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: VR1M1

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1807912.779656
FMO2-HF: Nuclear repulsion 1738445.198886
FMO2-HF: Total energy -69467.580771
FMO2-MP2: Total energy -69668.261089


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.
-1.584-0.08-0.019-0.685-0.8010.002
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 : -0.024 / q_NPA : -0.029
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].
3B694SER0-0.023-0.0373.883-0.0391.465-0.019-0.685-0.8010.002
4B695PRO00.027-0.0096.1580.2540.2540.0000.0000.0000.000
5B696LEU00.0150.0099.3900.0750.0750.0000.0000.0000.000
6B697GLU-1-0.808-0.8806.547-1.325-1.3250.0000.0000.0000.000
7B698VAL0-0.0100.0087.0440.1420.1420.0000.0000.0000.000
8B699LEU00.0200.0249.6100.0180.0180.0000.0000.0000.000
9B700ALA00.0140.01212.8630.0020.0020.0000.0000.0000.000
10B701SER0-0.071-0.06210.6610.0620.0620.0000.0000.0000.000
11B702TRP00.000-0.00611.502-0.030-0.0300.0000.0000.0000.000
12B703TYR00.0570.03715.214-0.018-0.0180.0000.0000.0000.000
13B704ALA00.0180.00215.427-0.014-0.0140.0000.0000.0000.000
14B705ALA0-0.024-0.02215.380-0.011-0.0110.0000.0000.0000.000
15B706ASP-1-0.894-0.94117.3650.2060.2060.0000.0000.0000.000
16B707LEU0-0.020-0.01020.508-0.017-0.0170.0000.0000.0000.000
17B708LEU0-0.047-0.02018.815-0.015-0.0150.0000.0000.0000.000
18B709ASP-1-0.859-0.96620.7540.2010.2010.0000.0000.0000.000
19B710ALA0-0.022-0.00722.714-0.011-0.0110.0000.0000.0000.000
20B711LEU00.0360.02324.618-0.008-0.0080.0000.0000.0000.000
21B712LEU0-0.044-0.02222.344-0.009-0.0090.0000.0000.0000.000
22B713MET00.0040.01226.479-0.005-0.0050.0000.0000.0000.000
23B714GLU-1-0.850-0.91129.0070.0490.0490.0000.0000.0000.000
24B715SER0-0.061-0.05229.389-0.007-0.0070.0000.0000.0000.000
25B716LEU0-0.041-0.00831.314-0.004-0.0040.0000.0000.0000.000
26B717SER0-0.113-0.07533.565-0.002-0.0020.0000.0000.0000.000
27B718ARG10.7560.86430.432-0.042-0.0420.0000.0000.0000.000
28B719LYS10.9380.96734.376-0.019-0.0190.0000.0000.0000.000
29B720VAL00.0180.01828.5950.0010.0010.0000.0000.0000.000
30B721GLU-1-0.919-0.93530.066-0.001-0.0010.0000.0000.0000.000
31B722ILE0-0.001-0.02126.1820.0040.0040.0000.0000.0000.000
32B723SER00.012-0.00726.052-0.002-0.0020.0000.0000.0000.000
33B724GLU-1-0.702-0.84726.1930.0260.0260.0000.0000.0000.000
34B725ILE0-0.013-0.01521.4240.0050.0050.0000.0000.0000.000
35B726GLU-1-0.962-0.96921.454-0.061-0.0610.0000.0000.0000.000
36B727GLU-1-0.912-0.93621.497-0.018-0.0180.0000.0000.0000.000
37B728ILE00.0270.02118.436-0.005-0.0050.0000.0000.0000.000
38B729ILE0-0.009-0.01216.863-0.001-0.0010.0000.0000.0000.000
39B730SER0-0.070-0.05416.546-0.039-0.0390.0000.0000.0000.000
40B731LEU00.0300.02517.219-0.039-0.0390.0000.0000.0000.000
41B732CYS0-0.076-0.02713.2140.0140.0140.0000.0000.0000.000
42B733PRO00.0180.0158.718-0.077-0.0770.0000.0000.0000.000
43B734LYS10.8410.89810.4110.2860.2860.0000.0000.0000.000
44B735ASN0-0.0080.0106.0820.1630.1630.0000.0000.0000.000
45B736SER00.0130.0036.360-0.007-0.0070.0000.0000.0000.000
46B737SER00.007-0.0158.238-0.075-0.0750.0000.0000.0000.000
47B738ILE00.0530.03910.638-0.079-0.0790.0000.0000.0000.000
48B739ILE00.0320.03511.870-0.034-0.0340.0000.0000.0000.000
49B740ARG10.9320.94910.290-0.140-0.1400.0000.0000.0000.000
50B741HIS0-0.065-0.03714.1330.0100.0100.0000.0000.0000.000
51B742ALA00.0890.04316.912-0.014-0.0140.0000.0000.0000.000
52B743LEU0-0.022-0.00816.620-0.013-0.0130.0000.0000.0000.000
53B744LEU0-0.039-0.02818.394-0.006-0.0060.0000.0000.0000.000
54B745ALA00.0360.01921.119-0.003-0.0030.0000.0000.0000.000
55B746LYS10.8120.90322.5160.0280.0280.0000.0000.0000.000
56B747LEU0-0.0170.00223.796-0.003-0.0030.0000.0000.0000.000
57B748VAL00.007-0.01525.632-0.002-0.0020.0000.0000.0000.000
58B749LEU0-0.021-0.00125.719-0.001-0.0010.0000.0000.0000.000
59B750PHE0-0.0060.00826.082-0.003-0.0030.0000.0000.0000.000
60B751PRO0-0.023-0.01130.160-0.003-0.0030.0000.0000.0000.000
61B752GLU-1-0.861-0.92732.5280.0000.0000.0000.0000.0000.000
62B753ASN0-0.0010.00227.178-0.002-0.0020.0000.0000.0000.000
63B754THR0-0.0010.00228.191-0.004-0.0040.0000.0000.0000.000
64B755ALA00.0010.00628.083-0.002-0.0020.0000.0000.0000.000
65B756ASP-1-0.864-0.93327.599-0.042-0.0420.0000.0000.0000.000
66B757SER00.008-0.03723.958-0.006-0.0060.0000.0000.0000.000
67B758LEU00.010-0.00223.0840.0010.0010.0000.0000.0000.000
68B759ASN0-0.049-0.01123.140-0.003-0.0030.0000.0000.0000.000
69B760GLU-1-0.807-0.88420.075-0.063-0.0630.0000.0000.0000.000
70B761VAL00.0090.00718.654-0.010-0.0100.0000.0000.0000.000
71B762LEU0-0.013-0.01418.3030.0010.0010.0000.0000.0000.000
72B763ALA00.0020.01018.583-0.011-0.0110.0000.0000.0000.000
73B764ALA00.0230.01214.444-0.033-0.0330.0000.0000.0000.000
74B765TYR0-0.018-0.02313.6570.0040.0040.0000.0000.0000.000
75B766LYS10.9320.95715.0360.0520.0520.0000.0000.0000.000
76B767ASN00.0450.02810.737-0.034-0.0340.0000.0000.0000.000
77B768THR0-0.051-0.0179.724-0.022-0.0220.0000.0000.0000.000
78B769LEU0-0.052-0.03611.1390.0140.0140.0000.0000.0000.000
79B770ASP-1-0.879-0.90713.903-0.329-0.3290.0000.0000.0000.000
80B771LEU00.0850.0258.441-0.024-0.0240.0000.0000.0000.000
81B772CYS0-0.147-0.0599.936-0.003-0.0030.0000.0000.0000.000
82B773SER0-0.098-0.04211.3330.0690.0690.0000.0000.0000.000
83B774GLN0-0.064-0.03310.4880.0190.0190.0000.0000.0000.000
84B782VAL00.0460.02713.345-0.009-0.0090.0000.0000.0000.000
85B783LEU0-0.013-0.02213.8610.0530.0530.0000.0000.0000.000
86B784LYS10.9400.96512.841-0.330-0.3300.0000.0000.0000.000
87B785ILE0-0.022-0.00915.0070.0470.0470.0000.0000.0000.000
88B786ASN0-0.012-0.00417.643-0.040-0.0400.0000.0000.0000.000
89B787LEU00.0900.04119.816-0.014-0.0140.0000.0000.0000.000
90B788SER00.038-0.01120.980-0.017-0.0170.0000.0000.0000.000
91B789LYS10.9470.98314.207-0.465-0.4650.0000.0000.0000.000
92B790LEU0-0.0020.00520.073-0.018-0.0180.0000.0000.0000.000
93B791PHE00.0630.02822.292-0.017-0.0170.0000.0000.0000.000
94B792THR0-0.0010.00021.501-0.013-0.0130.0000.0000.0000.000
95B793LEU0-0.027-0.01918.257-0.015-0.0150.0000.0000.0000.000
96B794HIS0-0.043-0.01522.646-0.017-0.0170.0000.0000.0000.000
97B795SER00.012-0.00826.101-0.011-0.0110.0000.0000.0000.000
98B796CYS0-0.036-0.00424.275-0.011-0.0110.0000.0000.0000.000
99B797LEU00.0150.00525.500-0.010-0.0100.0000.0000.0000.000
100B798SER00.024-0.00527.164-0.008-0.0080.0000.0000.0000.000
101B799LEU0-0.003-0.00729.506-0.006-0.0060.0000.0000.0000.000
102B800ALA00.0140.00727.825-0.005-0.0050.0000.0000.0000.000
103B801LEU0-0.011-0.01429.954-0.006-0.0060.0000.0000.0000.000
104B802GLN0-0.043-0.02232.338-0.002-0.0020.0000.0000.0000.000
105B803ARG10.8340.92430.114-0.029-0.0290.0000.0000.0000.000
106B804LEU0-0.0150.00130.420-0.004-0.0040.0000.0000.0000.000
107B805GLY00.0130.01934.719-0.003-0.0030.0000.0000.0000.000
108B806TYR0-0.042-0.02333.010-0.001-0.0010.0000.0000.0000.000
109B807GLY00.0250.00637.3720.0010.0010.0000.0000.0000.000
110B808ASP-1-0.840-0.92438.5490.0160.0160.0000.0000.0000.000
111B809VAL00.0130.01533.9710.0030.0030.0000.0000.0000.000
112B810SER00.011-0.00534.0430.0030.0030.0000.0000.0000.000
113B811LYS10.8590.92934.846-0.012-0.0120.0000.0000.0000.000
114B812ARG10.8270.89036.101-0.029-0.0290.0000.0000.0000.000
115B813MET0-0.0170.00929.6340.0030.0030.0000.0000.0000.000
116B814TYR00.0540.00232.7020.0070.0070.0000.0000.0000.000
117B815GLN0-0.091-0.06533.8820.0030.0030.0000.0000.0000.000
118B816GLU-1-0.846-0.89132.4730.0440.0440.0000.0000.0000.000
119B817ILE0-0.073-0.01229.3120.0060.0060.0000.0000.0000.000
120B818PHE00.0110.00327.9430.0000.0000.0000.0000.0000.000
121B819VAL0-0.022-0.01828.6180.0080.0080.0000.0000.0000.000
122B820PRO0-0.044-0.02526.2600.0000.0000.0000.0000.0000.000
123B821ASP-1-0.810-0.90428.9800.1330.1330.0000.0000.0000.000
124B822SER0-0.117-0.07530.404-0.010-0.0100.0000.0000.0000.000
125B823ASP-1-0.883-0.91726.1330.1930.1930.0000.0000.0000.000
126B824ALA0-0.027-0.03224.910-0.003-0.0030.0000.0000.0000.000
127B825ASP-1-0.869-0.87820.9710.3010.3010.0000.0000.0000.000
128B826ILE0-0.061-0.02723.358-0.013-0.0130.0000.0000.0000.000
129B827THR00.0400.02119.7500.0090.0090.0000.0000.0000.000
130B828PRO00.0390.02322.536-0.018-0.0180.0000.0000.0000.000
131B829LEU00.0250.02619.511-0.014-0.0140.0000.0000.0000.000
132B830SER00.0160.00122.908-0.017-0.0170.0000.0000.0000.000
133B831PHE00.0340.02724.465-0.014-0.0140.0000.0000.0000.000
134B832ILE00.0320.03026.690-0.011-0.0110.0000.0000.0000.000
135B833ILE0-0.0050.01223.171-0.012-0.0120.0000.0000.0000.000
136B834SER0-0.018-0.02427.405-0.010-0.0100.0000.0000.0000.000
137B835TRP00.0500.01629.693-0.008-0.0080.0000.0000.0000.000
138B836THR0-0.027-0.03229.971-0.008-0.0080.0000.0000.0000.000
139B837ALA00.0380.01830.483-0.006-0.0060.0000.0000.0000.000
140B838LEU0-0.029-0.01232.505-0.004-0.0040.0000.0000.0000.000
141B839ASN0-0.044-0.04135.379-0.008-0.0080.0000.0000.0000.000
142B840THR0-0.024-0.01434.715-0.002-0.0020.0000.0000.0000.000
143B841PHE0-0.010-0.01733.250-0.004-0.0040.0000.0000.0000.000
144B842ALA00.0160.03238.158-0.001-0.0010.0000.0000.0000.000
145B843PRO0-0.045-0.00740.432-0.001-0.0010.0000.0000.0000.000
146B844ILE0-0.033-0.02039.447-0.003-0.0030.0000.0000.0000.000
147B845CYS0-0.039-0.03137.831-0.002-0.0020.0000.0000.0000.000
148B846THR0-0.036-0.01741.5170.0000.0000.0000.0000.0000.000
149B847SER0-0.0440.00244.268-0.001-0.0010.0000.0000.0000.000
150B848PRO00.013-0.01443.728-0.001-0.0010.0000.0000.0000.000
151B849LYS10.8650.94044.904-0.033-0.0330.0000.0000.0000.000
152B850GLU-1-0.883-0.94045.4620.0300.0300.0000.0000.0000.000
153B851ASN0-0.031-0.00938.9110.0040.0040.0000.0000.0000.000
154B852ASP-1-0.773-0.88639.6180.0400.0400.0000.0000.0000.000
155B853VAL00.0050.00033.7860.0020.0020.0000.0000.0000.000
156B854VAL0-0.019-0.00936.9000.0050.0050.0000.0000.0000.000
157B855GLU-1-0.844-0.90638.3350.0590.0590.0000.0000.0000.000
158B856LYS10.8740.91235.586-0.057-0.0570.0000.0000.0000.000
159B857MET00.0110.01830.4940.0090.0090.0000.0000.0000.000
160B858ALA00.0120.00034.3900.0040.0040.0000.0000.0000.000
161B859MET0-0.079-0.04036.5480.0040.0040.0000.0000.0000.000
162B860TYR00.0770.04826.4720.0060.0060.0000.0000.0000.000
163B861VAL00.0220.00631.6650.0060.0060.0000.0000.0000.000
164B862ARG10.9090.97033.130-0.082-0.0820.0000.0000.0000.000
165B863THR0-0.007-0.02131.854-0.001-0.0010.0000.0000.0000.000
166B864ALA00.0060.03329.2380.0070.0070.0000.0000.0000.000
167B865ILE00.0230.00730.4450.0050.0050.0000.0000.0000.000
168B866GLY0-0.0230.00132.631-0.001-0.0010.0000.0000.0000.000
169B867THR0-0.007-0.03529.2340.0030.0030.0000.0000.0000.000
170B868LEU00.0240.02425.8670.0060.0060.0000.0000.0000.000
171B869LYS10.9930.99429.551-0.074-0.0740.0000.0000.0000.000
172B870ILE0-0.047-0.01932.215-0.004-0.0040.0000.0000.0000.000
173B871GLN0-0.026-0.02026.1740.0110.0110.0000.0000.0000.000
174B872ASP-1-0.880-0.92730.3100.1010.1010.0000.0000.0000.000
175B873LEU00.0020.00731.168-0.004-0.0040.0000.0000.0000.000
176B874LYS10.7390.84631.386-0.111-0.1110.0000.0000.0000.000
177B875LEU0-0.0120.01727.840-0.002-0.0020.0000.0000.0000.000