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: 392GL

Calculation Name: 5BV0-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BV0

Chain ID: B

ChEMBL ID:

UniProt ID: G0SCM5

Base Structure: X-ray

Registration Date: 2023-09-20

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2093557.600604
FMO2-HF: Nuclear repulsion 2011540.614701
FMO2-HF: Total energy -82016.985903
FMO2-MP2: Total energy -82258.219033


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:524:GLU)


Summations of interaction energy for fragment #1(B:524:GLU)
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.
52.8255.297-0.024-1.201-1.2520.002
Interaction energy analysis for fragmet #1(B:524:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.953 / q_NPA : -0.981
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].
3B526LEU0-0.0040.0183.795-2.929-0.452-0.024-1.201-1.2520.002
4B527ASN0-0.053-0.0415.823-9.713-9.7130.0000.0000.0000.000
5B528HIS0-0.010-0.0147.782-1.558-1.5580.0000.0000.0000.000
6B529GLU-1-0.953-0.91010.05824.45924.4590.0000.0000.0000.000
7B530PRO00.020-0.02110.7931.2971.2970.0000.0000.0000.000
8B531ARG10.9670.96114.237-15.505-15.5050.0000.0000.0000.000
9B532ALA00.0610.02514.8660.0280.0280.0000.0000.0000.000
10B533GLY00.0520.02715.907-0.998-0.9980.0000.0000.0000.000
11B534ARG10.8940.92617.399-15.227-15.2270.0000.0000.0000.000
12B535GLN00.0750.03911.241-0.686-0.6860.0000.0000.0000.000
13B536VAL00.0590.03213.0951.1221.1220.0000.0000.0000.000
14B537PRO0-0.029-0.01715.422-0.056-0.0560.0000.0000.0000.000
15B538LEU0-0.0050.01311.164-0.397-0.3970.0000.0000.0000.000
16B539LEU00.0530.0329.0510.3710.3710.0000.0000.0000.000
17B540LEU0-0.0180.00512.6650.0210.0210.0000.0000.0000.000
18B541SER0-0.103-0.06214.635-0.494-0.4940.0000.0000.0000.000
19B542MET0-0.060-0.0257.7970.0600.0600.0000.0000.0000.000
20B543GLU-1-0.890-0.94212.43917.58817.5880.0000.0000.0000.000
21B544GLU-1-0.929-0.9558.32831.63731.6370.0000.0000.0000.000
22B545ASP-1-0.803-0.90412.32916.67516.6750.0000.0000.0000.000
23B546GLU-1-0.829-0.90113.65617.55317.5530.0000.0000.0000.000
24B547LEU00.0250.0207.861-0.263-0.2630.0000.0000.0000.000
25B548ALA00.000-0.00912.422-0.294-0.2940.0000.0000.0000.000
26B549LEU0-0.026-0.01714.626-0.757-0.7570.0000.0000.0000.000
27B550ASP-1-0.776-0.88213.87217.71817.7180.0000.0000.0000.000
28B551LYS10.7880.87810.698-24.179-24.1790.0000.0000.0000.000
29B552ALA00.0010.00215.257-0.655-0.6550.0000.0000.0000.000
30B553ILE0-0.022-0.00418.602-0.935-0.9350.0000.0000.0000.000
31B554GLU-1-0.855-0.91113.58320.36820.3680.0000.0000.0000.000
32B555SER0-0.065-0.03718.271-0.535-0.5350.0000.0000.0000.000
33B556GLY0-0.021-0.00320.052-0.493-0.4930.0000.0000.0000.000
34B557ASP-1-0.878-0.95022.96211.86911.8690.0000.0000.0000.000
35B558THR0-0.008-0.02824.2080.1450.1450.0000.0000.0000.000
36B559ASP-1-0.941-0.95726.60211.42811.4280.0000.0000.0000.000
37B560LEU0-0.036-0.01819.1710.2380.2380.0000.0000.0000.000
38B561ILE00.001-0.00221.9620.4160.4160.0000.0000.0000.000
39B562TYR00.0180.00123.157-0.014-0.0140.0000.0000.0000.000
40B563PHE0-0.032-0.00820.3410.0180.0180.0000.0000.0000.000
41B564VAL0-0.005-0.00118.5680.0580.0580.0000.0000.0000.000
42B565ILE00.0060.00621.5830.0060.0060.0000.0000.0000.000
43B566HIS0-0.014-0.00824.184-0.266-0.2660.0000.0000.0000.000
44B567GLN0-0.018-0.01320.6330.1500.1500.0000.0000.0000.000
45B568LEU00.0340.01018.829-0.151-0.1510.0000.0000.0000.000
46B569ARG10.9220.97422.943-10.024-10.0240.0000.0000.0000.000
47B570ARG10.8680.94626.509-10.646-10.6460.0000.0000.0000.000
48B571LYS10.7970.89317.934-16.899-16.8990.0000.0000.0000.000
49B572LEU0-0.012-0.00120.755-0.022-0.0220.0000.0000.0000.000
50B573PRO00.0130.00724.880-0.455-0.4550.0000.0000.0000.000
51B574LEU00.0560.02326.6100.3570.3570.0000.0000.0000.000
52B575ALA00.0780.04127.7330.1990.1990.0000.0000.0000.000
53B576SER0-0.036-0.00922.2060.3480.3480.0000.0000.0000.000
54B577PHE00.005-0.00323.2650.3830.3830.0000.0000.0000.000
55B578PHE00.014-0.02124.5200.1700.1700.0000.0000.0000.000
56B579ARG10.8740.93718.684-14.422-14.4220.0000.0000.0000.000
57B580VAL0-0.034-0.01319.2100.2610.2610.0000.0000.0000.000
58B581VAL0-0.019-0.02021.2960.2960.2960.0000.0000.0000.000
59B582SER0-0.043-0.01723.6710.0300.0300.0000.0000.0000.000
60B583SER0-0.037-0.00720.3770.0960.0960.0000.0000.0000.000
61B584ARG10.8110.88815.406-16.975-16.9750.0000.0000.0000.000
62B585PRO00.0480.01221.948-0.253-0.2530.0000.0000.0000.000
63B586THR00.0180.00223.341-0.406-0.4060.0000.0000.0000.000
64B587ALA00.0120.01422.561-0.263-0.2630.0000.0000.0000.000
65B588SER00.0530.02724.657-0.405-0.4050.0000.0000.0000.000
66B589ALA0-0.034-0.01627.429-0.398-0.3980.0000.0000.0000.000
67B590MET0-0.0210.00027.534-0.234-0.2340.0000.0000.0000.000
68B591VAL0-0.008-0.01527.207-0.274-0.2740.0000.0000.0000.000
69B592GLU-1-0.750-0.84729.9458.9758.9750.0000.0000.0000.000
70B593ALA0-0.052-0.01932.573-0.327-0.3270.0000.0000.0000.000
71B594LEU00.0200.00330.506-0.264-0.2640.0000.0000.0000.000
72B595ALA0-0.0190.00634.428-0.192-0.1920.0000.0000.0000.000
73B596ARG10.8240.90935.078-8.803-8.8030.0000.0000.0000.000
74B597ASN0-0.042-0.04537.969-0.176-0.1760.0000.0000.0000.000
75B598SER0-0.0370.00038.3200.2070.2070.0000.0000.0000.000
76B599ASP-1-0.858-0.89639.8356.9016.9010.0000.0000.0000.000
77B600GLY0-0.076-0.03841.647-0.033-0.0330.0000.0000.0000.000
78B601ASP-1-0.866-0.93741.6767.2097.2090.0000.0000.0000.000
79B602GLY0-0.024-0.02943.421-0.024-0.0240.0000.0000.0000.000
80B603ASN0-0.089-0.03344.462-0.017-0.0170.0000.0000.0000.000
81B604GLU-1-0.788-0.87741.2317.7167.7160.0000.0000.0000.000
82B605ASP-1-0.871-0.93636.3838.4598.4590.0000.0000.0000.000
83B606THR00.013-0.02638.2630.1510.1510.0000.0000.0000.000
84B607ALA0-0.034-0.01539.3020.0230.0230.0000.0000.0000.000
85B608LEU00.0100.02231.9750.1510.1510.0000.0000.0000.000
86B609LEU0-0.018-0.00934.7850.1860.1860.0000.0000.0000.000
87B610LYS10.8060.89936.104-7.131-7.1310.0000.0000.0000.000
88B611ASP-1-0.918-0.95234.1498.5598.5590.0000.0000.0000.000
89B612LEU0-0.045-0.02029.5430.1670.1670.0000.0000.0000.000
90B613TYR0-0.044-0.05932.1000.0520.0520.0000.0000.0000.000
91B614TYR0-0.050-0.00934.666-0.035-0.0350.0000.0000.0000.000
92B615GLN0-0.019-0.02930.4980.2640.2640.0000.0000.0000.000
93B616ASP-1-0.839-0.91928.62810.74310.7430.0000.0000.0000.000
94B617ASP-1-0.849-0.89731.2978.3868.3860.0000.0000.0000.000
95B618ARG10.7870.89330.918-9.568-9.5680.0000.0000.0000.000
96B619ARG10.8060.86235.332-8.242-8.2420.0000.0000.0000.000
97B620LEU00.0080.00838.761-0.180-0.1800.0000.0000.0000.000
98B621ASP-1-0.816-0.88535.7868.3898.3890.0000.0000.0000.000
99B622GLY00.0430.01138.542-0.065-0.0650.0000.0000.0000.000
100B623ALA0-0.025-0.01439.770-0.169-0.1690.0000.0000.0000.000
101B624SER0-0.031-0.03841.317-0.218-0.2180.0000.0000.0000.000
102B625VAL0-0.0270.00939.712-0.118-0.1180.0000.0000.0000.000
103B626PHE00.0180.00542.906-0.133-0.1330.0000.0000.0000.000
104B627ILE00.008-0.00945.941-0.175-0.1750.0000.0000.0000.000
105B628ARG10.8170.87340.484-7.621-7.6210.0000.0000.0000.000
106B629GLU-1-0.734-0.84945.4926.7086.7080.0000.0000.0000.000
107B630ALA0-0.045-0.02148.377-0.143-0.1430.0000.0000.0000.000
108B631LEU0-0.048-0.02048.951-0.145-0.1450.0000.0000.0000.000
109B632GLN0-0.029-0.00749.055-0.007-0.0070.0000.0000.0000.000
110B633GLN0-0.103-0.04551.568-0.109-0.1090.0000.0000.0000.000
111B634PRO00.0160.01954.963-0.043-0.0430.0000.0000.0000.000
112B635GLU-1-0.906-0.94758.3275.0555.0550.0000.0000.0000.000
113B636THR00.037-0.00258.4210.1310.1310.0000.0000.0000.000
114B637ARG10.8460.91658.004-5.304-5.3040.0000.0000.0000.000
115B638THR00.0450.02155.5320.0330.0330.0000.0000.0000.000
116B639ALA00.0100.00554.2140.1230.1230.0000.0000.0000.000
117B640SER0-0.021-0.03853.9760.0910.0910.0000.0000.0000.000
118B641ASP-1-0.824-0.89254.1735.6235.6230.0000.0000.0000.000
119B642LYS10.8300.91649.002-6.254-6.2540.0000.0000.0000.000
120B643LEU00.0220.00649.7100.1330.1330.0000.0000.0000.000
121B644ASP-1-0.805-0.88550.9785.7625.7620.0000.0000.0000.000
122B645LEU0-0.042-0.01347.4530.0680.0680.0000.0000.0000.000
123B646ALA00.0250.01146.1890.1260.1260.0000.0000.0000.000
124B647ALA0-0.023-0.01846.3980.0910.0910.0000.0000.0000.000
125B648ASN0-0.017-0.02047.891-0.013-0.0130.0000.0000.0000.000
126B649LEU0-0.0160.00641.2400.0620.0620.0000.0000.0000.000
127B650LEU0-0.0060.00343.0830.0990.0990.0000.0000.0000.000
128B651GLN0-0.117-0.04745.114-0.075-0.0750.0000.0000.0000.000
129B652GLY00.0610.01444.194-0.055-0.0550.0000.0000.0000.000
130B653ASN0-0.070-0.02739.6470.1020.1020.0000.0000.0000.000
131B654GLN00.1340.07243.572-0.097-0.0970.0000.0000.0000.000
132B655LYS10.8950.94341.503-7.308-7.3080.0000.0000.0000.000
133B656GLU-1-0.895-0.95040.5317.4387.4380.0000.0000.0000.000
134B657HIS0-0.0010.00940.6500.1200.1200.0000.0000.0000.000
135B658VAL0-0.014-0.00845.626-0.119-0.1190.0000.0000.0000.000
136B659PHE00.0070.00547.123-0.156-0.1560.0000.0000.0000.000
137B660GLU-1-0.787-0.90244.1626.7276.7270.0000.0000.0000.000
138B661LEU0-0.036-0.01148.087-0.107-0.1070.0000.0000.0000.000
139B662GLY0-0.005-0.00450.370-0.121-0.1210.0000.0000.0000.000
140B663ALA00.0110.00750.742-0.118-0.1180.0000.0000.0000.000
141B664LEU0-0.005-0.00548.237-0.102-0.1020.0000.0000.0000.000
142B665LYS10.8660.92452.649-5.967-5.9670.0000.0000.0000.000
143B666GLU-1-0.897-0.95255.7745.3175.3170.0000.0000.0000.000
144B667ALA0-0.0030.00154.751-0.109-0.1090.0000.0000.0000.000
145B668LYS10.8440.89655.489-5.647-5.6470.0000.0000.0000.000
146B669MET0-0.075-0.03158.117-0.078-0.0780.0000.0000.0000.000
147B670LEU0-0.003-0.00659.671-0.103-0.1030.0000.0000.0000.000
148B671LEU00.0380.02656.905-0.081-0.0810.0000.0000.0000.000
149B672ARG10.9780.99461.440-5.001-5.0010.0000.0000.0000.000
150B673MET0-0.059-0.03364.162-0.071-0.0710.0000.0000.0000.000
151B674GLN0-0.007-0.02162.059-0.041-0.0410.0000.0000.0000.000
152B675GLU-1-0.808-0.90464.4184.9184.9180.0000.0000.0000.000
153B676THR0-0.059-0.03367.013-0.102-0.1020.0000.0000.0000.000
154B677PHE0-0.022-0.02467.966-0.077-0.0770.0000.0000.0000.000
155B678GLU-1-0.724-0.84666.5374.7294.7290.0000.0000.0000.000
156B679ARG10.8050.91470.546-4.478-4.4780.0000.0000.0000.000
157B680ASP-1-0.863-0.91572.9674.2364.2360.0000.0000.0000.000
158B681LEU0-0.065-0.04072.960-0.057-0.0570.0000.0000.0000.000
159B682THR0-0.054-0.00574.124-0.049-0.0490.0000.0000.0000.000
160B683ASP-1-0.784-0.88671.6174.4434.4430.0000.0000.0000.000
161B684SER00.0120.00466.7390.0470.0470.0000.0000.0000.000
162B685PHE0-0.090-0.08266.524-0.044-0.0440.0000.0000.0000.000
163B686VAL00.006-0.00261.4780.0600.0600.0000.0000.0000.000
164B687GLY00.0120.01959.4160.0240.0240.0000.0000.0000.000
165B688LEU0-0.074-0.01259.3530.0660.0660.0000.0000.0000.000
166B689SER00.0660.03058.904-0.006-0.0060.0000.0000.0000.000
167B690VAL00.1070.04859.845-0.103-0.1030.0000.0000.0000.000
168B691ASN0-0.003-0.02061.549-0.091-0.0910.0000.0000.0000.000
169B692GLN00.0490.02560.266-0.071-0.0710.0000.0000.0000.000
170B693THR00.0290.01863.798-0.078-0.0780.0000.0000.0000.000
171B694MET0-0.057-0.02666.213-0.070-0.0700.0000.0000.0000.000
172B695PHE00.0230.01667.428-0.084-0.0840.0000.0000.0000.000
173B696LYS10.8210.91168.548-4.663-4.6630.0000.0000.0000.000
174B697LEU0-0.006-0.00369.730-0.078-0.0780.0000.0000.0000.000
175B698ILE0-0.064-0.03671.069-0.076-0.0760.0000.0000.0000.000
176B699LYS10.9260.97371.925-4.469-4.4690.0000.0000.0000.000
177B700LEU0-0.028-0.00573.418-0.046-0.0460.0000.0000.0000.000
178B701GLY00.0020.01076.419-0.048-0.0480.0000.0000.0000.000
179B702TYR00.0300.02175.100-0.059-0.0590.0000.0000.0000.000
180B703HIS00.037-0.00575.1210.1060.1060.0000.0000.0000.000
181B704GLY0-0.019-0.00875.6490.0270.0270.0000.0000.0000.000
182B705ARG10.8840.92872.560-4.204-4.2040.0000.0000.0000.000
183B706ALA00.0320.02370.9340.0640.0640.0000.0000.0000.000
184B707LYS10.9010.94970.648-4.295-4.2950.0000.0000.0000.000
185B708LYS10.9030.94469.579-4.498-4.4980.0000.0000.0000.000
186B709ILE00.0610.03265.5360.0480.0480.0000.0000.0000.000
187B710GLN00.0650.03566.418-0.015-0.0150.0000.0000.0000.000
188B711SER0-0.096-0.04966.7130.0280.0280.0000.0000.0000.000
189B712GLU-1-0.902-0.93364.9514.7284.7280.0000.0000.0000.000
190B713PHE0-0.010-0.02260.6650.0260.0260.0000.0000.0000.000
191B714LYS10.9140.97061.994-4.881-4.8810.0000.0000.0000.000
192B715VAL00.0140.01762.9870.0390.0390.0000.0000.0000.000
193B716PRO00.0340.00961.184-0.087-0.0870.0000.0000.0000.000
194B717GLU-1-0.888-0.94764.2634.4724.4720.0000.0000.0000.000
195B718ARG10.9620.97464.332-4.810-4.8100.0000.0000.0000.000
196B719VAL00.0310.01761.937-0.020-0.0200.0000.0000.0000.000
197B720ALA00.0350.01765.275-0.037-0.0370.0000.0000.0000.000
198B721TRP0-0.042-0.01968.169-0.036-0.0360.0000.0000.0000.000
199B722TRP00.0350.00266.790-0.056-0.0560.0000.0000.0000.000
200B723ILE0-0.027-0.00164.636-0.020-0.0200.0000.0000.0000.000
201B724ARG10.9150.94868.644-4.402-4.4020.0000.0000.0000.000
202B725LEU0-0.0050.00671.959-0.052-0.0520.0000.0000.0000.000
203B726GLN0-0.012-0.01766.158-0.019-0.0190.0000.0000.0000.000
204B727ALA0-0.025-0.00671.387-0.013-0.0130.0000.0000.0000.000
205B728LEU0-0.037-0.02172.785-0.037-0.0370.0000.0000.0000.000
206B729VAL0-0.0280.00674.142-0.047-0.0470.0000.0000.0000.000
207B730ALA0-0.0150.00473.231-0.029-0.0290.0000.0000.0000.000