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: 2LZ7R

Calculation Name: 1VC1-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VC1

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1F5

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 OptH
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 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -885517.607906
FMO2-HF: Nuclear repulsion 842855.38487
FMO2-HF: Total energy -42662.223037
FMO2-MP2: Total energy -42787.746539


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(A:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-11.213-4.5243.907-5.678-4.918-0.002
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.077 / q_NPA : -0.018
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].
4A2ASN0-0.192-0.0282.548-2.832-1.4250.692-1.113-0.986-0.011
5A3ASN00.1730.0013.778-4.073-0.688-0.032-2.153-1.2010.012
6A3ASN0-0.0610.0387.9480.0590.0590.0000.0000.0000.000
7A4LEU00.212-0.0866.2870.0010.0010.0000.0000.0000.000
8A4LEU0-0.0730.1447.825-0.029-0.0290.0000.0000.0000.000
9A5LYS00.072-0.0959.110-0.302-0.3020.0000.0000.0000.000
10A5LYS10.8361.07112.5280.5850.5850.0000.0000.0000.000
11A6LEU0-0.018-0.14712.5430.1100.1100.0000.0000.0000.000
12A6LEU0-0.0470.13913.1230.0140.0140.0000.0000.0000.000
13A7ASP00.134-0.06715.338-0.040-0.0400.0000.0000.0000.000
14A7ASP-1-1.005-0.88418.713-0.361-0.3610.0000.0000.0000.000
15A8ILE00.107-0.09318.9210.0450.0450.0000.0000.0000.000
16A8ILE0-0.1130.10117.770-0.003-0.0030.0000.0000.0000.000
17A9VAL00.078-0.13221.151-0.009-0.0090.0000.0000.0000.000
18A9VAL0-0.0820.11623.8930.0040.0040.0000.0000.0000.000
19A10GLU00.112-0.08024.9570.0100.0100.0000.0000.0000.000
20A10GLU-1-0.958-0.83725.573-0.268-0.2680.0000.0000.0000.000
21A11GLN00.001-0.10827.617-0.001-0.0010.0000.0000.0000.000
22A11GLN0-0.0430.08929.498-0.009-0.0090.0000.0000.0000.000
23A12ASP00.051-0.09131.061-0.003-0.0030.0000.0000.0000.000
24A12ASP-1-1.003-0.90132.480-0.126-0.1260.0000.0000.0000.000
25A13ASP00.073-0.10132.817-0.008-0.0080.0000.0000.0000.000
26A13ASP-1-0.870-0.80233.413-0.115-0.1150.0000.0000.0000.000
27A14LYS0-0.072-0.14228.9190.0010.0010.0000.0000.0000.000
28A14LYS10.7681.00327.9460.1230.1230.0000.0000.0000.000
29A15ALA00.200-0.10425.1620.0020.0020.0000.0000.0000.000
30A15ALA0-0.1020.09824.343-0.004-0.0040.0000.0000.0000.000
31A16ILE00.053-0.12823.814-0.001-0.0010.0000.0000.0000.000
32A16ILE0-0.1100.10523.1190.0040.0040.0000.0000.0000.000
33A17VAL00.117-0.10219.279-0.018-0.0180.0000.0000.0000.000
34A17VAL0-0.1000.10817.335-0.006-0.0060.0000.0000.0000.000
35A18ARG00.085-0.08019.1720.0330.0330.0000.0000.0000.000
36A18ARG10.8231.05819.4620.2510.2510.0000.0000.0000.000
37A19VAL00.061-0.12115.157-0.079-0.0790.0000.0000.0000.000
38A19VAL0-0.0420.12313.137-0.001-0.0010.0000.0000.0000.000
39A20GLN00.110-0.09514.2030.0930.0930.0000.0000.0000.000
40A20GLN0-0.1480.07413.941-0.061-0.0610.0000.0000.0000.000
41A21GLY0-0.034-0.10810.627-0.158-0.1580.0000.0000.0000.000
42A22ASP00.102-0.0139.674-0.023-0.0230.0000.0000.0000.000
43A22ASP-1-0.941-0.8139.7120.2150.2150.0000.0000.0000.000
44A23ILE00.183-0.0448.987-0.074-0.0740.0000.0000.0000.000
45A23ILE0-0.1480.08411.338-0.005-0.0050.0000.0000.0000.000
46A24ASP00.091-0.1018.205-0.071-0.0710.0000.0000.0000.000
47A24ASP-1-0.909-0.8426.4291.3431.3430.0000.0000.0000.000
48A25ALA00.099-0.1277.150-0.421-0.4210.0000.0000.0000.000
49A25ALA0-0.0740.0897.3250.0250.0250.0000.0000.0000.000
50A26TYR0-0.021-0.1063.1110.193-0.1370.0310.516-0.2170.000
51A26TYR0-0.1310.0632.361-1.600-0.7062.534-2.037-1.3910.009
52A27ASN00.034-0.1202.781-3.182-1.8490.682-0.891-1.123-0.012
53A27ASN0-0.0500.0794.9870.1610.1610.0000.0000.0000.000
54A28SER00.076-0.0695.411-0.364-0.3640.0000.0000.0000.000
55A28SER0-0.0600.0668.182-0.007-0.0070.0000.0000.0000.000
56A29SER00.031-0.0967.4800.0730.0730.0000.0000.0000.000
57A29SER0-0.0200.0806.8740.0140.0140.0000.0000.0000.000
58A30GLU00.089-0.1057.1630.2070.2070.0000.0000.0000.000
59A30GLU-1-0.967-0.8286.281-2.124-2.1240.0000.0000.0000.000
60A31LEU00.095-0.1248.4000.1240.1240.0000.0000.0000.000
61A31LEU0-0.0860.12010.4930.0370.0370.0000.0000.0000.000
62A32LYS00.136-0.10111.2030.0850.0850.0000.0000.0000.000
63A32LYS10.8591.08412.3830.2870.2870.0000.0000.0000.000
64A33GLU00.035-0.13211.6910.1750.1750.0000.0000.0000.000
65A33GLU-1-0.922-0.80611.171-0.675-0.6750.0000.0000.0000.000
66A34GLN00.035-0.13012.5390.0870.0870.0000.0000.0000.000
67A34GLN0-0.0410.12010.5910.2310.2310.0000.0000.0000.000
68A35LEU00.032-0.12614.3770.0610.0610.0000.0000.0000.000
69A35LEU0-0.0720.12515.0380.0160.0160.0000.0000.0000.000
70A36ARG00.166-0.08116.1760.0690.0690.0000.0000.0000.000
71A36ARG10.7751.04215.9370.4690.4690.0000.0000.0000.000
72A37ASN00.107-0.08217.1000.0640.0640.0000.0000.0000.000
73A37ASN0-0.1090.08115.7280.0510.0510.0000.0000.0000.000
74A38PHE00.130-0.05918.4310.0420.0420.0000.0000.0000.000
75A38PHE0-0.0410.12418.9720.0020.0020.0000.0000.0000.000
76A39ILE00.058-0.12020.3560.0300.0300.0000.0000.0000.000
77A39ILE0-0.0810.10120.4760.0100.0100.0000.0000.0000.000
78A40SER0-0.078-0.11821.8960.0390.0390.0000.0000.0000.000
79A40SER0-0.0660.04621.931-0.006-0.0060.0000.0000.0000.000
80A41THR0-0.034-0.09623.4790.0200.0200.0000.0000.0000.000
81A41THR0-0.0920.05022.735-0.002-0.0020.0000.0000.0000.000
82A42THR00.033-0.05624.4370.0210.0210.0000.0000.0000.000
83A42THR0-0.0340.05324.4850.0120.0120.0000.0000.0000.000
84A43SER00.032-0.08326.3380.0070.0070.0000.0000.0000.000
85A43SER0-0.0290.06030.9990.0000.0000.0000.0000.0000.000
86A44LYS00.034-0.13228.6030.0200.0200.0000.0000.0000.000
87A44LYS10.8341.10627.7470.1900.1900.0000.0000.0000.000
88A45LYS00.039-0.13328.896-0.009-0.0090.0000.0000.0000.000
89A45LYS10.8701.09730.4210.1470.1470.0000.0000.0000.000
90A46LYS00.078-0.11828.3590.0030.0030.0000.0000.0000.000
91A46LYS10.8181.04828.5350.1000.1000.0000.0000.0000.000
92A47ILE00.087-0.09223.759-0.009-0.0090.0000.0000.0000.000
93A47ILE0-0.0750.11121.679-0.003-0.0030.0000.0000.0000.000
94A48VAL00.001-0.12523.9550.0170.0170.0000.0000.0000.000
95A48VAL0-0.0280.11824.1610.0020.0020.0000.0000.0000.000
96A49LEU00.062-0.08919.546-0.030-0.0300.0000.0000.0000.000
97A49LEU0-0.0530.10317.090-0.003-0.0030.0000.0000.0000.000
98A50ASP00.127-0.08220.4800.0410.0410.0000.0000.0000.000
99A50ASP-1-0.909-0.79421.108-0.169-0.1690.0000.0000.0000.000
100A51LEU00.063-0.11818.138-0.049-0.0490.0000.0000.0000.000
101A51LEU0-0.1130.08516.7120.0070.0070.0000.0000.0000.000
102A52SER00.099-0.06219.0690.0290.0290.0000.0000.0000.000
103A52SER0-0.0680.05921.905-0.003-0.0030.0000.0000.0000.000
104A53SER0-0.051-0.12617.7840.0360.0360.0000.0000.0000.000
105A53SER0-0.0440.06517.057-0.012-0.0120.0000.0000.0000.000
106A54VAL00.060-0.12714.922-0.012-0.0120.0000.0000.0000.000
107A54VAL0-0.1020.12514.1570.0020.0020.0000.0000.0000.000
108A55SER0-0.001-0.10914.9990.0100.0100.0000.0000.0000.000
109A55SER0-0.0090.08615.654-0.005-0.0050.0000.0000.0000.000
110A56TYR00.043-0.07313.561-0.005-0.0050.0000.0000.0000.000
111A56TYR0-0.0750.08710.5550.0480.0480.0000.0000.0000.000
112A57MET00.105-0.10212.555-0.036-0.0360.0000.0000.0000.000
113A57MET0-0.0920.09413.862-0.018-0.0180.0000.0000.0000.000
114A58ASP00.053-0.06812.040-0.044-0.0440.0000.0000.0000.000
115A58ASP-1-0.796-0.7719.7801.0361.0360.0000.0000.0000.000
116A59SER00.090-0.09113.150-0.098-0.0980.0000.0000.0000.000
117A59SER0-0.0370.08814.2750.0330.0330.0000.0000.0000.000
118A60ALA00.019-0.12710.642-0.146-0.1460.0000.0000.0000.000
119A60ALA0-0.0250.13210.0420.0460.0460.0000.0000.0000.000
120A61GLY0-0.003-0.09011.652-0.141-0.1410.0000.0000.0000.000
121A62LEU00.077-0.04112.267-0.118-0.1180.0000.0000.0000.000
122A62LEU0-0.0680.12815.876-0.003-0.0030.0000.0000.0000.000
123A63GLY0-0.018-0.09415.312-0.052-0.0520.0000.0000.0000.000
124A64THR00.060-0.01213.177-0.030-0.0300.0000.0000.0000.000
125A64THR0-0.0370.10012.226-0.036-0.0360.0000.0000.0000.000
126A65LEU00.096-0.10714.585-0.068-0.0680.0000.0000.0000.000
127A65LEU0-0.0720.11715.188-0.001-0.0010.0000.0000.0000.000
128A66VAL00.096-0.09516.954-0.034-0.0340.0000.0000.0000.000
129A66VAL0-0.0970.10519.2820.0030.0030.0000.0000.0000.000
130A67VAL00.045-0.14418.188-0.006-0.0060.0000.0000.0000.000
131A67VAL0-0.1020.10116.717-0.003-0.0030.0000.0000.0000.000
132A68ILE00.073-0.07417.963-0.009-0.0090.0000.0000.0000.000
133A68ILE0-0.0270.10714.582-0.006-0.0060.0000.0000.0000.000
134A69LEU00.130-0.09018.976-0.022-0.0220.0000.0000.0000.000
135A69LEU0-0.1100.10422.2030.0030.0030.0000.0000.0000.000
136A70LYS00.106-0.11122.158-0.002-0.0020.0000.0000.0000.000
137A70LYS10.7621.02921.4200.1000.1000.0000.0000.0000.000
138A71ASP00.080-0.11521.2090.0150.0150.0000.0000.0000.000
139A71ASP-1-0.930-0.80719.476-0.189-0.1890.0000.0000.0000.000
140A72ALA00.046-0.11522.528-0.011-0.0110.0000.0000.0000.000
141A72ALA0-0.0480.12022.6160.0000.0000.0000.0000.0000.000
142A73LYS00.064-0.07923.913-0.006-0.0060.0000.0000.0000.000
143A73LYS10.8471.04726.4240.0570.0570.0000.0000.0000.000
144A74ILE00.046-0.07026.0750.0090.0090.0000.0000.0000.000
145A74ILE0-0.0880.07724.2560.0020.0020.0000.0000.0000.000
146A75ASN0-0.013-0.11426.1980.0090.0090.0000.0000.0000.000
147A75ASN0-0.1180.07723.5650.0000.0000.0000.0000.0000.000
148A76GLY00.018-0.11027.413-0.005-0.0050.0000.0000.0000.000
149A77LYS0-0.009-0.04127.2410.0080.0080.0000.0000.0000.000
150A77LYS10.7941.05325.6490.1960.1960.0000.0000.0000.000
151A78GLU00.079-0.13827.9870.0070.0070.0000.0000.0000.000
152A78GLU-1-0.987-0.83629.129-0.089-0.0890.0000.0000.0000.000
153A79PHE00.128-0.05224.021-0.017-0.0170.0000.0000.0000.000
154A79PHE0-0.1070.06618.935-0.001-0.0010.0000.0000.0000.000
155A80ILE0-0.020-0.18524.3980.0200.0200.0000.0000.0000.000
156A80ILE0-0.0270.11926.0000.0020.0020.0000.0000.0000.000
157A81LEU00.003-0.08122.232-0.027-0.0270.0000.0000.0000.000
158A81LEU0-0.0660.10019.9920.0040.0040.0000.0000.0000.000
159A82SER00.042-0.07622.7390.0220.0220.0000.0000.0000.000
160A82SER0-0.0090.07024.537-0.007-0.0070.0000.0000.0000.000
161A83SER00.003-0.04122.684-0.007-0.0070.0000.0000.0000.000
162A83SER0-0.0050.06023.5510.0000.0000.0000.0000.0000.000
163A84LEU00.097-0.09621.696-0.013-0.0130.0000.0000.0000.000
164A84LEU0-0.0860.09521.3080.0040.0040.0000.0000.0000.000
165A85LYS00.153-0.02921.172-0.003-0.0030.0000.0000.0000.000
166A85LYS10.8571.05819.0430.0150.0150.0000.0000.0000.000
167A86GLU00.128-0.13022.4870.0060.0060.0000.0000.0000.000
168A86GLU-1-0.988-0.83325.0910.0390.0390.0000.0000.0000.000
169A87SER00.009-0.09620.2470.0080.0080.0000.0000.0000.000
170A87SER0-0.0610.05118.663-0.010-0.0100.0000.0000.0000.000
171A88ILE00.069-0.13919.6220.0370.0370.0000.0000.0000.000
172A88ILE0-0.0430.15216.452-0.002-0.0020.0000.0000.0000.000
173A89SER00.113-0.07020.3050.0050.0050.0000.0000.0000.000
174A89SER0-0.0330.09824.8360.0000.0000.0000.0000.0000.000
175A90ARG00.031-0.08923.658-0.003-0.0030.0000.0000.0000.000
176A90ARG10.8471.03722.713-0.184-0.1840.0000.0000.0000.000
177A91ILE00.076-0.09820.095-0.002-0.0020.0000.0000.0000.000
178A91ILE0-0.0700.11417.7130.0040.0040.0000.0000.0000.000
179A92LEU00.037-0.10321.6210.0200.0200.0000.0000.0000.000
180A92LEU0-0.0150.10519.724-0.003-0.0030.0000.0000.0000.000
181A93LYS00.111-0.04722.866-0.003-0.0030.0000.0000.0000.000
182A93LYS10.8581.03326.537-0.052-0.0520.0000.0000.0000.000
183A94LEU00.028-0.10624.970-0.008-0.0080.0000.0000.0000.000
184A94LEU0-0.0960.08523.5450.0040.0040.0000.0000.0000.000
185A95THR0-0.009-0.08322.7870.0050.0050.0000.0000.0000.000
186A95THR0-0.0680.04320.802-0.003-0.0030.0000.0000.0000.000
187A96HIS00.080-0.04724.2430.0020.0020.0000.0000.0000.000
188A96HIS0-0.1140.05827.419-0.010-0.0100.0000.0000.0000.000
189A97LEU00.157-0.10722.952-0.013-0.0130.0000.0000.0000.000
190A97LEU0-0.1120.11520.3690.0000.0000.0000.0000.0000.000
191A98ASP00.048-0.10924.448-0.019-0.0190.0000.0000.0000.000
192A98ASP-1-0.906-0.83226.4340.0590.0590.0000.0000.0000.000
193A99LYS00.000-0.10326.649-0.012-0.0120.0000.0000.0000.000
194A99LYS10.8831.03828.752-0.052-0.0520.0000.0000.0000.000
195A100ILE0-0.030-0.08925.755-0.006-0.0060.0000.0000.0000.000
196A100ILE0-0.0970.05524.2280.0000.0000.0000.0000.0000.000
197A101PHE00.042-0.10324.149-0.014-0.0140.0000.0000.0000.000
198A101PHE0-0.0720.08719.805-0.001-0.0010.0000.0000.0000.000
199A102LYS00.162-0.05225.4190.0120.0120.0000.0000.0000.000
200A102LYS10.8631.07827.5700.0630.0630.0000.0000.0000.000
201A103ILE00.073-0.14525.815-0.015-0.0150.0000.0000.0000.000
202A103ILE0-0.0910.10224.3800.0030.0030.0000.0000.0000.000
203A104THR0-0.041-0.08626.7280.0110.0110.0000.0000.0000.000
204A104THR0-0.0630.04728.291-0.004-0.0040.0000.0000.0000.000
205A105ASP00.169-0.10327.177-0.002-0.0020.0000.0000.0000.000
206A105ASP-1-1.012-0.82129.845-0.032-0.0320.0000.0000.0000.000
207A106THR0-0.017-0.10128.029-0.002-0.0020.0000.0000.0000.000
208A106THR00.0160.08929.845-0.004-0.0040.0000.0000.0000.000
209A107VAL00.119-0.08026.9130.0060.0060.0000.0000.0000.000
210A107VAL0-0.0600.12025.009-0.002-0.0020.0000.0000.0000.000
211A108GLU00.000-0.17827.729-0.007-0.0070.0000.0000.0000.000
212A108GLU-1-0.902-0.77830.123-0.116-0.1160.0000.0000.0000.000
213A109GLU00.005-0.18131.350-0.002-0.0020.0000.0000.0000.000
214A109GLU-1-0.888-0.77731.396-0.050-0.0500.0000.0000.0000.000
215A110ALA0-0.127-0.11729.0320.0090.0090.0000.0000.0000.000
216A110ALA00.0940.05228.496-0.003-0.0030.0000.0000.0000.000