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: 497LN

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2231183.250223
FMO2-HF: Nuclear repulsion 2155061.748744
FMO2-HF: Total energy -76121.501479
FMO2-MP2: Total energy -76348.85102


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.
-6.515-2.5070.442-1.905-2.5450.007
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 : -0.032 / q_NPA : -0.034
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].
3A6PHE00.0270.0053.780-2.3540.030-0.039-1.181-1.164-0.003
4A7GLY0-0.028-0.0135.0851.2311.307-0.001-0.002-0.0720.000
5A8LYS10.8080.9282.698-5.543-3.9950.482-0.722-1.3090.010
6A9THR00.002-0.0116.892-0.781-0.7810.0000.0000.0000.000
7A10LEU0-0.030-0.0099.1560.1130.1130.0000.0000.0000.000
8A11ALA0-0.012-0.0029.788-0.084-0.0840.0000.0000.0000.000
9A12ALA00.0200.01411.333-0.040-0.0400.0000.0000.0000.000
10A13ARG10.7890.8766.125-0.182-0.1820.0000.0000.0000.000
11A14PRO00.0290.00412.523-0.086-0.0860.0000.0000.0000.000
12A15VAL00.0050.01912.995-0.059-0.0590.0000.0000.0000.000
13A16GLU-1-0.959-0.98715.268-0.276-0.2760.0000.0000.0000.000
14A17ALA00.0160.01917.5160.0340.0340.0000.0000.0000.000
15A18ILE00.0080.00218.1290.0250.0250.0000.0000.0000.000
16A19PRO00.0450.02519.5420.0210.0210.0000.0000.0000.000
17A20GLY00.015-0.00120.974-0.004-0.0040.0000.0000.0000.000
18A21MET0-0.0120.00915.457-0.003-0.0030.0000.0000.0000.000
19A22LEU0-0.045-0.01514.9460.0220.0220.0000.0000.0000.000
20A23GLU-1-0.747-0.8577.508-1.540-1.5400.0000.0000.0000.000
21A24PHE00.016-0.01610.8810.1350.1350.0000.0000.0000.000
22A25ASP-1-0.799-0.8695.4971.9481.9480.0000.0000.0000.000
23A26ILE0-0.015-0.0258.351-0.065-0.0650.0000.0000.0000.000
24A27PRO0-0.023-0.0158.7210.3460.3460.0000.0000.0000.000
25A28VAL0-0.0080.0138.445-0.423-0.4230.0000.0000.0000.000
26A29HIS00.005-0.0019.1040.6640.6640.0000.0000.0000.000
27A30GLY00.0340.00511.165-0.295-0.2950.0000.0000.0000.000
28A31ASP-1-0.781-0.8579.9281.1381.1380.0000.0000.0000.000
29A32ASN00.010-0.01210.653-0.070-0.0700.0000.0000.0000.000
30A33ARG10.7850.85611.690-0.779-0.7790.0000.0000.0000.000
31A34GLY00.0040.01113.948-0.100-0.1000.0000.0000.0000.000
32A35TRP0-0.045-0.02211.6890.1900.1900.0000.0000.0000.000
33A36PHE0-0.008-0.00313.993-0.125-0.1250.0000.0000.0000.000
34A37LYS10.7980.87312.548-0.097-0.0970.0000.0000.0000.000
35A38GLU-1-0.937-0.95714.6570.5220.5220.0000.0000.0000.000
36A39ASN0-0.012-0.01815.0510.0620.0620.0000.0000.0000.000
37A40PHE00.0430.00916.064-0.033-0.0330.0000.0000.0000.000
38A41GLN00.0280.01518.481-0.021-0.0210.0000.0000.0000.000
39A42LYS10.8540.92320.210-0.136-0.1360.0000.0000.0000.000
40A43GLU-1-0.866-0.92322.7440.3940.3940.0000.0000.0000.000
41A44LYS10.8730.92218.386-0.540-0.5400.0000.0000.0000.000
42A45MET0-0.045-0.00315.8080.0260.0260.0000.0000.0000.000
43A46LEU0-0.0120.00919.110-0.027-0.0270.0000.0000.0000.000
44A47PRO0-0.043-0.02720.832-0.025-0.0250.0000.0000.0000.000
45A48LEU0-0.052-0.01614.6930.0120.0120.0000.0000.0000.000
46A49GLY00.0220.01617.534-0.024-0.0240.0000.0000.0000.000
47A50PHE0-0.021-0.00418.338-0.047-0.0470.0000.0000.0000.000
48A51PRO00.0090.01420.2740.0170.0170.0000.0000.0000.000
49A52GLU-1-0.734-0.87823.7320.1270.1270.0000.0000.0000.000
50A53SER0-0.019-0.01326.908-0.001-0.0010.0000.0000.0000.000
51A54PHE0-0.028-0.00923.831-0.008-0.0080.0000.0000.0000.000
52A55PHE00.030-0.01923.903-0.001-0.0010.0000.0000.0000.000
53A56ALA0-0.0240.00228.9460.0040.0040.0000.0000.0000.000
54A57GLU-1-0.856-0.92432.043-0.010-0.0100.0000.0000.0000.000
55A58GLY0-0.048-0.01432.364-0.001-0.0010.0000.0000.0000.000
56A59LYS10.7570.89031.4700.0200.0200.0000.0000.0000.000
57A60LEU0-0.024-0.02225.9330.0050.0050.0000.0000.0000.000
58A61GLN0-0.013-0.02227.8180.0050.0050.0000.0000.0000.000
59A62ASN0-0.066-0.04322.7070.0160.0160.0000.0000.0000.000
60A63ASN00.0120.02924.7080.0200.0200.0000.0000.0000.000
61A64VAL00.022-0.01122.205-0.005-0.0050.0000.0000.0000.000
62A65SER0-0.0220.00521.9930.0030.0030.0000.0000.0000.000
63A66PHE0-0.003-0.00620.433-0.021-0.0210.0000.0000.0000.000
64A67SER0-0.047-0.02121.2520.0100.0100.0000.0000.0000.000
65A68ARG10.8940.92920.8880.2760.2760.0000.0000.0000.000
66A69LYS10.8650.91917.4130.6450.6450.0000.0000.0000.000
67A70ASN00.0050.00419.714-0.010-0.0100.0000.0000.0000.000
68A71VAL0-0.0340.01121.3840.0190.0190.0000.0000.0000.000
69A72LEU00.0100.00720.811-0.069-0.0690.0000.0000.0000.000
70A73ARG10.8000.90021.7150.3870.3870.0000.0000.0000.000
71A74GLY00.0500.03122.104-0.047-0.0470.0000.0000.0000.000
72A75LEU0-0.0340.00321.1080.0060.0060.0000.0000.0000.000
73A76HIS0-0.042-0.06324.4660.0330.0330.0000.0000.0000.000
74A77ALA0-0.0130.00924.833-0.015-0.0150.0000.0000.0000.000
75A78GLU-1-0.759-0.85726.433-0.149-0.1490.0000.0000.0000.000
76A79PRO0-0.014-0.00427.851-0.001-0.0010.0000.0000.0000.000
77A80TRP0-0.031-0.03926.3140.0230.0230.0000.0000.0000.000
78A81ASP-1-0.826-0.89423.727-0.093-0.0930.0000.0000.0000.000
79A82LYS10.8290.89121.0750.2180.2180.0000.0000.0000.000
80A83TYR00.0140.02915.364-0.013-0.0130.0000.0000.0000.000
81A84ILE0-0.011-0.00515.7380.0260.0260.0000.0000.0000.000
82A85SER00.004-0.00714.2290.0290.0290.0000.0000.0000.000
83A86VAL00.0090.01613.059-0.029-0.0290.0000.0000.0000.000
84A87ALA0-0.014-0.01214.5260.1170.1170.0000.0000.0000.000
85A88ASP-1-0.787-0.89715.835-0.212-0.2120.0000.0000.0000.000
86A89GLY0-0.024-0.01812.1420.0160.0160.0000.0000.0000.000
87A90GLY0-0.0080.00511.858-0.134-0.1340.0000.0000.0000.000
88A91LYS10.9320.9478.9702.0632.0630.0000.0000.0000.000
89A92VAL0-0.014-0.00312.2060.1210.1210.0000.0000.0000.000
90A93LEU00.0190.02611.813-0.272-0.2720.0000.0000.0000.000
91A94GLY0-0.011-0.01212.5980.2030.2030.0000.0000.0000.000
92A95THR00.0170.00914.247-0.139-0.1390.0000.0000.0000.000
93A96TRP0-0.029-0.03013.0230.0460.0460.0000.0000.0000.000
94A97VAL00.0500.02618.996-0.032-0.0320.0000.0000.0000.000
95A98ASP-1-0.768-0.84022.178-0.208-0.2080.0000.0000.0000.000
96A99LEU00.0270.01823.9330.0050.0050.0000.0000.0000.000
97A100ARG10.7390.84022.9040.2300.2300.0000.0000.0000.000
98A101GLU-1-0.868-0.96128.910-0.137-0.1370.0000.0000.0000.000
99A102GLY0-0.035-0.02530.6950.0120.0120.0000.0000.0000.000
100A103GLU-1-0.966-0.99128.803-0.157-0.1570.0000.0000.0000.000
101A104THR0-0.023-0.02524.083-0.003-0.0030.0000.0000.0000.000
102A105PHE0-0.0370.00425.218-0.028-0.0280.0000.0000.0000.000
103A106GLY00.014-0.00625.956-0.001-0.0010.0000.0000.0000.000
104A107ASN0-0.051-0.01721.414-0.037-0.0370.0000.0000.0000.000
105A108THR0-0.049-0.04119.3190.0120.0120.0000.0000.0000.000
106A109TYR0-0.050-0.0479.533-0.050-0.0500.0000.0000.0000.000
107A110GLN00.019-0.00913.7130.0570.0570.0000.0000.0000.000
108A111THR0-0.0180.0148.335-0.488-0.4880.0000.0000.0000.000
109A112VAL00.0060.0067.0030.2570.2570.0000.0000.0000.000
110A113ILE0-0.0030.0118.018-0.210-0.2100.0000.0000.0000.000
111A114ASP-1-0.762-0.8696.690-2.144-2.1440.0000.0000.0000.000
112A115ALA0-0.0020.00210.1130.2070.2070.0000.0000.0000.000
113A116SER0-0.006-0.0276.2090.4250.4250.0000.0000.0000.000
114A117LYS10.7960.8975.3303.6563.6560.0000.0000.0000.000
115A118SER0-0.010-0.0098.754-0.102-0.1020.0000.0000.0000.000
116A119ILE0-0.009-0.00910.741-0.038-0.0380.0000.0000.0000.000
117A120PHE0-0.012-0.00414.0600.0480.0480.0000.0000.0000.000
118A121VAL00.013-0.00317.412-0.045-0.0450.0000.0000.0000.000
119A122PRO0-0.033-0.00619.6650.0280.0280.0000.0000.0000.000
120A123ARG10.9250.95522.9850.0630.0630.0000.0000.0000.000
121A124GLY0-0.016-0.03026.1810.0070.0070.0000.0000.0000.000
122A125VAL0-0.044-0.00920.326-0.015-0.0150.0000.0000.0000.000
123A126ALA0-0.0070.00223.2650.0080.0080.0000.0000.0000.000
124A127ASN00.015-0.01419.053-0.065-0.0650.0000.0000.0000.000
125A128GLY00.0530.00919.4680.0490.0490.0000.0000.0000.000
126A129PHE0-0.077-0.03816.772-0.063-0.0630.0000.0000.0000.000
127A130GLN00.0330.02116.8120.0170.0170.0000.0000.0000.000
128A131VAL0-0.079-0.02916.114-0.131-0.1310.0000.0000.0000.000
129A132LEU00.0270.01511.550-0.020-0.0200.0000.0000.0000.000
130A133SER0-0.059-0.03413.599-0.031-0.0310.0000.0000.0000.000
131A134ASP-1-0.829-0.92015.324-0.469-0.4690.0000.0000.0000.000
132A135PHE00.005-0.01317.6930.0490.0490.0000.0000.0000.000
133A136VAL0-0.0080.02715.308-0.060-0.0600.0000.0000.0000.000
134A137ALA00.0150.01717.5850.0390.0390.0000.0000.0000.000
135A138TYR00.0450.02716.6820.0320.0320.0000.0000.0000.000
136A139SER00.0240.00918.3760.0360.0360.0000.0000.0000.000
137A140TYR00.0320.02018.798-0.001-0.0010.0000.0000.0000.000
138A141LEU0-0.0190.00820.8870.0240.0240.0000.0000.0000.000
139A142VAL0-0.018-0.01822.824-0.024-0.0240.0000.0000.0000.000
140A143ASN00.001-0.00725.5850.0030.0030.0000.0000.0000.000
141A144ASP-1-0.796-0.89828.239-0.034-0.0340.0000.0000.0000.000
142A145TYR0-0.033-0.00530.580-0.003-0.0030.0000.0000.0000.000
143A146TRP00.0120.00533.3000.0020.0020.0000.0000.0000.000
144A147ALA00.0470.01934.7570.0090.0090.0000.0000.0000.000
145A148LEU0-0.012-0.01137.890-0.008-0.0080.0000.0000.0000.000
146A149GLU-1-0.952-0.98339.382-0.051-0.0510.0000.0000.0000.000
147A150LEU00.0310.00733.805-0.004-0.0040.0000.0000.0000.000
148A151LYS10.9650.99935.6110.0960.0960.0000.0000.0000.000
149A152PRO0-0.070-0.05436.282-0.010-0.0100.0000.0000.0000.000
150A153LYS10.8300.91134.0710.0870.0870.0000.0000.0000.000
151A154TYR0-0.035-0.00830.4320.0010.0010.0000.0000.0000.000
152A155ALA0-0.036-0.00329.9840.0050.0050.0000.0000.0000.000
153A156PHE0-0.014-0.01728.823-0.006-0.0060.0000.0000.0000.000
154A157VAL00.0010.00626.0410.0110.0110.0000.0000.0000.000
155A158ASN0-0.053-0.03627.223-0.042-0.0420.0000.0000.0000.000
156A159TYR0-0.024-0.04623.728-0.035-0.0350.0000.0000.0000.000
157A160ALA00.0530.03924.375-0.044-0.0440.0000.0000.0000.000
158A161ASP-1-0.793-0.86226.893-0.307-0.3070.0000.0000.0000.000
159A162PRO0-0.031-0.02526.456-0.026-0.0260.0000.0000.0000.000
160A163SER0-0.141-0.09626.625-0.014-0.0140.0000.0000.0000.000
161A164LEU00.0120.01723.5110.0010.0010.0000.0000.0000.000
162A165ASP-1-0.933-0.95320.873-0.630-0.6300.0000.0000.0000.000
163A166ILE0-0.023-0.00518.697-0.067-0.0670.0000.0000.0000.000
164A167LYS10.8730.92217.7920.6860.6860.0000.0000.0000.000
165A168TRP00.010-0.01017.365-0.109-0.1090.0000.0000.0000.000
166A169GLU-1-0.962-0.97814.575-1.354-1.3540.0000.0000.0000.000
167A170ASN0-0.026-0.03217.4180.0550.0550.0000.0000.0000.000
168A171LEU00.0450.03320.9250.0300.0300.0000.0000.0000.000
169A172GLU-1-0.935-0.97723.644-0.509-0.5090.0000.0000.0000.000
170A173GLU-1-0.925-0.95123.990-0.461-0.4610.0000.0000.0000.000
171A174ALA0-0.048-0.01023.739-0.002-0.0020.0000.0000.0000.000
172A175GLU-1-0.802-0.88324.545-0.268-0.2680.0000.0000.0000.000
173A176VAL00.0260.01025.666-0.016-0.0160.0000.0000.0000.000
174A177SER0-0.078-0.05227.7650.0300.0300.0000.0000.0000.000
175A178GLU-1-0.827-0.93730.483-0.212-0.2120.0000.0000.0000.000
176A179ALA0-0.051-0.02032.1010.0020.0020.0000.0000.0000.000
177A180ASP-1-0.779-0.87527.675-0.289-0.2890.0000.0000.0000.000
178A181GLU-1-0.820-0.89129.725-0.328-0.3280.0000.0000.0000.000
179A182ASN0-0.104-0.05631.4450.0080.0080.0000.0000.0000.000
180A183HIS0-0.0380.00928.7450.0240.0240.0000.0000.0000.000
181A184PRO00.0100.01232.408-0.008-0.0080.0000.0000.0000.000
182A185PHE00.0700.02130.934-0.019-0.0190.0000.0000.0000.000
183A186LEU00.0600.02027.4660.0170.0170.0000.0000.0000.000
184A187LYS10.7670.86130.7970.2210.2210.0000.0000.0000.000
185A188ASP-1-0.864-0.91034.171-0.187-0.1870.0000.0000.0000.000
186A189VAL0-0.0200.00730.4040.0100.0100.0000.0000.0000.000
187A190LYS10.8350.91733.6580.1430.1430.0000.0000.0000.000
188A191PRO0-0.043-0.01532.0100.0010.0010.0000.0000.0000.000
189A192LEU00.0190.02429.2570.0170.0170.0000.0000.0000.000
190A193ARG10.8570.90332.2400.0950.0950.0000.0000.0000.000
191A194LYS10.9710.96830.6950.1090.1090.0000.0000.0000.000
192A195GLU-1-0.823-0.88534.668-0.080-0.0800.0000.0000.0000.000
193A196ASP-1-0.813-0.88934.151-0.104-0.1040.0000.0000.0000.000
194A197LEU0-0.0230.01929.179-0.002-0.0020.0000.0000.0000.000