Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: MVKKZ

Calculation Name: 1PVT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PVT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0G1

Base Structure: X-ray

Registration Date: 2023-09-20

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

DOI:


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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2987328.429763
FMO2-HF: Nuclear repulsion 2895134.786731
FMO2-HF: Total energy -92193.643032
FMO2-MP2: Total energy -92462.262621


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:GLY)


Summations of interaction energy for fragment #1(A:2:GLY)
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.
3.1116.7272.706-3.026-3.295-0.01
Interaction energy analysis for fragmet #1(A:2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.019
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].
3A1MET00.0160.0243.902-0.6910.233-0.004-0.440-0.4800.001
4A2ARG10.8980.9102.2341.0941.9561.391-1.099-1.1540.002
5A3GLU-1-0.863-0.9034.298-0.576-0.322-0.001-0.048-0.2040.000
6A4THR0-0.015-0.0256.0810.7130.7130.0000.0000.0000.000
7A5ILE0-0.0070.0048.2870.2460.2460.0000.0000.0000.000
8A6ARG10.9060.9346.1131.3541.3540.0000.0000.0000.000
9A7GLU-1-0.782-0.86410.719-0.135-0.1350.0000.0000.0000.000
10A8ILE00.012-0.00212.5800.0900.0900.0000.0000.0000.000
11A9GLN0-0.040-0.01513.4630.0100.0100.0000.0000.0000.000
12A10LYS10.9450.97715.0840.2090.2090.0000.0000.0000.000
13A11VAL0-0.002-0.00116.8950.0370.0370.0000.0000.0000.000
14A12ALA00.002-0.00418.5870.0260.0260.0000.0000.0000.000
15A13TYR00.0250.01019.8440.0230.0230.0000.0000.0000.000
16A14TRP0-0.041-0.02320.0930.0230.0230.0000.0000.0000.000
17A15LEU0-0.0120.00122.8450.0150.0150.0000.0000.0000.000
18A16ALA0-0.015-0.00924.4400.0120.0120.0000.0000.0000.000
19A17ILE0-0.066-0.02425.1800.0110.0110.0000.0000.0000.000
20A18LYS10.8120.87926.9340.0800.0800.0000.0000.0000.000
21A19GLY00.0170.01829.3420.0070.0070.0000.0000.0000.000
22A20LEU0-0.0040.00826.7060.0050.0050.0000.0000.0000.000
23A21SER0-0.027-0.00426.703-0.003-0.0030.0000.0000.0000.000
24A22GLU-1-0.898-0.93628.730-0.079-0.0790.0000.0000.0000.000
25A23ALA0-0.030-0.02730.138-0.001-0.0010.0000.0000.0000.000
26A24ASN00.005-0.00427.316-0.005-0.0050.0000.0000.0000.000
27A25ALA0-0.0020.01927.974-0.002-0.0020.0000.0000.0000.000
28A26GLY00.0170.00626.0790.0070.0070.0000.0000.0000.000
29A27ASN0-0.0370.00422.767-0.022-0.0220.0000.0000.0000.000
30A28ILE00.0430.02217.3830.0150.0150.0000.0000.0000.000
31A29SER0-0.0110.00517.068-0.005-0.0050.0000.0000.0000.000
32A30VAL00.0120.00312.5150.0310.0310.0000.0000.0000.000
33A31ARG10.8380.92813.831-0.037-0.0370.0000.0000.0000.000
34A32LEU0-0.030-0.0328.421-0.021-0.0210.0000.0000.0000.000
35A33ASP-1-0.881-0.93210.2450.2120.2120.0000.0000.0000.000
36A34GLU-1-0.908-0.9535.8151.1581.1580.0000.0000.0000.000
37A35ARG10.7770.8458.935-0.136-0.1360.0000.0000.0000.000
38A36PRO0-0.034-0.0216.6310.0290.0290.0000.0000.0000.000
39A37GLU-1-0.810-0.8882.759-0.2991.2771.320-1.439-1.457-0.013
40A38GLY00.0170.0175.8390.0820.0820.0000.0000.0000.000
41A39TYR0-0.064-0.0448.105-0.042-0.0420.0000.0000.0000.000
42A40GLU-1-0.936-0.97111.108-0.275-0.2750.0000.0000.0000.000
43A41VAL0-0.039-0.01513.572-0.015-0.0150.0000.0000.0000.000
44A42LYS10.9340.96716.6240.1900.1900.0000.0000.0000.000
45A43SER0-0.028-0.01718.4820.0180.0180.0000.0000.0000.000
46A44VAL00.0290.01420.398-0.008-0.0080.0000.0000.0000.000
47A45ASN0-0.039-0.01322.4780.0080.0080.0000.0000.0000.000
48A46GLU-1-0.805-0.89225.114-0.055-0.0550.0000.0000.0000.000
49A47TYR0-0.085-0.05322.656-0.014-0.0140.0000.0000.0000.000
50A48GLY0-0.034-0.00627.322-0.001-0.0010.0000.0000.0000.000
51A49PHE0-0.047-0.03326.9840.0040.0040.0000.0000.0000.000
52A50ASP-1-0.878-0.95530.074-0.035-0.0350.0000.0000.0000.000
53A51TYR0-0.056-0.04722.3640.0000.0000.0000.0000.0000.000
54A52ASP-1-0.884-0.93627.288-0.008-0.0080.0000.0000.0000.000
55A53GLY00.0360.00825.6150.0020.0020.0000.0000.0000.000
56A54PRO0-0.018-0.01221.453-0.001-0.0010.0000.0000.0000.000
57A55GLU-1-0.749-0.82717.623-0.011-0.0110.0000.0000.0000.000
58A56MET0-0.068-0.02916.1140.0200.0200.0000.0000.0000.000
59A57TYR00.0570.02712.0400.0050.0050.0000.0000.0000.000
60A58LEU00.0010.00913.6910.0220.0220.0000.0000.0000.000
61A59LEU00.0300.0349.528-0.012-0.0120.0000.0000.0000.000
62A60ILE0-0.040-0.03213.9310.0550.0550.0000.0000.0000.000
63A61THR00.0180.01717.449-0.019-0.0190.0000.0000.0000.000
64A62ALA00.0480.02219.4250.0200.0200.0000.0000.0000.000
65A63THR0-0.028-0.01621.1520.0130.0130.0000.0000.0000.000
66A64GLY0-0.036-0.01424.740-0.006-0.0060.0000.0000.0000.000
67A65SER0-0.052-0.02421.7790.0000.0000.0000.0000.0000.000
68A66ARG10.8790.89123.3830.1440.1440.0000.0000.0000.000
69A67MET00.0380.02722.302-0.018-0.0180.0000.0000.0000.000
70A68ARG10.9350.93922.3180.1060.1060.0000.0000.0000.000
71A69GLU-1-0.751-0.82422.772-0.139-0.1390.0000.0000.0000.000
72A70VAL00.003-0.00218.292-0.013-0.0130.0000.0000.0000.000
73A71TYR0-0.084-0.05717.289-0.039-0.0390.0000.0000.0000.000
74A72GLU-1-0.906-0.91317.604-0.202-0.2020.0000.0000.0000.000
75A73ASP-1-0.849-0.90517.712-0.280-0.2800.0000.0000.0000.000
76A74ASP-1-0.811-0.91111.978-0.541-0.5410.0000.0000.0000.000
77A75SER0-0.032-0.02514.9060.0000.0000.0000.0000.0000.000
78A76LYS10.8270.91216.6270.2200.2200.0000.0000.0000.000
79A77ILE0-0.032-0.02313.8460.0320.0320.0000.0000.0000.000
80A78CYS0-0.0240.01214.895-0.020-0.0200.0000.0000.0000.000
81A79LEU00.0000.0029.453-0.023-0.0230.0000.0000.0000.000
82A80LEU0-0.027-0.01813.4920.0420.0420.0000.0000.0000.000
83A81HIS10.8200.90514.4450.0700.0700.0000.0000.0000.000
84A82VAL0-0.0030.00716.3100.0100.0100.0000.0000.0000.000
85A83LEU00.0200.00019.1210.0130.0130.0000.0000.0000.000
86A84PRO00.0440.02821.602-0.006-0.0060.0000.0000.0000.000
87A85GLY00.0390.04725.250-0.002-0.0020.0000.0000.0000.000
88A86LYS10.8780.90927.5110.0420.0420.0000.0000.0000.000
89A87HIS0-0.052-0.02825.146-0.006-0.0060.0000.0000.0000.000
90A88TYR00.0330.02920.156-0.002-0.0020.0000.0000.0000.000
91A89GLU-1-0.826-0.90316.611-0.113-0.1130.0000.0000.0000.000
92A90ILE0-0.030-0.02416.883-0.010-0.0100.0000.0000.0000.000
93A91LEU0-0.020-0.01411.3170.0180.0180.0000.0000.0000.000
94A92HIS00.006-0.00611.3110.0230.0230.0000.0000.0000.000
95A93GLY00.0340.02913.8310.0230.0230.0000.0000.0000.000
96A94ASN0-0.051-0.04716.6260.0280.0280.0000.0000.0000.000
97A95GLY0-0.029-0.01220.0250.0240.0240.0000.0000.0000.000
98A96LYS10.9090.95120.7500.0940.0940.0000.0000.0000.000
99A97PRO00.0660.02520.170-0.007-0.0070.0000.0000.0000.000
100A98THR0-0.033-0.02121.9610.0220.0220.0000.0000.0000.000
101A99SER00.0370.00324.2870.0030.0030.0000.0000.0000.000
102A100GLU-1-0.779-0.84225.278-0.094-0.0940.0000.0000.0000.000
103A101PHE00.0140.00220.6980.0010.0010.0000.0000.0000.000
104A102PRO00.0230.01124.2690.0020.0020.0000.0000.0000.000
105A103THR0-0.045-0.02926.6980.0040.0040.0000.0000.0000.000
106A104HIS10.8360.87621.2970.1280.1280.0000.0000.0000.000
107A105LEU0-0.0110.01421.9090.0010.0010.0000.0000.0000.000
108A106MET0-0.0060.01123.1890.0110.0110.0000.0000.0000.000
109A107ILE00.0090.02023.2550.0070.0070.0000.0000.0000.000
110A108HIS00.010-0.00918.1740.0230.0230.0000.0000.0000.000
111A109ALA0-0.018-0.00221.1210.0130.0130.0000.0000.0000.000
112A110LYS10.8510.89622.9400.0150.0150.0000.0000.0000.000
113A111PHE00.0120.00121.8770.0100.0100.0000.0000.0000.000
114A112LYS10.8660.92516.587-0.007-0.0070.0000.0000.0000.000
115A113GLU-1-0.855-0.89821.0520.0180.0180.0000.0000.0000.000
116A114MET00.0120.01324.4620.0100.0100.0000.0000.0000.000
117A115ASN0-0.063-0.03524.0460.0000.0000.0000.0000.0000.000
118A116PRO00.0510.02619.887-0.006-0.0060.0000.0000.0000.000
119A117GLU-1-0.831-0.90618.5880.1060.1060.0000.0000.0000.000
120A118LYS10.8220.92518.433-0.004-0.0040.0000.0000.0000.000
121A119LYS10.8580.93611.1510.1670.1670.0000.0000.0000.000
122A120ALA0-0.0220.00116.438-0.043-0.0430.0000.0000.0000.000
123A121ILE0-0.002-0.00717.8980.0240.0240.0000.0000.0000.000
124A122VAL0-0.0110.00120.300-0.028-0.0280.0000.0000.0000.000
125A123HIS10.8060.88722.5380.1010.1010.0000.0000.0000.000
126A124THR00.004-0.03325.764-0.013-0.0130.0000.0000.0000.000
127A125HIS0-0.068-0.05128.1690.0120.0120.0000.0000.0000.000
128A126PRO00.0210.02430.1430.0000.0000.0000.0000.0000.000
129A127LEU00.0920.05132.6740.0040.0040.0000.0000.0000.000
130A128ASN0-0.051-0.04136.1240.0060.0060.0000.0000.0000.000
131A129LEU00.019-0.00432.6850.0030.0030.0000.0000.0000.000
132A130LEU0-0.010-0.01034.6820.0020.0020.0000.0000.0000.000
133A131THR0-0.074-0.03937.8400.0030.0030.0000.0000.0000.000
134A132LEU0-0.017-0.00938.9800.0020.0020.0000.0000.0000.000
135A133MET0-0.0240.00635.3270.0020.0020.0000.0000.0000.000
136A134ASN0-0.043-0.01740.9460.0010.0010.0000.0000.0000.000
137A135LEU0-0.0340.00243.8980.0010.0010.0000.0000.0000.000
138A136GLU-1-0.903-0.95945.819-0.024-0.0240.0000.0000.0000.000
139A137GLU-1-0.931-0.96947.808-0.017-0.0170.0000.0000.0000.000
140A138PHE0-0.023-0.02438.5920.0010.0010.0000.0000.0000.000
141A139GLN00.008-0.00541.3620.0010.0010.0000.0000.0000.000
142A140GLU-1-0.894-0.95044.131-0.012-0.0120.0000.0000.0000.000
143A141LEU0-0.010-0.00144.0460.0010.0010.0000.0000.0000.000
144A142LEU0-0.0140.00838.0120.0000.0000.0000.0000.0000.000
145A143PRO00.001-0.00540.6460.0010.0010.0000.0000.0000.000
146A144LYS10.8720.93842.1910.0110.0110.0000.0000.0000.000
147A145MET00.0120.01037.5950.0000.0000.0000.0000.0000.000
148A146MET0-0.014-0.01135.3770.0000.0000.0000.0000.0000.000
149A147LYS10.9190.96537.8310.0010.0010.0000.0000.0000.000
150A148ILE0-0.0300.00939.4940.0010.0010.0000.0000.0000.000
151A149HIS0-0.014-0.01733.3730.0030.0030.0000.0000.0000.000
152A150PRO00.020-0.00835.5350.0000.0000.0000.0000.0000.000
153A151GLU-1-0.774-0.86631.202-0.019-0.0190.0000.0000.0000.000
154A152VAL00.0460.02131.4850.0000.0000.0000.0000.0000.000
155A153LEU0-0.028-0.01732.9630.0010.0010.0000.0000.0000.000
156A154ILE0-0.039-0.01429.0330.0030.0030.0000.0000.0000.000
157A155PHE00.0160.00624.3310.0050.0050.0000.0000.0000.000
158A156PHE0-0.016-0.01128.365-0.003-0.0030.0000.0000.0000.000
159A157PRO00.0210.03130.634-0.001-0.0010.0000.0000.0000.000
160A158GLN0-0.043-0.02230.8820.0020.0020.0000.0000.0000.000
161A159GLY0-0.006-0.00434.675-0.002-0.0020.0000.0000.0000.000
162A160ILE00.010-0.00531.9900.0000.0000.0000.0000.0000.000
163A161SER0-0.063-0.04734.0280.0020.0020.0000.0000.0000.000
164A162VAL00.0180.01034.941-0.004-0.0040.0000.0000.0000.000
165A163VAL0-0.0230.00233.4020.0020.0020.0000.0000.0000.000
166A164GLU-1-0.743-0.86236.605-0.028-0.0280.0000.0000.0000.000
167A165PHE0-0.021-0.01232.883-0.002-0.0020.0000.0000.0000.000
168A166GLU-1-0.833-0.90137.397-0.030-0.0300.0000.0000.0000.000
169A167LYS10.8090.88136.4170.0330.0330.0000.0000.0000.000
170A168PRO00.0290.00933.626-0.002-0.0020.0000.0000.0000.000
171A169GLY0-0.0150.00729.6470.0000.0000.0000.0000.0000.000
172A170SER00.0330.00729.676-0.001-0.0010.0000.0000.0000.000
173A171VAL00.0710.02729.423-0.002-0.0020.0000.0000.0000.000
174A172GLU-1-0.770-0.87231.092-0.032-0.0320.0000.0000.0000.000
175A173LEU00.0190.02231.2730.0030.0030.0000.0000.0000.000
176A174GLY00.0220.01629.1320.0000.0000.0000.0000.0000.000
177A175LEU0-0.024-0.01729.7630.0030.0030.0000.0000.0000.000
178A176LYS10.7860.88031.9220.0320.0320.0000.0000.0000.000
179A177THR0-0.014-0.02628.8290.0010.0010.0000.0000.0000.000
180A178VAL0-0.011-0.01527.7460.0030.0030.0000.0000.0000.000
181A179GLU-1-0.895-0.94930.356-0.015-0.0150.0000.0000.0000.000
182A180LYS10.8040.89933.9510.0260.0260.0000.0000.0000.000
183A181SER0-0.0100.00528.624-0.001-0.0010.0000.0000.0000.000
184A182GLU-1-0.872-0.91329.8020.0090.0090.0000.0000.0000.000
185A183GLY0-0.016-0.00629.5410.0000.0000.0000.0000.0000.000
186A184LYS10.7810.90129.8980.0100.0100.0000.0000.0000.000
187A185ASP-1-0.789-0.90626.159-0.002-0.0020.0000.0000.0000.000
188A186ALA0-0.019-0.02226.574-0.008-0.0080.0000.0000.0000.000
189A187VAL0-0.035-0.00328.9590.0060.0060.0000.0000.0000.000
190A188LEU00.0190.00431.113-0.007-0.0070.0000.0000.0000.000
191A189TRP0-0.015-0.02128.4130.0000.0000.0000.0000.0000.000
192A190ASP-1-0.778-0.90334.628-0.034-0.0340.0000.0000.0000.000
193A191LYS10.9050.94438.2710.0300.0300.0000.0000.0000.000
194A192HIS10.7910.89234.3630.0460.0460.0000.0000.0000.000
195A193GLY00.0600.03732.247-0.005-0.0050.0000.0000.0000.000
196A194VAL0-0.015-0.00628.8660.0050.0050.0000.0000.0000.000
197A195VAL0-0.015-0.01325.819-0.011-0.0110.0000.0000.0000.000
198A196ALA00.0210.01824.9570.0100.0100.0000.0000.0000.000
199A197PHE00.011-0.01322.234-0.015-0.0150.0000.0000.0000.000
200A198GLY00.0390.00720.5670.0050.0050.0000.0000.0000.000
201A199LYS10.8600.91717.639-0.082-0.0820.0000.0000.0000.000
202A200ASP-1-0.870-0.93514.355-0.042-0.0420.0000.0000.0000.000
203A201VAL00.007-0.02114.8670.0110.0110.0000.0000.0000.000
204A202ALA0-0.020-0.00816.6980.0000.0000.0000.0000.0000.000
205A203GLU-1-0.788-0.87218.3260.0160.0160.0000.0000.0000.000
206A204ALA0-0.038-0.01919.9860.0060.0060.0000.0000.0000.000
207A205TYR0-0.057-0.06420.932-0.003-0.0030.0000.0000.0000.000
208A206ASP-1-0.869-0.94522.426-0.048-0.0480.0000.0000.0000.000
209A207ARG10.7440.86423.1970.0230.0230.0000.0000.0000.000
210A208VAL0-0.002-0.00725.5850.0040.0040.0000.0000.0000.000
211A209GLU-1-0.768-0.83425.679-0.067-0.0670.0000.0000.0000.000
212A210ILE0-0.039-0.00727.8750.0040.0040.0000.0000.0000.000
213A211LEU0-0.009-0.00730.1620.0040.0040.0000.0000.0000.000
214A212GLU-1-0.727-0.86231.550-0.049-0.0490.0000.0000.0000.000
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216A214ALA0-0.039-0.01834.5070.0030.0030.0000.0000.0000.000
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