FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: VV2N1

Calculation Name: 1V2Z-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V2Z

Chain ID: A

ChEMBL ID:

UniProt ID: Q79V62

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 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 210
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -863167.029717
FMO2-HF: Nuclear repulsion 819122.92946
FMO2-HF: Total energy -44044.100256
FMO2-MP2: Total energy -44171.908898


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(A:173:SER)


Summations of interaction energy for fragment #1(A:173:SER)
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.
6.5056.9240.0340.968-1.420.003
Interaction energy analysis for fragmet #1(A:173:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.143 / q_NPA : 0.075
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].
4A174THR00.0040.0844.356-0.1450.1870.000-0.143-0.1880.000
5A175ALA00.177-0.0573.620-0.7910.3790.002-0.605-0.5670.002
6A175ALA0-0.0730.1194.1550.0530.126-0.001-0.022-0.0510.000
7A176PHE00.096-0.0722.9902.6962.212-0.0050.626-0.1370.000
8A176PHE0-0.1150.0603.1420.842-0.1990.0391.214-0.2120.001
9A177PHE00.082-0.0804.4341.0871.307-0.001-0.067-0.1520.000
10A177PHE0-0.0950.0845.1150.2280.2280.0000.0000.0000.000
11A178PHE00.060-0.1106.3520.4840.4840.0000.0000.0000.000
12A178PHE0-0.0490.1157.7450.1160.1160.0000.0000.0000.000
13A179ARG00.202-0.0517.7270.4500.4500.0000.0000.0000.000
14A179ARG10.7080.9547.8271.4781.4780.0000.0000.0000.000
15A180ARG0-0.012-0.1418.5420.3140.3140.0000.0000.0000.000
16A180ARG10.7921.0318.6220.8990.8990.0000.0000.0000.000
17A181MET00.091-0.08710.3960.1770.1770.0000.0000.0000.000
18A181MET0-0.0950.09710.2320.0470.0470.0000.0000.0000.000
19A182SER0-0.008-0.07512.1820.1700.1700.0000.0000.0000.000
20A182SER0-0.0100.09312.6990.0090.0090.0000.0000.0000.000
21A183PRO0-0.036-0.11514.0790.0110.0110.0000.0000.0000.000
22A184ALA00.1760.02517.782-0.045-0.0450.0000.0000.0000.000
23A184ALA0-0.0890.09820.0630.0070.0070.0000.0000.0000.000
24A185ASP00.078-0.08719.798-0.008-0.0080.0000.0000.0000.000
25A185ASP-1-0.927-0.80423.337-0.215-0.2150.0000.0000.0000.000
26A186LYS00.059-0.12919.4890.0330.0330.0000.0000.0000.000
27A186LYS10.7601.03514.0490.7360.7360.0000.0000.0000.000
28A187ARG00.064-0.06820.471-0.001-0.0010.0000.0000.0000.000
29A187ARG10.8240.97524.8950.2020.2020.0000.0000.0000.000
30A188LYS00.123-0.04823.8550.0050.0050.0000.0000.0000.000
31A188LYS10.8611.04023.0800.1860.1860.0000.0000.0000.000
32A189LEU00.080-0.07619.4750.0360.0360.0000.0000.0000.000
33A189LEU0-0.0540.09616.927-0.010-0.0100.0000.0000.0000.000
34A190LEU00.110-0.07820.8810.0050.0050.0000.0000.0000.000
35A190LEU0-0.0840.09020.320-0.003-0.0030.0000.0000.0000.000
36A191ASP00.094-0.09622.5010.0090.0090.0000.0000.0000.000
37A191ASP-1-0.924-0.80725.955-0.165-0.1650.0000.0000.0000.000
38A192GLU00.070-0.12722.7970.0200.0200.0000.0000.0000.000
39A192GLU-1-0.904-0.80621.034-0.143-0.1430.0000.0000.0000.000
40A193LEU00.061-0.07721.3980.0300.0300.0000.0000.0000.000
41A193LEU0-0.0960.09418.144-0.004-0.0040.0000.0000.0000.000
42A194ARG00.098-0.09022.3880.0080.0080.0000.0000.0000.000
43A194ARG10.6980.93825.8570.1840.1840.0000.0000.0000.000
44A195SER00.075-0.04726.0470.0090.0090.0000.0000.0000.000
45A195SER0-0.0820.04726.2470.0040.0040.0000.0000.0000.000
46A196ILE00.085-0.09923.3470.0150.0150.0000.0000.0000.000
47A196ILE0-0.1010.10521.006-0.002-0.0020.0000.0000.0000.000
48A197TYR00.144-0.06024.7030.0180.0180.0000.0000.0000.000
49A197TYR0-0.0810.06823.285-0.004-0.0040.0000.0000.0000.000
50A198ARG00.112-0.08225.6040.0060.0060.0000.0000.0000.000
51A198ARG10.7561.00029.6680.0720.0720.0000.0000.0000.000
52A199THR0-0.076-0.08928.2480.0040.0040.0000.0000.0000.000
53A199THR0-0.0350.05726.8140.0030.0030.0000.0000.0000.000
54A200ILE00.127-0.06125.9330.0130.0130.0000.0000.0000.000
55A200ILE0-0.0980.08322.613-0.002-0.0020.0000.0000.0000.000
56A201VAL00.116-0.07527.2390.0090.0090.0000.0000.0000.000
57A201VAL0-0.1000.07928.474-0.002-0.0020.0000.0000.0000.000
58A202LEU00.003-0.12630.2020.0020.0020.0000.0000.0000.000
59A202LEU0-0.1120.07532.0440.0000.0000.0000.0000.0000.000
60A203GLU00.104-0.09430.3110.0050.0050.0000.0000.0000.000
61A203GLU-1-0.950-0.84528.960-0.016-0.0160.0000.0000.0000.000
62A204TYR00.114-0.06529.7440.0100.0100.0000.0000.0000.000
63A204TYR0-0.1560.02225.913-0.003-0.0030.0000.0000.0000.000
64A205PHE0-0.023-0.13530.4320.0000.0000.0000.0000.0000.000
65A205PHE0-0.0770.09532.122-0.001-0.0010.0000.0000.0000.000
66A206ASN00.147-0.07433.0680.0040.0040.0000.0000.0000.000
67A206ASN0-0.1640.06733.772-0.004-0.0040.0000.0000.0000.000
68A207THR00.039-0.06533.1770.0020.0020.0000.0000.0000.000
69A207THR0-0.0290.05335.1250.0000.0000.0000.0000.0000.000
70A208ASP0-0.006-0.10234.252-0.003-0.0030.0000.0000.0000.000
71A208ASP-1-0.980-0.85436.0550.0260.0260.0000.0000.0000.000
72A209ALA00.137-0.10732.1420.0080.0080.0000.0000.0000.000
73A209ALA0-0.0670.12731.604-0.002-0.0020.0000.0000.0000.000
74A210LYS00.051-0.07528.317-0.004-0.0040.0000.0000.0000.000
75A210LYS10.7290.97224.497-0.079-0.0790.0000.0000.0000.000
76A211VAL00.137-0.11026.5090.0070.0070.0000.0000.0000.000
77A211VAL0-0.0510.12226.265-0.001-0.0010.0000.0000.0000.000
78A212ASN00.040-0.07423.443-0.016-0.0160.0000.0000.0000.000
79A212ASN0-0.1200.04521.3190.0110.0110.0000.0000.0000.000
80A213GLU00.146-0.09521.915-0.005-0.0050.0000.0000.0000.000
81A213GLU-1-0.899-0.77422.8600.0770.0770.0000.0000.0000.000
82A214ARG00.090-0.11321.556-0.001-0.0010.0000.0000.0000.000
83A214ARG10.7500.99724.5690.0270.0270.0000.0000.0000.000
84A215ILE00.083-0.09521.276-0.026-0.0260.0000.0000.0000.000
85A215ILE0-0.0920.09819.821-0.003-0.0030.0000.0000.0000.000
86A216ASP00.103-0.12017.666-0.046-0.0460.0000.0000.0000.000
87A216ASP-1-0.956-0.82317.9240.0680.0680.0000.0000.0000.000
88A217GLU00.061-0.12816.843-0.012-0.0120.0000.0000.0000.000
89A217GLU-1-0.920-0.80720.329-0.009-0.0090.0000.0000.0000.000
90A218PHE00.084-0.07517.811-0.028-0.0280.0000.0000.0000.000
91A218PHE0-0.0890.07718.772-0.006-0.0060.0000.0000.0000.000
92A219VAL00.049-0.11715.851-0.066-0.0660.0000.0000.0000.000
93A219VAL0-0.0880.12213.873-0.001-0.0010.0000.0000.0000.000
94A220SER00.105-0.07113.012-0.104-0.1040.0000.0000.0000.000
95A220SER0-0.0730.06914.1140.0050.0050.0000.0000.0000.000
96A221LYS00.055-0.10713.210-0.080-0.0800.0000.0000.0000.000
97A221LYS10.7501.00717.3470.1520.1520.0000.0000.0000.000
98A222ALA00.077-0.11315.310-0.053-0.0530.0000.0000.0000.000
99A222ALA0-0.0460.10815.5640.0040.0040.0000.0000.0000.000
100A223PHE00.085-0.09110.935-0.106-0.1060.0000.0000.0000.000
101A223PHE0-0.1090.0895.762-0.068-0.0680.0000.0000.0000.000
102A224PHE00.077-0.10810.637-0.281-0.2810.0000.0000.0000.000
103A224PHE0-0.1410.07512.1430.0260.0260.0000.0000.0000.000
104A225ALA00.094-0.11611.987-0.091-0.0910.0000.0000.0000.000
105A225ALA0-0.0870.10215.8010.0210.0210.0000.0000.0000.000
106A226ASP00.083-0.04211.4860.0600.0600.0000.0000.0000.000
107A226ASP-1-0.898-0.79010.511-1.434-1.4340.0000.0000.0000.000
108A227ILE0-0.011-0.12412.324-0.002-0.0020.0000.0000.0000.000
109A227ILE0-0.0630.09916.1810.0190.0190.0000.0000.0000.000
110A228SER00.108-0.06914.748-0.059-0.0590.0000.0000.0000.000
111A228SER0-0.0670.04417.2060.0270.0270.0000.0000.0000.000
112A229VAL00.108-0.11216.6710.0380.0380.0000.0000.0000.000
113A229VAL0-0.0600.12516.266-0.005-0.0050.0000.0000.0000.000
114A230SER00.056-0.07918.4600.0440.0440.0000.0000.0000.000
115A230SER0-0.0130.08321.2380.0020.0020.0000.0000.0000.000
116A231GLN00.073-0.06720.0510.0410.0410.0000.0000.0000.000
117A231GLN0-0.0220.12718.640-0.055-0.0550.0000.0000.0000.000
118A232VAL00.078-0.08720.2480.0260.0260.0000.0000.0000.000
119A232VAL0-0.0760.08918.443-0.001-0.0010.0000.0000.0000.000
120A233LEU00.108-0.07621.3880.0310.0310.0000.0000.0000.000
121A233LEU0-0.1170.08123.937-0.001-0.0010.0000.0000.0000.000
122A234GLU00.119-0.10324.1670.0290.0290.0000.0000.0000.000
123A234GLU-1-1.050-0.86424.244-0.271-0.2710.0000.0000.0000.000
124A235ILE00.131-0.06924.4330.0210.0210.0000.0000.0000.000
125A235ILE0-0.1070.09022.089-0.001-0.0010.0000.0000.0000.000
126A236HIS00.130-0.08125.5860.0200.0200.0000.0000.0000.000
127A236HIS0-0.0770.11426.002-0.001-0.0010.0000.0000.0000.000
128A237VAL00.043-0.11327.3760.0180.0180.0000.0000.0000.000
129A237VAL0-0.0740.10328.803-0.001-0.0010.0000.0000.0000.000
130A238GLU00.084-0.12129.2220.0140.0140.0000.0000.0000.000
131A238GLU-1-0.882-0.79227.760-0.179-0.1790.0000.0000.0000.000
132A239LEU00.023-0.09229.8640.0120.0120.0000.0000.0000.000
133A239LEU0-0.0960.11228.3140.0030.0030.0000.0000.0000.000
134A240MET00.049-0.12331.3550.0130.0130.0000.0000.0000.000
135A240MET0-0.1100.10730.6390.0030.0030.0000.0000.0000.000
136A241ASP00.198-0.09333.4500.0120.0120.0000.0000.0000.000
137A241ASP-1-1.005-0.82534.532-0.115-0.1150.0000.0000.0000.000
138A242THR0-0.011-0.11534.4060.0080.0080.0000.0000.0000.000
139A242THR0-0.1200.04533.8370.0020.0020.0000.0000.0000.000
140A243PHE00.068-0.10435.2430.0060.0060.0000.0000.0000.000
141A243PHE0-0.0480.09731.7080.0010.0010.0000.0000.0000.000
142A244SER00.085-0.05336.8740.0070.0070.0000.0000.0000.000
143A244SER0-0.0030.08038.4670.0010.0010.0000.0000.0000.000
144A245LYS00.124-0.05439.0760.0060.0060.0000.0000.0000.000
145A245LYS10.7501.01936.6610.0870.0870.0000.0000.0000.000
146A246GLN00.042-0.10839.5660.0030.0030.0000.0000.0000.000
147A246GLN0-0.0790.08336.715-0.001-0.0010.0000.0000.0000.000
148A247LEU00.011-0.12740.8630.0040.0040.0000.0000.0000.000
149A247LEU0-0.0530.11039.2700.0000.0000.0000.0000.0000.000
150A248LYS0-0.018-0.06642.6050.0020.0020.0000.0000.0000.000
151A248LYS10.8521.01845.4210.0510.0510.0000.0000.0000.000
152A249LEU00.117-0.08842.9480.0040.0040.0000.0000.0000.000
153A249LEU0-0.1360.07240.3860.0000.0000.0000.0000.0000.000
154A250GLU00.132-0.09744.300-0.004-0.0040.0000.0000.0000.000
155A250GLU-1-1.032-0.87347.456-0.055-0.0550.0000.0000.0000.000
156A251GLY00.063-0.03445.1560.0030.0030.0000.0000.0000.000
157A252ARG0-0.039-0.06444.900-0.003-0.0030.0000.0000.0000.000
158A252ARG10.8011.01545.6380.0540.0540.0000.0000.0000.000
159A253SER00.036-0.07144.4880.0010.0010.0000.0000.0000.000
160A253SER0-0.0520.06844.5920.0010.0010.0000.0000.0000.000
161A254GLU00.054-0.14840.5640.0030.0030.0000.0000.0000.000
162A254GLU-1-0.814-0.75739.878-0.066-0.0660.0000.0000.0000.000
163A255ASP00.085-0.10339.293-0.006-0.0060.0000.0000.0000.000
164A255ASP-1-0.928-0.81842.053-0.061-0.0610.0000.0000.0000.000
165A256ILE00.061-0.10139.491-0.001-0.0010.0000.0000.0000.000
166A256ILE0-0.0830.09539.2230.0010.0010.0000.0000.0000.000
167A257LEU00.002-0.12436.1220.0040.0040.0000.0000.0000.000
168A257LEU0-0.0750.09435.384-0.001-0.0010.0000.0000.0000.000
169A258LEU00.069-0.10634.490-0.008-0.0080.0000.0000.0000.000
170A258LEU0-0.0920.10136.497-0.001-0.0010.0000.0000.0000.000
171A259ASP00.126-0.11033.764-0.010-0.0100.0000.0000.0000.000
172A259ASP-1-0.968-0.82334.281-0.053-0.0530.0000.0000.0000.000
173A260TYR00.034-0.10830.8950.0010.0010.0000.0000.0000.000
174A260TYR0-0.0720.09430.653-0.002-0.0020.0000.0000.0000.000
175A261ARG00.112-0.09929.190-0.012-0.0120.0000.0000.0000.000
176A261ARG10.8661.05330.4370.1000.1000.0000.0000.0000.000
177A262LEU00.011-0.12727.974-0.016-0.0160.0000.0000.0000.000
178A262LEU0-0.0370.12329.4070.0010.0010.0000.0000.0000.000
179A263THR00.045-0.07726.628-0.003-0.0030.0000.0000.0000.000
180A263THR0-0.0080.08226.4260.0020.0020.0000.0000.0000.000
181A264LEU00.157-0.05724.686-0.004-0.0040.0000.0000.0000.000
182A264LEU0-0.1340.09123.600-0.002-0.0020.0000.0000.0000.000
183A265ILE00.053-0.11223.147-0.027-0.0270.0000.0000.0000.000
184A265ILE0-0.1100.08324.2480.0000.0000.0000.0000.0000.000
185A266ASP00.080-0.09722.238-0.018-0.0180.0000.0000.0000.000
186A266ASP-1-0.880-0.76622.598-0.058-0.0580.0000.0000.0000.000
187A267VAL00.093-0.09320.3960.0010.0010.0000.0000.0000.000
188A267VAL0-0.0760.10719.955-0.003-0.0030.0000.0000.0000.000
189A268ILE00.099-0.08818.604-0.026-0.0260.0000.0000.0000.000
190A268ILE0-0.1130.07518.917-0.009-0.0090.0000.0000.0000.000
191A269ALA00.071-0.12217.577-0.057-0.0570.0000.0000.0000.000
192A269ALA0-0.0660.11919.9730.0070.0070.0000.0000.0000.000
193A270HIS00.057-0.10616.849-0.013-0.0130.0000.0000.0000.000
194A270HIS0-0.1130.07617.3360.0240.0240.0000.0000.0000.000
195A271LEU00.140-0.09714.2560.0290.0290.0000.0000.0000.000
196A271LEU0-0.1020.10912.973-0.004-0.0040.0000.0000.0000.000
197A272CYS00.114-0.12712.840-0.102-0.1020.0000.0000.0000.000
198A272CYS0-0.1510.09514.433-0.010-0.0100.0000.0000.0000.000
199A273GLU00.041-0.12512.565-0.079-0.0790.0000.0000.0000.000
200A273GLU-1-0.857-0.75314.4030.0040.0040.0000.0000.0000.000
201A274MET00.110-0.08410.9210.1120.1120.0000.0000.0000.000
202A274MET0-0.0890.1069.4220.0450.0450.0000.0000.0000.000
203A275TYR00.019-0.1107.8970.1090.1090.0000.0000.0000.000
204A275TYR0-0.0880.0827.4980.0020.0020.0000.0000.0000.000
205A276ARG00.070-0.0807.883-0.052-0.0520.0000.0000.0000.000
206A276ARG10.7791.00512.0690.0670.0670.0000.0000.0000.000
207A277ARG00.001-0.1109.7250.0370.0370.0000.0000.0000.000
208A277ARG10.7971.01010.772-0.136-0.1360.0000.0000.0000.000
209A278SER0-0.111-0.1764.192-0.0920.0570.000-0.035-0.1130.000
210A278SER00.0440.0435.134-0.073-0.0730.0000.0000.0000.000