FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 16N8Z

Calculation Name: 2NX4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NX4

Chain ID: A

ChEMBL ID:

UniProt ID: Q0SCU8

Base Structure: X-ray

Registration Date: 2023-09-27

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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2088980.899059
FMO2-HF: Nuclear repulsion 2010786.39883
FMO2-HF: Total energy -78194.500229
FMO2-MP2: Total energy -78416.298822


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:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
-0.4050.889-0.007-0.674-0.6130.004
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.007
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].
3A2PRO00.0170.0073.803-0.2001.094-0.007-0.674-0.6130.004
4A3LYS10.9830.9856.3671.2241.2240.0000.0000.0000.000
5A4LEU00.0050.0068.6320.2020.2020.0000.0000.0000.000
6A5VAL00.0570.0308.2340.1430.1430.0000.0000.0000.000
7A6ASP-1-0.837-0.9047.551-0.529-0.5290.0000.0000.0000.000
8A7HIS0-0.083-0.0859.4480.3120.3120.0000.0000.0000.000
9A8ASP-1-0.864-0.91712.850-0.617-0.6170.0000.0000.0000.000
10A9GLU-1-0.936-0.9699.728-0.922-0.9220.0000.0000.0000.000
11A10ARG10.8820.94111.9810.4180.4180.0000.0000.0000.000
12A11ARG10.8190.88215.0050.4910.4910.0000.0000.0000.000
13A12ARG10.8320.87416.1110.4690.4690.0000.0000.0000.000
14A13SER0-0.042-0.02315.9500.0550.0550.0000.0000.0000.000
15A14ILE0-0.041-0.02118.5150.0400.0400.0000.0000.0000.000
16A15THR0-0.0170.00620.9360.0170.0170.0000.0000.0000.000
17A16ALA00.0180.01221.7670.0200.0200.0000.0000.0000.000
18A17ALA0-0.062-0.02723.0990.0190.0190.0000.0000.0000.000
19A18ALA00.0250.02324.8860.0140.0140.0000.0000.0000.000
20A19TRP0-0.0110.00026.3430.0100.0100.0000.0000.0000.000
21A20ARG10.8530.88828.1380.1120.1120.0000.0000.0000.000
22A21LEU00.0020.02930.6140.0080.0080.0000.0000.0000.000
23A22ILE0-0.043-0.04328.5780.0060.0060.0000.0000.0000.000
24A23ALA00.0020.01432.4870.0050.0050.0000.0000.0000.000
25A24ALA0-0.028-0.01134.5660.0060.0060.0000.0000.0000.000
26A25ARG10.8340.90835.1010.0760.0760.0000.0000.0000.000
27A26GLY00.0470.03436.1750.0040.0040.0000.0000.0000.000
28A27ILE00.009-0.00931.0930.0020.0020.0000.0000.0000.000
29A28GLU-1-0.841-0.93134.767-0.108-0.1080.0000.0000.0000.000
30A29ALA0-0.0120.00237.4630.0030.0030.0000.0000.0000.000
31A30ALA0-0.0250.01032.4180.0040.0040.0000.0000.0000.000
32A31ASN0-0.030-0.02532.751-0.003-0.0030.0000.0000.0000.000
33A32MET00.0790.02627.575-0.002-0.0020.0000.0000.0000.000
34A33ARG10.8950.95128.3650.0540.0540.0000.0000.0000.000
35A34ASP-1-0.825-0.87829.810-0.060-0.0600.0000.0000.0000.000
36A35ILE00.0480.02925.7850.0030.0030.0000.0000.0000.000
37A36ALA0-0.029-0.01125.165-0.003-0.0030.0000.0000.0000.000
38A37THR0-0.058-0.05825.7380.0090.0090.0000.0000.0000.000
39A38GLU-1-0.878-0.94927.618-0.082-0.0820.0000.0000.0000.000
40A39ALA00.0160.02322.6040.0000.0000.0000.0000.0000.000
41A40GLY0-0.0280.00022.529-0.001-0.0010.0000.0000.0000.000
42A41TYR0-0.040-0.01817.048-0.009-0.0090.0000.0000.0000.000
43A42THR00.013-0.00122.4880.0000.0000.0000.0000.0000.000
44A43ASN00.048-0.00923.759-0.010-0.0100.0000.0000.0000.000
45A44GLY00.0050.01023.713-0.013-0.0130.0000.0000.0000.000
46A45ALA0-0.003-0.00319.293-0.019-0.0190.0000.0000.0000.000
47A46LEU00.0310.01719.814-0.031-0.0310.0000.0000.0000.000
48A47SER0-0.005-0.01221.751-0.017-0.0170.0000.0000.0000.000
49A48HIS0-0.104-0.03014.8570.0130.0130.0000.0000.0000.000
50A49TYR0-0.033-0.01812.942-0.004-0.0040.0000.0000.0000.000
51A50PHE00.0130.01818.831-0.029-0.0290.0000.0000.0000.000
52A51ALA00.0120.01322.3600.0210.0210.0000.0000.0000.000
53A52GLY00.009-0.01125.0520.0220.0220.0000.0000.0000.000
54A53LYS10.8350.90826.9980.0940.0940.0000.0000.0000.000
55A54ASP-1-0.812-0.89729.164-0.173-0.1730.0000.0000.0000.000
56A55GLU-1-0.773-0.86822.366-0.326-0.3260.0000.0000.0000.000
57A56ILE00.0040.00324.426-0.011-0.0110.0000.0000.0000.000
58A57LEU0-0.0140.01626.0270.0010.0010.0000.0000.0000.000
59A58ARG10.8760.92222.2000.3200.3200.0000.0000.0000.000
60A59THR0-0.013-0.02121.433-0.001-0.0010.0000.0000.0000.000
61A60SER0-0.020-0.04324.3430.0010.0010.0000.0000.0000.000
62A61TYR00.020-0.00526.8820.0090.0090.0000.0000.0000.000
63A62GLU-1-0.809-0.89522.903-0.322-0.3220.0000.0000.0000.000
64A63HIS0-0.0020.00023.185-0.002-0.0020.0000.0000.0000.000
65A64ILE0-0.005-0.00225.1530.0050.0050.0000.0000.0000.000
66A65SER0-0.0260.00427.3810.0120.0120.0000.0000.0000.000
67A66GLU-1-0.800-0.86221.542-0.349-0.3490.0000.0000.0000.000
68A67ALA0-0.051-0.01825.7250.0070.0070.0000.0000.0000.000
69A68THR00.018-0.00727.3140.0140.0140.0000.0000.0000.000
70A69ASP-1-0.844-0.92027.398-0.186-0.1860.0000.0000.0000.000
71A70ARG10.7490.84724.0810.1500.1500.0000.0000.0000.000
72A71ARG10.7470.84427.5210.1300.1300.0000.0000.0000.000
73A72ILE00.0180.01730.8760.0100.0100.0000.0000.0000.000
74A73ALA0-0.029-0.02028.4020.0070.0070.0000.0000.0000.000
75A74GLU-1-0.902-0.93026.634-0.123-0.1230.0000.0000.0000.000
76A75ALA0-0.024-0.00330.8300.0090.0090.0000.0000.0000.000
77A76LEU0-0.054-0.02033.5740.0060.0060.0000.0000.0000.000
78A77GLY00.0030.00934.2190.0060.0060.0000.0000.0000.000
79A78ASP-1-0.984-1.00235.574-0.071-0.0710.0000.0000.0000.000
80A79ALA0-0.0170.00738.2660.0030.0030.0000.0000.0000.000
81A80THR0-0.031-0.01939.513-0.005-0.0050.0000.0000.0000.000
82A81GLY00.0480.02742.1010.0030.0030.0000.0000.0000.000
83A82LEU00.002-0.02443.459-0.004-0.0040.0000.0000.0000.000
84A83ASP-1-0.906-0.94143.628-0.061-0.0610.0000.0000.0000.000
85A84ALA00.0050.00539.217-0.002-0.0020.0000.0000.0000.000
86A85LEU0-0.005-0.00639.745-0.005-0.0050.0000.0000.0000.000
87A86ARG10.8190.88441.3360.0570.0570.0000.0000.0000.000
88A87ILE0-0.045-0.01336.825-0.001-0.0010.0000.0000.0000.000
89A88LEU00.0430.02436.020-0.003-0.0030.0000.0000.0000.000
90A89CYS0-0.006-0.02537.559-0.004-0.0040.0000.0000.0000.000
91A90ARG10.8930.94939.8460.0690.0690.0000.0000.0000.000
92A91GLU-1-0.858-0.91334.278-0.097-0.0970.0000.0000.0000.000
93A92VAL00.0130.01535.440-0.005-0.0050.0000.0000.0000.000
94A93MET0-0.0140.00837.0990.0010.0010.0000.0000.0000.000
95A94PRO0-0.0100.01139.3340.0000.0000.0000.0000.0000.000
96A95ILE00.0140.00740.3480.0060.0060.0000.0000.0000.000
97A96ASN0-0.042-0.02837.4810.0040.0040.0000.0000.0000.000
98A97GLU-1-0.864-0.94638.411-0.073-0.0730.0000.0000.0000.000
99A98GLU-1-0.768-0.85231.436-0.105-0.1050.0000.0000.0000.000
100A99GLN00.0470.01635.006-0.005-0.0050.0000.0000.0000.000
101A100LEU00.0060.01836.616-0.004-0.0040.0000.0000.0000.000
102A101LEU0-0.070-0.03234.309-0.003-0.0030.0000.0000.0000.000
103A102GLU-1-0.818-0.89831.190-0.139-0.1390.0000.0000.0000.000
104A103ALA00.0510.03434.137-0.006-0.0060.0000.0000.0000.000
105A104ARG10.8650.94236.5860.0790.0790.0000.0000.0000.000
106A105ILE0-0.055-0.01930.355-0.002-0.0020.0000.0000.0000.000
107A106ALA00.0400.01333.788-0.006-0.0060.0000.0000.0000.000
108A107ALA0-0.0030.00134.927-0.002-0.0020.0000.0000.0000.000
109A108SER0-0.052-0.02634.8690.0030.0030.0000.0000.0000.000
110A109LEU0-0.032-0.01230.774-0.001-0.0010.0000.0000.0000.000
111A110TRP00.004-0.00934.0620.0010.0010.0000.0000.0000.000
112A111PRO00.008-0.00436.822-0.001-0.0010.0000.0000.0000.000
113A112ARG10.8090.87733.4020.1350.1350.0000.0000.0000.000
114A113ALA00.0370.02533.633-0.004-0.0040.0000.0000.0000.000
115A114MET0-0.076-0.01934.8630.0010.0010.0000.0000.0000.000
116A115TYR0-0.073-0.03237.0240.0080.0080.0000.0000.0000.000
117A116ASP-1-0.828-0.92630.845-0.209-0.2090.0000.0000.0000.000
118A117GLU-1-0.882-0.92131.377-0.179-0.1790.0000.0000.0000.000
119A118GLN0-0.046-0.02224.660-0.035-0.0350.0000.0000.0000.000
120A119MET0-0.087-0.05528.355-0.011-0.0110.0000.0000.0000.000
121A120ALA00.0520.04130.1330.0060.0060.0000.0000.0000.000
122A121ALA0-0.076-0.03827.6750.0010.0010.0000.0000.0000.000
123A122THR0-0.040-0.04225.0840.0050.0050.0000.0000.0000.000
124A123ASN00.0580.05728.0840.0060.0060.0000.0000.0000.000
125A124ARG10.8840.92331.7550.1730.1730.0000.0000.0000.000
126A125ARG10.9340.97825.2840.2960.2960.0000.0000.0000.000
127A126THR00.0450.03329.618-0.002-0.0020.0000.0000.0000.000
128A127MET0-0.028-0.00931.2140.0120.0120.0000.0000.0000.000
129A128ASP-1-0.782-0.88533.679-0.149-0.1490.0000.0000.0000.000
130A129ASN00.0050.01730.3560.0080.0080.0000.0000.0000.000
131A130TRP0-0.006-0.02831.7780.0120.0120.0000.0000.0000.000
132A131ARG10.8030.86035.4120.1340.1340.0000.0000.0000.000
133A132GLU-1-0.966-0.98033.665-0.158-0.1580.0000.0000.0000.000
134A133GLN0-0.015-0.00732.4940.0060.0060.0000.0000.0000.000
135A134MET0-0.017-0.01036.8340.0060.0060.0000.0000.0000.000
136A135ALA00.0210.00340.1280.0070.0070.0000.0000.0000.000
137A136ILE0-0.029-0.00336.7150.0050.0050.0000.0000.0000.000
138A137PHE0-0.008-0.00836.4440.0040.0040.0000.0000.0000.000
139A138LEU00.005-0.01142.1350.0060.0060.0000.0000.0000.000
140A139GLU-1-0.820-0.89644.363-0.072-0.0720.0000.0000.0000.000
141A140GLN00.0150.00740.6860.0030.0030.0000.0000.0000.000
142A141ALA00.0280.01445.6690.0040.0040.0000.0000.0000.000
143A142ARG10.7340.84248.2030.0720.0720.0000.0000.0000.000
144A143GLU-1-1.007-0.99847.402-0.069-0.0690.0000.0000.0000.000
145A144GLU-1-0.919-0.97246.381-0.063-0.0630.0000.0000.0000.000
146A145GLY0-0.045-0.01150.9770.0030.0030.0000.0000.0000.000
147A146SER0-0.076-0.03649.5600.0020.0020.0000.0000.0000.000
148A147VAL0-0.045-0.01850.1210.0000.0000.0000.0000.0000.000
149A148GLY00.004-0.00553.0260.0010.0010.0000.0000.0000.000
150A149ASP-1-0.869-0.92253.605-0.062-0.0620.0000.0000.0000.000
151A150ILE0-0.042-0.02048.8390.0000.0000.0000.0000.0000.000
152A151ASP-1-0.853-0.93049.979-0.078-0.0780.0000.0000.0000.000
153A152VAL00.0400.00844.918-0.002-0.0020.0000.0000.0000.000
154A153THR00.0050.00044.674-0.004-0.0040.0000.0000.0000.000
155A154ILE0-0.012-0.00545.880-0.003-0.0030.0000.0000.0000.000
156A155VAL00.0100.01547.280-0.001-0.0010.0000.0000.0000.000
157A156VAL00.0070.00841.499-0.001-0.0010.0000.0000.0000.000
158A157GLU-1-0.798-0.86542.911-0.111-0.1110.0000.0000.0000.000
159A158GLN0-0.031-0.01645.0340.0000.0000.0000.0000.0000.000
160A159LEU00.0280.01743.5110.0010.0010.0000.0000.0000.000
161A160LEU00.0270.01538.458-0.001-0.0010.0000.0000.0000.000
162A161ASN0-0.070-0.06242.280-0.002-0.0020.0000.0000.0000.000
163A162MET0-0.036-0.00344.4650.0010.0010.0000.0000.0000.000
164A163MET00.0170.00340.1020.0020.0020.0000.0000.0000.000
165A164MET0-0.0170.00237.727-0.004-0.0040.0000.0000.0000.000
166A165GLY00.0260.00841.5470.0000.0000.0000.0000.0000.000
167A166MET0-0.025-0.01843.2510.0020.0020.0000.0000.0000.000
168A167GLN0-0.044-0.01738.2520.0010.0010.0000.0000.0000.000
169A168ILE0-0.033-0.01241.2770.0010.0010.0000.0000.0000.000
170A169LEU00.019-0.00143.6950.0030.0030.0000.0000.0000.000
171A170GLY00.0340.02544.4890.0040.0040.0000.0000.0000.000
172A171VAL0-0.057-0.02740.7390.0030.0030.0000.0000.0000.000
173A172LEU0-0.064-0.03944.0810.0040.0040.0000.0000.0000.000
174A173THR0-0.075-0.02946.9880.0030.0030.0000.0000.0000.000
175A174PRO00.0390.01946.9280.0010.0010.0000.0000.0000.000
176A175GLY0-0.008-0.00148.8190.0010.0010.0000.0000.0000.000
177A176GLU-1-0.955-0.99052.467-0.048-0.0480.0000.0000.0000.000
178A177THR0-0.033-0.01547.360-0.001-0.0010.0000.0000.0000.000
179A178SER00.013-0.00947.608-0.004-0.0040.0000.0000.0000.000
180A179SER00.010-0.01844.312-0.001-0.0010.0000.0000.0000.000
181A180GLU-1-0.826-0.90846.550-0.050-0.0500.0000.0000.0000.000
182A181ARG10.8970.95849.5880.0490.0490.0000.0000.0000.000
183A182GLN0-0.003-0.01643.786-0.003-0.0030.0000.0000.0000.000
184A183LEU0-0.014-0.00944.218-0.001-0.0010.0000.0000.0000.000
185A184GLU-1-0.861-0.90647.763-0.047-0.0470.0000.0000.0000.000
186A185MET0-0.064-0.03649.2190.0000.0000.0000.0000.0000.000
187A186LEU00.0180.00944.316-0.001-0.0010.0000.0000.0000.000
188A187GLU-1-0.812-0.88648.184-0.059-0.0590.0000.0000.0000.000
189A188GLN0-0.083-0.06150.7360.0010.0010.0000.0000.0000.000
190A189PHE0-0.028-0.01347.7970.0010.0010.0000.0000.0000.000
191A190VAL00.016-0.00847.4960.0000.0000.0000.0000.0000.000
192A191ALA0-0.027-0.00650.7850.0010.0010.0000.0000.0000.000
193A192ALA0-0.064-0.02254.2960.0020.0020.0000.0000.0000.000
194A193LEU0-0.0380.01549.4260.0010.0010.0000.0000.0000.000