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: 2N65R

Calculation Name: 4FMR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FMR

Chain ID: A

ChEMBL ID:

UniProt ID: A6L2B2

Base Structure: X-ray

Registration Date: 2023-09-24

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2471752.891525
FMO2-HF: Nuclear repulsion 2383515.12886
FMO2-HF: Total energy -88237.762664
FMO2-MP2: Total energy -88495.567768


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:3:LYS)


Summations of interaction energy for fragment #1(A:3: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.
-90.108-90.4625.097-13.8-10.944-0.151
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.811 / q_NPA : 0.881
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].
3A5VAL00.001-0.0073.8557.2438.900-0.008-0.820-0.8280.003
4A6LEU0-0.0140.0006.7880.7190.7190.0000.0000.0000.000
5A7LYS10.8580.9209.85519.56619.5660.0000.0000.0000.000
6A8ALA0-0.025-0.01512.9730.1870.1870.0000.0000.0000.000
7A9TRP00.0370.01815.5330.5890.5890.0000.0000.0000.000
8A10LEU0-0.013-0.00119.025-0.289-0.2890.0000.0000.0000.000
9A11VAL0-0.028-0.02521.3080.4090.4090.0000.0000.0000.000
10A12ASP-1-0.795-0.88524.479-10.232-10.2320.0000.0000.0000.000
11A13ASN0-0.028-0.00526.393-0.154-0.1540.0000.0000.0000.000
12A21THR0-0.018-0.01930.0860.0710.0710.0000.0000.0000.000
13A22ASP-1-0.850-0.91926.313-10.435-10.4350.0000.0000.0000.000
14A23LYS10.7900.87523.65910.65610.6560.0000.0000.0000.000
15A24ILE00.0100.00821.388-0.267-0.2670.0000.0000.0000.000
16A25PHE00.022-0.00116.513-0.011-0.0110.0000.0000.0000.000
17A26GLN0-0.038-0.01918.647-0.080-0.0800.0000.0000.0000.000
18A27LEU00.0120.00512.927-0.080-0.0800.0000.0000.0000.000
19A28GLU-1-0.833-0.91116.001-16.326-16.3260.0000.0000.0000.000
20A29THR0-0.016-0.01517.161-0.914-0.9140.0000.0000.0000.000
21A30THR0-0.042-0.00815.098-0.211-0.2110.0000.0000.0000.000
22A31ARG10.9310.95313.33621.38921.3890.0000.0000.0000.000
23A32SER00.0450.03416.797-0.718-0.7180.0000.0000.0000.000
24A33ILE0-0.056-0.03612.874-0.426-0.4260.0000.0000.0000.000
25A34ASP-1-0.723-0.86217.216-15.102-15.1020.0000.0000.0000.000
26A35LYS10.8090.87517.86112.57312.5730.0000.0000.0000.000
27A36GLU-1-0.821-0.88019.344-13.804-13.8040.0000.0000.0000.000
28A37ILE0-0.018-0.01915.378-0.847-0.8470.0000.0000.0000.000
29A38ILE0-0.063-0.03913.921-1.696-1.6960.0000.0000.0000.000
30A39LEU00.0370.01115.145-1.018-1.0180.0000.0000.0000.000
31A40ASP-1-0.853-0.90116.609-16.019-16.0190.0000.0000.0000.000
32A41ARG10.8730.93911.14222.90222.9020.0000.0000.0000.000
33A42MET0-0.038-0.01312.419-1.406-1.4060.0000.0000.0000.000
34A43VAL00.0200.01614.369-0.301-0.3010.0000.0000.0000.000
35A44ALA0-0.025-0.01413.6240.0570.0570.0000.0000.0000.000
36A45LYS10.8660.9326.95333.61633.6160.0000.0000.0000.000
37A46ASN0-0.014-0.00612.185-0.069-0.0690.0000.0000.0000.000
38A47PRO00.0460.02115.0970.7280.7280.0000.0000.0000.000
39A48GLY0-0.0100.01518.1560.8740.8740.0000.0000.0000.000
40A49VAL0-0.059-0.02817.3660.4500.4500.0000.0000.0000.000
41A50ARG10.8840.92720.28010.95710.9570.0000.0000.0000.000
42A51ARG10.8320.87420.28214.33614.3360.0000.0000.0000.000
43A52GLU-1-0.761-0.87822.414-12.071-12.0710.0000.0000.0000.000
44A53THR0-0.019-0.00623.8290.1520.1520.0000.0000.0000.000
45A54MET0-0.028-0.01418.954-0.435-0.4350.0000.0000.0000.000
46A55ALA00.0240.01121.446-0.239-0.2390.0000.0000.0000.000
47A56LEU00.0160.01223.1350.0590.0590.0000.0000.0000.000
48A57GLY0-0.0040.00022.4660.2000.2000.0000.0000.0000.000
49A58ILE0-0.042-0.02518.350-0.320-0.3200.0000.0000.0000.000
50A59GLU-1-0.807-0.89821.521-13.012-13.0120.0000.0000.0000.000
51A60LEU00.0590.04125.0490.1440.1440.0000.0000.0000.000
52A61MET0-0.070-0.03318.213-0.269-0.2690.0000.0000.0000.000
53A62GLU-1-0.866-0.93521.500-14.096-14.0960.0000.0000.0000.000
54A63GLU-1-0.917-0.95424.259-10.384-10.3840.0000.0000.0000.000
55A64VAL00.0310.01626.1980.1960.1960.0000.0000.0000.000
56A65VAL0-0.052-0.03122.0720.0480.0480.0000.0000.0000.000
57A66ALA0-0.001-0.00125.5030.1470.1470.0000.0000.0000.000
58A67GLU-1-0.923-0.96228.034-9.404-9.4040.0000.0000.0000.000
59A68ALA00.0270.02127.4910.2670.2670.0000.0000.0000.000
60A69LEU0-0.076-0.04024.5370.1590.1590.0000.0000.0000.000
61A70MET0-0.084-0.04628.9790.3210.3210.0000.0000.0000.000
62A71ASN0-0.050-0.02332.3520.6060.6060.0000.0000.0000.000
63A72GLY0-0.028-0.00432.3720.2190.2190.0000.0000.0000.000
64A73GLU-1-0.926-0.95429.083-10.604-10.6040.0000.0000.0000.000
65A74SER0-0.083-0.06726.500-0.238-0.2380.0000.0000.0000.000
66A75VAL00.0500.04722.006-0.351-0.3510.0000.0000.0000.000
67A76ASN0-0.006-0.01819.232-0.635-0.6350.0000.0000.0000.000
68A77THR00.0070.01017.010-0.336-0.3360.0000.0000.0000.000
69A78GLY00.004-0.00613.604-0.378-0.3780.0000.0000.0000.000
70A79LEU00.011-0.00510.505-1.758-1.7580.0000.0000.0000.000
71A80PHE00.0380.01513.414-0.544-0.5440.0000.0000.0000.000
72A81ARG10.9370.98116.79213.27713.2770.0000.0000.0000.000
73A82GLY00.017-0.00520.251-0.187-0.1870.0000.0000.0000.000
74A83VAL0-0.021-0.01523.4560.1440.1440.0000.0000.0000.000
75A84ALA00.0460.04827.274-0.135-0.1350.0000.0000.0000.000
76A85GLN0-0.035-0.02129.5020.1170.1170.0000.0000.0000.000
77A86PHE00.0450.02031.9290.0970.0970.0000.0000.0000.000
78A87ARG10.8330.93929.86410.03310.0330.0000.0000.0000.000
79A88GLY00.0470.03236.2440.1880.1880.0000.0000.0000.000
80A89VAL0-0.006-0.01239.617-0.050-0.0500.0000.0000.0000.000
81A90ALA00.0570.04042.7040.0320.0320.0000.0000.0000.000
82A91LYS10.8540.91844.3877.1507.1500.0000.0000.0000.000
83A92GLN0-0.008-0.01447.647-0.073-0.0730.0000.0000.0000.000
84A93ASN0-0.0220.00347.7850.0090.0090.0000.0000.0000.000
85A94ALA00.0100.01347.3880.0020.0020.0000.0000.0000.000
86A95TRP0-0.0080.00037.446-0.166-0.1660.0000.0000.0000.000
87A96ASP-1-0.775-0.89244.384-6.890-6.8900.0000.0000.0000.000
88A97ALA00.024-0.00342.561-0.162-0.1620.0000.0000.0000.000
89A98ALA00.0020.01842.363-0.131-0.1310.0000.0000.0000.000
90A99THR0-0.122-0.06842.234-0.022-0.0220.0000.0000.0000.000
91A100ASN0-0.064-0.03639.6550.0250.0250.0000.0000.0000.000
92A101SER00.018-0.00235.338-0.066-0.0660.0000.0000.0000.000
93A102ILE00.0330.01132.716-0.068-0.0680.0000.0000.0000.000
94A103TYR0-0.022-0.01428.428-0.187-0.1870.0000.0000.0000.000
95A104VAL00.0690.03424.9160.1210.1210.0000.0000.0000.000
96A105SER0-0.047-0.01125.797-0.394-0.3940.0000.0000.0000.000
97A106LEU00.0500.00920.404-0.146-0.1460.0000.0000.0000.000
98A107THR0-0.035-0.01219.365-0.254-0.2540.0000.0000.0000.000
99A108GLN00.0430.01213.841-1.039-1.0390.0000.0000.0000.000
100A109GLY00.0400.03014.3891.0061.0060.0000.0000.0000.000
101A110LYS10.9380.95912.60120.28020.2800.0000.0000.0000.000
102A111ALA00.0110.0009.000-1.538-1.5380.0000.0000.0000.000
103A112LEU00.0300.0238.088-4.732-4.7320.0000.0000.0000.000
104A113ARG10.8610.9119.19921.45921.4590.0000.0000.0000.000
105A114GLU-1-0.815-0.8858.308-25.753-25.7530.0000.0000.0000.000
106A115ALA00.0150.0074.953-3.441-3.4410.0000.0000.0000.000
107A116ILE0-0.014-0.0025.797-4.935-4.9350.0000.0000.0000.000
108A117LYS10.8760.9307.07728.77328.7730.0000.0000.0000.000
109A118ASP-1-0.862-0.8971.658-126.642-128.21317.554-9.247-6.736-0.107
110A119THR0-0.029-0.0161.984-23.536-24.2297.552-3.729-3.130-0.047
111A120ARG10.8410.9103.86429.70829.963-0.001-0.004-0.2500.000
112A121VAL00.0300.0086.160-1.207-1.2070.0000.0000.0000.000
113A122ASP-1-0.865-0.9179.744-20.359-20.3590.0000.0000.0000.000
114A123VAL00.0180.00311.7040.4470.4470.0000.0000.0000.000
115A124LEU00.0070.00215.2680.4520.4520.0000.0000.0000.000
116A125GLY00.0370.03417.8900.6780.6780.0000.0000.0000.000
117A126GLU-1-0.818-0.89220.764-11.031-11.0310.0000.0000.0000.000
118A127ARG10.8830.94322.07613.19013.1900.0000.0000.0000.000
119A128PRO00.0160.00924.8130.3520.3520.0000.0000.0000.000
120A129THR0-0.028-0.01727.9620.4980.4980.0000.0000.0000.000
121A130LYS10.8030.89528.40010.02010.0200.0000.0000.0000.000
122A131PHE0-0.030-0.02530.2550.3280.3280.0000.0000.0000.000
123A132TYR00.0320.01626.686-0.319-0.3190.0000.0000.0000.000
124A133ILE00.0670.05726.7020.3100.3100.0000.0000.0000.000
125A134GLY0-0.026-0.01925.808-0.449-0.4490.0000.0000.0000.000
126A135SER00.011-0.00224.898-0.455-0.4550.0000.0000.0000.000
127A136GLY00.0790.02526.7080.3540.3540.0000.0000.0000.000
128A137GLN0-0.0090.01028.2220.1130.1130.0000.0000.0000.000
129A138ASP-1-0.668-0.79129.794-9.791-9.7910.0000.0000.0000.000
130A139ALA0-0.040-0.02031.4310.0380.0380.0000.0000.0000.000
131A140THR0-0.024-0.00333.5700.3490.3490.0000.0000.0000.000
132A141THR00.011-0.02928.864-0.024-0.0240.0000.0000.0000.000
133A142ARG10.7840.88330.3989.4089.4080.0000.0000.0000.000
134A143ALA00.0430.04925.589-0.081-0.0810.0000.0000.0000.000
135A144THR0-0.007-0.03825.6770.2900.2900.0000.0000.0000.000
136A145ASP-1-0.846-0.89120.808-14.092-14.0920.0000.0000.0000.000
137A146PHE0-0.071-0.04321.707-0.403-0.4030.0000.0000.0000.000
138A147SER00.0200.00323.4920.1040.1040.0000.0000.0000.000
139A148ALA0-0.041-0.03825.0680.3810.3810.0000.0000.0000.000
140A149THR0-0.015-0.01528.786-0.169-0.1690.0000.0000.0000.000
141A150ALA00.0490.02531.7670.2330.2330.0000.0000.0000.000
142A151GLY0-0.001-0.01334.0510.1430.1430.0000.0000.0000.000
143A152ARG10.8500.92635.0878.7048.7040.0000.0000.0000.000
144A153ASN00.0390.01636.004-0.086-0.0860.0000.0000.0000.000
145A154PHE00.0190.01527.467-0.202-0.2020.0000.0000.0000.000
146A155THR0-0.040-0.01132.3690.3980.3980.0000.0000.0000.000
147A156LEU00.0000.00229.540-0.458-0.4580.0000.0000.0000.000
148A157PHE00.0420.02530.0530.4280.4280.0000.0000.0000.000
149A158GLY00.0370.00229.741-0.470-0.4700.0000.0000.0000.000
150A159LYS10.7990.92730.4539.9349.9340.0000.0000.0000.000
151A160ASN0-0.017-0.02932.7640.1060.1060.0000.0000.0000.000
152A161LEU00.0460.01431.2760.0010.0010.0000.0000.0000.000
153A162THR00.0010.02135.360-0.049-0.0490.0000.0000.0000.000
154A163VAL00.0570.05637.8010.0100.0100.0000.0000.0000.000
155A164ALA00.0200.01140.1190.2160.2160.0000.0000.0000.000
156A165GLY0-0.021-0.02342.576-0.146-0.1460.0000.0000.0000.000
157A166THR0-0.018-0.01644.7980.1400.1400.0000.0000.0000.000
158A167ASP-1-0.824-0.87541.703-7.568-7.5680.0000.0000.0000.000
159A168PRO00.0520.01643.159-0.109-0.1090.0000.0000.0000.000
160A169SER0-0.061-0.04937.907-0.167-0.1670.0000.0000.0000.000
161A170VAL0-0.055-0.02638.524-0.246-0.2460.0000.0000.0000.000
162A171GLY00.0550.03238.5510.1910.1910.0000.0000.0000.000
163A172VAL0-0.015-0.00433.361-0.224-0.2240.0000.0000.0000.000
164A173THR0-0.032-0.01932.9050.1370.1370.0000.0000.0000.000
165A174LEU00.0370.01629.594-0.296-0.2960.0000.0000.0000.000
166A175ALA00.0100.01328.0130.2330.2330.0000.0000.0000.000
167A176SER00.0380.02727.238-0.573-0.5730.0000.0000.0000.000
168A177ALA0-0.008-0.02122.5180.0340.0340.0000.0000.0000.000
169A178ALA00.0060.01324.060-0.316-0.3160.0000.0000.0000.000
170A179THR00.0020.00525.6670.3350.3350.0000.0000.0000.000
171A180GLY0-0.0140.00427.8900.2550.2550.0000.0000.0000.000
172A181THR0-0.014-0.02529.1720.3580.3580.0000.0000.0000.000
173A182VAL0-0.031-0.01631.662-0.214-0.2140.0000.0000.0000.000
174A183THR00.0400.03033.1010.4030.4030.0000.0000.0000.000
175A184LYS10.7830.87734.5987.8657.8650.0000.0000.0000.000
176A185ILE0-0.021-0.01333.8560.1130.1130.0000.0000.0000.000
177A186ASP-1-0.868-0.93338.034-7.209-7.2090.0000.0000.0000.000
178A187ASN00.010-0.02141.305-0.268-0.2680.0000.0000.0000.000
179A188ASP-1-0.871-0.92542.978-6.831-6.8310.0000.0000.0000.000
180A189MET0-0.074-0.03240.301-0.017-0.0170.0000.0000.0000.000
181A190ILE0-0.066-0.02838.609-0.277-0.2770.0000.0000.0000.000
182A191VAL0-0.0010.00040.4130.1370.1370.0000.0000.0000.000
183A192LEU0-0.037-0.01139.7500.1400.1400.0000.0000.0000.000
184A193ASN00.018-0.00239.706-0.430-0.4300.0000.0000.0000.000
185A194GLU-1-0.750-0.84339.111-7.671-7.6710.0000.0000.0000.000
186A195PRO00.000-0.00637.930-0.256-0.2560.0000.0000.0000.000
187A196SER0-0.054-0.05534.079-0.174-0.1740.0000.0000.0000.000
188A197ARG10.8200.87234.2347.8277.8270.0000.0000.0000.000
189A198LEU0-0.0010.03234.5720.2490.2490.0000.0000.0000.000
190A199ILE0-0.036-0.02735.505-0.250-0.2500.0000.0000.0000.000
191A200ILE00.0010.00132.5650.1860.1860.0000.0000.0000.000
192A201LEU00.0140.01836.308-0.200-0.2000.0000.0000.0000.000
193A202LEU0-0.003-0.00231.3800.0260.0260.0000.0000.0000.000
194A203PRO00.023-0.00135.2240.1270.1270.0000.0000.0000.000
195A204ALA00.023-0.00635.949-0.218-0.2180.0000.0000.0000.000
196A205SER0-0.038-0.00937.233-0.067-0.0670.0000.0000.0000.000
197A206LEU0-0.058-0.02132.055-0.011-0.0110.0000.0000.0000.000
198A207GLU-1-0.845-0.90729.787-10.074-10.0740.0000.0000.0000.000
199A208ASP-1-0.809-0.87127.124-11.733-11.7330.0000.0000.0000.000
200A209GLY00.0300.01124.666-0.259-0.2590.0000.0000.0000.000
201A210GLU-1-0.856-0.89721.018-14.768-14.7680.0000.0000.0000.000
202A211TYR0-0.049-0.04723.9130.4430.4430.0000.0000.0000.000
203A212MET0-0.032-0.01521.689-0.362-0.3620.0000.0000.0000.000
204A213LEU00.0170.02325.8220.5490.5490.0000.0000.0000.000
205A214THR0-0.023-0.00927.815-0.423-0.4230.0000.0000.0000.000
206A215VAL00.0060.02330.3320.3500.3500.0000.0000.0000.000
207A216THR00.0480.02433.198-0.268-0.2680.0000.0000.0000.000
208A217THR00.010-0.02035.8270.3210.3210.0000.0000.0000.000
209A218GLN00.0620.02238.646-0.061-0.0610.0000.0000.0000.000
210A219TYR0-0.015-0.00738.6220.1240.1240.0000.0000.0000.000
211A220ARG10.8600.92339.3336.9136.9130.0000.0000.0000.000
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