FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: NN3LQ

Calculation Name: 3MVP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MVP

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DWD0

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2274856.538855
FMO2-HF: Nuclear repulsion 2193692.500438
FMO2-HF: Total energy -81164.038417
FMO2-MP2: Total energy -81406.744628


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:14:LYS)


Summations of interaction energy for fragment #1(A:14:LYS)
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.
81.76685.0880.333-1.22-2.4340.001
Interaction energy analysis for fragmet #1(A:14:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.991 / q_NPA : 0.982
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].
3A16ILE00.0650.0442.63011.14814.4350.334-1.211-2.4100.001
4A17ARG10.9600.9774.83719.31719.352-0.001-0.009-0.0240.000
5A18LYS10.8770.9375.04746.73146.7310.0000.0000.0000.000
6A19PRO00.0400.0217.681-1.562-1.5620.0000.0000.0000.000
7A20LYS10.9970.9766.85926.71626.7160.0000.0000.0000.000
8A21GLN00.0130.0227.875-0.794-0.7940.0000.0000.0000.000
9A22GLU-1-0.776-0.8875.661-44.215-44.2150.0000.0000.0000.000
10A23ARG10.9280.9429.19323.85823.8580.0000.0000.0000.000
11A24SER00.0080.00411.2481.7121.7120.0000.0000.0000.000
12A25ILE00.0390.01811.9391.8271.8270.0000.0000.0000.000
13A26GLU-1-0.823-0.88413.274-21.419-21.4190.0000.0000.0000.000
14A27LYS10.9420.97215.52018.81618.8160.0000.0000.0000.000
15A28ARG10.9721.00016.97815.95415.9540.0000.0000.0000.000
16A29ASN00.0330.00717.0301.6771.6770.0000.0000.0000.000
17A30LYS10.9411.00119.63013.96213.9620.0000.0000.0000.000
18A31ILE0-0.016-0.01620.9430.7010.7010.0000.0000.0000.000
19A32LEU0-0.031-0.00421.6590.5300.5300.0000.0000.0000.000
20A33GLN0-0.034-0.02524.0220.1810.1810.0000.0000.0000.000
21A34VAL0-0.015-0.02025.5980.4700.4700.0000.0000.0000.000
22A35ALA00.0160.00527.3290.4370.4370.0000.0000.0000.000
23A36LYS10.8610.92528.58810.84510.8450.0000.0000.0000.000
24A37ASP-1-0.833-0.89329.563-10.418-10.4180.0000.0000.0000.000
25A38LEU0-0.041-0.02230.7530.3020.3020.0000.0000.0000.000
26A39PHE0-0.030-0.03831.1710.2810.2810.0000.0000.0000.000
27A40SER0-0.029-0.03633.7650.3080.3080.0000.0000.0000.000
28A41ASP-1-0.959-0.95036.138-8.222-8.2220.0000.0000.0000.000
29A42LYS10.8820.91436.8668.7358.7350.0000.0000.0000.000
30A43THR0-0.018-0.00538.5320.2770.2770.0000.0000.0000.000
31A44TYR0-0.024-0.05433.408-0.180-0.1800.0000.0000.0000.000
32A45PHE0-0.002-0.01037.180-0.187-0.1870.0000.0000.0000.000
33A46ASN0-0.0270.00939.8060.1210.1210.0000.0000.0000.000
34A47VAL00.0000.02233.296-0.104-0.1040.0000.0000.0000.000
35A48THR00.0130.00435.151-0.107-0.1070.0000.0000.0000.000
36A49THR00.0660.00929.725-0.157-0.1570.0000.0000.0000.000
37A50ASN0-0.012-0.00830.340-0.591-0.5910.0000.0000.0000.000
38A51GLU-1-0.846-0.89731.096-9.209-9.2090.0000.0000.0000.000
39A52ILE00.0230.01127.173-0.261-0.2610.0000.0000.0000.000
40A53ALA0-0.005-0.00426.306-0.415-0.4150.0000.0000.0000.000
41A54LYS10.8700.93226.48510.86110.8610.0000.0000.0000.000
42A55LYS10.9730.99027.9869.9539.9530.0000.0000.0000.000
43A56ALA0-0.045-0.02223.558-0.265-0.2650.0000.0000.0000.000
44A57ASP-1-0.903-0.94122.957-12.869-12.8690.0000.0000.0000.000
45A58VAL0-0.060-0.02320.617-0.896-0.8960.0000.0000.0000.000
46A59SER00.0420.02823.0170.4590.4590.0000.0000.0000.000
47A60VAL00.1010.02924.906-0.277-0.2770.0000.0000.0000.000
48A61GLY00.0200.01225.345-0.020-0.0200.0000.0000.0000.000
49A62THR0-0.036-0.03319.605-0.574-0.5740.0000.0000.0000.000
50A63LEU0-0.016-0.00321.926-0.435-0.4350.0000.0000.0000.000
51A64TYR00.010-0.00724.154-0.028-0.0280.0000.0000.0000.000
52A65ALA0-0.0440.00020.5040.0140.0140.0000.0000.0000.000
53A66TYR0-0.142-0.07115.865-0.672-0.6720.0000.0000.0000.000
54A67PHE0-0.031-0.03621.545-0.150-0.1500.0000.0000.0000.000
55A68ALA00.0620.04125.1970.1700.1700.0000.0000.0000.000
56A69SER0-0.008-0.03027.9420.4330.4330.0000.0000.0000.000
57A70LYS10.8710.91729.5198.4938.4930.0000.0000.0000.000
58A71GLU-1-0.742-0.86331.236-9.212-9.2120.0000.0000.0000.000
59A72ASP-1-0.872-0.89627.378-10.780-10.7800.0000.0000.0000.000
60A73ILE0-0.059-0.03626.579-0.402-0.4020.0000.0000.0000.000
61A74LEU00.0340.01927.993-0.232-0.2320.0000.0000.0000.000
62A75THR0-0.0020.00228.7080.0260.0260.0000.0000.0000.000
63A76ALA0-0.083-0.04324.805-0.136-0.1360.0000.0000.0000.000
64A77LEU0-0.033-0.01726.781-0.229-0.2290.0000.0000.0000.000
65A78LEU00.0300.02328.6150.0510.0510.0000.0000.0000.000
66A79LYS10.9350.96726.98711.41511.4150.0000.0000.0000.000
67A80ARG10.9000.94620.21714.10114.1010.0000.0000.0000.000
68A81TYR00.017-0.00627.665-0.105-0.1050.0000.0000.0000.000
69A82ASN00.0010.01230.9720.5830.5830.0000.0000.0000.000
70A83ASP-1-0.877-0.93926.924-11.323-11.3230.0000.0000.0000.000
71A84PHE0-0.0020.02429.656-0.009-0.0090.0000.0000.0000.000
72A85PHE00.0200.02130.6640.2090.2090.0000.0000.0000.000
73A86LEU0-0.003-0.01232.1240.2140.2140.0000.0000.0000.000
74A87THR0-0.080-0.07028.3460.0780.0780.0000.0000.0000.000
75A88THR0-0.068-0.04230.9380.1100.1100.0000.0000.0000.000
76A89ILE00.0220.02933.4750.2290.2290.0000.0000.0000.000
77A90PHE0-0.041-0.03236.4380.2560.2560.0000.0000.0000.000
78A91ALA0-0.0080.00234.4300.2090.2090.0000.0000.0000.000
79A92ASP-1-0.889-0.93836.591-8.440-8.4400.0000.0000.0000.000
80A93ILE0-0.019-0.00439.1470.2450.2450.0000.0000.0000.000
81A94ASN0-0.011-0.00239.0060.4720.4720.0000.0000.0000.000
82A95SER00.0590.03540.527-0.110-0.1100.0000.0000.0000.000
83A96GLN0-0.017-0.02542.3110.0780.0780.0000.0000.0000.000
84A97ASP-1-0.813-0.87443.619-7.042-7.0420.0000.0000.0000.000
85A98SER0-0.047-0.04144.5020.1900.1900.0000.0000.0000.000
86A99LEU0-0.009-0.00846.4280.1560.1560.0000.0000.0000.000
87A100ASP-1-0.804-0.89548.630-6.388-6.3880.0000.0000.0000.000
88A101ARG10.7710.87645.4277.0957.0950.0000.0000.0000.000
89A102PHE00.001-0.01650.9910.1480.1480.0000.0000.0000.000
90A103LYS10.7820.88352.9345.9555.9550.0000.0000.0000.000
91A104LYS10.8190.91753.0036.0886.0880.0000.0000.0000.000
92A105ASN00.013-0.02655.2490.1760.1760.0000.0000.0000.000
93A106PRO00.0560.04054.903-0.105-0.1050.0000.0000.0000.000
94A107LYS10.8710.93154.6705.3145.3140.0000.0000.0000.000
95A108GLU-1-0.883-0.91451.468-6.168-6.1680.0000.0000.0000.000
96A109TRP00.009-0.00548.128-0.094-0.0940.0000.0000.0000.000
97A110LEU00.0160.01749.704-0.144-0.1440.0000.0000.0000.000
98A111ASN0-0.053-0.03650.326-0.106-0.1060.0000.0000.0000.000
99A112VAL0-0.016-0.00845.481-0.096-0.0960.0000.0000.0000.000
100A113LEU00.0450.03344.971-0.173-0.1730.0000.0000.0000.000
101A114ILE00.0230.00045.582-0.146-0.1460.0000.0000.0000.000
102A115ASN00.0170.01145.415-0.016-0.0160.0000.0000.0000.000
103A116GLN00.0310.01141.435-0.023-0.0230.0000.0000.0000.000
104A117LEU0-0.035-0.02041.267-0.204-0.2040.0000.0000.0000.000
105A118LEU0-0.023-0.00742.499-0.098-0.0980.0000.0000.0000.000
106A119ALA0-0.039-0.01739.825-0.077-0.0770.0000.0000.0000.000
107A120ALA0-0.0110.02037.946-0.279-0.2790.0000.0000.0000.000
108A121GLU-1-0.815-0.89034.346-8.659-8.6590.0000.0000.0000.000
109A122ASP-1-0.886-0.94732.557-9.952-9.9520.0000.0000.0000.000
110A123LYS10.9180.93435.2448.1218.1210.0000.0000.0000.000
111A124ILE00.0330.02335.8050.0950.0950.0000.0000.0000.000
112A125PHE0-0.004-0.01632.105-0.010-0.0100.0000.0000.0000.000
113A126HIS00.0020.00635.899-0.222-0.2220.0000.0000.0000.000
114A127ALA00.0740.04838.0040.1230.1230.0000.0000.0000.000
115A128GLN00.0140.00736.8150.1380.1380.0000.0000.0000.000
116A129ILE0-0.042-0.02734.4560.0190.0190.0000.0000.0000.000
117A130GLU-1-0.795-0.89938.438-7.329-7.3290.0000.0000.0000.000
118A131MET0-0.050-0.01541.0010.1680.1680.0000.0000.0000.000
119A132LEU0-0.038-0.03036.5490.0730.0730.0000.0000.0000.000
120A133ALA00.0060.01840.7030.0120.0120.0000.0000.0000.000
121A134TYR0-0.030-0.01242.4460.1630.1630.0000.0000.0000.000
122A135ALA0-0.032-0.01742.2170.1100.1100.0000.0000.0000.000
123A136ILE0-0.038-0.01836.712-0.078-0.0780.0000.0000.0000.000
124A137PRO00.0420.00939.617-0.055-0.0550.0000.0000.0000.000
125A138GLN0-0.007-0.02332.399-0.122-0.1220.0000.0000.0000.000
126A139ALA00.0140.01837.087-0.117-0.1170.0000.0000.0000.000
127A140LYS10.8470.90438.1687.0837.0830.0000.0000.0000.000
128A141ALA0-0.009-0.00438.5060.0670.0670.0000.0000.0000.000
129A142LEU0-0.022-0.00634.253-0.011-0.0110.0000.0000.0000.000
130A143LEU00.0260.01537.806-0.007-0.0070.0000.0000.0000.000
131A144GLU-1-0.792-0.87440.558-6.999-6.9990.0000.0000.0000.000
132A145GLU-1-0.883-0.91837.944-7.904-7.9040.0000.0000.0000.000
133A146HIS10.8750.92735.2228.8338.8330.0000.0000.0000.000
134A147ASN00.0550.03140.3490.1770.1770.0000.0000.0000.000
135A148ASN00.0310.00943.4410.2970.2970.0000.0000.0000.000
136A149ASN0-0.096-0.06239.315-0.027-0.0270.0000.0000.0000.000
137A150LEU00.0120.01341.9050.0630.0630.0000.0000.0000.000
138A151LYS10.8250.91344.5806.6706.6700.0000.0000.0000.000
139A152ASN0-0.033-0.01844.7820.3010.3010.0000.0000.0000.000
140A153LEU0-0.023-0.00644.0230.1100.1100.0000.0000.0000.000
141A154THR00.0440.01646.2610.1240.1240.0000.0000.0000.000
142A155TYR00.004-0.00949.5720.1550.1550.0000.0000.0000.000
143A156LYS10.8880.94343.5337.3887.3880.0000.0000.0000.000
144A157CYS0-0.040-0.01048.6790.0360.0360.0000.0000.0000.000
145A158LEU00.0210.01151.2670.1080.1080.0000.0000.0000.000
146A159LEU0-0.060-0.02552.0070.1150.1150.0000.0000.0000.000
147A160TYR00.000-0.01651.2830.1240.1240.0000.0000.0000.000
148A161TYR0-0.020-0.00453.8000.0640.0640.0000.0000.0000.000
149A162SER0-0.034-0.01856.7060.0980.0980.0000.0000.0000.000
150A163ASP-1-0.866-0.90655.806-5.685-5.6850.0000.0000.0000.000
151A164GLN0-0.0110.00656.9200.0020.0020.0000.0000.0000.000
152A165ALA00.0210.00554.607-0.109-0.1090.0000.0000.0000.000
153A166ALA0-0.022-0.03254.021-0.125-0.1250.0000.0000.0000.000
154A167ASN00.0580.04356.0520.1330.1330.0000.0000.0000.000
155A168PRO00.0480.01357.244-0.073-0.0730.0000.0000.0000.000
156A169SER0-0.011-0.01658.203-0.033-0.0330.0000.0000.0000.000
157A170PHE00.0680.02356.077-0.040-0.0400.0000.0000.0000.000
158A171LYS10.8950.97049.4806.3506.3500.0000.0000.0000.000
159A172THR00.0000.01154.424-0.083-0.0830.0000.0000.0000.000
160A173LEU00.0260.02256.495-0.039-0.0390.0000.0000.0000.000
161A174SER0-0.063-0.05051.576-0.087-0.0870.0000.0000.0000.000
162A175LEU0-0.029-0.01351.297-0.113-0.1130.0000.0000.0000.000
163A176VAL00.0560.02753.055-0.055-0.0550.0000.0000.0000.000
164A177VAL00.0040.00152.876-0.026-0.0260.0000.0000.0000.000
165A178PHE00.018-0.01145.458-0.060-0.0600.0000.0000.0000.000
166A179ASP-1-0.811-0.88550.295-6.455-6.4550.0000.0000.0000.000
167A180PHE0-0.035-0.01852.1110.0200.0200.0000.0000.0000.000
168A181ILE0-0.005-0.00648.679-0.008-0.0080.0000.0000.0000.000
169A182SER0-0.021-0.01547.373-0.109-0.1090.0000.0000.0000.000
170A183ALA00.0200.02049.010-0.054-0.0540.0000.0000.0000.000
171A184LEU0-0.045-0.01051.8070.0300.0300.0000.0000.0000.000
172A185VAL0-0.009-0.02545.295-0.021-0.0210.0000.0000.0000.000
173A186ASP-1-0.864-0.93946.601-6.981-6.9810.0000.0000.0000.000
174A187GLU-1-0.939-0.95348.556-5.982-5.9820.0000.0000.0000.000
175A188LEU0-0.047-0.03949.2650.0200.0200.0000.0000.0000.000
176A189LEU0-0.075-0.02643.085-0.089-0.0890.0000.0000.0000.000
177A190TYR0-0.088-0.04642.153-0.222-0.2220.0000.0000.0000.000
178A191HIS0-0.023-0.00447.2980.1000.1000.0000.0000.0000.000
179A192GLU-1-0.970-0.97250.305-6.473-6.4730.0000.0000.0000.000
180A193HIS0-0.014-0.01651.8410.2180.2180.0000.0000.0000.000
181A194THR00.0040.00352.592-0.083-0.0830.0000.0000.0000.000
182A195GLN00.0330.00049.328-0.038-0.0380.0000.0000.0000.000
183A196GLU-1-0.874-0.93753.517-5.528-5.5280.0000.0000.0000.000
184A197GLU-1-0.912-0.95756.531-5.385-5.3850.0000.0000.0000.000
185A198ALA00.0520.02451.8710.0060.0060.0000.0000.0000.000
186A199HIS0-0.068-0.02854.025-0.116-0.1160.0000.0000.0000.000
187A200GLN00.012-0.00555.2500.0650.0650.0000.0000.0000.000
188A201ILE00.0450.04954.6480.0660.0660.0000.0000.0000.000
189A202LYS10.9300.96849.8186.4416.4410.0000.0000.0000.000
190A203LYS10.8640.94054.5655.2965.2960.0000.0000.0000.000
191A204THR00.014-0.01157.5320.0860.0860.0000.0000.0000.000
192A205GLY00.0370.02956.1330.0570.0570.0000.0000.0000.000
193A206ILE0-0.015-0.01152.2750.0210.0210.0000.0000.0000.000
194A207ASP-1-0.853-0.92956.329-5.343-5.3430.0000.0000.0000.000
195A208SER0-0.039-0.03559.6440.1060.1060.0000.0000.0000.000
196A209LEU0-0.015-0.01353.9430.0380.0380.0000.0000.0000.000
197A210ASP-1-0.808-0.90258.027-5.460-5.4600.0000.0000.0000.000
198A211LEU0-0.0100.00659.1090.0460.0460.0000.0000.0000.000
199A212ILE00.0240.00459.7430.0500.0500.0000.0000.0000.000
200A213ILE0-0.0020.01855.1820.0290.0290.0000.0000.0000.000
201A214LYS10.8090.87359.4625.4175.4170.0000.0000.0000.000
202A215SER0-0.104-0.04562.1510.0800.0800.0000.0000.0000.000
203A216TYR0-0.025-0.01861.2330.0760.0760.0000.0000.0000.000
204A217LEU0-0.058-0.00557.9530.0220.0220.0000.0000.0000.000