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: ZN2KN

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 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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2942989.457804
FMO2-HF: Nuclear repulsion 2849067.676519
FMO2-HF: Total energy -93921.781285
FMO2-MP2: Total energy -94202.444333


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.
-2.0220.3351.225-1.457-2.126-0.002
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 : 0.000 / 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].
3A2LYS11.0221.0002.969-1.3400.8861.226-1.450-2.002-0.002
4A3ASN00.0350.0145.2581.3081.439-0.001-0.007-0.1240.000
5A4PRO00.038-0.0057.5530.0300.0300.0000.0000.0000.000
6A5TYR00.0390.03511.0450.1460.1460.0000.0000.0000.000
7A6SER00.014-0.0068.058-0.158-0.1580.0000.0000.0000.000
8A7ASN00.0080.0079.042-0.008-0.0080.0000.0000.0000.000
9A8GLN0-0.020-0.00410.9100.1110.1110.0000.0000.0000.000
10A9ILE00.0480.02312.8750.1270.1270.0000.0000.0000.000
11A10GLU-1-0.931-0.9659.564-2.061-2.0610.0000.0000.0000.000
12A11ARG10.8170.89512.9270.7530.7530.0000.0000.0000.000
13A12GLU-1-0.940-0.97715.631-0.620-0.6200.0000.0000.0000.000
14A13GLU-1-0.889-0.93815.758-0.734-0.7340.0000.0000.0000.000
15A14LEU0-0.041-0.01614.8700.1090.1090.0000.0000.0000.000
16A15ILE0-0.027-0.02318.0400.0960.0960.0000.0000.0000.000
17A16LEU00.018-0.02321.0000.0730.0730.0000.0000.0000.000
18A17LYS10.9290.97818.8190.6180.6180.0000.0000.0000.000
19A18TYR0-0.003-0.01819.6680.0380.0380.0000.0000.0000.000
20A19LEU00.0390.04024.2590.0440.0440.0000.0000.0000.000
21A20PRO0-0.020-0.01226.2960.0370.0370.0000.0000.0000.000
22A21LEU0-0.0030.00525.9280.0300.0300.0000.0000.0000.000
23A22VAL00.0210.01227.7380.0270.0270.0000.0000.0000.000
24A23LYS10.9460.98930.3550.2230.2230.0000.0000.0000.000
25A24ALA00.007-0.00332.3450.0190.0190.0000.0000.0000.000
26A25ILE0-0.006-0.00229.7300.0190.0190.0000.0000.0000.000
27A26ALA00.0370.02233.9800.0140.0140.0000.0000.0000.000
28A27THR0-0.037-0.03536.2090.0110.0110.0000.0000.0000.000
29A28ASN00.002-0.00537.0400.0120.0120.0000.0000.0000.000
30A29ILE00.0020.00035.3640.0090.0090.0000.0000.0000.000
31A30LYS10.8890.92139.4230.1260.1260.0000.0000.0000.000
32A31LYS10.8300.93341.7850.1230.1230.0000.0000.0000.000
33A32HIS0-0.019-0.00242.0400.0120.0120.0000.0000.0000.000
34A33LEU0-0.029-0.00541.0470.0040.0040.0000.0000.0000.000
35A34PRO00.0110.01445.4060.0000.0000.0000.0000.0000.000
36A35GLU-1-0.915-0.97147.077-0.097-0.0970.0000.0000.0000.000
37A36ASP-1-0.920-0.97047.623-0.094-0.0940.0000.0000.0000.000
38A37VAL00.0120.02842.357-0.004-0.0040.0000.0000.0000.000
39A38ASP-1-0.733-0.85541.936-0.149-0.1490.0000.0000.0000.000
40A39ILE0-0.011-0.01137.820-0.004-0.0040.0000.0000.0000.000
41A40ARG10.8880.92137.2480.1470.1470.0000.0000.0000.000
42A41ASP-1-0.843-0.89636.575-0.151-0.1510.0000.0000.0000.000
43A42LEU0-0.051-0.02636.386-0.006-0.0060.0000.0000.0000.000
44A43ILE00.003-0.00932.210-0.008-0.0080.0000.0000.0000.000
45A44SER0-0.010-0.00832.089-0.019-0.0190.0000.0000.0000.000
46A45TYR0-0.002-0.00831.699-0.013-0.0130.0000.0000.0000.000
47A46GLY00.013-0.00330.676-0.004-0.0040.0000.0000.0000.000
48A47VAL0-0.010-0.00426.777-0.017-0.0170.0000.0000.0000.000
49A48ILE0-0.0080.00526.672-0.021-0.0210.0000.0000.0000.000
50A49GLY0-0.012-0.01926.096-0.007-0.0070.0000.0000.0000.000
51A50LEU0-0.025-0.01022.6410.0010.0010.0000.0000.0000.000
52A51ILE00.007-0.00321.850-0.027-0.0270.0000.0000.0000.000
53A52LYS10.9390.96921.0820.1550.1550.0000.0000.0000.000
54A53ALA0-0.027-0.00520.7740.0100.0100.0000.0000.0000.000
55A54VAL0-0.010-0.01016.972-0.005-0.0050.0000.0000.0000.000
56A55ASP-1-0.796-0.87716.397-0.517-0.5170.0000.0000.0000.000
57A56ASN0-0.110-0.04915.9760.0320.0320.0000.0000.0000.000
58A57LEU00.0280.02615.0300.0620.0620.0000.0000.0000.000
59A58SER0-0.001-0.02311.7650.0040.0040.0000.0000.0000.000
60A59THR0-0.045-0.01211.7110.0300.0300.0000.0000.0000.000
61A60GLU-1-0.853-0.9118.944-1.118-1.1180.0000.0000.0000.000
62A61ASN0-0.030-0.03113.0250.0370.0370.0000.0000.0000.000
63A62PRO00.0560.01715.1210.0470.0470.0000.0000.0000.000
64A63LYS10.9500.98618.0090.1190.1190.0000.0000.0000.000
65A64ARG10.7520.85118.7410.0420.0420.0000.0000.0000.000
66A65ALA00.0200.02916.8960.0200.0200.0000.0000.0000.000
67A66GLU-1-0.936-0.96718.964-0.276-0.2760.0000.0000.0000.000
68A67ALA0-0.031-0.02022.2440.0170.0170.0000.0000.0000.000
69A68TYR00.0660.04120.1990.0140.0140.0000.0000.0000.000
70A69ILE00.0260.01019.6430.0170.0170.0000.0000.0000.000
71A70LYS10.9350.95523.3170.1810.1810.0000.0000.0000.000
72A71LEU0-0.0110.00325.8670.0100.0100.0000.0000.0000.000
73A72ARG10.9080.95022.8320.1700.1700.0000.0000.0000.000
74A73ILE0-0.0110.01626.2160.0080.0080.0000.0000.0000.000
75A74LYS10.9500.96528.7100.1440.1440.0000.0000.0000.000
76A75GLY00.0180.02630.2550.0100.0100.0000.0000.0000.000
77A76ALA00.0480.01829.4840.0090.0090.0000.0000.0000.000
78A77ILE0-0.028-0.01131.4570.0050.0050.0000.0000.0000.000
79A78TYR0-0.013-0.02434.4360.0050.0050.0000.0000.0000.000
80A79ASP-1-0.872-0.90432.187-0.086-0.0860.0000.0000.0000.000
81A80TYR0-0.0060.00135.5650.0070.0070.0000.0000.0000.000
82A81LEU0-0.004-0.00637.4330.0060.0060.0000.0000.0000.000
83A82ARG10.8240.89236.9450.0690.0690.0000.0000.0000.000
84A83SER0-0.105-0.04239.4310.0060.0060.0000.0000.0000.000
85A84LEU00.0090.01341.3950.0020.0020.0000.0000.0000.000
86A85ASP-1-0.861-0.93244.321-0.062-0.0620.0000.0000.0000.000
87A86PHE00.0410.00943.6580.0040.0040.0000.0000.0000.000
88A87GLY00.0100.02846.9410.0030.0030.0000.0000.0000.000
89A88SER0-0.0190.00248.3730.0050.0050.0000.0000.0000.000
90A89ARG10.9120.92051.1860.0300.0300.0000.0000.0000.000
91A90GLN00.0490.01154.7060.0020.0020.0000.0000.0000.000
92A91VAL00.0300.02451.1910.0000.0000.0000.0000.0000.000
93A92ARG10.9280.96049.6090.0420.0420.0000.0000.0000.000
94A93GLU-1-0.841-0.87855.216-0.028-0.0280.0000.0000.0000.000
95A94LYS10.9580.96356.3740.0530.0530.0000.0000.0000.000
96A95GLU-1-0.779-0.86354.422-0.040-0.0400.0000.0000.0000.000
97A96ARG10.8490.92057.6710.0280.0280.0000.0000.0000.000
98A97ARG10.9530.97060.7030.0370.0370.0000.0000.0000.000
99A98ILE00.0310.01958.1280.0000.0000.0000.0000.0000.000
100A99LYS10.9300.97256.4790.0340.0340.0000.0000.0000.000
101A100GLU-1-0.908-0.94662.131-0.027-0.0270.0000.0000.0000.000
102A101VAL0-0.0020.00164.9560.0010.0010.0000.0000.0000.000
103A102VAL0-0.029-0.02261.9500.0000.0000.0000.0000.0000.000
104A103GLU-1-0.875-0.95863.526-0.032-0.0320.0000.0000.0000.000
105A104LYS10.8880.94467.1700.0310.0310.0000.0000.0000.000
106A105LEU0-0.078-0.05967.6620.0010.0010.0000.0000.0000.000
107A106LYS10.8630.94263.7180.0350.0350.0000.0000.0000.000
108A107GLU-1-0.958-0.96969.581-0.023-0.0230.0000.0000.0000.000
109A108LYS10.9060.95972.8440.0330.0330.0000.0000.0000.000
110A109LEU0-0.072-0.03770.5900.0000.0000.0000.0000.0000.000
111A110GLY00.0070.02573.3250.0000.0000.0000.0000.0000.000
112A111ARG10.7970.88869.3120.0380.0380.0000.0000.0000.000
113A112GLU-1-0.834-0.92463.323-0.039-0.0390.0000.0000.0000.000
114A113PRO0-0.013-0.00465.271-0.001-0.0010.0000.0000.0000.000
115A114THR00.0370.02164.678-0.002-0.0020.0000.0000.0000.000
116A115ASP-1-0.698-0.87760.150-0.054-0.0540.0000.0000.0000.000
117A116GLU-1-0.873-0.95762.788-0.055-0.0550.0000.0000.0000.000
118A117GLU-1-0.917-0.94965.478-0.039-0.0390.0000.0000.0000.000
119A118VAL00.0220.01862.2010.0020.0020.0000.0000.0000.000
120A119ALA00.004-0.00262.9800.0010.0010.0000.0000.0000.000
121A120LYS10.9340.97864.4720.0420.0420.0000.0000.0000.000
122A121GLU-1-0.907-0.96068.199-0.033-0.0330.0000.0000.0000.000
123A122LEU0-0.055-0.01462.2190.0010.0010.0000.0000.0000.000
124A123GLY0-0.0260.00966.3530.0000.0000.0000.0000.0000.000
125A124ILE0-0.058-0.02660.764-0.001-0.0010.0000.0000.0000.000
126A125SER00.0380.01861.1010.0000.0000.0000.0000.0000.000
127A126THR00.0590.00860.7380.0000.0000.0000.0000.0000.000
128A127GLU-1-0.804-0.87655.372-0.077-0.0770.0000.0000.0000.000
129A128GLU-1-0.933-0.96756.485-0.063-0.0630.0000.0000.0000.000
130A129LEU0-0.011-0.00457.1480.0000.0000.0000.0000.0000.000
131A130PHE00.000-0.01954.4700.0010.0010.0000.0000.0000.000
132A131LYS10.8350.92252.2780.0790.0790.0000.0000.0000.000
133A132THR0-0.039-0.03252.3160.0000.0000.0000.0000.0000.000
134A133LEU0-0.002-0.00953.4710.0020.0020.0000.0000.0000.000
135A134ASP-1-0.788-0.87949.039-0.077-0.0770.0000.0000.0000.000
136A135LYS10.8460.92048.7290.0640.0640.0000.0000.0000.000
137A136ILE0-0.0210.00649.0550.0010.0010.0000.0000.0000.000
138A137ASN0-0.016-0.03848.6980.0040.0040.0000.0000.0000.000
139A138PHE00.0290.01640.419-0.001-0.0010.0000.0000.0000.000
140A139SER0-0.031-0.03444.780-0.001-0.0010.0000.0000.0000.000
141A140TYR0-0.054-0.06345.8030.0030.0030.0000.0000.0000.000
142A141ILE0-0.0120.01041.3560.0010.0010.0000.0000.0000.000
143A142LEU0-0.011-0.00740.2440.0000.0000.0000.0000.0000.000
144A143SER0-0.006-0.00640.9880.0030.0030.0000.0000.0000.000
145A144LEU00.0090.01241.1290.0040.0040.0000.0000.0000.000
146A145GLU-1-0.807-0.88634.978-0.074-0.0740.0000.0000.0000.000
147A146GLU-1-0.929-0.97437.016-0.039-0.0390.0000.0000.0000.000
148A147VAL00.0300.03237.4750.0030.0030.0000.0000.0000.000
149A148PHE0-0.035-0.02935.3610.0030.0030.0000.0000.0000.000
150A149ARG10.7230.83932.2080.0760.0760.0000.0000.0000.000
151A150ASP-1-0.894-0.94132.553-0.013-0.0130.0000.0000.0000.000
152A151PHE0-0.002-0.00633.1820.0050.0050.0000.0000.0000.000
153A152ALA0-0.006-0.01429.4290.0050.0050.0000.0000.0000.000
154A153ARG10.9030.96128.3090.0210.0210.0000.0000.0000.000
155A154ASP-1-0.853-0.90928.1910.0280.0280.0000.0000.0000.000
156A155TYR0-0.019-0.01726.9260.0030.0030.0000.0000.0000.000
157A156SER0-0.139-0.08324.340-0.001-0.0010.0000.0000.0000.000
158A157GLU-1-0.882-0.93522.8930.0440.0440.0000.0000.0000.000
159A158LEU0-0.034-0.02122.8870.0240.0240.0000.0000.0000.000
160A159ILE0-0.027-0.02521.0050.0100.0100.0000.0000.0000.000
161A160PRO0-0.029-0.01017.887-0.006-0.0060.0000.0000.0000.000
162A161SER0-0.031-0.00817.7590.0220.0220.0000.0000.0000.000
163A162SER0-0.0060.03419.4630.0150.0150.0000.0000.0000.000
164A163THR00.027-0.01320.838-0.025-0.0250.0000.0000.0000.000
165A164ASN0-0.015-0.02821.094-0.024-0.0240.0000.0000.0000.000
166A165VAL00.0100.00724.081-0.012-0.0120.0000.0000.0000.000
167A166GLU-1-0.798-0.89924.5940.1120.1120.0000.0000.0000.000
168A167GLU-1-0.775-0.86523.522-0.079-0.0790.0000.0000.0000.000
169A168GLU-1-0.828-0.89226.581-0.043-0.0430.0000.0000.0000.000
170A169VAL0-0.012-0.01129.552-0.004-0.0040.0000.0000.0000.000
171A170ILE00.0190.00826.883-0.003-0.0030.0000.0000.0000.000
172A171LYS10.7960.87929.8770.0380.0380.0000.0000.0000.000
173A172ARG10.9470.95631.6440.0030.0030.0000.0000.0000.000
174A173GLU-1-0.823-0.89134.0050.0050.0050.0000.0000.0000.000
175A174LEU00.0090.02233.084-0.002-0.0020.0000.0000.0000.000
176A175THR0-0.029-0.04235.138-0.004-0.0040.0000.0000.0000.000
177A176GLU-1-0.946-0.97737.620-0.016-0.0160.0000.0000.0000.000
178A177LYS10.8780.95236.593-0.001-0.0010.0000.0000.0000.000
179A178VAL0-0.010-0.00838.497-0.001-0.0010.0000.0000.0000.000
180A179LYS10.8990.94941.4570.0240.0240.0000.0000.0000.000
181A180GLU-1-0.885-0.93543.607-0.005-0.0050.0000.0000.0000.000
182A181ALA00.0060.01344.7840.0000.0000.0000.0000.0000.000
183A182VAL0-0.012-0.01144.065-0.001-0.0010.0000.0000.0000.000
184A183SER0-0.081-0.06447.0330.0000.0000.0000.0000.0000.000
185A184LYS10.9320.97249.6530.0070.0070.0000.0000.0000.000
186A185LEU0-0.0310.00048.1460.0000.0000.0000.0000.0000.000
187A186PRO0-0.007-0.00652.4000.0000.0000.0000.0000.0000.000
188A187GLU-1-0.828-0.92054.422-0.031-0.0310.0000.0000.0000.000
189A188ARG10.9160.95254.8650.0390.0390.0000.0000.0000.000
190A189GLU-1-0.786-0.91652.513-0.035-0.0350.0000.0000.0000.000
191A190LYS10.9180.98449.4980.0260.0260.0000.0000.0000.000
192A191LEU00.0090.01149.955-0.003-0.0030.0000.0000.0000.000
193A192VAL00.002-0.00250.804-0.004-0.0040.0000.0000.0000.000
194A193ILE0-0.016-0.01045.845-0.005-0.0050.0000.0000.0000.000
195A194GLN00.0010.00346.280-0.002-0.0020.0000.0000.0000.000
196A195LEU00.0350.00546.337-0.005-0.0050.0000.0000.0000.000
197A196ILE0-0.015-0.00445.199-0.004-0.0040.0000.0000.0000.000
198A197PHE0-0.070-0.05341.278-0.005-0.0050.0000.0000.0000.000
199A198TYR0-0.084-0.02141.322-0.005-0.0050.0000.0000.0000.000
200A199GLU-1-0.890-0.95542.689-0.083-0.0830.0000.0000.0000.000
201A200GLU-1-1.014-0.98338.780-0.130-0.1300.0000.0000.0000.000
202A201LEU00.0010.01343.529-0.005-0.0050.0000.0000.0000.000
203A202PRO00.0290.00046.3090.0040.0040.0000.0000.0000.000
204A203ALA00.0420.00948.1020.0030.0030.0000.0000.0000.000
205A204LYS10.8850.93050.3030.0820.0820.0000.0000.0000.000
206A205GLU-1-0.854-0.93549.924-0.083-0.0830.0000.0000.0000.000
207A206VAL0-0.009-0.00450.3140.0030.0030.0000.0000.0000.000
208A207ALA0-0.030-0.02053.0760.0030.0030.0000.0000.0000.000
209A208LYS10.9060.96054.4010.0800.0800.0000.0000.0000.000
210A209ILE0-0.0130.00852.1260.0020.0020.0000.0000.0000.000
211A210LEU0-0.087-0.05755.0440.0030.0030.0000.0000.0000.000
212A211GLU-1-0.930-0.93958.310-0.045-0.0450.0000.0000.0000.000
213A212THR0-0.037-0.01558.8280.0030.0030.0000.0000.0000.000
214A213SER00.0100.01360.400-0.002-0.0020.0000.0000.0000.000
215A214VAL00.042-0.00554.7210.0000.0000.0000.0000.0000.000
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217A216ARG10.8870.96157.9300.0400.0400.0000.0000.0000.000
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