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: 53KMZ

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1808211.220729
FMO2-HF: Nuclear repulsion 1738746.329989
FMO2-HF: Total energy -69464.89074
FMO2-MP2: Total energy -69665.940514


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.
-1.550.237-0.033-0.798-0.9560.002
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 : -0.021 / q_NPA : -0.027
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].
3B694SER00.0080.0113.805-0.2881.499-0.033-0.798-0.9560.002
4B695PRO00.0260.0126.1990.3540.3540.0000.0000.0000.000
5B696LEU00.0120.0039.5040.0660.0660.0000.0000.0000.000
6B697GLU-1-0.885-0.9636.989-1.111-1.1110.0000.0000.0000.000
7B698VAL00.0140.0147.4350.1120.1120.0000.0000.0000.000
8B699LEU00.0290.0239.9260.0160.0160.0000.0000.0000.000
9B700ALA00.0150.02612.644-0.008-0.0080.0000.0000.0000.000
10B701SER0-0.063-0.04610.6340.0470.0470.0000.0000.0000.000
11B702TRP00.014-0.00112.054-0.029-0.0290.0000.0000.0000.000
12B703TYR00.0210.01815.165-0.031-0.0310.0000.0000.0000.000
13B704ALA00.0180.00115.299-0.014-0.0140.0000.0000.0000.000
14B705ALA0-0.044-0.03815.366-0.014-0.0140.0000.0000.0000.000
15B706ASP-1-0.848-0.91117.3130.2200.2200.0000.0000.0000.000
16B707LEU0-0.036-0.01520.372-0.019-0.0190.0000.0000.0000.000
17B708LEU0-0.036-0.01918.994-0.016-0.0160.0000.0000.0000.000
18B709ASP-1-0.888-0.96220.7980.1990.1990.0000.0000.0000.000
19B710ALA0-0.034-0.01622.863-0.011-0.0110.0000.0000.0000.000
20B711LEU00.0420.02224.499-0.008-0.0080.0000.0000.0000.000
21B712LEU0-0.040-0.01422.345-0.008-0.0080.0000.0000.0000.000
22B713MET0-0.0040.02926.551-0.006-0.0060.0000.0000.0000.000
23B714GLU-1-0.840-0.91628.8920.0470.0470.0000.0000.0000.000
24B715SER0-0.068-0.17529.327-0.008-0.0080.0000.0000.0000.000
25B716LEU0-0.070-0.02631.214-0.004-0.0040.0000.0000.0000.000
26B717SER0-0.080-0.05833.375-0.002-0.0020.0000.0000.0000.000
27B718ARG10.7990.89929.605-0.039-0.0390.0000.0000.0000.000
28B719LYS10.9060.95634.936-0.018-0.0180.0000.0000.0000.000
29B720VAL0-0.0250.11528.799-0.001-0.0010.0000.0000.0000.000
30B721GLU-1-0.907-0.97430.348-0.001-0.0010.0000.0000.0000.000
31B722ILE0-0.003-0.01525.8910.0040.0040.0000.0000.0000.000
32B723SER0-0.0020.00526.252-0.002-0.0020.0000.0000.0000.000
33B724GLU-1-0.689-0.84726.1850.0220.0220.0000.0000.0000.000
34B725ILE0-0.043-0.03821.6510.0030.0030.0000.0000.0000.000
35B726GLU-1-0.977-0.97921.549-0.074-0.0740.0000.0000.0000.000
36B727GLU-1-0.901-0.94421.520-0.027-0.0270.0000.0000.0000.000
37B728ILE00.0290.02618.290-0.001-0.0010.0000.0000.0000.000
38B729ILE0-0.025-0.03016.680-0.007-0.0070.0000.0000.0000.000
39B730SER0-0.081-0.04316.231-0.037-0.0370.0000.0000.0000.000
40B731LEU00.0610.03116.791-0.042-0.0420.0000.0000.0000.000
41B732CYS0-0.133-0.04313.3100.0210.0210.0000.0000.0000.000
42B733PRO00.011-0.0059.081-0.079-0.0790.0000.0000.0000.000
43B734LYS10.8970.93810.6310.3370.3370.0000.0000.0000.000
44B735ASN0-0.0200.0026.8390.1680.1680.0000.0000.0000.000
45B736SER00.0400.0226.643-0.027-0.0270.0000.0000.0000.000
46B737SER0-0.026-0.0278.437-0.067-0.0670.0000.0000.0000.000
47B738ILE00.0980.03310.725-0.074-0.0740.0000.0000.0000.000
48B739ILE00.0320.04211.604-0.033-0.0330.0000.0000.0000.000
49B740ARG10.9350.96011.184-0.068-0.0680.0000.0000.0000.000
50B741HIS0-0.071-0.02614.4350.0270.0270.0000.0000.0000.000
51B742ALA00.0890.04416.666-0.010-0.0100.0000.0000.0000.000
52B743LEU0-0.047-0.01816.470-0.013-0.0130.0000.0000.0000.000
53B744LEU0-0.018-0.03218.455-0.003-0.0030.0000.0000.0000.000
54B745ALA00.0370.02121.073-0.002-0.0020.0000.0000.0000.000
55B746LYS10.8410.91722.3330.0440.0440.0000.0000.0000.000
56B747LEU0-0.020-0.01023.677-0.005-0.0050.0000.0000.0000.000
57B748VAL0-0.022-0.01625.511-0.002-0.0020.0000.0000.0000.000
58B749LEU0-0.017-0.00725.624-0.002-0.0020.0000.0000.0000.000
59B750PHE00.0240.05125.892-0.005-0.0050.0000.0000.0000.000
60B751PRO0-0.010-0.00529.737-0.004-0.0040.0000.0000.0000.000
61B752GLU-1-0.874-0.94132.246-0.011-0.0110.0000.0000.0000.000
62B753ASN00.0250.02027.955-0.008-0.0080.0000.0000.0000.000
63B754THR00.0460.07528.378-0.005-0.0050.0000.0000.0000.000
64B755ALA00.0030.00927.965-0.003-0.0030.0000.0000.0000.000
65B756ASP-1-0.906-0.95427.718-0.062-0.0620.0000.0000.0000.000
66B757SER0-0.043-0.09324.409-0.005-0.0050.0000.0000.0000.000
67B758LEU0-0.049-0.03723.2660.0000.0000.0000.0000.0000.000
68B759ASN00.0150.00923.519-0.001-0.0010.0000.0000.0000.000
69B760GLU-1-0.788-0.89219.701-0.090-0.0900.0000.0000.0000.000
70B761VAL0-0.0080.01018.770-0.011-0.0110.0000.0000.0000.000
71B762LEU0-0.013-0.01218.6470.0030.0030.0000.0000.0000.000
72B763ALA00.0150.02718.778-0.014-0.0140.0000.0000.0000.000
73B764ALA00.0410.01014.260-0.035-0.0350.0000.0000.0000.000
74B765TYR0-0.035-0.03013.9450.0000.0000.0000.0000.0000.000
75B766LYS10.9230.94615.6080.0730.0730.0000.0000.0000.000
76B767ASN00.0570.03812.188-0.033-0.0330.0000.0000.0000.000
77B768THR0-0.080-0.03010.303-0.026-0.0260.0000.0000.0000.000
78B769LEU0-0.053-0.04711.4880.0110.0110.0000.0000.0000.000
79B770ASP-1-0.920-0.93513.761-0.339-0.3390.0000.0000.0000.000
80B771LEU00.0410.0018.277-0.033-0.0330.0000.0000.0000.000
81B772CYS0-0.118-0.04210.4030.0160.0160.0000.0000.0000.000
82B773SER0-0.057-0.02211.7040.0580.0580.0000.0000.0000.000
83B774GLN0-0.0370.00310.5220.0300.0300.0000.0000.0000.000
84B782VAL00.012-0.01013.481-0.014-0.0140.0000.0000.0000.000
85B783LEU00.0120.01813.7690.0430.0430.0000.0000.0000.000
86B784LYS10.9720.97613.504-0.332-0.3320.0000.0000.0000.000
87B785ILE0-0.026-0.00815.1780.0520.0520.0000.0000.0000.000
88B786ASN00.0240.01417.655-0.024-0.0240.0000.0000.0000.000
89B787LEU00.1220.06019.784-0.019-0.0190.0000.0000.0000.000
90B788SER00.1040.05221.937-0.014-0.0140.0000.0000.0000.000
91B789LYS10.9290.96214.087-0.430-0.4300.0000.0000.0000.000
92B790LEU00.0130.01220.266-0.019-0.0190.0000.0000.0000.000
93B791PHE00.0500.02522.611-0.016-0.0160.0000.0000.0000.000
94B792THR00.0160.03321.429-0.013-0.0130.0000.0000.0000.000
95B793LEU0-0.027-0.02218.475-0.015-0.0150.0000.0000.0000.000
96B794HIS0-0.053-0.00922.866-0.015-0.0150.0000.0000.0000.000
97B795SER00.026-0.03626.274-0.009-0.0090.0000.0000.0000.000
98B796CYS0-0.044-0.00823.473-0.011-0.0110.0000.0000.0000.000
99B797LEU00.0100.01525.737-0.011-0.0110.0000.0000.0000.000
100B798SER00.0370.00327.275-0.007-0.0070.0000.0000.0000.000
101B799LEU0-0.026-0.01929.497-0.005-0.0050.0000.0000.0000.000
102B800ALA0-0.010-0.00527.809-0.005-0.0050.0000.0000.0000.000
103B801LEU00.007-0.00129.923-0.006-0.0060.0000.0000.0000.000
104B802GLN00.0080.00032.384-0.003-0.0030.0000.0000.0000.000
105B803ARG10.8020.90230.113-0.020-0.0200.0000.0000.0000.000
106B804LEU0-0.0190.00831.551-0.004-0.0040.0000.0000.0000.000
107B805GLY0-0.0060.00635.086-0.002-0.0020.0000.0000.0000.000
108B806TYR0-0.029-0.00432.822-0.002-0.0020.0000.0000.0000.000
109B807GLY00.0280.00437.8240.0010.0010.0000.0000.0000.000
110B808ASP-1-0.906-0.92938.5310.0080.0080.0000.0000.0000.000
111B809VAL00.002-0.01834.2700.0030.0030.0000.0000.0000.000
112B810SER0-0.012-0.02434.2780.0010.0010.0000.0000.0000.000
113B811LYS10.9570.97134.900-0.010-0.0100.0000.0000.0000.000
114B812ARG10.8710.94636.734-0.023-0.0230.0000.0000.0000.000
115B813MET0-0.021-0.00430.0280.0030.0030.0000.0000.0000.000
116B814TYR00.0630.00632.5470.0070.0070.0000.0000.0000.000
117B815GLN0-0.120-0.09033.9310.0030.0030.0000.0000.0000.000
118B816GLU-1-0.902-0.92532.8490.0410.0410.0000.0000.0000.000
119B817ILE0-0.080-0.00729.1800.0060.0060.0000.0000.0000.000
120B818PHE0-0.012-0.00527.938-0.001-0.0010.0000.0000.0000.000
121B819VAL0-0.046-0.02628.7910.0080.0080.0000.0000.0000.000
122B820PRO0-0.028-0.02426.3360.0000.0000.0000.0000.0000.000
123B821ASP-1-0.844-0.90228.9040.1320.1320.0000.0000.0000.000
124B822SER0-0.153-0.13530.464-0.010-0.0100.0000.0000.0000.000
125B823ASP-1-0.826-0.87226.1870.1740.1740.0000.0000.0000.000
126B824ALA0-0.047-0.03224.463-0.005-0.0050.0000.0000.0000.000
127B825ASP-1-0.953-0.96421.3990.2730.2730.0000.0000.0000.000
128B826ILE0-0.034-0.00923.341-0.020-0.0200.0000.0000.0000.000
129B827THR00.0180.01119.786-0.001-0.0010.0000.0000.0000.000
130B828PRO00.1060.03222.880-0.018-0.0180.0000.0000.0000.000
131B829LEU00.0270.03019.561-0.015-0.0150.0000.0000.0000.000
132B830SER0-0.035-0.02022.993-0.016-0.0160.0000.0000.0000.000
133B831PHE00.0520.02724.444-0.014-0.0140.0000.0000.0000.000
134B832ILE00.0280.02826.478-0.011-0.0110.0000.0000.0000.000
135B833ILE0-0.024-0.00723.451-0.012-0.0120.0000.0000.0000.000
136B834SER0-0.010-0.02927.669-0.009-0.0090.0000.0000.0000.000
137B835TRP0-0.0110.00230.069-0.007-0.0070.0000.0000.0000.000
138B836THR00.000-0.02730.244-0.008-0.0080.0000.0000.0000.000
139B837ALA00.006-0.00230.636-0.007-0.0070.0000.0000.0000.000
140B838LEU00.0190.00832.694-0.004-0.0040.0000.0000.0000.000
141B839ASN0-0.014-0.01435.437-0.003-0.0030.0000.0000.0000.000
142B840THR0-0.102-0.05134.625-0.004-0.0040.0000.0000.0000.000
143B841PHE00.0330.00233.355-0.005-0.0050.0000.0000.0000.000
144B842ALA00.0090.02438.037-0.001-0.0010.0000.0000.0000.000
145B843PRO0-0.026-0.00940.433-0.001-0.0010.0000.0000.0000.000
146B844ILE0-0.041-0.02339.365-0.003-0.0030.0000.0000.0000.000
147B845CYS0-0.063-0.05138.916-0.002-0.0020.0000.0000.0000.000
148B846THR0-0.0320.00741.6380.0000.0000.0000.0000.0000.000
149B847SER00.0200.01644.248-0.001-0.0010.0000.0000.0000.000
150B848PRO0-0.051-0.02044.4540.0000.0000.0000.0000.0000.000
151B849LYS10.9140.95845.227-0.030-0.0300.0000.0000.0000.000
152B850GLU-1-0.912-0.97345.3890.0290.0290.0000.0000.0000.000
153B851ASN0-0.0270.00839.0730.0040.0040.0000.0000.0000.000
154B852ASP-1-0.783-0.88739.8630.0330.0330.0000.0000.0000.000
155B853VAL00.0260.01334.1740.0020.0020.0000.0000.0000.000
156B854VAL0-0.008-0.00137.0000.0040.0040.0000.0000.0000.000
157B855GLU-1-0.911-0.96038.5290.0560.0560.0000.0000.0000.000
158B856LYS10.9850.98435.129-0.060-0.0600.0000.0000.0000.000
159B857MET0-0.002-0.00131.0780.0080.0080.0000.0000.0000.000
160B858ALA00.012-0.00534.3650.0040.0040.0000.0000.0000.000
161B859MET0-0.067-0.04036.6840.0030.0030.0000.0000.0000.000
162B860TYR00.0740.04526.1910.0060.0060.0000.0000.0000.000
163B861VAL00.0260.00431.8980.0060.0060.0000.0000.0000.000
164B862ARG10.9090.97233.315-0.083-0.0830.0000.0000.0000.000
165B863THR0-0.069-0.04732.2310.0030.0030.0000.0000.0000.000
166B864ALA00.0550.04629.8490.0080.0080.0000.0000.0000.000
167B865ILE00.010-0.00130.7020.0060.0060.0000.0000.0000.000
168B866GLY0-0.015-0.00232.768-0.002-0.0020.0000.0000.0000.000
169B867THR0-0.030-0.02529.2620.0030.0030.0000.0000.0000.000
170B868LEU00.0680.02726.0050.0040.0040.0000.0000.0000.000
171B869LYS10.9950.99429.833-0.073-0.0730.0000.0000.0000.000
172B870ILE0-0.070-0.02132.146-0.003-0.0030.0000.0000.0000.000
173B871GLN0-0.020-0.02926.0590.0050.0050.0000.0000.0000.000
174B872ASP-1-0.933-0.95129.8760.1090.1090.0000.0000.0000.000
175B873LEU0-0.0120.00531.077-0.004-0.0040.0000.0000.0000.000
176B874LYS10.8090.90731.733-0.118-0.1180.0000.0000.0000.000
177B875LEU00.0120.02328.0740.0000.0000.0000.0000.0000.000