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: K9N23

Calculation Name: 1NXM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NXM

Chain ID: A

ChEMBL ID:

UniProt ID: Q8GIQ0

Base Structure: X-ray

Registration Date: 2023-09-20

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2228205.184061
FMO2-HF: Nuclear repulsion 2152084.397316
FMO2-HF: Total energy -76120.786745
FMO2-MP2: Total energy -76347.94096


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:4:ASN)


Summations of interaction energy for fragment #1(A:4:ASN)
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.
-4.608-0.2390.229-2.007-2.5910.005
Interaction energy analysis for fragmet #1(A:4:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.017
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].
3A6PHE00.0330.0093.780-2.462-0.057-0.040-1.192-1.173-0.003
4A7GLY0-0.023-0.0105.1031.2661.353-0.001-0.002-0.0840.000
5A8LYS10.8560.9493.034-1.0320.8450.270-0.813-1.3340.008
6A9THR00.002-0.0067.029-0.842-0.8420.0000.0000.0000.000
7A10LEU0-0.027-0.0119.4970.0000.0000.0000.0000.0000.000
8A11ALA0-0.013-0.0039.7890.0160.0160.0000.0000.0000.000
9A12ALA00.0280.01711.234-0.128-0.1280.0000.0000.0000.000
10A13ARG10.7630.8656.3020.6540.6540.0000.0000.0000.000
11A14PRO00.0360.01012.460-0.109-0.1090.0000.0000.0000.000
12A15VAL00.0180.02213.161-0.060-0.0600.0000.0000.0000.000
13A16GLU-1-0.966-0.99115.312-0.313-0.3130.0000.0000.0000.000
14A17ALA00.0160.02117.5840.0430.0430.0000.0000.0000.000
15A18ILE00.0060.00418.2140.0300.0300.0000.0000.0000.000
16A19PRO00.0410.02519.6070.0060.0060.0000.0000.0000.000
17A20GLY00.010-0.00220.990-0.002-0.0020.0000.0000.0000.000
18A21MET0-0.0090.01615.454-0.021-0.0210.0000.0000.0000.000
19A22LEU0-0.055-0.02014.9610.0300.0300.0000.0000.0000.000
20A23GLU-1-0.775-0.8687.643-2.132-2.1320.0000.0000.0000.000
21A24PHE00.007-0.01510.8630.1800.1800.0000.0000.0000.000
22A25ASP-1-0.825-0.8865.9960.0810.0810.0000.0000.0000.000
23A26ILE0-0.026-0.0338.3310.1950.1950.0000.0000.0000.000
24A27PRO0-0.036-0.0228.9810.1550.1550.0000.0000.0000.000
25A28VAL00.0030.0168.435-0.314-0.3140.0000.0000.0000.000
26A29HIS00.002-0.0049.1200.6430.6430.0000.0000.0000.000
27A30GLY00.0370.00711.182-0.276-0.2760.0000.0000.0000.000
28A31ASP-1-0.783-0.8759.9291.0781.0780.0000.0000.0000.000
29A32ASN00.011-0.01410.827-0.073-0.0730.0000.0000.0000.000
30A33ARG10.7840.87311.707-0.711-0.7110.0000.0000.0000.000
31A34GLY00.0070.01413.977-0.093-0.0930.0000.0000.0000.000
32A35TRP0-0.046-0.01911.6770.1770.1770.0000.0000.0000.000
33A36PHE0-0.002-0.00114.017-0.113-0.1130.0000.0000.0000.000
34A37LYS10.8030.88712.6280.3780.3780.0000.0000.0000.000
35A38GLU-1-0.927-0.95514.6640.3560.3560.0000.0000.0000.000
36A39ASN00.008-0.00215.458-0.023-0.0230.0000.0000.0000.000
37A40PHE00.0370.01816.261-0.053-0.0530.0000.0000.0000.000
38A41GLN00.0440.02418.746-0.002-0.0020.0000.0000.0000.000
39A42LYS10.9901.00020.499-0.033-0.0330.0000.0000.0000.000
40A43GLU-1-0.954-0.97122.8750.2170.2170.0000.0000.0000.000
41A44LYS10.9420.96018.526-0.469-0.4690.0000.0000.0000.000
42A45MET0-0.0230.00115.8410.0260.0260.0000.0000.0000.000
43A46LEU00.0090.02019.125-0.026-0.0260.0000.0000.0000.000
44A47PRO0-0.034-0.02321.032-0.019-0.0190.0000.0000.0000.000
45A48LEU0-0.058-0.02014.7410.0210.0210.0000.0000.0000.000
46A49GLY00.0200.01417.440-0.034-0.0340.0000.0000.0000.000
47A50PHE0-0.023-0.00418.324-0.048-0.0480.0000.0000.0000.000
48A51PRO00.0090.01220.2400.0330.0330.0000.0000.0000.000
49A52GLU-1-0.866-0.95823.7110.0220.0220.0000.0000.0000.000
50A53SER0-0.023-0.01626.8760.0000.0000.0000.0000.0000.000
51A54PHE0-0.0070.00223.907-0.006-0.0060.0000.0000.0000.000
52A55PHE00.005-0.02423.774-0.001-0.0010.0000.0000.0000.000
53A56ALA0-0.0140.00528.9530.0090.0090.0000.0000.0000.000
54A57GLU-1-0.874-0.93032.050-0.077-0.0770.0000.0000.0000.000
55A58GLY0-0.053-0.01832.3840.0020.0020.0000.0000.0000.000
56A59LYS10.7560.88531.6380.0950.0950.0000.0000.0000.000
57A60LEU0-0.009-0.01425.968-0.002-0.0020.0000.0000.0000.000
58A61GLN0-0.019-0.01427.9070.0160.0160.0000.0000.0000.000
59A62ASN0-0.070-0.03822.6470.0110.0110.0000.0000.0000.000
60A63ASN00.0250.03024.5830.0370.0370.0000.0000.0000.000
61A64VAL00.021-0.00822.027-0.022-0.0220.0000.0000.0000.000
62A65SER0-0.059-0.01421.7170.0070.0070.0000.0000.0000.000
63A66PHE00.007-0.00520.540-0.035-0.0350.0000.0000.0000.000
64A67SER0-0.030-0.00620.8610.0330.0330.0000.0000.0000.000
65A68ARG10.9050.94220.7270.3340.3340.0000.0000.0000.000
66A69LYS10.9700.97517.6750.7290.7290.0000.0000.0000.000
67A70ASN00.0130.00519.613-0.006-0.0060.0000.0000.0000.000
68A71VAL0-0.0140.02021.3000.0240.0240.0000.0000.0000.000
69A72LEU00.0110.00620.646-0.086-0.0860.0000.0000.0000.000
70A73ARG10.8840.95921.5090.4820.4820.0000.0000.0000.000
71A74GLY00.0230.01921.886-0.062-0.0620.0000.0000.0000.000
72A75LEU0-0.0340.00320.9480.0100.0100.0000.0000.0000.000
73A76HIS0-0.047-0.07324.2720.0390.0390.0000.0000.0000.000
74A77ALA0-0.0070.00824.791-0.027-0.0270.0000.0000.0000.000
75A78GLU-1-0.834-0.91226.499-0.264-0.2640.0000.0000.0000.000
76A79PRO0-0.018-0.00827.994-0.005-0.0050.0000.0000.0000.000
77A80TRP0-0.026-0.03126.2720.0300.0300.0000.0000.0000.000
78A81ASP-1-0.822-0.89723.778-0.211-0.2110.0000.0000.0000.000
79A82LYS10.8230.89621.2850.3670.3670.0000.0000.0000.000
80A83TYR0-0.0200.00215.334-0.037-0.0370.0000.0000.0000.000
81A84ILE0-0.011-0.00915.4460.0380.0380.0000.0000.0000.000
82A85SER0-0.007-0.01714.134-0.023-0.0230.0000.0000.0000.000
83A86VAL00.0060.01312.6540.0190.0190.0000.0000.0000.000
84A87ALA0-0.022-0.02114.4710.0730.0730.0000.0000.0000.000
85A88ASP-1-0.795-0.90215.852-0.436-0.4360.0000.0000.0000.000
86A89GLY0-0.028-0.02012.164-0.036-0.0360.0000.0000.0000.000
87A90GLY0-0.0040.00611.876-0.134-0.1340.0000.0000.0000.000
88A91LYS10.9280.9468.7872.2642.2640.0000.0000.0000.000
89A92VAL0-0.013-0.00111.9220.1860.1860.0000.0000.0000.000
90A93LEU00.0020.01311.593-0.346-0.3460.0000.0000.0000.000
91A94GLY0-0.020-0.01112.3990.2230.2230.0000.0000.0000.000
92A95THR00.0320.00714.086-0.160-0.1600.0000.0000.0000.000
93A96TRP0-0.032-0.02313.0760.0350.0350.0000.0000.0000.000
94A97VAL00.0540.02419.041-0.023-0.0230.0000.0000.0000.000
95A98ASP-1-0.762-0.84622.294-0.298-0.2980.0000.0000.0000.000
96A99LEU00.0210.01324.0800.0140.0140.0000.0000.0000.000
97A100ARG10.7490.85323.0340.3240.3240.0000.0000.0000.000
98A101GLU-1-0.939-0.99029.033-0.171-0.1710.0000.0000.0000.000
99A102GLY0-0.027-0.02030.7830.0100.0100.0000.0000.0000.000
100A103GLU-1-0.975-0.99728.967-0.189-0.1890.0000.0000.0000.000
101A104THR0-0.038-0.03024.1520.0010.0010.0000.0000.0000.000
102A105PHE0-0.0280.00925.342-0.034-0.0340.0000.0000.0000.000
103A106GLY00.006-0.01026.1170.0040.0040.0000.0000.0000.000
104A107ASN0-0.051-0.02421.540-0.028-0.0280.0000.0000.0000.000
105A108THR0-0.046-0.03919.3060.0020.0020.0000.0000.0000.000
106A109TYR0-0.063-0.0609.724-0.025-0.0250.0000.0000.0000.000
107A110GLN00.015-0.01013.6460.0760.0760.0000.0000.0000.000
108A111THR0-0.0210.0038.294-0.522-0.5220.0000.0000.0000.000
109A112VAL00.0040.0106.8660.2470.2470.0000.0000.0000.000
110A113ILE0-0.0020.0127.701-0.417-0.4170.0000.0000.0000.000
111A114ASP-1-0.752-0.8846.351-3.510-3.5100.0000.0000.0000.000
112A115ALA0-0.0050.0019.7350.1820.1820.0000.0000.0000.000
113A116SER0-0.015-0.0086.2590.1770.1770.0000.0000.0000.000
114A117LYS10.8290.9184.9084.7244.7240.0000.0000.0000.000
115A118SER0-0.019-0.0078.847-0.004-0.0040.0000.0000.0000.000
116A119ILE00.001-0.00610.933-0.070-0.0700.0000.0000.0000.000
117A120PHE0-0.007-0.00314.1580.0770.0770.0000.0000.0000.000
118A121VAL00.011-0.00517.484-0.042-0.0420.0000.0000.0000.000
119A122PRO0-0.018-0.00119.7720.0390.0390.0000.0000.0000.000
120A123ARG10.9640.98323.0730.1430.1430.0000.0000.0000.000
121A124GLY0-0.018-0.02826.2910.0130.0130.0000.0000.0000.000
122A125VAL0-0.038-0.00720.470-0.009-0.0090.0000.0000.0000.000
123A126ALA0-0.0070.00223.4230.0010.0010.0000.0000.0000.000
124A127ASN00.006-0.01518.911-0.097-0.0970.0000.0000.0000.000
125A128GLY00.0490.00519.2540.0660.0660.0000.0000.0000.000
126A129PHE0-0.073-0.03516.522-0.086-0.0860.0000.0000.0000.000
127A130GLN00.0380.02516.6370.0320.0320.0000.0000.0000.000
128A131VAL0-0.078-0.02815.960-0.160-0.1600.0000.0000.0000.000
129A132LEU00.0160.00611.481-0.004-0.0040.0000.0000.0000.000
130A133SER0-0.074-0.04313.486-0.023-0.0230.0000.0000.0000.000
131A134ASP-1-0.881-0.95015.223-0.524-0.5240.0000.0000.0000.000
132A135PHE0-0.004-0.01917.7010.0630.0630.0000.0000.0000.000
133A136VAL0-0.0040.02815.047-0.084-0.0840.0000.0000.0000.000
134A137ALA00.0230.02417.4070.0640.0640.0000.0000.0000.000
135A138TYR00.0470.02816.4330.0070.0070.0000.0000.0000.000
136A139SER00.0140.00318.0140.0690.0690.0000.0000.0000.000
137A140TYR00.0310.01918.654-0.025-0.0250.0000.0000.0000.000
138A141LEU0-0.0170.00620.8330.0410.0410.0000.0000.0000.000
139A142VAL0-0.012-0.01622.926-0.032-0.0320.0000.0000.0000.000
140A143ASN0-0.002-0.00825.6870.0040.0040.0000.0000.0000.000
141A144ASP-1-0.794-0.89928.317-0.106-0.1060.0000.0000.0000.000
142A145TYR0-0.025-0.00230.694-0.009-0.0090.0000.0000.0000.000
143A146TRP0-0.0010.00133.0790.0070.0070.0000.0000.0000.000
144A147ALA00.0660.02334.7790.0120.0120.0000.0000.0000.000
145A148LEU0-0.020-0.01237.953-0.008-0.0080.0000.0000.0000.000
146A149GLU-1-0.951-0.98139.587-0.102-0.1020.0000.0000.0000.000
147A150LEU00.0360.01033.858-0.003-0.0030.0000.0000.0000.000
148A151LYS10.9640.99735.7380.1430.1430.0000.0000.0000.000
149A152PRO0-0.083-0.06236.312-0.011-0.0110.0000.0000.0000.000
150A153LYS10.8760.96034.1590.1380.1380.0000.0000.0000.000
151A154TYR00.0020.01930.829-0.010-0.0100.0000.0000.0000.000
152A155ALA0-0.0210.00230.0770.0100.0100.0000.0000.0000.000
153A156PHE0-0.021-0.01628.699-0.012-0.0120.0000.0000.0000.000
154A157VAL00.0000.00425.8740.0160.0160.0000.0000.0000.000
155A158ASN0-0.059-0.04327.069-0.048-0.0480.0000.0000.0000.000
156A159TYR0-0.016-0.03023.595-0.033-0.0330.0000.0000.0000.000
157A160ALA00.0480.03324.335-0.045-0.0450.0000.0000.0000.000
158A161ASP-1-0.795-0.87426.874-0.340-0.3400.0000.0000.0000.000
159A162PRO0-0.040-0.02726.472-0.028-0.0280.0000.0000.0000.000
160A163SER0-0.137-0.08826.718-0.010-0.0100.0000.0000.0000.000
161A164LEU00.0000.01023.4700.0020.0020.0000.0000.0000.000
162A165ASP-1-0.935-0.95520.811-0.662-0.6620.0000.0000.0000.000
163A166ILE0-0.017-0.00118.745-0.077-0.0770.0000.0000.0000.000
164A167LYS10.9080.94617.8310.7010.7010.0000.0000.0000.000
165A168TRP00.010-0.01017.412-0.136-0.1360.0000.0000.0000.000
166A169GLU-1-0.977-0.98314.847-1.306-1.3060.0000.0000.0000.000
167A170ASN0-0.003-0.00917.4940.0670.0670.0000.0000.0000.000
168A171LEU00.0340.01920.9950.0230.0230.0000.0000.0000.000
169A172GLU-1-0.943-0.97523.691-0.535-0.5350.0000.0000.0000.000
170A173GLU-1-0.960-0.97924.050-0.480-0.4800.0000.0000.0000.000
171A174ALA0-0.057-0.01323.671-0.009-0.0090.0000.0000.0000.000
172A175GLU-1-0.880-0.93224.450-0.340-0.3400.0000.0000.0000.000
173A176VAL00.0150.00125.556-0.026-0.0260.0000.0000.0000.000
174A177SER0-0.072-0.02827.6210.0340.0340.0000.0000.0000.000
175A178GLU-1-0.816-0.93230.291-0.260-0.2600.0000.0000.0000.000
176A179ALA0-0.057-0.02431.8580.0040.0040.0000.0000.0000.000
177A180ASP-1-0.781-0.89126.786-0.384-0.3840.0000.0000.0000.000
178A181GLU-1-0.829-0.90629.584-0.373-0.3730.0000.0000.0000.000
179A182ASN0-0.106-0.05531.3240.0120.0120.0000.0000.0000.000
180A183HIS0-0.0160.01928.8330.0260.0260.0000.0000.0000.000
181A184PRO00.0130.01732.249-0.005-0.0050.0000.0000.0000.000
182A185PHE00.0710.01730.861-0.021-0.0210.0000.0000.0000.000
183A186LEU00.0670.02527.6950.0180.0180.0000.0000.0000.000
184A187LYS10.7980.88130.7330.2490.2490.0000.0000.0000.000
185A188ASP-1-0.890-0.92334.075-0.210-0.2100.0000.0000.0000.000
186A189VAL0-0.0290.00430.3740.0090.0090.0000.0000.0000.000
187A190LYS10.9230.96233.6860.1790.1790.0000.0000.0000.000
188A191PRO0-0.032-0.01532.156-0.002-0.0020.0000.0000.0000.000
189A192LEU0-0.0010.01229.4080.0170.0170.0000.0000.0000.000
190A193ARG10.9830.99732.3570.1350.1350.0000.0000.0000.000
191A194LYS10.9670.96530.6590.1500.1500.0000.0000.0000.000
192A195GLU-1-0.958-0.97534.752-0.119-0.1190.0000.0000.0000.000
193A196ASP-1-0.848-0.93134.272-0.154-0.1540.0000.0000.0000.000
194A197LEU0-0.031-0.00329.249-0.005-0.0050.0000.0000.0000.000