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

tag_button

FMODB ID: 94552

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 OptHSide
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 -2990618.873186
FMO2-HF: Nuclear repulsion 2898426.581754
FMO2-HF: Total energy -92192.291432
FMO2-MP2: Total energy -92461.161447


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.
2.5715.7191.799-2.207-2.74-0.001
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 : 0.047 / q_NPA : 0.009
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].
3A1MET00.0400.0353.819-0.6950.4750.000-0.533-0.6360.000
4A2ARG10.9240.9232.234-0.0800.8001.759-1.274-1.3660.001
5A3GLU-1-0.882-0.9124.240-0.587-0.334-0.001-0.041-0.2110.000
6A4THR00.010-0.0096.0540.7270.7270.0000.0000.0000.000
7A5ILE0-0.0050.0037.9020.2650.2650.0000.0000.0000.000
8A6ARG10.9320.9645.5241.3711.3710.0000.0000.0000.000
9A7GLU-1-0.854-0.93610.407-0.186-0.1860.0000.0000.0000.000
10A8ILE0-0.021-0.01612.2130.0980.0980.0000.0000.0000.000
11A9GLN0-0.062-0.03112.9390.0140.0140.0000.0000.0000.000
12A10LYS10.9590.97714.7060.2400.2400.0000.0000.0000.000
13A11VAL00.000-0.00316.4840.0390.0390.0000.0000.0000.000
14A12ALA0-0.007-0.00118.0270.0280.0280.0000.0000.0000.000
15A13TYR00.0260.00819.3000.0230.0230.0000.0000.0000.000
16A14TRP0-0.039-0.02519.8040.0230.0230.0000.0000.0000.000
17A15LEU00.0120.01022.5380.0150.0150.0000.0000.0000.000
18A16ALA0-0.027-0.01524.0080.0120.0120.0000.0000.0000.000
19A17ILE0-0.054-0.01225.0400.0110.0110.0000.0000.0000.000
20A18LYS10.8010.88026.4140.0880.0880.0000.0000.0000.000
21A19GLY00.0090.00828.7900.0070.0070.0000.0000.0000.000
22A20LEU0-0.035-0.00426.2440.0030.0030.0000.0000.0000.000
23A21SER0-0.043-0.01826.043-0.003-0.0030.0000.0000.0000.000
24A22GLU-1-0.903-0.95028.048-0.075-0.0750.0000.0000.0000.000
25A23ALA0-0.034-0.02329.8830.0000.0000.0000.0000.0000.000
26A24ASN0-0.031-0.02826.849-0.004-0.0040.0000.0000.0000.000
27A25ALA00.0040.01427.183-0.003-0.0030.0000.0000.0000.000
28A26GLY00.0270.00325.7110.0040.0040.0000.0000.0000.000
29A27ASN0-0.062-0.00922.089-0.017-0.0170.0000.0000.0000.000
30A28ILE00.0530.02117.0490.0110.0110.0000.0000.0000.000
31A29SER00.0030.00517.2520.0010.0010.0000.0000.0000.000
32A30VAL00.0110.01012.5330.0240.0240.0000.0000.0000.000
33A31ARG10.8420.91814.3090.0210.0210.0000.0000.0000.000
34A32LEU0-0.015-0.0348.635-0.013-0.0130.0000.0000.0000.000
35A33ASP-1-0.882-0.93410.7050.1100.1100.0000.0000.0000.000
36A34GLU-1-0.939-0.9636.8120.7780.7780.0000.0000.0000.000
37A35ARG10.8000.8548.733-0.102-0.1020.0000.0000.0000.000
38A36PRO0-0.033-0.0176.7270.0260.0260.0000.0000.0000.000
39A37GLU-1-0.853-0.9103.4850.6401.4850.041-0.359-0.527-0.002
40A38GLY00.0040.0246.0950.0360.0360.0000.0000.0000.000
41A39TYR0-0.067-0.0548.016-0.075-0.0750.0000.0000.0000.000
42A40GLU-1-0.931-0.97110.957-0.146-0.1460.0000.0000.0000.000
43A41VAL0-0.042-0.00413.717-0.023-0.0230.0000.0000.0000.000
44A42LYS10.9350.97916.7290.1240.1240.0000.0000.0000.000
45A43SER0-0.020-0.02818.5370.0120.0120.0000.0000.0000.000
46A44VAL00.0670.05120.331-0.007-0.0070.0000.0000.0000.000
47A45ASN0-0.037-0.02022.2630.0050.0050.0000.0000.0000.000
48A46GLU-1-0.816-0.91624.983-0.043-0.0430.0000.0000.0000.000
49A47TYR0-0.100-0.05722.628-0.010-0.0100.0000.0000.0000.000
50A48GLY0-0.048-0.00227.150-0.002-0.0020.0000.0000.0000.000
51A49PHE0-0.053-0.05126.7080.0030.0030.0000.0000.0000.000
52A50ASP-1-0.915-0.97429.745-0.030-0.0300.0000.0000.0000.000
53A51TYR0-0.087-0.03922.465-0.001-0.0010.0000.0000.0000.000
54A52ASP-1-0.880-0.94127.785-0.012-0.0120.0000.0000.0000.000
55A53GLY00.0280.02525.3840.0040.0040.0000.0000.0000.000
56A54PRO00.005-0.01921.6460.0000.0000.0000.0000.0000.000
57A55GLU-1-0.735-0.81317.752-0.008-0.0080.0000.0000.0000.000
58A56MET0-0.059-0.03116.2190.0090.0090.0000.0000.0000.000
59A57TYR00.0620.02112.0290.0110.0110.0000.0000.0000.000
60A58LEU0-0.0030.01413.625-0.007-0.0070.0000.0000.0000.000
61A59LEU00.0230.0149.4260.0040.0040.0000.0000.0000.000
62A60ILE0-0.042-0.02613.9250.0350.0350.0000.0000.0000.000
63A61THR00.0240.03017.224-0.012-0.0120.0000.0000.0000.000
64A62ALA00.0240.01518.8280.0180.0180.0000.0000.0000.000
65A63THR0-0.021-0.00520.6810.0070.0070.0000.0000.0000.000
66A64GLY0-0.038-0.01124.446-0.001-0.0010.0000.0000.0000.000
67A65SER0-0.054-0.04021.2860.0000.0000.0000.0000.0000.000
68A66ARG10.9010.92123.3410.1230.1230.0000.0000.0000.000
69A67MET00.0610.04321.442-0.017-0.0170.0000.0000.0000.000
70A68ARG10.9280.95621.7810.0980.0980.0000.0000.0000.000
71A69GLU-1-0.762-0.86522.089-0.124-0.1240.0000.0000.0000.000
72A70VAL00.0080.00917.702-0.011-0.0110.0000.0000.0000.000
73A71TYR0-0.086-0.05116.737-0.038-0.0380.0000.0000.0000.000
74A72GLU-1-0.909-0.92617.069-0.184-0.1840.0000.0000.0000.000
75A73ASP-1-0.837-0.90417.057-0.238-0.2380.0000.0000.0000.000
76A74ASP-1-0.851-0.92911.589-0.439-0.4390.0000.0000.0000.000
77A75SER0-0.041-0.03313.919-0.007-0.0070.0000.0000.0000.000
78A76LYS10.7960.88716.1120.1890.1890.0000.0000.0000.000
79A77ILE0-0.033-0.02713.1280.0200.0200.0000.0000.0000.000
80A78CYS0-0.0240.00514.453-0.005-0.0050.0000.0000.0000.000
81A79LEU0-0.0160.0239.185-0.018-0.0180.0000.0000.0000.000
82A80LEU0-0.023-0.01713.1360.0410.0410.0000.0000.0000.000
83A81HIS10.8410.93714.7780.0550.0550.0000.0000.0000.000
84A82VAL0-0.040-0.02816.2530.0080.0080.0000.0000.0000.000
85A83LEU00.0280.00919.3900.0120.0120.0000.0000.0000.000
86A84PRO00.0550.03721.728-0.005-0.0050.0000.0000.0000.000
87A85GLY00.0410.04425.201-0.001-0.0010.0000.0000.0000.000
88A86LYS10.9310.94027.9350.0340.0340.0000.0000.0000.000
89A87HIS0-0.051-0.03224.801-0.005-0.0050.0000.0000.0000.000
90A88TYR00.0460.04020.173-0.001-0.0010.0000.0000.0000.000
91A89GLU-1-0.847-0.93316.864-0.074-0.0740.0000.0000.0000.000
92A90ILE0-0.055-0.04516.844-0.012-0.0120.0000.0000.0000.000
93A91LEU0-0.030-0.01311.3100.0120.0120.0000.0000.0000.000
94A92HIS00.0320.01011.0390.0370.0370.0000.0000.0000.000
95A93GLY00.0380.01013.5030.0120.0120.0000.0000.0000.000
96A94ASN0-0.012-0.01216.3540.0220.0220.0000.0000.0000.000
97A95GLY0-0.026-0.00719.6850.0190.0190.0000.0000.0000.000
98A96LYS10.8890.94820.7750.0790.0790.0000.0000.0000.000
99A97PRO00.0720.02019.764-0.005-0.0050.0000.0000.0000.000
100A98THR00.0120.00321.5790.0190.0190.0000.0000.0000.000
101A99SER00.0720.02324.0230.0030.0030.0000.0000.0000.000
102A100GLU-1-0.818-0.87025.066-0.097-0.0970.0000.0000.0000.000
103A101PHE00.0110.00220.925-0.001-0.0010.0000.0000.0000.000
104A102PRO00.0380.01624.1470.0000.0000.0000.0000.0000.000
105A103THR0-0.052-0.03026.5670.0030.0030.0000.0000.0000.000
106A104HIS10.8400.87721.3440.1260.1260.0000.0000.0000.000
107A105LEU0-0.0030.01722.2660.0010.0010.0000.0000.0000.000
108A106MET0-0.0080.00723.5550.0070.0070.0000.0000.0000.000
109A107ILE00.0150.01323.7320.0060.0060.0000.0000.0000.000
110A108HIS0-0.001-0.01018.2170.0180.0180.0000.0000.0000.000
111A109ALA0-0.030-0.00721.8420.0090.0090.0000.0000.0000.000
112A110LYS10.8720.90423.4290.0230.0230.0000.0000.0000.000
113A111PHE00.0140.01321.6460.0080.0080.0000.0000.0000.000
114A112LYS10.8590.92316.8760.0150.0150.0000.0000.0000.000
115A113GLU-1-0.867-0.90621.4030.0030.0030.0000.0000.0000.000
116A114MET0-0.011-0.00424.7980.0090.0090.0000.0000.0000.000
117A115ASN0-0.071-0.05424.3000.0010.0010.0000.0000.0000.000
118A116PRO00.0690.03320.056-0.009-0.0090.0000.0000.0000.000
119A117GLU-1-0.853-0.90818.7310.0500.0500.0000.0000.0000.000
120A118LYS10.8310.93918.5930.0140.0140.0000.0000.0000.000
121A119LYS10.9651.01311.2620.2300.2300.0000.0000.0000.000
122A120ALA0-0.046-0.00716.284-0.038-0.0380.0000.0000.0000.000
123A121ILE0-0.002-0.00117.9130.0230.0230.0000.0000.0000.000
124A122VAL0-0.0110.00320.162-0.022-0.0220.0000.0000.0000.000
125A123HIS10.8150.90222.3040.1040.1040.0000.0000.0000.000
126A124THR00.0420.00525.472-0.007-0.0070.0000.0000.0000.000
127A125HIS0-0.048-0.03027.5880.0110.0110.0000.0000.0000.000
128A126PRO00.0240.03129.8960.0000.0000.0000.0000.0000.000
129A127LEU00.1170.05932.2100.0040.0040.0000.0000.0000.000
130A128ASN0-0.050-0.02035.5390.0070.0070.0000.0000.0000.000
131A129LEU00.0220.00332.4760.0030.0030.0000.0000.0000.000
132A130LEU0-0.050-0.01934.1590.0020.0020.0000.0000.0000.000
133A131THR0-0.057-0.04937.2500.0030.0030.0000.0000.0000.000
134A132LEU0-0.009-0.00438.8450.0030.0030.0000.0000.0000.000
135A133MET0-0.0270.02434.9500.0020.0020.0000.0000.0000.000
136A134ASN0-0.049-0.04440.6190.0020.0020.0000.0000.0000.000
137A135LEU0-0.041-0.00243.4420.0010.0010.0000.0000.0000.000
138A136GLU-1-0.882-0.94945.753-0.025-0.0250.0000.0000.0000.000
139A137GLU-1-0.948-0.95747.446-0.020-0.0200.0000.0000.0000.000
140A138PHE0-0.012-0.02538.5850.0000.0000.0000.0000.0000.000
141A139GLN00.021-0.01241.2530.0000.0000.0000.0000.0000.000
142A140GLU-1-0.928-0.96243.980-0.017-0.0170.0000.0000.0000.000
143A141LEU00.0040.01043.6730.0010.0010.0000.0000.0000.000
144A142LEU0-0.0130.00237.8670.0000.0000.0000.0000.0000.000
145A143PRO00.0250.01940.1640.0000.0000.0000.0000.0000.000
146A144LYS10.9520.97441.6760.0160.0160.0000.0000.0000.000
147A145MET00.0060.00437.5490.0000.0000.0000.0000.0000.000
148A146MET0-0.004-0.00735.261-0.001-0.0010.0000.0000.0000.000
149A147LYS10.8900.95037.6160.0110.0110.0000.0000.0000.000
150A148ILE0-0.0360.01238.8670.0020.0020.0000.0000.0000.000
151A149HIS0-0.006-0.01633.5470.0020.0020.0000.0000.0000.000
152A150PRO00.007-0.00435.622-0.001-0.0010.0000.0000.0000.000
153A151GLU-1-0.783-0.89430.928-0.035-0.0350.0000.0000.0000.000
154A152VAL00.0050.02231.422-0.001-0.0010.0000.0000.0000.000
155A153LEU00.020-0.00332.4300.0010.0010.0000.0000.0000.000
156A154ILE0-0.025-0.00729.1080.0020.0020.0000.0000.0000.000
157A155PHE00.0370.02424.3900.0030.0030.0000.0000.0000.000
158A156PHE0-0.069-0.03828.546-0.003-0.0030.0000.0000.0000.000
159A157PRO0-0.0020.01230.4060.0010.0010.0000.0000.0000.000
160A158GLN0-0.014-0.01131.3240.0020.0020.0000.0000.0000.000
161A159GLY00.0040.01733.6490.0000.0000.0000.0000.0000.000
162A160ILE00.002-0.02332.138-0.001-0.0010.0000.0000.0000.000
163A161SER0-0.057-0.03234.0090.0020.0020.0000.0000.0000.000
164A162VAL00.0140.02234.681-0.004-0.0040.0000.0000.0000.000
165A163VAL0-0.039-0.01733.6670.0020.0020.0000.0000.0000.000
166A164GLU-1-0.786-0.89536.612-0.032-0.0320.0000.0000.0000.000
167A165PHE0-0.012-0.00632.748-0.002-0.0020.0000.0000.0000.000
168A166GLU-1-0.842-0.90837.184-0.030-0.0300.0000.0000.0000.000
169A167LYS10.8430.90036.0780.0330.0330.0000.0000.0000.000
170A168PRO00.018-0.01033.276-0.002-0.0020.0000.0000.0000.000
171A169GLY0-0.0040.00629.463-0.001-0.0010.0000.0000.0000.000
172A170SER00.0280.02630.1620.0010.0010.0000.0000.0000.000
173A171VAL00.0790.02329.518-0.002-0.0020.0000.0000.0000.000
174A172GLU-1-0.794-0.89031.213-0.034-0.0340.0000.0000.0000.000
175A173LEU00.0240.03530.9620.0010.0010.0000.0000.0000.000
176A174GLY00.0130.01629.2210.0000.0000.0000.0000.0000.000
177A175LEU00.003-0.00529.9160.0020.0020.0000.0000.0000.000
178A176LYS10.7910.88432.0770.0340.0340.0000.0000.0000.000
179A177THR0-0.022-0.03628.9020.0010.0010.0000.0000.0000.000
180A178VAL0-0.016-0.01527.7730.0010.0010.0000.0000.0000.000
181A179GLU-1-0.907-0.94630.299-0.020-0.0200.0000.0000.0000.000
182A180LYS10.8660.93733.8450.0310.0310.0000.0000.0000.000
183A181SER0-0.069-0.03428.478-0.001-0.0010.0000.0000.0000.000
184A182GLU-1-0.892-0.93629.646-0.009-0.0090.0000.0000.0000.000
185A183GLY00.0060.00928.9280.0020.0020.0000.0000.0000.000
186A184LYS10.8500.92929.7510.0220.0220.0000.0000.0000.000
187A185ASP-1-0.814-0.91325.915-0.029-0.0290.0000.0000.0000.000
188A186ALA0-0.013-0.01926.948-0.007-0.0070.0000.0000.0000.000
189A187VAL0-0.0360.00229.0620.0050.0050.0000.0000.0000.000
190A188LEU00.0210.00230.852-0.006-0.0060.0000.0000.0000.000
191A189TRP0-0.015-0.01628.1380.0010.0010.0000.0000.0000.000
192A190ASP-1-0.777-0.89834.273-0.037-0.0370.0000.0000.0000.000
193A191LYS10.9160.94837.8090.0340.0340.0000.0000.0000.000
194A192HIS10.7400.86233.7420.0480.0480.0000.0000.0000.000
195A193GLY00.0540.02431.915-0.005-0.0050.0000.0000.0000.000
196A194VAL0-0.015-0.00528.5630.0050.0050.0000.0000.0000.000
197A195VAL0-0.001-0.01125.505-0.010-0.0100.0000.0000.0000.000
198A196ALA00.0090.01324.5500.0090.0090.0000.0000.0000.000
199A197PHE00.032-0.00622.243-0.015-0.0150.0000.0000.0000.000
200A198GLY00.0560.01420.8320.0050.0050.0000.0000.0000.000
201A199LYS10.8390.90417.780-0.034-0.0340.0000.0000.0000.000
202A200ASP-1-0.876-0.96114.213-0.105-0.1050.0000.0000.0000.000
203A201VAL0-0.008-0.00914.1620.0150.0150.0000.0000.0000.000
204A202ALA00.0080.00016.0330.0170.0170.0000.0000.0000.000
205A203GLU-1-0.765-0.84617.752-0.018-0.0180.0000.0000.0000.000
206A204ALA0-0.047-0.01819.8320.0100.0100.0000.0000.0000.000
207A205TYR0-0.070-0.08620.5840.0040.0040.0000.0000.0000.000
208A206ASP-1-0.866-0.93921.982-0.071-0.0710.0000.0000.0000.000
209A207ARG10.7420.86823.3080.0510.0510.0000.0000.0000.000
210A208VAL0-0.023-0.00725.1460.0050.0050.0000.0000.0000.000
211A209GLU-1-0.751-0.82525.258-0.075-0.0750.0000.0000.0000.000
212A210ILE0-0.0190.00827.7360.0060.0060.0000.0000.0000.000
213A211LEU0-0.017-0.01229.8790.0050.0050.0000.0000.0000.000
214A212GLU-1-0.736-0.88630.929-0.053-0.0530.0000.0000.0000.000
215A213LYS10.8270.91131.7700.0430.0430.0000.0000.0000.000
216A214ALA0-0.022-0.01034.0940.0030.0030.0000.0000.0000.000
217A215ALA00.0370.00935.7430.0030.0030.0000.0000.0000.000
218A216GLU-1-0.903-0.95035.945-0.046-0.0460.0000.0000.0000.000
219A217ILE0-0.048-0.03137.0360.0030.0030.0000.0000.0000.000
220A218LEU0-0.009-0.01140.0800.0020.0020.0000.0000.0000.000
221A219LEU00.0430.00740.4030.0020.0020.0000.0000.0000.000
222A220ARG10.9420.99642.4910.0320.0320.0000.0000.0000.000
223A221VAL0-0.021-0.01544.2070.0020.0020.0000.0000.0000.000
224A222LEU00.0210.00845.4640.0020.0020.0000.0000.0000.000
225A223SER0-0.060-0.02846.1900.0010.0010.0000.0000.0000.000
226A224LEU0-0.076-0.03948.2620.0000.0000.0000.0000.0000.000
227A225GLY0-0.024-0.00250.9830.0010.0010.0000.0000.0000.000
228A226ARG10.8900.93950.3460.0180.0180.0000.0000.0000.000
229A227ASN00.021-0.02046.8750.0000.0000.0000.0000.0000.000
230A228PRO0-0.077-0.04148.6450.0000.0000.0000.0000.0000.000
231A229THR00.0420.05148.8280.0000.0000.0000.0000.0000.000
232A230GLY00.0200.02549.7260.0000.0000.0000.0000.0000.000