FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: LNNK9

Calculation Name: 1XFS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XFS

Chain ID: A

ChEMBL ID:

UniProt ID: Q82XK1

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 154
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1536760.308443
FMO2-HF: Nuclear repulsion 1474267.417687
FMO2-HF: Total energy -62492.890756
FMO2-MP2: Total energy -62672.687553


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:6:ILE)


Summations of interaction energy for fragment #1(A:6:ILE)
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.
-8.565-1.9376.059-4.367-8.319-0.026
Interaction energy analysis for fragmet #1(A:6:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.025
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].
3A8ALA0-0.021-0.0173.579-0.1502.0620.004-0.848-1.3680.002
4A9GLU-1-0.846-0.9344.453-0.611-0.438-0.001-0.010-0.1610.000
5A10LEU0-0.055-0.0046.0400.6980.6980.0000.0000.0000.000
6A11ASP-1-0.787-0.9042.573-8.389-5.2772.741-2.645-3.208-0.030
7A12LEU0-0.0390.0024.110-0.225-0.0370.002-0.039-0.1500.000
8A13MET0-0.019-0.0182.626-0.7900.4820.934-0.374-1.8330.001
9A14LEU0-0.0150.0044.601-0.212-0.179-0.001-0.010-0.0220.000
10A15LYS10.8930.9418.255-0.551-0.5510.0000.0000.0000.000
11A16ARG10.8690.91910.113-0.374-0.3740.0000.0000.0000.000
12A17GLU-1-0.795-0.87213.8200.6350.6350.0000.0000.0000.000
13A18LEU00.0370.03316.280-0.042-0.0420.0000.0000.0000.000
14A19ALA0-0.027-0.00519.4060.0140.0140.0000.0000.0000.000
15A20VAL0-0.011-0.02521.883-0.029-0.0290.0000.0000.0000.000
16A21PRO0-0.0070.01621.7230.0290.0290.0000.0000.0000.000
17A22VAL00.0740.02318.313-0.006-0.0060.0000.0000.0000.000
18A23ASN00.0660.03720.9130.0080.0080.0000.0000.0000.000
19A24LEU0-0.047-0.02623.586-0.010-0.0100.0000.0000.0000.000
20A25VAL00.0250.00317.374-0.009-0.0090.0000.0000.0000.000
21A26TRP0-0.0110.00516.0510.0130.0130.0000.0000.0000.000
22A27ARG10.8520.89920.250-0.189-0.1890.0000.0000.0000.000
23A28GLY0-0.003-0.00121.818-0.018-0.0180.0000.0000.0000.000
24A29LEU0-0.035-0.02515.399-0.010-0.0100.0000.0000.0000.000
25A30THR00.016-0.00419.212-0.014-0.0140.0000.0000.0000.000
26A31GLU-1-0.783-0.84021.5940.1530.1530.0000.0000.0000.000
27A32PRO00.0330.01125.007-0.003-0.0030.0000.0000.0000.000
28A33GLU-1-0.844-0.91426.2010.0850.0850.0000.0000.0000.000
29A34LEU0-0.008-0.01124.834-0.007-0.0070.0000.0000.0000.000
30A35LEU00.0410.01719.781-0.006-0.0060.0000.0000.0000.000
31A36LYS10.7820.87623.231-0.095-0.0950.0000.0000.0000.000
32A37LYS10.8230.91825.396-0.120-0.1200.0000.0000.0000.000
33A38TRP0-0.073-0.03616.5930.0040.0040.0000.0000.0000.000
34A39PHE00.006-0.00116.2740.0000.0000.0000.0000.0000.000
35A40VAL00.0300.03518.720-0.005-0.0050.0000.0000.0000.000
36A41PRO0-0.0050.01618.9120.0100.0100.0000.0000.0000.000
37A42LYS10.9480.97621.433-0.101-0.1010.0000.0000.0000.000
38A43PRO0-0.027-0.03024.418-0.002-0.0020.0000.0000.0000.000
39A44TRP00.0120.02523.3210.0010.0010.0000.0000.0000.000
40A45SER00.000-0.01025.7190.0100.0100.0000.0000.0000.000
41A46ILE0-0.008-0.00122.310-0.005-0.0050.0000.0000.0000.000
42A47SER0-0.047-0.02226.676-0.001-0.0010.0000.0000.0000.000
43A48ASP-1-0.865-0.94128.0640.0510.0510.0000.0000.0000.000
44A49CYS0-0.045-0.01224.0290.0060.0060.0000.0000.0000.000
45A50ARG10.9030.95726.058-0.066-0.0660.0000.0000.0000.000
46A51VAL00.0410.01322.7040.0000.0000.0000.0000.0000.000
47A52ASP-1-0.870-0.90224.6310.1100.1100.0000.0000.0000.000
48A53LEU00.024-0.00520.2810.0020.0020.0000.0000.0000.000
49A54ARG10.8450.92122.868-0.104-0.1040.0000.0000.0000.000
50A55PRO00.0160.01320.286-0.011-0.0110.0000.0000.0000.000
51A56GLY00.004-0.01020.800-0.019-0.0190.0000.0000.0000.000
52A57GLY0-0.024-0.01122.510-0.024-0.0240.0000.0000.0000.000
53A58GLU-1-0.880-0.94322.0790.0500.0500.0000.0000.0000.000
54A59PHE00.0010.00717.4080.0090.0090.0000.0000.0000.000
55A60TYR0-0.030-0.02421.903-0.018-0.0180.0000.0000.0000.000
56A61THR00.024-0.00221.8540.0160.0160.0000.0000.0000.000
57A62VAL0-0.0190.01324.385-0.013-0.0130.0000.0000.0000.000
58A63MET00.0100.01620.3340.0060.0060.0000.0000.0000.000
59A64GLN00.0130.01125.139-0.004-0.0040.0000.0000.0000.000
60A65ASP-1-0.716-0.84026.193-0.022-0.0220.0000.0000.0000.000
61A66PRO0-0.031-0.03826.8230.0040.0040.0000.0000.0000.000
62A67GLU-1-0.970-0.97529.395-0.043-0.0430.0000.0000.0000.000
63A68GLY0-0.053-0.01330.9500.0010.0010.0000.0000.0000.000
64A69ASN0-0.092-0.05129.1230.0030.0030.0000.0000.0000.000
65A70LYS10.8550.89828.796-0.007-0.0070.0000.0000.0000.000
66A71PHE0-0.010-0.00724.627-0.008-0.0080.0000.0000.0000.000
67A72PRO0-0.023-0.00325.0950.0090.0090.0000.0000.0000.000
68A73ASN00.0330.00820.8430.0000.0000.0000.0000.0000.000
69A74SER0-0.017-0.01422.2680.0150.0150.0000.0000.0000.000
70A75GLY00.0520.03119.071-0.019-0.0190.0000.0000.0000.000
71A76CYS0-0.093-0.02818.3830.0030.0030.0000.0000.0000.000
72A77PHE00.0360.01117.4660.0150.0150.0000.0000.0000.000
73A78LEU0-0.039-0.03113.452-0.032-0.0320.0000.0000.0000.000
74A79GLU-1-0.814-0.87614.0660.7490.7490.0000.0000.0000.000
75A80VAL00.000-0.00316.3260.0130.0130.0000.0000.0000.000
76A81THR0-0.048-0.03416.384-0.052-0.0520.0000.0000.0000.000
77A82ASP-1-0.829-0.93717.8010.3400.3400.0000.0000.0000.000
78A83GLU-1-0.919-0.98119.0230.3370.3370.0000.0000.0000.000
79A84LYS10.7890.90212.239-1.013-1.0130.0000.0000.0000.000
80A85ARG10.7720.84710.711-1.006-1.0060.0000.0000.0000.000
81A86LEU00.0070.02612.950-0.092-0.0920.0000.0000.0000.000
82A87ILE00.0060.00910.9220.0770.0770.0000.0000.0000.000
83A88TRP00.0420.02313.007-0.040-0.0400.0000.0000.0000.000
84A89THR0-0.009-0.01813.073-0.015-0.0150.0000.0000.0000.000
85A90SER00.0450.02114.7560.0020.0020.0000.0000.0000.000
86A91ALA00.0020.00515.320-0.018-0.0180.0000.0000.0000.000
87A92LEU0-0.041-0.02117.242-0.005-0.0050.0000.0000.0000.000
88A93VAL00.0230.00819.7130.0120.0120.0000.0000.0000.000
89A94LYS10.8780.92022.521-0.046-0.0460.0000.0000.0000.000
90A95ASN0-0.058-0.04624.863-0.004-0.0040.0000.0000.0000.000
91A96TYR00.0560.03019.7630.0030.0030.0000.0000.0000.000
92A97ARG10.9300.99522.544-0.002-0.0020.0000.0000.0000.000
93A98PRO00.0330.00721.6330.0020.0020.0000.0000.0000.000
94A99ALA00.0130.01420.7190.0100.0100.0000.0000.0000.000
95A100VAL0-0.029-0.01722.588-0.012-0.0120.0000.0000.0000.000
96A101PRO00.0070.01423.0590.0000.0000.0000.0000.0000.000
97A113VAL0-0.039-0.02714.5580.0130.0130.0000.0000.0000.000
98A114MET00.0060.00910.684-0.052-0.0520.0000.0000.0000.000
99A115THR00.0110.0179.5770.0810.0810.0000.0000.0000.000
100A116ALA0-0.0100.0198.715-0.027-0.0270.0000.0000.0000.000
101A117VAL00.0260.0066.791-0.001-0.0010.0000.0000.0000.000
102A118ILE0-0.033-0.0178.0380.1040.1040.0000.0000.0000.000
103A119GLU-1-0.763-0.8588.2101.4671.4670.0000.0000.0000.000
104A120LEU0-0.042-0.02010.879-0.051-0.0510.0000.0000.0000.000
105A121GLN00.024-0.00113.8620.0130.0130.0000.0000.0000.000
106A122PRO00.0210.03015.701-0.026-0.0260.0000.0000.0000.000
107A123THR0-0.007-0.01817.7680.0150.0150.0000.0000.0000.000
108A124SER0-0.005-0.01120.397-0.015-0.0150.0000.0000.0000.000
109A125SER0-0.020-0.01322.674-0.015-0.0150.0000.0000.0000.000
110A126GLY00.000-0.00321.703-0.025-0.0250.0000.0000.0000.000
111A127THR0-0.024-0.00816.3350.0210.0210.0000.0000.0000.000
112A128ARG10.7900.88012.385-0.665-0.6650.0000.0000.0000.000
113A129TYR00.0350.00211.7550.0700.0700.0000.0000.0000.000
114A130THR00.014-0.0046.269-0.015-0.0150.0000.0000.0000.000
115A131ALA00.0070.0158.1300.0370.0370.0000.0000.0000.000
116A132CYS0-0.013-0.0062.737-0.093-0.7052.379-0.410-1.3570.001
117A133ALA00.0210.0235.378-0.049-0.0490.0000.0000.0000.000
118A134MET00.003-0.0063.809-0.0880.1620.001-0.031-0.2200.000
119A135HIS0-0.006-0.0106.6630.4320.4320.0000.0000.0000.000
120A136ASN0-0.004-0.0109.249-0.186-0.1860.0000.0000.0000.000
121A137THR00.012-0.00511.989-0.032-0.0320.0000.0000.0000.000
122A138PRO00.0850.03810.9750.0370.0370.0000.0000.0000.000
123A139GLY0-0.0120.00412.0180.0600.0600.0000.0000.0000.000
124A140GLN00.0090.00713.2170.0720.0720.0000.0000.0000.000
125A141ARG10.7760.8907.1311.2611.2610.0000.0000.0000.000
126A142LYS10.8630.92010.5090.5160.5160.0000.0000.0000.000
127A143LEU00.0230.00913.0240.0700.0700.0000.0000.0000.000
128A144HIS0-0.027-0.04110.4600.1220.1220.0000.0000.0000.000
129A145GLU-1-0.809-0.89110.668-0.575-0.5750.0000.0000.0000.000
130A146GLU-1-0.955-0.98212.898-0.275-0.2750.0000.0000.0000.000
131A147MET0-0.051-0.01215.5460.0390.0390.0000.0000.0000.000
132A148GLY00.0300.02315.9690.0300.0300.0000.0000.0000.000
133A149PHE0-0.017-0.0037.5900.0180.0180.0000.0000.0000.000
134A150HIS0-0.004-0.00710.4170.0380.0380.0000.0000.0000.000
135A151GLU-1-0.901-0.94812.3230.0260.0260.0000.0000.0000.000
136A152GLY00.0440.02815.7860.0300.0300.0000.0000.0000.000
137A153TRP00.032-0.00610.6430.0550.0550.0000.0000.0000.000
138A154GLY00.0180.01613.9840.0490.0490.0000.0000.0000.000
139A155THR0-0.037-0.03015.0530.0220.0220.0000.0000.0000.000
140A156THR0-0.055-0.02415.7860.0160.0160.0000.0000.0000.000
141A157ILE00.009-0.00213.7850.0160.0160.0000.0000.0000.000
142A158THR0-0.013-0.00717.1930.0170.0170.0000.0000.0000.000
143A159GLN0-0.027-0.01420.204-0.017-0.0170.0000.0000.0000.000
144A160LEU00.0240.02317.613-0.003-0.0030.0000.0000.0000.000
145A161GLU-1-0.835-0.91920.4470.2360.2360.0000.0000.0000.000
146A162GLU-1-0.958-0.98022.1590.1020.1020.0000.0000.0000.000
147A163LEU00.0060.00624.394-0.008-0.0080.0000.0000.0000.000
148A164LEU0-0.001-0.01021.816-0.005-0.0050.0000.0000.0000.000
149A165LYS10.8480.92123.964-0.199-0.1990.0000.0000.0000.000
150A166GLN0-0.044-0.02027.864-0.002-0.0020.0000.0000.0000.000
151A167GLU-1-0.875-0.92428.9050.1080.1080.0000.0000.0000.000
152A168LYS10.9150.97428.638-0.169-0.1690.0000.0000.0000.000
153A169ALA0-0.078-0.03930.1850.0010.0010.0000.0000.0000.000
154A170TYR0-0.011-0.00231.987-0.002-0.0020.0000.0000.0000.000