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: YVN12

Calculation Name: 2P2O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P2O

Chain ID: A

ChEMBL ID:

UniProt ID: Q75TD0

Base Structure: X-ray

Registration Date: 2023-09-22

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 OptAll
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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1937678.638643
FMO2-HF: Nuclear repulsion 1866347.552295
FMO2-HF: Total energy -71331.086349
FMO2-MP2: Total energy -71540.917567


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:2:LYS)


Summations of interaction energy for fragment #1(A:2:LYS)
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.
-184.784-177.65128.384-16.17-19.346-0.172
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.853 / q_NPA : 0.926
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].
3A4GLU-1-0.752-0.8793.200-46.136-43.3440.079-1.508-1.3620.001
4A5LYS10.8600.9195.88725.87625.8760.0000.0000.0000.000
5A6GLU-1-0.789-0.8702.017-69.875-66.2097.725-5.256-6.135-0.045
6A7LYS10.7730.8831.8993.2654.9998.611-4.651-5.694-0.064
7A8MET0-0.0070.0213.6391.5701.7420.0080.042-0.2220.000
8A9LEU0-0.026-0.0105.5042.5002.5000.0000.0000.0000.000
9A10ALA0-0.045-0.0142.438-0.2840.2440.702-0.453-0.777-0.004
10A11GLY00.0240.0124.3331.8951.959-0.001-0.012-0.0510.000
11A12HIS0-0.070-0.0261.923-29.594-31.41711.260-4.332-5.105-0.060
12A13LEU00.010-0.0056.0462.5432.5430.0000.0000.0000.000
13A14TYR0-0.042-0.0507.154-4.846-4.8460.0000.0000.0000.000
14A15ASN00.0620.0218.5954.1214.1210.0000.0000.0000.000
15A16PRO00.0420.02210.960-0.758-0.7580.0000.0000.0000.000
16A17ALA0-0.021-0.00913.2200.8630.8630.0000.0000.0000.000
17A18ASP-1-0.830-0.9159.803-26.197-26.1970.0000.0000.0000.000
18A19LEU00.0200.00112.1430.8580.8580.0000.0000.0000.000
19A20GLU-1-0.871-0.9129.824-25.854-25.8540.0000.0000.0000.000
20A21LEU0-0.009-0.0169.0011.1671.1670.0000.0000.0000.000
21A22VAL0-0.0010.00412.7601.2281.2280.0000.0000.0000.000
22A23LYS10.8440.92115.86915.98715.9870.0000.0000.0000.000
23A24GLU-1-0.795-0.86412.851-22.403-22.4030.0000.0000.0000.000
24A25ARG10.8710.93814.27320.65920.6590.0000.0000.0000.000
25A26GLU-1-0.878-0.93318.211-13.586-13.5860.0000.0000.0000.000
26A27ARG10.8670.92116.18718.52118.5210.0000.0000.0000.000
27A28ALA00.0400.02318.9290.7050.7050.0000.0000.0000.000
28A29ARG10.7910.86519.07416.44316.4430.0000.0000.0000.000
29A30ARG10.8450.93623.85312.61812.6180.0000.0000.0000.000
30A31LEU00.0130.01522.6730.5890.5890.0000.0000.0000.000
31A32VAL00.0190.01423.5060.4840.4840.0000.0000.0000.000
32A33ARG10.8210.89826.38010.59410.5940.0000.0000.0000.000
33A34LEU0-0.002-0.00928.7490.3720.3720.0000.0000.0000.000
34A35TYR0-0.033-0.02928.5490.2970.2970.0000.0000.0000.000
35A36ASN0-0.047-0.02828.6740.4900.4900.0000.0000.0000.000
36A37GLU-1-0.858-0.90032.263-9.327-9.3270.0000.0000.0000.000
37A38THR0-0.088-0.04233.1950.3070.3070.0000.0000.0000.000
38A39LEU00.0250.00835.9010.0130.0130.0000.0000.0000.000
39A40GLU-1-0.858-0.91738.227-7.840-7.8400.0000.0000.0000.000
40A41THR0-0.009-0.02739.953-0.018-0.0180.0000.0000.0000.000
41A42GLU-1-0.807-0.87737.350-8.503-8.5030.0000.0000.0000.000
42A43TYR00.002-0.01236.214-0.249-0.2490.0000.0000.0000.000
43A44ASP-1-0.880-0.92534.736-8.801-8.8010.0000.0000.0000.000
44A45LYS10.7870.89033.6648.5178.5170.0000.0000.0000.000
45A46ARG10.8260.89031.7798.7508.7500.0000.0000.0000.000
46A47THR00.005-0.01630.162-0.427-0.4270.0000.0000.0000.000
47A48GLY0-0.019-0.00829.179-0.377-0.3770.0000.0000.0000.000
48A49LEU0-0.005-0.01027.886-0.417-0.4170.0000.0000.0000.000
49A50LEU0-0.012-0.01125.551-0.552-0.5520.0000.0000.0000.000
50A51LYS10.8040.90724.28110.28910.2890.0000.0000.0000.000
51A52GLU-1-0.903-0.93924.038-12.555-12.5550.0000.0000.0000.000
52A53LEU0-0.062-0.03020.826-0.654-0.6540.0000.0000.0000.000
53A54PHE0-0.020-0.02419.880-0.699-0.6990.0000.0000.0000.000
54A55GLY00.0160.01817.1400.0920.0920.0000.0000.0000.000
55A56SER0-0.092-0.06618.0850.2460.2460.0000.0000.0000.000
56A57THR0-0.015-0.03120.888-0.078-0.0780.0000.0000.0000.000
57A58GLY00.0140.03224.3460.0430.0430.0000.0000.0000.000
58A59GLU-1-0.884-0.96427.504-10.329-10.3290.0000.0000.0000.000
59A60ARG10.8660.94530.5328.9298.9290.0000.0000.0000.000
60A61LEU00.0220.01026.331-0.223-0.2230.0000.0000.0000.000
61A62PHE0-0.025-0.01130.3730.1790.1790.0000.0000.0000.000
62A63ILE00.0230.00826.477-0.198-0.1980.0000.0000.0000.000
63A64GLU-1-0.821-0.87531.052-8.586-8.5860.0000.0000.0000.000
64A65PRO0-0.0350.00532.050-0.264-0.2640.0000.0000.0000.000
65A66ASN0-0.053-0.04830.5100.0980.0980.0000.0000.0000.000
66A67PHE00.0500.02722.967-0.038-0.0380.0000.0000.0000.000
67A68ARG10.8340.90024.51711.20511.2050.0000.0000.0000.000
68A69CYS00.0080.02519.8540.1150.1150.0000.0000.0000.000
69A70ASP-1-0.868-0.92016.362-17.193-17.1930.0000.0000.0000.000
70A71TYR00.013-0.01413.228-0.076-0.0760.0000.0000.0000.000
71A72GLY00.0030.00716.4630.3200.3200.0000.0000.0000.000
72A73TYR00.007-0.02811.167-0.465-0.4650.0000.0000.0000.000
73A74ASN0-0.037-0.02610.780-1.272-1.2720.0000.0000.0000.000
74A75ILE0-0.043-0.01314.4410.0850.0850.0000.0000.0000.000
75A76HIS0-0.0140.00714.3751.2451.2450.0000.0000.0000.000
76A77VAL0-0.029-0.01319.5920.1220.1220.0000.0000.0000.000
77A78GLY00.0740.03723.2480.0500.0500.0000.0000.0000.000
78A79GLU-1-0.838-0.92825.977-10.364-10.3640.0000.0000.0000.000
79A80ASN0-0.108-0.06729.6010.1530.1530.0000.0000.0000.000
80A81PHE00.0390.04225.8390.1400.1400.0000.0000.0000.000
81A82PHE00.0170.00029.3440.1920.1920.0000.0000.0000.000
82A83MET0-0.0300.00125.828-0.310-0.3100.0000.0000.0000.000
83A84ASN00.0260.00730.1400.1730.1730.0000.0000.0000.000
84A85PHE00.0270.00631.740-0.252-0.2520.0000.0000.0000.000
85A86ASP-1-0.844-0.90831.418-9.474-9.4740.0000.0000.0000.000
86A87GLY00.0070.01528.317-0.119-0.1190.0000.0000.0000.000
87A88VAL0-0.057-0.04523.161-0.165-0.1650.0000.0000.0000.000
88A89ILE00.022-0.00219.312-0.003-0.0030.0000.0000.0000.000
89A90LEU00.0170.01318.256-0.306-0.3060.0000.0000.0000.000
90A91ASP-1-0.684-0.83815.550-19.168-19.1680.0000.0000.0000.000
91A92VAL00.0330.01610.997-0.962-0.9620.0000.0000.0000.000
92A93CYS0-0.047-0.0158.831-2.718-2.7180.0000.0000.0000.000
93A94GLU-1-0.788-0.87211.008-21.441-21.4410.0000.0000.0000.000
94A95VAL0-0.013-0.00713.2480.4270.4270.0000.0000.0000.000
95A96ARG10.8040.89013.94820.52620.5260.0000.0000.0000.000
96A97ILE0-0.007-0.01418.7470.3230.3230.0000.0000.0000.000
97A98GLY00.0250.02022.5760.0000.0000.0000.0000.0000.000
98A99ASP-1-0.837-0.92925.277-11.202-11.2020.0000.0000.0000.000
99A100HIS0-0.046-0.03528.5990.2270.2270.0000.0000.0000.000
100A101CYS0-0.067-0.00227.6810.1330.1330.0000.0000.0000.000
101A102PHE00.0100.01029.6400.0730.0730.0000.0000.0000.000
102A103ILE00.027-0.00226.056-0.048-0.0480.0000.0000.0000.000
103A104GLY0-0.007-0.00230.4900.2180.2180.0000.0000.0000.000
104A105PRO00.0170.01231.512-0.263-0.2630.0000.0000.0000.000
105A106GLY00.035-0.00131.3590.0840.0840.0000.0000.0000.000
106A107VAL0-0.089-0.02626.694-0.078-0.0780.0000.0000.0000.000
107A108HIS00.0120.01824.682-0.574-0.5740.0000.0000.0000.000
108A109ILE00.0080.00219.7400.1330.1330.0000.0000.0000.000
109A110TYR0-0.045-0.03919.005-0.118-0.1180.0000.0000.0000.000
110A111THR0-0.001-0.00913.591-0.514-0.5140.0000.0000.0000.000
111A112ALA00.0400.02613.902-1.497-1.4970.0000.0000.0000.000
112A113THR0-0.040-0.02313.8841.8901.8900.0000.0000.0000.000
113A114HIS0-0.024-0.02114.766-0.726-0.7260.0000.0000.0000.000
114A115PRO00.0330.02515.2640.1830.1830.0000.0000.0000.000
115A116LEU00.0150.00717.3500.8880.8880.0000.0000.0000.000
116A117ASP-1-0.781-0.88320.429-12.926-12.9260.0000.0000.0000.000
117A118PRO0-0.041-0.02921.355-0.494-0.4940.0000.0000.0000.000
118A119HIS00.0030.00520.8220.1170.1170.0000.0000.0000.000
119A120GLU-1-0.899-0.96417.482-17.951-17.9510.0000.0000.0000.000
120A121ARG10.8010.91517.40713.75313.7530.0000.0000.0000.000
121A122ASN0-0.020-0.01918.887-0.409-0.4090.0000.0000.0000.000
122A123SER0-0.047-0.02615.627-0.200-0.2000.0000.0000.0000.000
123A124GLY0-0.021-0.00516.146-0.329-0.3290.0000.0000.0000.000
124A125LEU0-0.064-0.02910.463-1.039-1.0390.0000.0000.0000.000
125A126GLU-1-0.824-0.87112.564-19.030-19.0300.0000.0000.0000.000
126A127TYR0-0.027-0.0319.754-2.135-2.1350.0000.0000.0000.000
127A128GLY00.022-0.0019.9782.0212.0210.0000.0000.0000.000
128A129LYS10.9100.95510.45618.03318.0330.0000.0000.0000.000
129A130PRO00.0410.02310.7491.2121.2120.0000.0000.0000.000
130A131VAL0-0.022-0.00213.4430.9080.9080.0000.0000.0000.000
131A132VAL0-0.021-0.00616.661-0.205-0.2050.0000.0000.0000.000
132A133ILE0-0.006-0.01319.2180.6630.6630.0000.0000.0000.000
133A134GLY00.0440.02422.946-0.114-0.1140.0000.0000.0000.000
134A135HIS00.0460.02525.5140.2630.2630.0000.0000.0000.000
135A136ASN0-0.071-0.05528.4110.3050.3050.0000.0000.0000.000
136A137VAL0-0.0230.01627.2130.2700.2700.0000.0000.0000.000
137A138TRP0-0.021-0.00230.1130.1390.1390.0000.0000.0000.000
138A139ILE00.014-0.00126.292-0.067-0.0670.0000.0000.0000.000
139A140GLY00.0280.01630.7460.1500.1500.0000.0000.0000.000
140A141GLY00.0440.00232.145-0.251-0.2510.0000.0000.0000.000
141A142ARG10.9170.94031.8169.7029.7020.0000.0000.0000.000
142A143ALA0-0.0340.01229.552-0.003-0.0030.0000.0000.0000.000
143A144VAL00.0130.00124.828-0.156-0.1560.0000.0000.0000.000
144A145ILE0-0.023-0.00921.7070.2190.2190.0000.0000.0000.000
145A146ASN0-0.013-0.02520.927-0.524-0.5240.0000.0000.0000.000
146A147PRO00.0300.01115.432-0.019-0.0190.0000.0000.0000.000
147A148GLY0-0.038-0.02615.5530.1290.1290.0000.0000.0000.000
148A149VAL0-0.0590.00416.4800.3570.3570.0000.0000.0000.000
149A150THR00.008-0.00419.514-0.588-0.5880.0000.0000.0000.000
150A151ILE0-0.042-0.03321.1650.7480.7480.0000.0000.0000.000
151A152GLY00.0220.01324.609-0.193-0.1930.0000.0000.0000.000
152A153ASP-1-0.769-0.90026.568-11.249-11.2490.0000.0000.0000.000
153A154ASN0-0.054-0.02629.0070.5620.5620.0000.0000.0000.000
154A155ALA0-0.0090.02229.1000.3280.3280.0000.0000.0000.000
155A156VAL0-0.016-0.01531.2220.0370.0370.0000.0000.0000.000
156A157ILE0-0.0010.00327.8750.0780.0780.0000.0000.0000.000
157A158ALA00.0100.00131.3970.1520.1520.0000.0000.0000.000
158A159SER00.0340.00533.059-0.192-0.1920.0000.0000.0000.000
159A160GLY0-0.063-0.02233.2150.2120.2120.0000.0000.0000.000
160A161ALA0-0.081-0.02331.254-0.049-0.0490.0000.0000.0000.000
161A162VAL00.0220.01027.131-0.275-0.2750.0000.0000.0000.000
162A163VAL00.0240.00224.6810.1460.1460.0000.0000.0000.000
163A164THR0-0.008-0.00123.671-0.478-0.4780.0000.0000.0000.000
164A165LYS10.9330.97122.93710.57810.5780.0000.0000.0000.000
165A166ASP-1-0.764-0.87021.276-14.683-14.6830.0000.0000.0000.000
166A167VAL0-0.063-0.02824.0110.6610.6610.0000.0000.0000.000
167A168PRO0-0.003-0.00726.762-0.169-0.1690.0000.0000.0000.000
168A169ALA00.0860.04228.7310.1130.1130.0000.0000.0000.000
169A170ASN0-0.043-0.03030.0750.1020.1020.0000.0000.0000.000
170A171ALA0-0.0090.00931.2760.3630.3630.0000.0000.0000.000
171A172VAL0-0.0010.00232.766-0.095-0.0950.0000.0000.0000.000
172A173VAL00.0220.00029.7570.1450.1450.0000.0000.0000.000
173A174GLY00.0410.01033.2280.0500.0500.0000.0000.0000.000
174A175GLY0-0.0100.00134.1680.0270.0270.0000.0000.0000.000
175A176ASN00.0280.01130.587-0.558-0.5580.0000.0000.0000.000
176A177PRO00.0480.01328.8950.2150.2150.0000.0000.0000.000
177A178ALA0-0.0480.00829.0820.3650.3650.0000.0000.0000.000
178A179LYS10.9210.95130.4088.2718.2710.0000.0000.0000.000
179A180VAL00.0410.01232.3690.0650.0650.0000.0000.0000.000
180A181ILE0-0.072-0.03534.3890.2060.2060.0000.0000.0000.000
181A182LYS10.9420.97837.1178.0998.0990.0000.0000.0000.000
182A183TRP00.0560.03232.722-0.306-0.3060.0000.0000.0000.000
183A184LEU0-0.0110.00735.6690.3050.3050.0000.0000.0000.000
184A185LYS10.8910.93835.5508.7978.7970.0000.0000.0000.000