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: 98LV2

Calculation Name: 4XCM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XCM

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLM7

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1625019.373221
FMO2-HF: Nuclear repulsion 1558651.856587
FMO2-HF: Total energy -66367.516635
FMO2-MP2: Total energy -66564.508434


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:17:ALA)


Summations of interaction energy for fragment #1(A:17: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.
-1.32.7950.452-2.027-2.519-0.003
Interaction energy analysis for fragmet #1(A:17:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / q_NPA : 0.002
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].
3A19TYR0-0.040-0.0303.8641.1692.981-0.023-1.053-0.7360.001
4A20THR0-0.004-0.0106.775-0.331-0.3310.0000.0000.0000.000
5A21VAL0-0.0160.00710.6150.0430.0430.0000.0000.0000.000
6A22ALA00.0650.04113.3030.0210.0210.0000.0000.0000.000
7A23PRO0-0.017-0.02515.619-0.043-0.0430.0000.0000.0000.000
8A24GLY00.0290.01519.3960.0080.0080.0000.0000.0000.000
9A25ASP-1-0.790-0.86013.2630.0660.0660.0000.0000.0000.000
10A26THR0-0.033-0.02515.448-0.029-0.0290.0000.0000.0000.000
11A27LEU00.0590.01913.593-0.009-0.0090.0000.0000.0000.000
12A28TYR00.0120.00513.789-0.036-0.0360.0000.0000.0000.000
13A29SER0-0.028-0.02314.689-0.028-0.0280.0000.0000.0000.000
14A30ILE00.0210.0178.8680.0090.0090.0000.0000.0000.000
15A31ALA0-0.0050.0019.820-0.062-0.0620.0000.0000.0000.000
16A32ARG10.8350.88811.1010.0080.0080.0000.0000.0000.000
17A33ARG10.8470.9149.075-0.282-0.2820.0000.0000.0000.000
18A34TYR0-0.058-0.0366.1670.2300.2300.0000.0000.0000.000
19A35GLY0-0.0040.0188.184-0.176-0.1760.0000.0000.0000.000
20A36THR00.0130.0068.8170.0110.0110.0000.0000.0000.000
21A37THR00.0430.01811.4840.0670.0670.0000.0000.0000.000
22A38VAL00.016-0.01012.930-0.062-0.0620.0000.0000.0000.000
23A39GLU-1-0.925-0.95514.732-0.330-0.3300.0000.0000.0000.000
24A40GLU-1-0.807-0.87510.296-0.826-0.8260.0000.0000.0000.000
25A41LEU0-0.0190.0008.722-0.100-0.1000.0000.0000.0000.000
26A42MET0-0.022-0.00311.148-0.023-0.0230.0000.0000.0000.000
27A43ARG10.8700.90710.3300.6840.6840.0000.0000.0000.000
28A44LEU0-0.062-0.0295.7010.0350.0350.0000.0000.0000.000
29A45ASN0-0.090-0.0618.341-0.119-0.1190.0000.0000.0000.000
30A46GLY00.0090.02311.4730.0800.0800.0000.0000.0000.000
31A47LEU0-0.042-0.01813.7640.0530.0530.0000.0000.0000.000
32A48GLU-1-0.899-0.94816.546-0.183-0.1830.0000.0000.0000.000
33A49SER0-0.060-0.03519.3850.0280.0280.0000.0000.0000.000
34A50PHE00.042-0.01218.871-0.025-0.0250.0000.0000.0000.000
35A51LEU0-0.0360.00219.5480.0120.0120.0000.0000.0000.000
36A52LEU0-0.001-0.00214.185-0.027-0.0270.0000.0000.0000.000
37A53GLN0-0.016-0.00317.4980.0270.0270.0000.0000.0000.000
38A54PRO00.008-0.01716.8580.0020.0020.0000.0000.0000.000
39A55GLY00.0030.00715.321-0.004-0.0040.0000.0000.0000.000
40A56GLN00.0230.02113.5250.0460.0460.0000.0000.0000.000
41A57VAL0-0.007-0.0048.3670.0150.0150.0000.0000.0000.000
42A58LEU0-0.045-0.0178.747-0.072-0.0720.0000.0000.0000.000
43A59LYS10.9700.9804.9410.8680.902-0.001-0.025-0.0080.000
44A60LEU0-0.014-0.0102.495-0.2661.0180.412-0.528-1.168-0.001
45A61PRO0-0.0090.0073.268-1.840-0.8750.064-0.421-0.607-0.003
46A117PRO00.015-0.0079.2680.0610.0610.0000.0000.0000.000
47A118PRO0-0.0050.01311.672-0.061-0.0610.0000.0000.0000.000
48A119PRO00.0380.01412.8240.0010.0010.0000.0000.0000.000
49A120PRO00.0170.00616.0570.0140.0140.0000.0000.0000.000
50A121GLU-1-0.766-0.83819.432-0.015-0.0150.0000.0000.0000.000
51A122PRO0-0.051-0.02320.9350.0050.0050.0000.0000.0000.000
52A123GLU-1-0.776-0.85124.3270.0240.0240.0000.0000.0000.000
53A124ALA0-0.019-0.03426.789-0.009-0.0090.0000.0000.0000.000
54A125LEU0-0.039-0.00328.5550.0060.0060.0000.0000.0000.000
55A126ASP-1-0.822-0.90428.8360.0230.0230.0000.0000.0000.000
56A127PRO0-0.010-0.02528.951-0.002-0.0020.0000.0000.0000.000
57A128GLU-1-0.820-0.88631.9790.0200.0200.0000.0000.0000.000
58A129SER0-0.024-0.00433.4160.0010.0010.0000.0000.0000.000
59A130PRO00.0330.00835.187-0.004-0.0040.0000.0000.0000.000
60A131LEU00.0520.03136.907-0.002-0.0020.0000.0000.0000.000
61A132LEU00.0120.00632.536-0.003-0.0030.0000.0000.0000.000
62A133ARG10.8190.87836.507-0.017-0.0170.0000.0000.0000.000
63A134ALA0-0.0080.00638.857-0.002-0.0020.0000.0000.0000.000
64A135VAL0-0.012-0.01438.062-0.002-0.0020.0000.0000.0000.000
65A136LEU0-0.023-0.02935.207-0.002-0.0020.0000.0000.0000.000
66A137ARG10.8260.91439.640-0.004-0.0040.0000.0000.0000.000
67A138TYR0-0.046-0.04642.884-0.001-0.0010.0000.0000.0000.000
68A139LEU0-0.0260.00737.035-0.002-0.0020.0000.0000.0000.000
69A140GLY00.0330.02341.506-0.001-0.0010.0000.0000.0000.000
70A141VAL00.003-0.00343.398-0.001-0.0010.0000.0000.0000.000
71A142PRO0-0.052-0.02246.8390.0000.0000.0000.0000.0000.000
72A143TYR0-0.004-0.00648.1480.0010.0010.0000.0000.0000.000
73A144LYS10.8450.90250.0340.0130.0130.0000.0000.0000.000
74A145TYR00.0180.01953.5910.0010.0010.0000.0000.0000.000
75A146GLY00.024-0.00155.5430.0010.0010.0000.0000.0000.000
76A147ALA0-0.024-0.01258.374-0.001-0.0010.0000.0000.0000.000
77A148ASN0-0.009-0.01059.343-0.001-0.0010.0000.0000.0000.000
78A149SER0-0.043-0.02455.4740.0000.0000.0000.0000.0000.000
79A150PRO00.0350.02155.742-0.001-0.0010.0000.0000.0000.000
80A151LEU00.0710.02548.1900.0010.0010.0000.0000.0000.000
81A152ALA00.0020.00050.8530.0000.0000.0000.0000.0000.000
82A153LEU0-0.047-0.00752.4220.0010.0010.0000.0000.0000.000
83A154ASP-1-0.691-0.79250.886-0.011-0.0110.0000.0000.0000.000
84A155CYS0-0.105-0.02746.8290.0010.0010.0000.0000.0000.000
85A156SER00.0610.00247.6080.0000.0000.0000.0000.0000.000
86A157ALA00.0050.01749.5600.0010.0010.0000.0000.0000.000
87A158PHE00.0060.00242.0020.0010.0010.0000.0000.0000.000
88A159VAL00.001-0.00944.0870.0010.0010.0000.0000.0000.000
89A160ALA00.013-0.00746.2060.0020.0020.0000.0000.0000.000
90A161GLN0-0.038-0.00348.0300.0010.0010.0000.0000.0000.000
91A162VAL0-0.004-0.00841.8380.0010.0010.0000.0000.0000.000
92A163TYR0-0.025-0.04440.4160.0010.0010.0000.0000.0000.000
93A164ALA00.0240.02645.6840.0020.0020.0000.0000.0000.000
94A165GLU-1-0.792-0.84945.8560.0020.0020.0000.0000.0000.000
95A166LEU0-0.076-0.03740.4690.0010.0010.0000.0000.0000.000
96A167GLY0-0.0150.00145.1050.0020.0020.0000.0000.0000.000
97A168VAL0-0.062-0.02944.8150.0000.0000.0000.0000.0000.000
98A169ALA00.0060.00148.045-0.001-0.0010.0000.0000.0000.000
99A170LEU00.004-0.00446.8730.0000.0000.0000.0000.0000.000
100A171PRO0-0.018-0.00350.7400.0000.0000.0000.0000.0000.000
101A172ARG10.9500.98652.2400.0010.0010.0000.0000.0000.000
102A173THR0-0.030-0.04053.097-0.001-0.0010.0000.0000.0000.000
103A174THR00.028-0.00248.6460.0010.0010.0000.0000.0000.000
104A175LYS10.8640.92350.4970.0080.0080.0000.0000.0000.000
105A176GLU-1-0.754-0.84652.792-0.002-0.0020.0000.0000.0000.000
106A177GLN0-0.045-0.04148.1700.0000.0000.0000.0000.0000.000
107A178TYR0-0.028-0.02645.6950.0010.0010.0000.0000.0000.000
108A179GLN0-0.045-0.03649.038-0.001-0.0010.0000.0000.0000.000
109A180ALA0-0.0170.00351.3350.0010.0010.0000.0000.0000.000
110A181PHE00.0010.01146.3620.0010.0010.0000.0000.0000.000
111A182PRO00.0230.01644.782-0.001-0.0010.0000.0000.0000.000
112A183PRO0-0.004-0.02943.9900.0000.0000.0000.0000.0000.000
113A184VAL0-0.047-0.01437.5250.0020.0020.0000.0000.0000.000
114A185GLU-1-0.920-0.95037.028-0.011-0.0110.0000.0000.0000.000
115A186ALA0-0.018-0.01332.876-0.003-0.0030.0000.0000.0000.000
116A187PRO0-0.052-0.01734.8230.0030.0030.0000.0000.0000.000
117A188ARG10.8170.85832.169-0.025-0.0250.0000.0000.0000.000
118A189PRO0-0.030-0.02730.657-0.002-0.0020.0000.0000.0000.000
119A190GLY00.0530.03133.7650.0040.0040.0000.0000.0000.000
120A191ASP-1-0.795-0.86336.9740.0070.0070.0000.0000.0000.000
121A192LEU00.0070.01438.924-0.002-0.0020.0000.0000.0000.000
122A193VAL0-0.032-0.02337.5810.0000.0000.0000.0000.0000.000
123A194PHE00.0260.00641.009-0.001-0.0010.0000.0000.0000.000
124A195PHE0-0.017-0.02339.658-0.002-0.0020.0000.0000.0000.000
125A196SER0-0.010-0.02345.1130.0010.0010.0000.0000.0000.000
126A197PHE0-0.023-0.03244.144-0.002-0.0020.0000.0000.0000.000
127A198GLY00.0080.01148.399-0.001-0.0010.0000.0000.0000.000
128A199GLY0-0.054-0.03049.8890.0000.0000.0000.0000.0000.000
129A200LYS10.8940.94350.9060.0170.0170.0000.0000.0000.000
130A201GLU-1-0.794-0.87752.614-0.009-0.0090.0000.0000.0000.000
131A202VAL0-0.0110.01147.699-0.001-0.0010.0000.0000.0000.000
132A203ASP-1-0.813-0.88849.384-0.015-0.0150.0000.0000.0000.000
133A204HIS00.0190.01744.6780.0000.0000.0000.0000.0000.000
134A205VAL00.0230.00844.7410.0000.0000.0000.0000.0000.000
135A206GLY0-0.003-0.00841.586-0.001-0.0010.0000.0000.0000.000
136A207ILE00.0110.01838.3490.0010.0010.0000.0000.0000.000
137A208TYR0-0.0080.00530.625-0.005-0.0050.0000.0000.0000.000
138A209LEU00.014-0.00232.8330.0040.0040.0000.0000.0000.000
139A210GLY00.0550.03029.8430.0040.0040.0000.0000.0000.000
140A211ARG10.8500.89822.6360.0020.0020.0000.0000.0000.000
141A212GLY00.0820.05527.680-0.007-0.0070.0000.0000.0000.000
142A213VAL0-0.039-0.02430.238-0.004-0.0040.0000.0000.0000.000
143A214PHE00.000-0.00832.6490.0050.0050.0000.0000.0000.000
144A215ALA00.0350.02736.176-0.003-0.0030.0000.0000.0000.000
145A216HIS10.8120.86738.8820.0240.0240.0000.0000.0000.000
146A217ALA00.0610.04642.502-0.001-0.0010.0000.0000.0000.000
147A218SER0-0.037-0.03243.312-0.001-0.0010.0000.0000.0000.000
148A219SER00.051-0.01045.0630.0020.0020.0000.0000.0000.000
149A220TYR0-0.0010.01742.4640.0010.0010.0000.0000.0000.000
150A221GLY00.0250.00147.7800.0000.0000.0000.0000.0000.000
151A222SER0-0.071-0.06948.4500.0010.0010.0000.0000.0000.000
152A223ARG10.8510.93145.5290.0220.0220.0000.0000.0000.000
153A224VAL00.0230.03541.552-0.002-0.0020.0000.0000.0000.000
154A225VAL0-0.0080.00439.521-0.001-0.0010.0000.0000.0000.000
155A226ILE00.011-0.00533.8950.0030.0030.0000.0000.0000.000
156A227GLU-1-0.817-0.86635.440-0.035-0.0350.0000.0000.0000.000
157A228SER00.0230.00431.5970.0010.0010.0000.0000.0000.000
158A229LEU00.015-0.00533.7080.0000.0000.0000.0000.0000.000
159A230GLU-1-0.804-0.87529.472-0.041-0.0410.0000.0000.0000.000
160A231ALA0-0.0200.00832.846-0.004-0.0040.0000.0000.0000.000
161A232PRO00.013-0.01334.7350.0040.0040.0000.0000.0000.000
162A233PHE0-0.0010.01237.5880.0020.0020.0000.0000.0000.000
163A234TYR00.013-0.02837.8150.0030.0030.0000.0000.0000.000
164A235ARG10.7990.86631.4350.0430.0430.0000.0000.0000.000
165A236LYS10.9130.97638.4420.0400.0400.0000.0000.0000.000
166A237VAL0-0.0150.00442.1560.0020.0020.0000.0000.0000.000
167A238TYR00.0400.02938.5470.0030.0030.0000.0000.0000.000
168A239ARG10.8470.91542.2200.0190.0190.0000.0000.0000.000
169A240GLY00.0480.04541.4790.0020.0020.0000.0000.0000.000
170A241ALA00.0200.00739.254-0.001-0.0010.0000.0000.0000.000
171A242ARG10.8090.90641.2760.0040.0040.0000.0000.0000.000
172A243ARG10.8640.94737.239-0.010-0.0100.0000.0000.0000.000
173A244VAL00.0190.00441.9840.0000.0000.0000.0000.0000.000
174A245MET0-0.0030.00740.4990.0000.0000.0000.0000.0000.000
175A246ALA00.0050.00638.1790.0010.0010.0000.0000.0000.000