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: R93M8

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2432390.366821
FMO2-HF: Nuclear repulsion 2350574.128707
FMO2-HF: Total energy -81816.238114
FMO2-MP2: Total energy -82050.725928


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.
-7.965-1.0825.197-4.263-7.816-0.025
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 : -0.059 / q_NPA : -0.033
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].
3A3THR00.002-0.0033.009-1.9080.6600.177-1.168-1.577-0.005
4A4VAL0-0.011-0.0044.6910.4540.504-0.001-0.008-0.0400.000
5A5LEU0-0.0050.0148.1270.1900.1900.0000.0000.0000.000
6A6CYS0-0.051-0.01411.1770.0510.0510.0000.0000.0000.000
7A7TYR0-0.004-0.01414.1490.0100.0100.0000.0000.0000.000
8A8GLY00.0900.01617.3140.0160.0160.0000.0000.0000.000
9A9ASP-1-0.798-0.91020.475-0.033-0.0330.0000.0000.0000.000
10A10SER0-0.018-0.01322.6630.0070.0070.0000.0000.0000.000
11A11LEU0-0.055-0.03623.7610.0090.0090.0000.0000.0000.000
12A12THR00.0390.04017.7550.0150.0150.0000.0000.0000.000
13A13TRP0-0.037-0.01219.3520.0160.0160.0000.0000.0000.000
14A14GLY00.0200.00921.1550.0120.0120.0000.0000.0000.000
15A15TYR0-0.050-0.02222.870-0.002-0.0020.0000.0000.0000.000
16A16ASP-1-0.810-0.89726.6370.0360.0360.0000.0000.0000.000
17A17ALA0-0.009-0.03628.840-0.005-0.0050.0000.0000.0000.000
18A18THR0-0.067-0.01532.039-0.003-0.0030.0000.0000.0000.000
19A19GLY00.0180.00332.191-0.002-0.0020.0000.0000.0000.000
20A20SER0-0.061-0.01732.167-0.004-0.0040.0000.0000.0000.000
21A21GLY00.0210.01429.268-0.005-0.0050.0000.0000.0000.000
22A22ARG10.8070.91218.984-0.004-0.0040.0000.0000.0000.000
23A23HIS00.0280.00622.7240.0050.0050.0000.0000.0000.000
24A24ALA00.0380.02221.457-0.005-0.0050.0000.0000.0000.000
25A25LEU00.020-0.00714.092-0.001-0.0010.0000.0000.0000.000
26A26GLU-1-0.878-0.95316.5290.1360.1360.0000.0000.0000.000
27A27ASP-1-0.869-0.92817.5900.1370.1370.0000.0000.0000.000
28A28ARG10.8290.92317.344-0.071-0.0710.0000.0000.0000.000
29A29TRP00.0560.00214.8100.0410.0410.0000.0000.0000.000
30A30PRO00.0280.00913.1980.0330.0330.0000.0000.0000.000
31A31SER0-0.002-0.00312.2320.0760.0760.0000.0000.0000.000
32A32VAL0-0.040-0.01312.9970.0710.0710.0000.0000.0000.000
33A33LEU00.0560.02711.3550.0420.0420.0000.0000.0000.000
34A34GLN0-0.012-0.0095.707-0.141-0.036-0.001-0.004-0.1000.000
35A35LYS10.8600.9289.291-0.176-0.1760.0000.0000.0000.000
36A36ALA0-0.021-0.00711.7390.0350.0350.0000.0000.0000.000
37A37LEU0-0.013-0.0047.8020.0080.0080.0000.0000.0000.000
38A38GLY0-0.016-0.0038.1640.1630.1630.0000.0000.0000.000
39A39SER0-0.014-0.0384.291-0.1630.0780.000-0.035-0.2050.000
40A40ASP-1-0.926-0.9343.5692.5943.8500.396-0.518-1.134-0.004
41A41ALA0-0.027-0.0132.583-3.926-1.7161.365-1.670-1.906-0.017
42A42HIS00.0200.0262.9300.7031.3563.231-1.105-2.7790.000
43A43VAL0-0.039-0.0274.281-1.530-1.7300.0300.245-0.0750.001
44A44ILE00.0130.0177.7440.0660.0660.0000.0000.0000.000
45A45ALA0-0.047-0.02910.488-0.036-0.0360.0000.0000.0000.000
46A46GLU-1-0.869-0.92914.188-0.212-0.2120.0000.0000.0000.000
47A47GLY0-0.023-0.01516.782-0.002-0.0020.0000.0000.0000.000
48A48LEU0-0.019-0.01219.9550.0060.0060.0000.0000.0000.000
49A49ASN00.034-0.01923.2330.0060.0060.0000.0000.0000.000
50A50GLY0-0.045-0.03426.537-0.005-0.0050.0000.0000.0000.000
51A51ARG10.9030.97719.8500.1170.1170.0000.0000.0000.000
52A52THR0-0.004-0.01026.4810.0050.0050.0000.0000.0000.000
53A53THR0-0.028-0.04825.740-0.012-0.0120.0000.0000.0000.000
54A54ALA0-0.025-0.01626.107-0.013-0.0130.0000.0000.0000.000
55A55TYR0-0.059-0.03728.6770.0020.0020.0000.0000.0000.000
56A56ASP-1-0.806-0.87430.926-0.079-0.0790.0000.0000.0000.000
57A57ASP-1-0.850-0.94331.818-0.039-0.0390.0000.0000.0000.000
58A58HIS0-0.004-0.00732.563-0.005-0.0050.0000.0000.0000.000
59A59LEU0-0.032-0.01534.7580.0020.0020.0000.0000.0000.000
60A60ALA0-0.071-0.04031.3410.0050.0050.0000.0000.0000.000
61A61ASP-1-0.935-0.95331.196-0.068-0.0680.0000.0000.0000.000
62A62CYS0-0.039-0.02126.953-0.003-0.0030.0000.0000.0000.000
63A63ASP-1-0.762-0.84926.949-0.099-0.0990.0000.0000.0000.000
64A64ARG10.8770.93326.4100.0420.0420.0000.0000.0000.000
65A65ASN0-0.0040.00127.590-0.003-0.0030.0000.0000.0000.000
66A66GLY00.0260.01824.028-0.011-0.0110.0000.0000.0000.000
67A67ALA00.0660.02223.279-0.019-0.0190.0000.0000.0000.000
68A68ARG10.6860.81124.6210.0870.0870.0000.0000.0000.000
69A69VAL00.0110.00421.255-0.011-0.0110.0000.0000.0000.000
70A70LEU0-0.0050.01517.548-0.018-0.0180.0000.0000.0000.000
71A71PRO00.0460.02118.826-0.033-0.0330.0000.0000.0000.000
72A72THR00.0300.01218.882-0.036-0.0360.0000.0000.0000.000
73A73VAL0-0.032-0.00615.378-0.029-0.0290.0000.0000.0000.000
74A74LEU00.001-0.00614.480-0.051-0.0510.0000.0000.0000.000
75A75HIS00.0340.02813.960-0.099-0.0990.0000.0000.0000.000
76A76THR0-0.103-0.04713.891-0.029-0.0290.0000.0000.0000.000
77A77HIS0-0.049-0.05210.256-0.068-0.0680.0000.0000.0000.000
78A78ALA0-0.0470.0269.339-0.202-0.2020.0000.0000.0000.000
79A79PRO0-0.0030.0057.6520.0480.0480.0000.0000.0000.000
80A80LEU0-0.002-0.0347.546-0.326-0.3260.0000.0000.0000.000
81A81ASP-1-0.797-0.8855.603-2.987-2.9870.0000.0000.0000.000
82A82LEU0-0.035-0.0088.6390.3450.3450.0000.0000.0000.000
83A83ILE0-0.0090.00710.571-0.058-0.0580.0000.0000.0000.000
84A84VAL0-0.004-0.01112.7470.0650.0650.0000.0000.0000.000
85A85PHE0-0.010-0.01015.315-0.004-0.0040.0000.0000.0000.000
86A86MET0-0.0160.00918.8230.0280.0280.0000.0000.0000.000
87A87LEU0-0.050-0.01821.237-0.001-0.0010.0000.0000.0000.000
88A88GLY00.1030.05524.2860.0040.0040.0000.0000.0000.000
89A89SER00.0280.01027.6880.0020.0020.0000.0000.0000.000
90A90ASN0-0.044-0.03127.6630.0050.0050.0000.0000.0000.000
91A91ASP-1-0.711-0.82429.449-0.052-0.0520.0000.0000.0000.000
92A92MET0-0.044-0.00632.0820.0030.0030.0000.0000.0000.000
93A93LYS10.9180.98432.4340.0320.0320.0000.0000.0000.000
94A94PRO00.0510.02236.430-0.004-0.0040.0000.0000.0000.000
95A95ILE0-0.044-0.02636.767-0.001-0.0010.0000.0000.0000.000
96A96ILE0-0.105-0.03132.599-0.003-0.0030.0000.0000.0000.000
97A97HIS00.0180.00632.4850.0010.0010.0000.0000.0000.000
98A98GLY0-0.0110.01936.1200.0030.0030.0000.0000.0000.000
99A99THR0-0.042-0.03136.2350.0040.0040.0000.0000.0000.000
100A100ALA00.0460.00633.335-0.003-0.0030.0000.0000.0000.000
101A101PHE0-0.012-0.01332.696-0.004-0.0040.0000.0000.0000.000
102A102GLY00.0630.03433.330-0.004-0.0040.0000.0000.0000.000
103A103ALA00.0090.01129.398-0.007-0.0070.0000.0000.0000.000
104A104VAL00.0210.00928.414-0.007-0.0070.0000.0000.0000.000
105A105LYS10.8540.90928.7390.0470.0470.0000.0000.0000.000
106A106GLY00.0270.01428.455-0.009-0.0090.0000.0000.0000.000
107A107ILE0-0.022-0.02623.212-0.015-0.0150.0000.0000.0000.000
108A108GLU-1-0.789-0.86624.233-0.075-0.0750.0000.0000.0000.000
109A109ARG10.8850.95125.5890.1130.1130.0000.0000.0000.000
110A110LEU0-0.007-0.00121.469-0.014-0.0140.0000.0000.0000.000
111A111VAL00.0370.02620.773-0.028-0.0280.0000.0000.0000.000
112A112ASN0-0.018-0.02521.227-0.024-0.0240.0000.0000.0000.000
113A113LEU0-0.086-0.03821.771-0.008-0.0080.0000.0000.0000.000
114A114VAL00.0440.02416.068-0.024-0.0240.0000.0000.0000.000
115A115ARG10.8250.90518.3820.1000.1000.0000.0000.0000.000
116A116ARG10.8550.92420.2960.1670.1670.0000.0000.0000.000
117A117HIS00.0010.00817.2380.0400.0400.0000.0000.0000.000
118A118ASP-1-0.977-0.98019.490-0.298-0.2980.0000.0000.0000.000
119A119TRP00.023-0.00313.920-0.054-0.0540.0000.0000.0000.000
120A120PRO0-0.0080.00214.1610.0250.0250.0000.0000.0000.000
121A121THR0-0.086-0.03813.5920.0020.0020.0000.0000.0000.000
122A122GLU-1-0.975-1.00515.448-0.352-0.3520.0000.0000.0000.000
123A123THR0-0.059-0.02113.467-0.080-0.0800.0000.0000.0000.000
124A124GLU-1-0.982-0.96212.463-0.284-0.2840.0000.0000.0000.000
125A125GLU-1-0.882-0.96612.070-0.179-0.1790.0000.0000.0000.000
126A126GLY0-0.057-0.02512.971-0.096-0.0960.0000.0000.0000.000
127A127PRO0-0.009-0.00411.7960.0260.0260.0000.0000.0000.000
128A128GLU-1-0.900-0.92812.5350.0080.0080.0000.0000.0000.000
129A129ILE0-0.020-0.03013.908-0.058-0.0580.0000.0000.0000.000
130A130LEU0-0.0170.00015.5170.0480.0480.0000.0000.0000.000
131A131ILE00.006-0.00217.474-0.015-0.0150.0000.0000.0000.000
132A132VAL00.0250.00018.8170.0220.0220.0000.0000.0000.000
133A133SER00.0060.00221.701-0.010-0.0100.0000.0000.0000.000
134A134PRO0-0.050-0.02324.9320.0110.0110.0000.0000.0000.000
135A135PRO0-0.028-0.02425.1200.0000.0000.0000.0000.0000.000
136A136PRO00.0330.02228.352-0.005-0.0050.0000.0000.0000.000
137A137LEU0-0.0060.00631.6930.0030.0030.0000.0000.0000.000
138A138CYS0-0.099-0.02434.0960.0020.0020.0000.0000.0000.000
139A139GLU-1-0.884-0.95236.9150.0070.0070.0000.0000.0000.000
140A140THR0-0.039-0.04338.6380.0020.0020.0000.0000.0000.000
141A141ALA0-0.0010.00440.743-0.002-0.0020.0000.0000.0000.000
142A142ASN0-0.0210.00338.941-0.004-0.0040.0000.0000.0000.000
143A143SER00.0760.01741.819-0.001-0.0010.0000.0000.0000.000
144A144ALA00.0160.01440.998-0.001-0.0010.0000.0000.0000.000
145A145PHE0-0.006-0.01533.786-0.003-0.0030.0000.0000.0000.000
146A146ALA00.0170.01039.065-0.001-0.0010.0000.0000.0000.000
147A147ALA0-0.036-0.00541.446-0.001-0.0010.0000.0000.0000.000
148A148MET0-0.040-0.01735.970-0.003-0.0030.0000.0000.0000.000
149A149PHE0-0.010-0.02532.653-0.003-0.0030.0000.0000.0000.000
150A150ALA00.0400.03338.0270.0020.0020.0000.0000.0000.000
151A151GLY00.0060.00040.707-0.002-0.0020.0000.0000.0000.000
152A152GLY00.0300.00236.9270.0000.0000.0000.0000.0000.000
153A153VAL0-0.0010.01836.2140.0010.0010.0000.0000.0000.000
154A154GLU-1-0.894-0.96337.2380.0050.0050.0000.0000.0000.000
155A155GLN00.0160.01036.370-0.001-0.0010.0000.0000.0000.000
156A156SER00.0340.00232.3000.0010.0010.0000.0000.0000.000
157A157ALA0-0.0070.01532.5820.0020.0020.0000.0000.0000.000
158A158MET0-0.069-0.04734.2700.0020.0020.0000.0000.0000.000
159A159LEU0-0.0010.00329.122-0.002-0.0020.0000.0000.0000.000
160A160ALA00.0080.01028.503-0.002-0.0020.0000.0000.0000.000
161A161PRO0-0.042-0.03129.2410.0010.0010.0000.0000.0000.000
162A162LEU00.0620.03831.179-0.002-0.0020.0000.0000.0000.000
163A163TYR0-0.037-0.05725.179-0.007-0.0070.0000.0000.0000.000
164A164ARG10.9190.97726.476-0.036-0.0360.0000.0000.0000.000
165A165ASP-1-0.904-0.95327.5800.0050.0050.0000.0000.0000.000
166A166LEU0-0.011-0.00525.938-0.004-0.0040.0000.0000.0000.000
167A167ALA0-0.065-0.04423.277-0.008-0.0080.0000.0000.0000.000
168A168ASP-1-0.934-0.95924.5810.0090.0090.0000.0000.0000.000
169A169GLU-1-0.974-0.97627.008-0.040-0.0400.0000.0000.0000.000
170A170LEU0-0.070-0.04224.217-0.009-0.0090.0000.0000.0000.000
171A171ASP-1-0.878-0.93322.146-0.039-0.0390.0000.0000.0000.000
172A172CYS0-0.103-0.01919.847-0.026-0.0260.0000.0000.0000.000
173A173GLY00.0580.01718.9610.0250.0250.0000.0000.0000.000
174A174PHE00.000-0.02119.995-0.015-0.0150.0000.0000.0000.000
175A175PHE0-0.016-0.01420.5420.0220.0220.0000.0000.0000.000
176A176ASP-1-0.801-0.90522.4740.0270.0270.0000.0000.0000.000
177A177GLY00.0170.00423.7950.0120.0120.0000.0000.0000.000
178A178GLY0-0.010-0.01724.5940.0070.0070.0000.0000.0000.000
179A179SER0-0.124-0.05125.6640.0050.0050.0000.0000.0000.000
180A180VAL0-0.038-0.02623.0860.0070.0070.0000.0000.0000.000
181A181ALA0-0.0190.00525.3420.0050.0050.0000.0000.0000.000
182A182ARG10.9330.96027.420-0.052-0.0520.0000.0000.0000.000
183A183THR00.007-0.00929.8280.0040.0040.0000.0000.0000.000
184A184THR0-0.025-0.01331.4040.0010.0010.0000.0000.0000.000
185A185PRO00.0820.02133.512-0.004-0.0040.0000.0000.0000.000
186A186ILE0-0.047-0.01134.430-0.003-0.0030.0000.0000.0000.000
187A187ASP-1-0.816-0.89733.4670.0080.0080.0000.0000.0000.000
188A188GLY00.0480.02935.661-0.003-0.0030.0000.0000.0000.000
189A189VAL0-0.028-0.01030.5040.0000.0000.0000.0000.0000.000
190A190HIS10.8030.87728.170-0.003-0.0030.0000.0000.0000.000
191A191LEU00.0610.03324.2910.0010.0010.0000.0000.0000.000
192A192ASP-1-0.832-0.89027.3140.0600.0600.0000.0000.0000.000
193A193ALA00.0760.03024.8950.0040.0040.0000.0000.0000.000
194A194GLU-1-0.849-0.92224.1250.1290.1290.0000.0000.0000.000
195A195ASN00.018-0.01424.8630.0100.0100.0000.0000.0000.000
196A196THR0-0.049-0.03420.725-0.002-0.0020.0000.0000.0000.000
197A197ARG10.8810.92818.894-0.155-0.1550.0000.0000.0000.000
198A198ALA0-0.038-0.00920.2480.0230.0230.0000.0000.0000.000
199A199VAL00.0530.02919.5660.0090.0090.0000.0000.0000.000
200A200GLY00.002-0.00217.1820.0040.0040.0000.0000.0000.000
201A201ARG10.8370.90916.813-0.138-0.1380.0000.0000.0000.000
202A202GLY0-0.021-0.01218.7180.0180.0180.0000.0000.0000.000
203A203LEU00.0050.00716.291-0.001-0.0010.0000.0000.0000.000
204A204GLU-1-0.830-0.89113.4580.4460.4460.0000.0000.0000.000
205A205PRO0-0.031-0.01514.2240.0310.0310.0000.0000.0000.000
206A206VAL00.0380.02015.7190.0190.0190.0000.0000.0000.000
207A207VAL00.0180.00510.853-0.014-0.0140.0000.0000.0000.000
208A208ARG10.8200.8999.977-0.725-0.7250.0000.0000.0000.000
209A209MET0-0.053-0.02611.9840.0220.0220.0000.0000.0000.000
210A210MET00.002-0.00713.3720.0220.0220.0000.0000.0000.000
211A211LEU00.0060.0166.987-0.063-0.0630.0000.0000.0000.000
212A212GLY0-0.019-0.0018.7210.2280.2280.0000.0000.0000.000
213A213LEU0-0.037-0.0156.2220.1220.1220.0000.0000.0000.000