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: LZ5R9

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2099822.680819
FMO2-HF: Nuclear repulsion 2017804.964204
FMO2-HF: Total energy -82017.716615
FMO2-MP2: Total energy -82258.978619


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.
53.25555.4910.001-0.861-1.3750.005
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 : -0.930 / q_NPA : -0.973
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].
3B526LEU0-0.002-0.0043.605-5.512-3.2760.001-0.861-1.3750.005
4B527ASN0-0.030-0.0216.019-9.845-9.8450.0000.0000.0000.000
5B528HIS0-0.032-0.0287.717-0.632-0.6320.0000.0000.0000.000
6B529GLU-1-0.927-0.91410.48523.34723.3470.0000.0000.0000.000
7B530PRO0-0.010-0.01111.0401.4031.4030.0000.0000.0000.000
8B531ARG10.9940.96614.515-14.774-14.7740.0000.0000.0000.000
9B532ALA00.0860.04215.7390.2410.2410.0000.0000.0000.000
10B533GLY00.0110.00116.709-0.674-0.6740.0000.0000.0000.000
11B534ARG10.7700.86417.928-14.668-14.6680.0000.0000.0000.000
12B535GLN00.0850.04311.272-0.423-0.4230.0000.0000.0000.000
13B536VAL00.0220.03013.7850.9570.9570.0000.0000.0000.000
14B537PRO0-0.021-0.01815.5810.0240.0240.0000.0000.0000.000
15B538LEU0-0.0030.01911.180-0.385-0.3850.0000.0000.0000.000
16B539LEU00.0290.0219.2020.3200.3200.0000.0000.0000.000
17B540LEU00.0050.00012.6690.0130.0130.0000.0000.0000.000
18B541SER0-0.105-0.06014.817-0.500-0.5000.0000.0000.0000.000
19B542MET0-0.046-0.0187.5090.1370.1370.0000.0000.0000.000
20B543GLU-1-0.891-0.94112.58617.84317.8430.0000.0000.0000.000
21B544GLU-1-0.907-0.9358.06932.69832.6980.0000.0000.0000.000
22B545ASP-1-0.827-0.94012.21616.66516.6650.0000.0000.0000.000
23B546GLU-1-0.812-0.87513.89517.43717.4370.0000.0000.0000.000
24B547LEU00.0510.0328.252-0.588-0.5880.0000.0000.0000.000
25B548ALA00.0160.00112.650-0.250-0.2500.0000.0000.0000.000
26B549LEU0-0.032-0.01414.702-0.924-0.9240.0000.0000.0000.000
27B550ASP-1-0.795-0.89213.97017.93517.9350.0000.0000.0000.000
28B551LYS10.7990.87510.754-24.439-24.4390.0000.0000.0000.000
29B552ALA0-0.0040.00615.363-0.603-0.6030.0000.0000.0000.000
30B553ILE0-0.019-0.01018.911-0.807-0.8070.0000.0000.0000.000
31B554GLU-1-0.847-0.90713.62920.54320.5430.0000.0000.0000.000
32B555SER0-0.058-0.03318.350-0.610-0.6100.0000.0000.0000.000
33B556GLY0-0.010-0.00120.383-0.556-0.5560.0000.0000.0000.000
34B557ASP-1-0.857-0.94323.00712.08712.0870.0000.0000.0000.000
35B558THR00.017-0.01024.2570.1400.1400.0000.0000.0000.000
36B559ASP-1-0.872-0.91526.16811.92911.9290.0000.0000.0000.000
37B560LEU0-0.033-0.00519.1470.1800.1800.0000.0000.0000.000
38B561ILE0-0.001-0.00522.1340.3930.3930.0000.0000.0000.000
39B562TYR0-0.002-0.01123.302-0.022-0.0220.0000.0000.0000.000
40B563PHE0-0.024-0.01720.1980.0030.0030.0000.0000.0000.000
41B564VAL00.0010.00118.7490.0550.0550.0000.0000.0000.000
42B565ILE0-0.0010.00821.628-0.073-0.0730.0000.0000.0000.000
43B566HIS00.0010.00524.277-0.290-0.2900.0000.0000.0000.000
44B567GLN0-0.007-0.00120.8170.1250.1250.0000.0000.0000.000
45B568LEU00.0290.00719.134-0.136-0.1360.0000.0000.0000.000
46B569ARG10.8310.91923.254-9.932-9.9320.0000.0000.0000.000
47B570ARG10.8490.92426.237-10.943-10.9430.0000.0000.0000.000
48B571LYS10.8070.89817.897-17.216-17.2160.0000.0000.0000.000
49B572LEU0-0.0050.00320.7490.0420.0420.0000.0000.0000.000
50B573PRO0-0.003-0.00824.889-0.452-0.4520.0000.0000.0000.000
51B574LEU00.0250.01226.7370.3810.3810.0000.0000.0000.000
52B575ALA00.0770.05128.0220.1860.1860.0000.0000.0000.000
53B576SER0-0.048-0.02022.0020.3620.3620.0000.0000.0000.000
54B577PHE00.0260.00723.3040.3590.3590.0000.0000.0000.000
55B578PHE00.003-0.01324.5890.2180.2180.0000.0000.0000.000
56B579ARG10.8480.91418.707-14.654-14.6540.0000.0000.0000.000
57B580VAL0-0.030-0.00119.4450.3480.3480.0000.0000.0000.000
58B581VAL0-0.006-0.01421.6170.1960.1960.0000.0000.0000.000
59B582SER0-0.049-0.03524.0660.0620.0620.0000.0000.0000.000
60B583SER0-0.071-0.03020.5770.1640.1640.0000.0000.0000.000
61B584ARG10.8200.89215.278-16.884-16.8840.0000.0000.0000.000
62B585PRO00.0510.01621.780-0.194-0.1940.0000.0000.0000.000
63B586THR00.007-0.00123.560-0.459-0.4590.0000.0000.0000.000
64B587ALA00.0150.01223.035-0.297-0.2970.0000.0000.0000.000
65B588SER00.0160.00725.119-0.354-0.3540.0000.0000.0000.000
66B589ALA0-0.015-0.00427.900-0.378-0.3780.0000.0000.0000.000
67B590MET0-0.0130.00427.736-0.221-0.2210.0000.0000.0000.000
68B591VAL00.001-0.00827.485-0.294-0.2940.0000.0000.0000.000
69B592GLU-1-0.730-0.84330.2019.1039.1030.0000.0000.0000.000
70B593ALA0-0.051-0.02232.770-0.323-0.3230.0000.0000.0000.000
71B594LEU00.006-0.00130.610-0.251-0.2510.0000.0000.0000.000
72B595ALA0-0.021-0.00534.299-0.237-0.2370.0000.0000.0000.000
73B596ARG10.8470.92934.696-8.885-8.8850.0000.0000.0000.000
74B597ASN0-0.019-0.03038.023-0.167-0.1670.0000.0000.0000.000
75B598SER0-0.0170.00238.4740.0980.0980.0000.0000.0000.000
76B599ASP-1-0.877-0.91439.7446.9286.9280.0000.0000.0000.000
77B600GLY0-0.089-0.03141.547-0.023-0.0230.0000.0000.0000.000
78B601ASP-1-0.882-0.94541.7547.2167.2160.0000.0000.0000.000
79B602GLY0-0.023-0.01143.530-0.036-0.0360.0000.0000.0000.000
80B603ASN0-0.084-0.05144.362-0.063-0.0630.0000.0000.0000.000
81B604GLU-1-0.772-0.86140.7027.7717.7710.0000.0000.0000.000
82B605ASP-1-0.790-0.88735.9088.6228.6220.0000.0000.0000.000
83B606THR00.002-0.02838.1750.1320.1320.0000.0000.0000.000
84B607ALA0-0.042-0.01439.145-0.018-0.0180.0000.0000.0000.000
85B608LEU00.0010.00731.7860.1050.1050.0000.0000.0000.000
86B609LEU0-0.023-0.00334.7540.1910.1910.0000.0000.0000.000
87B610LYS10.8130.90236.099-7.136-7.1360.0000.0000.0000.000
88B611ASP-1-0.861-0.93634.4148.9148.9140.0000.0000.0000.000
89B612LEU0-0.0050.00429.7580.1590.1590.0000.0000.0000.000
90B613TYR0-0.058-0.07032.537-0.015-0.0150.0000.0000.0000.000
91B614TYR0-0.053-0.01934.882-0.021-0.0210.0000.0000.0000.000
92B615GLN0-0.060-0.05030.4900.2940.2940.0000.0000.0000.000
93B616ASP-1-0.829-0.90228.64210.82310.8230.0000.0000.0000.000
94B617ASP-1-0.835-0.88131.2448.4228.4220.0000.0000.0000.000
95B618ARG10.8000.91430.786-9.726-9.7260.0000.0000.0000.000
96B619ARG10.7830.84635.381-8.286-8.2860.0000.0000.0000.000
97B620LEU00.0040.01138.570-0.196-0.1960.0000.0000.0000.000
98B621ASP-1-0.815-0.87835.4788.4388.4380.0000.0000.0000.000
99B622GLY00.0570.01138.520-0.104-0.1040.0000.0000.0000.000
100B623ALA0-0.037-0.02239.951-0.169-0.1690.0000.0000.0000.000
101B624SER0-0.020-0.03841.100-0.223-0.2230.0000.0000.0000.000
102B625VAL0-0.050-0.00939.986-0.079-0.0790.0000.0000.0000.000
103B626PHE00.0310.01642.968-0.142-0.1420.0000.0000.0000.000
104B627ILE00.008-0.00845.678-0.184-0.1840.0000.0000.0000.000
105B628ARG10.8080.87240.644-7.630-7.6300.0000.0000.0000.000
106B629GLU-1-0.764-0.86046.0826.6776.6770.0000.0000.0000.000
107B630ALA0-0.023-0.01548.581-0.148-0.1480.0000.0000.0000.000
108B631LEU0-0.056-0.02148.736-0.142-0.1420.0000.0000.0000.000
109B632GLN0-0.028-0.01049.0690.0190.0190.0000.0000.0000.000
110B633GLN0-0.077-0.04051.618-0.071-0.0710.0000.0000.0000.000
111B634PRO00.0080.01154.928-0.049-0.0490.0000.0000.0000.000
112B635GLU-1-0.900-0.94758.4635.0785.0780.0000.0000.0000.000
113B636THR00.030-0.01458.6790.1310.1310.0000.0000.0000.000
114B637ARG10.8130.89657.871-5.333-5.3330.0000.0000.0000.000
115B638THR00.019-0.00155.8630.0530.0530.0000.0000.0000.000
116B639ALA00.0260.00754.5100.1240.1240.0000.0000.0000.000
117B640SER0-0.034-0.03754.1160.0930.0930.0000.0000.0000.000
118B641ASP-1-0.801-0.86453.8595.6835.6830.0000.0000.0000.000
119B642LYS10.8400.92849.498-6.217-6.2170.0000.0000.0000.000
120B643LEU00.0240.01149.8290.1300.1300.0000.0000.0000.000
121B644ASP-1-0.798-0.87251.0455.7855.7850.0000.0000.0000.000
122B645LEU0-0.033-0.01647.7450.0840.0840.0000.0000.0000.000
123B646ALA00.0170.00846.1620.1440.1440.0000.0000.0000.000
124B647ALA0-0.010-0.01046.2590.0900.0900.0000.0000.0000.000
125B648ASN0-0.015-0.01847.759-0.013-0.0130.0000.0000.0000.000
126B649LEU0-0.0030.01541.2380.0760.0760.0000.0000.0000.000
127B650LEU00.0120.01442.7950.1310.1310.0000.0000.0000.000
128B651GLN0-0.082-0.04644.891-0.046-0.0460.0000.0000.0000.000
129B652GLY00.010-0.00644.055-0.071-0.0710.0000.0000.0000.000
130B653ASN00.0360.03039.4350.1290.1290.0000.0000.0000.000
131B654GLN00.0150.03243.209-0.126-0.1260.0000.0000.0000.000
132B655LYS10.8850.91940.775-7.448-7.4480.0000.0000.0000.000
133B656GLU-1-0.893-0.94340.4767.4757.4750.0000.0000.0000.000
134B657HIS0-0.025-0.02640.6980.0150.0150.0000.0000.0000.000
135B658VAL0-0.031-0.02045.591-0.120-0.1200.0000.0000.0000.000
136B659PHE00.0010.00847.281-0.159-0.1590.0000.0000.0000.000
137B660GLU-1-0.770-0.88744.1746.7516.7510.0000.0000.0000.000
138B661LEU0-0.039-0.01647.805-0.109-0.1090.0000.0000.0000.000
139B662GLY00.0080.00950.396-0.120-0.1200.0000.0000.0000.000
140B663ALA00.0290.01151.005-0.114-0.1140.0000.0000.0000.000
141B664LEU0-0.013-0.00748.065-0.091-0.0910.0000.0000.0000.000
142B665LYS10.8590.91752.496-6.002-6.0020.0000.0000.0000.000
143B666GLU-1-0.897-0.96455.8475.3395.3390.0000.0000.0000.000
144B667ALA0-0.0040.00654.835-0.107-0.1070.0000.0000.0000.000
145B668LYS10.8630.90555.743-5.667-5.6670.0000.0000.0000.000
146B669MET0-0.088-0.03458.434-0.086-0.0860.0000.0000.0000.000
147B670LEU0-0.004-0.00859.562-0.102-0.1020.0000.0000.0000.000
148B671LEU00.0320.02457.024-0.089-0.0890.0000.0000.0000.000
149B672ARG10.9940.99961.566-5.014-5.0140.0000.0000.0000.000
150B673MET0-0.078-0.03364.229-0.079-0.0790.0000.0000.0000.000
151B674GLN0-0.006-0.01761.874-0.040-0.0400.0000.0000.0000.000
152B675GLU-1-0.792-0.89364.6604.9044.9040.0000.0000.0000.000
153B676THR0-0.071-0.02666.989-0.103-0.1030.0000.0000.0000.000
154B677PHE0-0.005-0.01867.984-0.084-0.0840.0000.0000.0000.000
155B678GLU-1-0.751-0.86266.4844.7484.7480.0000.0000.0000.000
156B679ARG10.8050.89670.702-4.500-4.5000.0000.0000.0000.000
157B680ASP-1-0.838-0.89272.9034.2544.2540.0000.0000.0000.000
158B681LEU0-0.080-0.04472.992-0.066-0.0660.0000.0000.0000.000
159B682THR0-0.059-0.01274.367-0.052-0.0520.0000.0000.0000.000
160B683ASP-1-0.782-0.88671.4684.4804.4800.0000.0000.0000.000
161B684SER0-0.0010.00166.9390.0420.0420.0000.0000.0000.000
162B685PHE0-0.081-0.07566.410-0.036-0.0360.0000.0000.0000.000
163B686VAL00.007-0.00661.2820.0600.0600.0000.0000.0000.000
164B687GLY00.0190.02059.2080.0300.0300.0000.0000.0000.000
165B688LEU0-0.073-0.00959.1920.0600.0600.0000.0000.0000.000
166B689SER00.0610.00758.8000.0090.0090.0000.0000.0000.000
167B690VAL00.0780.03660.028-0.104-0.1040.0000.0000.0000.000
168B691ASN00.011-0.00861.361-0.088-0.0880.0000.0000.0000.000
169B692GLN00.0810.06060.671-0.045-0.0450.0000.0000.0000.000
170B693THR00.0340.01763.732-0.078-0.0780.0000.0000.0000.000
171B694MET0-0.066-0.03266.222-0.070-0.0700.0000.0000.0000.000
172B695PHE0-0.004-0.00567.329-0.080-0.0800.0000.0000.0000.000
173B696LYS10.8110.89668.499-4.670-4.6700.0000.0000.0000.000
174B697LEU0-0.004-0.00169.766-0.077-0.0770.0000.0000.0000.000
175B698ILE0-0.058-0.03071.048-0.074-0.0740.0000.0000.0000.000
176B699LYS10.9220.97071.730-4.486-4.4860.0000.0000.0000.000
177B700LEU0-0.0220.00073.333-0.041-0.0410.0000.0000.0000.000
178B701GLY00.0180.02176.427-0.050-0.0500.0000.0000.0000.000
179B702TYR00.0330.02374.863-0.050-0.0500.0000.0000.0000.000
180B703HIS00.028-0.01375.0920.1030.1030.0000.0000.0000.000
181B704GLY0-0.0010.00475.1280.0340.0340.0000.0000.0000.000
182B705ARG10.8870.93372.355-4.218-4.2180.0000.0000.0000.000
183B706ALA00.0380.03070.6820.0680.0680.0000.0000.0000.000
184B707LYS10.8970.93970.338-4.314-4.3140.0000.0000.0000.000
185B708LYS10.8340.91569.494-4.509-4.5090.0000.0000.0000.000
186B709ILE00.0610.03965.6140.0560.0560.0000.0000.0000.000
187B710GLN00.0260.00466.347-0.012-0.0120.0000.0000.0000.000
188B711SER0-0.088-0.05466.8750.0280.0280.0000.0000.0000.000
189B712GLU-1-0.801-0.89764.9294.6914.6910.0000.0000.0000.000
190B713PHE00.003-0.00360.4780.0280.0280.0000.0000.0000.000
191B714LYS10.8580.93562.082-4.878-4.8780.0000.0000.0000.000
192B715VAL00.0190.02363.0960.0230.0230.0000.0000.0000.000
193B716PRO00.0580.01861.319-0.100-0.1000.0000.0000.0000.000
194B717GLU-1-0.899-0.94864.5514.4754.4750.0000.0000.0000.000
195B718ARG10.9780.97864.311-4.805-4.8050.0000.0000.0000.000
196B719VAL00.0180.01262.106-0.022-0.0220.0000.0000.0000.000
197B720ALA00.0340.00865.477-0.029-0.0290.0000.0000.0000.000
198B721TRP0-0.0370.00468.233-0.056-0.0560.0000.0000.0000.000
199B722TRP00.0330.00466.699-0.053-0.0530.0000.0000.0000.000
200B723ILE00.0050.01464.570-0.035-0.0350.0000.0000.0000.000
201B724ARG10.8870.94368.592-4.418-4.4180.0000.0000.0000.000
202B725LEU00.0150.01172.216-0.052-0.0520.0000.0000.0000.000
203B726GLN0-0.016-0.02366.234-0.013-0.0130.0000.0000.0000.000
204B727ALA0-0.021-0.00471.412-0.007-0.0070.0000.0000.0000.000
205B728LEU0-0.035-0.02772.813-0.042-0.0420.0000.0000.0000.000
206B729VAL0-0.0450.00373.989-0.056-0.0560.0000.0000.0000.000
207B730ALA0-0.013-0.00173.847-0.015-0.0150.0000.0000.0000.000