MET0-0.0150.01330.803-0.005-0.0050.0000.0000.0000.000
166A814TYR00.010-0.06026.704-0.008-0.0080.0000.0000.0000.000
167A815GLN0-0.011-0.02129.952-0.005-0.0050.0000.0000.0000.000
168A816GLU-1-0.859-0.91531.214-0.160-0.1600.0000.0000.0000.000
169A817ILE0-0.0120.01724.875-0.013-0.0130.0000.0000.0000.000
170A818PHE0-0.036-0.02122.9490.0080.0080.0000.0000.0000.000
171A819VAL0-0.014-0.01622.186-0.028-0.0280.0000.0000.0000.000
172A820PRO0-0.046-0.03517.6790.0090.0090.0000.0000.0000.000
173A821ASP-1-0.866-0.91818.342-0.282-0.2820.0000.0000.0000.000
174A822SER0-0.102-0.04015.963-0.031-0.0310.0000.0000.0000.000
175A823ASP-1-0.885-0.96112.352-0.638-0.6380.0000.0000.0000.000
176A824ALA0-0.034-0.0217.1550.0630.0630.0000.0000.0000.000
177A825ASP-1-0.909-0.9558.109-2.417-2.4170.0000.0000.0000.000
178A826ILE0-0.037-0.0218.9820.3420.3420.0000.0000.0000.000
179A827THR00.0200.02510.1060.1630.1630.0000.0000.0000.000
180A828PRO00.1130.04410.3570.1270.1270.0000.0000.0000.000
181A829LEU00.0310.02213.3170.0820.0820.0000.0000.0000.000
182A830SER0-0.079-0.05414.2220.0470.0470.0000.0000.0000.000
183A831PHE00.0660.03714.7680.0560.0560.0000.0000.0000.000
184A832ILE00.0540.03216.5360.0550.0550.0000.0000.0000.000
185A833ILE0-0.035-0.00319.1300.0370.0370.0000.0000.0000.000
186A834SER00.0120.00219.1880.0270.0270.0000.0000.0000.000
187A835TRP00.0050.01120.5350.0300.0300.0000.0000.0000.000
188A836THR0-0.022-0.03922.1470.0230.0230.0000.0000.0000.000
189A837ALA00.0130.03524.1660.0170.0170.0000.0000.0000.000
190A838LEU00.0040.01224.7300.0130.0130.0000.0000.0000.000
191A839ASN00.005-0.01526.0070.0170.0170.0000.0000.0000.000
192A840THR0-0.102-0.08728.2030.0080.0080.0000.0000.0000.000
193A841PHE0-0.049-0.03129.1850.0070.0070.0000.0000.0000.000
194A842ALA0-0.0030.01430.1380.0020.0020.0000.0000.0000.000
195A843PRO0-0.046-0.01031.7980.0050.0050.0000.0000.0000.000
196A844ILE0-0.013-0.01134.5460.0020.0020.0000.0000.0000.000
197A845CYS0-0.083-0.02732.5680.0020.0020.0000.0000.0000.000
198A846THR00.0920.05135.2490.0030.0030.0000.0000.0000.000
199A847SER00.0020.03637.8270.0000.0000.0000.0000.0000.000
200A848PRO0-0.054-0.06238.795-0.004-0.0040.0000.0000.0000.000
201A849LYS10.8050.89034.9220.1440.1440.0000.0000.0000.000
202A850GLU-1-0.796-0.90433.441-0.106-0.1060.0000.0000.0000.000
203A851ASN0-0.073-0.05233.581-0.006-0.0060.0000.0000.0000.000
204A852ASP-1-0.849-0.93930.648-0.154-0.1540.0000.0000.0000.000
205A853VAL0-0.0460.00727.519-0.007-0.0070.0000.0000.0000.000
206A854VAL00.0720.03527.297-0.011-0.0110.0000.0000.0000.000
207A855GLU-1-0.909-0.95227.327-0.110-0.1100.0000.0000.0000.000
208A856LYS10.9460.97325.2660.2080.2080.0000.0000.0000.000
209A857MET0-0.0270.05422.940-0.017-0.0170.0000.0000.0000.000
210A858ALA0-0.010-0.02122.546-0.011-0.0110.0000.0000.0000.000
211A859MET0-0.046-0.03622.7940.0070.0070.0000.0000.0000.000
212A860TYR00.0300.01515.1980.0020.0020.0000.0000.0000.000
213A861VAL00.0220.00618.026-0.019-0.0190.0000.0000.0000.000
214A862ARG10.9150.96318.2950.0550.0550.0000.0000.0000.000
215A863THR0-0.086-0.03316.8380.0240.0240.0000.0000.0000.000
216A864ALA0-0.0100.01514.003-0.010-0.0100.0000.0000.0000.000
217A865ILE0-0.010-0.01614.1640.0300.0300.0000.0000.0000.000
218A866GLY00.0050.01910.6470.0710.0710.0000.0000.0000.000
219A867THR0-0.006-0.00510.8820.0750.0750.0000.0000.0000.000
220A868LEU0-0.001-0.00613.1780.0470.0470.0000.0000.0000.000
221A869LYS10.9320.96514.892-0.526-0.5260.0000.0000.0000.000
222A870ILE00.0360.02816.993-0.004-0.0040.0000.0000.0000.000