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: JQ999

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2091002.097439
FMO2-HF: Nuclear repulsion 2018413.430715
FMO2-HF: Total energy -72588.666724
FMO2-MP2: Total energy -72803.586724


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.
-25.844-14.6151.607-5.794-7.042-0.033
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 : 0.018 / q_NPA : 0.015
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].
3A3LYS10.8930.9223.0851.5044.4450.066-1.378-1.6300.005
4A4LEU0-0.054-0.0224.7560.1750.274-0.001-0.007-0.0910.000
5A5ILE00.0300.0228.3610.0420.0420.0000.0000.0000.000
6A6VAL0-0.028-0.02510.823-0.049-0.0490.0000.0000.0000.000
7A7GLY00.0360.02014.2950.0640.0640.0000.0000.0000.000
8A8LEU0-0.063-0.04117.574-0.029-0.0290.0000.0000.0000.000
9A9ALA00.015-0.00120.4390.0220.0220.0000.0000.0000.000
10A10ASN0-0.0180.01123.909-0.024-0.0240.0000.0000.0000.000
11A11PRO00.0400.02426.8660.0060.0060.0000.0000.0000.000
12A12GLY00.0560.02327.9730.0030.0030.0000.0000.0000.000
13A13ALA0-0.003-0.02130.6940.0060.0060.0000.0000.0000.000
14A14GLU-1-0.902-0.92332.675-0.017-0.0170.0000.0000.0000.000
15A15TYR0-0.028-0.04229.8990.0050.0050.0000.0000.0000.000
16A16ALA0-0.0060.01728.5140.0070.0070.0000.0000.0000.000
17A17ALA0-0.004-0.00228.2500.0070.0070.0000.0000.0000.000
18A18THR0-0.063-0.03729.5700.0080.0080.0000.0000.0000.000
19A19ARG10.9190.93527.515-0.060-0.0600.0000.0000.0000.000
20A20HIS0-0.079-0.06425.702-0.003-0.0030.0000.0000.0000.000
21A21ASN0-0.0070.00724.226-0.012-0.0120.0000.0000.0000.000
22A22ALA00.0380.02422.4030.0030.0030.0000.0000.0000.000
23A23GLY0-0.010-0.00918.7270.0200.0200.0000.0000.0000.000
24A24ALA0-0.008-0.01218.5160.0120.0120.0000.0000.0000.000
25A25TRP00.0140.01520.4460.0110.0110.0000.0000.0000.000
26A26PHE00.007-0.00312.4430.0000.0000.0000.0000.0000.000
27A27VAL0-0.003-0.00414.9140.0200.0200.0000.0000.0000.000
28A28ASP-1-0.895-0.94916.879-0.010-0.0100.0000.0000.0000.000
29A29LEU0-0.051-0.01518.540-0.006-0.0060.0000.0000.0000.000
30A30LEU0-0.025-0.01712.2980.0050.0050.0000.0000.0000.000
31A31ALA00.0240.01315.994-0.021-0.0210.0000.0000.0000.000
32A32GLU-1-0.883-0.93517.6440.0450.0450.0000.0000.0000.000
33A33ARG10.8320.88617.691-0.207-0.2070.0000.0000.0000.000
34A34LEU0-0.0020.00912.981-0.008-0.0080.0000.0000.0000.000
35A35ARG10.7800.87917.457-0.047-0.0470.0000.0000.0000.000
36A36ALA00.0140.01716.761-0.024-0.0240.0000.0000.0000.000
37A37PRO0-0.023-0.02318.5720.0030.0030.0000.0000.0000.000
38A38LEU00.0140.02417.106-0.030-0.0300.0000.0000.0000.000
39A39ARG10.8590.91420.3890.2360.2360.0000.0000.0000.000
40A40GLU-1-0.849-0.90521.211-0.135-0.1350.0000.0000.0000.000
41A41GLU-1-0.838-0.89118.835-0.296-0.2960.0000.0000.0000.000
42A42ALA00.0450.00322.322-0.007-0.0070.0000.0000.0000.000
43A43LYS10.8310.93119.6110.3530.3530.0000.0000.0000.000
44A44PHE0-0.013-0.01717.297-0.027-0.0270.0000.0000.0000.000
45A45PHE0-0.010-0.01619.9060.0050.0050.0000.0000.0000.000
46A46GLY00.1240.05620.6590.0140.0140.0000.0000.0000.000
47A47TYR0-0.037-0.00620.420-0.012-0.0120.0000.0000.0000.000
48A48THR0-0.045-0.03516.075-0.004-0.0040.0000.0000.0000.000
49A49SER00.017-0.00515.3170.0140.0140.0000.0000.0000.000
50A50ARG10.7700.84611.0090.7620.7620.0000.0000.0000.000
51A51VAL00.0050.00410.6580.0520.0520.0000.0000.0000.000
52A52THR0-0.0040.0059.524-0.093-0.0930.0000.0000.0000.000
53A53LEU0-0.016-0.0087.7320.1470.1470.0000.0000.0000.000
54A54GLY00.0490.0276.870-0.039-0.0390.0000.0000.0000.000
55A55GLY0-0.067-0.0317.476-0.110-0.1100.0000.0000.0000.000
56A56GLU-1-0.893-0.9472.372-21.802-16.1971.007-3.536-3.076-0.045
57A57ASP-1-0.842-0.8825.784-0.261-0.2610.0000.0000.0000.000
58A58VAL00.0080.0095.576-0.278-0.2780.0000.0000.0000.000
59A59ARG10.9200.9647.7620.8830.8830.0000.0000.0000.000
60A60LEU00.0130.00710.3410.0690.0690.0000.0000.0000.000
61A61LEU0-0.007-0.01513.114-0.049-0.0490.0000.0000.0000.000
62A62VAL00.0400.03215.6490.0350.0350.0000.0000.0000.000
63A63PRO0-0.044-0.02818.305-0.013-0.0130.0000.0000.0000.000
64A64THR0-0.030-0.03421.0010.0160.0160.0000.0000.0000.000
65A65THR0-0.056-0.03223.3560.0010.0010.0000.0000.0000.000
66A66PHE00.0470.02325.7730.0060.0060.0000.0000.0000.000
67A67MET00.0550.03923.524-0.019-0.0190.0000.0000.0000.000
68A68ASN0-0.034-0.02724.456-0.007-0.0070.0000.0000.0000.000
69A69LEU0-0.0230.00225.718-0.005-0.0050.0000.0000.0000.000
70A70SER00.006-0.01420.525-0.015-0.0150.0000.0000.0000.000
71A71GLY0-0.023-0.02019.582-0.026-0.0260.0000.0000.0000.000
72A72LYS10.8990.96419.5400.1210.1210.0000.0000.0000.000
73A73ALA00.0380.02519.235-0.024-0.0240.0000.0000.0000.000
74A74VAL00.0000.00413.992-0.039-0.0390.0000.0000.0000.000
75A75ALA00.0320.02015.090-0.074-0.0740.0000.0000.0000.000
76A76ALA0-0.0050.01416.728-0.043-0.0430.0000.0000.0000.000
77A77MET0-0.006-0.00112.526-0.049-0.0490.0000.0000.0000.000
78A78ALA00.0060.00211.831-0.077-0.0770.0000.0000.0000.000
79A79SER0-0.015-0.01712.777-0.073-0.0730.0000.0000.0000.000
80A80PHE0-0.008-0.01215.4180.0070.0070.0000.0000.0000.000
81A81PHE0-0.026-0.03010.4960.0190.0190.0000.0000.0000.000
82A82ARG10.9070.96810.5390.5340.5340.0000.0000.0000.000
83A83ILE0-0.0290.0006.831-0.137-0.1370.0000.0000.0000.000
84A84ASN00.0300.0147.1530.4550.4550.0000.0000.0000.000
85A85PRO00.009-0.0198.262-0.198-0.1980.0000.0000.0000.000
86A86ASP-1-0.890-0.9446.167-1.137-1.1370.0000.0000.0000.000
87A87GLU-1-0.780-0.8653.462-4.363-3.8210.004-0.108-0.4380.000
88A88ILE0-0.029-0.0155.2260.5640.581-0.001-0.008-0.0080.000
89A89LEU00.0080.0078.0100.1080.1080.0000.0000.0000.000
90A90VAL0-0.025-0.0189.786-0.004-0.0040.0000.0000.0000.000
91A91ALA00.0150.01513.6050.0620.0620.0000.0000.0000.000
92A92HIS0-0.053-0.05515.637-0.039-0.0390.0000.0000.0000.000
93A93ASP-1-0.746-0.83519.1470.0790.0790.0000.0000.0000.000
94A94GLU-1-0.820-0.90621.0260.1130.1130.0000.0000.0000.000
95A95LEU00.0290.00523.0760.0050.0050.0000.0000.0000.000
96A96ASP-1-0.945-0.97224.5420.1060.1060.0000.0000.0000.000
97A97LEU0-0.074-0.02620.5520.0180.0180.0000.0000.0000.000
98A98PRO00.0210.01025.070-0.013-0.0130.0000.0000.0000.000
99A99PRO00.0310.00425.6260.0160.0160.0000.0000.0000.000
100A100GLY00.0140.01825.146-0.003-0.0030.0000.0000.0000.000
101A101VAL0-0.051-0.02521.8030.0230.0230.0000.0000.0000.000
102A102ALA00.0470.01517.782-0.021-0.0210.0000.0000.0000.000
103A103LYS10.8730.94416.597-0.313-0.3130.0000.0000.0000.000
104A104PHE00.0810.04211.241-0.030-0.0300.0000.0000.0000.000
105A105LYS10.8480.92312.860-0.204-0.2040.0000.0000.0000.000
106A106LEU00.0520.0418.269-0.021-0.0210.0000.0000.0000.000
107A107GLY00.0310.02811.6040.0150.0150.0000.0000.0000.000
108A108GLY0-0.045-0.03414.0030.0400.0400.0000.0000.0000.000
109A109GLY00.0350.01317.764-0.032-0.0320.0000.0000.0000.000
110A110HIS00.0590.02419.3340.0120.0120.0000.0000.0000.000
111A111GLY00.0070.00621.4430.0080.0080.0000.0000.0000.000
112A112GLY0-0.010-0.00424.0770.0060.0060.0000.0000.0000.000
113A113HIS00.012-0.00322.373-0.021-0.0210.0000.0000.0000.000
114A114ASN00.013-0.03923.457-0.017-0.0170.0000.0000.0000.000
115A115GLY00.0730.05622.439-0.014-0.0140.0000.0000.0000.000
116A116LEU0-0.011-0.00817.204-0.029-0.0290.0000.0000.0000.000
117A117LYS10.9050.95519.7460.0190.0190.0000.0000.0000.000
118A118ASP-1-0.794-0.87721.993-0.149-0.1490.0000.0000.0000.000
119A119ILE00.0280.01315.733-0.022-0.0220.0000.0000.0000.000
120A120ILE0-0.021-0.00117.486-0.030-0.0300.0000.0000.0000.000
121A121SER0-0.048-0.01418.588-0.017-0.0170.0000.0000.0000.000
122A122LYS10.8570.90220.0920.1370.1370.0000.0000.0000.000
123A123LEU0-0.0230.01413.521-0.028-0.0280.0000.0000.0000.000
124A124GLY0-0.0040.00016.952-0.023-0.0230.0000.0000.0000.000
125A125ASN0-0.068-0.04119.5470.0200.0200.0000.0000.0000.000
126A126ASN00.0690.04013.4590.0520.0520.0000.0000.0000.000
127A127PRO00.0180.00015.466-0.031-0.0310.0000.0000.0000.000
128A128ASN0-0.078-0.03111.3310.1040.1040.0000.0000.0000.000
129A129PHE00.0690.0539.419-0.105-0.1050.0000.0000.0000.000
130A130HIS00.028-0.0085.0020.6850.6850.0000.0000.0000.000
131A131ARG10.7740.8869.840-0.056-0.0560.0000.0000.0000.000
132A132LEU0-0.0010.01212.8360.0960.0960.0000.0000.0000.000
133A133ARG10.8110.88114.305-0.250-0.2500.0000.0000.0000.000
134A134ILE00.0470.01017.9010.0350.0350.0000.0000.0000.000
135A135GLY00.0040.00420.263-0.029-0.0290.0000.0000.0000.000
136A136ILE0-0.032-0.01123.617-0.005-0.0050.0000.0000.0000.000
137A137GLY00.0050.00726.747-0.009-0.0090.0000.0000.0000.000
138A138HIS00.0470.01429.231-0.009-0.0090.0000.0000.0000.000
139A139PRO0-0.029-0.00931.4660.0000.0000.0000.0000.0000.000
140A140GLY00.0160.01534.710-0.002-0.0020.0000.0000.0000.000
141A141ASP-1-0.828-0.90936.2250.0360.0360.0000.0000.0000.000
142A142LYS11.0040.96832.693-0.031-0.0310.0000.0000.0000.000
143A143ASN0-0.062-0.02435.457-0.006-0.0060.0000.0000.0000.000
144A144LYS10.9080.94937.142-0.041-0.0410.0000.0000.0000.000
145A145VAL00.0000.00630.9160.0010.0010.0000.0000.0000.000
146A146VAL00.0130.01133.0440.0010.0010.0000.0000.0000.000
147A147GLY00.0410.01434.101-0.001-0.0010.0000.0000.0000.000
148A148PHE0-0.0020.00529.942-0.001-0.0010.0000.0000.0000.000
149A149VAL00.037-0.00228.7730.0040.0040.0000.0000.0000.000
150A150LEU0-0.035-0.00730.076-0.001-0.0010.0000.0000.0000.000
151A151GLY00.0470.03532.559-0.004-0.0040.0000.0000.0000.000
152A152LYS10.9310.96632.021-0.031-0.0310.0000.0000.0000.000
153A153PRO00.0000.00929.596-0.001-0.0010.0000.0000.0000.000
154A154PRO00.0130.00932.726-0.004-0.0040.0000.0000.0000.000
155A155VAL00.031-0.00333.5260.0060.0060.0000.0000.0000.000
156A156SER00.0060.00033.0480.0050.0050.0000.0000.0000.000
157A157GLU-1-0.810-0.89430.6750.0870.0870.0000.0000.0000.000
158A158GLN0-0.053-0.04027.0470.0020.0020.0000.0000.0000.000
159A159LYS10.9480.98128.093-0.075-0.0750.0000.0000.0000.000
160A160LEU00.0200.01627.7360.0120.0120.0000.0000.0000.000
161A161ILE00.002-0.00623.6860.0200.0200.0000.0000.0000.000
162A162ASP-1-0.851-0.92623.3090.1260.1260.0000.0000.0000.000
163A163GLU-1-0.874-0.92223.1710.1970.1970.0000.0000.0000.000
164A164ALA0-0.035-0.01321.1230.0290.0290.0000.0000.0000.000
165A165ILE0-0.0040.00618.9170.0470.0470.0000.0000.0000.000
166A166ASP-1-0.763-0.82518.1310.2790.2790.0000.0000.0000.000
167A167GLU-1-0.769-0.86017.9460.4660.4660.0000.0000.0000.000
168A168ALA00.0140.00215.1860.0830.0830.0000.0000.0000.000
169A169ALA0-0.0090.00813.6530.1290.1290.0000.0000.0000.000
170A170ARG10.8460.90713.140-0.198-0.1980.0000.0000.0000.000
171A171CYS0-0.051-0.02612.8860.0860.0860.0000.0000.0000.000
172A172THR0-0.015-0.0318.7670.2220.2220.0000.0000.0000.000
173A173GLU-1-0.890-0.9408.3150.9060.9060.0000.0000.0000.000
174A174MET0-0.009-0.0108.8740.1160.1160.0000.0000.0000.000
175A175TRP0-0.023-0.0093.576-0.676-0.4180.002-0.050-0.2090.000
176A176PHE0-0.034-0.0212.849-0.8000.8950.531-0.707-1.5190.007
177A177THR00.0010.0105.547-0.575-0.503-0.0010.000-0.0710.000
178A178ASP-1-0.885-0.9368.4790.7520.7520.0000.0000.0000.000
179A179GLY00.0240.0226.647-0.105-0.1050.0000.0000.0000.000
180A180LEU00.0220.0006.292-0.432-0.4320.0000.0000.0000.000
181A181THR00.0020.0047.906-0.321-0.3210.0000.0000.0000.000
182A182LYS10.9020.94311.294-1.091-1.0910.0000.0000.0000.000
183A183ALA00.0320.0339.616-0.187-0.1870.0000.0000.0000.000
184A184THR0-0.028-0.03710.938-0.206-0.2060.0000.0000.0000.000
185A185ASN0-0.046-0.02513.144-0.123-0.1230.0000.0000.0000.000
186A186ARG10.8380.89915.291-0.607-0.6070.0000.0000.0000.000
187A187LEU00.0420.01614.210-0.078-0.0780.0000.0000.0000.000
188A188HIS0-0.079-0.05215.914-0.071-0.0710.0000.0000.0000.000
189A189ALA00.0460.03118.689-0.044-0.0440.0000.0000.0000.000
190A190PHE00.0280.02420.260-0.043-0.0430.0000.0000.0000.000
191A191LYS10.7770.87022.026-0.220-0.2200.0000.0000.0000.000
192A192ALA0-0.0220.00123.800-0.019-0.0190.0000.0000.0000.000
193A193GLN0-0.0230.00225.2380.0010.0010.0000.0000.0000.000