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: RY168

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2943662.492367
FMO2-HF: Nuclear repulsion 2849739.193329
FMO2-HF: Total energy -93923.299038
FMO2-MP2: Total energy -94203.960423


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.
-2.706-0.4161.048-1.432-1.907-0.001
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 : 0.002 / q_NPA : -0.009
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].
3A2LYS10.9260.9373.151-1.8530.4371.048-1.432-1.907-0.001
4A3ASN00.0180.0055.4481.4531.4530.0000.0000.0000.000
5A4PRO00.0520.0027.6070.0250.0250.0000.0000.0000.000
6A5TYR00.0320.02911.1180.0890.0890.0000.0000.0000.000
7A6SER00.0190.0018.137-0.117-0.1170.0000.0000.0000.000
8A7ASN0-0.006-0.0029.007-0.089-0.0890.0000.0000.0000.000
9A8GLN0-0.080-0.04111.0750.1120.1120.0000.0000.0000.000
10A9ILE00.0390.01613.0230.1180.1180.0000.0000.0000.000
11A10GLU-1-0.849-0.9098.959-2.291-2.2910.0000.0000.0000.000
12A11ARG10.8040.86513.0420.6720.6720.0000.0000.0000.000
13A12GLU-1-0.879-0.93715.779-0.619-0.6190.0000.0000.0000.000
14A13GLU-1-0.875-0.93715.874-0.730-0.7300.0000.0000.0000.000
15A14LEU0-0.040-0.01115.5570.1020.1020.0000.0000.0000.000
16A15ILE0-0.027-0.02818.1540.0900.0900.0000.0000.0000.000
17A16LEU0-0.004-0.00821.1150.0690.0690.0000.0000.0000.000
18A17LYS10.9170.96219.2790.5740.5740.0000.0000.0000.000
19A18TYR0-0.014-0.02020.1180.0330.0330.0000.0000.0000.000
20A19LEU00.0540.03524.3660.0450.0450.0000.0000.0000.000
21A20PRO0-0.019-0.01426.3930.0360.0360.0000.0000.0000.000
22A21LEU0-0.0140.00026.0010.0290.0290.0000.0000.0000.000
23A22VAL00.0240.01427.8570.0260.0260.0000.0000.0000.000
24A23LYS10.9550.99330.4820.2170.2170.0000.0000.0000.000
25A24ALA00.0090.00932.4090.0180.0180.0000.0000.0000.000
26A25ILE0-0.003-0.00229.6670.0180.0180.0000.0000.0000.000
27A26ALA00.0290.02133.9900.0140.0140.0000.0000.0000.000
28A27THR0-0.041-0.04836.2240.0100.0100.0000.0000.0000.000
29A28ASN0-0.042-0.04136.9130.0130.0130.0000.0000.0000.000
30A29ILE00.0040.00535.3570.0090.0090.0000.0000.0000.000
31A30LYS10.8440.90639.4380.1150.1150.0000.0000.0000.000
32A31LYS10.7980.93440.8960.1230.1230.0000.0000.0000.000
33A32HIS0-0.020-0.00241.8480.0120.0120.0000.0000.0000.000
34A33LEU0-0.0240.00341.1230.0040.0040.0000.0000.0000.000
35A34PRO00.0150.01345.4270.0000.0000.0000.0000.0000.000
36A35GLU-1-0.899-0.95447.099-0.092-0.0920.0000.0000.0000.000
37A36ASP-1-0.912-0.96647.761-0.086-0.0860.0000.0000.0000.000
38A37VAL00.0050.02442.394-0.004-0.0040.0000.0000.0000.000
39A38ASP-1-0.707-0.82941.859-0.142-0.1420.0000.0000.0000.000
40A39ILE00.013-0.00138.069-0.003-0.0030.0000.0000.0000.000
41A40ARG10.8840.90837.3970.1370.1370.0000.0000.0000.000
42A41ASP-1-0.821-0.86236.724-0.135-0.1350.0000.0000.0000.000
43A42LEU0-0.048-0.02636.417-0.005-0.0050.0000.0000.0000.000
44A43ILE00.003-0.01032.310-0.007-0.0070.0000.0000.0000.000
45A44SER0-0.013-0.01432.240-0.017-0.0170.0000.0000.0000.000
46A45TYR0-0.003-0.00731.847-0.011-0.0110.0000.0000.0000.000
47A46GLY00.013-0.00330.710-0.002-0.0020.0000.0000.0000.000
48A47VAL0-0.009-0.00626.952-0.016-0.0160.0000.0000.0000.000
49A48ILE0-0.0100.00226.733-0.018-0.0180.0000.0000.0000.000
50A49GLY0-0.003-0.01126.134-0.004-0.0040.0000.0000.0000.000
51A50LEU0-0.027-0.01122.8000.0030.0030.0000.0000.0000.000
52A51ILE00.009-0.00522.042-0.024-0.0240.0000.0000.0000.000
53A52LYS10.9370.97221.1200.1310.1310.0000.0000.0000.000
54A53ALA0-0.032-0.00920.8160.0140.0140.0000.0000.0000.000
55A54VAL0-0.010-0.01017.074-0.003-0.0030.0000.0000.0000.000
56A55ASP-1-0.775-0.84216.431-0.450-0.4500.0000.0000.0000.000
57A56ASN0-0.088-0.02716.0240.0360.0360.0000.0000.0000.000
58A57LEU00.0420.03314.9200.0540.0540.0000.0000.0000.000
59A58SER0-0.004-0.02511.6900.0270.0270.0000.0000.0000.000
60A59THR0-0.033-0.01211.7260.0300.0300.0000.0000.0000.000
61A60GLU-1-0.847-0.9139.055-1.080-1.0800.0000.0000.0000.000
62A61ASN0-0.044-0.03713.0130.0470.0470.0000.0000.0000.000
63A62PRO00.0700.02615.0920.0530.0530.0000.0000.0000.000
64A63LYS10.9210.97917.9920.1150.1150.0000.0000.0000.000
65A64ARG10.7500.84318.6620.0300.0300.0000.0000.0000.000
66A65ALA00.0120.02716.8860.0220.0220.0000.0000.0000.000
67A66GLU-1-0.814-0.89618.967-0.268-0.2680.0000.0000.0000.000
68A67ALA0-0.031-0.01822.2440.0150.0150.0000.0000.0000.000
69A68TYR00.0730.04220.5040.0090.0090.0000.0000.0000.000
70A69ILE00.005-0.00119.8320.0150.0150.0000.0000.0000.000
71A70LYS10.8430.89723.3320.2190.2190.0000.0000.0000.000
72A71LEU0-0.0080.00925.9230.0090.0090.0000.0000.0000.000
73A72ARG10.8940.93522.2880.1340.1340.0000.0000.0000.000
74A73ILE0-0.0180.01126.1520.0070.0070.0000.0000.0000.000
75A74LYS10.9680.97428.7330.1300.1300.0000.0000.0000.000
76A75GLY00.0210.02730.2730.0090.0090.0000.0000.0000.000
77A76ALA00.0480.01829.4870.0090.0090.0000.0000.0000.000
78A77ILE0-0.032-0.01331.4920.0040.0040.0000.0000.0000.000
79A78TYR0-0.017-0.02434.4660.0040.0040.0000.0000.0000.000
80A79ASP-1-0.869-0.90932.214-0.065-0.0650.0000.0000.0000.000
81A80TYR0-0.065-0.04335.6030.0080.0080.0000.0000.0000.000
82A81LEU0-0.002-0.00137.4710.0060.0060.0000.0000.0000.000
83A82ARG10.7480.84637.2180.0550.0550.0000.0000.0000.000
84A83SER0-0.106-0.04739.4770.0050.0050.0000.0000.0000.000
85A84LEU00.0080.00941.4380.0020.0020.0000.0000.0000.000
86A85ASP-1-0.833-0.90544.360-0.053-0.0530.0000.0000.0000.000
87A86PHE00.0420.01943.9800.0030.0030.0000.0000.0000.000
88A87GLY00.0140.02446.9780.0020.0020.0000.0000.0000.000
89A88SER0-0.028-0.00748.4090.0050.0050.0000.0000.0000.000
90A89ARG10.9020.91351.2250.0230.0230.0000.0000.0000.000
91A90GLN00.0680.02354.7460.0010.0010.0000.0000.0000.000
92A91VAL00.0410.03251.2690.0000.0000.0000.0000.0000.000
93A92ARG10.9160.94949.4230.0350.0350.0000.0000.0000.000
94A93GLU-1-0.830-0.87655.249-0.023-0.0230.0000.0000.0000.000
95A94LYS10.8560.90956.7910.0490.0490.0000.0000.0000.000
96A95GLU-1-0.749-0.82454.163-0.034-0.0340.0000.0000.0000.000
97A96ARG10.8450.92657.6980.0220.0220.0000.0000.0000.000
98A97ARG10.9310.95760.4390.0320.0320.0000.0000.0000.000
99A98ILE00.0170.01058.3130.0000.0000.0000.0000.0000.000
100A99LYS10.8900.94256.0570.0300.0300.0000.0000.0000.000
101A100GLU-1-0.891-0.94262.154-0.023-0.0230.0000.0000.0000.000
102A101VAL0-0.008-0.00365.0500.0010.0010.0000.0000.0000.000
103A102VAL0-0.033-0.02561.9720.0000.0000.0000.0000.0000.000
104A103GLU-1-0.820-0.94163.371-0.030-0.0300.0000.0000.0000.000
105A104LYS10.8680.93367.1880.0280.0280.0000.0000.0000.000
106A105LEU0-0.067-0.05267.8470.0000.0000.0000.0000.0000.000
107A106LYS10.8400.93064.0520.0320.0320.0000.0000.0000.000
108A107GLU-1-0.957-0.96669.594-0.021-0.0210.0000.0000.0000.000
109A108LYS10.8280.91972.8580.0300.0300.0000.0000.0000.000
110A109LEU0-0.061-0.03070.5930.0000.0000.0000.0000.0000.000
111A110GLY00.0020.02273.3390.0000.0000.0000.0000.0000.000
112A111ARG10.7710.85668.9940.0360.0360.0000.0000.0000.000
113A112GLU-1-0.847-0.93263.477-0.035-0.0350.0000.0000.0000.000
114A113PRO00.0050.00865.245-0.001-0.0010.0000.0000.0000.000
115A114THR00.0420.01364.679-0.001-0.0010.0000.0000.0000.000
116A115ASP-1-0.678-0.83360.197-0.051-0.0510.0000.0000.0000.000
117A116GLU-1-0.868-0.95662.802-0.052-0.0520.0000.0000.0000.000
118A117GLU-1-0.893-0.91365.493-0.037-0.0370.0000.0000.0000.000
119A118VAL00.0270.01562.2250.0020.0020.0000.0000.0000.000
120A119ALA0-0.002-0.00462.9300.0010.0010.0000.0000.0000.000
121A120LYS10.9430.98064.4930.0400.0400.0000.0000.0000.000
122A121GLU-1-0.850-0.91668.219-0.029-0.0290.0000.0000.0000.000
123A122LEU0-0.041-0.00862.3130.0010.0010.0000.0000.0000.000
124A123GLY0-0.0270.00866.3790.0000.0000.0000.0000.0000.000
125A124ILE0-0.054-0.02560.762-0.001-0.0010.0000.0000.0000.000
126A125SER00.0390.01761.0190.0000.0000.0000.0000.0000.000
127A126THR00.0650.01160.6180.0000.0000.0000.0000.0000.000
128A127GLU-1-0.835-0.89355.348-0.073-0.0730.0000.0000.0000.000
129A128GLU-1-0.858-0.92956.507-0.056-0.0560.0000.0000.0000.000
130A129LEU0-0.012-0.00557.1730.0010.0010.0000.0000.0000.000
131A130PHE00.009-0.01854.5010.0010.0010.0000.0000.0000.000
132A131LYS10.8450.91152.2140.0750.0750.0000.0000.0000.000
133A132THR0-0.0050.00152.3400.0010.0010.0000.0000.0000.000
134A133LEU00.005-0.00153.4960.0020.0020.0000.0000.0000.000
135A134ASP-1-0.774-0.87249.007-0.072-0.0720.0000.0000.0000.000
136A135LYS10.8140.88948.7520.0600.0600.0000.0000.0000.000
137A136ILE0-0.0110.00549.0830.0020.0020.0000.0000.0000.000
138A137ASN0-0.047-0.04948.6780.0030.0030.0000.0000.0000.000
139A138PHE00.0370.01740.4190.0000.0000.0000.0000.0000.000
140A139SER0-0.014-0.02044.8050.0000.0000.0000.0000.0000.000
141A140TYR0-0.058-0.06345.8310.0040.0040.0000.0000.0000.000
142A141ILE0-0.0160.00541.3130.0010.0010.0000.0000.0000.000
143A142LEU0-0.019-0.00840.0800.0000.0000.0000.0000.0000.000
144A143SER00.005-0.01141.0160.0030.0030.0000.0000.0000.000
145A144LEU0-0.0040.00441.2470.0040.0040.0000.0000.0000.000
146A145GLU-1-0.772-0.86335.005-0.062-0.0620.0000.0000.0000.000
147A146GLU-1-0.839-0.91637.041-0.033-0.0330.0000.0000.0000.000
148A147VAL00.0170.02037.5050.0040.0040.0000.0000.0000.000
149A148PHE0-0.021-0.02235.4200.0030.0030.0000.0000.0000.000
150A149ARG10.7250.83732.3140.0600.0600.0000.0000.0000.000
151A150ASP-1-0.801-0.88132.5810.0020.0020.0000.0000.0000.000
152A151PHE0-0.006-0.00333.2090.0060.0060.0000.0000.0000.000
153A152ALA00.003-0.01129.5040.0060.0060.0000.0000.0000.000
154A153ARG10.7910.89428.333-0.002-0.0020.0000.0000.0000.000
155A154ASP-1-0.854-0.91028.2220.0480.0480.0000.0000.0000.000
156A155TYR0-0.027-0.01726.9620.0040.0040.0000.0000.0000.000
157A156SER0-0.136-0.09024.284-0.001-0.0010.0000.0000.0000.000
158A157GLU-1-0.894-0.94522.9180.0790.0790.0000.0000.0000.000
159A158LEU0-0.023-0.01022.9120.0250.0250.0000.0000.0000.000
160A159ILE0-0.039-0.02621.2210.0090.0090.0000.0000.0000.000
161A160PRO0-0.018-0.00817.857-0.009-0.0090.0000.0000.0000.000
162A161SER00.0100.01217.7650.0150.0150.0000.0000.0000.000
163A162SER0-0.0490.01119.4720.0150.0150.0000.0000.0000.000
164A163THR00.013-0.04920.831-0.026-0.0260.0000.0000.0000.000
165A164ASN0-0.017-0.02720.858-0.026-0.0260.0000.0000.0000.000
166A165VAL00.0180.00824.061-0.011-0.0110.0000.0000.0000.000
167A166GLU-1-0.767-0.85124.5750.1170.1170.0000.0000.0000.000
168A167GLU-1-0.780-0.86623.431-0.074-0.0740.0000.0000.0000.000
169A168GLU-1-0.775-0.86026.574-0.041-0.0410.0000.0000.0000.000
170A169VAL0-0.015-0.01229.539-0.004-0.0040.0000.0000.0000.000
171A170ILE00.0270.01226.999-0.003-0.0030.0000.0000.0000.000
172A171LYS10.8270.89629.8250.0350.0350.0000.0000.0000.000
173A172ARG10.8620.90931.6410.0060.0060.0000.0000.0000.000
174A173GLU-1-0.811-0.87933.9320.0120.0120.0000.0000.0000.000
175A174LEU00.0190.02932.861-0.002-0.0020.0000.0000.0000.000
176A175THR0-0.034-0.04035.170-0.004-0.0040.0000.0000.0000.000
177A176GLU-1-0.834-0.90337.618-0.018-0.0180.0000.0000.0000.000
178A177LYS10.8450.92536.695-0.011-0.0110.0000.0000.0000.000
179A178VAL00.002-0.00738.666-0.001-0.0010.0000.0000.0000.000
180A179LYS10.7970.87740.9860.0190.0190.0000.0000.0000.000
181A180GLU-1-0.844-0.90543.606-0.002-0.0020.0000.0000.0000.000
182A181ALA0-0.0040.00344.7530.0000.0000.0000.0000.0000.000
183A182VAL0-0.005-0.01244.194-0.001-0.0010.0000.0000.0000.000
184A183SER0-0.066-0.04147.036-0.001-0.0010.0000.0000.0000.000
185A184LYS10.8690.93349.6530.0030.0030.0000.0000.0000.000
186A185LEU0-0.0160.00948.1640.0000.0000.0000.0000.0000.000
187A186PRO00.005-0.00652.4050.0000.0000.0000.0000.0000.000
188A187GLU-1-0.785-0.88454.424-0.029-0.0290.0000.0000.0000.000
189A188ARG10.9310.96654.8640.0380.0380.0000.0000.0000.000
190A189GLU-1-0.723-0.84252.580-0.031-0.0310.0000.0000.0000.000
191A190LYS10.8390.92049.7110.0240.0240.0000.0000.0000.000
192A191LEU00.0280.01949.954-0.003-0.0030.0000.0000.0000.000
193A192VAL00.002-0.00150.911-0.004-0.0040.0000.0000.0000.000
194A193ILE0-0.008-0.00945.763-0.004-0.0040.0000.0000.0000.000
195A194GLN0-0.039-0.01346.278-0.001-0.0010.0000.0000.0000.000
196A195LEU00.0320.00246.333-0.005-0.0050.0000.0000.0000.000
197A196ILE0-0.026-0.01445.419-0.005-0.0050.0000.0000.0000.000
198A197PHE0-0.057-0.04641.459-0.005-0.0050.0000.0000.0000.000
199A198TYR0-0.073-0.01441.412-0.005-0.0050.0000.0000.0000.000
200A199GLU-1-0.860-0.94042.681-0.080-0.0800.0000.0000.0000.000
201A200GLU-1-0.946-0.94638.699-0.129-0.1290.0000.0000.0000.000
202A201LEU00.0170.01343.527-0.005-0.0050.0000.0000.0000.000
203A202PRO00.0350.00146.4330.0040.0040.0000.0000.0000.000
204A203ALA00.0390.00848.1080.0030.0030.0000.0000.0000.000
205A204LYS10.8570.91350.5570.0770.0770.0000.0000.0000.000
206A205GLU-1-0.793-0.87550.167-0.080-0.0800.0000.0000.0000.000
207A206VAL00.0080.00550.2830.0030.0030.0000.0000.0000.000
208A207ALA0-0.034-0.02153.0770.0030.0030.0000.0000.0000.000
209A208LYS10.8360.89954.2230.0790.0790.0000.0000.0000.000
210A209ILE0-0.0090.00952.2270.0020.0020.0000.0000.0000.000
211A210LEU0-0.092-0.05454.8110.0030.0030.0000.0000.0000.000
212A211GLU-1-0.935-0.94658.308-0.045-0.0450.0000.0000.0000.000
213A212THR0-0.054-0.02758.8750.0030.0030.0000.0000.0000.000
214A213SER00.0210.02260.405-0.002-0.0020.0000.0000.0000.000
215A214VAL00.026-0.02454.7160.0000.0000.0000.0000.0000.000
216A215SER0-0.029-0.03456.3490.0000.0000.0000.0000.0000.000
217A216ARG10.8970.95857.9440.0370.0370.0000.0000.0000.000
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