FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: LQL59

Calculation Name: 3MVB-O-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3MVB

Chain ID: O

ChEMBL ID:

UniProt ID: Q99551

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 628
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4644158.821361
FMO2-HF: Nuclear repulsion 4514837.267042
FMO2-HF: Total energy -129321.554319
FMO2-MP2: Total energy -129697.202179


3D Structure Molmil
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(O:73:GLU)


Summations of interaction energy for fragment #1(O:73: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.
-9.847-5.9960.437-1.764-2.5220.012
Interaction energy analysis for fragmet #1(O:73:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.153 / q_NPA : 0.036
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].
4O74ASP-1-0.878-0.7844.362-2.429-2.041-0.001-0.123-0.2640.000
5O75LEU00.170-0.0752.543-3.395-1.3320.234-0.956-1.3410.008
6O75LEU0-0.1210.0923.0860.0230.8850.204-0.565-0.5000.004
7O76LEU00.076-0.1194.243-1.928-1.7050.002-0.060-0.1640.000
8O76LEU0-0.0560.1005.915-0.043-0.0430.0000.0000.0000.000
9O77LYS00.072-0.0896.562-0.297-0.2970.0000.0000.0000.000
10O77LYS10.8231.0136.6821.2521.2520.0000.0000.0000.000
11O78ASN00.109-0.0407.382-0.236-0.2360.0000.0000.0000.000
12O78ASN0-0.0690.0766.2890.0420.0420.0000.0000.0000.000
13O79LEU00.096-0.0758.550-0.326-0.3260.0000.0000.0000.000
14O79LEU0-0.0960.0738.271-0.001-0.0010.0000.0000.0000.000
15O80LEU00.161-0.07810.593-0.171-0.1710.0000.0000.0000.000
16O80LEU0-0.0740.11211.8100.0130.0130.0000.0000.0000.000
17O81THR0-0.036-0.11412.314-0.057-0.0570.0000.0000.0000.000
18O81THR0-0.0830.04312.252-0.074-0.0740.0000.0000.0000.000
19O82MET0-0.016-0.12113.232-0.117-0.1170.0000.0000.0000.000
20O82MET0-0.1450.06210.3490.0050.0050.0000.0000.0000.000
21O83GLY00.002-0.08614.811-0.065-0.0650.0000.0000.0000.000
22O84VAL00.0590.01413.868-0.066-0.0660.0000.0000.0000.000
23O84VAL0-0.1520.06712.6650.0260.0260.0000.0000.0000.000
24O85ASP00.176-0.09015.2550.0170.0170.0000.0000.0000.000
25O85ASP-1-0.997-0.83218.0520.6570.6570.0000.0000.0000.000
26O86ILE00.101-0.10812.499-0.014-0.0140.0000.0000.0000.000
27O86ILE0-0.0950.09310.2170.0770.0770.0000.0000.0000.000
28O87ASP00.139-0.11013.4950.1590.1590.0000.0000.0000.000
29O87ASP-1-0.970-0.80515.0890.9190.9190.0000.0000.0000.000
30O88MET00.071-0.12715.7640.0230.0230.0000.0000.0000.000
31O88MET0-0.1080.10118.462-0.022-0.0220.0000.0000.0000.000
32O89ALA00.106-0.11114.054-0.104-0.1040.0000.0000.0000.000
33O89ALA0-0.0970.09413.4200.0290.0290.0000.0000.0000.000
34O90ARG00.062-0.12313.0330.0370.0370.0000.0000.0000.000
35O90ARG10.8811.0837.955-2.730-2.7300.0000.0000.0000.000
36O91LYS00.082-0.08313.750-0.008-0.0080.0000.0000.0000.000
37O91LYS10.8551.06718.507-0.544-0.5440.0000.0000.0000.000
38O92ARG00.014-0.08017.329-0.060-0.0600.0000.0000.0000.000
39O92ARG10.7691.01117.202-0.635-0.6350.0000.0000.0000.000
40O93GLN00.036-0.09315.234-0.095-0.0950.0000.0000.0000.000
41O93GLN0-0.0840.08314.6400.0470.0470.0000.0000.0000.000
42O94PRO00.120-0.07012.7500.2200.2200.0000.0000.0000.000
43O95GLY0-0.002-0.01411.1520.2510.2510.0000.0000.0000.000
44O96VAL00.071-0.00110.2450.1040.1040.0000.0000.0000.000
45O96VAL0-0.0930.1019.424-0.063-0.0630.0000.0000.0000.000
46O97PHE00.133-0.0627.0830.2100.2100.0000.0000.0000.000
47O97PHE0-0.1410.0397.368-0.062-0.0620.0000.0000.0000.000
48O98HIS00.006-0.0706.0281.5051.5050.0000.0000.0000.000
49O98HIS0-0.1120.0749.3110.1840.1840.0000.0000.0000.000
50O99ARG00.139-0.1246.302-0.742-0.7420.0000.0000.0000.000
51O99ARG10.7661.0227.080-1.048-1.0480.0000.0000.0000.000
52O100MET00.117-0.0444.1711.3121.458-0.002-0.014-0.1300.000
53O100MET0-0.1050.0825.949-0.099-0.0990.0000.0000.0000.000
54O101ILE00.100-0.0884.043-0.827-0.6580.000-0.046-0.1230.000
55O101ILE0-0.0480.1265.9900.0420.0420.0000.0000.0000.000
56O102THR0-0.023-0.1336.0940.3030.3030.0000.0000.0000.000
57O102THR0-0.0140.0665.6400.3530.3530.0000.0000.0000.000
58O103ASN00.085-0.0347.378-0.234-0.2340.0000.0000.0000.000
59O103ASN0-0.1250.04910.594-0.061-0.0610.0000.0000.0000.000
60O104GLU00.135-0.0968.677-0.172-0.1720.0000.0000.0000.000
61O104GLU-1-0.842-0.7876.9121.0221.0220.0000.0000.0000.000
62O105GLN00.045-0.10510.0440.0410.0410.0000.0000.0000.000
63O105GLN0-0.0380.1088.053-0.006-0.0060.0000.0000.0000.000
64O106ASP00.105-0.13111.685-0.020-0.0200.0000.0000.0000.000
65O106ASP-1-0.951-0.82613.423-0.133-0.1330.0000.0000.0000.000
66O107LEU00.065-0.09213.526-0.047-0.0470.0000.0000.0000.000
67O107LEU0-0.0940.09613.7700.0150.0150.0000.0000.0000.000
68O108LYS00.143-0.07114.273-0.014-0.0140.0000.0000.0000.000
69O108LYS10.8811.07314.371-0.134-0.1340.0000.0000.0000.000
70O109MET00.087-0.12416.0250.0060.0060.0000.0000.0000.000
71O109MET0-0.0760.12615.903-0.002-0.0020.0000.0000.0000.000
72O110PHE00.144-0.03917.758-0.023-0.0230.0000.0000.0000.000
73O110PHE0-0.1180.07018.5360.0030.0030.0000.0000.0000.000
74O111LEU00.006-0.09019.051-0.025-0.0250.0000.0000.0000.000
75O111LEU0-0.0550.07718.2250.0090.0090.0000.0000.0000.000
76O112LEU00.040-0.09119.9970.0050.0050.0000.0000.0000.000
77O112LEU0-0.0570.08118.925-0.003-0.0030.0000.0000.0000.000
78O113SER0-0.027-0.09921.651-0.006-0.0060.0000.0000.0000.000
79O113SER0-0.0770.03222.311-0.008-0.0080.0000.0000.0000.000
80O114LYS00.073-0.07723.618-0.017-0.0170.0000.0000.0000.000
81O114LYS10.7761.03423.799-0.070-0.0700.0000.0000.0000.000
82O115GLY00.017-0.12525.6420.0090.0090.0000.0000.0000.000
83O116ALA00.0720.02123.177-0.006-0.0060.0000.0000.0000.000
84O116ALA0-0.0870.08922.3190.0070.0070.0000.0000.0000.000
85O117SER00.083-0.05223.504-0.012-0.0120.0000.0000.0000.000
86O117SER0-0.0230.06624.8110.0090.0090.0000.0000.0000.000
87O118LYS00.201-0.05820.4890.0250.0250.0000.0000.0000.000
88O118LYS10.7521.00219.353-0.179-0.1790.0000.0000.0000.000
89O119GLU00.030-0.14619.7950.0490.0490.0000.0000.0000.000
90O119GLU-1-0.853-0.76522.7420.1840.1840.0000.0000.0000.000
91O120VAL00.127-0.09621.5160.0490.0490.0000.0000.0000.000
92O120VAL0-0.0970.12522.600-0.001-0.0010.0000.0000.0000.000
93O121ILE00.105-0.09218.6910.0420.0420.0000.0000.0000.000
94O121ILE0-0.0890.11216.5510.0040.0040.0000.0000.0000.000
95O122ALA00.111-0.10516.5820.0790.0790.0000.0000.0000.000
96O122ALA0-0.0390.14417.749-0.006-0.0060.0000.0000.0000.000
97O123SER00.071-0.05817.4470.1050.1050.0000.0000.0000.000
98O123SER0-0.0360.08521.7130.0000.0000.0000.0000.0000.000
99O124ILE00.003-0.13019.5350.0400.0400.0000.0000.0000.000
100O124ILE0-0.0870.09418.116-0.004-0.0040.0000.0000.0000.000
101O125ILE00.078-0.09814.745-0.004-0.0040.0000.0000.0000.000
102O125ILE0-0.0690.10512.6240.0230.0230.0000.0000.0000.000
103O126SER00.033-0.12615.2400.1450.1450.0000.0000.0000.000
104O126SER0-0.0420.09117.1090.0080.0080.0000.0000.0000.000
105O127ARG00.015-0.10316.8750.0450.0450.0000.0000.0000.000
106O127ARG10.7190.99020.575-0.386-0.3860.0000.0000.0000.000
107O128TYR00.043-0.09817.660-0.001-0.0010.0000.0000.0000.000
108O128TYR0-0.1200.08217.911-0.007-0.0070.0000.0000.0000.000
109O129PRO00.125-0.03812.180-0.047-0.0470.0000.0000.0000.000
110O130ARG00.2020.05412.7590.0860.0860.0000.0000.0000.000
111O130ARG10.8041.03814.913-0.648-0.6480.0000.0000.0000.000
112O131ALA00.077-0.11014.217-0.060-0.0600.0000.0000.0000.000
113O131ALA0-0.0310.11615.593-0.011-0.0110.0000.0000.0000.000
114O132ILE0-0.030-0.14411.002-0.198-0.1980.0000.0000.0000.000
115O132ILE0-0.0210.1248.6380.0160.0160.0000.0000.0000.000
116O133THR0-0.020-0.06911.033-0.017-0.0170.0000.0000.0000.000
117O133THR0-0.1020.01710.332-0.020-0.0200.0000.0000.0000.000
118O134ARG00.041-0.12112.218-0.082-0.0820.0000.0000.0000.000
119O134ARG10.8271.05016.066-0.418-0.4180.0000.0000.0000.000
120O135THR00.009-0.05814.5780.0110.0110.0000.0000.0000.000
121O135THR0-0.0420.02914.9430.0190.0190.0000.0000.0000.000
122O136PRO00.097-0.07115.5950.0310.0310.0000.0000.0000.000
123O137GLU00.0830.02018.6750.0110.0110.0000.0000.0000.000
124O137GLU-1-0.885-0.76219.4330.0040.0040.0000.0000.0000.000
125O138ASN00.108-0.07820.038-0.001-0.0010.0000.0000.0000.000
126O138ASN0-0.1420.05819.0250.0100.0100.0000.0000.0000.000
127O139LEU00.060-0.12619.8570.0090.0090.0000.0000.0000.000
128O139LEU0-0.0590.11116.7110.0060.0060.0000.0000.0000.000
129O140SER00.091-0.10621.0510.0150.0150.0000.0000.0000.000
130O140SER00.0170.11523.069-0.008-0.0080.0000.0000.0000.000
131O141LYS00.034-0.06023.854-0.005-0.0050.0000.0000.0000.000
132O141LYS10.8181.04925.023-0.060-0.0600.0000.0000.0000.000
133O142ARG00.111-0.11024.479-0.010-0.0100.0000.0000.0000.000
134O142ARG10.7431.02923.225-0.194-0.1940.0000.0000.0000.000
135O143TRP00.128-0.09924.9170.0050.0050.0000.0000.0000.000
136O143TRP0-0.1170.08223.5990.0040.0040.0000.0000.0000.000
137O144ASP00.137-0.11326.4040.0040.0040.0000.0000.0000.000
138O144ASP-1-0.999-0.81528.6010.0480.0480.0000.0000.0000.000
139O145LEU0-0.011-0.14028.883-0.009-0.0090.0000.0000.0000.000
140O145LEU0-0.1300.06128.3810.0000.0000.0000.0000.0000.000
141O146TRP00.152-0.06029.347-0.007-0.0070.0000.0000.0000.000
142O146TRP0-0.0910.08527.5320.0030.0030.0000.0000.0000.000
143O147ARG00.031-0.12030.8400.0020.0020.0000.0000.0000.000
144O147ARG10.7901.03330.354-0.067-0.0670.0000.0000.0000.000
145O148LYS0-0.021-0.11732.698-0.008-0.0080.0000.0000.0000.000
146O148LYS10.8911.06733.343-0.046-0.0460.0000.0000.0000.000
147O149ILE00.016-0.11934.591-0.007-0.0070.0000.0000.0000.000
148O149ILE0-0.0840.11333.8680.0010.0010.0000.0000.0000.000
149O150VAL00.140-0.09534.151-0.007-0.0070.0000.0000.0000.000
150O150VAL0-0.1260.12332.7590.0010.0010.0000.0000.0000.000
151O151THR0-0.032-0.13435.224-0.003-0.0030.0000.0000.0000.000
152O151THR0-0.0330.06937.625-0.002-0.0020.0000.0000.0000.000
153O152SER00.007-0.05834.292-0.009-0.0090.0000.0000.0000.000
154O152SER0-0.0520.02734.5790.0020.0020.0000.0000.0000.000
155O153ASP00.108-0.11729.9230.0090.0090.0000.0000.0000.000
156O153ASP-1-0.826-0.76228.8790.0710.0710.0000.0000.0000.000
157O154LEU00.140-0.06929.4460.0160.0160.0000.0000.0000.000
158O154LEU0-0.0550.11630.803-0.002-0.0020.0000.0000.0000.000
159O155GLU00.035-0.11830.9560.0130.0130.0000.0000.0000.000
160O155GLU-1-0.795-0.76033.5060.0850.0850.0000.0000.0000.000
161O156ILE00.129-0.07928.9550.0120.0120.0000.0000.0000.000
162O156ILE0-0.1290.08026.8400.0000.0000.0000.0000.0000.000
163O157VAL00.056-0.13226.2040.0210.0210.0000.0000.0000.000
164O157VAL0-0.0720.12025.6060.0010.0010.0000.0000.0000.000
165O158ASN00.116-0.04426.7920.0240.0240.0000.0000.0000.000
166O158ASN0-0.1150.06230.5570.0030.0030.0000.0000.0000.000
167O159ILE00.098-0.07428.9860.0150.0150.0000.0000.0000.000
168O159ILE0-0.0740.09428.7230.0000.0000.0000.0000.0000.000
169O160LEU0-0.028-0.14724.6700.0130.0130.0000.0000.0000.000
170O160LEU0-0.0970.09422.6630.0040.0040.0000.0000.0000.000
171O161GLU00.135-0.12824.3400.0410.0410.0000.0000.0000.000
172O161GLU-1-0.954-0.80725.2940.2180.2180.0000.0000.0000.000
173O162ALA00.090-0.09225.5930.0330.0330.0000.0000.0000.000
174O162ALA0-0.0570.13129.584-0.005-0.0050.0000.0000.0000.000
175O163SER0-0.056-0.11426.5160.0150.0150.0000.0000.0000.000
176O163SER0-0.0580.08527.400-0.004-0.0040.0000.0000.0000.000
177O164PRO00.105-0.05521.114-0.005-0.0050.0000.0000.0000.000
178O165GLU00.092-0.01522.244-0.003-0.0030.0000.0000.0000.000
179O165GLU-1-0.895-0.77222.4740.3700.3700.0000.0000.0000.000
180O166SER0-0.010-0.12223.2740.0050.0050.0000.0000.0000.000
181O166SER0-0.0340.09426.462-0.011-0.0110.0000.0000.0000.000
182O167PHE00.124-0.10423.886-0.018-0.0180.0000.0000.0000.000
183O167PHE0-0.0820.12321.3910.0000.0000.0000.0000.0000.000
184O168PHE00.013-0.10019.754-0.031-0.0310.0000.0000.0000.000
185O168PHE0-0.0180.12218.5020.0150.0150.0000.0000.0000.000
186O169ARG00.032-0.10019.7950.0430.0430.0000.0000.0000.000
187O169ARG10.7980.99722.695-0.321-0.3210.0000.0000.0000.000
188O170SER00.028-0.10021.8200.0050.0050.0000.0000.0000.000
189O170SER0-0.0330.07424.435-0.008-0.0080.0000.0000.0000.000
190O171ASN00.068-0.05620.5640.0040.0040.0000.0000.0000.000
191O171ASN0-0.0750.07519.7790.0130.0130.0000.0000.0000.000
192O172ASN00.160-0.05521.911-0.023-0.0230.0000.0000.0000.000
193O172ASN0-0.1080.07825.341-0.012-0.0120.0000.0000.0000.000
194O173ASN00.130-0.06925.3710.0030.0030.0000.0000.0000.000
195O173ASN0-0.0580.10723.3210.0100.0100.0000.0000.0000.000
196O174LEU00.164-0.08527.107-0.005-0.0050.0000.0000.0000.000
197O174LEU0-0.0580.12629.4890.0000.0000.0000.0000.0000.000
198O175ASN00.126-0.05929.220-0.009-0.0090.0000.0000.0000.000
199O175ASN0-0.1110.07229.2640.0060.0060.0000.0000.0000.000
200O176LEU00.165-0.07229.269-0.005-0.0050.0000.0000.0000.000
201O176LEU0-0.1390.09028.0430.0010.0010.0000.0000.0000.000
202O177GLU00.114-0.10930.5760.0000.0000.0000.0000.0000.000
203O177GLU-1-0.916-0.80031.6590.0550.0550.0000.0000.0000.000
204O178ASN00.069-0.06432.983-0.007-0.0070.0000.0000.0000.000
205O178ASN0-0.0690.07334.167-0.005-0.0050.0000.0000.0000.000
206O179ASN00.162-0.04933.805-0.007-0.0070.0000.0000.0000.000
207O179ASN0-0.1100.08532.430-0.006-0.0060.0000.0000.0000.000
208O180ILE00.100-0.09534.552-0.001-0.0010.0000.0000.0000.000
209O180ILE0-0.1280.07432.5580.0000.0000.0000.0000.0000.000
210O181LYS00.072-0.09036.294-0.003-0.0030.0000.0000.0000.000
211O181LYS10.7520.98635.570-0.059-0.0590.0000.0000.0000.000
212O182PHE00.112-0.06138.416-0.005-0.0050.0000.0000.0000.000
213O182PHE0-0.0780.08538.4210.0010.0010.0000.0000.0000.000
214O183LEU00.128-0.05538.905-0.005-0.0050.0000.0000.0000.000
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