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: 729KK

Calculation Name: 4RNS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RNS

Chain ID: A

ChEMBL ID:

UniProt ID: P52679

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2527542.129738
FMO2-HF: Nuclear repulsion 2443387.488522
FMO2-HF: Total energy -84154.641216
FMO2-MP2: Total energy -84404.267108


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:89:ARG)


Summations of interaction energy for fragment #1(A:89:ARG)
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.
-76.949-72.51515.893-9.377-10.951-0.093
Interaction energy analysis for fragmet #1(A:89:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.873 / q_NPA : 0.912
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].
3A91ASP-1-0.770-0.8633.799-24.325-20.837-0.044-1.819-1.625-0.005
4A92PRO0-0.033-0.0096.4230.3860.3860.0000.0000.0000.000
5A93GLY00.0530.03410.0720.6010.6010.0000.0000.0000.000
6A94THR0-0.073-0.0648.4170.4520.4520.0000.0000.0000.000
7A95SER0-0.063-0.0117.452-0.709-0.7090.0000.0000.0000.000
8A96ASN00.0370.0109.508-0.175-0.1750.0000.0000.0000.000
9A97ARG10.7730.8793.76047.20947.365-0.001-0.016-0.1390.000
10A98ASN0-0.001-0.0109.7172.6702.6700.0000.0000.0000.000
11A99PHE0-0.015-0.0087.829-1.867-1.8670.0000.0000.0000.000
12A100ARG10.8600.91811.58322.40122.4010.0000.0000.0000.000
13A101ILE00.0210.00213.376-0.802-0.8020.0000.0000.0000.000
14A102ALA00.0040.02416.0030.9610.9610.0000.0000.0000.000
15A103ALA00.031-0.00318.617-0.024-0.0240.0000.0000.0000.000
16A104SER00.0510.03421.9100.0190.0190.0000.0000.0000.000
17A105ASP-1-0.690-0.84724.941-10.729-10.7290.0000.0000.0000.000
18A106PHE0-0.001-0.01126.806-0.138-0.1380.0000.0000.0000.000
19A107GLY00.0220.01024.393-0.076-0.0760.0000.0000.0000.000
20A108GLN0-0.030-0.03821.541-0.483-0.4830.0000.0000.0000.000
21A109ALA00.0170.00923.403-0.251-0.2510.0000.0000.0000.000
22A110LEU0-0.062-0.02225.7220.1740.1740.0000.0000.0000.000
23A111MET0-0.021-0.00519.193-0.144-0.1440.0000.0000.0000.000
24A112LEU00.0360.00719.433-0.218-0.2180.0000.0000.0000.000
25A113PRO00.0280.02121.642-0.256-0.2560.0000.0000.0000.000
26A114ARG10.8240.91922.85811.64911.6490.0000.0000.0000.000
27A115LEU0-0.026-0.02616.903-0.407-0.4070.0000.0000.0000.000
28A116TYR0-0.078-0.05219.668-0.334-0.3340.0000.0000.0000.000
29A117ALA00.0690.03321.295-0.204-0.2040.0000.0000.0000.000
30A118THR00.020-0.00216.3230.1180.1180.0000.0000.0000.000
31A119LEU0-0.0240.00415.442-0.852-0.8520.0000.0000.0000.000
32A120GLU-1-0.834-0.88317.965-14.074-14.0740.0000.0000.0000.000
33A121GLU-1-1.000-1.00019.781-12.718-12.7180.0000.0000.0000.000
34A122THR0-0.124-0.08314.971-0.435-0.4350.0000.0000.0000.000
35A123ALA0-0.057-0.03113.128-1.238-1.2380.0000.0000.0000.000
36A124PRO00.1100.06114.518-0.538-0.5380.0000.0000.0000.000
37A125GLN0-0.055-0.02214.1240.8270.8270.0000.0000.0000.000
38A126VAL0-0.070-0.01811.186-1.218-1.2180.0000.0000.0000.000
39A127ARG10.9370.97413.57619.36719.3670.0000.0000.0000.000
40A128VAL00.0330.01513.889-1.543-1.5430.0000.0000.0000.000
41A129THR0-0.030-0.02015.5471.2311.2310.0000.0000.0000.000
42A130GLY00.0060.01216.965-0.655-0.6550.0000.0000.0000.000
43A131VAL0-0.039-0.02616.9180.4310.4310.0000.0000.0000.000
44A132ASN00.0510.01919.990-0.171-0.1710.0000.0000.0000.000
45A133LEU00.0170.02822.063-0.609-0.6090.0000.0000.0000.000
46A134ARG10.8880.93122.00913.65913.6590.0000.0000.0000.000
47A135HIS00.0890.04024.719-0.031-0.0310.0000.0000.0000.000
48A136GLY0-0.0230.00923.8500.1290.1290.0000.0000.0000.000
49A137PRO00.0550.02421.966-0.071-0.0710.0000.0000.0000.000
50A138LEU00.0410.02218.326-0.727-0.7270.0000.0000.0000.000
51A139VAL00.023-0.00717.833-1.024-1.0240.0000.0000.0000.000
52A140GLU-1-0.882-0.94616.558-15.327-15.3270.0000.0000.0000.000
53A141GLU-1-0.863-0.90015.721-18.489-18.4890.0000.0000.0000.000
54A142LEU0-0.063-0.03213.060-1.507-1.5070.0000.0000.0000.000
55A143GLU-1-0.877-0.92111.669-24.449-24.4490.0000.0000.0000.000
56A144SER0-0.008-0.02811.678-2.112-2.1120.0000.0000.0000.000
57A145GLY0-0.056-0.0249.252-1.789-1.7890.0000.0000.0000.000
58A146SER0-0.069-0.02810.039-1.113-1.1130.0000.0000.0000.000
59A147ILE0-0.014-0.01312.5401.2501.2500.0000.0000.0000.000
60A148ASP-1-0.811-0.8788.112-33.559-33.5590.0000.0000.0000.000
61A149ILE0-0.022-0.01810.721-0.363-0.3630.0000.0000.0000.000
62A150ALA00.0180.03113.7580.6420.6420.0000.0000.0000.000
63A151PHE0-0.024-0.02417.437-0.049-0.0490.0000.0000.0000.000
64A152GLY00.0150.00420.0910.5030.5030.0000.0000.0000.000
65A153GLY00.0600.02323.639-0.180-0.1800.0000.0000.0000.000
66A154PHE00.0110.00821.2820.2160.2160.0000.0000.0000.000
67A155PRO00.0010.00924.224-0.376-0.3760.0000.0000.0000.000
68A156THR00.0110.00624.335-0.049-0.0490.0000.0000.0000.000
69A157LEU0-0.058-0.01519.089-0.393-0.3930.0000.0000.0000.000
70A158SER0-0.014-0.01722.0040.2010.2010.0000.0000.0000.000
71A159ALA00.0420.02020.897-0.478-0.4780.0000.0000.0000.000
72A160GLY00.0320.02417.679-0.307-0.3070.0000.0000.0000.000
73A161ILE0-0.068-0.03015.886-1.508-1.5080.0000.0000.0000.000
74A162LYS10.8750.94214.16620.46520.4650.0000.0000.0000.000
75A163THR0-0.006-0.01616.827-0.055-0.0550.0000.0000.0000.000
76A164GLN00.0330.01418.149-0.621-0.6210.0000.0000.0000.000
77A165THR0-0.006-0.01120.279-0.220-0.2200.0000.0000.0000.000
78A166LEU0-0.047-0.01719.896-0.062-0.0620.0000.0000.0000.000
79A167PHE0-0.028-0.01624.0230.3300.3300.0000.0000.0000.000
80A168ARG10.8790.92927.6889.5319.5310.0000.0000.0000.000
81A169GLU-1-0.809-0.88930.426-9.642-9.6420.0000.0000.0000.000
82A170GLU-1-0.753-0.84132.265-8.746-8.7460.0000.0000.0000.000
83A171TYR0-0.017-0.04233.391-0.154-0.1540.0000.0000.0000.000
84A172VAL0-0.046-0.02337.5430.1820.1820.0000.0000.0000.000
85A173CYS0-0.0270.00140.379-0.106-0.1060.0000.0000.0000.000
86A174VAL00.0030.00440.7390.0160.0160.0000.0000.0000.000
87A175MET00.0010.01143.6140.0140.0140.0000.0000.0000.000
88A176ARG10.8810.91846.3486.4006.4000.0000.0000.0000.000
89A177GLN0-0.071-0.04647.4530.2450.2450.0000.0000.0000.000
90A178SER0-0.012-0.00550.0040.1010.1010.0000.0000.0000.000
91A179HIS00.0740.05449.4790.0990.0990.0000.0000.0000.000
92A180PRO00.009-0.00852.6140.0500.0500.0000.0000.0000.000
93A181ALA0-0.010-0.02252.7800.0830.0830.0000.0000.0000.000
94A182LEU0-0.0400.00950.587-0.026-0.0260.0000.0000.0000.000
95A183THR0-0.059-0.02653.5550.0190.0190.0000.0000.0000.000
96A184HIS0-0.043-0.01156.1550.1300.1300.0000.0000.0000.000
97A185GLY00.0370.02654.852-0.082-0.0820.0000.0000.0000.000
98A186LEU0-0.046-0.04750.0020.0090.0090.0000.0000.0000.000
99A187ASP-1-0.847-0.91252.302-5.789-5.7890.0000.0000.0000.000
100A188LEU00.037-0.00349.545-0.042-0.0420.0000.0000.0000.000
101A189GLU-1-0.765-0.85352.254-5.887-5.8870.0000.0000.0000.000
102A190ALA00.0090.01554.8860.0090.0090.0000.0000.0000.000
103A191PHE00.030-0.00245.050-0.069-0.0690.0000.0000.0000.000
104A192ARG10.7980.87250.4385.9335.9330.0000.0000.0000.000
105A193GLN0-0.024-0.00351.477-0.030-0.0300.0000.0000.0000.000
106A194CYS0-0.077-0.02050.4240.0490.0490.0000.0000.0000.000
107A195ARG10.8740.93548.9646.0326.0320.0000.0000.0000.000
108A196HIS10.8650.94144.5246.7056.7050.0000.0000.0000.000
109A197ILE00.0030.01239.7150.0400.0400.0000.0000.0000.000
110A198ILE00.0140.00538.746-0.049-0.0490.0000.0000.0000.000
111A199VAL0-0.020-0.01433.201-0.037-0.0370.0000.0000.0000.000
112A200THR0-0.048-0.04034.2070.1020.1020.0000.0000.0000.000
113A201ALA0-0.026-0.04530.369-0.281-0.2810.0000.0000.0000.000
114A202HIS00.016-0.01230.605-0.324-0.3240.0000.0000.0000.000
115A203GLU-1-0.852-0.90030.740-9.683-9.6830.0000.0000.0000.000
116A204PHE0-0.091-0.03826.391-0.432-0.4320.0000.0000.0000.000
117A205ASN0-0.051-0.02026.141-0.647-0.6470.0000.0000.0000.000
118A206HIS00.0400.02125.336-0.132-0.1320.0000.0000.0000.000
119A207VAL00.040-0.00927.7330.3370.3370.0000.0000.0000.000
120A208HIS0-0.0250.01229.7530.1930.1930.0000.0000.0000.000
121A209GLU-1-0.867-0.93230.416-9.840-9.8400.0000.0000.0000.000
122A210GLN0-0.021-0.01332.4890.4380.4380.0000.0000.0000.000
123A211VAL0-0.010-0.00735.3740.2890.2890.0000.0000.0000.000
124A212GLU-1-0.797-0.88535.300-8.519-8.5190.0000.0000.0000.000
125A213ALA00.013-0.00437.6600.2420.2420.0000.0000.0000.000
126A214ARG10.8700.92839.5737.6537.6530.0000.0000.0000.000
127A215LEU0-0.034-0.02139.8690.2240.2240.0000.0000.0000.000
128A216LEU0-0.012-0.00940.0820.2020.2020.0000.0000.0000.000
129A217GLU-1-0.974-0.96543.743-6.911-6.9110.0000.0000.0000.000
130A218LEU0-0.042-0.01645.6270.1820.1820.0000.0000.0000.000
131A219LEU0-0.052-0.03544.9120.1890.1890.0000.0000.0000.000
132A220PRO00.0140.02248.344-0.025-0.0250.0000.0000.0000.000
133A221PRO00.0830.04648.485-0.077-0.0770.0000.0000.0000.000
134A222GLU-1-0.896-0.95249.087-6.039-6.0390.0000.0000.0000.000
135A223SER0-0.075-0.05549.6660.0590.0590.0000.0000.0000.000
136A224ILE0-0.023-0.00643.770-0.091-0.0910.0000.0000.0000.000
137A225ARG10.9080.97446.2586.3466.3460.0000.0000.0000.000
138A226PHE00.000-0.01242.2690.0040.0040.0000.0000.0000.000
139A227THR00.0290.00538.317-0.008-0.0080.0000.0000.0000.000
140A228THR0-0.038-0.02135.768-0.085-0.0850.0000.0000.0000.000
141A229GLU-1-0.846-0.91431.108-9.861-9.8610.0000.0000.0000.000
142A230ASN0-0.094-0.03529.983-0.568-0.5680.0000.0000.0000.000
143A231PHE00.0480.00629.8410.3010.3010.0000.0000.0000.000
144A232LEU00.000-0.00229.3840.3170.3170.0000.0000.0000.000
145A233VAL0-0.005-0.00133.4680.2360.2360.0000.0000.0000.000
146A234SER0-0.007-0.03035.7500.2840.2840.0000.0000.0000.000
147A235ALA00.006-0.00236.4830.2350.2350.0000.0000.0000.000
148A236VAL00.0170.01237.0090.1930.1930.0000.0000.0000.000
149A237ILE00.0220.00639.5320.2120.2120.0000.0000.0000.000
150A238ALA0-0.027-0.00541.4220.2150.2150.0000.0000.0000.000
151A239GLU-1-0.777-0.87140.913-7.587-7.5870.0000.0000.0000.000
152A240GLU-1-0.940-0.96043.692-6.850-6.8500.0000.0000.0000.000
153A241THR0-0.111-0.06845.6400.1820.1820.0000.0000.0000.000
154A242ASP-1-0.806-0.88647.398-6.273-6.2730.0000.0000.0000.000
155A243VAL0-0.084-0.03444.3710.0710.0710.0000.0000.0000.000
156A244ILE0-0.019-0.01744.785-0.056-0.0560.0000.0000.0000.000
157A245LEU0-0.0120.00737.957-0.058-0.0580.0000.0000.0000.000
158A246THR00.002-0.00639.2220.1170.1170.0000.0000.0000.000
159A247ILE0-0.011-0.00935.567-0.213-0.2130.0000.0000.0000.000
160A248PRO00.0200.01131.6280.1450.1450.0000.0000.0000.000
161A249SER00.003-0.00734.3980.0880.0880.0000.0000.0000.000
162A250ARG10.8140.88330.00910.28310.2830.0000.0000.0000.000
163A251LEU0-0.0120.00932.345-0.006-0.0060.0000.0000.0000.000
164A252ALA00.0520.01933.9640.1430.1430.0000.0000.0000.000
165A253ARG10.9060.94336.1817.9987.9980.0000.0000.0000.000
166A254TRP0-0.050-0.02032.5030.1570.1570.0000.0000.0000.000
167A255PHE00.0340.00434.511-0.001-0.0010.0000.0000.0000.000
168A256ALA00.0230.02038.5880.2020.2020.0000.0000.0000.000
169A257ASN0-0.057-0.01537.5720.3450.3450.0000.0000.0000.000
170A258ARG10.8220.88138.9217.9197.9190.0000.0000.0000.000
171A259GLY0-0.040-0.01742.5770.1260.1260.0000.0000.0000.000
172A260GLY00.0500.03944.0580.1690.1690.0000.0000.0000.000
173A261LEU0-0.029-0.01140.7210.1150.1150.0000.0000.0000.000
174A262THR0-0.017-0.01344.713-0.054-0.0540.0000.0000.0000.000
175A263ILE0-0.015-0.01540.477-0.072-0.0720.0000.0000.0000.000
176A264PHE0-0.016-0.00944.3090.1480.1480.0000.0000.0000.000
177A265PRO00.0340.00244.254-0.167-0.1670.0000.0000.0000.000
178A266VAL00.0200.00641.4660.1000.1000.0000.0000.0000.000
179A267PRO0-0.0160.00644.8200.0200.0200.0000.0000.0000.000
180A268ILE0-0.007-0.00643.4960.1130.1130.0000.0000.0000.000
181A269GLU-1-0.895-0.94042.896-7.348-7.3480.0000.0000.0000.000
182A270LEU0-0.024-0.01438.812-0.053-0.0530.0000.0000.0000.000
183A271PRO00.0220.01635.6980.0150.0150.0000.0000.0000.000
184A272SER0-0.027-0.02634.645-0.205-0.2050.0000.0000.0000.000
185A273ILE0-0.019-0.01729.247-0.210-0.2100.0000.0000.0000.000
186A274GLU-1-0.844-0.90927.456-10.857-10.8570.0000.0000.0000.000
187A275VAL0-0.0210.00424.176-0.285-0.2850.0000.0000.0000.000
188A276LYS10.8730.93021.67811.93811.9380.0000.0000.0000.000
189A277GLN0-0.016-0.00916.005-0.642-0.6420.0000.0000.0000.000
190A278TYR0-0.011-0.01817.0140.2190.2190.0000.0000.0000.000
191A279TRP0-0.023-0.03011.343-0.194-0.1940.0000.0000.0000.000
192A280HIS00.1430.06811.570-0.245-0.2450.0000.0000.0000.000
193A281GLU-1-0.888-0.95211.349-20.089-20.0890.0000.0000.0000.000
194A282ARG10.7970.9068.93525.86325.8630.0000.0000.0000.000
195A283TYR0-0.038-0.0245.359-6.324-6.3240.0000.0000.0000.000
196A284ASP-1-0.833-0.9007.747-24.640-24.6400.0000.0000.0000.000
197A285LYS10.9650.9706.61029.50129.5010.0000.0000.0000.000
198A286ASP-1-0.749-0.8571.778-111.877-111.87111.218-6.032-5.192-0.085
199A287PRO00.006-0.0072.0453.1603.7654.721-1.478-3.849-0.003
200A288GLY00.0410.0314.3526.6446.823-0.001-0.032-0.1460.000
201A289ASN0-0.018-0.0175.5368.0738.0730.0000.0000.0000.000
202A290ILE0-0.0210.0066.9114.3324.3320.0000.0000.0000.000
203A291TRP0-0.016-0.0118.4942.5882.5880.0000.0000.0000.000
204A292LEU00.0370.01810.1072.4922.4920.0000.0000.0000.000
205A293ARG10.8860.9409.29028.42928.4290.0000.0000.0000.000
206A294ARG10.9050.96213.08218.78118.7810.0000.0000.0000.000
207A295VAL00.0110.00014.0651.5181.5180.0000.0000.0000.000
208A296ILE00.0540.01715.1911.2791.2790.0000.0000.0000.000
209A297ALA0-0.048-0.02417.6300.9920.9920.0000.0000.0000.000
210A298LYS10.8640.93717.68916.11516.1150.0000.0000.0000.000
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