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: M8MYZ

Calculation Name: 2VH2-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2VH2

Chain ID: A

ChEMBL ID:

UniProt ID: A1JJJ6

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2114926.488462
FMO2-HF: Nuclear repulsion 2033409.540655
FMO2-HF: Total energy -81516.947807
FMO2-MP2: Total energy -81755.631417


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:57:PRO)


Summations of interaction energy for fragment #1(A:57:PRO)
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.
1.2693.004-0.021-0.819-0.895-0.002
Interaction energy analysis for fragmet #1(A:57:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.868 / q_NPA : 0.911
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].
3A59SER00.0820.0633.8580.1721.907-0.021-0.819-0.895-0.002
4A60LYS10.9120.9566.79229.34929.3490.0000.0000.0000.000
5A61LEU00.0230.01310.0670.1500.1500.0000.0000.0000.000
6A62VAL0-0.0110.00413.2840.7320.7320.0000.0000.0000.000
7A63VAL00.008-0.00216.3640.6020.6020.0000.0000.0000.000
8A64THR0-0.030-0.04118.8630.3180.3180.0000.0000.0000.000
9A65GLY00.0570.02522.649-0.028-0.0280.0000.0000.0000.000
10A66GLU-1-0.958-0.98125.359-10.327-10.3270.0000.0000.0000.000
11A67ARG10.8770.95418.57115.39715.3970.0000.0000.0000.000
12A68HIS0-0.036-0.01025.0290.2140.2140.0000.0000.0000.000
13A69TYR0-0.046-0.03726.6000.2600.2600.0000.0000.0000.000
14A70THR0-0.037-0.02820.654-0.339-0.3390.0000.0000.0000.000
15A71THR0-0.040-0.01218.260-0.098-0.0980.0000.0000.0000.000
16A72ASN0-0.035-0.04314.5220.5570.5570.0000.0000.0000.000
17A73ASP-1-0.931-0.97813.796-23.097-23.0970.0000.0000.0000.000
18A74ASP-1-0.731-0.86815.499-16.182-16.1820.0000.0000.0000.000
19A75ILE0-0.024-0.00414.981-0.190-0.1900.0000.0000.0000.000
20A76ARG10.8800.9388.24231.09131.0910.0000.0000.0000.000
21A77GLN00.0270.00511.927-1.751-1.7510.0000.0000.0000.000
22A78ALA00.0300.03414.3920.2990.2990.0000.0000.0000.000
23A79ILE0-0.065-0.04410.891-0.095-0.0950.0000.0000.0000.000
24A80LEU0-0.043-0.0238.449-1.160-1.1600.0000.0000.0000.000
25A81SER00.0030.01111.7060.4070.4070.0000.0000.0000.000
26A82LEU0-0.042-0.00613.8741.1771.1770.0000.0000.0000.000
27A83GLY00.0170.01512.388-1.988-1.9880.0000.0000.0000.000
28A84ALA0-0.031-0.02711.6350.8680.8680.0000.0000.0000.000
29A85PRO0-0.021-0.0176.522-2.132-2.1320.0000.0000.0000.000
30A86GLY00.0320.0245.8361.2011.2010.0000.0000.0000.000
31A87THR00.007-0.0136.6232.0462.0460.0000.0000.0000.000
32A88PHE00.0030.0047.9373.0553.0550.0000.0000.0000.000
33A89MET0-0.0240.00710.3092.0812.0810.0000.0000.0000.000
34A90THR00.0020.01012.2911.8151.8150.0000.0000.0000.000
35A91GLN00.0130.00714.5420.0460.0460.0000.0000.0000.000
36A92ASP-1-0.831-0.93117.044-15.994-15.9940.0000.0000.0000.000
37A93VAL00.0540.01918.1410.1090.1090.0000.0000.0000.000
38A94ASN00.0090.00617.9590.9940.9940.0000.0000.0000.000
39A95ILE0-0.026-0.00414.029-0.281-0.2810.0000.0000.0000.000
40A96ILE0-0.034-0.02217.9000.0960.0960.0000.0000.0000.000
41A97GLN00.0070.00821.3510.1630.1630.0000.0000.0000.000
42A98GLN00.0210.00117.609-0.220-0.2200.0000.0000.0000.000
43A99GLN00.020-0.01017.6950.4610.4610.0000.0000.0000.000
44A100ILE0-0.067-0.01920.9010.4320.4320.0000.0000.0000.000
45A101GLU-1-0.968-0.97323.703-11.970-11.9700.0000.0000.0000.000
46A102ARG10.9060.95724.56710.49010.4900.0000.0000.0000.000
47A103LEU00.0250.03321.4290.0380.0380.0000.0000.0000.000
48A104PRO0-0.029-0.01625.304-0.069-0.0690.0000.0000.0000.000
49A105TRP0-0.005-0.01823.3540.5100.5100.0000.0000.0000.000
50A106ILE0-0.024-0.00523.8370.0990.0990.0000.0000.0000.000
51A107GLN0-0.031-0.00827.3300.2170.2170.0000.0000.0000.000
52A108GLN00.006-0.01627.7250.2520.2520.0000.0000.0000.000
53A109ALA00.0380.01622.433-0.154-0.1540.0000.0000.0000.000
54A110SER0-0.068-0.03923.1900.4810.4810.0000.0000.0000.000
55A111VAL00.0030.00416.797-0.395-0.3950.0000.0000.0000.000
56A112ARG10.9310.96418.55114.82314.8230.0000.0000.0000.000
57A113LYS10.8610.93013.84718.72318.7230.0000.0000.0000.000
58A114GLN0-0.0390.00214.7651.7991.7990.0000.0000.0000.000
59A115TRP00.062-0.00312.712-1.444-1.4440.0000.0000.0000.000
60A116PRO0-0.046-0.00412.529-0.765-0.7650.0000.0000.0000.000
61A117ASP-1-0.804-0.9196.732-37.479-37.4790.0000.0000.0000.000
62A118GLU-1-0.929-0.9719.423-20.596-20.5960.0000.0000.0000.000
63A119LEU00.0190.00111.3281.4031.4030.0000.0000.0000.000
64A120LYS10.8370.93513.52514.59414.5940.0000.0000.0000.000
65A121ILE00.0210.01215.0130.3410.3410.0000.0000.0000.000
66A122HIS00.0070.01918.894-0.135-0.1350.0000.0000.0000.000
67A123LEU00.0120.00121.371-0.003-0.0030.0000.0000.0000.000
68A124VAL0-0.026-0.01224.5880.2200.2200.0000.0000.0000.000
69A125GLU-1-0.680-0.81525.708-12.233-12.2330.0000.0000.0000.000
70A126TYR0-0.031-0.00729.0190.4100.4100.0000.0000.0000.000
71A127VAL00.0170.01232.459-0.104-0.1040.0000.0000.0000.000
72A128PRO0-0.049-0.01934.3840.2020.2020.0000.0000.0000.000
73A129PHE0-0.007-0.01537.2310.1380.1380.0000.0000.0000.000
74A130ALA00.001-0.01040.6870.2200.2200.0000.0000.0000.000
75A131ARG10.9470.96537.3908.0428.0420.0000.0000.0000.000
76A132TRP0-0.0020.00440.1000.1650.1650.0000.0000.0000.000
77A133ASN00.0540.01241.3210.2700.2700.0000.0000.0000.000
78A134ASP-1-0.846-0.89941.131-7.390-7.3900.0000.0000.0000.000
79A135LEU0-0.046-0.02635.850-0.149-0.1490.0000.0000.0000.000
80A136HIS0-0.037-0.02235.484-0.240-0.2400.0000.0000.0000.000
81A137MET0-0.072-0.03834.7680.1610.1610.0000.0000.0000.000
82A138VAL00.0460.03837.369-0.088-0.0880.0000.0000.0000.000
83A139ASP-1-0.701-0.83136.889-8.613-8.6130.0000.0000.0000.000
84A140GLU-1-0.942-0.99039.003-7.255-7.2550.0000.0000.0000.000
85A141GLN0-0.112-0.05438.482-0.027-0.0270.0000.0000.0000.000
86A142GLY00.0130.01141.0840.1320.1320.0000.0000.0000.000
87A143ARG10.7980.88935.6028.9518.9510.0000.0000.0000.000
88A144SER00.008-0.02237.216-0.136-0.1360.0000.0000.0000.000
89A145PHE0-0.039-0.02032.006-0.258-0.2580.0000.0000.0000.000
90A146SER00.007-0.00731.6840.1890.1890.0000.0000.0000.000
91A147VAL00.0630.01728.358-0.311-0.3110.0000.0000.0000.000
92A148PRO00.0510.03626.2850.4050.4050.0000.0000.0000.000
93A149SER0-0.020-0.00629.6280.0860.0860.0000.0000.0000.000
94A150GLU-1-0.881-0.94726.404-12.035-12.0350.0000.0000.0000.000
95A151ARG10.8810.93628.27210.71310.7130.0000.0000.0000.000
96A152VAL00.0420.01928.698-0.132-0.1320.0000.0000.0000.000
97A153GLY00.0150.02731.5450.2390.2390.0000.0000.0000.000
98A154LYS10.8680.92835.1348.6148.6140.0000.0000.0000.000
99A155GLN00.0660.02837.143-0.090-0.0900.0000.0000.0000.000
100A156LYS10.8640.92939.7007.4047.4040.0000.0000.0000.000
101A157LEU00.0300.03339.4370.0140.0140.0000.0000.0000.000
102A158PRO00.0180.01342.730-0.009-0.0090.0000.0000.0000.000
103A159LEU0-0.0010.01243.904-0.181-0.1810.0000.0000.0000.000
104A160LEU0-0.008-0.00544.6730.2130.2130.0000.0000.0000.000
105A161TYR0-0.038-0.03444.925-0.078-0.0780.0000.0000.0000.000
106A162GLY00.0210.00446.3410.1790.1790.0000.0000.0000.000
107A163PRO0-0.056-0.01146.342-0.094-0.0940.0000.0000.0000.000
108A164GLU-1-0.915-0.96541.304-7.794-7.7940.0000.0000.0000.000
109A165GLY00.0080.01643.0160.1350.1350.0000.0000.0000.000
110A166SER0-0.013-0.01944.2160.1710.1710.0000.0000.0000.000
111A167GLU-1-0.825-0.90640.315-7.765-7.7650.0000.0000.0000.000
112A168GLN0-0.005-0.01443.7590.0210.0210.0000.0000.0000.000
113A169ASP-1-0.874-0.92446.090-6.421-6.4210.0000.0000.0000.000
114A170VAL0-0.051-0.03247.3400.1670.1670.0000.0000.0000.000
115A171LEU0-0.0080.00943.4950.1050.1050.0000.0000.0000.000
116A172GLU-1-0.925-0.96447.440-6.308-6.3080.0000.0000.0000.000
117A173GLY0-0.040-0.02550.3230.1330.1330.0000.0000.0000.000
118A174TYR00.0110.00046.3230.1510.1510.0000.0000.0000.000
119A175ARG10.9740.98948.0516.7296.7290.0000.0000.0000.000
120A176ALA0-0.019-0.00650.4210.0610.0610.0000.0000.0000.000
121A177ILE0-0.016-0.01653.9010.1110.1110.0000.0000.0000.000
122A178ASN00.006-0.00549.9870.1530.1530.0000.0000.0000.000
123A179LYS10.9220.96452.5326.1286.1280.0000.0000.0000.000
124A180VAL00.0030.00655.3440.0700.0700.0000.0000.0000.000
125A181LEU0-0.011-0.00655.8450.0800.0800.0000.0000.0000.000
126A182ALA00.004-0.00353.4750.0330.0330.0000.0000.0000.000
127A183ALA0-0.0190.01055.506-0.003-0.0030.0000.0000.0000.000
128A184ASN0-0.0080.00558.7070.0750.0750.0000.0000.0000.000
129A185LYS10.9580.97857.8165.3335.3330.0000.0000.0000.000
130A186TYR0-0.072-0.04657.4760.0350.0350.0000.0000.0000.000
131A187GLN0-0.019-0.02251.777-0.120-0.1200.0000.0000.0000.000
132A188LEU0-0.010-0.00150.7440.0230.0230.0000.0000.0000.000
133A189LYS10.8480.92049.7016.2266.2260.0000.0000.0000.000
134A190MET0-0.051-0.01648.836-0.174-0.1740.0000.0000.0000.000
135A191VAL00.017-0.00749.3790.1810.1810.0000.0000.0000.000
136A192ALA00.0360.01749.454-0.152-0.1520.0000.0000.0000.000
137A193MET0-0.0080.03550.1130.2050.2050.0000.0000.0000.000
138A194SER00.004-0.01251.219-0.115-0.1150.0000.0000.0000.000
139A195ALA00.0450.00452.1660.0440.0440.0000.0000.0000.000
140A196ARG10.9080.95453.1945.5965.5960.0000.0000.0000.000
141A197HIS00.026-0.00852.8540.1630.1630.0000.0000.0000.000
142A198SER0-0.086-0.04656.0650.1070.1070.0000.0000.0000.000
143A199TRP00.0360.00751.983-0.125-0.1250.0000.0000.0000.000
144A200GLN0-0.082-0.05055.0520.0360.0360.0000.0000.0000.000
145A201LEU00.0220.01053.910-0.120-0.1200.0000.0000.0000.000
146A202ALA00.0130.01353.3810.1100.1100.0000.0000.0000.000
147A203LEU0-0.021-0.00153.958-0.093-0.0930.0000.0000.0000.000
148A204ASP-1-0.872-0.93353.730-6.016-6.0160.0000.0000.0000.000
149A205ASN00.0270.01354.341-0.049-0.0490.0000.0000.0000.000
150A206ASP-1-0.846-0.90153.516-6.094-6.0940.0000.0000.0000.000
151A207VAL0-0.103-0.04356.4570.0700.0700.0000.0000.0000.000
152A208ARG10.8660.91557.5285.3355.3350.0000.0000.0000.000
153A209LEU00.017-0.00258.2720.1170.1170.0000.0000.0000.000
154A210GLU-1-0.804-0.86858.680-5.530-5.5300.0000.0000.0000.000
155A211LEU00.029-0.00958.6600.0880.0880.0000.0000.0000.000
156A212GLY0-0.0180.00460.7550.0580.0580.0000.0000.0000.000
157A213ARG10.9310.94859.8365.0805.0800.0000.0000.0000.000
158A214ASP-1-0.858-0.89660.730-5.020-5.0200.0000.0000.0000.000
159A215ASP-1-0.796-0.89762.082-5.112-5.1120.0000.0000.0000.000
160A216ARG10.9310.97953.9115.8605.8600.0000.0000.0000.000
161A217MET0-0.025-0.01261.075-0.060-0.0600.0000.0000.0000.000
162A218GLY00.0470.02162.2960.0150.0150.0000.0000.0000.000
163A219ARG10.8040.88163.6445.0065.0060.0000.0000.0000.000
164A220LEU00.001-0.00358.6460.0060.0060.0000.0000.0000.000
165A221GLN00.0050.00162.640-0.022-0.0220.0000.0000.0000.000
166A222ARG10.9070.95565.0484.7104.7100.0000.0000.0000.000
167A223PHE0-0.014-0.01260.8060.0450.0450.0000.0000.0000.000
168A224ILE0-0.024-0.01561.4150.0010.0010.0000.0000.0000.000
169A225GLU-1-0.935-0.94465.184-4.526-4.5260.0000.0000.0000.000
170A226LEU0-0.040-0.03068.9340.0460.0460.0000.0000.0000.000
171A227TYR00.0010.00262.691-0.060-0.0600.0000.0000.0000.000
172A228PRO00.009-0.01168.1230.0130.0130.0000.0000.0000.000
173A229MET0-0.0150.01970.1650.0430.0430.0000.0000.0000.000
174A230LEU0-0.005-0.03166.655-0.001-0.0010.0000.0000.0000.000
175A231GLN0-0.0140.00367.9140.0950.0950.0000.0000.0000.000
176A232GLN0-0.010-0.01066.628-0.109-0.1090.0000.0000.0000.000
177A233GLN00.0020.01468.641-0.065-0.0650.0000.0000.0000.000
178A234PRO0-0.028-0.01166.615-0.062-0.0620.0000.0000.0000.000
179A235ASP-1-0.825-0.92065.854-4.748-4.7480.0000.0000.0000.000
180A236LYS10.8830.96367.3724.4944.4940.0000.0000.0000.000
181A237ARG10.9470.97262.4375.0845.0840.0000.0000.0000.000
182A238VAL0-0.020-0.01164.1590.0380.0380.0000.0000.0000.000
183A239SER0-0.046-0.01761.829-0.078-0.0780.0000.0000.0000.000
184A240TYR0-0.005-0.01661.451-0.102-0.1020.0000.0000.0000.000
185A241VAL00.0250.01762.8750.1020.1020.0000.0000.0000.000
186A242ASP-1-0.824-0.91863.462-5.097-5.0970.0000.0000.0000.000
187A243LEU00.019-0.00363.5740.0980.0980.0000.0000.0000.000
188A244ARG10.8620.94361.2485.2295.2290.0000.0000.0000.000
189A245TYR0-0.026-0.00166.6300.0280.0280.0000.0000.0000.000
190A246GLU-1-0.896-0.93669.451-4.494-4.4940.0000.0000.0000.000
191A247THR00.0100.00272.037-0.024-0.0240.0000.0000.0000.000
192A248GLY00.0310.00972.4210.0150.0150.0000.0000.0000.000
193A249ALA0-0.050-0.02568.142-0.057-0.0570.0000.0000.0000.000
194A250ALA00.0070.01468.9240.0750.0750.0000.0000.0000.000
195A251ILE00.0090.00367.798-0.093-0.0930.0000.0000.0000.000
196A252GLY00.0350.02466.9760.0680.0680.0000.0000.0000.000
197A253TRP0-0.026-0.03666.634-0.026-0.0260.0000.0000.0000.000
198A254ALA00.0310.00963.552-0.010-0.0100.0000.0000.0000.000
199A255PRO0-0.033-0.01964.3710.0580.0580.0000.0000.0000.000
200A256VAL0-0.0120.00664.997-0.082-0.0820.0000.0000.0000.000
201A257PHE0-0.030-0.01964.1290.0420.0420.0000.0000.0000.000
202A258ILE-1-0.935-0.95466.087-4.819-4.8190.0000.0000.0000.000