Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: LNRL9

Calculation Name: 3TFX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3TFX

Chain ID: A

ChEMBL ID:

UniProt ID: Q5FJB3

Base Structure: X-ray

Registration Date: 2023-09-23

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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2696143.87048
FMO2-HF: Nuclear repulsion 2608127.813193
FMO2-HF: Total energy -88016.057287
FMO2-MP2: Total energy -88272.656525


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:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
18.99321.8650.292-1.684-1.48-0.004
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.927 / q_NPA : -0.965
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].
3A4PRO0-0.0060.0013.860-2.118-0.363-0.012-0.853-0.8900.004
4A5VAL00.0100.0076.366-2.774-2.7740.0000.0000.0000.000
5A6ILE0-0.038-0.0139.436-0.194-0.1940.0000.0000.0000.000
6A7VAL00.029-0.00612.441-1.086-1.0860.0000.0000.0000.000
7A8ALA0-0.052-0.03415.656-0.249-0.2490.0000.0000.0000.000
8A9LEU0-0.048-0.03218.817-0.438-0.4380.0000.0000.0000.000
9A10ASP-1-0.944-0.95921.48312.52112.5210.0000.0000.0000.000
10A11LEU0-0.042-0.03623.898-0.244-0.2440.0000.0000.0000.000
11A12ASP-1-0.825-0.90327.1409.7889.7880.0000.0000.0000.000
12A13ASN00.004-0.01328.995-0.147-0.1470.0000.0000.0000.000
13A14GLU-1-0.887-0.96827.26910.95310.9530.0000.0000.0000.000
14A15GLU-1-0.930-0.95827.4979.5039.5030.0000.0000.0000.000
15A16GLN0-0.049-0.01827.341-0.089-0.0890.0000.0000.0000.000
16A17LEU0-0.015-0.00321.6080.4180.4180.0000.0000.0000.000
17A18ASN00.0430.00223.3800.9350.9350.0000.0000.0000.000
18A19LYS10.9480.99124.472-9.803-9.8030.0000.0000.0000.000
19A20ILE0-0.036-0.00620.7050.1890.1890.0000.0000.0000.000
20A21LEU00.0600.01919.0380.5530.5530.0000.0000.0000.000
21A22SER0-0.082-0.03619.7890.4740.4740.0000.0000.0000.000
22A23LYS10.9100.95221.101-11.721-11.7210.0000.0000.0000.000
23A24LEU0-0.006-0.01215.9590.2550.2550.0000.0000.0000.000
24A25GLY0-0.029-0.02015.3331.1101.1100.0000.0000.0000.000
25A26ASP-1-0.876-0.92114.50917.03217.0320.0000.0000.0000.000
26A27PRO00.010-0.01614.1521.3061.3060.0000.0000.0000.000
27A28HIS0-0.004-0.00111.7461.6471.6470.0000.0000.0000.000
28A29ASP-1-0.917-0.9339.67228.42828.4280.0000.0000.0000.000
29A30VAL0-0.080-0.04510.5770.3350.3350.0000.0000.0000.000
30A31PHE00.007-0.0028.4630.0450.0450.0000.0000.0000.000
31A32VAL00.0030.01611.950-0.491-0.4910.0000.0000.0000.000
32A33LYS10.8900.95015.386-14.304-14.3040.0000.0000.0000.000
33A34VAL00.0340.03017.549-0.545-0.5450.0000.0000.0000.000
34A35GLY00.0490.01521.1530.2930.2930.0000.0000.0000.000
35A36MET0-0.027-0.02223.833-0.230-0.2300.0000.0000.0000.000
36A37GLU-1-0.925-0.94227.08910.35310.3530.0000.0000.0000.000
37A38LEU00.0550.03523.503-0.201-0.2010.0000.0000.0000.000
38A39PHE0-0.001-0.00925.011-0.270-0.2700.0000.0000.0000.000
39A40TYR0-0.017-0.03526.894-0.069-0.0690.0000.0000.0000.000
40A41ASN0-0.0150.00930.003-0.581-0.5810.0000.0000.0000.000
41A42ALA0-0.020-0.01127.544-0.165-0.1650.0000.0000.0000.000
42A43GLY00.0050.01828.809-0.136-0.1360.0000.0000.0000.000
43A44ILE0-0.022-0.04126.3880.4460.4460.0000.0000.0000.000
44A45ASP-1-0.893-0.93825.88510.71310.7130.0000.0000.0000.000
45A46VAL00.0220.01324.4420.4150.4150.0000.0000.0000.000
46A47ILE00.0120.00420.5750.5000.5000.0000.0000.0000.000
47A48LYS10.9530.97821.449-11.641-11.6410.0000.0000.0000.000
48A49LYS10.9510.96922.350-10.525-10.5250.0000.0000.0000.000
49A50LEU0-0.031-0.01519.3570.3860.3860.0000.0000.0000.000
50A51THR00.004-0.01717.2560.4810.4810.0000.0000.0000.000
51A52GLN0-0.044-0.01817.6950.4490.4490.0000.0000.0000.000
52A53GLN0-0.051-0.02719.3790.3000.3000.0000.0000.0000.000
53A54GLY00.0070.01015.4360.3270.3270.0000.0000.0000.000
54A55TYR0-0.0210.01213.6171.2351.2350.0000.0000.0000.000
55A56LYS10.9540.9837.404-31.525-31.5250.0000.0000.0000.000
56A57ILE00.0390.01612.939-0.500-0.5000.0000.0000.0000.000
57A58PHE0-0.032-0.02114.3230.3650.3650.0000.0000.0000.000
58A59LEU00.0480.01815.972-0.624-0.6240.0000.0000.0000.000
59A60ASP-1-0.846-0.89819.66613.83913.8390.0000.0000.0000.000
60A61LEU00.012-0.01421.231-0.476-0.4760.0000.0000.0000.000
61A62LYS10.8320.93123.187-13.227-13.2270.0000.0000.0000.000
62A63MET00.0100.01523.968-0.579-0.5790.0000.0000.0000.000
63A64HIS00.021-0.00927.3070.3520.3520.0000.0000.0000.000
64A65ASP-1-0.819-0.88530.1128.7438.7430.0000.0000.0000.000
65A66ILE0-0.002-0.02232.1590.2030.2030.0000.0000.0000.000
66A67PRO00.011-0.00931.1610.1690.1690.0000.0000.0000.000
67A68ASN00.0360.01531.2910.4030.4030.0000.0000.0000.000
68A69THR00.0130.00632.8860.0890.0890.0000.0000.0000.000
69A70VAL00.0370.01727.1110.2350.2350.0000.0000.0000.000
70A71TYR00.0000.01828.0470.3660.3660.0000.0000.0000.000
71A72ASN0-0.021-0.02728.3120.4480.4480.0000.0000.0000.000
72A73GLY00.0150.01528.7600.0920.0920.0000.0000.0000.000
73A74ALA00.036-0.00124.0390.3150.3150.0000.0000.0000.000
74A75LYS10.9350.98724.166-10.167-10.1670.0000.0000.0000.000
75A76ALA0-0.083-0.05125.6140.2110.2110.0000.0000.0000.000
76A77LEU00.019-0.00122.4400.1490.1490.0000.0000.0000.000
77A78ALA00.0210.02220.7790.5100.5100.0000.0000.0000.000
78A79LYS10.9290.97221.361-10.599-10.5990.0000.0000.0000.000
79A80LEU0-0.075-0.03521.936-0.127-0.1270.0000.0000.0000.000
80A81GLY00.0290.04318.7300.1650.1650.0000.0000.0000.000
81A82ILE0-0.026-0.00116.7800.7790.7790.0000.0000.0000.000
82A83THR00.001-0.00310.5010.0810.0810.0000.0000.0000.000
83A84PHE0-0.015-0.0029.5100.7550.7550.0000.0000.0000.000
84A85THR00.001-0.02215.132-0.912-0.9120.0000.0000.0000.000
85A86THR00.002-0.01818.7990.2530.2530.0000.0000.0000.000
86A87VAL0-0.0190.00221.028-0.463-0.4630.0000.0000.0000.000
87A88HIS00.0230.01023.6040.4050.4050.0000.0000.0000.000
88A89ALA00.0340.01424.539-0.169-0.1690.0000.0000.0000.000
89A90LEU00.0050.00026.306-0.278-0.2780.0000.0000.0000.000
90A91GLY00.0070.00329.044-0.361-0.3610.0000.0000.0000.000
91A92GLY0-0.037-0.01529.536-0.244-0.2440.0000.0000.0000.000
92A93SER0-0.004-0.02527.9890.1810.1810.0000.0000.0000.000
93A94GLN00.001-0.01628.0030.5070.5070.0000.0000.0000.000
94A95MET00.0120.04326.9470.0800.0800.0000.0000.0000.000
95A96ILE0-0.0040.00822.9760.2760.2760.0000.0000.0000.000
96A97LYS10.9810.99124.523-10.389-10.3890.0000.0000.0000.000
97A98SER00.0050.00825.8600.0890.0890.0000.0000.0000.000
98A99ALA0-0.0010.00524.1440.0990.0990.0000.0000.0000.000
99A100LYS10.8680.93016.876-17.301-17.3010.0000.0000.0000.000
100A101ASP-1-0.881-0.94022.67712.36712.3670.0000.0000.0000.000
101A102GLY0-0.019-0.01525.418-0.067-0.0670.0000.0000.0000.000
102A103LEU0-0.041-0.03819.5600.0550.0550.0000.0000.0000.000
103A104ILE0-0.0070.00620.7010.4130.4130.0000.0000.0000.000
104A105ALA0-0.029-0.00622.349-0.017-0.0170.0000.0000.0000.000
105A106GLY0-0.059-0.03624.457-0.337-0.3370.0000.0000.0000.000
106A107THR0-0.025-0.02618.2570.4020.4020.0000.0000.0000.000
107A108PRO0-0.0240.00020.388-0.405-0.4050.0000.0000.0000.000
108A109ALA00.0770.03020.3580.7430.7430.0000.0000.0000.000
109A110GLY0-0.028-0.00718.601-0.103-0.1030.0000.0000.0000.000
110A111HIS0-0.059-0.03216.2641.2431.2430.0000.0000.0000.000
111A112SER00.0150.00812.6540.4830.4830.0000.0000.0000.000
112A113VAL0-0.030-0.01214.661-0.409-0.4090.0000.0000.0000.000
113A114PRO0-0.027-0.00214.9821.3141.3140.0000.0000.0000.000
114A115LYS10.9150.95010.400-27.054-27.0540.0000.0000.0000.000
115A116LEU0-0.009-0.00714.934-0.521-0.5210.0000.0000.0000.000
116A117LEU0-0.028-0.01113.6890.2620.2620.0000.0000.0000.000
117A118ALA00.0200.00217.840-0.766-0.7660.0000.0000.0000.000
118A119VAL0-0.014-0.02520.4170.4520.4520.0000.0000.0000.000
119A120THR00.0270.01022.808-0.351-0.3510.0000.0000.0000.000
120A121GLU-1-0.774-0.88424.7069.6739.6730.0000.0000.0000.000
121A122LEU0-0.022-0.01425.6570.4500.4500.0000.0000.0000.000
122A123THR00.007-0.00724.489-0.223-0.2230.0000.0000.0000.000
123A124SER0-0.013-0.00927.326-0.104-0.1040.0000.0000.0000.000
124A125ILE0-0.0230.01130.187-0.328-0.3280.0000.0000.0000.000
125A126SER00.0430.02131.1100.1990.1990.0000.0000.0000.000
126A127ASP-1-0.870-0.96233.4229.1009.1000.0000.0000.0000.000
127A128ASP-1-0.936-0.96235.0377.4377.4370.0000.0000.0000.000
128A129VAL00.0390.03835.195-0.094-0.0940.0000.0000.0000.000
129A130LEU0-0.036-0.02632.077-0.030-0.0300.0000.0000.0000.000
130A131ARG10.8830.94635.333-7.500-7.5000.0000.0000.0000.000
131A132ASN0-0.057-0.05938.653-0.193-0.1930.0000.0000.0000.000
132A133GLU-1-0.924-0.93538.3427.7157.7150.0000.0000.0000.000
133A134GLN0-0.096-0.06432.1460.0180.0180.0000.0000.0000.000
134A135ASN00.0100.00237.424-0.090-0.0900.0000.0000.0000.000
135A136CYS0-0.082-0.00433.576-0.001-0.0010.0000.0000.0000.000
136A137ARG10.9930.98836.493-8.398-8.3980.0000.0000.0000.000
137A138LEU0-0.082-0.05432.434-0.126-0.1260.0000.0000.0000.000
138A139PRO00.0770.03833.6580.0480.0480.0000.0000.0000.000
139A140MET00.1030.05028.6350.3350.3350.0000.0000.0000.000
140A141ALA0-0.066-0.04027.6170.3390.3390.0000.0000.0000.000
141A142GLU-1-0.908-0.96227.4829.4009.4000.0000.0000.0000.000
142A143GLN00.0060.00329.1710.0630.0630.0000.0000.0000.000
143A144VAL00.0120.00223.7040.2600.2600.0000.0000.0000.000
144A145LEU00.0030.00423.5900.4420.4420.0000.0000.0000.000
145A146SER0-0.037-0.01324.9190.3410.3410.0000.0000.0000.000
146A147LEU00.0170.00225.4120.0990.0990.0000.0000.0000.000
147A148ALA00.0070.01220.8160.3120.3120.0000.0000.0000.000
148A149LYS10.9650.97221.861-11.606-11.6060.0000.0000.0000.000
149A150MET0-0.0180.01023.5920.0150.0150.0000.0000.0000.000
150A151ALA00.0120.01121.491-0.001-0.0010.0000.0000.0000.000
151A152LYS10.8960.95316.570-16.890-16.8900.0000.0000.0000.000
152A153HIS0-0.044-0.02820.6970.2990.2990.0000.0000.0000.000
153A154SER0-0.087-0.05923.355-0.652-0.6520.0000.0000.0000.000
154A155GLY00.0300.01221.129-0.253-0.2530.0000.0000.0000.000
155A156ALA0-0.022-0.00219.2320.4310.4310.0000.0000.0000.000
156A157ASP-1-0.772-0.87613.87719.07019.0700.0000.0000.0000.000
157A158GLY00.0350.01114.0241.4701.4700.0000.0000.0000.000
158A159VAL0-0.0390.00015.410-1.171-1.1710.0000.0000.0000.000
159A160ILE0-0.031-0.00816.1080.9120.9120.0000.0000.0000.000
160A161CYS0-0.026-0.00117.322-0.504-0.5040.0000.0000.0000.000
161A162SER00.000-0.00518.2400.6520.6520.0000.0000.0000.000
162A163PRO00.048-0.01316.7540.1970.1970.0000.0000.0000.000
163A164LEU00.0170.00817.9180.2950.2950.0000.0000.0000.000
164A165GLU-1-0.949-0.96620.38512.53712.5370.0000.0000.0000.000
165A166VAL00.0110.01414.192-0.233-0.2330.0000.0000.0000.000
166A167LYS10.9751.00017.572-15.590-15.5900.0000.0000.0000.000
167A168LYS11.0111.01319.245-11.927-11.9270.0000.0000.0000.000
168A169LEU00.0000.01118.542-0.264-0.2640.0000.0000.0000.000
169A170HIS0-0.062-0.04214.145-1.010-1.0100.0000.0000.0000.000
170A171GLU-1-0.920-0.96617.54312.95112.9510.0000.0000.0000.000
171A172ASN0-0.111-0.06520.665-0.763-0.7630.0000.0000.0000.000
172A173ILE0-0.093-0.04317.255-0.427-0.4270.0000.0000.0000.000
173A174GLY00.0050.01716.7530.1680.1680.0000.0000.0000.000
174A175ASP-1-0.812-0.90311.69121.37221.3720.0000.0000.0000.000
175A176ASP-1-0.976-0.96311.46222.36322.3630.0000.0000.0000.000
176A177PHE0-0.002-0.01212.115-1.802-1.8020.0000.0000.0000.000
177A178LEU0-0.033-0.0128.5571.5771.5770.0000.0000.0000.000
178A179TYR00.032-0.01811.485-2.282-2.2820.0000.0000.0000.000
179A180VAL00.0090.01011.7611.2061.2060.0000.0000.0000.000
180A181THR00.005-0.00513.597-1.199-1.1990.0000.0000.0000.000
181A182PRO00.0350.01515.0570.6100.6100.0000.0000.0000.000
182A183GLY0-0.062-0.02317.565-0.332-0.3320.0000.0000.0000.000
183A184ILE0-0.0150.00313.882-0.623-0.6230.0000.0000.0000.000
184A185ARG10.9340.94517.121-13.091-13.0910.0000.0000.0000.000
185A186PRO00.0190.03416.659-0.263-0.2630.0000.0000.0000.000
186A198ALA00.0350.01717.961-0.205-0.2050.0000.0000.0000.000
187A199THR0-0.001-0.00415.7140.2000.2000.0000.0000.0000.000
188A200PRO00.0650.01411.3450.3970.3970.0000.0000.0000.000
189A201LYS10.9030.95911.796-14.874-14.8740.0000.0000.0000.000
190A202MET0-0.021-0.01513.3050.2510.2510.0000.0000.0000.000
191A203ALA00.0020.01012.2880.0500.0500.0000.0000.0000.000
192A204LYS10.8800.9398.442-22.373-22.3730.0000.0000.0000.000
193A205GLU-1-0.905-0.95010.69116.95516.9550.0000.0000.0000.000
194A206TRP0-0.097-0.06913.703-0.600-0.6000.0000.0000.0000.000
195A207GLY00.0390.02911.527-0.724-0.7240.0000.0000.0000.000
196A208SER0-0.031-0.01311.4800.8910.8910.0000.0000.0000.000
197A209SER00.0420.0297.8951.1681.1680.0000.0000.0000.000
198A210ALA00.0160.0037.1703.3423.3420.0000.0000.0000.000
199A211ILE0-0.0200.0199.576-2.436-2.4360.0000.0000.0000.000
200A212VAL0-0.021-0.01311.9520.5980.5980.0000.0000.0000.000
201A213VAL00.0120.01113.543-0.904-0.9040.0000.0000.0000.000
202A214GLY00.0760.04616.2150.0380.0380.0000.0000.0000.000
203A215ARG10.9780.97619.606-10.711-10.7110.0000.0000.0000.000
204A216PRO0-0.041-0.02018.247-0.212-0.2120.0000.0000.0000.000
205A217ILE00.0450.03414.2170.0250.0250.0000.0000.0000.000
206A218THR00.009-0.00718.712-0.403-0.4030.0000.0000.0000.000
207A219LEU0-0.032-0.01921.287-0.494-0.4940.0000.0000.0000.000
208A220ALA0-0.0150.01220.824-0.418-0.4180.0000.0000.0000.000
209A221SER0-0.010-0.02922.774-0.249-0.2490.0000.0000.0000.000
210A222ASP-1-0.881-0.93820.61513.58713.5870.0000.0000.0000.000
211A223PRO0-0.045-0.02119.4890.6050.6050.0000.0000.0000.000
212A224LYS11.0411.03115.790-16.074-16.0740.0000.0000.0000.000
213A225ALA00.0080.00915.2961.2441.2440.0000.0000.0000.000
214A226ALA0-0.021-0.01315.8370.5500.5500.0000.0000.0000.000
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