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: YYK32

Calculation Name: 5GPD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GPD

Chain ID: B

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1807939.996072
FMO2-HF: Nuclear repulsion 1738473.32537
FMO2-HF: Total energy -69466.670703
FMO2-MP2: Total energy -69667.570488


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(B:692:VAL)


Summations of interaction energy for fragment #1(B:692:VAL)
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.
-1.6570.181-0.033-0.838-0.9680.001
Interaction energy analysis for fragmet #1(B:692:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.034
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].
3B694SER0-0.043-0.0383.805-0.3731.465-0.033-0.838-0.9680.001
4B695PRO00.0370.0176.1610.3300.3300.0000.0000.0000.000
5B696LEU00.0100.0079.5000.0680.0680.0000.0000.0000.000
6B697GLU-1-0.829-0.9157.075-1.032-1.0320.0000.0000.0000.000
7B698VAL00.0120.0127.3220.1120.1120.0000.0000.0000.000
8B699LEU00.0320.0279.8950.0110.0110.0000.0000.0000.000
9B700ALA00.0130.02112.743-0.010-0.0100.0000.0000.0000.000
10B701SER0-0.064-0.04510.7230.0490.0490.0000.0000.0000.000
11B702TRP00.013-0.00511.731-0.038-0.0380.0000.0000.0000.000
12B703TYR00.0430.02815.222-0.025-0.0250.0000.0000.0000.000
13B704ALA00.0160.00215.379-0.016-0.0160.0000.0000.0000.000
14B705ALA0-0.042-0.03815.413-0.015-0.0150.0000.0000.0000.000
15B706ASP-1-0.875-0.92417.3800.2230.2230.0000.0000.0000.000
16B707LEU0-0.022-0.00920.500-0.019-0.0190.0000.0000.0000.000
17B708LEU0-0.044-0.02518.907-0.016-0.0160.0000.0000.0000.000
18B709ASP-1-0.874-0.96221.0160.1960.1960.0000.0000.0000.000
19B710ALA0-0.031-0.01122.927-0.012-0.0120.0000.0000.0000.000
20B711LEU00.0290.01524.656-0.009-0.0090.0000.0000.0000.000
21B712LEU0-0.042-0.01522.387-0.009-0.0090.0000.0000.0000.000
22B713MET00.0120.01726.611-0.007-0.0070.0000.0000.0000.000
23B714GLU-1-0.846-0.91628.9550.0530.0530.0000.0000.0000.000
24B715SER0-0.100-0.07629.388-0.008-0.0080.0000.0000.0000.000
25B716LEU0-0.041-0.00631.273-0.005-0.0050.0000.0000.0000.000
26B717SER0-0.090-0.06333.433-0.002-0.0020.0000.0000.0000.000
27B718ARG10.7740.88030.042-0.048-0.0480.0000.0000.0000.000
28B719LYS10.9250.96634.995-0.022-0.0220.0000.0000.0000.000
29B720VAL00.0070.01928.785-0.001-0.0010.0000.0000.0000.000
30B721GLU-1-0.896-0.92630.3590.0030.0030.0000.0000.0000.000
31B722ILE00.017-0.00925.8820.0050.0050.0000.0000.0000.000
32B723SER0-0.020-0.01426.305-0.001-0.0010.0000.0000.0000.000
33B724GLU-1-0.711-0.85926.4210.0330.0330.0000.0000.0000.000
34B725ILE0-0.034-0.03321.6450.0050.0050.0000.0000.0000.000
35B726GLU-1-0.982-0.97421.604-0.053-0.0530.0000.0000.0000.000
36B727GLU-1-0.906-0.94021.573-0.008-0.0080.0000.0000.0000.000
37B728ILE00.0530.03018.5500.0020.0020.0000.0000.0000.000
38B729ILE0-0.007-0.00916.696-0.004-0.0040.0000.0000.0000.000
39B730SER0-0.076-0.06116.283-0.031-0.0310.0000.0000.0000.000
40B731LEU00.0750.04816.844-0.037-0.0370.0000.0000.0000.000
41B732CYS0-0.131-0.04513.3390.0280.0280.0000.0000.0000.000
42B733PRO00.011-0.0069.216-0.074-0.0740.0000.0000.0000.000
43B734LYS10.8560.90310.7720.2560.2560.0000.0000.0000.000
44B735ASN0-0.0220.0006.5150.0960.0960.0000.0000.0000.000
45B736SER00.0370.0246.6800.0040.0040.0000.0000.0000.000
46B737SER00.013-0.0088.485-0.073-0.0730.0000.0000.0000.000
47B738ILE00.0690.03510.765-0.076-0.0760.0000.0000.0000.000
48B739ILE00.0290.04111.933-0.040-0.0400.0000.0000.0000.000
49B740ARG10.9520.96510.655-0.111-0.1110.0000.0000.0000.000
50B741HIS0-0.081-0.04114.4020.0060.0060.0000.0000.0000.000
51B742ALA00.0830.03916.717-0.014-0.0140.0000.0000.0000.000
52B743LEU0-0.037-0.01416.743-0.015-0.0150.0000.0000.0000.000
53B744LEU0-0.024-0.03218.647-0.005-0.0050.0000.0000.0000.000
54B745ALA00.0290.01521.120-0.003-0.0030.0000.0000.0000.000
55B746LYS10.8320.92322.4320.0260.0260.0000.0000.0000.000
56B747LEU0-0.032-0.01023.716-0.005-0.0050.0000.0000.0000.000
57B748VAL0-0.010-0.01525.550-0.003-0.0030.0000.0000.0000.000
58B749LEU0-0.022-0.00125.808-0.003-0.0030.0000.0000.0000.000
59B750PHE00.0180.02125.836-0.004-0.0040.0000.0000.0000.000
60B751PRO0-0.022-0.00429.777-0.003-0.0030.0000.0000.0000.000
61B752GLU-1-0.850-0.92632.286-0.001-0.0010.0000.0000.0000.000
62B753ASN00.0140.01127.408-0.004-0.0040.0000.0000.0000.000
63B754THR00.0540.03628.411-0.004-0.0040.0000.0000.0000.000
64B755ALA00.0000.01027.992-0.003-0.0030.0000.0000.0000.000
65B756ASP-1-0.909-0.96227.768-0.046-0.0460.0000.0000.0000.000
66B757SER0-0.052-0.05524.380-0.005-0.0050.0000.0000.0000.000
67B758LEU0-0.022-0.02923.2950.0010.0010.0000.0000.0000.000
68B759ASN0-0.0170.00223.537-0.003-0.0030.0000.0000.0000.000
69B760GLU-1-0.786-0.89219.775-0.063-0.0630.0000.0000.0000.000
70B761VAL0-0.0010.01218.791-0.008-0.0080.0000.0000.0000.000
71B762LEU00.002-0.00718.6640.0040.0040.0000.0000.0000.000
72B763ALA00.0030.02218.786-0.013-0.0130.0000.0000.0000.000
73B764ALA00.0440.01114.344-0.032-0.0320.0000.0000.0000.000
74B765TYR0-0.021-0.02013.9530.0030.0030.0000.0000.0000.000
75B766LYS10.9330.94715.6040.0570.0570.0000.0000.0000.000
76B767ASN00.0380.03611.430-0.034-0.0340.0000.0000.0000.000
77B768THR0-0.074-0.03210.190-0.026-0.0260.0000.0000.0000.000
78B769LEU0-0.055-0.04511.4700.0050.0050.0000.0000.0000.000
79B770ASP-1-0.905-0.92613.812-0.337-0.3370.0000.0000.0000.000
80B771LEU00.0470.0028.341-0.034-0.0340.0000.0000.0000.000
81B772CYS0-0.134-0.05610.2330.0100.0100.0000.0000.0000.000
82B773SER0-0.060-0.02111.5480.0530.0530.0000.0000.0000.000
83B774GLN0-0.0370.00210.6360.0170.0170.0000.0000.0000.000
84B782VAL00.0380.02413.399-0.007-0.0070.0000.0000.0000.000
85B783LEU0-0.021-0.01713.7830.0390.0390.0000.0000.0000.000
86B784LYS10.9660.96813.271-0.289-0.2890.0000.0000.0000.000
87B785ILE0-0.025-0.00515.1740.0500.0500.0000.0000.0000.000
88B786ASN0-0.017-0.01917.661-0.029-0.0290.0000.0000.0000.000
89B787LEU00.1140.06219.800-0.017-0.0170.0000.0000.0000.000
90B788SER00.0760.03921.715-0.015-0.0150.0000.0000.0000.000
91B789LYS10.9410.98014.148-0.425-0.4250.0000.0000.0000.000
92B790LEU00.0060.01120.291-0.018-0.0180.0000.0000.0000.000
93B791PHE00.0570.03322.627-0.015-0.0150.0000.0000.0000.000
94B792THR00.000-0.01221.598-0.011-0.0110.0000.0000.0000.000
95B793LEU0-0.026-0.02218.491-0.014-0.0140.0000.0000.0000.000
96B794HIS0-0.056-0.01422.890-0.015-0.0150.0000.0000.0000.000
97B795SER00.017-0.00826.294-0.010-0.0100.0000.0000.0000.000
98B796CYS0-0.029-0.00624.369-0.009-0.0090.0000.0000.0000.000
99B797LEU00.0220.01425.704-0.010-0.0100.0000.0000.0000.000
100B798SER00.0270.00027.297-0.007-0.0070.0000.0000.0000.000
101B799LEU0-0.030-0.02229.555-0.005-0.0050.0000.0000.0000.000
102B800ALA00.0050.00027.830-0.005-0.0050.0000.0000.0000.000
103B801LEU0-0.036-0.01829.951-0.006-0.0060.0000.0000.0000.000
104B802GLN00.019-0.00432.405-0.002-0.0020.0000.0000.0000.000
105B803ARG10.7860.89330.088-0.027-0.0270.0000.0000.0000.000
106B804LEU0-0.0220.00330.830-0.004-0.0040.0000.0000.0000.000
107B805GLY00.0010.01335.110-0.002-0.0020.0000.0000.0000.000
108B806TYR0-0.025-0.01533.170-0.002-0.0020.0000.0000.0000.000
109B807GLY00.0380.01537.8410.0010.0010.0000.0000.0000.000
110B808ASP-1-0.842-0.90038.5500.0120.0120.0000.0000.0000.000
111B809VAL00.007-0.01434.3460.0030.0030.0000.0000.0000.000
112B810SER00.004-0.00334.2970.0010.0010.0000.0000.0000.000
113B811LYS10.8850.93734.920-0.011-0.0110.0000.0000.0000.000
114B812ARG10.8240.90236.610-0.024-0.0240.0000.0000.0000.000
115B813MET0-0.0150.00229.7910.0030.0030.0000.0000.0000.000
116B814TYR00.0750.00932.5630.0060.0060.0000.0000.0000.000
117B815GLN0-0.082-0.06633.9520.0030.0030.0000.0000.0000.000
118B816GLU-1-0.869-0.90132.8930.0390.0390.0000.0000.0000.000
119B817ILE0-0.067-0.00529.3710.0050.0050.0000.0000.0000.000
120B818PHE0-0.010-0.00428.113-0.001-0.0010.0000.0000.0000.000
121B819VAL0-0.037-0.02728.8120.0080.0080.0000.0000.0000.000
122B820PRO0-0.037-0.02426.2800.0000.0000.0000.0000.0000.000
123B821ASP-1-0.854-0.92028.9300.1250.1250.0000.0000.0000.000
124B822SER0-0.114-0.08030.467-0.009-0.0090.0000.0000.0000.000
125B823ASP-1-0.839-0.90126.3210.1820.1820.0000.0000.0000.000
126B824ALA0-0.033-0.02624.495-0.004-0.0040.0000.0000.0000.000
127B825ASP-1-0.893-0.92521.3270.2760.2760.0000.0000.0000.000
128B826ILE0-0.055-0.02723.382-0.019-0.0190.0000.0000.0000.000
129B827THR00.0300.01219.7180.0000.0000.0000.0000.0000.000
130B828PRO00.0620.02822.720-0.018-0.0180.0000.0000.0000.000
131B829LEU00.0110.02719.670-0.014-0.0140.0000.0000.0000.000
132B830SER00.0290.00822.957-0.018-0.0180.0000.0000.0000.000
133B831PHE00.0420.02224.489-0.015-0.0150.0000.0000.0000.000
134B832ILE00.0300.02426.640-0.012-0.0120.0000.0000.0000.000
135B833ILE0-0.015-0.00523.286-0.012-0.0120.0000.0000.0000.000
136B834SER0-0.001-0.01727.713-0.009-0.0090.0000.0000.0000.000
137B835TRP00.0320.01630.110-0.007-0.0070.0000.0000.0000.000
138B836THR0-0.018-0.01830.249-0.008-0.0080.0000.0000.0000.000
139B837ALA00.0350.01530.679-0.006-0.0060.0000.0000.0000.000
140B838LEU0-0.028-0.01632.731-0.005-0.0050.0000.0000.0000.000
141B839ASN0-0.037-0.03235.443-0.007-0.0070.0000.0000.0000.000
142B840THR0-0.041-0.01935.060-0.002-0.0020.0000.0000.0000.000
143B841PHE0-0.009-0.02033.184-0.004-0.0040.0000.0000.0000.000
144B842ALA00.0120.03238.070-0.001-0.0010.0000.0000.0000.000
145B843PRO0-0.0370.00240.496-0.001-0.0010.0000.0000.0000.000
146B844ILE0-0.029-0.02139.405-0.003-0.0030.0000.0000.0000.000
147B845CYS0-0.060-0.03337.933-0.002-0.0020.0000.0000.0000.000
148B846THR0-0.027-0.02041.6640.0000.0000.0000.0000.0000.000
149B847SER0-0.056-0.01544.277-0.001-0.0010.0000.0000.0000.000
150B848PRO00.0200.01144.4090.0000.0000.0000.0000.0000.000
151B849LYS10.9010.94845.383-0.030-0.0300.0000.0000.0000.000
152B850GLU-1-0.907-0.96645.5070.0280.0280.0000.0000.0000.000
153B851ASN0-0.0320.00339.1160.0030.0030.0000.0000.0000.000
154B852ASP-1-0.774-0.89139.6940.0370.0370.0000.0000.0000.000
155B853VAL00.0180.01134.1190.0020.0020.0000.0000.0000.000
156B854VAL0-0.020-0.00537.0290.0050.0050.0000.0000.0000.000
157B855GLU-1-0.926-0.96538.5630.0540.0540.0000.0000.0000.000
158B856LYS10.9420.96135.389-0.056-0.0560.0000.0000.0000.000
159B857MET0-0.0030.00730.7420.0080.0080.0000.0000.0000.000
160B858ALA00.012-0.00734.4030.0040.0040.0000.0000.0000.000
161B859MET0-0.066-0.03936.7360.0030.0030.0000.0000.0000.000
162B860TYR00.0540.04026.3950.0060.0060.0000.0000.0000.000
163B861VAL00.020-0.00531.8220.0060.0060.0000.0000.0000.000
164B862ARG10.9120.97133.360-0.080-0.0800.0000.0000.0000.000
165B863THR0-0.001-0.01232.048-0.001-0.0010.0000.0000.0000.000
166B864ALA00.0070.02729.7830.0080.0080.0000.0000.0000.000
167B865ILE00.0230.01030.7550.0060.0060.0000.0000.0000.000
168B866GLY0-0.021-0.00332.822-0.002-0.0020.0000.0000.0000.000
169B867THR0-0.016-0.02529.4810.0030.0030.0000.0000.0000.000
170B868LEU00.0300.01426.1570.0050.0050.0000.0000.0000.000
171B869LYS11.0071.00329.891-0.073-0.0730.0000.0000.0000.000
172B870ILE0-0.041-0.01132.287-0.003-0.0030.0000.0000.0000.000
173B871GLN00.001-0.01526.0010.0100.0100.0000.0000.0000.000
174B872ASP-1-0.930-0.94929.8760.1100.1100.0000.0000.0000.000
175B873LEU0-0.015-0.00331.082-0.004-0.0040.0000.0000.0000.000
176B874LYS10.7540.88131.670-0.115-0.1150.0000.0000.0000.000
177B875LEU00.0160.02428.0670.0000.0000.0000.0000.0000.000