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: LZ559

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2991761.385228
FMO2-HF: Nuclear repulsion 2899571.120118
FMO2-HF: Total energy -92190.26511
FMO2-MP2: Total energy -92459.284301


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.
2.2123.9843.781-2.881-2.6720.007
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 : 0.042 / q_NPA : 0.000
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].
3A1MET00.0420.0303.819-0.4580.6760.000-0.513-0.6210.000
4A2ARG10.9930.9651.938-0.496-0.4403.782-2.244-1.5950.007
5A3GLU-1-0.990-0.9804.456-0.1760.054-0.001-0.037-0.1910.000
6A4THR00.0450.0176.0650.6760.6760.0000.0000.0000.000
7A5ILE0-0.012-0.0067.5150.2480.2480.0000.0000.0000.000
8A6ARG10.9790.9995.5891.0351.0350.0000.0000.0000.000
9A7GLU-1-0.842-0.93310.413-0.210-0.2100.0000.0000.0000.000
10A8ILE0-0.023-0.00812.2090.0900.0900.0000.0000.0000.000
11A9GLN0-0.042-0.02412.5780.0090.0090.0000.0000.0000.000
12A10LYS10.9610.97914.7010.2270.2270.0000.0000.0000.000
13A11VAL00.0110.00716.4940.0350.0350.0000.0000.0000.000
14A12ALA0-0.0030.00118.0250.0250.0250.0000.0000.0000.000
15A13TYR00.0150.00319.2950.0210.0210.0000.0000.0000.000
16A14TRP0-0.034-0.02319.8020.0200.0200.0000.0000.0000.000
17A15LEU00.0250.00721.7590.0140.0140.0000.0000.0000.000
18A16ALA0-0.027-0.01424.0050.0110.0110.0000.0000.0000.000
19A17ILE0-0.059-0.01325.2360.0100.0100.0000.0000.0000.000
20A18LYS10.8020.88726.5650.0830.0830.0000.0000.0000.000
21A19GLY00.0150.01228.7990.0050.0050.0000.0000.0000.000
22A20LEU0-0.0160.00626.5380.0030.0030.0000.0000.0000.000
23A21SER0-0.028-0.00826.038-0.001-0.0010.0000.0000.0000.000
24A22GLU-1-0.889-0.93828.048-0.062-0.0620.0000.0000.0000.000
25A23ALA0-0.059-0.02729.8860.0000.0000.0000.0000.0000.000
26A24ASN0-0.039-0.03726.841-0.004-0.0040.0000.0000.0000.000
27A25ALA00.0040.01227.189-0.003-0.0030.0000.0000.0000.000
28A26GLY00.0340.00425.7140.0030.0030.0000.0000.0000.000
29A27ASN0-0.066-0.02022.091-0.011-0.0110.0000.0000.0000.000
30A28ILE00.0480.02217.0810.0080.0080.0000.0000.0000.000
31A29SER0-0.024-0.00217.2810.0050.0050.0000.0000.0000.000
32A30VAL00.0140.01112.5750.0200.0200.0000.0000.0000.000
33A31ARG10.8590.94514.3090.0600.0600.0000.0000.0000.000
34A32LEU0-0.025-0.0378.549-0.018-0.0180.0000.0000.0000.000
35A33ASP-1-0.876-0.94010.253-0.013-0.0130.0000.0000.0000.000
36A34GLU-1-0.963-0.9747.3940.4940.4940.0000.0000.0000.000
37A35ARG10.8850.9338.733-0.054-0.0540.0000.0000.0000.000
38A36PRO0-0.039-0.0216.737-0.005-0.0050.0000.0000.0000.000
39A37GLU-1-0.913-0.9434.0390.6951.0470.000-0.087-0.2650.000
40A38GLY0-0.0100.0216.1070.0320.0320.0000.0000.0000.000
41A39TYR0-0.0240.0008.013-0.092-0.0920.0000.0000.0000.000
42A40GLU-1-0.927-0.97410.4600.0060.0060.0000.0000.0000.000
43A41VAL0-0.028-0.00113.715-0.022-0.0220.0000.0000.0000.000
44A42LYS10.9370.98016.7350.0680.0680.0000.0000.0000.000
45A43SER0-0.030-0.03818.5560.0080.0080.0000.0000.0000.000
46A44VAL00.0890.06920.330-0.007-0.0070.0000.0000.0000.000
47A45ASN0-0.066-0.04422.0380.0030.0030.0000.0000.0000.000
48A46GLU-1-0.876-0.95124.982-0.035-0.0350.0000.0000.0000.000
49A47TYR0-0.102-0.04522.555-0.009-0.0090.0000.0000.0000.000
50A48GLY0-0.0350.00427.149-0.002-0.0020.0000.0000.0000.000
51A49PHE0-0.072-0.05726.6300.0020.0020.0000.0000.0000.000
52A50ASP-1-0.948-0.98829.745-0.026-0.0260.0000.0000.0000.000
53A51TYR0-0.104-0.04422.430-0.002-0.0020.0000.0000.0000.000
54A52ASP-1-0.871-0.94627.785-0.015-0.0150.0000.0000.0000.000
55A53GLY00.0280.03525.3860.0030.0030.0000.0000.0000.000
56A54PRO00.013-0.01421.7780.0000.0000.0000.0000.0000.000
57A55GLU-1-0.835-0.89417.559-0.018-0.0180.0000.0000.0000.000
58A56MET0-0.085-0.05216.2710.0010.0010.0000.0000.0000.000
59A57TYR00.051-0.02012.0200.0110.0110.0000.0000.0000.000
60A58LEU0-0.0020.01213.625-0.015-0.0150.0000.0000.0000.000
61A59LEU00.0130.0089.3090.0080.0080.0000.0000.0000.000
62A60ILE0-0.039-0.02113.9330.0250.0250.0000.0000.0000.000
63A61THR00.0160.02917.232-0.007-0.0070.0000.0000.0000.000
64A62ALA00.0220.00818.8360.0140.0140.0000.0000.0000.000
65A63THR0-0.046-0.02820.6920.0050.0050.0000.0000.0000.000
66A64GLY0-0.016-0.00424.4570.0000.0000.0000.0000.0000.000
67A65SER0-0.053-0.02021.261-0.001-0.0010.0000.0000.0000.000
68A66ARG10.9350.95523.3480.0920.0920.0000.0000.0000.000
69A67MET00.0530.04421.702-0.013-0.0130.0000.0000.0000.000
70A68ARG10.9820.98421.8030.0760.0760.0000.0000.0000.000
71A69GLU-1-0.884-0.95622.092-0.097-0.0970.0000.0000.0000.000
72A70VAL00.0160.01616.939-0.008-0.0080.0000.0000.0000.000
73A71TYR0-0.047-0.01616.740-0.031-0.0310.0000.0000.0000.000
74A72GLU-1-0.977-0.98917.069-0.141-0.1410.0000.0000.0000.000
75A73ASP-1-0.829-0.90317.060-0.163-0.1630.0000.0000.0000.000
76A74ASP-1-0.896-0.95911.355-0.298-0.2980.0000.0000.0000.000
77A75SER0-0.054-0.03013.928-0.010-0.0100.0000.0000.0000.000
78A76LYS10.8460.91716.1230.1370.1370.0000.0000.0000.000
79A77ILE0-0.028-0.02312.8300.0090.0090.0000.0000.0000.000
80A78CYS0-0.030-0.00314.4640.0020.0020.0000.0000.0000.000
81A79LEU0-0.0160.0289.437-0.026-0.0260.0000.0000.0000.000
82A80LEU0-0.032-0.02613.1490.0400.0400.0000.0000.0000.000
83A81HIS10.8600.95314.7780.0460.0460.0000.0000.0000.000
84A82VAL0-0.022-0.01916.2520.0090.0090.0000.0000.0000.000
85A83LEU00.0220.00519.3900.0080.0080.0000.0000.0000.000
86A84PRO00.0370.01521.728-0.003-0.0030.0000.0000.0000.000
87A85GLY00.0560.04425.2010.0010.0010.0000.0000.0000.000
88A86LYS10.9780.95927.9350.0220.0220.0000.0000.0000.000
89A87HIS0-0.026-0.01524.753-0.003-0.0030.0000.0000.0000.000
90A88TYR00.0420.04120.100-0.002-0.0020.0000.0000.0000.000
91A89GLU-1-0.873-0.95117.429-0.044-0.0440.0000.0000.0000.000
92A90ILE0-0.072-0.05416.958-0.013-0.0130.0000.0000.0000.000
93A91LEU0-0.029-0.01411.0740.0110.0110.0000.0000.0000.000
94A92HIS00.0710.03911.1640.0360.0360.0000.0000.0000.000
95A93GLY00.0330.01013.519-0.001-0.0010.0000.0000.0000.000
96A94ASN00.007-0.00116.3680.0120.0120.0000.0000.0000.000
97A95GLY0-0.023-0.01019.6990.0140.0140.0000.0000.0000.000
98A96LYS10.8960.96120.7900.0600.0600.0000.0000.0000.000
99A97PRO00.0810.02419.737-0.004-0.0040.0000.0000.0000.000
100A98THR00.0200.01621.5910.0160.0160.0000.0000.0000.000
101A99SER00.0760.02024.0320.0010.0010.0000.0000.0000.000
102A100GLU-1-0.844-0.91225.135-0.084-0.0840.0000.0000.0000.000
103A101PHE00.000-0.00221.523-0.002-0.0020.0000.0000.0000.000
104A102PRO00.0390.01524.156-0.002-0.0020.0000.0000.0000.000
105A103THR0-0.037-0.00626.5680.0020.0020.0000.0000.0000.000
106A104HIS10.8380.89021.3130.1160.1160.0000.0000.0000.000
107A105LEU00.0190.01721.692-0.001-0.0010.0000.0000.0000.000
108A106MET0-0.0310.01223.5550.0050.0050.0000.0000.0000.000
109A107ILE00.0260.01824.0270.0040.0040.0000.0000.0000.000
110A108HIS00.010-0.00818.1420.0120.0120.0000.0000.0000.000
111A109ALA0-0.0050.00721.8430.0060.0060.0000.0000.0000.000
112A110LYS10.9920.97423.4310.0330.0330.0000.0000.0000.000
113A111PHE00.0220.01621.6520.0060.0060.0000.0000.0000.000
114A112LYS10.8830.95117.0750.0430.0430.0000.0000.0000.000
115A113GLU-1-0.971-0.97721.404-0.007-0.0070.0000.0000.0000.000
116A114MET0-0.024-0.01224.8000.0070.0070.0000.0000.0000.000
117A115ASN0-0.083-0.05724.3020.0000.0000.0000.0000.0000.000
118A116PRO00.0340.01420.002-0.009-0.0090.0000.0000.0000.000
119A117GLU-1-0.909-0.95618.7330.0070.0070.0000.0000.0000.000
120A118LYS10.8010.93818.5930.0270.0270.0000.0000.0000.000
121A119LYS10.9701.00611.3110.2660.2660.0000.0000.0000.000
122A120ALA0-0.043-0.00616.293-0.033-0.0330.0000.0000.0000.000
123A121ILE00.0010.00017.9130.0220.0220.0000.0000.0000.000
124A122VAL0-0.0100.00120.234-0.017-0.0170.0000.0000.0000.000
125A123HIS10.8320.91822.3040.0920.0920.0000.0000.0000.000
126A124THR00.027-0.00925.474-0.008-0.0080.0000.0000.0000.000
127A125HIS0-0.055-0.03227.5890.0080.0080.0000.0000.0000.000
128A126PRO00.0350.03429.8930.0010.0010.0000.0000.0000.000
129A127LEU00.1220.05732.2080.0030.0030.0000.0000.0000.000
130A128ASN0-0.0140.01135.5370.0060.0060.0000.0000.0000.000
131A129LEU00.0570.01732.6710.0030.0030.0000.0000.0000.000
132A130LEU0-0.048-0.02534.7890.0020.0020.0000.0000.0000.000
133A131THR0-0.079-0.05937.2490.0030.0030.0000.0000.0000.000
134A132LEU0-0.016-0.00838.6480.0020.0020.0000.0000.0000.000
135A133MET0-0.0660.00034.7300.0020.0020.0000.0000.0000.000
136A134ASN0-0.087-0.06440.5110.0010.0010.0000.0000.0000.000
137A135LEU0-0.0270.00243.4420.0010.0010.0000.0000.0000.000
138A136GLU-1-0.884-0.95045.753-0.023-0.0230.0000.0000.0000.000
139A137GLU-1-0.929-0.94947.446-0.020-0.0200.0000.0000.0000.000
140A138PHE0-0.003-0.02238.607-0.001-0.0010.0000.0000.0000.000
141A139GLN00.037-0.00441.682-0.001-0.0010.0000.0000.0000.000
142A140GLU-1-0.938-0.97243.980-0.018-0.0180.0000.0000.0000.000
143A141LEU00.0070.01943.4950.0000.0000.0000.0000.0000.000
144A142LEU0-0.014-0.00437.6960.0000.0000.0000.0000.0000.000
145A143PRO00.0230.01840.1640.0000.0000.0000.0000.0000.000
146A144LYS10.9510.97141.6730.0180.0180.0000.0000.0000.000
147A145MET00.000-0.01137.546-0.001-0.0010.0000.0000.0000.000
148A146MET0-0.008-0.00135.390-0.002-0.0020.0000.0000.0000.000
149A147LYS10.9050.94437.5930.0160.0160.0000.0000.0000.000
150A148ILE0-0.0530.01238.8080.0020.0020.0000.0000.0000.000
151A149HIS00.003-0.00933.6460.0020.0020.0000.0000.0000.000
152A150PRO00.008-0.01235.621-0.001-0.0010.0000.0000.0000.000
153A151GLU-1-0.871-0.96129.933-0.040-0.0400.0000.0000.0000.000
154A152VAL0-0.0060.02331.415-0.002-0.0020.0000.0000.0000.000
155A153LEU00.010-0.00132.4240.0000.0000.0000.0000.0000.000
156A154ILE0-0.0150.00428.9760.0010.0010.0000.0000.0000.000
157A155PHE00.0320.02424.7920.0020.0020.0000.0000.0000.000
158A156PHE0-0.089-0.04728.894-0.003-0.0030.0000.0000.0000.000
159A157PRO0-0.0180.00430.4040.0020.0020.0000.0000.0000.000
160A158GLN00.019-0.00332.1920.0020.0020.0000.0000.0000.000
161A159GLY0-0.0020.01833.6590.0010.0010.0000.0000.0000.000
162A160ILE0-0.012-0.02432.065-0.002-0.0020.0000.0000.0000.000
163A161SER0-0.051-0.02833.7630.0030.0030.0000.0000.0000.000
164A162VAL00.0250.02434.681-0.003-0.0030.0000.0000.0000.000
165A163VAL0-0.067-0.03233.4830.0020.0020.0000.0000.0000.000
166A164GLU-1-0.807-0.92336.612-0.031-0.0310.0000.0000.0000.000
167A165PHE0-0.036-0.01532.680-0.002-0.0020.0000.0000.0000.000
168A166GLU-1-0.898-0.94237.226-0.028-0.0280.0000.0000.0000.000
169A167LYS10.9220.95435.8660.0310.0310.0000.0000.0000.000
170A168PRO00.004-0.01833.287-0.002-0.0020.0000.0000.0000.000
171A169GLY00.0190.00929.3960.0000.0000.0000.0000.0000.000
172A170SER00.0290.02630.1710.0010.0010.0000.0000.0000.000
173A171VAL00.0920.02029.555-0.002-0.0020.0000.0000.0000.000
174A172GLU-1-0.890-0.95431.213-0.033-0.0330.0000.0000.0000.000
175A173LEU00.0340.03830.7820.0010.0010.0000.0000.0000.000
176A174GLY00.0320.02329.231-0.001-0.0010.0000.0000.0000.000
177A175LEU0-0.018-0.01429.9160.0010.0010.0000.0000.0000.000
178A176LYS10.9120.96732.0780.0320.0320.0000.0000.0000.000
179A177THR0-0.033-0.04228.9000.0010.0010.0000.0000.0000.000
180A178VAL0-0.028-0.02527.9660.0000.0000.0000.0000.0000.000
181A179GLU-1-0.913-0.95330.299-0.023-0.0230.0000.0000.0000.000
182A180LYS10.8840.94833.8060.0320.0320.0000.0000.0000.000
183A181SER0-0.097-0.06428.463-0.001-0.0010.0000.0000.0000.000
184A182GLU-1-0.906-0.92629.646-0.020-0.0200.0000.0000.0000.000
185A183GLY0-0.007-0.00528.9300.0020.0020.0000.0000.0000.000
186A184LYS10.8710.94229.7510.0260.0260.0000.0000.0000.000
187A185ASP-1-0.810-0.92925.472-0.048-0.0480.0000.0000.0000.000
188A186ALA0-0.025-0.02226.948-0.007-0.0070.0000.0000.0000.000
189A187VAL0-0.0360.00329.0620.0050.0050.0000.0000.0000.000
190A188LEU00.0150.00330.852-0.005-0.0050.0000.0000.0000.000
191A189TRP00.000-0.00328.3200.0020.0020.0000.0000.0000.000
192A190ASP-1-0.773-0.89934.273-0.035-0.0350.0000.0000.0000.000
193A191LYS10.9660.98137.8090.0330.0330.0000.0000.0000.000
194A192HIS10.7620.87833.6010.0440.0440.0000.0000.0000.000
195A193GLY00.0560.02631.916-0.004-0.0040.0000.0000.0000.000
196A194VAL00.006-0.00228.6850.0040.0040.0000.0000.0000.000
197A195VAL0-0.030-0.01225.428-0.008-0.0080.0000.0000.0000.000
198A196ALA00.0080.01124.5370.0080.0080.0000.0000.0000.000
199A197PHE00.023-0.00822.235-0.014-0.0140.0000.0000.0000.000
200A198GLY00.0630.03020.8260.0060.0060.0000.0000.0000.000
201A199LYS10.9110.95017.8640.0070.0070.0000.0000.0000.000
202A200ASP-1-0.835-0.95014.281-0.148-0.1480.0000.0000.0000.000
203A201VAL0-0.034-0.02114.6340.0200.0200.0000.0000.0000.000
204A202ALA00.0190.00816.0270.0210.0210.0000.0000.0000.000
205A203GLU-1-0.736-0.82017.752-0.039-0.0390.0000.0000.0000.000
206A204ALA0-0.048-0.02219.8320.0120.0120.0000.0000.0000.000
207A205TYR0-0.041-0.04220.6620.0090.0090.0000.0000.0000.000
208A206ASP-1-0.849-0.92621.968-0.077-0.0770.0000.0000.0000.000
209A207ARG10.7370.86023.0300.0660.0660.0000.0000.0000.000
210A208VAL0-0.038-0.01025.1690.0060.0060.0000.0000.0000.000
211A209GLU-1-0.816-0.90025.927-0.074-0.0740.0000.0000.0000.000
212A210ILE0-0.0020.01827.7650.0060.0060.0000.0000.0000.000
213A211LEU0-0.024-0.01730.0180.0050.0050.0000.0000.0000.000
214A212GLU-1-0.763-0.90130.882-0.048-0.0480.0000.0000.0000.000
215A213LYS10.9630.99532.0860.0490.0490.0000.0000.0000.000
216A214ALA0-0.015-0.00634.0950.0030.0030.0000.0000.0000.000
217A215ALA00.0370.01635.7440.0030.0030.0000.0000.0000.000
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