Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 3JVVL

Calculation Name: 2PTH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PTH

Chain ID: A

ChEMBL ID:

UniProt ID: P0A7D1

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:


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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2102005.410064
FMO2-HF: Nuclear repulsion 2029416.602666
FMO2-HF: Total energy -72588.807398
FMO2-MP2: Total energy -72803.749393


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:1:THR)


Summations of interaction energy for fragment #1(A:1:THR)
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.
-38.634-35.33516.528-10.777-9.051-0.077
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.023
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].
3A3LYS10.8690.9202.9350.9803.5900.095-1.115-1.5910.003
4A4LEU0-0.054-0.0224.426-0.0810.038-0.001-0.014-0.1040.000
5A5ILE00.0240.0207.9670.0390.0390.0000.0000.0000.000
6A6VAL0-0.023-0.02410.625-0.087-0.0870.0000.0000.0000.000
7A7GLY00.0330.01214.0510.0530.0530.0000.0000.0000.000
8A8LEU0-0.080-0.04617.514-0.030-0.0300.0000.0000.0000.000
9A9ALA00.0240.00020.4430.0170.0170.0000.0000.0000.000
10A10ASN0-0.0160.01023.878-0.020-0.0200.0000.0000.0000.000
11A11PRO00.0440.02926.5650.0070.0070.0000.0000.0000.000
12A12GLY00.0530.02227.5770.0020.0020.0000.0000.0000.000
13A13ALA0-0.002-0.02430.2830.0060.0060.0000.0000.0000.000
14A14GLU-1-0.907-0.92132.480-0.002-0.0020.0000.0000.0000.000
15A15TYR0-0.010-0.03729.5100.0050.0050.0000.0000.0000.000
16A16ALA0-0.0030.02228.1130.0080.0080.0000.0000.0000.000
17A17ALA0-0.018-0.00428.2280.0090.0090.0000.0000.0000.000
18A18THR0-0.062-0.04129.7150.0050.0050.0000.0000.0000.000
19A19ARG10.8900.91127.886-0.061-0.0610.0000.0000.0000.000
20A20HIS0-0.085-0.07226.092-0.001-0.0010.0000.0000.0000.000
21A21ASN00.0170.00624.629-0.010-0.0100.0000.0000.0000.000
22A22ALA00.0250.01323.0440.0040.0040.0000.0000.0000.000
23A23GLY0-0.019-0.00819.2270.0230.0230.0000.0000.0000.000
24A24ALA0-0.013-0.00518.7240.0180.0180.0000.0000.0000.000
25A25TRP00.0270.01419.8510.0180.0180.0000.0000.0000.000
26A26PHE00.004-0.00712.5500.0020.0020.0000.0000.0000.000
27A27VAL0-0.0020.00414.8810.0300.0300.0000.0000.0000.000
28A28ASP-1-0.879-0.94916.6950.0390.0390.0000.0000.0000.000
29A29LEU0-0.052-0.02118.555-0.009-0.0090.0000.0000.0000.000
30A30LEU0-0.011-0.00812.2560.0080.0080.0000.0000.0000.000
31A31ALA00.0180.00415.885-0.023-0.0230.0000.0000.0000.000
32A32GLU-1-0.860-0.92317.6860.0710.0710.0000.0000.0000.000
33A33ARG10.8100.89617.843-0.213-0.2130.0000.0000.0000.000
34A34LEU00.0040.00612.812-0.012-0.0120.0000.0000.0000.000
35A35ARG10.7680.86517.073-0.076-0.0760.0000.0000.0000.000
36A36ALA00.0340.02716.674-0.025-0.0250.0000.0000.0000.000
37A37PRO0-0.030-0.01618.4800.0080.0080.0000.0000.0000.000
38A38LEU00.0180.02217.231-0.024-0.0240.0000.0000.0000.000
39A39ARG10.8510.90519.8000.1750.1750.0000.0000.0000.000
40A40GLU-1-0.830-0.87921.025-0.083-0.0830.0000.0000.0000.000
41A41GLU-1-0.825-0.87418.597-0.229-0.2290.0000.0000.0000.000
42A42ALA00.0510.01421.961-0.005-0.0050.0000.0000.0000.000
43A43LYS10.8270.93618.7240.2950.2950.0000.0000.0000.000
44A44PHE0-0.012-0.01916.584-0.025-0.0250.0000.0000.0000.000
45A45PHE00.024-0.00219.6370.0100.0100.0000.0000.0000.000
46A46GLY00.1330.05920.3550.0120.0120.0000.0000.0000.000
47A47TYR0-0.055-0.02620.452-0.012-0.0120.0000.0000.0000.000
48A48THR0-0.050-0.05016.0630.0080.0080.0000.0000.0000.000
49A49SER00.015-0.01315.2650.0040.0040.0000.0000.0000.000
50A50ARG10.7880.85610.7090.6600.6600.0000.0000.0000.000
51A51VAL00.0090.00910.4100.0180.0180.0000.0000.0000.000
52A52THR0-0.0030.0099.270-0.037-0.0370.0000.0000.0000.000
53A53LEU0-0.017-0.0067.6210.1300.1300.0000.0000.0000.000
54A54GLY00.009-0.0086.7390.0420.0420.0000.0000.0000.000
55A55GLY0-0.043-0.0188.119-0.026-0.0260.0000.0000.0000.000
56A56GLU-1-0.863-0.9021.666-33.985-36.29016.028-8.557-5.166-0.090
57A57ASP-1-0.800-0.8685.3350.0330.056-0.001-0.003-0.0190.000
58A58VAL00.0000.0125.211-0.156-0.1560.0000.0000.0000.000
59A59ARG10.8410.9137.6130.6810.6810.0000.0000.0000.000
60A60LEU00.0230.01410.1430.1140.1140.0000.0000.0000.000
61A61LEU0-0.013-0.01712.995-0.060-0.0600.0000.0000.0000.000
62A62VAL00.0460.02115.4260.0350.0350.0000.0000.0000.000
63A63PRO0-0.047-0.01918.130-0.015-0.0150.0000.0000.0000.000
64A64THR0-0.010-0.03120.8620.0120.0120.0000.0000.0000.000
65A65THR0-0.093-0.05522.9310.0000.0000.0000.0000.0000.000
66A66PHE00.0390.01625.4250.0030.0030.0000.0000.0000.000
67A67MET00.0710.07523.825-0.015-0.0150.0000.0000.0000.000
68A68ASN0-0.045-0.03324.105-0.004-0.0040.0000.0000.0000.000
69A69LEU0-0.0220.00124.994-0.006-0.0060.0000.0000.0000.000
70A70SER00.018-0.00419.956-0.012-0.0120.0000.0000.0000.000
71A71GLY0-0.013-0.01218.939-0.017-0.0170.0000.0000.0000.000
72A72LYS10.8470.94419.0030.0900.0900.0000.0000.0000.000
73A73ALA00.0260.01918.927-0.020-0.0200.0000.0000.0000.000
74A74VAL00.0060.00113.516-0.028-0.0280.0000.0000.0000.000
75A75ALA00.0300.02014.566-0.058-0.0580.0000.0000.0000.000
76A76ALA0-0.0030.01716.106-0.039-0.0390.0000.0000.0000.000
77A77MET0-0.005-0.00212.009-0.052-0.0520.0000.0000.0000.000
78A78ALA00.0080.00011.191-0.062-0.0620.0000.0000.0000.000
79A79SER0-0.028-0.02112.029-0.076-0.0760.0000.0000.0000.000
80A80PHE0-0.012-0.02514.475-0.015-0.0150.0000.0000.0000.000
81A81PHE0-0.014-0.02210.1250.0130.0130.0000.0000.0000.000
82A82ARG10.9160.9689.6390.4540.4540.0000.0000.0000.000
83A83ILE0-0.0140.0086.396-0.169-0.1690.0000.0000.0000.000
84A84ASN00.0380.0207.3760.3570.3570.0000.0000.0000.000
85A85PRO00.010-0.0178.499-0.127-0.1270.0000.0000.0000.000
86A86ASP-1-0.887-0.9436.315-1.058-1.0580.0000.0000.0000.000
87A87GLU-1-0.765-0.8543.578-3.841-3.2220.004-0.137-0.4860.000
88A88ILE0-0.039-0.0235.4950.6410.6410.0000.0000.0000.000
89A89LEU0-0.005-0.0018.2890.0280.0280.0000.0000.0000.000
90A90VAL0-0.022-0.01810.0790.0230.0230.0000.0000.0000.000
91A91ALA00.0200.02013.9380.0320.0320.0000.0000.0000.000
92A92HIS0-0.057-0.05315.920-0.036-0.0360.0000.0000.0000.000
93A93ASP-1-0.738-0.82619.4540.0870.0870.0000.0000.0000.000
94A94GLU-1-0.814-0.89521.6140.1070.1070.0000.0000.0000.000
95A95LEU00.0260.00923.6730.0010.0010.0000.0000.0000.000
96A96ASP-1-0.885-0.93324.5160.1070.1070.0000.0000.0000.000
97A97LEU0-0.058-0.02220.8950.0130.0130.0000.0000.0000.000
98A98PRO00.0120.01125.414-0.010-0.0100.0000.0000.0000.000
99A99PRO00.0240.00526.0890.0140.0140.0000.0000.0000.000
100A100GLY00.0230.02125.729-0.005-0.0050.0000.0000.0000.000
101A101VAL0-0.058-0.03322.1530.0180.0180.0000.0000.0000.000
102A102ALA00.0510.02218.357-0.018-0.0180.0000.0000.0000.000
103A103LYS10.8380.93216.935-0.267-0.2670.0000.0000.0000.000
104A104PHE00.0810.03811.755-0.031-0.0310.0000.0000.0000.000
105A105LYS10.8200.89913.296-0.174-0.1740.0000.0000.0000.000
106A106LEU00.0540.0498.828-0.026-0.0260.0000.0000.0000.000
107A107GLY00.0370.03211.8110.0200.0200.0000.0000.0000.000
108A108GLY0-0.022-0.01914.2180.0380.0380.0000.0000.0000.000
109A109GLY00.0280.00718.063-0.023-0.0230.0000.0000.0000.000
110A110HIS00.0700.03519.7340.0130.0130.0000.0000.0000.000
111A111GLY00.0320.02421.8330.0070.0070.0000.0000.0000.000
112A112GLY0-0.023-0.00924.4590.0040.0040.0000.0000.0000.000
113A113HIS00.003-0.02422.700-0.020-0.0200.0000.0000.0000.000
114A114ASN00.022-0.02123.700-0.017-0.0170.0000.0000.0000.000
115A115GLY00.0690.05222.947-0.012-0.0120.0000.0000.0000.000
116A116LEU00.0090.00517.515-0.022-0.0220.0000.0000.0000.000
117A117LYS10.8740.93219.8570.0030.0030.0000.0000.0000.000
118A118ASP-1-0.791-0.87222.272-0.111-0.1110.0000.0000.0000.000
119A119ILE00.0350.01815.808-0.020-0.0200.0000.0000.0000.000
120A120ILE0-0.026-0.00517.927-0.027-0.0270.0000.0000.0000.000
121A121SER0-0.049-0.01118.931-0.017-0.0170.0000.0000.0000.000
122A122LYS10.8390.88719.9220.1000.1000.0000.0000.0000.000
123A123LEU00.0090.02213.500-0.025-0.0250.0000.0000.0000.000
124A124GLY0-0.017-0.00316.925-0.025-0.0250.0000.0000.0000.000
125A125ASN0-0.065-0.04319.6860.0160.0160.0000.0000.0000.000
126A126ASN00.0500.03814.0970.0370.0370.0000.0000.0000.000
127A127PRO00.0200.00015.697-0.023-0.0230.0000.0000.0000.000
128A128ASN0-0.079-0.02411.8000.0790.0790.0000.0000.0000.000
129A129PHE00.0780.0409.867-0.090-0.0900.0000.0000.0000.000
130A130HIS0-0.002-0.0195.3440.5830.5830.0000.0000.0000.000
131A131ARG10.7750.88110.291-0.035-0.0350.0000.0000.0000.000
132A132LEU0-0.008-0.00313.1590.0780.0780.0000.0000.0000.000
133A133ARG10.7900.87114.851-0.198-0.1980.0000.0000.0000.000
134A134ILE00.0390.00617.8860.0310.0310.0000.0000.0000.000
135A135GLY0-0.008-0.01220.515-0.024-0.0240.0000.0000.0000.000
136A136ILE0-0.042-0.02023.945-0.003-0.0030.0000.0000.0000.000
137A137GLY00.0080.01027.006-0.009-0.0090.0000.0000.0000.000
138A138HIS00.0570.01429.532-0.007-0.0070.0000.0000.0000.000
139A139PRO0-0.0370.00031.8600.0000.0000.0000.0000.0000.000
140A140GLY00.0220.01534.936-0.004-0.0040.0000.0000.0000.000
141A141ASP-1-0.831-0.92236.4410.0360.0360.0000.0000.0000.000
142A142LYS10.9960.97133.119-0.031-0.0310.0000.0000.0000.000
143A143ASN0-0.051-0.02235.727-0.005-0.0050.0000.0000.0000.000
144A144LYS10.9060.95537.380-0.041-0.0410.0000.0000.0000.000
145A145VAL0-0.0030.00431.1410.0010.0010.0000.0000.0000.000
146A146VAL00.0180.01333.0980.0020.0020.0000.0000.0000.000
147A147GLY00.0410.01634.239-0.001-0.0010.0000.0000.0000.000
148A148PHE0-0.018-0.00930.284-0.001-0.0010.0000.0000.0000.000
149A149VAL00.0180.00028.9570.0040.0040.0000.0000.0000.000
150A150LEU0-0.016-0.00530.4490.0010.0010.0000.0000.0000.000
151A151GLY00.0470.04032.756-0.004-0.0040.0000.0000.0000.000
152A152LYS10.9400.97432.272-0.041-0.0410.0000.0000.0000.000
153A153PRO00.0070.00929.656-0.001-0.0010.0000.0000.0000.000
154A154PRO0-0.009-0.00132.708-0.003-0.0030.0000.0000.0000.000
155A155VAL00.0220.00333.6360.0060.0060.0000.0000.0000.000
156A156SER00.0250.01233.2030.0050.0050.0000.0000.0000.000
157A157GLU-1-0.795-0.88530.8440.0860.0860.0000.0000.0000.000
158A158GLN0-0.036-0.02927.4600.0020.0020.0000.0000.0000.000
159A159LYS10.8660.93128.288-0.084-0.0840.0000.0000.0000.000
160A160LEU00.0180.01727.9680.0110.0110.0000.0000.0000.000
161A161ILE00.000-0.00623.9170.0170.0170.0000.0000.0000.000
162A162ASP-1-0.825-0.91123.6370.1260.1260.0000.0000.0000.000
163A163GLU-1-0.836-0.91523.4910.1900.1900.0000.0000.0000.000
164A164ALA0-0.025-0.00421.6090.0260.0260.0000.0000.0000.000
165A165ILE00.0160.01219.0960.0420.0420.0000.0000.0000.000
166A166ASP-1-0.767-0.82118.2590.2780.2780.0000.0000.0000.000
167A167GLU-1-0.774-0.86518.1410.4310.4310.0000.0000.0000.000
168A168ALA00.0340.01915.5600.0720.0720.0000.0000.0000.000
169A169ALA00.0030.01813.9040.1190.1190.0000.0000.0000.000
170A170ARG10.8260.88813.337-0.181-0.1810.0000.0000.0000.000
171A171CYS0-0.071-0.03613.2550.0710.0710.0000.0000.0000.000
172A172THR0-0.015-0.0359.1320.1790.1790.0000.0000.0000.000
173A173GLU-1-0.866-0.9238.7100.8290.8290.0000.0000.0000.000
174A174MET00.0140.0168.9390.1590.1590.0000.0000.0000.000
175A175TRP0-0.006-0.0113.946-0.534-0.365-0.001-0.020-0.1480.000
176A176PHE0-0.036-0.0222.925-1.8860.1780.404-0.931-1.5370.010
177A177THR0-0.025-0.0215.961-0.438-0.4380.0000.0000.0000.000
178A178ASP-1-0.875-0.9109.1980.6650.6650.0000.0000.0000.000
179A179GLY00.0390.0316.765-0.086-0.0860.0000.0000.0000.000
180A180LEU00.0240.0056.703-0.425-0.4250.0000.0000.0000.000
181A181THR00.0030.0088.263-0.254-0.2540.0000.0000.0000.000
182A182LYS10.8940.94211.424-0.977-0.9770.0000.0000.0000.000
183A183ALA00.0340.0289.989-0.160-0.1600.0000.0000.0000.000
184A184THR0-0.029-0.03711.358-0.171-0.1710.0000.0000.0000.000
185A185ASN0-0.037-0.02413.571-0.100-0.1000.0000.0000.0000.000
186A186ARG10.8270.89015.447-0.559-0.5590.0000.0000.0000.000
187A187LEU00.0420.01414.757-0.064-0.0640.0000.0000.0000.000
188A188HIS0-0.078-0.04715.979-0.049-0.0490.0000.0000.0000.000
189A189ALA00.0690.03118.909-0.042-0.0420.0000.0000.0000.000
190A190PHE00.0080.01420.522-0.032-0.0320.0000.0000.0000.000
191A191LYS10.7710.87222.312-0.198-0.1980.0000.0000.0000.000
192A192ALA0-0.029-0.00124.058-0.016-0.0160.0000.0000.0000.000
193A193GLN0-0.0240.00225.264-0.001-0.0010.0000.0000.0000.000