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: NNGGQ

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2089520.773116
FMO2-HF: Nuclear repulsion 2016932.686956
FMO2-HF: Total energy -72588.086161
FMO2-MP2: Total energy -72802.954777


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.
-8.398-2.2290.406-2.288-4.2870.007
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 : 0.044 / 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].
3A3LYS10.9470.9642.9022.0234.9540.108-1.333-1.7060.005
4A4LEU0-0.041-0.0144.7700.2300.329-0.001-0.008-0.0910.000
5A5ILE00.0260.0198.367-0.032-0.0320.0000.0000.0000.000
6A6VAL0-0.025-0.02110.851-0.021-0.0210.0000.0000.0000.000
7A7GLY00.0320.01514.2990.0490.0490.0000.0000.0000.000
8A8LEU0-0.063-0.04217.585-0.021-0.0210.0000.0000.0000.000
9A9ALA00.017-0.00220.4390.0240.0240.0000.0000.0000.000
10A10ASN0-0.0250.01123.914-0.026-0.0260.0000.0000.0000.000
11A11PRO00.0350.02026.8310.0070.0070.0000.0000.0000.000
12A12GLY00.0580.02527.9900.0030.0030.0000.0000.0000.000
13A13ALA0-0.004-0.02030.7310.0040.0040.0000.0000.0000.000
14A14GLU-1-0.967-0.97032.724-0.025-0.0250.0000.0000.0000.000
15A15TYR00.0320.00429.8440.0020.0020.0000.0000.0000.000
16A16ALA00.0010.02028.5600.0050.0050.0000.0000.0000.000
17A17ALA0-0.0010.00228.2590.0070.0070.0000.0000.0000.000
18A18THR0-0.069-0.04429.6640.0060.0060.0000.0000.0000.000
19A19ARG10.9390.96227.513-0.036-0.0360.0000.0000.0000.000
20A20HIS0-0.074-0.06325.703-0.005-0.0050.0000.0000.0000.000
21A21ASN00.0130.02124.237-0.018-0.0180.0000.0000.0000.000
22A22ALA00.0320.01822.3980.0040.0040.0000.0000.0000.000
23A23GLY0-0.008-0.00718.7240.0190.0190.0000.0000.0000.000
24A24ALA0-0.008-0.01218.5070.0130.0130.0000.0000.0000.000
25A25TRP00.0180.01620.4700.0130.0130.0000.0000.0000.000
26A26PHE0-0.005-0.00312.6350.0050.0050.0000.0000.0000.000
27A27VAL00.001-0.00514.9460.0260.0260.0000.0000.0000.000
28A28ASP-1-0.893-0.94816.9040.0080.0080.0000.0000.0000.000
29A29LEU0-0.047-0.01218.5340.0020.0020.0000.0000.0000.000
30A30LEU0-0.029-0.02112.1200.0130.0130.0000.0000.0000.000
31A31ALA00.0200.01216.029-0.007-0.0070.0000.0000.0000.000
32A32GLU-1-0.962-0.97617.6760.0670.0670.0000.0000.0000.000
33A33ARG10.8680.91517.725-0.226-0.2260.0000.0000.0000.000
34A34LEU0-0.0010.00913.167-0.002-0.0020.0000.0000.0000.000
35A35ARG10.8480.93417.491-0.080-0.0800.0000.0000.0000.000
36A36ALA00.0160.02116.804-0.022-0.0220.0000.0000.0000.000
37A37PRO0-0.035-0.03018.5980.0000.0000.0000.0000.0000.000
38A38LEU00.0250.02917.317-0.024-0.0240.0000.0000.0000.000
39A39ARG10.9510.97220.4670.1750.1750.0000.0000.0000.000
40A40GLU-1-0.895-0.93121.268-0.132-0.1320.0000.0000.0000.000
41A41GLU-1-0.941-0.96118.917-0.254-0.2540.0000.0000.0000.000
42A42ALA00.0470.00422.329-0.010-0.0100.0000.0000.0000.000
43A43LYS10.8900.95720.2220.2900.2900.0000.0000.0000.000
44A44PHE00.002-0.01017.402-0.027-0.0270.0000.0000.0000.000
45A45PHE0-0.018-0.01619.8850.0000.0000.0000.0000.0000.000
46A46GLY00.1200.05220.6680.0070.0070.0000.0000.0000.000
47A47TYR0-0.0080.00620.366-0.008-0.0080.0000.0000.0000.000
48A48THR0-0.037-0.03016.153-0.004-0.0040.0000.0000.0000.000
49A49SER00.024-0.00615.3890.0180.0180.0000.0000.0000.000
50A50ARG10.7770.86811.3260.5090.5090.0000.0000.0000.000
51A51VAL00.0030.00510.6650.0320.0320.0000.0000.0000.000
52A52THR00.0050.0119.553-0.062-0.0620.0000.0000.0000.000
53A53LEU0-0.001-0.0087.6500.0620.0620.0000.0000.0000.000
54A54GLY00.0500.0256.9060.0750.0750.0000.0000.0000.000
55A55GLY0-0.040-0.0187.506-0.046-0.0460.0000.0000.0000.000
56A56GLU-1-0.923-0.9572.854-5.058-4.3280.046-0.228-0.548-0.002
57A57ASP-1-0.847-0.9005.805-0.164-0.1640.0000.0000.0000.000
58A58VAL00.0060.0095.677-0.179-0.1790.0000.0000.0000.000
59A59ARG10.9130.9567.8860.6190.6190.0000.0000.0000.000
60A60LEU00.0120.00710.4010.0370.0370.0000.0000.0000.000
61A61LEU00.006-0.01513.179-0.044-0.0440.0000.0000.0000.000
62A62VAL00.0280.03215.6770.0220.0220.0000.0000.0000.000
63A63PRO0-0.040-0.02718.355-0.007-0.0070.0000.0000.0000.000
64A64THR0-0.018-0.01720.9960.0150.0150.0000.0000.0000.000
65A65THR0-0.052-0.03023.3380.0020.0020.0000.0000.0000.000
66A66PHE00.0430.02025.7450.0050.0050.0000.0000.0000.000
67A67MET00.0580.03923.510-0.023-0.0230.0000.0000.0000.000
68A68ASN0-0.031-0.02424.494-0.013-0.0130.0000.0000.0000.000
69A69LEU0-0.0240.00225.655-0.007-0.0070.0000.0000.0000.000
70A70SER00.006-0.01720.505-0.012-0.0120.0000.0000.0000.000
71A71GLY0-0.017-0.01919.629-0.027-0.0270.0000.0000.0000.000
72A72LYS10.8970.96119.4550.1280.1280.0000.0000.0000.000
73A73ALA00.0440.02819.196-0.021-0.0210.0000.0000.0000.000
74A74VAL0-0.0010.00513.939-0.034-0.0340.0000.0000.0000.000
75A75ALA00.0200.01315.014-0.075-0.0750.0000.0000.0000.000
76A76ALA0-0.0050.00416.636-0.038-0.0380.0000.0000.0000.000
77A77MET0-0.023-0.00112.818-0.017-0.0170.0000.0000.0000.000
78A78ALA00.0150.00411.749-0.062-0.0620.0000.0000.0000.000
79A79SER0-0.013-0.00712.677-0.072-0.0720.0000.0000.0000.000
80A80PHE0-0.050-0.02615.1970.0150.0150.0000.0000.0000.000
81A81PHE0-0.041-0.03610.4340.0280.0280.0000.0000.0000.000
82A82ARG10.9030.96610.4700.5520.5520.0000.0000.0000.000
83A83ILE0-0.0310.0016.782-0.130-0.1300.0000.0000.0000.000
84A84ASN00.0380.0117.1450.5750.5750.0000.0000.0000.000
85A85PRO00.009-0.0198.209-0.241-0.2410.0000.0000.0000.000
86A86ASP-1-0.910-0.9546.258-1.656-1.6560.0000.0000.0000.000
87A87GLU-1-0.846-0.9103.267-4.972-4.3260.010-0.142-0.5140.000
88A88ILE0-0.031-0.0145.2830.7020.718-0.001-0.008-0.0060.000
89A89LEU00.0100.0058.1040.0670.0670.0000.0000.0000.000
90A90VAL0-0.028-0.0209.7930.0450.0450.0000.0000.0000.000
91A91ALA00.0080.01013.6130.0520.0520.0000.0000.0000.000
92A92HIS0-0.049-0.05115.639-0.040-0.0400.0000.0000.0000.000
93A93ASP-1-0.758-0.84619.1530.0320.0320.0000.0000.0000.000
94A94GLU-1-0.840-0.93121.0600.0370.0370.0000.0000.0000.000
95A95LEU00.021-0.00323.0880.0090.0090.0000.0000.0000.000
96A96ASP-1-0.942-0.96624.5800.0520.0520.0000.0000.0000.000
97A97LEU0-0.085-0.03720.6020.0170.0170.0000.0000.0000.000
98A98PRO00.0190.01125.083-0.011-0.0110.0000.0000.0000.000
99A99PRO00.0370.00925.6310.0130.0130.0000.0000.0000.000
100A100GLY00.0140.01825.146-0.001-0.0010.0000.0000.0000.000
101A101VAL0-0.029-0.01621.8590.0210.0210.0000.0000.0000.000
102A102ALA00.0470.01417.718-0.020-0.0200.0000.0000.0000.000
103A103LYS10.8770.94616.632-0.221-0.2210.0000.0000.0000.000
104A104PHE00.0800.04411.090-0.040-0.0400.0000.0000.0000.000
105A105LYS10.8590.92312.853-0.058-0.0580.0000.0000.0000.000
106A106LEU00.0500.0388.506-0.029-0.0290.0000.0000.0000.000
107A107GLY00.0120.02111.5950.0340.0340.0000.0000.0000.000
108A108GLY0-0.031-0.02214.0080.0500.0500.0000.0000.0000.000
109A109GLY00.0290.00417.768-0.032-0.0320.0000.0000.0000.000
110A110HIS00.0550.02219.3460.0050.0050.0000.0000.0000.000
111A111GLY00.0040.00221.4600.0100.0100.0000.0000.0000.000
112A112GLY0-0.009-0.00624.0860.0100.0100.0000.0000.0000.000
113A113HIS00.0250.01422.375-0.017-0.0170.0000.0000.0000.000
114A114ASN00.014-0.03523.481-0.020-0.0200.0000.0000.0000.000
115A115GLY00.0560.04822.470-0.012-0.0120.0000.0000.0000.000
116A116LEU0-0.013-0.00917.212-0.032-0.0320.0000.0000.0000.000
117A117LYS10.9190.96019.7780.0590.0590.0000.0000.0000.000
118A118ASP-1-0.799-0.88522.030-0.190-0.1900.0000.0000.0000.000
119A119ILE00.0310.01415.719-0.019-0.0190.0000.0000.0000.000
120A120ILE0-0.0200.00117.530-0.033-0.0330.0000.0000.0000.000
121A121SER0-0.064-0.02218.627-0.016-0.0160.0000.0000.0000.000
122A122LYS10.8730.91720.0380.1780.1780.0000.0000.0000.000
123A123LEU0-0.0250.01313.482-0.024-0.0240.0000.0000.0000.000
124A124GLY0-0.0040.00017.004-0.030-0.0300.0000.0000.0000.000
125A125ASN0-0.065-0.04019.5920.0140.0140.0000.0000.0000.000
126A126ASN00.0590.03813.3500.0360.0360.0000.0000.0000.000
127A127PRO00.011-0.00915.504-0.036-0.0360.0000.0000.0000.000
128A128ASN0-0.054-0.02311.2540.0960.0960.0000.0000.0000.000
129A129PHE00.0600.0499.447-0.134-0.1340.0000.0000.0000.000
130A130HIS00.0410.0025.2280.6710.6710.0000.0000.0000.000
131A131ARG10.7920.9069.8480.1240.1240.0000.0000.0000.000
132A132LEU00.0030.01312.9150.0790.0790.0000.0000.0000.000
133A133ARG10.8290.89814.313-0.156-0.1560.0000.0000.0000.000
134A134ILE00.0510.01317.7040.0360.0360.0000.0000.0000.000
135A135GLY00.0020.00420.267-0.025-0.0250.0000.0000.0000.000
136A136ILE0-0.030-0.00923.6230.0000.0000.0000.0000.0000.000
137A137GLY00.0040.00626.752-0.005-0.0050.0000.0000.0000.000
138A138HIS00.0490.01229.242-0.008-0.0080.0000.0000.0000.000
139A139PRO0-0.032-0.01231.4780.0020.0020.0000.0000.0000.000
140A140GLY00.0230.02034.7230.0000.0000.0000.0000.0000.000
141A141ASP-1-0.821-0.90536.2390.0140.0140.0000.0000.0000.000
142A142LYS10.9960.96232.6340.0010.0010.0000.0000.0000.000
143A143ASN0-0.0290.00435.465-0.006-0.0060.0000.0000.0000.000
144A144LYS10.8770.92237.260-0.018-0.0180.0000.0000.0000.000
145A145VAL00.0030.01130.9370.0010.0010.0000.0000.0000.000
146A146VAL00.0170.01333.0540.0010.0010.0000.0000.0000.000
147A147GLY00.0340.01034.109-0.001-0.0010.0000.0000.0000.000
148A148PHE0-0.0050.00730.0540.0000.0000.0000.0000.0000.000
149A149VAL00.0380.00228.8050.0040.0040.0000.0000.0000.000
150A150LEU0-0.031-0.00730.079-0.001-0.0010.0000.0000.0000.000
151A151GLY00.0490.03532.562-0.002-0.0020.0000.0000.0000.000
152A152LYS10.9280.96532.020-0.023-0.0230.0000.0000.0000.000
153A153PRO00.0050.00529.441-0.001-0.0010.0000.0000.0000.000
154A154PRO00.0080.00532.722-0.001-0.0010.0000.0000.0000.000
155A155VAL00.0400.00533.5190.0050.0050.0000.0000.0000.000
156A156SER0-0.016-0.01533.0380.0050.0050.0000.0000.0000.000
157A157GLU-1-0.814-0.91630.7280.0660.0660.0000.0000.0000.000
158A158GLN0-0.050-0.02027.120-0.002-0.0020.0000.0000.0000.000
159A159LYS10.9400.96928.083-0.067-0.0670.0000.0000.0000.000
160A160LEU00.0320.02027.7250.0120.0120.0000.0000.0000.000
161A161ILE0-0.002-0.00723.6660.0170.0170.0000.0000.0000.000
162A162ASP-1-0.857-0.93323.3000.1130.1130.0000.0000.0000.000
163A163GLU-1-0.911-0.95523.1560.1700.1700.0000.0000.0000.000
164A164ALA0-0.034-0.01421.0350.0280.0280.0000.0000.0000.000
165A165ILE0-0.0040.00418.8790.0410.0410.0000.0000.0000.000
166A166ASP-1-0.840-0.91818.1160.2730.2730.0000.0000.0000.000
167A167GLU-1-0.826-0.91117.8700.4280.4280.0000.0000.0000.000
168A168ALA00.002-0.00915.1530.0760.0760.0000.0000.0000.000
169A169ALA0-0.0120.00213.6390.1140.1140.0000.0000.0000.000
170A170ARG10.9300.96913.195-0.193-0.1930.0000.0000.0000.000
171A171CYS0-0.031-0.01112.8050.0910.0910.0000.0000.0000.000
172A172THR0-0.020-0.0238.6130.1830.1830.0000.0000.0000.000
173A173GLU-1-0.958-0.9708.3731.0011.0010.0000.0000.0000.000
174A174MET0-0.015-0.0058.9340.1400.1400.0000.0000.0000.000
175A175TRP0-0.036-0.0153.725-0.513-0.2620.000-0.046-0.2050.000
176A176PHE0-0.042-0.0253.014-0.5410.8880.245-0.523-1.1510.004
177A177THR00.0000.0095.607-0.433-0.366-0.0010.000-0.0660.000
178A178ASP-1-0.942-0.9688.5080.7790.7790.0000.0000.0000.000
179A179GLY00.0040.0136.647-0.100-0.1000.0000.0000.0000.000
180A180LEU00.010-0.0066.341-0.385-0.3850.0000.0000.0000.000
181A181THR00.002-0.0047.919-0.291-0.2910.0000.0000.0000.000
182A182LYS10.9890.98911.286-0.949-0.9490.0000.0000.0000.000
183A183ALA00.0530.0359.621-0.165-0.1650.0000.0000.0000.000
184A184THR0-0.023-0.02810.909-0.191-0.1910.0000.0000.0000.000
185A185ASN0-0.034-0.01913.155-0.127-0.1270.0000.0000.0000.000
186A186ARG10.8540.93315.299-0.551-0.5510.0000.0000.0000.000
187A187LEU00.0490.01814.220-0.066-0.0660.0000.0000.0000.000
188A188HIS0-0.074-0.05015.909-0.060-0.0600.0000.0000.0000.000
189A189ALA00.0350.02918.698-0.038-0.0380.0000.0000.0000.000
190A190PHE00.0150.01720.220-0.034-0.0340.0000.0000.0000.000
191A191LYS10.8060.90222.026-0.189-0.1890.0000.0000.0000.000
192A192ALA0-0.0180.00123.848-0.017-0.0170.0000.0000.0000.000
193A193GLN0-0.031-0.00125.2530.0060.0060.0000.0000.0000.000