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: 76NKK

Calculation Name: 1JY5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JY5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9M7C7

Base Structure: X-ray

Registration Date: 2023-09-23

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2363121.266821
FMO2-HF: Nuclear repulsion 2280217.893144
FMO2-HF: Total energy -82903.373676
FMO2-MP2: Total energy -83136.655024


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:2:HIS)


Summations of interaction energy for fragment #1(A:2: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.
-27.838-19.7069.737-6.76-11.109-0.021
Interaction energy analysis for fragmet #1(A:2:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.004
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].
3A4GLU-1-0.853-0.9121.911-21.549-19.9916.673-4.186-4.044-0.029
4A5PHE0-0.016-0.0043.8121.1321.505-0.001-0.022-0.3500.000
5A6ASP-1-0.761-0.8675.388-3.151-3.114-0.001-0.001-0.0350.000
6A7TYR0-0.044-0.0298.9440.4210.4210.0000.0000.0000.000
7A8PHE00.0280.0079.293-0.260-0.2600.0000.0000.0000.000
8A9THR00.007-0.02012.0300.1410.1410.0000.0000.0000.000
9A10LEU0-0.038-0.01614.3600.0670.0670.0000.0000.0000.000
10A11ALA00.0070.00716.8710.0130.0130.0000.0000.0000.000
11A12LEU0-0.002-0.00518.7080.0540.0540.0000.0000.0000.000
12A13THR00.0480.00422.143-0.010-0.0100.0000.0000.0000.000
13A14TRP0-0.045-0.02324.6190.0020.0020.0000.0000.0000.000
14A15SER00.0650.00928.3520.0120.0120.0000.0000.0000.000
15A16GLY00.019-0.00129.9030.0140.0140.0000.0000.0000.000
16A17THR0-0.052-0.05229.9510.0110.0110.0000.0000.0000.000
17A18GLU-1-0.889-0.93526.438-0.007-0.0070.0000.0000.0000.000
18A19CYS0-0.129-0.04430.0550.0070.0070.0000.0000.0000.000
19A20LEU00.0620.03333.4160.0000.0000.0000.0000.0000.000
20A21SER0-0.050-0.02635.5350.0080.0080.0000.0000.0000.000
21A22VAL0-0.016-0.01133.6220.0060.0060.0000.0000.0000.000
22A23LYS10.9060.95134.083-0.056-0.0560.0000.0000.0000.000
23A24ASP-1-0.756-0.86031.7950.1050.1050.0000.0000.0000.000
24A25SER0-0.020-0.03535.351-0.012-0.0120.0000.0000.0000.000
25A26CYS0-0.094-0.02628.3180.0170.0170.0000.0000.0000.000
26A27PRO00.0300.01032.780-0.007-0.0070.0000.0000.0000.000
27A28THR00.0230.00426.961-0.010-0.0100.0000.0000.0000.000
28A29ASN0-0.008-0.00528.963-0.015-0.0150.0000.0000.0000.000
29A30ALA00.0350.01429.444-0.005-0.0050.0000.0000.0000.000
30A32SER0-0.066-0.02333.589-0.009-0.0090.0000.0000.0000.000
31A33ARG10.9120.96429.238-0.073-0.0730.0000.0000.0000.000
32A34SER00.009-0.00436.059-0.007-0.0070.0000.0000.0000.000
33A35GLU-1-0.939-0.96436.2250.0060.0060.0000.0000.0000.000
34A36VAL0-0.017-0.00232.073-0.006-0.0060.0000.0000.0000.000
35A37GLU-1-0.905-0.94735.286-0.064-0.0640.0000.0000.0000.000
36A38THR0-0.079-0.03233.3430.0040.0040.0000.0000.0000.000
37A39GLY00.0730.03031.214-0.007-0.0070.0000.0000.0000.000
38A40PHE0-0.019-0.00925.7650.0090.0090.0000.0000.0000.000
39A41THR0-0.0220.02725.1280.0140.0140.0000.0000.0000.000
40A42ILE00.011-0.00618.807-0.025-0.0250.0000.0000.0000.000
41A43LYS10.8320.94418.016-0.006-0.0060.0000.0000.0000.000
42A44GLY0-0.006-0.03315.7120.0850.0850.0000.0000.0000.000
43A45LEU00.0140.03212.060-0.071-0.0710.0000.0000.0000.000
44A46TRP0-0.068-0.06510.6300.1360.1360.0000.0000.0000.000
45A47PRO00.0090.0295.880-0.075-0.0750.0000.0000.0000.000
46A48ASP-1-0.767-0.8747.955-1.161-1.1610.0000.0000.0000.000
47A49TYR0-0.039-0.0512.367-0.0592.0910.419-1.027-1.542-0.006
48A50ASP-1-0.881-0.9568.745-1.534-1.5340.0000.0000.0000.000
49A51ASP-1-0.965-0.95510.023-1.618-1.6180.0000.0000.0000.000
50A52GLY00.0010.00612.4460.2280.2280.0000.0000.0000.000
51A53THR0-0.109-0.0678.7930.1760.1760.0000.0000.0000.000
52A54TRP0-0.024-0.0267.496-0.223-0.2230.0000.0000.0000.000
53A55PRO0-0.0380.0063.186-0.3330.9840.187-0.379-1.1250.002
54A56SER0-0.027-0.0495.214-0.0950.018-0.001-0.005-0.1070.000
55A57CYS0-0.086-0.0406.1780.4570.4570.0000.0000.0000.000
56A58CYS0-0.079-0.0033.020-1.3460.6062.462-0.974-3.4400.013
57A59GLU-1-0.902-0.9494.2091.4631.692-0.001-0.034-0.1940.000
58A60GLY00.0330.0046.2360.2360.2360.0000.0000.0000.000
59A61ALA0-0.049-0.0128.931-0.189-0.1890.0000.0000.0000.000
60A62LYS10.9290.96712.301-0.658-0.6580.0000.0000.0000.000
61A63TYR00.0720.01814.400-0.101-0.1010.0000.0000.0000.000
62A64ASP-1-0.881-0.94416.1740.4680.4680.0000.0000.0000.000
63A65GLN00.0060.00519.140-0.064-0.0640.0000.0000.0000.000
64A66ASN0-0.059-0.03821.838-0.075-0.0750.0000.0000.0000.000
65A67GLU-1-0.889-0.93516.9840.4680.4680.0000.0000.0000.000
66A68ILE00.0080.00518.324-0.042-0.0420.0000.0000.0000.000
67A69SER00.0160.01521.380-0.041-0.0410.0000.0000.0000.000
68A70ILE0-0.034-0.01224.388-0.015-0.0150.0000.0000.0000.000
69A71LEU00.0080.01420.266-0.022-0.0220.0000.0000.0000.000
70A72SER0-0.041-0.02524.352-0.014-0.0140.0000.0000.0000.000
71A73ASN0-0.006-0.01425.9850.0030.0030.0000.0000.0000.000
72A74ASP-1-0.837-0.92525.159-0.019-0.0190.0000.0000.0000.000
73A75LEU0-0.022-0.01120.117-0.014-0.0140.0000.0000.0000.000
74A76SER0-0.049-0.01123.9020.0020.0020.0000.0000.0000.000
75A77LYS10.8780.93526.932-0.001-0.0010.0000.0000.0000.000
76A78TYR00.013-0.00324.784-0.010-0.0100.0000.0000.0000.000
77A79TRP0-0.0130.00515.322-0.034-0.0340.0000.0000.0000.000
78A80PRO0-0.0210.00723.0440.0320.0320.0000.0000.0000.000
79A81SER00.0420.04024.322-0.010-0.0100.0000.0000.0000.000
80A82TYR00.002-0.05725.441-0.007-0.0070.0000.0000.0000.000
81A83SER00.008-0.00727.087-0.002-0.0020.0000.0000.0000.000
82A85PRO0-0.055-0.00927.7660.0190.0190.0000.0000.0000.000
83A86SER0-0.018-0.01023.5570.0080.0080.0000.0000.0000.000
84A87SER00.0260.02219.943-0.023-0.0230.0000.0000.0000.000
85A88SER0-0.032-0.02218.9810.0300.0300.0000.0000.0000.000
86A89ALA00.0140.00013.851-0.048-0.0480.0000.0000.0000.000
87A91GLY00.0180.01912.6260.0630.0630.0000.0000.0000.000
88A92SER0-0.029-0.00615.624-0.035-0.0350.0000.0000.0000.000
89A93PHE0-0.030-0.02318.0320.0040.0040.0000.0000.0000.000
90A94ASP-1-0.822-0.91717.1310.6820.6820.0000.0000.0000.000
91A95ALA0-0.040-0.03020.244-0.055-0.0550.0000.0000.0000.000
92A96SER0-0.014-0.02021.132-0.029-0.0290.0000.0000.0000.000
93A97ASP-1-0.766-0.89119.9680.2340.2340.0000.0000.0000.000
94A98LEU0-0.0030.00118.1140.0280.0280.0000.0000.0000.000
95A99ALA0-0.023-0.01416.4990.0600.0600.0000.0000.0000.000
96A100TYR0-0.0090.01215.2600.1110.1110.0000.0000.0000.000
97A101GLU-1-0.795-0.90913.9840.2180.2180.0000.0000.0000.000
98A102TRP0-0.0220.01010.2850.0120.0120.0000.0000.0000.000
99A103ALA0-0.0010.01110.5780.2370.2370.0000.0000.0000.000
100A104LYS10.9340.9489.4400.0340.0340.0000.0000.0000.000
101A105HIS10.9130.9538.3620.3920.3920.0000.0000.0000.000
102A106GLY00.0510.0217.673-0.158-0.1580.0000.0000.0000.000
103A107THR0-0.0220.0106.704-0.297-0.2970.0000.0000.0000.000
104A109SER0-0.013-0.0233.902-3.317-3.0290.001-0.118-0.171-0.001
105A110SER0-0.0260.0335.463-0.344-0.3440.0000.0000.0000.000
106A111PRO0-0.032-0.0444.368-1.269-1.154-0.001-0.014-0.1010.000
107A112VAL0-0.021-0.0097.5500.2790.2790.0000.0000.0000.000
108A113LEU0-0.025-0.0108.8810.2260.2260.0000.0000.0000.000
109A114GLY00.0380.0159.3280.1230.1230.0000.0000.0000.000
110A115ASN0-0.076-0.04411.3590.2270.2270.0000.0000.0000.000
111A116GLN00.0930.02412.897-0.115-0.1150.0000.0000.0000.000
112A117TYR00.0430.02414.316-0.080-0.0800.0000.0000.0000.000
113A118GLU-1-0.848-0.89713.990-0.122-0.1220.0000.0000.0000.000
114A119TYR0-0.012-0.00110.9610.0050.0050.0000.0000.0000.000
115A120PHE00.014-0.00413.433-0.079-0.0790.0000.0000.0000.000
116A121SER0-0.021-0.03416.712-0.060-0.0600.0000.0000.0000.000
117A122THR00.000-0.01014.901-0.043-0.0430.0000.0000.0000.000
118A123THR0-0.029-0.02315.194-0.066-0.0660.0000.0000.0000.000
119A124LEU0-0.012-0.01017.265-0.011-0.0110.0000.0000.0000.000
120A125MET0-0.0310.00618.9510.0010.0010.0000.0000.0000.000
121A126LEU0-0.027-0.01316.2910.0010.0010.0000.0000.0000.000
122A127TYR0-0.046-0.04220.6400.0080.0080.0000.0000.0000.000
123A128PHE0-0.039-0.02522.4840.0110.0110.0000.0000.0000.000
124A129LYS10.8640.95323.1040.3910.3910.0000.0000.0000.000
125A130TYR00.000-0.01221.791-0.010-0.0100.0000.0000.0000.000
126A131ASN00.0640.03125.318-0.003-0.0030.0000.0000.0000.000
127A132ILE00.0450.00624.6840.0040.0040.0000.0000.0000.000
128A133SER00.013-0.00527.9570.0060.0060.0000.0000.0000.000
129A134GLU-1-0.888-0.92730.743-0.148-0.1480.0000.0000.0000.000
130A135ILE00.0500.03028.4020.0020.0020.0000.0000.0000.000
131A136LEU0-0.030-0.01230.3790.0040.0040.0000.0000.0000.000
132A137SER0-0.035-0.01733.5570.0100.0100.0000.0000.0000.000
133A138GLU-1-0.970-0.98035.911-0.146-0.1460.0000.0000.0000.000
134A139SER0-0.073-0.04235.438-0.004-0.0040.0000.0000.0000.000
135A140GLY0-0.056-0.02337.8860.0010.0010.0000.0000.0000.000
136A141TYR0-0.055-0.02235.2680.0090.0090.0000.0000.0000.000
137A142LEU00.0380.02335.919-0.003-0.0030.0000.0000.0000.000
138A143PRO00.0420.02335.4190.0010.0010.0000.0000.0000.000
139A144SER00.000-0.00637.3940.0070.0070.0000.0000.0000.000
140A145ASN00.0030.00539.340-0.005-0.0050.0000.0000.0000.000
141A146THR0-0.046-0.03541.4170.0030.0030.0000.0000.0000.000
142A147ALA0-0.0350.00240.747-0.001-0.0010.0000.0000.0000.000
143A148GLU-1-0.901-0.93939.579-0.079-0.0790.0000.0000.0000.000
144A149TYR0-0.061-0.06536.714-0.002-0.0020.0000.0000.0000.000
145A150LYS10.9710.99237.3610.1350.1350.0000.0000.0000.000
146A151VAL00.0520.02930.974-0.007-0.0070.0000.0000.0000.000
147A152GLU-1-0.948-0.99032.790-0.189-0.1890.0000.0000.0000.000
148A153GLY00.0560.03534.175-0.011-0.0110.0000.0000.0000.000
149A154ILE00.0040.00130.450-0.005-0.0050.0000.0000.0000.000
150A155MET0-0.044-0.01926.624-0.010-0.0100.0000.0000.0000.000
151A156SER0-0.019-0.00530.325-0.023-0.0230.0000.0000.0000.000
152A157ALA00.0150.02132.838-0.007-0.0070.0000.0000.0000.000
153A158ILE00.0170.00226.430-0.005-0.0050.0000.0000.0000.000
154A159GLN00.0490.02028.218-0.024-0.0240.0000.0000.0000.000
155A160SER0-0.103-0.05229.311-0.011-0.0110.0000.0000.0000.000
156A161ALA0-0.0170.00330.1830.0020.0020.0000.0000.0000.000
157A162LEU0-0.051-0.03324.142-0.006-0.0060.0000.0000.0000.000
158A163ARG10.8560.92526.3960.3010.3010.0000.0000.0000.000
159A164VAL0-0.0040.01822.335-0.026-0.0260.0000.0000.0000.000
160A165THR0-0.036-0.03224.4180.0610.0610.0000.0000.0000.000
161A166PRO0-0.0220.00422.951-0.041-0.0410.0000.0000.0000.000
162A167VAL00.014-0.00320.1140.0230.0230.0000.0000.0000.000
163A168VAL00.003-0.01222.9770.0180.0180.0000.0000.0000.000
164A169LYS10.9180.97320.3960.3620.3620.0000.0000.0000.000
165A170CYS0-0.057-0.00525.5850.0280.0280.0000.0000.0000.000
166A171LYS10.8490.91828.4850.0270.0270.0000.0000.0000.000
167A172SER00.002-0.01030.4560.0090.0090.0000.0000.0000.000
168A173ASP-1-0.982-1.00233.672-0.088-0.0880.0000.0000.0000.000
169A174ALA00.0210.03333.152-0.007-0.0070.0000.0000.0000.000
170A175VAL00.0340.00128.495-0.005-0.0050.0000.0000.0000.000
171A176GLU-1-0.871-0.90425.639-0.053-0.0530.0000.0000.0000.000
172A177GLN00.004-0.00419.909-0.040-0.0400.0000.0000.0000.000
173A178VAL00.0080.01323.532-0.013-0.0130.0000.0000.0000.000
174A179GLN0-0.041-0.03218.252-0.030-0.0300.0000.0000.0000.000
175A180ILE00.0450.02619.4340.0000.0000.0000.0000.0000.000
176A181CYS0-0.0390.01416.312-0.123-0.1230.0000.0000.0000.000
177A182PHE00.021-0.00615.2900.1110.1110.0000.0000.0000.000
178A183ASP-1-0.659-0.78514.046-1.178-1.1780.0000.0000.0000.000
179A184LYS10.7990.8828.3303.5043.5040.0000.0000.0000.000
180A185THR0-0.123-0.06312.5810.0740.0740.0000.0000.0000.000
181A186LEU0-0.060-0.03714.1860.1460.1460.0000.0000.0000.000
182A187GLN0-0.094-0.05316.8270.1940.1940.0000.0000.0000.000
183A188LEU0-0.032-0.00518.316-0.079-0.0790.0000.0000.0000.000
184A189GLN0-0.026-0.02215.239-0.093-0.0930.0000.0000.0000.000
185A190GLU-1-0.799-0.90219.849-0.496-0.4960.0000.0000.0000.000
186A192PRO00.0680.03614.6820.0720.0720.0000.0000.0000.000
187A193SER0-0.023-0.01217.7490.0810.0810.0000.0000.0000.000
188A194THR0-0.032-0.02319.931-0.016-0.0160.0000.0000.0000.000
189A195ALA0-0.033-0.00522.0210.0240.0240.0000.0000.0000.000
190A196SER00.021-0.00125.094-0.009-0.0090.0000.0000.0000.000
191A197THR0-0.008-0.01725.2150.0150.0150.0000.0000.0000.000
192A199PRO00.0410.02330.596-0.007-0.0070.0000.0000.0000.000
193A200SER0-0.002-0.01234.123-0.009-0.0090.0000.0000.0000.000
194A201LEU0-0.074-0.03536.345-0.008-0.0080.0000.0000.0000.000
195A202VAL00.0510.02532.5500.0010.0010.0000.0000.0000.000
196A203SER00.0450.02835.2700.0020.0020.0000.0000.0000.000
197A204LEU0-0.006-0.00131.878-0.006-0.0060.0000.0000.0000.000
198A205PRO00.0300.03033.9690.0050.0050.0000.0000.0000.000
199A206ILE00.0260.00535.157-0.003-0.0030.0000.0000.0000.000
200A207LYS10.8500.92532.7210.0150.0150.0000.0000.0000.000
201A208ASN0-0.034-0.01036.386-0.004-0.0040.0000.0000.0000.000