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: QY9MY

Calculation Name: 4TX1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4TX1

Chain ID: A

ChEMBL ID:

UniProt ID: Q7APD5

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 -2433124.049096
FMO2-HF: Nuclear repulsion 2351306.695387
FMO2-HF: Total energy -81817.353709
FMO2-MP2: Total energy -82051.76611


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.
-6.254-2.05510.015-3.711-10.501-0.038
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 : -0.085 / q_NPA : -0.035
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].
3A3THR00.0090.0013.381-0.7602.2210.228-1.310-1.899-0.006
4A4VAL0-0.008-0.0114.8660.1290.173-0.001-0.006-0.0360.000
5A5LEU0-0.0070.0168.3810.1290.1290.0000.0000.0000.000
6A6CYS0-0.042-0.00511.3450.0250.0250.0000.0000.0000.000
7A7TYR00.003-0.01414.377-0.009-0.0090.0000.0000.0000.000
8A8GLY00.0950.02117.4900.0090.0090.0000.0000.0000.000
9A9ASP-1-0.779-0.89620.6790.0110.0110.0000.0000.0000.000
10A10SER0-0.0010.00122.5870.0050.0050.0000.0000.0000.000
11A11LEU0-0.070-0.04123.6110.0030.0030.0000.0000.0000.000
12A12THR00.0360.03217.5640.0120.0120.0000.0000.0000.000
13A13TRP0-0.058-0.01919.1370.0100.0100.0000.0000.0000.000
14A14GLY00.0280.01621.0100.0050.0050.0000.0000.0000.000
15A15TYR0-0.048-0.02222.667-0.005-0.0050.0000.0000.0000.000
16A16ASP-1-0.770-0.87026.4510.0300.0300.0000.0000.0000.000
17A17ALA0-0.017-0.03528.415-0.004-0.0040.0000.0000.0000.000
18A18THR0-0.092-0.03731.445-0.002-0.0020.0000.0000.0000.000
19A19GLY00.006-0.00731.665-0.002-0.0020.0000.0000.0000.000
20A20SER0-0.056-0.01331.796-0.003-0.0030.0000.0000.0000.000
21A21GLY00.0200.01428.951-0.004-0.0040.0000.0000.0000.000
22A22ARG10.7980.90719.111-0.020-0.0200.0000.0000.0000.000
23A23HIS00.0280.00522.281-0.002-0.0020.0000.0000.0000.000
24A24ALA00.0310.02621.101-0.002-0.0020.0000.0000.0000.000
25A25LEU00.0300.00113.9880.0060.0060.0000.0000.0000.000
26A26GLU-1-0.850-0.93115.8730.0690.0690.0000.0000.0000.000
27A27ASP-1-0.862-0.92616.9530.0830.0830.0000.0000.0000.000
28A28ARG10.8250.91516.886-0.050-0.0500.0000.0000.0000.000
29A29TRP00.0610.01014.7360.0260.0260.0000.0000.0000.000
30A30PRO00.0350.00912.9390.0240.0240.0000.0000.0000.000
31A31SER0-0.018-0.01811.9510.0690.0690.0000.0000.0000.000
32A32VAL0-0.039-0.01212.1430.0220.0220.0000.0000.0000.000
33A33LEU00.0570.02910.7760.0090.0090.0000.0000.0000.000
34A34GLN0-0.012-0.0074.9940.2340.2340.0000.0000.0000.000
35A35LYS10.8660.9308.261-0.118-0.1180.0000.0000.0000.000
36A36ALA0-0.021-0.00310.585-0.019-0.0190.0000.0000.0000.000
37A37LEU0-0.010-0.0037.601-0.004-0.0040.0000.0000.0000.000
38A38GLY0-0.0130.0026.9820.1010.1010.0000.0000.0000.000
39A39SER0-0.013-0.0343.134-0.1350.2990.035-0.089-0.3790.000
40A40ASP-1-0.929-0.9442.769-1.529-0.0851.465-1.054-1.854-0.013
41A41ALA0-0.007-0.0062.600-1.965-0.1262.395-1.495-2.740-0.017
42A42HIS00.0110.0202.9970.423-1.4985.853-0.505-3.427-0.003
43A43VAL0-0.037-0.0274.067-0.940-1.5620.0400.748-0.1660.001
44A44ILE00.0100.0167.832-0.066-0.0660.0000.0000.0000.000
45A45ALA0-0.039-0.02810.518-0.041-0.0410.0000.0000.0000.000
46A46GLU-1-0.835-0.90914.063-0.103-0.1030.0000.0000.0000.000
47A47GLY0-0.021-0.00816.899-0.003-0.0030.0000.0000.0000.000
48A48LEU0-0.025-0.01620.001-0.002-0.0020.0000.0000.0000.000
49A49ASN00.033-0.01423.3580.0080.0080.0000.0000.0000.000
50A50GLY0-0.031-0.02426.545-0.005-0.0050.0000.0000.0000.000
51A51ARG10.8560.94519.8530.0330.0330.0000.0000.0000.000
52A52THR0-0.011-0.01426.6200.0050.0050.0000.0000.0000.000
53A53THR0-0.024-0.04425.896-0.006-0.0060.0000.0000.0000.000
54A54ALA0-0.030-0.02126.224-0.007-0.0070.0000.0000.0000.000
55A55TYR0-0.056-0.03328.780-0.002-0.0020.0000.0000.0000.000
56A56ASP-1-0.777-0.85931.018-0.035-0.0350.0000.0000.0000.000
57A57ASP-1-0.812-0.91231.869-0.009-0.0090.0000.0000.0000.000
58A58HIS0-0.012-0.01432.627-0.002-0.0020.0000.0000.0000.000
59A59LEU0-0.030-0.01234.7770.0000.0000.0000.0000.0000.000
60A60ALA0-0.060-0.03631.4540.0020.0020.0000.0000.0000.000
61A61ASP-1-0.937-0.95331.401-0.038-0.0380.0000.0000.0000.000
62A62CYS0-0.039-0.02626.979-0.001-0.0010.0000.0000.0000.000
63A63ASP-1-0.752-0.83326.930-0.045-0.0450.0000.0000.0000.000
64A64ARG10.8520.91426.4480.0130.0130.0000.0000.0000.000
65A65ASN0-0.012-0.01227.6870.0020.0020.0000.0000.0000.000
66A66GLY00.0350.02324.111-0.006-0.0060.0000.0000.0000.000
67A67ALA00.0500.01823.336-0.010-0.0100.0000.0000.0000.000
68A68ARG10.6970.80024.6300.0370.0370.0000.0000.0000.000
69A69VAL00.0130.01221.246-0.008-0.0080.0000.0000.0000.000
70A70LEU0-0.0130.00817.576-0.012-0.0120.0000.0000.0000.000
71A71PRO00.0510.02618.797-0.019-0.0190.0000.0000.0000.000
72A72THR00.0270.01118.778-0.026-0.0260.0000.0000.0000.000
73A73VAL0-0.032-0.00415.402-0.022-0.0220.0000.0000.0000.000
74A74LEU0-0.001-0.00314.429-0.027-0.0270.0000.0000.0000.000
75A75HIS00.0280.01713.837-0.074-0.0740.0000.0000.0000.000
76A76THR0-0.105-0.05214.139-0.031-0.0310.0000.0000.0000.000
77A77HIS0-0.068-0.06110.233-0.034-0.0340.0000.0000.0000.000
78A78ALA0-0.0450.0259.192-0.132-0.1320.0000.0000.0000.000
79A79PRO00.0020.0077.3960.0300.0300.0000.0000.0000.000
80A80LEU0-0.001-0.0317.403-0.246-0.2460.0000.0000.0000.000
81A81ASP-1-0.775-0.8815.839-1.678-1.6780.0000.0000.0000.000
82A82LEU0-0.036-0.0148.7670.2410.2410.0000.0000.0000.000
83A83ILE0-0.0050.01510.776-0.025-0.0250.0000.0000.0000.000
84A84VAL0-0.005-0.01313.1200.0370.0370.0000.0000.0000.000
85A85PHE0-0.006-0.00315.585-0.009-0.0090.0000.0000.0000.000
86A86MET0-0.0090.00819.0660.0180.0180.0000.0000.0000.000
87A87LEU0-0.042-0.01621.510-0.006-0.0060.0000.0000.0000.000
88A88GLY00.1040.05624.5210.0040.0040.0000.0000.0000.000
89A89SER00.0280.01227.926-0.001-0.0010.0000.0000.0000.000
90A90ASN0-0.041-0.03328.027-0.003-0.0030.0000.0000.0000.000
91A91ASP-1-0.717-0.83229.637-0.005-0.0050.0000.0000.0000.000
92A92MET0-0.049-0.00632.2840.0010.0010.0000.0000.0000.000
93A93LYS10.8760.96632.2530.0030.0030.0000.0000.0000.000
94A94PRO00.0620.02636.637-0.002-0.0020.0000.0000.0000.000
95A95ILE0-0.052-0.02737.041-0.001-0.0010.0000.0000.0000.000
96A96ILE0-0.107-0.03532.733-0.002-0.0020.0000.0000.0000.000
97A97HIS00.0190.00432.6640.0000.0000.0000.0000.0000.000
98A98GLY0-0.0150.01636.3140.0010.0010.0000.0000.0000.000
99A99THR0-0.038-0.02636.4450.0030.0030.0000.0000.0000.000
100A100ALA00.0420.00433.591-0.001-0.0010.0000.0000.0000.000
101A101PHE0-0.010-0.01232.9360.0000.0000.0000.0000.0000.000
102A102GLY00.0610.03533.535-0.002-0.0020.0000.0000.0000.000
103A103ALA00.0000.00729.770-0.004-0.0040.0000.0000.0000.000
104A104VAL00.0250.01228.661-0.002-0.0020.0000.0000.0000.000
105A105LYS10.8250.89728.9350.0000.0000.0000.0000.0000.000
106A106GLY00.0360.01628.607-0.005-0.0050.0000.0000.0000.000
107A107ILE0-0.027-0.03023.372-0.008-0.0080.0000.0000.0000.000
108A108GLU-1-0.762-0.84824.395-0.011-0.0110.0000.0000.0000.000
109A109ARG10.9050.96325.7100.0450.0450.0000.0000.0000.000
110A110LEU0-0.0020.00021.595-0.010-0.0100.0000.0000.0000.000
111A111VAL00.0360.02420.904-0.015-0.0150.0000.0000.0000.000
112A112ASN0-0.055-0.05021.313-0.015-0.0150.0000.0000.0000.000
113A113LEU0-0.072-0.03021.710-0.008-0.0080.0000.0000.0000.000
114A114VAL00.0410.02116.073-0.018-0.0180.0000.0000.0000.000
115A115ARG10.8160.89518.375-0.010-0.0100.0000.0000.0000.000
116A116ARG10.8620.92420.3210.0800.0800.0000.0000.0000.000
117A117HIS00.0010.01317.0570.0290.0290.0000.0000.0000.000
118A118ASP-1-0.980-0.98119.373-0.185-0.1850.0000.0000.0000.000
119A119TRP00.023-0.00313.412-0.041-0.0410.0000.0000.0000.000
120A120PRO0-0.0100.00413.9830.0190.0190.0000.0000.0000.000
121A121THR0-0.044-0.02113.537-0.003-0.0030.0000.0000.0000.000
122A122GLU-1-0.994-1.01015.390-0.232-0.2320.0000.0000.0000.000
123A123THR0-0.071-0.04313.024-0.048-0.0480.0000.0000.0000.000
124A124GLU-1-0.962-0.95112.485-0.156-0.1560.0000.0000.0000.000
125A125GLU-1-0.914-0.97411.964-0.073-0.0730.0000.0000.0000.000
126A126GLY0-0.042-0.01713.007-0.069-0.0690.0000.0000.0000.000
127A127PRO0-0.0120.00211.9320.0270.0270.0000.0000.0000.000
128A128GLU-1-0.875-0.92812.7010.1390.1390.0000.0000.0000.000
129A129ILE0-0.035-0.03314.101-0.039-0.0390.0000.0000.0000.000
130A130LEU00.0040.00115.7150.0280.0280.0000.0000.0000.000
131A131ILE0-0.011-0.00317.768-0.012-0.0120.0000.0000.0000.000
132A132VAL00.0310.00618.9280.0130.0130.0000.0000.0000.000
133A133SER00.000-0.00122.001-0.011-0.0110.0000.0000.0000.000
134A134PRO0-0.055-0.02724.9030.0090.0090.0000.0000.0000.000
135A135PRO0-0.021-0.01824.897-0.002-0.0020.0000.0000.0000.000
136A136PRO00.0120.01728.137-0.004-0.0040.0000.0000.0000.000
137A137LEU00.0150.01831.5780.0010.0010.0000.0000.0000.000
138A138CYS0-0.101-0.03933.9330.0010.0010.0000.0000.0000.000
139A139GLU-1-0.873-0.94436.5950.0180.0180.0000.0000.0000.000
140A140THR0-0.048-0.05338.3220.0010.0010.0000.0000.0000.000
141A141ALA0-0.0060.00340.429-0.001-0.0010.0000.0000.0000.000
142A142ASN0-0.040-0.00338.254-0.004-0.0040.0000.0000.0000.000
143A143SER00.0770.01741.5480.0000.0000.0000.0000.0000.000
144A144ALA00.0100.01040.796-0.001-0.0010.0000.0000.0000.000
145A145PHE00.007-0.01033.490-0.001-0.0010.0000.0000.0000.000
146A146ALA00.0130.01038.8720.0000.0000.0000.0000.0000.000
147A147ALA0-0.040-0.01041.2920.0000.0000.0000.0000.0000.000
148A148MET0-0.038-0.01136.426-0.001-0.0010.0000.0000.0000.000
149A149PHE0-0.005-0.02432.802-0.001-0.0010.0000.0000.0000.000
150A150ALA00.0330.03138.1030.0020.0020.0000.0000.0000.000
151A151GLY00.0130.00540.922-0.001-0.0010.0000.0000.0000.000
152A152GLY00.0330.00137.0440.0010.0010.0000.0000.0000.000
153A153VAL0-0.0250.01236.3150.0030.0030.0000.0000.0000.000
154A154GLU-1-0.883-0.95737.2800.0210.0210.0000.0000.0000.000
155A155GLN00.0290.01536.6170.0010.0010.0000.0000.0000.000
156A156SER00.023-0.00832.4300.0030.0030.0000.0000.0000.000
157A157ALA0-0.0110.00932.7510.0040.0040.0000.0000.0000.000
158A158MET0-0.074-0.04634.4550.0020.0020.0000.0000.0000.000
159A159LEU0-0.003-0.00329.4670.0000.0000.0000.0000.0000.000
160A160ALA00.0130.01828.8090.0010.0010.0000.0000.0000.000
161A161PRO0-0.051-0.03529.5710.0030.0030.0000.0000.0000.000
162A162LEU00.0640.04031.4890.0000.0000.0000.0000.0000.000
163A163TYR0-0.047-0.06925.406-0.004-0.0040.0000.0000.0000.000
164A164ARG10.9110.97526.763-0.067-0.0670.0000.0000.0000.000
165A165ASP-1-0.906-0.95327.8480.0450.0450.0000.0000.0000.000
166A166LEU0-0.009-0.00626.106-0.001-0.0010.0000.0000.0000.000
167A167ALA0-0.060-0.04023.568-0.004-0.0040.0000.0000.0000.000
168A168ASP-1-0.934-0.95424.8330.0630.0630.0000.0000.0000.000
169A169GLU-1-0.971-0.97527.1450.0130.0130.0000.0000.0000.000
170A170LEU0-0.064-0.04924.464-0.006-0.0060.0000.0000.0000.000
171A171ASP-1-0.905-0.93522.4820.0580.0580.0000.0000.0000.000
172A172CYS0-0.093-0.02420.100-0.012-0.0120.0000.0000.0000.000
173A173GLY00.0600.02719.1140.0130.0130.0000.0000.0000.000
174A174PHE00.018-0.01120.095-0.016-0.0160.0000.0000.0000.000
175A175PHE0-0.020-0.01220.5810.0180.0180.0000.0000.0000.000
176A176ASP-1-0.797-0.91122.6280.0570.0570.0000.0000.0000.000
177A177GLY00.0330.02223.5440.0080.0080.0000.0000.0000.000
178A178GLY0-0.003-0.00924.3920.0010.0010.0000.0000.0000.000
179A179SER0-0.134-0.07025.5510.0000.0000.0000.0000.0000.000
180A180VAL0-0.032-0.01722.5940.0030.0030.0000.0000.0000.000
181A181ALA0-0.024-0.00224.9320.0000.0000.0000.0000.0000.000
182A182ARG10.9220.95727.012-0.050-0.0500.0000.0000.0000.000
183A183THR00.0220.00029.4750.0010.0010.0000.0000.0000.000
184A184THR0-0.007-0.00931.052-0.001-0.0010.0000.0000.0000.000
185A185PRO00.0710.01733.206-0.002-0.0020.0000.0000.0000.000
186A186ILE0-0.044-0.00133.861-0.003-0.0030.0000.0000.0000.000
187A187ASP-1-0.808-0.90233.0910.0200.0200.0000.0000.0000.000
188A188GLY00.0580.03635.352-0.002-0.0020.0000.0000.0000.000
189A189VAL0-0.026-0.01530.3420.0020.0020.0000.0000.0000.000
190A190HIS10.8070.88927.910-0.018-0.0180.0000.0000.0000.000
191A191LEU00.0670.03723.9130.0000.0000.0000.0000.0000.000
192A192ASP-1-0.816-0.88126.9890.0520.0520.0000.0000.0000.000
193A193ALA00.0720.02824.2870.0050.0050.0000.0000.0000.000
194A194GLU-1-0.801-0.88123.4530.1000.1000.0000.0000.0000.000
195A195ASN0-0.002-0.02524.2490.0120.0120.0000.0000.0000.000
196A196THR0-0.045-0.03220.4600.0050.0050.0000.0000.0000.000
197A197ARG10.8530.90918.164-0.085-0.0850.0000.0000.0000.000
198A198ALA0-0.031-0.00519.7240.0200.0200.0000.0000.0000.000
199A199VAL00.0500.02519.2540.0100.0100.0000.0000.0000.000
200A200GLY00.002-0.00116.7790.0130.0130.0000.0000.0000.000
201A201ARG10.7870.86116.388-0.095-0.0950.0000.0000.0000.000
202A202GLY0-0.019-0.01118.3470.0170.0170.0000.0000.0000.000
203A203LEU00.0080.01016.0200.0030.0030.0000.0000.0000.000
204A204GLU-1-0.828-0.88413.4720.3690.3690.0000.0000.0000.000
205A205PRO0-0.018-0.00814.2460.0440.0440.0000.0000.0000.000
206A206VAL00.0290.02415.7430.0260.0260.0000.0000.0000.000
207A207VAL00.012-0.00310.8410.0050.0050.0000.0000.0000.000
208A208ARG10.8280.89310.103-0.524-0.5240.0000.0000.0000.000
209A209MET0-0.061-0.02912.0080.0360.0360.0000.0000.0000.000
210A210MET0-0.005-0.00513.4530.0200.0200.0000.0000.0000.000
211A211LEU00.0010.0147.154-0.046-0.0460.0000.0000.0000.000
212A212GLY00.0100.0158.7490.2520.2520.0000.0000.0000.000
213A213LEU0-0.087-0.0467.0600.3790.3790.0000.0000.0000.000