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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: X638Z

Calculation Name: 2PTH-A-Xray13

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: 2018-03-01

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 193
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2089588.918496
FMO2-HF: Nuclear repulsion 2017000.931166
FMO2-HF: Total energy -72587.98733
FMO2-MP2: Total energy -72802.864384


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.
-36.311-30.8270.394-1.774-4.104-0.002
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 : 1 / q_Mulliken : 0.862 / q_NPA : 0.919
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].
3A3LYS10.9590.9752.89948.55250.8120.104-0.857-1.508-0.002
4A4LEU0-0.029-0.0064.7695.0675.173-0.001-0.008-0.0960.000
5A5ILE00.0250.0198.366-1.682-1.6820.0000.0000.0000.000
6A6VAL0-0.024-0.02010.8511.7401.7400.0000.0000.0000.000
7A7GLY00.0340.01614.298-0.315-0.3150.0000.0000.0000.000
8A8LEU0-0.064-0.04217.5930.6650.6650.0000.0000.0000.000
9A9ALA00.0190.00020.4460.2230.2230.0000.0000.0000.000
10A10ASN0-0.0240.01023.914-0.107-0.1070.0000.0000.0000.000
11A11PRO00.0340.01926.831-0.092-0.0920.0000.0000.0000.000
12A12GLY00.0580.02527.9890.3470.3470.0000.0000.0000.000
13A13ALA0-0.003-0.02030.731-0.145-0.1450.0000.0000.0000.000
14A14GLU-1-0.966-0.97032.724-8.790-8.7900.0000.0000.0000.000
15A15TYR00.0320.00429.8430.0180.0180.0000.0000.0000.000
16A16ALA0-0.0010.01928.560-0.290-0.2900.0000.0000.0000.000
17A17ALA00.0000.00328.270-0.293-0.2930.0000.0000.0000.000
18A18THR0-0.069-0.04429.6720.0590.0590.0000.0000.0000.000
19A19ARG10.9410.96427.5199.4459.4450.0000.0000.0000.000
20A20HIS0-0.074-0.06225.709-0.376-0.3760.0000.0000.0000.000
21A21ASN00.0110.01924.245-0.455-0.4550.0000.0000.0000.000
22A22ALA00.0350.02022.404-0.354-0.3540.0000.0000.0000.000
23A23GLY0-0.008-0.00718.732-0.463-0.4630.0000.0000.0000.000
24A24ALA0-0.011-0.01418.517-0.804-0.8040.0000.0000.0000.000
25A25TRP00.0210.01820.470-0.187-0.1870.0000.0000.0000.000
26A26PHE0-0.003-0.00212.647-0.119-0.1190.0000.0000.0000.000
27A27VAL0-0.004-0.00814.945-0.478-0.4780.0000.0000.0000.000
28A28ASP-1-0.894-0.94816.905-13.805-13.8050.0000.0000.0000.000
29A29LEU0-0.043-0.01018.5340.2090.2090.0000.0000.0000.000
30A30LEU0-0.031-0.02312.119-0.024-0.0240.0000.0000.0000.000
31A31ALA00.0170.01016.030-0.040-0.0400.0000.0000.0000.000
32A32GLU-1-0.960-0.97517.658-12.138-12.1380.0000.0000.0000.000
33A33ARG10.8690.91617.71514.95514.9550.0000.0000.0000.000
34A34LEU0-0.0050.00713.1510.1410.1410.0000.0000.0000.000
35A35ARG10.8510.93617.47812.71912.7190.0000.0000.0000.000
36A36ALA00.0140.02016.7850.3150.3150.0000.0000.0000.000
37A37PRO0-0.034-0.02918.577-0.468-0.4680.0000.0000.0000.000
38A38LEU00.0240.02917.314-0.447-0.4470.0000.0000.0000.000
39A39ARG10.9530.97220.46613.70813.7080.0000.0000.0000.000
40A40GLU-1-0.893-0.93021.268-12.200-12.2000.0000.0000.0000.000
41A41GLU-1-0.941-0.96118.917-14.442-14.4420.0000.0000.0000.000
42A42ALA00.0490.00622.327-0.282-0.2820.0000.0000.0000.000
43A43LYS10.8900.95720.21913.94813.9480.0000.0000.0000.000
44A44PHE00.000-0.01217.401-0.394-0.3940.0000.0000.0000.000
45A45PHE0-0.017-0.01619.883-0.243-0.2430.0000.0000.0000.000
46A46GLY00.1210.05220.666-0.055-0.0550.0000.0000.0000.000
47A47TYR0-0.0050.00720.3660.1850.1850.0000.0000.0000.000
48A48THR0-0.039-0.03216.152-0.734-0.7340.0000.0000.0000.000
49A49SER00.027-0.00415.3890.7430.7430.0000.0000.0000.000
50A50ARG10.7780.86811.32820.24420.2440.0000.0000.0000.000
51A51VAL00.0070.00810.6451.3921.3920.0000.0000.0000.000
52A52THR00.0060.0119.537-1.050-1.0500.0000.0000.0000.000
53A53LEU00.003-0.0067.6381.8121.8120.0000.0000.0000.000
54A54GLY00.0510.0256.900-2.744-2.7440.0000.0000.0000.000
55A55GLY0-0.036-0.0167.511-1.111-1.1110.0000.0000.0000.000
56A56GLU-1-0.935-0.9642.854-46.192-45.3750.043-0.272-0.588-0.002
57A57ASP-1-0.844-0.8985.795-22.224-22.2240.0000.0000.0000.000
58A58VAL0-0.0030.0045.654-3.850-3.8500.0000.0000.0000.000
59A59ARG10.9170.9587.88725.62925.6290.0000.0000.0000.000
60A60LEU00.0130.00810.400-1.328-1.3280.0000.0000.0000.000
61A61LEU00.006-0.01513.1790.8350.8350.0000.0000.0000.000
62A62VAL00.0310.03315.677-0.437-0.4370.0000.0000.0000.000
63A63PRO0-0.041-0.02718.3540.5130.5130.0000.0000.0000.000
64A64THR0-0.017-0.01720.9950.1360.1360.0000.0000.0000.000
65A65THR0-0.053-0.03123.3350.3430.3430.0000.0000.0000.000
66A66PHE00.0450.02225.7440.3860.3860.0000.0000.0000.000
67A67MET00.0590.03923.516-0.581-0.5810.0000.0000.0000.000
68A68ASN0-0.029-0.02424.550-0.756-0.7560.0000.0000.0000.000
69A69LEU0-0.0240.00225.6520.0200.0200.0000.0000.0000.000
70A70SER00.006-0.01720.503-0.252-0.2520.0000.0000.0000.000
71A71GLY0-0.019-0.02019.633-0.761-0.7610.0000.0000.0000.000
72A72LYS10.8990.96219.45211.24311.2430.0000.0000.0000.000
73A73ALA00.0460.02919.193-0.192-0.1920.0000.0000.0000.000
74A74VAL0-0.0030.00413.935-0.666-0.6660.0000.0000.0000.000
75A75ALA00.0190.01215.011-1.119-1.1190.0000.0000.0000.000
76A76ALA0-0.0030.00516.633-0.375-0.3750.0000.0000.0000.000
77A77MET0-0.0220.00012.8150.1450.1450.0000.0000.0000.000
78A78ALA00.0110.00111.745-0.844-0.8440.0000.0000.0000.000
79A79SER0-0.011-0.00712.674-0.715-0.7150.0000.0000.0000.000
80A80PHE0-0.046-0.02415.1940.5570.5570.0000.0000.0000.000
81A81PHE0-0.040-0.03610.4320.4110.4110.0000.0000.0000.000
82A82ARG10.9060.96710.46719.52719.5270.0000.0000.0000.000
83A83ILE0-0.036-0.0026.778-1.991-1.9910.0000.0000.0000.000
84A84ASN00.0390.0127.1616.5496.5490.0000.0000.0000.000
85A85PRO00.020-0.0128.238-2.596-2.5960.0000.0000.0000.000
86A86ASP-1-0.902-0.9476.279-43.431-43.4310.0000.0000.0000.000
87A87GLU-1-0.888-0.9373.293-61.668-60.9960.007-0.158-0.521-0.001
88A88ILE0-0.018-0.0085.3512.3352.364-0.001-0.009-0.0190.000
89A89LEU00.0070.0048.109-0.188-0.1880.0000.0000.0000.000
90A90VAL0-0.026-0.0189.7971.6271.6270.0000.0000.0000.000
91A91ALA00.0100.01113.6160.2640.2640.0000.0000.0000.000
92A92HIS0-0.051-0.05115.645-0.037-0.0370.0000.0000.0000.000
93A93ASP-1-0.754-0.84419.157-13.224-13.2240.0000.0000.0000.000
94A94GLU-1-0.842-0.93221.060-14.282-14.2820.0000.0000.0000.000
95A95LEU00.020-0.00323.0890.3690.3690.0000.0000.0000.000
96A96ASP-1-0.943-0.96724.591-11.405-11.4050.0000.0000.0000.000
97A97LEU0-0.083-0.03620.601-0.173-0.1730.0000.0000.0000.000
98A98PRO00.0220.01225.0830.1340.1340.0000.0000.0000.000
99A99PRO00.0330.00725.635-0.493-0.4930.0000.0000.0000.000
100A100GLY00.0160.01925.1520.3320.3320.0000.0000.0000.000
101A101VAL0-0.016-0.00721.861-0.284-0.2840.0000.0000.0000.000
102A102ALA00.0410.01017.723-0.009-0.0090.0000.0000.0000.000
103A103LYS10.8860.95116.63315.02515.0250.0000.0000.0000.000
104A104PHE00.0700.03911.096-0.361-0.3610.0000.0000.0000.000
105A105LYS10.8670.92712.85618.90918.9090.0000.0000.0000.000
106A106LEU00.0400.0328.503-0.989-0.9890.0000.0000.0000.000
107A107GLY00.0120.02011.5991.3641.3640.0000.0000.0000.000
108A108GLY0-0.027-0.01914.0230.7480.7480.0000.0000.0000.000
109A109GLY00.0290.00417.781-0.193-0.1930.0000.0000.0000.000
110A110HIS00.0540.02219.373-0.615-0.6150.0000.0000.0000.000
111A111GLY00.0050.00321.4920.0680.0680.0000.0000.0000.000
112A112GLY0-0.008-0.00524.1100.3690.3690.0000.0000.0000.000
113A113HIS00.0270.01422.4110.2790.2790.0000.0000.0000.000
114A114ASN00.015-0.03523.522-0.513-0.5130.0000.0000.0000.000
115A115GLY00.0560.04822.5210.0110.0110.0000.0000.0000.000
116A116LEU0-0.015-0.01017.253-0.549-0.5490.0000.0000.0000.000
117A117LYS10.9210.96119.82511.01911.0190.0000.0000.0000.000
118A118ASP-1-0.798-0.88422.079-13.450-13.4500.0000.0000.0000.000
119A119ILE00.0300.01315.774-0.086-0.0860.0000.0000.0000.000
120A120ILE0-0.0220.00017.570-0.441-0.4410.0000.0000.0000.000
121A121SER0-0.062-0.02118.6750.0370.0370.0000.0000.0000.000
122A122LYS10.8740.91820.10013.10413.1040.0000.0000.0000.000
123A123LEU0-0.0300.01013.540-0.218-0.2180.0000.0000.0000.000
124A124GLY0-0.0040.00017.057-0.596-0.5960.0000.0000.0000.000
125A125ASN0-0.062-0.03819.637-0.055-0.0550.0000.0000.0000.000
126A126ASN00.0570.03713.388-0.298-0.2980.0000.0000.0000.000
127A127PRO00.015-0.00615.547-0.636-0.6360.0000.0000.0000.000
128A128ASN0-0.053-0.02211.274-0.076-0.0760.0000.0000.0000.000
129A129PHE00.0540.0449.487-1.963-1.9630.0000.0000.0000.000
130A130HIS00.032-0.0035.2706.3116.3110.0000.0000.0000.000
131A131ARG10.7960.9089.87521.18821.1880.0000.0000.0000.000
132A132LEU00.0040.01312.921-0.560-0.5600.0000.0000.0000.000
133A133ARG10.8290.89914.31716.23016.2300.0000.0000.0000.000
134A134ILE00.0520.01417.7110.1330.1330.0000.0000.0000.000
135A135GLY00.0040.00620.2720.3990.3990.0000.0000.0000.000
136A136ILE0-0.033-0.01023.6260.2300.2300.0000.0000.0000.000
137A137GLY00.0080.00926.7570.4940.4940.0000.0000.0000.000
138A138HIS00.0480.01129.2440.0800.0800.0000.0000.0000.000
139A139PRO0-0.033-0.01231.4790.2390.2390.0000.0000.0000.000
140A140GLY00.0240.02034.7250.3070.3070.0000.0000.0000.000
141A141ASP-1-0.821-0.90436.258-8.078-8.0780.0000.0000.0000.000
142A142LYS10.9950.96132.6599.2769.2760.0000.0000.0000.000
143A143ASN0-0.0300.00435.492-0.131-0.1310.0000.0000.0000.000
144A144LYS10.8770.92137.2617.9187.9180.0000.0000.0000.000
145A145VAL00.0040.01230.969-0.089-0.0890.0000.0000.0000.000
146A146VAL00.0160.01233.056-0.201-0.2010.0000.0000.0000.000
147A147GLY00.0340.01034.112-0.114-0.1140.0000.0000.0000.000
148A148PHE0-0.0040.00830.0560.0610.0610.0000.0000.0000.000
149A149VAL00.0380.00228.808-0.105-0.1050.0000.0000.0000.000
150A150LEU0-0.033-0.00830.084-0.292-0.2920.0000.0000.0000.000
151A151GLY00.0490.03532.5670.2740.2740.0000.0000.0000.000
152A152LYS10.9280.96532.0278.6098.6090.0000.0000.0000.000
153A153PRO00.0050.00529.4500.2900.2900.0000.0000.0000.000
154A154PRO00.0090.00532.7300.1240.1240.0000.0000.0000.000
155A155VAL00.0390.00433.527-0.249-0.2490.0000.0000.0000.000
156A156SER0-0.015-0.01433.047-0.255-0.2550.0000.0000.0000.000
157A157GLU-1-0.812-0.91530.735-9.823-9.8230.0000.0000.0000.000
158A158GLN0-0.054-0.02127.130-0.053-0.0530.0000.0000.0000.000
159A159LYS10.9400.96928.0939.0959.0950.0000.0000.0000.000
160A160LEU00.0370.02327.733-0.312-0.3120.0000.0000.0000.000
161A161ILE0-0.004-0.00823.674-0.477-0.4770.0000.0000.0000.000
162A162ASP-1-0.861-0.93623.310-12.166-12.1660.0000.0000.0000.000
163A163GLU-1-0.908-0.95423.167-11.529-11.5290.0000.0000.0000.000
164A164ALA0-0.028-0.01021.042-0.524-0.5240.0000.0000.0000.000
165A165ILE0-0.0090.00118.891-1.006-1.0060.0000.0000.0000.000
166A166ASP-1-0.840-0.91918.126-14.858-14.8580.0000.0000.0000.000
167A167GLU-1-0.817-0.90517.876-16.112-16.1120.0000.0000.0000.000
168A168ALA00.002-0.00815.163-1.078-1.0780.0000.0000.0000.000
169A169ALA0-0.016-0.00113.649-1.754-1.7540.0000.0000.0000.000
170A170ARG10.9320.97013.19413.13513.1350.0000.0000.0000.000
171A171CYS0-0.023-0.00512.811-0.783-0.7830.0000.0000.0000.000
172A172THR0-0.028-0.0288.624-2.259-2.2590.0000.0000.0000.000
173A173GLU-1-0.962-0.9728.373-23.057-23.0570.0000.0000.0000.000
174A174MET0-0.0060.0008.935-0.910-0.9100.0000.0000.0000.000
175A175TRP0-0.045-0.0173.798-0.425-0.1660.000-0.054-0.2050.000
176A176PHE0-0.060-0.0363.021-4.859-3.5880.243-0.416-1.0980.003
177A177THR00.0030.0105.608-1.871-1.801-0.0010.000-0.0690.000
178A178ASP-1-0.932-0.9628.526-21.286-21.2860.0000.0000.0000.000
179A179GLY0-0.0070.0076.6450.5050.5050.0000.0000.0000.000
180A180LEU00.001-0.0126.3362.6852.6850.0000.0000.0000.000
181A181THR00.005-0.0027.9152.0412.0410.0000.0000.0000.000
182A182LYS10.9940.99311.28321.52421.5240.0000.0000.0000.000
183A183ALA00.0480.0329.6231.6231.6230.0000.0000.0000.000
184A184THR0-0.027-0.03010.9061.3001.3000.0000.0000.0000.000
185A185ASN0-0.032-0.01813.1531.3251.3250.0000.0000.0000.000
186A186ARG10.8610.93615.30017.51217.5120.0000.0000.0000.000
187A187LEU00.0430.01414.2250.8760.8760.0000.0000.0000.000
188A188HIS0-0.083-0.05715.9060.3800.3800.0000.0000.0000.000
189A189ALA00.0460.03518.6990.6300.6300.0000.0000.0000.000
190A190PHE00.0190.02120.2250.7680.7680.0000.0000.0000.000
191A191LYS10.8010.89822.03011.57511.5750.0000.0000.0000.000
192A192ALA0-0.055-0.02323.8490.3790.3790.0000.0000.0000.000
193A193GLN-1-0.963-0.96125.256-11.147-11.1470.0000.0000.0000.000