FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 6YR4Z

Calculation Name: 1VHC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VHC

Chain ID: A

ChEMBL ID:

UniProt ID: P44480

Base Structure: X-ray

Registration Date: 2023-09-23

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2383834.501346
FMO2-HF: Nuclear repulsion 2304301.141627
FMO2-HF: Total energy -79533.359718
FMO2-MP2: Total energy -79767.146912


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
-0.2581.179-0.021-0.575-0.8420.003
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.020
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].
3A4THR00.0500.0133.777-1.0930.216-0.020-0.565-0.7250.003
4A5THR00.0840.0116.4100.1860.1860.0000.0000.0000.000
5A6GLN00.0010.0109.2840.1060.1060.0000.0000.0000.000
6A7GLN00.0570.0316.447-0.399-0.3990.0000.0000.0000.000
7A8ILE00.0030.0145.4510.1570.1570.0000.0000.0000.000
8A9ILE0-0.022-0.0089.2370.1410.1410.0000.0000.0000.000
9A10GLU-1-0.831-0.93712.556-0.136-0.1360.0000.0000.0000.000
10A11LYS10.9550.9906.7390.1710.1710.0000.0000.0000.000
11A12LEU0-0.037-0.02512.1640.0570.0570.0000.0000.0000.000
12A13ARG10.8920.96914.5270.1820.1820.0000.0000.0000.000
13A14GLU-1-0.975-0.99414.0400.0100.0100.0000.0000.0000.000
14A15LEU0-0.019-0.00213.1260.0160.0160.0000.0000.0000.000
15A16LYS10.9140.95817.5430.0550.0550.0000.0000.0000.000
16A17ILE0-0.031-0.01619.619-0.004-0.0040.0000.0000.0000.000
17A18VAL0-0.003-0.00216.1260.0060.0060.0000.0000.0000.000
18A19PRO00.0130.01117.494-0.004-0.0040.0000.0000.0000.000
19A20VAL0-0.053-0.02418.4790.0060.0060.0000.0000.0000.000
20A21ILE00.0400.01018.416-0.002-0.0020.0000.0000.0000.000
21A22ALA0-0.052-0.03720.6720.0040.0040.0000.0000.0000.000
22A23LEU0-0.015-0.00220.395-0.003-0.0030.0000.0000.0000.000
23A24ASP-1-0.861-0.94424.1270.0590.0590.0000.0000.0000.000
24A25ASN00.0150.01126.0480.0070.0070.0000.0000.0000.000
25A26ALA00.0340.00420.9720.0020.0020.0000.0000.0000.000
26A27ASP-1-0.877-0.93921.5380.1510.1510.0000.0000.0000.000
27A28ASP-1-0.874-0.94423.4860.0970.0970.0000.0000.0000.000
28A29ILE0-0.083-0.04917.229-0.004-0.0040.0000.0000.0000.000
29A30LEU0-0.0120.00418.1910.0080.0080.0000.0000.0000.000
30A31PRO00.0640.03520.4830.0000.0000.0000.0000.0000.000
31A32LEU0-0.0060.01320.895-0.010-0.0100.0000.0000.0000.000
32A33ALA00.020-0.00316.679-0.009-0.0090.0000.0000.0000.000
33A34ASP-1-0.820-0.90218.5900.1710.1710.0000.0000.0000.000
34A35THR0-0.069-0.04320.517-0.009-0.0090.0000.0000.0000.000
35A36LEU0-0.031-0.00618.310-0.010-0.0100.0000.0000.0000.000
36A37ALA00.0350.03116.964-0.010-0.0100.0000.0000.0000.000
37A38LYS10.8700.93618.581-0.102-0.1020.0000.0000.0000.000
38A39ASN0-0.089-0.04622.031-0.011-0.0110.0000.0000.0000.000
39A40GLY00.0450.03219.713-0.010-0.0100.0000.0000.0000.000
40A41LEU0-0.008-0.00517.786-0.010-0.0100.0000.0000.0000.000
41A42SER0-0.014-0.01613.3780.0040.0040.0000.0000.0000.000
42A43VAL0-0.020-0.01012.6530.0000.0000.0000.0000.0000.000
43A44ALA0-0.0010.00413.4270.0000.0000.0000.0000.0000.000
44A45GLU-1-0.897-0.93613.6550.0040.0040.0000.0000.0000.000
45A46ILE0-0.002-0.01214.830-0.008-0.0080.0000.0000.0000.000
46A47THR0-0.027-0.00116.8310.0000.0000.0000.0000.0000.000
47A48PHE00.0730.00115.3760.0080.0080.0000.0000.0000.000
48A49ARG10.8710.94120.152-0.034-0.0340.0000.0000.0000.000
49A50SER0-0.046-0.02322.584-0.006-0.0060.0000.0000.0000.000
50A51GLU-1-0.886-0.94622.2940.0790.0790.0000.0000.0000.000
51A52ALA00.0180.02222.4770.0090.0090.0000.0000.0000.000
52A53ALA0-0.034-0.01218.0590.0210.0210.0000.0000.0000.000
53A54ALA00.0470.01216.2230.0290.0290.0000.0000.0000.000
54A55ASP-1-0.841-0.92716.3380.2140.2140.0000.0000.0000.000
55A56ALA0-0.002-0.00617.8860.0210.0210.0000.0000.0000.000
56A57ILE0-0.023-0.01111.5660.0210.0210.0000.0000.0000.000
57A58ARG10.9180.96613.018-0.194-0.1940.0000.0000.0000.000
58A59LEU0-0.027-0.00614.3110.0380.0380.0000.0000.0000.000
59A60LEU0-0.0030.00013.0880.0050.0050.0000.0000.0000.000
60A61ARG10.8070.9187.081-0.878-0.8780.0000.0000.0000.000
61A62ALA0-0.015-0.01211.3030.0350.0350.0000.0000.0000.000
62A63ASN0-0.048-0.02413.437-0.014-0.0140.0000.0000.0000.000
63A64ARG10.8460.91812.854-0.245-0.2450.0000.0000.0000.000
64A65PRO00.0230.0129.3730.0230.0230.0000.0000.0000.000
65A66ASP-1-0.947-0.9737.4580.4570.4570.0000.0000.0000.000
66A67PHE0-0.026-0.0208.619-0.105-0.1050.0000.0000.0000.000
67A68LEU0-0.017-0.0037.7300.0260.0260.0000.0000.0000.000
68A69ILE0-0.005-0.0178.522-0.020-0.0200.0000.0000.0000.000
69A70ALA00.0160.0289.0460.0330.0330.0000.0000.0000.000
70A71ALA00.0210.02511.5740.0210.0210.0000.0000.0000.000
71A72GLY00.0390.00713.686-0.045-0.0450.0000.0000.0000.000
72A73THR0-0.090-0.06116.8250.0150.0150.0000.0000.0000.000
73A74VAL00.0310.03415.0490.0070.0070.0000.0000.0000.000
74A75LEU0-0.009-0.01518.454-0.021-0.0210.0000.0000.0000.000
75A76THR0-0.048-0.02820.566-0.009-0.0090.0000.0000.0000.000
76A77ALA00.0520.00118.4020.0020.0020.0000.0000.0000.000
77A78GLU-1-0.866-0.93017.7040.0310.0310.0000.0000.0000.000
78A79GLN00.0210.01017.9140.0090.0090.0000.0000.0000.000
79A80VAL00.0190.02513.0570.0330.0330.0000.0000.0000.000
80A81VAL00.0270.00913.1490.0460.0460.0000.0000.0000.000
81A82LEU0-0.0020.00613.3680.0570.0570.0000.0000.0000.000
82A83ALA00.0240.00512.1220.0640.0640.0000.0000.0000.000
83A84LYS10.9140.9665.608-0.181-0.1810.0000.0000.0000.000
84A85SER0-0.045-0.0228.9010.2440.2440.0000.0000.0000.000
85A86SER0-0.030-0.02111.1990.0420.0420.0000.0000.0000.000
86A87GLY00.0150.0168.142-0.001-0.0010.0000.0000.0000.000
87A88ALA0-0.023-0.0107.5470.1640.1640.0000.0000.0000.000
88A89ASP-1-0.823-0.9074.6170.6560.784-0.001-0.010-0.1170.000
89A90PHE0-0.065-0.0455.828-0.334-0.3340.0000.0000.0000.000
90A91VAL00.0170.0118.5590.1030.1030.0000.0000.0000.000
91A92VAL00.0200.01912.197-0.066-0.0660.0000.0000.0000.000
92A93THR0-0.056-0.06315.4440.0190.0190.0000.0000.0000.000
93A94PRO0-0.005-0.00618.864-0.009-0.0090.0000.0000.0000.000
94A95GLY00.0580.03622.397-0.001-0.0010.0000.0000.0000.000
95A96LEU00.0360.03920.553-0.007-0.0070.0000.0000.0000.000
96A97ASN0-0.0030.00221.3260.0000.0000.0000.0000.0000.000
97A98PRO00.1190.03320.654-0.008-0.0080.0000.0000.0000.000
98A99LYS10.9880.99720.0940.0450.0450.0000.0000.0000.000
99A100ILE0-0.033-0.00617.083-0.007-0.0070.0000.0000.0000.000
100A101VAL00.0210.01115.970-0.012-0.0120.0000.0000.0000.000
101A102LYS10.9290.97115.1190.2270.2270.0000.0000.0000.000
102A103LEU00.0050.00514.557-0.030-0.0300.0000.0000.0000.000
103A104CYS0-0.027-0.01211.2930.0060.0060.0000.0000.0000.000
104A105GLN0-0.018-0.00610.485-0.069-0.0690.0000.0000.0000.000
105A106ASP-1-0.866-0.93611.394-0.372-0.3720.0000.0000.0000.000
106A107LEU0-0.085-0.03410.022-0.010-0.0100.0000.0000.0000.000
107A108ASN0-0.065-0.0314.9430.1000.1000.0000.0000.0000.000
108A109PHE0-0.074-0.0325.670-0.259-0.2590.0000.0000.0000.000
109A110PRO00.0390.0105.6480.1350.1350.0000.0000.0000.000
110A111ILE00.0500.0148.6750.1550.1550.0000.0000.0000.000
111A112THR0-0.041-0.02112.332-0.025-0.0250.0000.0000.0000.000
112A113PRO00.0260.02314.9620.0370.0370.0000.0000.0000.000
113A114GLY00.0170.02518.268-0.003-0.0030.0000.0000.0000.000
114A115VAL0-0.021-0.01721.5440.0010.0010.0000.0000.0000.000
115A116ASN0-0.027-0.03624.6330.0010.0010.0000.0000.0000.000
116A117ASN0-0.018-0.01228.0300.0010.0010.0000.0000.0000.000
117A118PRO00.1050.02828.783-0.006-0.0060.0000.0000.0000.000
118A119MET00.0020.02329.359-0.005-0.0050.0000.0000.0000.000
119A120ALA0-0.005-0.00525.748-0.006-0.0060.0000.0000.0000.000
120A121ILE0-0.0010.00224.641-0.011-0.0110.0000.0000.0000.000
121A122GLU-1-0.827-0.88524.591-0.111-0.1110.0000.0000.0000.000
122A123ILE0-0.0140.00723.244-0.007-0.0070.0000.0000.0000.000
123A124ALA00.006-0.01120.476-0.013-0.0130.0000.0000.0000.000
124A125LEU0-0.045-0.01120.442-0.025-0.0250.0000.0000.0000.000
125A126GLU-1-0.926-0.94522.129-0.158-0.1580.0000.0000.0000.000
126A127MET0-0.101-0.04418.729-0.002-0.0020.0000.0000.0000.000
127A128GLY00.0200.01917.742-0.036-0.0360.0000.0000.0000.000
128A129ILE0-0.075-0.04215.439-0.038-0.0380.0000.0000.0000.000
129A130SER00.0510.01817.2080.0220.0220.0000.0000.0000.000
130A131ALA0-0.040-0.01615.2990.0230.0230.0000.0000.0000.000
131A132VAL00.0250.01316.904-0.014-0.0140.0000.0000.0000.000
132A133LYS10.8520.89115.4260.1330.1330.0000.0000.0000.000
133A134PHE0-0.0120.00620.2210.0010.0010.0000.0000.0000.000
134A135PHE0-0.0200.00923.7640.0110.0110.0000.0000.0000.000
135A136PRO0-0.027-0.02125.558-0.003-0.0030.0000.0000.0000.000
136A137ALA00.0470.01026.5790.0000.0000.0000.0000.0000.000
137A138GLU-1-0.819-0.89428.467-0.026-0.0260.0000.0000.0000.000
138A139ALA0-0.027-0.01331.9360.0000.0000.0000.0000.0000.000
139A140SER0-0.023-0.02430.223-0.001-0.0010.0000.0000.0000.000
140A141GLY0-0.013-0.01232.613-0.003-0.0030.0000.0000.0000.000
141A142GLY00.0100.00631.2370.0010.0010.0000.0000.0000.000
142A143VAL00.0290.00930.670-0.005-0.0050.0000.0000.0000.000
143A144LYS10.9480.97332.1140.0280.0280.0000.0000.0000.000
144A145MET0-0.0040.01331.206-0.003-0.0030.0000.0000.0000.000
145A146ILE00.0290.01526.542-0.004-0.0040.0000.0000.0000.000
146A147LYS10.9680.97830.0370.0360.0360.0000.0000.0000.000
147A148ALA0-0.027-0.00232.320-0.002-0.0020.0000.0000.0000.000
148A149LEU0-0.006-0.01128.689-0.002-0.0020.0000.0000.0000.000
149A150LEU0-0.021-0.01426.197-0.005-0.0050.0000.0000.0000.000
150A151GLY0-0.0270.00430.054-0.001-0.0010.0000.0000.0000.000
151A152PRO0-0.028-0.01231.996-0.002-0.0020.0000.0000.0000.000
152A153TYR0-0.077-0.08726.863-0.004-0.0040.0000.0000.0000.000
153A154ALA00.0610.03927.132-0.006-0.0060.0000.0000.0000.000
154A155GLN0-0.024-0.02123.8530.0080.0080.0000.0000.0000.000
155A156LEU00.0040.01422.083-0.018-0.0180.0000.0000.0000.000
156A157GLN0-0.013-0.01116.6680.0180.0180.0000.0000.0000.000
157A158ILE00.004-0.00119.903-0.008-0.0080.0000.0000.0000.000
158A159MET00.0270.04215.7690.0030.0030.0000.0000.0000.000
159A160PRO00.0330.02520.1900.0050.0050.0000.0000.0000.000
160A161THR00.0280.00821.6320.0080.0080.0000.0000.0000.000
161A162GLY00.0340.01623.921-0.002-0.0020.0000.0000.0000.000
162A163GLY00.0100.00927.323-0.003-0.0030.0000.0000.0000.000
163A164ILE0-0.010-0.00325.326-0.001-0.0010.0000.0000.0000.000
164A165GLY00.023-0.00428.6550.0050.0050.0000.0000.0000.000
165A166LEU00.0160.00430.121-0.004-0.0040.0000.0000.0000.000
166A167HIS0-0.002-0.00331.7050.0000.0000.0000.0000.0000.000
167A168ASN00.0530.03930.711-0.001-0.0010.0000.0000.0000.000
168A169ILE00.0020.00024.959-0.005-0.0050.0000.0000.0000.000
169A170ARG10.8990.94328.2570.0030.0030.0000.0000.0000.000
170A171ASP-1-0.913-0.95530.390-0.023-0.0230.0000.0000.0000.000
171A172TYR0-0.108-0.08726.606-0.008-0.0080.0000.0000.0000.000
172A173LEU0-0.002-0.01223.210-0.006-0.0060.0000.0000.0000.000
173A174ALA0-0.0150.01326.722-0.002-0.0020.0000.0000.0000.000
174A175ILE0-0.081-0.03727.128-0.002-0.0020.0000.0000.0000.000
175A176PRO00.0690.02625.978-0.005-0.0050.0000.0000.0000.000
176A177ASN0-0.059-0.02623.5530.0010.0010.0000.0000.0000.000
177A178ILE0-0.081-0.03222.246-0.015-0.0150.0000.0000.0000.000
178A179VAL0-0.0190.00116.3690.0030.0030.0000.0000.0000.000
179A180ALA0-0.018-0.02017.8190.0100.0100.0000.0000.0000.000
180A181CYS0-0.044-0.00619.894-0.008-0.0080.0000.0000.0000.000
181A182GLY00.0400.03520.7250.0040.0040.0000.0000.0000.000
182A183GLY0-0.020-0.02821.344-0.002-0.0020.0000.0000.0000.000
183A184SER00.0180.00923.0130.0040.0040.0000.0000.0000.000
184A185TRP00.0140.01025.1630.0040.0040.0000.0000.0000.000
185A186PHE00.0510.01722.0460.0030.0030.0000.0000.0000.000
186A187VAL0-0.015-0.00422.2340.0060.0060.0000.0000.0000.000
187A188GLU-1-0.815-0.89325.5630.0370.0370.0000.0000.0000.000
188A189LYS10.9100.95227.129-0.045-0.0450.0000.0000.0000.000
189A190LYS10.8550.90528.608-0.028-0.0280.0000.0000.0000.000
190A191LEU0-0.006-0.00429.4950.0010.0010.0000.0000.0000.000
191A192ILE00.0030.00424.2010.0030.0030.0000.0000.0000.000
192A193GLN00.0490.03228.0850.0040.0040.0000.0000.0000.000
193A194SER0-0.070-0.01430.6260.0000.0000.0000.0000.0000.000
194A195ASN0-0.029-0.02429.188-0.001-0.0010.0000.0000.0000.000
195A196ASN0-0.0070.01130.4610.0020.0020.0000.0000.0000.000
196A197TRP00.067-0.00125.640-0.002-0.0020.0000.0000.0000.000
197A198ASP-1-0.892-0.93228.3230.0610.0610.0000.0000.0000.000
198A199GLU-1-0.863-0.92930.8260.0340.0340.0000.0000.0000.000
199A200ILE0-0.0120.00125.056-0.002-0.0020.0000.0000.0000.000
200A201GLY00.032-0.00326.139-0.002-0.0020.0000.0000.0000.000
201A202ARG10.7840.89227.179-0.035-0.0350.0000.0000.0000.000
202A203LEU00.0090.00028.552-0.003-0.0030.0000.0000.0000.000
203A204VAL0-0.020-0.00822.920-0.005-0.0050.0000.0000.0000.000
204A205ARG10.9460.96825.871-0.056-0.0560.0000.0000.0000.000
205A206GLU-1-0.885-0.93627.4980.0170.0170.0000.0000.0000.000
206A207VAL0-0.031-0.01825.087-0.005-0.0050.0000.0000.0000.000
207A208ILE0-0.022-0.01922.398-0.007-0.0070.0000.0000.0000.000
208A209ASP-1-0.870-0.93225.8740.0230.0230.0000.0000.0000.000
209A210ILE0-0.0090.00329.210-0.004-0.0040.0000.0000.0000.000
210A211ILE0-0.037-0.02324.339-0.005-0.0050.0000.0000.0000.000
211A212LYS10.7760.89723.158-0.013-0.0130.0000.0000.0000.000
212A213GLU-1-0.947-0.96128.2950.0040.0040.0000.0000.0000.000