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: 94982

Calculation Name: 4PO4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PO4

Chain ID: A

ChEMBL ID:

UniProt ID: A0A088

Base Structure: X-ray

Registration Date: 2023-09-19

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2611053.473619
FMO2-HF: Nuclear repulsion 2523726.172616
FMO2-HF: Total energy -87327.301003
FMO2-MP2: Total energy -87578.389255


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-6.899-0.71415.864-9.824-12.228-0.007
Interaction energy analysis for fragmet #1(A:1:ALA)
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 : -0.010
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].
3A3PHE00.0420.0143.7881.5083.045-0.012-0.810-0.7150.003
4A4ALA0-0.079-0.0466.2070.2540.2540.0000.0000.0000.000
5A5ALA00.0280.0207.940-0.157-0.1570.0000.0000.0000.000
6A6GLY0-0.032-0.0229.416-0.027-0.0270.0000.0000.0000.000
7A7LYS10.9340.9658.7300.0810.0810.0000.0000.0000.000
8A8ASP-1-0.777-0.8996.442-1.032-1.0320.0000.0000.0000.000
9A9ASP-1-0.928-0.9342.547-4.721-2.9600.261-0.585-1.437-0.007
10A10LEU0-0.051-0.0121.8191.045-0.0907.981-4.399-2.4470.002
11A11CYS0-0.192-0.1072.7350.3220.9073.272-1.325-2.533-0.002
12A12THR00.0500.0294.246-0.148-0.1280.000-0.017-0.0040.000
13A14SER00.0240.0157.2140.1130.1130.0000.0000.0000.000
14A15ASN00.029-0.00810.6490.0910.0910.0000.0000.0000.000
15A16LYS10.9500.99013.035-0.074-0.0740.0000.0000.0000.000
16A17THR0-0.032-0.04015.707-0.006-0.0060.0000.0000.0000.000
17A18GLU-1-0.953-0.98918.8240.0050.0050.0000.0000.0000.000
18A19SER0-0.070-0.03920.9350.0030.0030.0000.0000.0000.000
19A20SER00.0430.05515.909-0.006-0.0060.0000.0000.0000.000
20A21PRO00.0150.00914.2940.0000.0000.0000.0000.0000.000
21A22GLU-1-0.845-0.9059.9770.2100.2100.0000.0000.0000.000
22A23THR0-0.031-0.0329.3950.0720.0720.0000.0000.0000.000
23A24VAL00.0200.0103.121-0.387-0.1070.057-0.089-0.2480.000
24A25ASP-1-0.813-0.8506.131-0.082-0.0820.0000.0000.0000.000
25A27SER0-0.033-0.0665.8520.0810.0810.0000.0000.0000.000
26A28SER0-0.027-0.0279.590-0.055-0.0550.0000.0000.0000.000
27A29LYS10.8680.9446.2290.5350.5350.0000.0000.0000.000
28A30LYS10.9130.9579.1560.1320.1320.0000.0000.0000.000
29A31LEU0-0.016-0.0045.3860.0070.0070.0000.0000.0000.000
30A32THR00.0330.0079.3590.0320.0320.0000.0000.0000.000
31A33THR0-0.016-0.0208.1240.0470.0470.0000.0000.0000.000
32A34VAL00.0310.0126.042-0.042-0.0420.0000.0000.0000.000
33A35PRO0-0.0190.0112.202-0.822-0.4772.318-0.920-1.7430.002
34A36THR00.003-0.0054.1620.3650.5830.000-0.039-0.1790.000
35A37GLY00.0570.0132.727-1.909-0.0890.573-1.037-1.356-0.003
36A38ILE0-0.023-0.0102.434-1.240-0.6341.401-0.585-1.423-0.002
37A39PRO00.0450.0413.729-0.489-0.3410.013-0.018-0.1430.000
38A40THR0-0.0180.0007.098-0.128-0.1280.0000.0000.0000.000
39A41SER0-0.064-0.03610.125-0.044-0.0440.0000.0000.0000.000
40A42THR0-0.034-0.0417.193-0.074-0.0740.0000.0000.0000.000
41A43GLU-1-0.952-0.9819.7990.1070.1070.0000.0000.0000.000
42A44LYS10.9530.99810.8600.0190.0190.0000.0000.0000.000
43A45LEU00.0250.0135.283-0.013-0.0130.0000.0000.0000.000
44A46GLN0-0.036-0.0197.581-0.041-0.0410.0000.0000.0000.000
45A47LEU00.0350.0125.558-0.006-0.0060.0000.0000.0000.000
46A48ASN00.0450.0228.8800.0010.0010.0000.0000.0000.000
47A49TYR0-0.030-0.02411.657-0.034-0.0340.0000.0000.0000.000
48A50ASN0-0.037-0.0038.897-0.075-0.0750.0000.0000.0000.000
49A51GLN0-0.009-0.02312.183-0.004-0.0040.0000.0000.0000.000
50A52LEU00.0200.0358.8560.0030.0030.0000.0000.0000.000
51A53THR00.0440.01312.9200.0000.0000.0000.0000.0000.000
52A54GLY00.002-0.00914.586-0.003-0.0030.0000.0000.0000.000
53A55ILE0-0.0010.00011.8930.0120.0120.0000.0000.0000.000
54A56PRO00.0280.02710.738-0.025-0.0250.0000.0000.0000.000
55A57PRO00.0280.00313.2880.0380.0380.0000.0000.0000.000
56A58THR00.0320.00313.019-0.005-0.0050.0000.0000.0000.000
57A59ALA0-0.032-0.0129.6350.0600.0600.0000.0000.0000.000
58A60PHE00.0140.0049.0670.1220.1220.0000.0000.0000.000
59A61GLN00.0150.01711.123-0.002-0.0020.0000.0000.0000.000
60A62GLY0-0.005-0.01411.199-0.052-0.0520.0000.0000.0000.000
61A63LEU00.0090.0308.036-0.041-0.0410.0000.0000.0000.000
62A64THR0-0.023-0.02011.801-0.057-0.0570.0000.0000.0000.000
63A65LYS10.9300.96213.895-0.199-0.1990.0000.0000.0000.000
64A66LEU00.0230.0309.896-0.017-0.0170.0000.0000.0000.000
65A67THR0-0.007-0.00313.840-0.021-0.0210.0000.0000.0000.000
66A68TYR0-0.0130.00312.553-0.023-0.0230.0000.0000.0000.000
67A69LEU00.0350.01310.6850.0350.0350.0000.0000.0000.000
68A70ASN00.0050.00011.579-0.016-0.0160.0000.0000.0000.000
69A71LEU00.024-0.01110.8190.0210.0210.0000.0000.0000.000
70A72ASP-1-0.747-0.85413.4970.0240.0240.0000.0000.0000.000
71A73SER0-0.065-0.04414.751-0.011-0.0110.0000.0000.0000.000
72A74ASN0-0.0110.01311.954-0.016-0.0160.0000.0000.0000.000
73A75GLN0-0.052-0.04315.618-0.005-0.0050.0000.0000.0000.000
74A76LEU00.0030.01114.0370.0030.0030.0000.0000.0000.000
75A77GLN0-0.010-0.00417.869-0.013-0.0130.0000.0000.0000.000
76A78TYR0-0.031-0.02419.895-0.005-0.0050.0000.0000.0000.000
77A79LEU00.0220.01417.0870.0080.0080.0000.0000.0000.000
78A80PRO0-0.0140.01117.014-0.012-0.0120.0000.0000.0000.000
79A81VAL00.012-0.03420.0840.0030.0030.0000.0000.0000.000
80A82GLY00.0590.03921.4760.0060.0060.0000.0000.0000.000
81A83VAL0-0.057-0.01415.5220.0140.0140.0000.0000.0000.000
82A84PHE00.0460.01214.9960.0270.0270.0000.0000.0000.000
83A85ASP-1-0.890-0.93418.0000.1360.1360.0000.0000.0000.000
84A86GLN0-0.070-0.05416.353-0.006-0.0060.0000.0000.0000.000
85A87LEU0-0.0150.01013.5340.0100.0100.0000.0000.0000.000
86A88LYS10.9700.96817.100-0.164-0.1640.0000.0000.0000.000
87A89ASN0-0.086-0.06017.873-0.029-0.0290.0000.0000.0000.000
88A90LEU0-0.041-0.00614.609-0.005-0.0050.0000.0000.0000.000
89A91ASN00.0250.02218.494-0.005-0.0050.0000.0000.0000.000
90A92GLU-1-0.895-0.95217.7710.0290.0290.0000.0000.0000.000
91A93LEU00.0210.00516.1210.0190.0190.0000.0000.0000.000
92A94ARG10.7800.89616.068-0.036-0.0360.0000.0000.0000.000
93A95LEU00.0260.00316.2060.0160.0160.0000.0000.0000.000
94A96ASP-1-0.753-0.86318.4270.0250.0250.0000.0000.0000.000
95A97PHE0-0.072-0.03919.0170.0000.0000.0000.0000.0000.000
96A98ASN0-0.012-0.00116.7820.0020.0020.0000.0000.0000.000
97A99LYS10.9130.95320.194-0.015-0.0150.0000.0000.0000.000
98A100LEU00.0490.04119.9530.0020.0020.0000.0000.0000.000
99A101LYS10.9530.96723.377-0.029-0.0290.0000.0000.0000.000
100A102SER0-0.036-0.01125.749-0.001-0.0010.0000.0000.0000.000
101A103LEU00.0480.01523.1230.0040.0040.0000.0000.0000.000
102A104PRO0-0.0020.01422.091-0.005-0.0050.0000.0000.0000.000
103A105PRO00.0310.00025.4360.0000.0000.0000.0000.0000.000
104A106ARG10.9340.95826.580-0.069-0.0690.0000.0000.0000.000
105A107VAL0-0.033-0.01121.3200.0070.0070.0000.0000.0000.000
106A108PHE00.1060.05121.0690.0100.0100.0000.0000.0000.000
107A109ASP-1-0.896-0.95223.9270.0750.0750.0000.0000.0000.000
108A110ARG10.9210.96022.621-0.110-0.1100.0000.0000.0000.000
109A111LEU0-0.0200.00119.4640.0060.0060.0000.0000.0000.000
110A112THR00.010-0.00622.817-0.005-0.0050.0000.0000.0000.000
111A113ASN0-0.038-0.01422.886-0.014-0.0140.0000.0000.0000.000
112A114LEU0-0.0190.00520.502-0.001-0.0010.0000.0000.0000.000
113A115THR00.0190.01323.170-0.003-0.0030.0000.0000.0000.000
114A116ALA00.0360.02621.914-0.007-0.0070.0000.0000.0000.000
115A117LEU00.0170.00621.6130.0100.0100.0000.0000.0000.000
116A118TYR0-0.056-0.02720.417-0.007-0.0070.0000.0000.0000.000
117A119LEU0-0.015-0.02621.2030.0080.0080.0000.0000.0000.000
118A120GLU-1-0.800-0.90323.4430.0100.0100.0000.0000.0000.000
119A121TYR0-0.038-0.00823.5050.0010.0010.0000.0000.0000.000
120A122ASN0-0.0060.00721.7740.0040.0040.0000.0000.0000.000
121A123GLN0-0.043-0.03524.947-0.004-0.0040.0000.0000.0000.000
122A124LEU00.0150.00125.3270.0000.0000.0000.0000.0000.000
123A125GLN0-0.004-0.01428.563-0.005-0.0050.0000.0000.0000.000
124A126SER0-0.065-0.01630.934-0.001-0.0010.0000.0000.0000.000
125A127ILE00.0230.01228.8420.0020.0020.0000.0000.0000.000
126A128PRO00.0030.00028.142-0.003-0.0030.0000.0000.0000.000
127A129LYS10.9620.96231.448-0.038-0.0380.0000.0000.0000.000
128A130GLY00.0870.05032.9780.0030.0030.0000.0000.0000.000
129A131VAL0-0.089-0.03227.2480.0030.0030.0000.0000.0000.000
130A132PHE00.0450.00926.6890.0050.0050.0000.0000.0000.000
131A133ASP-1-0.861-0.92430.0240.0470.0470.0000.0000.0000.000
132A134LYS10.8690.92028.410-0.069-0.0690.0000.0000.0000.000
133A135LEU0-0.0150.01325.3060.0020.0020.0000.0000.0000.000
134A136VAL00.0470.01028.608-0.004-0.0040.0000.0000.0000.000
135A137ASN0-0.113-0.07527.427-0.008-0.0080.0000.0000.0000.000
136A138LEU00.0010.03425.301-0.001-0.0010.0000.0000.0000.000
137A139GLU-1-0.919-0.95827.4750.0300.0300.0000.0000.0000.000
138A140THR0-0.015-0.01525.985-0.004-0.0040.0000.0000.0000.000
139A141LEU0-0.0020.00526.3950.0050.0050.0000.0000.0000.000
140A142TRP00.0150.00225.115-0.008-0.0080.0000.0000.0000.000
141A143LEU00.0340.00726.1200.0040.0040.0000.0000.0000.000
142A144ARG10.8420.92327.238-0.007-0.0070.0000.0000.0000.000
143A145GLU-1-0.939-0.98828.1090.0070.0070.0000.0000.0000.000
144A146ASN00.0080.03226.7290.0040.0040.0000.0000.0000.000
145A147LYS10.9040.92229.841-0.014-0.0140.0000.0000.0000.000
146A148LEU0-0.0010.02431.2700.0010.0010.0000.0000.0000.000
147A149GLN00.0200.01334.123-0.003-0.0030.0000.0000.0000.000
148A150SER00.0190.00336.992-0.001-0.0010.0000.0000.0000.000
149A151VAL0-0.002-0.00334.2450.0020.0020.0000.0000.0000.000
150A152PRO0-0.052-0.03734.888-0.001-0.0010.0000.0000.0000.000
151A153ASP-1-0.912-0.96237.8180.0260.0260.0000.0000.0000.000
152A154GLY00.0940.02639.3530.0020.0020.0000.0000.0000.000
153A155ALA0-0.106-0.03534.3030.0020.0020.0000.0000.0000.000
154A156PHE00.021-0.01932.6570.0030.0030.0000.0000.0000.000
155A157ASP-1-0.841-0.89035.3220.0290.0290.0000.0000.0000.000
156A158SER0-0.0110.00333.779-0.002-0.0020.0000.0000.0000.000
157A159LEU0-0.078-0.02530.0790.0020.0020.0000.0000.0000.000
158A160THR0-0.019-0.01833.599-0.002-0.0020.0000.0000.0000.000
159A161LYS10.9170.94831.422-0.041-0.0410.0000.0000.0000.000
160A162VAL00.0000.02630.7320.0000.0000.0000.0000.0000.000
161A163GLU-1-0.937-0.95531.8300.0180.0180.0000.0000.0000.000
162A164MET0-0.068-0.03630.384-0.003-0.0030.0000.0000.0000.000
163A165LEU00.0320.01530.9040.0030.0030.0000.0000.0000.000
164A166GLN0-0.064-0.01729.633-0.003-0.0030.0000.0000.0000.000
165A167LEU00.0670.01231.1090.0020.0020.0000.0000.0000.000
166A168HIS0-0.063-0.04232.925-0.001-0.0010.0000.0000.0000.000
167A169ASN00.000-0.00132.4940.0010.0010.0000.0000.0000.000
168A170ASN00.0590.02531.2550.0020.0020.0000.0000.0000.000
169A171PRO0-0.0530.01234.656-0.001-0.0010.0000.0000.0000.000
170A172TRP0-0.011-0.02634.4220.0020.0020.0000.0000.0000.000
171A173ASP-1-0.841-0.92539.6230.0120.0120.0000.0000.0000.000
172A174CYS0-0.169-0.06640.2110.0020.0020.0000.0000.0000.000
173A175ALA00.0140.00645.383-0.001-0.0010.0000.0000.0000.000
174A221CYS0-0.0620.03143.140-0.001-0.0010.0000.0000.0000.000
175A177SER00.0550.01146.6520.0000.0000.0000.0000.0000.000
176A178ASP-1-0.884-0.97641.6030.0230.0230.0000.0000.0000.000
177A179ILE0-0.0310.00341.1700.0010.0010.0000.0000.0000.000
178A180ILE0-0.017-0.01143.2380.0000.0000.0000.0000.0000.000
179A181TYR0-0.034-0.01937.948-0.001-0.0010.0000.0000.0000.000
180A182LEU00.0270.01737.7870.0000.0000.0000.0000.0000.000
181A183ARG10.8820.96241.087-0.014-0.0140.0000.0000.0000.000
182A184THR0-0.034-0.03844.207-0.001-0.0010.0000.0000.0000.000
183A185PHE00.0040.00437.111-0.001-0.0010.0000.0000.0000.000
184A186ILE00.040-0.00239.2340.0000.0000.0000.0000.0000.000
185A187ALA0-0.067-0.03441.702-0.001-0.0010.0000.0000.0000.000
186A188LYS10.9100.96243.907-0.020-0.0200.0000.0000.0000.000
187A189ASN0-0.033-0.02140.0000.0000.0000.0000.0000.0000.000
188A190THR0-0.004-0.01240.4220.0010.0010.0000.0000.0000.000
189A191ASP-1-0.902-0.92941.7330.0100.0100.0000.0000.0000.000
190A192LYS10.8340.89839.600-0.018-0.0180.0000.0000.0000.000
191A193ILE00.0200.03134.7350.0010.0010.0000.0000.0000.000
192A194SER00.0380.00734.550-0.002-0.0020.0000.0000.0000.000
193A195GLY0-0.011-0.01834.3230.0010.0010.0000.0000.0000.000
194A196MET00.0370.04235.4100.0010.0010.0000.0000.0000.000
195A197GLU-1-0.898-0.95937.4670.0080.0080.0000.0000.0000.000
196A198SER0-0.0470.00636.606-0.001-0.0010.0000.0000.0000.000
197A199ALA0-0.039-0.00738.058-0.001-0.0010.0000.0000.0000.000
198A200GLN00.0500.00438.955-0.001-0.0010.0000.0000.0000.000
199A202ASN00.032-0.00440.671-0.002-0.0020.0000.0000.0000.000
200A203GLY0-0.022-0.00341.7790.0000.0000.0000.0000.0000.000
201A204THR0-0.015-0.00143.935-0.001-0.0010.0000.0000.0000.000
202A205SER00.0290.01144.3060.0000.0000.0000.0000.0000.000
203A206THR0-0.062-0.02645.8400.0000.0000.0000.0000.0000.000
204A207ALA00.0820.03443.7410.0010.0010.0000.0000.0000.000
205A208VAL00.038-0.00540.4510.0000.0000.0000.0000.0000.000
206A209LYS10.9440.96543.513-0.007-0.0070.0000.0000.0000.000
207A210ASP-1-0.881-0.93445.1050.0080.0080.0000.0000.0000.000
208A211VAL0-0.057-0.02546.067-0.001-0.0010.0000.0000.0000.000
209A212LYS10.9420.97048.936-0.007-0.0070.0000.0000.0000.000
210A213THR00.0650.00748.9060.0000.0000.0000.0000.0000.000
211A214GLU-1-0.937-0.95751.2200.0140.0140.0000.0000.0000.000
212A215PRO0-0.056-0.05553.7870.0000.0000.0000.0000.0000.000
213A216ILE00.0080.00748.1070.0000.0000.0000.0000.0000.000
214A217LYS10.9560.98550.740-0.015-0.0150.0000.0000.0000.000
215A218ASN0-0.0140.00551.5550.0010.0010.0000.0000.0000.000
216A219VAL0-0.0030.01749.5680.0000.0000.0000.0000.0000.000
217A220PRO00.0220.00147.8450.0000.0000.0000.0000.0000.000