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: 89JKY

Calculation Name: 3P0L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P0L

Chain ID: A

ChEMBL ID:

UniProt ID: P49675

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptHSide
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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2520787.746789
FMO2-HF: Nuclear repulsion 2435768.998724
FMO2-HF: Total energy -85018.748065
FMO2-MP2: Total energy -85261.603644


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:64:SER)


Summations of interaction energy for fragment #1(A:64:SER)
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.
-1.2291.173-0.019-1.267-1.1150.006
Interaction energy analysis for fragmet #1(A:64:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.014
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].
3A66THR0-0.009-0.0053.789-2.473-0.071-0.019-1.267-1.1150.006
4A67LEU0-0.025-0.0206.2900.3620.3620.0000.0000.0000.000
5A68TYR0-0.028-0.0158.587-0.067-0.0670.0000.0000.0000.000
6A69SER0-0.005-0.02513.1360.1010.1010.0000.0000.0000.000
7A70ASP-1-0.854-0.94616.462-0.200-0.2000.0000.0000.0000.000
8A71GLN00.0090.00419.3320.0110.0110.0000.0000.0000.000
9A72GLU-1-0.858-0.90215.115-0.552-0.5520.0000.0000.0000.000
10A73LEU00.0360.00914.587-0.002-0.0020.0000.0000.0000.000
11A74ALA00.0300.03617.9880.0200.0200.0000.0000.0000.000
12A75TYR0-0.034-0.04819.9490.0070.0070.0000.0000.0000.000
13A76LEU0-0.030-0.02714.0310.0020.0020.0000.0000.0000.000
14A77GLN0-0.038-0.01718.6790.0150.0150.0000.0000.0000.000
15A78GLN00.1000.07821.2300.0160.0160.0000.0000.0000.000
16A79GLY0-0.026-0.01020.9530.0140.0140.0000.0000.0000.000
17A80GLU-1-0.897-0.96918.191-0.263-0.2630.0000.0000.0000.000
18A81GLU-1-0.907-0.94722.195-0.124-0.1240.0000.0000.0000.000
19A82ALA0-0.026-0.02025.3720.0170.0170.0000.0000.0000.000
20A83MET0-0.028-0.01622.1210.0070.0070.0000.0000.0000.000
21A84GLN00.004-0.00722.7850.0270.0270.0000.0000.0000.000
22A85LYS10.8810.93426.8090.0850.0850.0000.0000.0000.000
23A86ALA0-0.0010.00928.9450.0090.0090.0000.0000.0000.000
24A87LEU00.015-0.00525.4830.0080.0080.0000.0000.0000.000
25A88GLY00.0170.01829.9710.0090.0090.0000.0000.0000.000
26A89ILE0-0.049-0.02532.2710.0080.0080.0000.0000.0000.000
27A90LEU0-0.055-0.03431.1130.0050.0050.0000.0000.0000.000
28A91SER0-0.019-0.01032.6390.0050.0050.0000.0000.0000.000
29A92ASN0-0.054-0.00734.5450.0070.0070.0000.0000.0000.000
30A93GLN00.0710.01537.935-0.004-0.0040.0000.0000.0000.000
31A94GLU-1-0.928-0.96239.613-0.031-0.0310.0000.0000.0000.000
32A95GLY00.020-0.00443.2420.0000.0000.0000.0000.0000.000
33A96TRP0-0.048-0.01937.6400.0010.0010.0000.0000.0000.000
34A97LYN00.0060.00744.2890.0010.0010.0000.0000.0000.000
35A98LYS10.8640.89445.8390.0360.0360.0000.0000.0000.000
36A99GLU-1-0.836-0.89445.701-0.047-0.0470.0000.0000.0000.000
37A100SER0-0.006-0.00546.3650.0010.0010.0000.0000.0000.000
38A101GLN0-0.031-0.02147.0950.0000.0000.0000.0000.0000.000
39A102GLN00.0050.00845.7090.0020.0020.0000.0000.0000.000
40A103ASP-1-0.821-0.90548.261-0.036-0.0360.0000.0000.0000.000
41A104ASN0-0.055-0.02644.8550.0020.0020.0000.0000.0000.000
42A105GLY0-0.0090.00145.1520.0000.0000.0000.0000.0000.000
43A106ASP-1-0.804-0.86942.645-0.055-0.0550.0000.0000.0000.000
44A107LYS10.9090.95742.4820.0470.0470.0000.0000.0000.000
45A108VAL00.0290.03141.859-0.003-0.0030.0000.0000.0000.000
46A109MET0-0.010-0.00341.5620.0040.0040.0000.0000.0000.000
47A110SER00.0550.02642.113-0.004-0.0040.0000.0000.0000.000
48A111LYS10.8650.94340.3100.0510.0510.0000.0000.0000.000
49A112VAL0-0.0050.00342.188-0.003-0.0030.0000.0000.0000.000
50A113VAL0-0.037-0.01437.2170.0030.0030.0000.0000.0000.000
51A114PRO0-0.005-0.00840.311-0.001-0.0010.0000.0000.0000.000
52A115ASP-1-0.818-0.90336.372-0.064-0.0640.0000.0000.0000.000
53A116VAL0-0.019-0.00135.309-0.002-0.0020.0000.0000.0000.000
54A117GLY00.1050.04438.4140.0020.0020.0000.0000.0000.000
55A118LYS10.6990.85741.1220.0550.0550.0000.0000.0000.000
56A119VAL0-0.0160.00537.214-0.003-0.0030.0000.0000.0000.000
57A120PHE00.011-0.00238.8490.0060.0060.0000.0000.0000.000
58A121ARG10.8230.91836.5890.0540.0540.0000.0000.0000.000
59A122LEU00.0290.02837.1380.0050.0050.0000.0000.0000.000
60A123GLU-1-0.851-0.90837.220-0.063-0.0630.0000.0000.0000.000
61A124VAL00.0610.02637.1750.0040.0040.0000.0000.0000.000
62A125VAL0-0.019-0.00836.934-0.003-0.0030.0000.0000.0000.000
63A126VAL00.0290.01434.7380.0020.0020.0000.0000.0000.000
64A127ASP-1-0.878-0.93336.968-0.046-0.0460.0000.0000.0000.000
65A128GLN0-0.002-0.01134.232-0.001-0.0010.0000.0000.0000.000
66A129PRO00.0410.01730.952-0.002-0.0020.0000.0000.0000.000
67A130MET00.0100.01925.009-0.002-0.0020.0000.0000.0000.000
68A131GLU-1-0.906-0.97422.523-0.144-0.1440.0000.0000.0000.000
69A132ARG10.8960.94726.2490.0720.0720.0000.0000.0000.000
70A133LEU00.0240.00528.780-0.005-0.0050.0000.0000.0000.000
71A134TYR00.0030.00619.828-0.013-0.0130.0000.0000.0000.000
72A135GLU-1-0.834-0.90724.304-0.132-0.1320.0000.0000.0000.000
73A136GLU-1-0.834-0.91925.244-0.114-0.1140.0000.0000.0000.000
74A137LEU0-0.060-0.02527.6010.0030.0030.0000.0000.0000.000
75A138VAL0-0.055-0.04622.589-0.007-0.0070.0000.0000.0000.000
76A139GLU-1-0.990-0.97720.800-0.220-0.2200.0000.0000.0000.000
77A140ARG10.7820.86723.0700.1210.1210.0000.0000.0000.000
78A141MET00.0180.01724.5470.0100.0100.0000.0000.0000.000
79A142GLU-1-0.821-0.89425.107-0.194-0.1940.0000.0000.0000.000
80A143ALA0-0.0100.00828.0560.0070.0070.0000.0000.0000.000
81A144MET0-0.024-0.01530.5610.0090.0090.0000.0000.0000.000
82A145GLY0-0.013-0.01632.3080.0060.0060.0000.0000.0000.000
83A146GLU-1-0.902-0.92133.791-0.100-0.1000.0000.0000.0000.000
84A147TRP0-0.073-0.03232.2030.0090.0090.0000.0000.0000.000
85A148ASN00.016-0.01235.9900.0070.0070.0000.0000.0000.000
86A149PRO00.0600.03438.253-0.002-0.0020.0000.0000.0000.000
87A150ASN0-0.068-0.03039.113-0.001-0.0010.0000.0000.0000.000
88A151VAL0-0.052-0.02034.628-0.003-0.0030.0000.0000.0000.000
89A152LYS10.9510.98537.1830.0910.0910.0000.0000.0000.000
90A153GLU-1-0.917-0.97632.397-0.131-0.1310.0000.0000.0000.000
91A154ILE0-0.0170.00428.325-0.002-0.0020.0000.0000.0000.000
92A155LYS10.8780.94227.7220.1630.1630.0000.0000.0000.000
93A156VAL0-0.030-0.03721.165-0.004-0.0040.0000.0000.0000.000
94A157LEU0-0.036-0.00223.877-0.006-0.0060.0000.0000.0000.000
95A158GLN00.0340.01017.1390.0260.0260.0000.0000.0000.000
96A159LYS10.9440.97516.2350.3790.3790.0000.0000.0000.000
97A160ILE00.0040.00914.301-0.040-0.0400.0000.0000.0000.000
98A161GLY00.0350.03210.9950.0140.0140.0000.0000.0000.000
99A162LYS10.8950.9327.6891.3461.3460.0000.0000.0000.000
100A163ASP-1-0.762-0.85812.847-0.366-0.3660.0000.0000.0000.000
101A164THR00.0190.00716.1080.0520.0520.0000.0000.0000.000
102A165PHE0-0.013-0.02217.307-0.040-0.0400.0000.0000.0000.000
103A166ILE0-0.0020.01619.8760.0310.0310.0000.0000.0000.000
104A167THR0-0.060-0.02123.155-0.002-0.0020.0000.0000.0000.000
105A168HIS00.005-0.03826.1040.0020.0020.0000.0000.0000.000
106A169GLU-1-0.854-0.90929.628-0.136-0.1360.0000.0000.0000.000
107A170LEU00.0370.01231.9600.0080.0080.0000.0000.0000.000
108A171ALA00.0150.00435.3720.0010.0010.0000.0000.0000.000
109A172ALA0-0.0110.00337.9570.0020.0020.0000.0000.0000.000
110A173GLU-1-0.901-0.95341.422-0.069-0.0690.0000.0000.0000.000
111A174ALA00.0130.00444.3210.0010.0010.0000.0000.0000.000
112A175ALA0-0.060-0.02845.7290.0020.0020.0000.0000.0000.000
113A176GLY00.0320.02747.8830.0030.0030.0000.0000.0000.000
114A177ASN0-0.032-0.02748.724-0.001-0.0010.0000.0000.0000.000
115A178LEU0-0.020-0.01450.6480.0010.0010.0000.0000.0000.000
116A179VAL0-0.069-0.02345.1820.0000.0000.0000.0000.0000.000
117A180GLY00.0170.00846.573-0.001-0.0010.0000.0000.0000.000
118A181PRO00.0580.01742.411-0.002-0.0020.0000.0000.0000.000
119A182ARG10.8430.91639.3910.0760.0760.0000.0000.0000.000
120A183ASP-1-0.766-0.84135.266-0.115-0.1150.0000.0000.0000.000
121A184PHE0-0.012-0.00832.5390.0030.0030.0000.0000.0000.000
122A185VAL00.0370.02128.297-0.008-0.0080.0000.0000.0000.000
123A186SER0-0.020-0.00628.0450.0090.0090.0000.0000.0000.000
124A187VAL00.0140.02721.900-0.015-0.0150.0000.0000.0000.000
125A188ARG10.8290.89622.8080.2020.2020.0000.0000.0000.000
126A189CYS00.0010.01419.130-0.047-0.0470.0000.0000.0000.000
127A190ALA00.0110.02319.4600.0330.0330.0000.0000.0000.000
128A191LYS10.8670.92416.1630.2940.2940.0000.0000.0000.000
129A192ARG10.9140.90915.4780.3660.3660.0000.0000.0000.000
130A193ARG10.8800.95818.9640.1100.1100.0000.0000.0000.000
131A194GLY00.0180.00820.3050.0210.0210.0000.0000.0000.000
132A195SER00.0030.00621.188-0.005-0.0050.0000.0000.0000.000
133A196THR00.0310.00824.0100.0010.0010.0000.0000.0000.000
134A197CYS0-0.0050.00622.892-0.015-0.0150.0000.0000.0000.000
135A198VAL0-0.032-0.02923.0880.0170.0170.0000.0000.0000.000
136A199LEU0-0.0120.01823.214-0.020-0.0200.0000.0000.0000.000
137A200ALA0-0.031-0.02223.7680.0190.0190.0000.0000.0000.000
138A201GLY00.0660.00425.469-0.013-0.0130.0000.0000.0000.000
139A202MET0-0.044-0.00426.7250.0180.0180.0000.0000.0000.000
140A203ALA0-0.001-0.00328.169-0.012-0.0120.0000.0000.0000.000
141A204THR0-0.029-0.02425.477-0.005-0.0050.0000.0000.0000.000
142A205ASP-1-0.855-0.91828.022-0.125-0.1250.0000.0000.0000.000
143A206PHE0-0.015-0.00322.753-0.010-0.0100.0000.0000.0000.000
144A207GLY00.0420.01127.6310.0070.0070.0000.0000.0000.000
145A208ASN0-0.082-0.03525.1030.0200.0200.0000.0000.0000.000
146A209MET0-0.0330.00628.441-0.001-0.0010.0000.0000.0000.000
147A210PRO00.0480.02930.7070.0020.0020.0000.0000.0000.000
148A211GLU-1-0.913-0.95133.899-0.093-0.0930.0000.0000.0000.000
149A212GLN00.001-0.01934.0880.0050.0050.0000.0000.0000.000
150A213LYS10.9370.95538.9610.0750.0750.0000.0000.0000.000
151A214GLY0-0.007-0.00542.636-0.001-0.0010.0000.0000.0000.000
152A215VAL0-0.033-0.00839.1050.0030.0030.0000.0000.0000.000
153A216ILE0-0.0160.00440.773-0.001-0.0010.0000.0000.0000.000
154A217ARG10.8540.89933.1360.1210.1210.0000.0000.0000.000
155A218ALA0-0.0300.01137.6720.0040.0040.0000.0000.0000.000
156A219GLU-1-0.773-0.88034.633-0.102-0.1020.0000.0000.0000.000
157A220HIS10.8200.89831.9650.1260.1260.0000.0000.0000.000
158A221GLY00.0820.04132.600-0.004-0.0040.0000.0000.0000.000
159A222PRO0-0.003-0.02630.311-0.007-0.0070.0000.0000.0000.000
160A223THR0-0.063-0.01330.0800.0120.0120.0000.0000.0000.000
161A224CYS0-0.055-0.02328.088-0.009-0.0090.0000.0000.0000.000
162A225MET00.0140.00128.1910.0130.0130.0000.0000.0000.000
163A226VAL0-0.028-0.01027.826-0.011-0.0110.0000.0000.0000.000
164A227LEU00.0160.01526.6030.0090.0090.0000.0000.0000.000
165A228HIS00.023-0.00328.045-0.008-0.0080.0000.0000.0000.000
166A229PRO00.0460.03428.7840.0040.0040.0000.0000.0000.000
167A230LEU0-0.029-0.00631.7500.0030.0030.0000.0000.0000.000
168A231ALA0-0.008-0.01635.1330.0020.0020.0000.0000.0000.000
169A232GLY00.0250.01636.7260.0030.0030.0000.0000.0000.000
170A233SER0-0.044-0.03636.3490.0010.0010.0000.0000.0000.000
171A234PRO00.0570.02532.008-0.004-0.0040.0000.0000.0000.000
172A235SER0-0.020-0.00532.829-0.005-0.0050.0000.0000.0000.000
173A236LYS10.8520.93735.3340.0390.0390.0000.0000.0000.000
174A237THR00.0230.01230.927-0.002-0.0020.0000.0000.0000.000
175A238LYS10.7640.86433.5550.0660.0660.0000.0000.0000.000
176A239LEU00.0310.02132.183-0.004-0.0040.0000.0000.0000.000
177A240THR0-0.043-0.03832.5530.0060.0060.0000.0000.0000.000
178A241TRP00.0420.01632.254-0.006-0.0060.0000.0000.0000.000
179A242LEU0-0.029-0.00332.7330.0070.0070.0000.0000.0000.000
180A243LEU00.0060.00033.344-0.008-0.0080.0000.0000.0000.000
181A244SER00.016-0.00134.6240.0070.0070.0000.0000.0000.000
182A245ILE0-0.015-0.01135.297-0.007-0.0070.0000.0000.0000.000
183A246ASP-1-0.828-0.91037.714-0.068-0.0680.0000.0000.0000.000
184A247LEU00.000-0.02039.840-0.002-0.0020.0000.0000.0000.000
185A248LYS10.8800.95838.4590.0850.0850.0000.0000.0000.000
186A249GLY00.001-0.01243.1300.0000.0000.0000.0000.0000.000
187A250TRP0-0.002-0.00446.3450.0000.0000.0000.0000.0000.000
188A251LEU0-0.052-0.01546.2380.0020.0020.0000.0000.0000.000
189A252PRO00.0440.01949.9040.0000.0000.0000.0000.0000.000
190A253LYS11.0221.00349.3510.0420.0420.0000.0000.0000.000
191A254SER0-0.015-0.00849.429-0.002-0.0020.0000.0000.0000.000
192A255ILE00.0600.01848.979-0.001-0.0010.0000.0000.0000.000
193A256ILE00.0370.02144.600-0.002-0.0020.0000.0000.0000.000
194A257ASN00.000-0.00845.548-0.004-0.0040.0000.0000.0000.000
195A258GLN00.0470.02546.041-0.002-0.0020.0000.0000.0000.000
196A259VAL00.0170.02144.607-0.001-0.0010.0000.0000.0000.000
197A260LEU00.0500.02940.218-0.003-0.0030.0000.0000.0000.000
198A261SER0-0.027-0.02541.737-0.002-0.0020.0000.0000.0000.000
199A262GLN0-0.033-0.03243.320-0.003-0.0030.0000.0000.0000.000
200A263THR00.0220.02039.212-0.002-0.0020.0000.0000.0000.000
201A264GLN0-0.054-0.02936.8050.0010.0010.0000.0000.0000.000
202A265VAL0-0.018-0.02139.985-0.001-0.0010.0000.0000.0000.000
203A266ASP-1-0.849-0.92042.149-0.062-0.0620.0000.0000.0000.000
204A267PHE0-0.007-0.01332.7110.0000.0000.0000.0000.0000.000
205A268ALA0-0.002-0.00237.880-0.002-0.0020.0000.0000.0000.000
206A269ASN0-0.016-0.00639.1880.0010.0010.0000.0000.0000.000
207A270HIS00.0300.00539.0360.0020.0020.0000.0000.0000.000
208A271LEU00.0420.03333.078-0.001-0.0010.0000.0000.0000.000
209A272ARG10.7800.83736.7340.0570.0570.0000.0000.0000.000
210A273LYS10.8800.95038.9310.0670.0670.0000.0000.0000.000
211A274ARG10.8600.92333.8910.0980.0980.0000.0000.0000.000
212A275LEU0-0.077-0.03332.845-0.001-0.0010.0000.0000.0000.000
213A276GLU-1-0.851-0.90536.300-0.057-0.0570.0000.0000.0000.000