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: N13LQ

Calculation Name: 4RLB-A-Xray322

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RLB

Chain ID: A

ChEMBL ID:

UniProt ID: Q5DL42

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 214
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2149441.668992
FMO2-HF: Nuclear repulsion 2070074.415401
FMO2-HF: Total energy -79367.253591
FMO2-MP2: Total energy -79603.042322


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:13:ACE )


Summations of interaction energy for fragment #1(A:13:ACE )
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.
0.7942.002-0.005-0.571-0.633-0.001
Interaction energy analysis for fragmet #1(A:13:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.012
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].
3A15GLN 00.0240.0263.8740.4501.658-0.005-0.571-0.633-0.001
4A16LEU 00.014-0.0075.813-0.157-0.1570.0000.0000.0000.000
5A17ILE 0-0.0130.0077.2930.1590.1590.0000.0000.0000.000
6A18PRO 0-0.0050.00010.572-0.025-0.0250.0000.0000.0000.000
7A19VAL 0-0.040-0.03513.6990.0100.0100.0000.0000.0000.000
8A20GLY 00.0760.04516.1970.0160.0160.0000.0000.0000.000
9A21ALA 0-0.040-0.01519.846-0.004-0.0040.0000.0000.0000.000
10A22ARG 10.7960.88022.3770.1530.1530.0000.0000.0000.000
11A23ALA 00.0020.02525.1570.0060.0060.0000.0000.0000.000
12A24GLU -1-0.761-0.83426.818-0.119-0.1190.0000.0000.0000.000
13A25VAL 00.0350.00730.3850.0060.0060.0000.0000.0000.000
14A26GLY 00.031-0.00233.420-0.005-0.0050.0000.0000.0000.000
15A27THR 00.0020.00734.9900.0020.0020.0000.0000.0000.000
16A28THR 0-0.0030.00632.5420.0040.0040.0000.0000.0000.000
17A29GLY 00.0530.02835.6840.0020.0020.0000.0000.0000.000
18A30TYR 0-0.032-0.02733.687-0.004-0.0040.0000.0000.0000.000
19A31GLY 00.0180.00131.1000.0020.0020.0000.0000.0000.000
20A32GLY 0-0.0030.00327.598-0.001-0.0010.0000.0000.0000.000
21A33ALA 0-0.026-0.00822.7370.0010.0010.0000.0000.0000.000
22A34LEU 00.0010.00819.7930.0020.0020.0000.0000.0000.000
23A35LEU 00.0190.00817.926-0.016-0.0160.0000.0000.0000.000
24A36TRP 0-0.014-0.01512.5910.0090.0090.0000.0000.0000.000
25A37GLN 0-0.019-0.01812.0070.0420.0420.0000.0000.0000.000
26A38ALA 0-0.0140.0067.3100.0070.0070.0000.0000.0000.000
27A39ASN 0-0.014-0.0296.8760.0260.0260.0000.0000.0000.000
28A40PRO 0-0.019-0.0089.4230.1420.1420.0000.0000.0000.000
29A41TYR 00.0040.00711.0840.1240.1240.0000.0000.0000.000
30A42VAL 00.0090.02310.6500.0780.0780.0000.0000.0000.000
31A43GLY 00.0580.02711.912-0.093-0.0930.0000.0000.0000.000
32A44LEU 0-0.063-0.03014.1530.0160.0160.0000.0000.0000.000
33A45ALA 00.0660.04416.2020.0120.0120.0000.0000.0000.000
34A46LEU 0-0.006-0.00919.6390.0060.0060.0000.0000.0000.000
35A47GLY 00.0260.01121.6370.0050.0050.0000.0000.0000.000
36A48TYR 0-0.0280.00825.2510.0060.0060.0000.0000.0000.000
37A49ASN 0-0.091-0.05628.982-0.006-0.0060.0000.0000.0000.000
38A50GLY 00.0520.01331.8950.0020.0020.0000.0000.0000.000
39A51GLY 0-0.017-0.01235.437-0.001-0.0010.0000.0000.0000.000
40A52ASP -1-0.903-0.94238.698-0.034-0.0340.0000.0000.0000.000
41A53ILE 0-0.085-0.03838.4910.0000.0000.0000.0000.0000.000
42A54SER 00.1160.07743.0120.0010.0010.0000.0000.0000.000
43A55TRP 0-0.115-0.07038.833-0.003-0.0030.0000.0000.0000.000
44A56SER 0-0.080-0.05844.256-0.001-0.0010.0000.0000.0000.000
45A57ASP -1-0.870-0.92147.699-0.031-0.0310.0000.0000.0000.000
46A58ASP -1-0.858-0.92251.191-0.027-0.0270.0000.0000.0000.000
47A59LEU 0-0.023-0.00148.8080.0000.0000.0000.0000.0000.000
48A60SER 0-0.077-0.04352.7440.0000.0000.0000.0000.0000.000
49A61ILE 00.011-0.00950.643-0.001-0.0010.0000.0000.0000.000
50A62ASN 0-0.056-0.03355.1750.0010.0010.0000.0000.0000.000
51A63GLY 00.0150.00558.1900.0000.0000.0000.0000.0000.000
52A64THR 00.003-0.00255.1730.0010.0010.0000.0000.0000.000
53A65LYS 10.9260.98555.3280.0250.0250.0000.0000.0000.000
54A66TYR 0-0.037-0.02050.1610.0000.0000.0000.0000.0000.000
55A67ASP -1-0.855-0.92850.465-0.031-0.0310.0000.0000.0000.000
56A68MET 0-0.082-0.06042.957-0.001-0.0010.0000.0000.0000.000
57A69ASP -1-0.803-0.88445.782-0.034-0.0340.0000.0000.0000.000
58A70MET 0-0.107-0.06839.705-0.002-0.0020.0000.0000.0000.000
59A71ASP -1-0.846-0.91441.521-0.036-0.0360.0000.0000.0000.000
60A72ASN 0-0.075-0.02936.4390.0010.0010.0000.0000.0000.000
61A73LYS 10.9310.96734.8640.0380.0380.0000.0000.0000.000
62A74LEU 0-0.0130.01729.445-0.001-0.0010.0000.0000.0000.000
63A75ALA 00.004-0.00427.581-0.002-0.0020.0000.0000.0000.000
64A76TYR 0-0.084-0.08823.526-0.004-0.0040.0000.0000.0000.000
65A77LEU 00.0050.00218.489-0.005-0.0050.0000.0000.0000.000
66A78ASN 0-0.024-0.02420.537-0.003-0.0030.0000.0000.0000.000
67A79ALA 00.0050.01416.267-0.018-0.0180.0000.0000.0000.000
68A80GLU -1-0.859-0.93216.700-0.197-0.1970.0000.0000.0000.000
69A81ILE 0-0.027-0.02115.362-0.068-0.0680.0000.0000.0000.000
70A82ARG 10.8830.93416.2020.3250.3250.0000.0000.0000.000
71A83PRO 0-0.011-0.00516.969-0.037-0.0370.0000.0000.0000.000
72A84TRP 00.0210.00618.467-0.010-0.0100.0000.0000.0000.000
73A85GLY 00.0310.01416.2360.0220.0220.0000.0000.0000.000
74A86ALA 0-0.022-0.01314.632-0.010-0.0100.0000.0000.0000.000
75A87SER 0-0.068-0.01616.4190.0380.0380.0000.0000.0000.000
76A88THR 00.020-0.00120.231-0.003-0.0030.0000.0000.0000.000
77A89ASN 00.0390.01522.2190.0180.0180.0000.0000.0000.000
78A90PRO 00.0510.01523.725-0.016-0.0160.0000.0000.0000.000
79A91TRP 0-0.006-0.01024.797-0.007-0.0070.0000.0000.0000.000
80A92ALA 00.0280.00623.6360.0000.0000.0000.0000.0000.000
81A93GLN 0-0.0030.00218.3980.0050.0050.0000.0000.0000.000
82A94GLY 0-0.0040.00020.376-0.022-0.0220.0000.0000.0000.000
83A95LEU 0-0.0320.00522.9250.0040.0040.0000.0000.0000.000
84A96TYR 0-0.071-0.08120.104-0.030-0.0300.0000.0000.0000.000
85A97VAL 00.0030.01720.7820.0250.0250.0000.0000.0000.000
86A98ALA 00.0200.01220.465-0.029-0.0290.0000.0000.0000.000
87A99ALA 0-0.006-0.01620.6010.0180.0180.0000.0000.0000.000
88A100GLY 0-0.029-0.02320.627-0.022-0.0220.0000.0000.0000.000
89A101ALA 0-0.021-0.00222.6540.0110.0110.0000.0000.0000.000
90A102ALA 0-0.031-0.02125.260-0.006-0.0060.0000.0000.0000.000
91A103TYR 00.0370.06028.0380.0040.0040.0000.0000.0000.000
92A104VAL 0-0.076-0.06530.583-0.003-0.0030.0000.0000.0000.000
93A105ASP -1-0.810-0.88433.697-0.036-0.0360.0000.0000.0000.000
94A106ASN 00.022-0.00135.3220.0010.0010.0000.0000.0000.000
95A107GLN 00.0030.00938.7710.0010.0010.0000.0000.0000.000
96A108TYR 00.0080.00137.859-0.002-0.0020.0000.0000.0000.000
97A109ASP -1-0.800-0.88444.268-0.030-0.0300.0000.0000.0000.000
98A110LEU 0-0.060-0.03945.955-0.001-0.0010.0000.0000.0000.000
99A111THR 0-0.001-0.01049.3840.0020.0020.0000.0000.0000.000
100A112LYS 10.9380.98451.7700.0330.0330.0000.0000.0000.000
101A113ASN 00.016-0.00254.6270.0020.0020.0000.0000.0000.000
102A114VAL 0-0.023-0.01858.0240.0000.0000.0000.0000.0000.000
103A115GLY 00.0550.02859.8170.0010.0010.0000.0000.0000.000
104A116THR 0-0.006-0.05262.5970.0000.0000.0000.0000.0000.000
105A117ASN 0-0.111-0.05065.5500.0000.0000.0000.0000.0000.000
106A118ALA 00.0040.02960.8050.0000.0000.0000.0000.0000.000
107A119SER 0-0.057-0.03660.8410.0000.0000.0000.0000.0000.000
108A120VAL 00.0360.01855.633-0.001-0.0010.0000.0000.0000.000
109A121GLU -1-0.850-0.93355.433-0.030-0.0300.0000.0000.0000.000
110A122ILE 0-0.037-0.01853.653-0.002-0.0020.0000.0000.0000.000
111A123ASP -1-0.780-0.87653.307-0.030-0.0300.0000.0000.0000.000
112A124GLY 00.0000.00254.3250.0010.0010.0000.0000.0000.000
113A125ASN 00.0110.03756.4330.0010.0010.0000.0000.0000.000
114A126ARG 10.8520.91958.6770.0260.0260.0000.0000.0000.000
115A127PHE 00.0050.01259.1730.0010.0010.0000.0000.0000.000
116A128ASN 0-0.028-0.02962.0110.0000.0000.0000.0000.0000.000
117A129GLY 00.0350.02763.8070.0010.0010.0000.0000.0000.000
118A130GLY 00.0100.01864.7960.0010.0010.0000.0000.0000.000
119A131ALA 00.032-0.00568.1140.0000.0000.0000.0000.0000.000
120A132ASN 0-0.048-0.01368.1560.0000.0000.0000.0000.0000.000
121A133GLY 00.0470.04664.1850.0000.0000.0000.0000.0000.000
122A134VAL 0-0.044-0.02560.9150.0010.0010.0000.0000.0000.000
123A135SER 0-0.059-0.02758.556-0.001-0.0010.0000.0000.0000.000
124A136ILE 0-0.003-0.01054.6650.0010.0010.0000.0000.0000.000
125A137ALA 00.0180.01053.612-0.001-0.0010.0000.0000.0000.000
126A138GLY 00.001-0.01150.3990.0000.0000.0000.0000.0000.000
127A139ASN 0-0.0400.00347.673-0.001-0.0010.0000.0000.0000.000
128A140LEU 0-0.017-0.02243.5500.0000.0000.0000.0000.0000.000
129A141LYS 10.8250.90740.1790.0390.0390.0000.0000.0000.000
130A142TYR 0-0.017-0.02437.8740.0000.0000.0000.0000.0000.000
131A143ASP -1-0.860-0.94537.661-0.039-0.0390.0000.0000.0000.000
132A144ASN 0-0.073-0.06233.3080.0000.0000.0000.0000.0000.000
133A145ASP -1-0.853-0.91531.946-0.045-0.0450.0000.0000.0000.000
134A146ILE 0-0.076-0.04125.948-0.005-0.0050.0000.0000.0000.000
135A147ALA 00.0270.02229.9090.0000.0000.0000.0000.0000.000
136A148PRO 0-0.028-0.01527.056-0.008-0.0080.0000.0000.0000.000
137A149TYR 0-0.051-0.05824.8750.0080.0080.0000.0000.0000.000
138A150ILE 0-0.006-0.00324.625-0.013-0.0130.0000.0000.0000.000
139A151GLY 00.0460.02325.4240.0130.0130.0000.0000.0000.000
140A152PHE 0-0.052-0.02325.189-0.016-0.0160.0000.0000.0000.000
141A153GLY 00.0580.03024.9660.0120.0120.0000.0000.0000.000
142A154PHE 0-0.063-0.02825.159-0.009-0.0090.0000.0000.0000.000
143A155ALA 00.0510.01022.3640.0090.0090.0000.0000.0000.000
144A156PRO 0-0.0260.00622.422-0.022-0.0220.0000.0000.0000.000
145A157LYS 10.9160.96617.5280.2320.2320.0000.0000.0000.000
146A158PHE 00.0160.00222.3820.0030.0030.0000.0000.0000.000
147A159SER 0-0.0030.00623.3900.0110.0110.0000.0000.0000.000
148A160LYS 10.9200.95116.8500.1270.1270.0000.0000.0000.000
149A161ASN 00.0250.01220.733-0.005-0.0050.0000.0000.0000.000
150A162TRP 00.0290.01823.3750.0020.0020.0000.0000.0000.000
151A163GLY 0-0.009-0.00724.441-0.009-0.0090.0000.0000.0000.000
152A164VAL 00.0160.02525.4340.0070.0070.0000.0000.0000.000
153A165PHE 0-0.033-0.02025.098-0.013-0.0130.0000.0000.0000.000
154A166GLY 00.0320.02027.1130.0120.0120.0000.0000.0000.000
155A167GLU -1-0.828-0.85324.833-0.163-0.1630.0000.0000.0000.000
156A168VAL 00.0020.00328.5970.0110.0110.0000.0000.0000.000
157A169GLY 00.0440.01229.227-0.010-0.0100.0000.0000.0000.000
158A170ALA 0-0.044-0.02029.9440.0090.0090.0000.0000.0000.000
159A171TYR 00.0370.01527.821-0.006-0.0060.0000.0000.0000.000
160A172TYR 0-0.0160.00631.1140.0060.0060.0000.0000.0000.000
161A173SER 0-0.020-0.03333.0010.0000.0000.0000.0000.0000.000
162A174GLY 00.0200.02135.0810.0030.0030.0000.0000.0000.000
163A175ASN 0-0.073-0.04137.959-0.001-0.0010.0000.0000.0000.000
164A176PRO 0-0.0020.02141.5410.0010.0010.0000.0000.0000.000
165A177LYS 10.9440.97042.6240.0330.0330.0000.0000.0000.000
166A178VAL 0-0.017-0.01745.735-0.001-0.0010.0000.0000.0000.000
167A179SER 0-0.0200.00248.2010.0020.0020.0000.0000.0000.000
168A180LEU 0-0.051-0.02750.461-0.001-0.0010.0000.0000.0000.000
169A181ALA 00.0260.02153.7430.0010.0010.0000.0000.0000.000
170A182SER 0-0.032-0.04956.943-0.001-0.0010.0000.0000.0000.000
171A183ASN 00.0260.02159.7320.0000.0000.0000.0000.0000.000
172A184ASN 0-0.026-0.03962.8210.0010.0010.0000.0000.0000.000
173A185ASP -1-0.767-0.84461.685-0.022-0.0220.0000.0000.0000.000
174A186ALA 00.001-0.00964.0320.0000.0000.0000.0000.0000.000
175A187LEU 0-0.028-0.00263.9740.0000.0000.0000.0000.0000.000
176A188ILE 0-0.020-0.01765.2650.0000.0000.0000.0000.0000.000
177A189GLY 00.0260.02563.2730.0000.0000.0000.0000.0000.000
178A190SER 0-0.039-0.01762.3320.0000.0000.0000.0000.0000.000
179A191ASP -1-0.858-0.93860.693-0.024-0.0240.0000.0000.0000.000
180A192GLY 0-0.001-0.00864.1000.0000.0000.0000.0000.0000.000
181A193ARG 10.7010.84357.0580.0270.0270.0000.0000.0000.000
182A194THR 00.0490.02164.0710.0000.0000.0000.0000.0000.000
183A195LEU 00.0280.04158.870-0.001-0.0010.0000.0000.0000.000
184A196GLY 00.0480.01259.884-0.001-0.0010.0000.0000.0000.000
185A197LYS 10.8840.95259.7490.0220.0220.0000.0000.0000.000
186A198THR 0-0.033-0.04857.017-0.001-0.0010.0000.0000.0000.000
187A199LEU 0-0.0010.00255.034-0.002-0.0020.0000.0000.0000.000
188A200ASP -1-0.860-0.92254.866-0.025-0.0250.0000.0000.0000.000
189A201ASP -1-0.881-0.94954.793-0.026-0.0260.0000.0000.0000.000
190A202GLN 0-0.037-0.02649.1020.0000.0000.0000.0000.0000.000
191A203GLU -1-0.849-0.92650.449-0.029-0.0290.0000.0000.0000.000
192A204ARG 10.9340.97649.9350.0250.0250.0000.0000.0000.000
193A205LYS 10.8790.93548.5330.0310.0310.0000.0000.0000.000
194A206ILE 0-0.0140.00045.043-0.002-0.0020.0000.0000.0000.000
195A207ALA 00.0460.02844.939-0.002-0.0020.0000.0000.0000.000
196A208ASN 0-0.096-0.06245.2510.0010.0010.0000.0000.0000.000
197A209ASP -1-0.916-0.95744.347-0.039-0.0390.0000.0000.0000.000
198A210ASP -1-0.858-0.94939.940-0.048-0.0480.0000.0000.0000.000
199A211LYS 10.8720.93839.6500.0440.0440.0000.0000.0000.000
200A212TYR 00.000-0.02139.843-0.002-0.0020.0000.0000.0000.000
201A213LYS 10.8630.96937.4540.0450.0450.0000.0000.0000.000
202A214TRP 0-0.0310.00030.980-0.004-0.0040.0000.0000.0000.000
203A215LEU 00.0150.01834.9630.0030.0030.0000.0000.0000.000
204A216PRO 0-0.029-0.01134.206-0.006-0.0060.0000.0000.0000.000
205A217VAL 0-0.004-0.01230.8770.0030.0030.0000.0000.0000.000
206A218GLY 00.0250.01332.533-0.005-0.0050.0000.0000.0000.000
207A219LYS 10.8910.96026.9270.1170.1170.0000.0000.0000.000
208A220VAL 00.0140.00930.408-0.006-0.0060.0000.0000.0000.000
209A221GLY 00.0390.01129.2250.0050.0050.0000.0000.0000.000
210A222VAL 0-0.062-0.02827.771-0.004-0.0040.0000.0000.0000.000
211A223ASN 0-0.015-0.01422.4640.0010.0010.0000.0000.0000.000
212A224PHE 0-0.004-0.01423.6710.0070.0070.0000.0000.0000.000
213A225TYR 0-0.072-0.04418.922-0.010-0.0100.0000.0000.0000.000
214A226TRP -1-0.918-0.95419.390-0.091-0.0910.0000.0000.0000.000