FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 3J16L

Calculation Name: 1P74-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P74

Chain ID: A

ChEMBL ID:

UniProt ID: P43876

Base Structure: X-ray

Registration Date: 2023-09-24

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 272
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3597533.7986
FMO2-HF: Nuclear repulsion 3492856.271292
FMO2-HF: Total energy -104677.527308
FMO2-MP2: Total energy -104982.109852


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-7.555-1.8576.502-3.275-8.926-0.016
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.030
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].
3A3LEU00.0440.0223.8050.4871.769-0.005-0.411-0.8670.003
4A4TYR00.0220.0175.3100.2860.343-0.001-0.002-0.0530.000
5A5ALA00.025-0.0018.6040.0560.0560.0000.0000.0000.000
6A6VAL0-0.0550.02111.3920.0260.0260.0000.0000.0000.000
7A7TRP00.0540.01413.948-0.003-0.0030.0000.0000.0000.000
8A8GLY0-0.004-0.01717.3930.0220.0220.0000.0000.0000.000
9A9ASN0-0.0680.00820.726-0.007-0.0070.0000.0000.0000.000
10A10PRO00.0870.01823.5110.0030.0030.0000.0000.0000.000
11A11ILE00.018-0.00817.5920.0080.0080.0000.0000.0000.000
12A12ALA00.0070.00719.4110.0120.0120.0000.0000.0000.000
13A13GLN00.0170.01420.4720.0040.0040.0000.0000.0000.000
14A14SER0-0.014-0.01017.6390.0190.0190.0000.0000.0000.000
15A15LYS10.9390.95517.437-0.037-0.0370.0000.0000.0000.000
16A16SER0-0.0090.00615.0800.0160.0160.0000.0000.0000.000
17A17PRO00.0470.01711.7640.0310.0310.0000.0000.0000.000
18A18LEU0-0.0110.00111.1450.0430.0430.0000.0000.0000.000
19A19ILE0-0.006-0.00612.7820.0120.0120.0000.0000.0000.000
20A20GLN00.028-0.00110.6540.0620.0620.0000.0000.0000.000
21A21ASN00.0150.0076.9140.1980.1980.0000.0000.0000.000
22A22LYS10.8730.9468.432-0.145-0.1450.0000.0000.0000.000
23A23LEU0-0.022-0.00511.1570.0010.0010.0000.0000.0000.000
24A24ALA00.0460.0156.5520.0150.0150.0000.0000.0000.000
25A25ALA0-0.0150.0027.9190.0360.0360.0000.0000.0000.000
26A26GLN0-0.010-0.0038.7010.0130.0130.0000.0000.0000.000
27A27THR0-0.024-0.00711.0480.0120.0120.0000.0000.0000.000
28A28HIS0-0.0030.0118.5350.0850.0850.0000.0000.0000.000
29A29GLN0-0.030-0.0146.9210.2480.2480.0000.0000.0000.000
30A30THR0-0.012-0.0132.307-1.415-1.0542.788-0.801-2.348-0.002
31A31MET0-0.065-0.0072.932-1.8070.6510.692-1.157-1.993-0.010
32A32GLU-1-0.896-0.9422.656-2.999-1.4423.015-1.004-3.568-0.007
33A33TYR0-0.018-0.0394.396-1.058-1.0750.0130.100-0.0970.000
34A34ILE00.0320.0077.8200.0080.0080.0000.0000.0000.000
35A35ALA0-0.029-0.01910.405-0.035-0.0350.0000.0000.0000.000
36A36LYS10.9290.97811.6310.4750.4750.0000.0000.0000.000
37A37LEU0-0.025-0.02215.2490.0230.0230.0000.0000.0000.000
38A38GLY00.0080.01418.975-0.019-0.0190.0000.0000.0000.000
39A39ASP-1-0.811-0.90320.580-0.102-0.1020.0000.0000.0000.000
40A40LEU0-0.035-0.04623.7140.0010.0010.0000.0000.0000.000
41A41ASP-1-0.886-0.92326.730-0.075-0.0750.0000.0000.0000.000
42A42ALA0-0.067-0.04324.096-0.001-0.0010.0000.0000.0000.000
43A43PHE0-0.009-0.00319.372-0.017-0.0170.0000.0000.0000.000
44A44GLU-1-0.785-0.89720.588-0.114-0.1140.0000.0000.0000.000
45A45GLN00.0360.01521.212-0.016-0.0160.0000.0000.0000.000
46A46GLN00.0030.01018.242-0.015-0.0150.0000.0000.0000.000
47A47LEU0-0.039-0.01915.783-0.047-0.0470.0000.0000.0000.000
48A48LEU00.0460.00516.201-0.039-0.0390.0000.0000.0000.000
49A49ALA00.0400.03816.976-0.026-0.0260.0000.0000.0000.000
50A50PHE00.016-0.00210.304-0.082-0.0820.0000.0000.0000.000
51A51PHE0-0.043-0.04011.989-0.113-0.1130.0000.0000.0000.000
52A52GLU-1-0.948-0.96612.783-0.347-0.3470.0000.0000.0000.000
53A53GLU-1-1.001-0.99210.876-0.756-0.7560.0000.0000.0000.000
54A54GLY0-0.030-0.0158.287-0.265-0.2650.0000.0000.0000.000
55A55ALA0-0.049-0.0088.077-0.140-0.1400.0000.0000.0000.000
56A56LYS10.9560.9707.2990.1080.1080.0000.0000.0000.000
57A57GLY00.0310.0089.9740.1660.1660.0000.0000.0000.000
58A58CYS0-0.046-0.01811.196-0.057-0.0570.0000.0000.0000.000
59A59ASN0-0.0090.00013.5340.0570.0570.0000.0000.0000.000
60A60ILE00.0150.02216.546-0.026-0.0260.0000.0000.0000.000
61A61THR0-0.055-0.03919.6140.0200.0200.0000.0000.0000.000
62A62SER0-0.0360.02822.400-0.006-0.0060.0000.0000.0000.000
63A63PRO00.024-0.01724.4170.0000.0000.0000.0000.0000.000
64A64PHE00.042-0.01621.546-0.001-0.0010.0000.0000.0000.000
65A65LYS10.9220.98023.711-0.005-0.0050.0000.0000.0000.000
66A66GLU-1-0.901-0.95624.820-0.027-0.0270.0000.0000.0000.000
67A67ARG10.8140.88225.4520.0840.0840.0000.0000.0000.000
68A68ALA00.003-0.00321.124-0.006-0.0060.0000.0000.0000.000
69A69TYR0-0.018-0.01922.961-0.001-0.0010.0000.0000.0000.000
70A70GLN0-0.027-0.01525.0580.0080.0080.0000.0000.0000.000
71A71LEU0-0.025-0.00221.883-0.004-0.0040.0000.0000.0000.000
72A72ALA0-0.093-0.03122.485-0.006-0.0060.0000.0000.0000.000
73A73ASP-1-0.816-0.87321.928-0.062-0.0620.0000.0000.0000.000
74A74GLU-1-0.874-0.94122.9650.0220.0220.0000.0000.0000.000
75A75TYR00.004-0.01923.9670.0000.0000.0000.0000.0000.000
76A76SER0-0.023-0.00224.5870.0010.0010.0000.0000.0000.000
77A77GLN00.0640.02426.413-0.002-0.0020.0000.0000.0000.000
78A78ARG10.8560.90523.895-0.076-0.0760.0000.0000.0000.000
79A79ALA0-0.0120.01325.346-0.005-0.0050.0000.0000.0000.000
80A80LYS10.9500.98127.404-0.008-0.0080.0000.0000.0000.000
81A81LEU0-0.031-0.01230.644-0.004-0.0040.0000.0000.0000.000
82A82ALA0-0.038-0.00329.260-0.002-0.0020.0000.0000.0000.000
83A83GLU-1-0.904-0.95130.855-0.007-0.0070.0000.0000.0000.000
84A84ALA00.0460.01327.139-0.007-0.0070.0000.0000.0000.000
85A85CYS0-0.0610.00022.5200.0060.0060.0000.0000.0000.000
86A86ASN0-0.0050.00321.544-0.010-0.0100.0000.0000.0000.000
87A87THR0-0.010-0.01616.9860.0090.0090.0000.0000.0000.000
88A88LEU00.0700.04516.7840.0040.0040.0000.0000.0000.000
89A89LYS10.8960.95013.858-0.193-0.1930.0000.0000.0000.000
90A90LYS10.9801.00410.8090.3690.3690.0000.0000.0000.000
91A91LEU0-0.092-0.04513.8620.0420.0420.0000.0000.0000.000
92A92ASP-1-0.937-0.97313.9020.2190.2190.0000.0000.0000.000
93A93ASP-1-0.915-0.96515.5830.0160.0160.0000.0000.0000.000
94A94GLY00.0130.00116.630-0.023-0.0230.0000.0000.0000.000
95A95LYS10.8660.95817.686-0.031-0.0310.0000.0000.0000.000
96A96LEU00.016-0.00716.9420.0030.0030.0000.0000.0000.000
97A97TYR0-0.019-0.01418.6650.0170.0170.0000.0000.0000.000
98A98ALA00.0350.00319.379-0.004-0.0040.0000.0000.0000.000
99A99ASP-1-0.781-0.86321.0800.0800.0800.0000.0000.0000.000
100A100ASN0-0.045-0.06122.460-0.007-0.0070.0000.0000.0000.000
101A101THR00.0270.00420.176-0.003-0.0030.0000.0000.0000.000
102A102ASP-1-0.843-0.92723.5370.0360.0360.0000.0000.0000.000
103A103GLY00.0540.02225.7520.0030.0030.0000.0000.0000.000
104A104ILE0-0.021-0.00423.5150.0000.0000.0000.0000.0000.000
105A105GLY00.0220.01324.5550.0080.0080.0000.0000.0000.000
106A106LEU0-0.028-0.01825.1870.0010.0010.0000.0000.0000.000
107A107VAL00.0230.00828.6940.0000.0000.0000.0000.0000.000
108A108THR00.0310.03024.3520.0050.0050.0000.0000.0000.000
109A109ASP-1-0.749-0.84127.0020.0680.0680.0000.0000.0000.000
110A110LEU00.0120.00428.166-0.002-0.0020.0000.0000.0000.000
111A111GLN0-0.021-0.01229.6790.0020.0020.0000.0000.0000.000
112A112ARG10.8610.93926.486-0.071-0.0710.0000.0000.0000.000
113A113LEU0-0.064-0.03830.015-0.002-0.0020.0000.0000.0000.000
114A114ASN0-0.068-0.02732.961-0.002-0.0020.0000.0000.0000.000
115A115TRP0-0.038-0.01834.909-0.004-0.0040.0000.0000.0000.000
116A116LEU00.0030.00532.977-0.002-0.0020.0000.0000.0000.000
117A117ARG10.9670.99036.500-0.046-0.0460.0000.0000.0000.000
118A118PRO00.0290.02239.235-0.002-0.0020.0000.0000.0000.000
119A119ASN0-0.032-0.02140.966-0.002-0.0020.0000.0000.0000.000
120A120GLN0-0.032-0.01538.728-0.002-0.0020.0000.0000.0000.000
121A121HIS00.0100.01243.047-0.001-0.0010.0000.0000.0000.000
122A122VAL0-0.012-0.01738.4270.0000.0000.0000.0000.0000.000
123A123LEU00.0040.01941.808-0.002-0.0020.0000.0000.0000.000
124A124ILE0-0.017-0.01036.9660.0010.0010.0000.0000.0000.000
125A125LEU00.0200.00139.936-0.002-0.0020.0000.0000.0000.000
126A126GLY0-0.012-0.03339.0450.0000.0000.0000.0000.0000.000
127A127ALA0-0.0090.00237.350-0.001-0.0010.0000.0000.0000.000
128A128GLY00.0260.00236.437-0.002-0.0020.0000.0000.0000.000
129A129GLY0-0.029-0.01634.7710.0010.0010.0000.0000.0000.000
130A130ALA00.000-0.00731.0400.0000.0000.0000.0000.0000.000
131A131THR00.0460.01130.3940.0010.0010.0000.0000.0000.000
132A132LYS10.8850.95832.4470.0060.0060.0000.0000.0000.000
133A133GLY00.0050.00929.4320.0010.0010.0000.0000.0000.000
134A134VAL00.019-0.00830.0130.0060.0060.0000.0000.0000.000
135A135LEU0-0.0070.00531.8960.0030.0030.0000.0000.0000.000
136A136LEU00.0300.02931.0240.0010.0010.0000.0000.0000.000
137A137PRO0-0.0040.00129.5600.0020.0020.0000.0000.0000.000
138A138LEU00.0170.01632.1120.0030.0030.0000.0000.0000.000
139A139LEU0-0.024-0.00135.1470.0010.0010.0000.0000.0000.000
140A140GLN0-0.050-0.04932.0200.0040.0040.0000.0000.0000.000
141A141ALA0-0.0440.00234.3030.0030.0030.0000.0000.0000.000
142A142GLN0-0.007-0.00336.1210.0010.0010.0000.0000.0000.000
143A143GLN0-0.049-0.04037.243-0.003-0.0030.0000.0000.0000.000
144A144ASN0-0.023-0.00340.212-0.002-0.0020.0000.0000.0000.000
145A145ILE00.004-0.00538.3670.0000.0000.0000.0000.0000.000
146A146VAL00.0350.02742.579-0.002-0.0020.0000.0000.0000.000
147A147LEU0-0.032-0.02339.4810.0000.0000.0000.0000.0000.000
148A148ALA00.0660.04743.314-0.001-0.0010.0000.0000.0000.000
149A149ASN0-0.019-0.00641.205-0.001-0.0010.0000.0000.0000.000
150A150ARG10.9510.98144.346-0.003-0.0030.0000.0000.0000.000
151A151THR0-0.0460.01543.954-0.002-0.0020.0000.0000.0000.000
152A152PHE00.0580.01545.9110.0000.0000.0000.0000.0000.000
153A153SER00.0120.00046.134-0.001-0.0010.0000.0000.0000.000
154A154LYS11.0871.00140.0440.0090.0090.0000.0000.0000.000
155A155THR0-0.002-0.01041.7970.0000.0000.0000.0000.0000.000
156A156LYS10.9980.99842.8640.0000.0000.0000.0000.0000.000
157A157GLU-1-0.911-0.94741.855-0.003-0.0030.0000.0000.0000.000
158A158LEU0-0.064-0.03037.0220.0010.0010.0000.0000.0000.000
159A159ALA00.005-0.00940.6250.0020.0020.0000.0000.0000.000
160A160GLU-1-0.924-0.96343.0930.0090.0090.0000.0000.0000.000
161A161ARG10.8550.94134.240-0.002-0.0020.0000.0000.0000.000
162A162PHE0-0.035-0.05534.6040.0020.0020.0000.0000.0000.000
163A163GLN00.0180.01939.8440.0040.0040.0000.0000.0000.000
164A164PRO0-0.028-0.01340.5490.0010.0010.0000.0000.0000.000
165A165TYR0-0.065-0.03836.6010.0030.0030.0000.0000.0000.000
166A166GLY00.0280.01839.5220.0030.0030.0000.0000.0000.000
167A167ASN0-0.0150.01141.910-0.003-0.0030.0000.0000.0000.000
168A168ILE00.0300.01440.0800.0010.0010.0000.0000.0000.000
169A169GLN00.0080.01743.954-0.001-0.0010.0000.0000.0000.000
170A170ALA0-0.031-0.00944.7180.0000.0000.0000.0000.0000.000
171A171VAL0-0.022-0.01146.289-0.001-0.0010.0000.0000.0000.000
172A172SER00.001-0.01047.780-0.001-0.0010.0000.0000.0000.000
173A173MET0-0.047-0.02344.3290.0010.0010.0000.0000.0000.000
174A174ASP-1-0.865-0.94449.2780.0060.0060.0000.0000.0000.000
175A175SER0-0.059-0.02451.8160.0000.0000.0000.0000.0000.000
176A176ILE0-0.038-0.02047.2420.0010.0010.0000.0000.0000.000
177A177PRO00.0210.01949.4600.0000.0000.0000.0000.0000.000
178A178LEU00.0390.01851.1930.0010.0010.0000.0000.0000.000
179A179GLN0-0.067-0.04848.5500.0000.0000.0000.0000.0000.000
180A180THR00.0460.02747.794-0.001-0.0010.0000.0000.0000.000
181A181TYR0-0.027-0.01644.3370.0000.0000.0000.0000.0000.000
182A182ASP-1-0.854-0.93442.5910.0300.0300.0000.0000.0000.000
183A183LEU0-0.030-0.01336.0870.0010.0010.0000.0000.0000.000
184A184VAL00.0290.02940.342-0.002-0.0020.0000.0000.0000.000
185A185ILE0-0.012-0.02335.0100.0010.0010.0000.0000.0000.000
186A186ASN0-0.028-0.01636.304-0.004-0.0040.0000.0000.0000.000
187A187ALA00.018-0.07034.7690.0020.0020.0000.0000.0000.000
188A188THR0-0.056-0.01235.239-0.003-0.0030.0000.0000.0000.000
189A189SER0-0.001-0.00132.5220.0010.0010.0000.0000.0000.000
190A190ALA0-0.042-0.02034.058-0.001-0.0010.0000.0000.0000.000
191A191GLY00.0470.01534.839-0.002-0.0020.0000.0000.0000.000
192A192LEU0-0.0030.01536.9100.0010.0010.0000.0000.0000.000
193A193SER0-0.003-0.00840.091-0.001-0.0010.0000.0000.0000.000
194A194GLY0-0.0050.00340.8050.0010.0010.0000.0000.0000.000
195A195GLY00.000-0.01937.9620.0000.0000.0000.0000.0000.000
196A196THR0-0.024-0.00337.2940.0000.0000.0000.0000.0000.000
197A197ALA0-0.001-0.00339.870-0.001-0.0010.0000.0000.0000.000
198A198SER0-0.013-0.01142.7720.0010.0010.0000.0000.0000.000
199A199VAL0-0.030-0.01043.743-0.001-0.0010.0000.0000.0000.000
200A200ASP-1-0.821-0.90646.5720.0090.0090.0000.0000.0000.000
201A201ALA00.0500.00548.8340.0010.0010.0000.0000.0000.000
202A202GLU-1-0.930-0.97749.9040.0130.0130.0000.0000.0000.000
203A203ILE0-0.058-0.01046.5090.0010.0010.0000.0000.0000.000
204A204LEU0-0.029-0.02743.6910.0010.0010.0000.0000.0000.000
205A205LYS10.9360.95546.599-0.015-0.0150.0000.0000.0000.000
206A206LEU0-0.0160.01848.2560.0010.0010.0000.0000.0000.000
207A207GLY0-0.0130.01244.7260.0010.0010.0000.0000.0000.000
208A208SER0-0.018-0.00443.910-0.001-0.0010.0000.0000.0000.000
209A209ALA0-0.001-0.00238.9170.0020.0020.0000.0000.0000.000
210A210PHE0-0.0310.00239.017-0.001-0.0010.0000.0000.0000.000
211A211TYR00.010-0.04428.9900.0010.0010.0000.0000.0000.000
212A212ASP-1-0.785-0.87533.6100.0170.0170.0000.0000.0000.000
213A213MET0-0.0130.04830.7650.0030.0030.0000.0000.0000.000
214A214GLN0-0.021-0.00129.0770.0030.0030.0000.0000.0000.000
215A215TYR00.0310.01823.4070.0040.0040.0000.0000.0000.000
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