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: G5YN1

Calculation Name: 5NR1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5NR1

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3007032.075879
FMO2-HF: Nuclear repulsion 2914385.855422
FMO2-HF: Total energy -92646.220457
FMO2-MP2: Total energy -92915.637967


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:VAL)


Summations of interaction energy for fragment #1(A:3:VAL)
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.
-17.309-7.8035.78-5.375-9.909-0.027
Interaction energy analysis for fragmet #1(A:3:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.010
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].
3A5ARG10.8580.9282.622-0.2424.1361.703-2.262-3.819-0.009
4A6THR00.0150.0174.3180.3660.4480.000-0.027-0.0540.000
5A7LEU0-0.038-0.0167.8440.1010.1010.0000.0000.0000.000
6A8HIS00.0380.01510.3250.1190.1190.0000.0000.0000.000
7A9HIS0-0.037-0.03913.5090.0690.0690.0000.0000.0000.000
8A10PHE00.0570.02516.1670.0210.0210.0000.0000.0000.000
9A11PRO00.0350.01019.6840.0010.0010.0000.0000.0000.000
10A12LEU0-0.040-0.01020.626-0.001-0.0010.0000.0000.0000.000
11A13ASP-1-0.737-0.85919.708-0.300-0.3000.0000.0000.0000.000
12A14PRO00.0290.01020.544-0.034-0.0340.0000.0000.0000.000
13A15ALA00.0370.02518.587-0.019-0.0190.0000.0000.0000.000
14A16SER0-0.007-0.04416.077-0.056-0.0560.0000.0000.0000.000
15A17ARG10.7960.86615.8050.2610.2610.0000.0000.0000.000
16A18GLN0-0.037-0.01817.305-0.023-0.0230.0000.0000.0000.000
17A19VAL0-0.0050.00711.189-0.017-0.0170.0000.0000.0000.000
18A20ARG10.8350.89712.6020.4600.4600.0000.0000.0000.000
19A21LEU0-0.015-0.00414.081-0.041-0.0410.0000.0000.0000.000
20A22ALA00.0060.00412.8150.0090.0090.0000.0000.0000.000
21A23LEU0-0.0030.0027.638-0.001-0.0010.0000.0000.0000.000
22A24GLY00.0280.01610.778-0.056-0.0560.0000.0000.0000.000
23A25GLU-1-0.838-0.90913.271-0.302-0.3020.0000.0000.0000.000
24A26LYS10.7420.84210.0940.4100.4100.0000.0000.0000.000
25A27ARG10.9020.96310.3220.3900.3900.0000.0000.0000.000
26A28LEU00.0060.0125.450-0.190-0.1900.0000.0000.0000.000
27A29PRO0-0.014-0.0116.0900.1670.1670.0000.0000.0000.000
28A30PHE0-0.042-0.0266.632-0.623-0.6230.0000.0000.0000.000
29A31VAL00.0290.0238.1700.3120.3120.0000.0000.0000.000
30A32GLU-1-0.898-0.95510.147-0.715-0.7150.0000.0000.0000.000
31A33MET0-0.005-0.00112.8150.0600.0600.0000.0000.0000.000
32A34GLN0-0.035-0.01714.9690.0500.0500.0000.0000.0000.000
33A35VAL00.0280.01217.9800.0250.0250.0000.0000.0000.000
34A36ARG10.8080.88419.8020.2310.2310.0000.0000.0000.000
35A37TYR00.0530.02121.1480.0220.0220.0000.0000.0000.000
36A38TRP00.0510.03123.0650.0110.0110.0000.0000.0000.000
37A39GLU-1-0.903-0.93926.115-0.185-0.1850.0000.0000.0000.000
38A40MET0-0.060-0.03024.8310.0120.0120.0000.0000.0000.000
39A41PRO00.0280.02621.7430.0120.0120.0000.0000.0000.000
40A42PRO00.0390.00722.536-0.013-0.0130.0000.0000.0000.000
41A43GLU-1-0.916-0.96918.484-0.284-0.2840.0000.0000.0000.000
42A44PHE0-0.0170.00815.686-0.021-0.0210.0000.0000.0000.000
43A45THR00.0140.00318.529-0.013-0.0130.0000.0000.0000.000
44A46SER0-0.112-0.05619.0400.0180.0180.0000.0000.0000.000
45A47LEU0-0.024-0.00913.0530.0070.0070.0000.0000.0000.000
46A48ASN0-0.032-0.04615.8150.0300.0300.0000.0000.0000.000
47A49PRO00.0080.01617.8400.0040.0040.0000.0000.0000.000
48A50SER0-0.060-0.03720.1500.0110.0110.0000.0000.0000.000
49A51GLY00.0050.00021.1570.0070.0070.0000.0000.0000.000
50A52MET0-0.015-0.00320.550-0.010-0.0100.0000.0000.0000.000
51A53PRO0-0.0680.01416.751-0.028-0.0280.0000.0000.0000.000
52A54PRO00.002-0.01513.5840.0260.0260.0000.0000.0000.000
53A55VAL00.022-0.00811.3630.0380.0380.0000.0000.0000.000
54A56LEU0-0.031-0.0106.003-0.062-0.0620.0000.0000.0000.000
55A57VAL0-0.010-0.0087.0660.1490.1490.0000.0000.0000.000
56A58GLU-1-0.785-0.8792.289-4.035-3.2421.973-0.893-1.874-0.004
57A59THR00.021-0.0033.0920.1900.8040.164-0.116-0.661-0.001
58A60LYS10.9690.9732.330-11.333-8.0051.941-2.033-3.236-0.013
59A61HIS0-0.014-0.0124.173-0.661-0.5140.001-0.036-0.1120.000
60A62GLN00.0290.0147.158-0.195-0.1950.0000.0000.0000.000
61A63ARG10.9050.9637.626-0.881-0.8810.0000.0000.0000.000
62A64ASN00.0490.0336.204-0.037-0.0370.0000.0000.0000.000
63A65LEU0-0.0130.0065.6130.1830.1830.0000.0000.0000.000
64A66VAL00.0130.0037.185-0.276-0.2760.0000.0000.0000.000
65A67ILE0-0.0080.0056.1780.1230.1230.0000.0000.0000.000
66A68CYS00.0120.00310.301-0.090-0.0900.0000.0000.0000.000
67A69GLU-1-0.796-0.88713.750-0.187-0.1870.0000.0000.0000.000
68A70THR00.0290.01114.379-0.006-0.0060.0000.0000.0000.000
69A71ARG10.9420.97715.1880.1060.1060.0000.0000.0000.000
70A72ALA00.0260.01012.8830.0240.0240.0000.0000.0000.000
71A73ILE0-0.009-0.0049.552-0.007-0.0070.0000.0000.0000.000
72A74LEU0-0.018-0.01810.561-0.053-0.0530.0000.0000.0000.000
73A75GLU-1-0.807-0.89612.761-0.101-0.1010.0000.0000.0000.000
74A76HIS00.0140.0044.6220.2740.320-0.001-0.003-0.0420.000
75A77ILE00.000-0.0027.7890.0380.0380.0000.0000.0000.000
76A78GLU-1-0.800-0.9099.157-0.112-0.1120.0000.0000.0000.000
77A79GLU-1-1.034-1.00910.7020.1340.1340.0000.0000.0000.000
78A80THR0-0.090-0.0495.8440.0420.0420.0000.0000.0000.000
79A81GLU-1-0.861-0.9204.752-0.297-0.179-0.001-0.005-0.1110.000
80A82THR0-0.012-0.0088.591-0.063-0.0630.0000.0000.0000.000
81A83GLU-1-1.009-0.98511.317-0.137-0.1370.0000.0000.0000.000
82A84PRO00.0090.01312.433-0.071-0.0710.0000.0000.0000.000
83A85PRO0-0.016-0.00314.620-0.043-0.0430.0000.0000.0000.000
84A86LEU0-0.015-0.02014.637-0.005-0.0050.0000.0000.0000.000
85A87LEU0-0.0120.00217.2210.0080.0080.0000.0000.0000.000
86A88GLY0-0.0010.00519.2930.0140.0140.0000.0000.0000.000
87A89ARG10.9180.94520.953-0.027-0.0270.0000.0000.0000.000
88A90ASP-1-0.846-0.91322.7630.0010.0010.0000.0000.0000.000
89A91PRO00.013-0.00925.155-0.011-0.0110.0000.0000.0000.000
90A92ALA00.0220.00726.183-0.008-0.0080.0000.0000.0000.000
91A93GLU-1-0.823-0.91924.798-0.050-0.0500.0000.0000.0000.000
92A94ARG10.8670.94017.367-0.003-0.0030.0000.0000.0000.000
93A95ALA0-0.013-0.00523.417-0.013-0.0130.0000.0000.0000.000
94A96GLU-1-0.748-0.83726.032-0.081-0.0810.0000.0000.0000.000
95A97ALA00.019-0.00522.262-0.010-0.0100.0000.0000.0000.000
96A98ARG10.8360.90118.1420.0480.0480.0000.0000.0000.000
97A99ARG10.7940.88823.0960.0720.0720.0000.0000.0000.000
98A100LEU0-0.011-0.01325.603-0.004-0.0040.0000.0000.0000.000
99A101LEU00.0360.01819.124-0.006-0.0060.0000.0000.0000.000
100A102GLN0-0.042-0.01323.085-0.001-0.0010.0000.0000.0000.000
101A103TRP0-0.043-0.02025.2650.0070.0070.0000.0000.0000.000
102A104PHE0-0.001-0.01924.9730.0040.0040.0000.0000.0000.000
103A105ASP-1-0.791-0.90121.172-0.227-0.2270.0000.0000.0000.000
104A106ARG10.9040.95924.6960.1080.1080.0000.0000.0000.000
105A107LYS10.8140.90827.8960.0880.0880.0000.0000.0000.000
106A108PHE00.001-0.00528.5950.0040.0040.0000.0000.0000.000
107A109ASP-1-0.838-0.91726.933-0.175-0.1750.0000.0000.0000.000
108A110ASN00.011-0.00628.941-0.002-0.0020.0000.0000.0000.000
109A111GLU-1-0.859-0.89332.002-0.086-0.0860.0000.0000.0000.000
110A112VAL0-0.010-0.00432.1170.0050.0050.0000.0000.0000.000
111A113ASN0-0.039-0.03127.3170.0050.0050.0000.0000.0000.000
112A114GLY00.0360.02531.203-0.002-0.0020.0000.0000.0000.000
113A115PHE0-0.047-0.01333.0870.0070.0070.0000.0000.0000.000
114A116LEU0-0.024-0.03433.6090.0000.0000.0000.0000.0000.000
115A117LEU0-0.003-0.00327.721-0.003-0.0030.0000.0000.0000.000
116A118HIS0-0.032-0.00631.7430.0030.0030.0000.0000.0000.000
117A119GLU-1-0.765-0.89433.348-0.103-0.1030.0000.0000.0000.000
118A120LYS10.7740.88434.4430.1410.1410.0000.0000.0000.000
119A121MET00.0040.01126.788-0.003-0.0030.0000.0000.0000.000
120A122GLU-1-0.862-0.92829.141-0.166-0.1660.0000.0000.0000.000
121A123LYS10.9060.95131.6600.1050.1050.0000.0000.0000.000
122A124ARG10.8910.96333.6260.1480.1480.0000.0000.0000.000
123A125LEU0-0.055-0.02927.8840.0030.0030.0000.0000.0000.000
124A126LEU00.0140.01130.8370.0010.0010.0000.0000.0000.000
125A127ARG10.8570.92633.8500.1270.1270.0000.0000.0000.000
126A128MET00.0110.00936.1800.0050.0050.0000.0000.0000.000
127A129GLY0-0.031-0.00338.8030.0050.0050.0000.0000.0000.000
128A130ALA0-0.020-0.01039.594-0.005-0.0050.0000.0000.0000.000
129A131PRO00.0280.00339.2820.0010.0010.0000.0000.0000.000
130A132ASP-1-0.841-0.91040.812-0.077-0.0770.0000.0000.0000.000
131A133LEU0-0.007-0.03642.248-0.002-0.0020.0000.0000.0000.000
132A134ALA0-0.043-0.01844.1970.0000.0000.0000.0000.0000.000
133A135ALA00.0560.03939.7750.0000.0000.0000.0000.0000.000
134A136LEU0-0.015-0.01238.276-0.003-0.0030.0000.0000.0000.000
135A137ARG10.9060.94640.4140.0730.0730.0000.0000.0000.000
136A138GLN00.0440.03939.7980.0040.0040.0000.0000.0000.000
137A139GLY00.0410.01337.600-0.001-0.0010.0000.0000.0000.000
138A140ARG10.8270.90837.5060.1060.1060.0000.0000.0000.000
139A141GLU-1-0.911-0.95039.415-0.079-0.0790.0000.0000.0000.000
140A142ALA00.0310.00536.8480.0010.0010.0000.0000.0000.000
141A143LEU0-0.015-0.00333.435-0.001-0.0010.0000.0000.0000.000
142A144ARG10.9320.96236.2330.0940.0940.0000.0000.0000.000
143A145MET0-0.0070.01738.5570.0040.0040.0000.0000.0000.000
144A146HIS0-0.023-0.03532.790-0.002-0.0020.0000.0000.0000.000
145A147LEU0-0.021-0.01133.449-0.002-0.0020.0000.0000.0000.000
146A148GLY00.0450.01935.5300.0010.0010.0000.0000.0000.000
147A149TYR00.0200.02631.8940.0030.0030.0000.0000.0000.000
148A150ILE00.0230.01330.6760.0020.0020.0000.0000.0000.000
149A151GLU-1-0.767-0.87233.566-0.094-0.0940.0000.0000.0000.000
150A152SER0-0.080-0.05336.3800.0050.0050.0000.0000.0000.000
151A153LEU0-0.025-0.01731.4510.0040.0040.0000.0000.0000.000
152A154LEU0-0.017-0.01830.1700.0020.0020.0000.0000.0000.000
153A155GLN0-0.072-0.02434.1460.0050.0050.0000.0000.0000.000
154A156THR0-0.103-0.04736.2770.0060.0060.0000.0000.0000.000
155A157ARG10.7960.87730.8050.0810.0810.0000.0000.0000.000
156A158ASP-1-0.930-0.94530.208-0.084-0.0840.0000.0000.0000.000
157A159TRP0-0.056-0.04226.249-0.018-0.0180.0000.0000.0000.000
158A160LEU00.0180.00626.6110.0120.0120.0000.0000.0000.000
159A161ALA0-0.021-0.00425.5580.0100.0100.0000.0000.0000.000
160A162GLY00.0130.00927.5680.0120.0120.0000.0000.0000.000
161A163ARG11.0060.99225.9400.0340.0340.0000.0000.0000.000
162A164ARG10.8900.95620.6410.0940.0940.0000.0000.0000.000
163A165MET0-0.0170.02119.7740.0010.0010.0000.0000.0000.000
164A166SER0-0.028-0.02420.4220.0020.0020.0000.0000.0000.000
165A167LEU00.0660.00915.358-0.014-0.0140.0000.0000.0000.000
166A168ALA00.0040.01819.439-0.007-0.0070.0000.0000.0000.000
167A169ASP-1-0.742-0.86723.005-0.161-0.1610.0000.0000.0000.000
168A170PHE00.0470.00616.6320.0000.0000.0000.0000.0000.000
169A171ALA00.0340.03121.127-0.013-0.0130.0000.0000.0000.000
170A172ALA00.0060.00422.1070.0010.0010.0000.0000.0000.000
171A173ALA0-0.004-0.01123.5190.0040.0040.0000.0000.0000.000
172A174ALA00.0050.00520.746-0.002-0.0020.0000.0000.0000.000
173A175HIS00.0160.00822.7840.0040.0040.0000.0000.0000.000
174A176LEU0-0.006-0.01025.6630.0080.0080.0000.0000.0000.000
175A177SER0-0.0110.01024.182-0.001-0.0010.0000.0000.0000.000
176A178VAL00.0080.00424.4740.0010.0010.0000.0000.0000.000
177A179ILE00.018-0.00127.0050.0110.0110.0000.0000.0000.000
178A180ASP-1-0.836-0.90529.422-0.168-0.1680.0000.0000.0000.000
179A181TYR0-0.041-0.02827.0260.0010.0010.0000.0000.0000.000
180A182PHE0-0.044-0.03128.8540.0080.0080.0000.0000.0000.000
181A183GLY00.001-0.00432.9780.0110.0110.0000.0000.0000.000
182A184ASP-1-0.806-0.88234.278-0.123-0.1230.0000.0000.0000.000
183A185VAL00.0150.00631.8130.0070.0070.0000.0000.0000.000
184A186PRO0-0.045-0.00735.2180.0010.0010.0000.0000.0000.000
185A187TRP00.064-0.00630.2510.0110.0110.0000.0000.0000.000
186A188LYS10.8650.93236.9670.0920.0920.0000.0000.0000.000
187A189ASP-1-0.882-0.94640.228-0.083-0.0830.0000.0000.0000.000
188A190PHE0-0.045-0.00237.1550.0040.0040.0000.0000.0000.000
189A191GLN00.0240.01337.188-0.009-0.0090.0000.0000.0000.000
190A192ALA00.0210.00835.671-0.005-0.0050.0000.0000.0000.000
191A193ALA00.0220.00133.017-0.008-0.0080.0000.0000.0000.000
192A194LYS10.8910.94332.4310.1060.1060.0000.0000.0000.000
193A195THR0-0.043-0.02632.937-0.009-0.0090.0000.0000.0000.000
194A196TRP0-0.067-0.04026.443-0.010-0.0100.0000.0000.0000.000
195A197TYR00.0300.01126.492-0.019-0.0190.0000.0000.0000.000
196A198MET00.0080.01128.204-0.014-0.0140.0000.0000.0000.000
197A199LYS10.9240.96427.8490.1130.1130.0000.0000.0000.000
198A200LEU0-0.012-0.01523.014-0.015-0.0150.0000.0000.0000.000
199A201LYS10.8170.93323.7510.1740.1740.0000.0000.0000.000
200A202SER00.0180.00625.272-0.011-0.0110.0000.0000.0000.000
201A203ARG10.7430.85619.7780.2610.2610.0000.0000.0000.000
202A204PRO0-0.013-0.02318.342-0.014-0.0140.0000.0000.0000.000
203A205CYS0-0.0230.00716.582-0.013-0.0130.0000.0000.0000.000
204A206PHE00.0760.03217.669-0.031-0.0310.0000.0000.0000.000
205A207ARG10.9400.98520.4330.3630.3630.0000.0000.0000.000
206A208PRO00.010-0.01316.8030.0230.0230.0000.0000.0000.000
207A209ILE00.0330.02518.0350.0160.0160.0000.0000.0000.000
208A210LEU0-0.034-0.00121.0380.0260.0260.0000.0000.0000.000
209A211ALA00.0170.01422.1840.0250.0250.0000.0000.0000.000
210A212ASP-1-0.793-0.85020.809-0.409-0.4090.0000.0000.0000.000
211A213ARG10.8190.89023.5200.2830.2830.0000.0000.0000.000
212A214TRP00.0310.01822.441-0.022-0.0220.0000.0000.0000.000
213A215PRO00.0360.01327.0780.0180.0180.0000.0000.0000.000
214A216GLY0-0.034-0.01330.1610.0040.0040.0000.0000.0000.000
215A217LEU0-0.053-0.02528.6080.0110.0110.0000.0000.0000.000
216A218ALA00.0010.02230.711-0.014-0.0140.0000.0000.0000.000
217A219PRO00.0170.01929.8760.0070.0070.0000.0000.0000.000
218A220ALA0-0.005-0.01231.9900.0090.0090.0000.0000.0000.000
219A221ALA0-0.007-0.01833.303-0.008-0.0080.0000.0000.0000.000
220A222HIS00.000-0.00733.3300.0010.0010.0000.0000.0000.000
221A223TYR0-0.081-0.02224.505-0.007-0.0070.0000.0000.0000.000
222A224ASP-1-0.877-0.95128.243-0.227-0.2270.0000.0000.0000.000
223A225ASP-1-0.837-0.89829.360-0.169-0.1690.0000.0000.0000.000
224A226LEU0-0.077-0.06627.322-0.004-0.0040.0000.0000.0000.000
225A227ASP-1-0.931-0.95531.106-0.132-0.1320.0000.0000.0000.000
226A228PHE00.0110.01031.6670.0050.0050.0000.0000.0000.000