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: QN8ZY

Calculation Name: 1RP3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RP3

Chain ID: A

ChEMBL ID:

UniProt ID: O67268

Base Structure: X-ray

Registration Date: 2023-09-26

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2955121.557181
FMO2-HF: Nuclear repulsion 2861197.734613
FMO2-HF: Total energy -93923.822568
FMO2-MP2: Total energy -94204.426752


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-2.845-0.3841.222-1.51-2.173-0.001
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.000
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].
3A2LYS10.9130.9283.159-2.3800.0811.222-1.510-2.173-0.001
4A3ASN00.0170.0105.6131.3441.3440.0000.0000.0000.000
5A4PRO00.0450.0087.8660.0540.0540.0000.0000.0000.000
6A5TYR00.0490.03411.5950.0590.0590.0000.0000.0000.000
7A6SER00.0130.0008.458-0.106-0.1060.0000.0000.0000.000
8A7ASN0-0.014-0.0219.128-0.127-0.1270.0000.0000.0000.000
9A8GLN0-0.066-0.03111.4250.1170.1170.0000.0000.0000.000
10A9ILE00.0360.01613.5500.0960.0960.0000.0000.0000.000
11A10GLU-1-0.859-0.9129.355-1.995-1.9950.0000.0000.0000.000
12A11ARG10.7990.86313.4100.5580.5580.0000.0000.0000.000
13A12GLU-1-0.882-0.94216.128-0.546-0.5460.0000.0000.0000.000
14A13GLU-1-0.872-0.94216.477-0.650-0.6500.0000.0000.0000.000
15A14LEU0-0.054-0.01815.4400.0870.0870.0000.0000.0000.000
16A15ILE0-0.013-0.01818.5650.0850.0850.0000.0000.0000.000
17A16LEU0-0.0040.00121.4120.0620.0620.0000.0000.0000.000
18A17LYS10.9080.94919.9540.4880.4880.0000.0000.0000.000
19A18TYR0-0.050-0.06720.1480.0270.0270.0000.0000.0000.000
20A19LEU00.0570.03324.9240.0410.0410.0000.0000.0000.000
21A20PRO0-0.002-0.00326.8170.0320.0320.0000.0000.0000.000
22A21LEU0-0.0120.00325.7500.0240.0240.0000.0000.0000.000
23A22VAL00.0150.01627.7090.0240.0240.0000.0000.0000.000
24A23LYS10.9580.99030.2880.1940.1940.0000.0000.0000.000
25A24ALA00.0010.01132.0910.0160.0160.0000.0000.0000.000
26A25ILE00.000-0.00329.5290.0160.0160.0000.0000.0000.000
27A26ALA00.0200.01233.7260.0130.0130.0000.0000.0000.000
28A27THR0-0.051-0.05536.0000.0080.0080.0000.0000.0000.000
29A28ASN0-0.064-0.05536.4680.0120.0120.0000.0000.0000.000
30A29ILE00.0200.01135.2860.0080.0080.0000.0000.0000.000
31A30LYS10.8010.87039.2650.0960.0960.0000.0000.0000.000
32A31LYS10.7540.89440.7370.1010.1010.0000.0000.0000.000
33A32HIS0-0.037-0.01041.4750.0110.0110.0000.0000.0000.000
34A33LEU0-0.0130.01440.9820.0050.0050.0000.0000.0000.000
35A34PRO00.0100.00945.061-0.001-0.0010.0000.0000.0000.000
36A35GLU-1-0.897-0.94246.674-0.079-0.0790.0000.0000.0000.000
37A36ASP-1-0.887-0.94547.237-0.069-0.0690.0000.0000.0000.000
38A37VAL00.0040.01342.090-0.004-0.0040.0000.0000.0000.000
39A38ASP-1-0.724-0.83242.045-0.123-0.1230.0000.0000.0000.000
40A39ILE00.0200.00338.059-0.001-0.0010.0000.0000.0000.000
41A40ARG10.8680.89837.6360.1190.1190.0000.0000.0000.000
42A41ASP-1-0.815-0.85336.703-0.111-0.1110.0000.0000.0000.000
43A42LEU0-0.022-0.01035.947-0.003-0.0030.0000.0000.0000.000
44A43ILE00.000-0.01132.601-0.006-0.0060.0000.0000.0000.000
45A44SER0-0.008-0.01132.004-0.016-0.0160.0000.0000.0000.000
46A45TYR0-0.005-0.01331.477-0.006-0.0060.0000.0000.0000.000
47A46GLY00.0230.01130.2660.0030.0030.0000.0000.0000.000
48A47VAL0-0.010-0.00627.195-0.012-0.0120.0000.0000.0000.000
49A48ILE0-0.013-0.00726.512-0.012-0.0120.0000.0000.0000.000
50A49GLY00.003-0.00326.3290.0060.0060.0000.0000.0000.000
51A50LEU0-0.019-0.01522.4970.0070.0070.0000.0000.0000.000
52A51ILE0-0.009-0.00422.106-0.015-0.0150.0000.0000.0000.000
53A52LYS10.9450.97021.0240.0860.0860.0000.0000.0000.000
54A53ALA0-0.0210.00821.2930.0280.0280.0000.0000.0000.000
55A54VAL00.005-0.00516.6860.0090.0090.0000.0000.0000.000
56A55ASP-1-0.792-0.85216.402-0.323-0.3230.0000.0000.0000.000
57A56ASN0-0.056-0.02217.3570.0720.0720.0000.0000.0000.000
58A57LEU00.0130.02814.4470.0550.0550.0000.0000.0000.000
59A58SER00.006-0.01111.3910.0230.0230.0000.0000.0000.000
60A59THR00.0130.01012.0110.0690.0690.0000.0000.0000.000
61A60GLU-1-0.851-0.9068.675-0.887-0.8870.0000.0000.0000.000
62A61ASN0-0.086-0.05912.5410.0670.0670.0000.0000.0000.000
63A62PRO00.0630.01415.0770.0360.0360.0000.0000.0000.000
64A63LYS10.8600.93717.7650.0570.0570.0000.0000.0000.000
65A64ARG10.7870.87118.450-0.047-0.0470.0000.0000.0000.000
66A65ALA00.0140.02416.6020.0170.0170.0000.0000.0000.000
67A66GLU-1-0.800-0.85118.656-0.244-0.2440.0000.0000.0000.000
68A67ALA0-0.026-0.01821.8520.0110.0110.0000.0000.0000.000
69A68TYR00.0700.04320.3500.0020.0020.0000.0000.0000.000
70A69ILE00.0080.00219.3970.0090.0090.0000.0000.0000.000
71A70LYS10.8540.90222.9770.1830.1830.0000.0000.0000.000
72A71LEU0-0.0130.00625.8180.0050.0050.0000.0000.0000.000
73A72ARG10.8520.90822.0300.0610.0610.0000.0000.0000.000
74A73ILE0-0.034-0.00625.7410.0020.0020.0000.0000.0000.000
75A74LYS10.9680.97528.3270.0930.0930.0000.0000.0000.000
76A75GLY00.0270.02430.0710.0060.0060.0000.0000.0000.000
77A76ALA00.0530.02929.5800.0070.0070.0000.0000.0000.000
78A77ILE0-0.034-0.01131.5730.0020.0020.0000.0000.0000.000
79A78TYR0-0.002-0.01834.3160.0010.0010.0000.0000.0000.000
80A79ASP-1-0.831-0.89732.894-0.025-0.0250.0000.0000.0000.000
81A80TYR0-0.064-0.04735.7050.0060.0060.0000.0000.0000.000
82A81LEU0-0.0120.00237.4970.0050.0050.0000.0000.0000.000
83A82ARG10.7330.83936.6560.0260.0260.0000.0000.0000.000
84A83SER0-0.086-0.04539.6700.0050.0050.0000.0000.0000.000
85A84LEU00.0080.01541.5610.0010.0010.0000.0000.0000.000
86A85ASP-1-0.823-0.90044.535-0.037-0.0370.0000.0000.0000.000
87A86PHE00.0310.02044.0380.0020.0020.0000.0000.0000.000
88A87GLY00.0360.03946.7970.0020.0020.0000.0000.0000.000
89A88SER0-0.040-0.01947.9260.0040.0040.0000.0000.0000.000
90A89ARG10.8740.89451.1090.0090.0090.0000.0000.0000.000
91A90GLN00.0760.04154.5110.0010.0010.0000.0000.0000.000
92A91VAL00.0410.03450.980-0.001-0.0010.0000.0000.0000.000
93A92ARG10.9140.94249.2330.0180.0180.0000.0000.0000.000
94A93GLU-1-0.817-0.85955.135-0.010-0.0100.0000.0000.0000.000
95A94LYS10.8020.86256.2210.0370.0370.0000.0000.0000.000
96A95GLU-1-0.742-0.82853.937-0.020-0.0200.0000.0000.0000.000
97A96ARG10.8380.92157.4560.0100.0100.0000.0000.0000.000
98A97ARG10.9280.95860.0540.0210.0210.0000.0000.0000.000
99A98ILE00.0210.01357.8690.0000.0000.0000.0000.0000.000
100A99LYS10.8820.94055.7100.0170.0170.0000.0000.0000.000
101A100GLU-1-0.864-0.94061.823-0.013-0.0130.0000.0000.0000.000
102A101VAL0-0.019-0.00464.7800.0000.0000.0000.0000.0000.000
103A102VAL0-0.019-0.01761.3880.0000.0000.0000.0000.0000.000
104A103GLU-1-0.791-0.91462.799-0.020-0.0200.0000.0000.0000.000
105A104LYS10.9150.95366.5810.0200.0200.0000.0000.0000.000
106A105LEU0-0.056-0.04567.3020.0000.0000.0000.0000.0000.000
107A106LYS10.7910.88864.1980.0220.0220.0000.0000.0000.000
108A107GLU-1-0.959-0.97069.394-0.013-0.0130.0000.0000.0000.000
109A108LYS10.8040.90372.6390.0230.0230.0000.0000.0000.000
110A109LEU0-0.050-0.02670.0800.0000.0000.0000.0000.0000.000
111A110GLY00.0130.02373.219-0.001-0.0010.0000.0000.0000.000
112A111ARG10.7520.84368.6910.0280.0280.0000.0000.0000.000
113A112GLU-1-0.776-0.87763.048-0.025-0.0250.0000.0000.0000.000
114A113PRO00.0100.01864.668-0.001-0.0010.0000.0000.0000.000
115A114THR0-0.010-0.03464.116-0.001-0.0010.0000.0000.0000.000
116A115ASP-1-0.677-0.82159.870-0.039-0.0390.0000.0000.0000.000
117A116GLU-1-0.802-0.89062.561-0.041-0.0410.0000.0000.0000.000
118A117GLU-1-0.847-0.87865.353-0.029-0.0290.0000.0000.0000.000
119A118VAL00.0420.01261.9210.0010.0010.0000.0000.0000.000
120A119ALA0-0.001-0.00862.5450.0010.0010.0000.0000.0000.000
121A120LYS10.8600.92864.2090.0330.0330.0000.0000.0000.000
122A121GLU-1-0.821-0.90167.998-0.021-0.0210.0000.0000.0000.000
123A122LEU0-0.057-0.01761.9540.0010.0010.0000.0000.0000.000
124A123GLY0-0.0170.01065.7430.0000.0000.0000.0000.0000.000
125A124ILE0-0.050-0.01860.627-0.001-0.0010.0000.0000.0000.000
126A125SER00.0360.01360.7550.0000.0000.0000.0000.0000.000
127A126THR00.0500.00660.4300.0010.0010.0000.0000.0000.000
128A127GLU-1-0.835-0.89255.086-0.060-0.0600.0000.0000.0000.000
129A128GLU-1-0.811-0.88756.266-0.043-0.0430.0000.0000.0000.000
130A129LEU0-0.0170.00556.9340.0010.0010.0000.0000.0000.000
131A130PHE0-0.010-0.02154.4030.0010.0010.0000.0000.0000.000
132A131LYS10.8670.90951.9110.0640.0640.0000.0000.0000.000
133A132THR0-0.016-0.01552.0190.0010.0010.0000.0000.0000.000
134A133LEU0-0.014-0.00753.1600.0020.0020.0000.0000.0000.000
135A134ASP-1-0.762-0.85748.728-0.056-0.0560.0000.0000.0000.000
136A135LYS10.8070.88748.5500.0460.0460.0000.0000.0000.000
137A136ILE0-0.0030.00748.7410.0020.0020.0000.0000.0000.000
138A137ASN0-0.048-0.04348.1950.0040.0040.0000.0000.0000.000
139A138PHE00.0430.01140.0780.0010.0010.0000.0000.0000.000
140A139SER0-0.020-0.02944.5350.0010.0010.0000.0000.0000.000
141A140TYR0-0.056-0.05145.6680.0040.0040.0000.0000.0000.000
142A141ILE0-0.0090.00140.9580.0020.0020.0000.0000.0000.000
143A142LEU0-0.020-0.00339.6790.0010.0010.0000.0000.0000.000
144A143SER00.000-0.01240.8420.0040.0040.0000.0000.0000.000
145A144LEU0-0.0230.00140.9050.0050.0050.0000.0000.0000.000
146A145GLU-1-0.781-0.87534.682-0.030-0.0300.0000.0000.0000.000
147A146GLU-1-0.818-0.90236.689-0.008-0.0080.0000.0000.0000.000
148A147VAL00.0510.03137.1400.0040.0040.0000.0000.0000.000
149A148PHE0-0.033-0.03035.3760.0040.0040.0000.0000.0000.000
150A149ARG10.7180.82832.2920.0270.0270.0000.0000.0000.000
151A150ASP-1-0.819-0.89032.5240.0370.0370.0000.0000.0000.000
152A151PHE00.018-0.00232.9870.0080.0080.0000.0000.0000.000
153A152ALA0-0.003-0.01029.6520.0070.0070.0000.0000.0000.000
154A153ARG10.7920.89828.305-0.042-0.0420.0000.0000.0000.000
155A154ASP-1-0.858-0.92227.8120.0870.0870.0000.0000.0000.000
156A155TYR0-0.032-0.01426.8100.0070.0070.0000.0000.0000.000
157A156SER0-0.118-0.08024.2420.0070.0070.0000.0000.0000.000
158A157GLU-1-0.894-0.94222.7770.1440.1440.0000.0000.0000.000
159A158LEU0-0.009-0.00422.5080.0280.0280.0000.0000.0000.000
160A159ILE0-0.044-0.02321.2820.0090.0090.0000.0000.0000.000
161A160PRO0-0.041-0.01917.662-0.010-0.0100.0000.0000.0000.000
162A161SER0-0.0190.00117.5310.0300.0300.0000.0000.0000.000
163A162SER00.0000.01719.4960.0070.0070.0000.0000.0000.000
164A163THR00.000-0.04720.572-0.026-0.0260.0000.0000.0000.000
165A164ASN00.002-0.03020.829-0.029-0.0290.0000.0000.0000.000
166A165VAL00.0030.00824.049-0.015-0.0150.0000.0000.0000.000
167A166GLU-1-0.770-0.85024.4390.1660.1660.0000.0000.0000.000
168A167GLU-1-0.751-0.84823.186-0.024-0.0240.0000.0000.0000.000
169A168GLU-1-0.760-0.84526.414-0.018-0.0180.0000.0000.0000.000
170A169VAL0-0.026-0.01829.530-0.007-0.0070.0000.0000.0000.000
171A170ILE00.0190.00626.776-0.004-0.0040.0000.0000.0000.000
172A171LYS10.8320.90529.8560.0080.0080.0000.0000.0000.000
173A172ARG10.8470.89931.524-0.018-0.0180.0000.0000.0000.000
174A173GLU-1-0.819-0.88433.6890.0390.0390.0000.0000.0000.000
175A174LEU00.0440.04033.079-0.003-0.0030.0000.0000.0000.000
176A175THR0-0.049-0.06034.976-0.004-0.0040.0000.0000.0000.000
177A176GLU-1-0.826-0.88737.482-0.001-0.0010.0000.0000.0000.000
178A177LYS10.8390.92536.440-0.039-0.0390.0000.0000.0000.000
179A178VAL00.0150.00338.323-0.002-0.0020.0000.0000.0000.000
180A179LYS10.7990.88440.5630.0010.0010.0000.0000.0000.000
181A180GLU-1-0.800-0.88643.4170.0120.0120.0000.0000.0000.000
182A181ALA00.0070.01944.145-0.001-0.0010.0000.0000.0000.000
183A182VAL0-0.008-0.01844.124-0.002-0.0020.0000.0000.0000.000
184A183SER0-0.086-0.05446.833-0.001-0.0010.0000.0000.0000.000
185A184LYS10.8350.90549.427-0.011-0.0110.0000.0000.0000.000
186A185LEU0-0.0190.00547.8940.0000.0000.0000.0000.0000.000
187A186PRO00.0150.00151.9850.0000.0000.0000.0000.0000.000
188A187GLU-1-0.777-0.87954.201-0.017-0.0170.0000.0000.0000.000
189A188ARG10.9250.96754.4100.0280.0280.0000.0000.0000.000
190A189GLU-1-0.727-0.84052.389-0.018-0.0180.0000.0000.0000.000
191A190LYS10.8020.89849.5540.0110.0110.0000.0000.0000.000
192A191LEU00.0280.02149.585-0.003-0.0030.0000.0000.0000.000
193A192VAL0-0.006-0.00450.453-0.004-0.0040.0000.0000.0000.000
194A193ILE00.001-0.00645.255-0.004-0.0040.0000.0000.0000.000
195A194GLN0-0.036-0.02245.9860.0000.0000.0000.0000.0000.000
196A195LEU00.027-0.00346.058-0.005-0.0050.0000.0000.0000.000
197A196ILE0-0.012-0.00545.424-0.004-0.0040.0000.0000.0000.000
198A197PHE0-0.051-0.04541.532-0.004-0.0040.0000.0000.0000.000
199A198TYR0-0.066-0.01441.119-0.001-0.0010.0000.0000.0000.000
200A199GLU-1-0.836-0.91842.404-0.067-0.0670.0000.0000.0000.000
201A200GLU-1-0.921-0.91638.504-0.105-0.1050.0000.0000.0000.000
202A201LEU00.0560.02843.410-0.006-0.0060.0000.0000.0000.000
203A202PRO00.0430.00546.0690.0040.0040.0000.0000.0000.000
204A203ALA00.0290.00447.8700.0020.0020.0000.0000.0000.000
205A204LYS10.8460.90550.4230.0630.0630.0000.0000.0000.000
206A205GLU-1-0.804-0.87950.178-0.068-0.0680.0000.0000.0000.000
207A206VAL00.0160.00749.8830.0020.0020.0000.0000.0000.000
208A207ALA0-0.030-0.01852.8130.0030.0030.0000.0000.0000.000
209A208LYS10.8200.88854.3030.0680.0680.0000.0000.0000.000
210A209ILE0-0.0110.00352.1420.0010.0010.0000.0000.0000.000
211A210LEU0-0.095-0.04154.2630.0030.0030.0000.0000.0000.000
212A211GLU-1-0.931-0.95957.884-0.037-0.0370.0000.0000.0000.000
213A212THR0-0.047-0.02358.5570.0030.0030.0000.0000.0000.000
214A213SER00.0100.00859.824-0.002-0.0020.0000.0000.0000.000
215A214VAL00.008-0.02254.4650.0000.0000.0000.0000.0000.000
216A215SER0-0.025-0.03955.9470.0010.0010.0000.0000.0000.000
217A216ARG10.8460.93357.5540.0260.0260.0000.0000.0000.000
218A217VAL00.0360.01252.5410.0020.0020.0000.0000.0000.000
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