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: LNN59

Calculation Name: 3L7O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L7O

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DTT9

Base Structure: X-ray

Registration Date: 2023-09-21

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2621999.391031
FMO2-HF: Nuclear repulsion 2536517.181878
FMO2-HF: Total energy -85482.209153
FMO2-MP2: Total energy -85732.776513


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:GLU)


Summations of interaction energy for fragment #1(A:2:GLU)
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.
-72.031-78.94740.547-17.991-15.6430.175
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.800 / q_NPA : -0.868
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].
3A4LEU00.0180.0113.173-4.822-2.4770.111-1.047-1.4100.005
4A5LYS10.8350.9011.815-145.988-150.81623.149-9.506-8.8150.114
5A6LYS11.0061.0034.219-35.601-35.264-0.001-0.115-0.2220.000
6A7ILE0-0.0040.0006.301-4.519-4.5190.0000.0000.0000.000
7A8ALA00.0140.0087.531-3.172-3.1720.0000.0000.0000.000
8A9GLY00.0170.0068.213-2.684-2.6840.0000.0000.0000.000
9A10VAL00.015-0.00510.021-2.525-2.5250.0000.0000.0000.000
10A11ARG10.8780.94511.769-19.588-19.5880.0000.0000.0000.000
11A12ALA00.006-0.00612.829-1.766-1.7660.0000.0000.0000.000
12A13ALA00.0360.01414.220-1.381-1.3810.0000.0000.0000.000
13A14GLN0-0.041-0.02716.073-1.107-1.1070.0000.0000.0000.000
14A15TYR0-0.051-0.02417.449-0.573-0.5730.0000.0000.0000.000
15A16VAL00.0150.00818.690-0.369-0.3690.0000.0000.0000.000
16A17GLU-1-0.929-0.98621.41112.04412.0440.0000.0000.0000.000
17A18ASP-1-0.848-0.93524.84311.99911.9990.0000.0000.0000.000
18A19GLY0-0.043-0.02527.299-0.359-0.3590.0000.0000.0000.000
19A20MET0-0.0720.01624.3930.0870.0870.0000.0000.0000.000
20A21ILE00.0230.01525.6730.1980.1980.0000.0000.0000.000
21A22VAL0-0.006-0.01319.5330.2370.2370.0000.0000.0000.000
22A23GLY00.0380.01520.5360.0330.0330.0000.0000.0000.000
23A24LEU0-0.062-0.04316.6390.9830.9830.0000.0000.0000.000
24A25GLY00.0710.02815.243-0.564-0.5640.0000.0000.0000.000
25A26THR0-0.067-0.02112.3511.0061.0060.0000.0000.0000.000
26A27GLY00.0840.0299.771-0.585-0.5850.0000.0000.0000.000
27A28SER0-0.045-0.0313.6863.0253.3640.003-0.166-0.1760.001
28A29THR0-0.0090.0074.36014.53114.747-0.001-0.010-0.2060.000
29A30ALA00.0520.0206.625-2.032-2.0320.0000.0000.0000.000
30A31TYR0-0.035-0.0226.814-1.487-1.4870.0000.0000.0000.000
31A32TYR0-0.012-0.0481.680-32.411-37.73617.286-7.147-4.8140.055
32A33PHE0-0.0010.0118.224-2.258-2.2580.0000.0000.0000.000
33A34VAL00.0170.01611.557-1.930-1.9300.0000.0000.0000.000
34A35GLU-1-0.837-0.9009.22624.35224.3520.0000.0000.0000.000
35A36GLU-1-0.854-0.88412.06618.84918.8490.0000.0000.0000.000
36A37VAL0-0.004-0.00813.535-1.498-1.4980.0000.0000.0000.000
37A38GLY00.0300.01015.736-1.185-1.1850.0000.0000.0000.000
38A39ARG10.7450.83114.464-18.625-18.6250.0000.0000.0000.000
39A40ARG10.8020.88616.857-16.197-16.1970.0000.0000.0000.000
40A41VAL0-0.007-0.00419.373-0.836-0.8360.0000.0000.0000.000
41A42GLN0-0.120-0.06217.855-0.478-0.4780.0000.0000.0000.000
42A43GLU-1-0.967-0.99118.77413.69813.6980.0000.0000.0000.000
43A44GLU-1-0.850-0.90619.84914.79814.7980.0000.0000.0000.000
44A45GLY0-0.0090.01323.553-0.487-0.4870.0000.0000.0000.000
45A46LEU0-0.0340.00420.931-0.366-0.3660.0000.0000.0000.000
46A47GLN0-0.065-0.05224.483-0.139-0.1390.0000.0000.0000.000
47A48VAL00.0070.00721.848-0.079-0.0790.0000.0000.0000.000
48A49ILE0-0.041-0.01525.241-0.083-0.0830.0000.0000.0000.000
49A50GLY00.0210.01121.6820.2020.2020.0000.0000.0000.000
50A51VAL00.018-0.00221.813-0.530-0.5300.0000.0000.0000.000
51A52THR00.0020.01118.6180.4940.4940.0000.0000.0000.000
52A53THR00.0020.00217.346-0.451-0.4510.0000.0000.0000.000
53A54SER00.010-0.00117.097-0.109-0.1090.0000.0000.0000.000
54A55SER00.0440.00819.0000.5550.5550.0000.0000.0000.000
55A56ARG10.9190.95514.928-19.201-19.2010.0000.0000.0000.000
56A57THR00.0350.00314.5690.2860.2860.0000.0000.0000.000
57A58THR0-0.027-0.01016.350-0.247-0.2470.0000.0000.0000.000
58A59ALA00.0200.01218.062-0.331-0.3310.0000.0000.0000.000
59A60GLN0-0.073-0.04511.039-0.668-0.6680.0000.0000.0000.000
60A61ALA00.0480.01116.077-0.144-0.1440.0000.0000.0000.000
61A62GLN0-0.021-0.01218.304-0.414-0.4140.0000.0000.0000.000
62A63ALA0-0.052-0.02017.581-0.540-0.5400.0000.0000.0000.000
63A64LEU0-0.051-0.01414.070-0.300-0.3000.0000.0000.0000.000
64A65GLY00.0010.01418.608-0.319-0.3190.0000.0000.0000.000
65A66ILE0-0.0130.00117.162-0.467-0.4670.0000.0000.0000.000
66A67PRO0-0.0050.00021.777-0.182-0.1820.0000.0000.0000.000
67A68LEU0-0.042-0.01820.9510.4900.4900.0000.0000.0000.000
68A69LYS10.8180.91325.051-10.612-10.6120.0000.0000.0000.000
69A70SER0-0.061-0.05125.8470.4810.4810.0000.0000.0000.000
70A71ILE00.035-0.00725.825-0.041-0.0410.0000.0000.0000.000
71A72ASP-1-0.922-0.96028.21610.14910.1490.0000.0000.0000.000
72A73GLU-1-0.888-0.90630.62110.03810.0380.0000.0000.0000.000
73A74VAL0-0.004-0.00228.037-0.087-0.0870.0000.0000.0000.000
74A75ASP-1-0.887-0.93331.4839.2769.2760.0000.0000.0000.000
75A76SER0-0.106-0.07329.688-0.153-0.1530.0000.0000.0000.000
76A77VAL00.0390.03123.2420.0640.0640.0000.0000.0000.000
77A78ASP-1-0.833-0.90225.84011.13211.1320.0000.0000.0000.000
78A79VAL00.0270.00320.0750.0600.0600.0000.0000.0000.000
79A80THR00.003-0.00618.6390.1540.1540.0000.0000.0000.000
80A81VAL0-0.0170.00613.3970.3280.3280.0000.0000.0000.000
81A82ASP-1-0.763-0.87014.12120.55920.5590.0000.0000.0000.000
82A83GLY0-0.0060.00911.6261.1281.1280.0000.0000.0000.000
83A84ALA0-0.013-0.01112.407-1.942-1.9420.0000.0000.0000.000
84A85ASP-1-0.841-0.92112.74724.36124.3610.0000.0000.0000.000
85A86GLU-1-0.790-0.89214.58017.44317.4430.0000.0000.0000.000
86A87VAL00.010-0.00715.652-0.563-0.5630.0000.0000.0000.000
87A88ASP-1-0.727-0.84818.21213.97913.9790.0000.0000.0000.000
88A89PRO0-0.032-0.01421.1760.0390.0390.0000.0000.0000.000
89A90ASN0-0.122-0.06922.797-0.696-0.6960.0000.0000.0000.000
90A91PHE0-0.050-0.02220.493-0.359-0.3590.0000.0000.0000.000
91A92ASN0-0.008-0.00122.891-0.351-0.3510.0000.0000.0000.000
92A93GLY00.0420.00219.6220.7450.7450.0000.0000.0000.000
93A94ILE0-0.071-0.01318.912-0.998-0.9980.0000.0000.0000.000
94A95LYS10.8110.89215.619-18.470-18.4700.0000.0000.0000.000
95A96GLY00.0710.03117.260-1.210-1.2100.0000.0000.0000.000
96A97GLY0-0.014-0.00515.717-0.675-0.6750.0000.0000.0000.000
97A98GLY0-0.043-0.02115.175-0.131-0.1310.0000.0000.0000.000
98A99GLY0-0.029-0.01415.686-0.460-0.4600.0000.0000.0000.000
99A100ALA00.006-0.00118.553-0.933-0.9330.0000.0000.0000.000
100A101LEU00.0330.02120.324-0.271-0.2710.0000.0000.0000.000
101A102LEU00.0330.02621.788-0.122-0.1220.0000.0000.0000.000
102A103MET0-0.008-0.00122.444-0.343-0.3430.0000.0000.0000.000
103A104GLU-1-0.844-0.93816.66119.14619.1460.0000.0000.0000.000
104A105LYS10.8350.92021.077-12.693-12.6930.0000.0000.0000.000
105A106ILE0-0.0040.01124.007-0.375-0.3750.0000.0000.0000.000
106A107VAL00.0100.00021.343-0.261-0.2610.0000.0000.0000.000
107A108GLY0-0.0010.00522.737-0.123-0.1230.0000.0000.0000.000
108A109THR0-0.058-0.05023.336-0.334-0.3340.0000.0000.0000.000
109A110LEU0-0.0230.00426.751-0.407-0.4070.0000.0000.0000.000
110A111THR0-0.048-0.00722.5280.1660.1660.0000.0000.0000.000
111A112LYS10.8190.91525.704-10.688-10.6880.0000.0000.0000.000
112A113ASP-1-0.777-0.87722.85414.00614.0060.0000.0000.0000.000
113A114TYR0-0.015-0.00818.5750.5490.5490.0000.0000.0000.000
114A115ILE00.004-0.00716.182-0.033-0.0330.0000.0000.0000.000
115A116TRP0-0.019-0.01614.9310.6970.6970.0000.0000.0000.000
116A117VAL0-0.009-0.00710.004-0.101-0.1010.0000.0000.0000.000
117A118VAL0-0.004-0.0049.3802.2182.2180.0000.0000.0000.000
118A119ASP-1-0.794-0.8656.42444.00144.0010.0000.0000.0000.000
119A120GLU-1-0.668-0.8188.44619.46619.4660.0000.0000.0000.000
120A121SER0-0.127-0.0729.200-2.160-2.1600.0000.0000.0000.000
121A122LYS10.8400.9058.343-37.448-37.4480.0000.0000.0000.000
122A123MET0-0.070-0.02013.288-1.473-1.4730.0000.0000.0000.000
123A124VAL00.0170.00415.527-0.021-0.0210.0000.0000.0000.000
124A125ASP-1-0.902-0.95718.54814.51314.5130.0000.0000.0000.000
125A126THR0-0.100-0.06221.970-1.032-1.0320.0000.0000.0000.000
126A127LEU0-0.0010.02020.6000.4490.4490.0000.0000.0000.000
127A128GLY0-0.011-0.03321.533-0.857-0.8570.0000.0000.0000.000
128A129ALA0-0.0310.00319.081-0.443-0.4430.0000.0000.0000.000
129A130PHE0-0.052-0.02614.7590.3850.3850.0000.0000.0000.000
130A131ARG10.8300.89018.894-14.741-14.7410.0000.0000.0000.000
131A132LEU00.0430.03221.0340.5690.5690.0000.0000.0000.000
132A133PRO00.0030.01820.232-0.704-0.7040.0000.0000.0000.000
133A134VAL00.009-0.00723.372-0.254-0.2540.0000.0000.0000.000
134A135GLU-1-0.765-0.85625.84112.32412.3240.0000.0000.0000.000
135A136VAL0-0.019-0.02427.704-0.435-0.4350.0000.0000.0000.000
136A137VAL00.0540.02531.3530.0600.0600.0000.0000.0000.000
137A138GLN0-0.034-0.03332.732-0.288-0.2880.0000.0000.0000.000
138A139TYR0-0.048-0.02134.947-0.165-0.1650.0000.0000.0000.000
139A140GLY00.0560.02238.585-0.077-0.0770.0000.0000.0000.000
140A141ALA00.0380.03233.224-0.024-0.0240.0000.0000.0000.000
141A142GLU-1-0.768-0.87334.8329.1959.1950.0000.0000.0000.000
142A143ARG10.7620.86136.506-8.076-8.0760.0000.0000.0000.000
143A144LEU00.0280.03433.947-0.142-0.1420.0000.0000.0000.000
144A145PHE00.0550.03030.107-0.016-0.0160.0000.0000.0000.000
145A146ARG10.8830.92934.417-8.512-8.5120.0000.0000.0000.000
146A147GLU-1-0.792-0.85537.1288.0988.0980.0000.0000.0000.000
147A148PHE00.0670.01131.317-0.061-0.0610.0000.0000.0000.000
148A149GLU-1-0.833-0.90134.0438.7958.7950.0000.0000.0000.000
149A150LYS10.7330.84734.985-8.357-8.3570.0000.0000.0000.000
150A151LYS10.8160.90735.779-8.956-8.9560.0000.0000.0000.000
151A152GLY00.0220.02234.5820.0650.0650.0000.0000.0000.000
152A153TYR0-0.013-0.02430.2970.2010.2010.0000.0000.0000.000
153A154LYS10.8290.90527.176-11.518-11.5180.0000.0000.0000.000
154A155PRO00.0000.01927.9960.4520.4520.0000.0000.0000.000
155A156SER0-0.003-0.00725.078-0.094-0.0940.0000.0000.0000.000
156A157PHE0-0.030-0.02826.3910.1530.1530.0000.0000.0000.000
157A158ARG10.7610.84718.708-16.320-16.3200.0000.0000.0000.000
158A159GLU-1-0.927-0.97623.76312.72112.7210.0000.0000.0000.000
159A160TYR00.0100.01617.8900.7100.7100.0000.0000.0000.000
160A161ASP-1-0.917-0.95022.17514.35714.3570.0000.0000.0000.000
161A162GLY0-0.0110.00424.426-0.564-0.5640.0000.0000.0000.000
162A163VAL0-0.075-0.03926.582-0.644-0.6440.0000.0000.0000.000
163A164ARG10.8070.89326.425-9.731-9.7310.0000.0000.0000.000
164A165PHE00.009-0.00421.901-0.160-0.1600.0000.0000.0000.000
165A166VAL0-0.032-0.02525.840-0.444-0.4440.0000.0000.0000.000
166A167THR0-0.018-0.01524.5490.1950.1950.0000.0000.0000.000
167A168ASP-1-0.811-0.90022.70813.79113.7910.0000.0000.0000.000
168A169MET0-0.026-0.01525.844-0.641-0.6410.0000.0000.0000.000
169A170LYS10.8290.91428.508-11.404-11.4040.0000.0000.0000.000
170A171ASN0-0.018-0.00128.835-0.806-0.8060.0000.0000.0000.000
171A172PHE00.007-0.00428.4650.2030.2030.0000.0000.0000.000
172A173ILE00.0420.01722.7680.0060.0060.0000.0000.0000.000
173A174ILE0-0.061-0.02626.566-0.215-0.2150.0000.0000.0000.000
174A175ASP-1-0.754-0.84222.17515.10715.1070.0000.0000.0000.000
175A176LEU0-0.011-0.01124.781-0.473-0.4730.0000.0000.0000.000
176A177ASP-1-0.789-0.85723.87014.03814.0380.0000.0000.0000.000
177A178LEU00.003-0.01625.469-0.430-0.4300.0000.0000.0000.000
178A179GLY0-0.0280.00524.465-0.486-0.4860.0000.0000.0000.000
179A180SER0-0.045-0.03124.7990.1390.1390.0000.0000.0000.000
180A181ILE0-0.010-0.00324.581-0.451-0.4510.0000.0000.0000.000
181A182PRO00.001-0.00427.4990.1480.1480.0000.0000.0000.000
182A183ASP-1-0.815-0.90229.54310.05410.0540.0000.0000.0000.000
183A184PRO00.0080.00226.355-0.190-0.1900.0000.0000.0000.000
184A185ILE00.0220.02528.559-0.003-0.0030.0000.0000.0000.000
185A186ALA00.0050.00731.170-0.205-0.2050.0000.0000.0000.000
186A187PHE0-0.003-0.01629.607-0.170-0.1700.0000.0000.0000.000
187A188GLY00.0210.00929.8310.0140.0140.0000.0000.0000.000
188A189ASN0-0.007-0.01130.496-0.411-0.4110.0000.0000.0000.000
189A190MET0-0.090-0.03633.510-0.386-0.3860.0000.0000.0000.000
190A191LEU0-0.046-0.03029.041-0.178-0.1780.0000.0000.0000.000
191A192ASP-1-0.829-0.90031.66210.39610.3960.0000.0000.0000.000
192A193HIS0-0.029-0.00833.919-0.307-0.3070.0000.0000.0000.000
193A194GLN0-0.067-0.01834.733-0.261-0.2610.0000.0000.0000.000
194A195VAL00.003-0.01535.9750.1860.1860.0000.0000.0000.000
195A196GLY0-0.015-0.01036.330-0.093-0.0930.0000.0000.0000.000
196A197VAL0-0.020-0.01330.5130.2490.2490.0000.0000.0000.000
197A198VAL0-0.085-0.03130.385-0.307-0.3070.0000.0000.0000.000
198A199GLU-1-0.770-0.87525.81811.98511.9850.0000.0000.0000.000
199A200HIS0-0.044-0.05726.1210.5320.5320.0000.0000.0000.000
200A201GLY00.0500.01522.3530.1320.1320.0000.0000.0000.000
201A202LEU0-0.026-0.00122.0130.6660.6660.0000.0000.0000.000
202A203PHE0-0.002-0.01321.090-0.498-0.4980.0000.0000.0000.000
203A204ASN00.003-0.03423.5730.6450.6450.0000.0000.0000.000
204A205GLY00.0210.01525.992-0.276-0.2760.0000.0000.0000.000
205A206MET0-0.0230.01023.394-0.076-0.0760.0000.0000.0000.000
206A207VAL0-0.0470.01018.938-0.219-0.2190.0000.0000.0000.000
207A208ASN00.003-0.00122.199-0.722-0.7220.0000.0000.0000.000
208A209ARG10.7350.82818.074-15.186-15.1860.0000.0000.0000.000
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