Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 2NJYR

Calculation Name: 3H8N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H8N

Chain ID: A

ChEMBL ID:

UniProt ID: P43632

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:


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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1988513.201181
FMO2-HF: Nuclear repulsion 1912152.667883
FMO2-HF: Total energy -76360.533298
FMO2-MP2: Total energy -76580.507881


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:ARG)


Summations of interaction energy for fragment #1(A:6:ARG)
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.
-84.686-77.7195.253-3.571-8.653-0.009
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.953 / q_NPA : 0.967
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].
3A8PRO00.001-0.0013.765-0.4141.141-0.020-0.564-0.9710.000
4A9SER0-0.021-0.0096.6061.8391.8390.0000.0000.0000.000
5A10PHE0-0.048-0.0498.653-0.151-0.1510.0000.0000.0000.000
6A11LEU00.0290.02211.7710.9050.9050.0000.0000.0000.000
7A12ALA00.0180.01515.199-0.150-0.1500.0000.0000.0000.000
8A13LEU0-0.0510.00218.8120.2800.2800.0000.0000.0000.000
9A14PRO00.044-0.00721.6730.0500.0500.0000.0000.0000.000
10A15GLY00.0570.01921.530-0.269-0.2690.0000.0000.0000.000
11A16HIS10.7830.85620.15212.30012.3000.0000.0000.0000.000
12A17LEU0-0.047-0.00122.0540.1160.1160.0000.0000.0000.000
13A18VAL00.0120.00225.3510.1300.1300.0000.0000.0000.000
14A19LYS10.9320.97427.8398.6468.6460.0000.0000.0000.000
15A20SER00.0630.01630.945-0.288-0.2880.0000.0000.0000.000
16A21GLU-1-1.019-1.01032.643-8.317-8.3170.0000.0000.0000.000
17A22GLU-1-0.880-0.92130.274-9.675-9.6750.0000.0000.0000.000
18A23THR0-0.023-0.01627.431-0.116-0.1160.0000.0000.0000.000
19A24VAL0-0.039-0.01022.3970.1050.1050.0000.0000.0000.000
20A25ILE0-0.009-0.00819.958-0.280-0.2800.0000.0000.0000.000
21A26LEU0-0.003-0.01117.165-0.177-0.1770.0000.0000.0000.000
22A27GLN0-0.017-0.01514.906-0.932-0.9320.0000.0000.0000.000
23A28CYS0-0.059-0.02110.3660.3560.3560.0000.0000.0000.000
24A29TRP00.025-0.00110.337-0.038-0.0380.0000.0000.0000.000
25A30SER0-0.041-0.0235.674-2.922-2.9220.0000.0000.0000.000
26A31ASP-1-0.855-0.9076.554-27.938-27.9380.0000.0000.0000.000
27A32VAL0-0.054-0.0243.037-1.421-0.4980.059-0.226-0.757-0.002
28A33MET00.0550.0226.0391.2621.2620.0000.0000.0000.000
29A34PHE0-0.067-0.0292.173-8.487-6.8451.010-0.960-1.693-0.005
30A35GLU-1-0.806-0.8756.587-24.368-24.3680.0000.0000.0000.000
31A36HIS10.7690.8598.28527.88027.8800.0000.0000.0000.000
32A37PHE00.0360.0108.007-4.313-4.3130.0000.0000.0000.000
33A38LEU0-0.024-0.01610.0912.7352.7350.0000.0000.0000.000
34A39LEU00.0030.00611.821-1.185-1.1850.0000.0000.0000.000
35A40HIS0-0.024-0.03113.7281.4081.4080.0000.0000.0000.000
36A41ARG10.8480.94815.24713.23013.2300.0000.0000.0000.000
37A42GLU-1-0.864-0.94915.026-17.489-17.4890.0000.0000.0000.000
38A43GLY00.0220.00719.0650.5890.5890.0000.0000.0000.000
39A44LYS10.9330.94322.53210.30810.3080.0000.0000.0000.000
40A45PHE00.0180.01024.915-0.126-0.1260.0000.0000.0000.000
41A46ASN00.0200.04719.6700.3690.3690.0000.0000.0000.000
42A47ASN00.017-0.01519.8470.3580.3580.0000.0000.0000.000
43A48THR0-0.0070.00714.753-0.618-0.6180.0000.0000.0000.000
44A49LEU0-0.0160.01116.7300.6710.6710.0000.0000.0000.000
45A50HIS00.0540.02012.747-2.317-2.3170.0000.0000.0000.000
46A51LEU0-0.0110.00313.8681.2731.2730.0000.0000.0000.000
47A52ILE0-0.005-0.00612.988-1.725-1.7250.0000.0000.0000.000
48A53GLY0-0.040-0.01413.0400.5550.5550.0000.0000.0000.000
49A54GLU-1-0.877-0.94012.396-21.763-21.7630.0000.0000.0000.000
50A55HIS00.0720.05310.346-1.444-1.4440.0000.0000.0000.000
51A56HIS0-0.127-0.06913.6611.7621.7620.0000.0000.0000.000
52A57ASP-1-0.881-0.94215.195-19.233-19.2330.0000.0000.0000.000
53A58GLY0-0.0410.00114.1331.0471.0470.0000.0000.0000.000
54A59VAL0-0.021-0.01111.667-1.554-1.5540.0000.0000.0000.000
55A60SER00.013-0.0109.0540.7650.7650.0000.0000.0000.000
56A61LYS10.9140.95411.07417.12817.1280.0000.0000.0000.000
57A62ALA00.0290.03013.0240.6090.6090.0000.0000.0000.000
58A63ASN0-0.016-0.01114.602-0.402-0.4020.0000.0000.0000.000
59A64PHE00.030-0.00713.6710.5930.5930.0000.0000.0000.000
60A65SER0-0.0010.01219.0340.3680.3680.0000.0000.0000.000
61A66ILE0-0.010-0.00920.476-0.151-0.1510.0000.0000.0000.000
62A67GLY00.0480.02124.0250.2660.2660.0000.0000.0000.000
63A68PRO0-0.003-0.02627.707-0.144-0.1440.0000.0000.0000.000
64A69MET0-0.067-0.00125.236-0.193-0.1930.0000.0000.0000.000
65A70MET00.0590.02628.8730.4440.4440.0000.0000.0000.000
66A71PRO00.0310.00728.651-0.455-0.4550.0000.0000.0000.000
67A72VAL0-0.0140.00527.637-0.194-0.1940.0000.0000.0000.000
68A73LEU0-0.063-0.03024.633-0.505-0.5050.0000.0000.0000.000
69A74ALA00.0390.03823.857-0.517-0.5170.0000.0000.0000.000
70A75GLY00.0300.00522.6650.0660.0660.0000.0000.0000.000
71A76THR0-0.013-0.02116.821-0.010-0.0100.0000.0000.0000.000
72A77TYR0-0.044-0.04516.128-0.357-0.3570.0000.0000.0000.000
73A78ARG10.8780.94510.70720.21820.2180.0000.0000.0000.000
74A80TYR0-0.0050.0017.081-1.633-1.6330.0000.0000.0000.000
75A81GLY00.0460.0225.3933.7183.7180.0000.0000.0000.000
76A82SER0-0.017-0.0204.317-6.134-6.002-0.001-0.011-0.1200.000
77A83VAL00.0730.0263.810-0.432-0.276-0.001-0.025-0.1310.000
78A84PRO0-0.0140.0105.8774.0994.0990.0000.0000.0000.000
79A85HIS00.002-0.0049.0670.8460.8460.0000.0000.0000.000
80A86SER0-0.0130.06411.715-0.875-0.8750.0000.0000.0000.000
81A87PRO0-0.005-0.04412.3900.6480.6480.0000.0000.0000.000
82A88TYR0-0.010-0.0378.2860.1650.1650.0000.0000.0000.000
83A89GLN00.009-0.0075.077-2.769-2.7690.0000.0000.0000.000
84A90LEU0-0.065-0.0134.564-6.306-6.196-0.001-0.007-0.1020.000
85A91SER0-0.019-0.0122.186-4.530-3.2682.007-0.918-2.3510.000
86A92ALA0-0.036-0.0212.0526.1507.1892.199-0.832-2.407-0.002
87A93PRO00.0580.0213.958-1.375-1.2270.001-0.028-0.1210.000
88A94SER00.0530.0426.110-1.825-1.8250.0000.0000.0000.000
89A95ASP-1-0.842-0.9108.367-20.832-20.8320.0000.0000.0000.000
90A96PRO0-0.027-0.01310.460-0.145-0.1450.0000.0000.0000.000
91A97LEU00.0030.00613.9430.5940.5940.0000.0000.0000.000
92A98ASP-1-0.832-0.89616.631-13.926-13.9260.0000.0000.0000.000
93A99MET0-0.0270.01318.8480.4620.4620.0000.0000.0000.000
94A100VAL00.006-0.00222.5790.2450.2450.0000.0000.0000.000
95A101ILE00.0320.03425.8860.0350.0350.0000.0000.0000.000
96A102ILE0-0.013-0.00728.8240.3160.3160.0000.0000.0000.000
97A103GLY0-0.071-0.06331.4550.0770.0770.0000.0000.0000.000
98A104LEU00.0210.01832.9820.0930.0930.0000.0000.0000.000
99A105TYR00.0370.02434.9200.2650.2650.0000.0000.0000.000
100A106GLU-1-0.868-0.90238.877-6.914-6.9140.0000.0000.0000.000
101A107LYS10.8220.90338.4737.0017.0010.0000.0000.0000.000
102A108PRO0-0.027-0.00436.4610.1780.1780.0000.0000.0000.000
103A109SER0-0.030-0.01539.715-0.012-0.0120.0000.0000.0000.000
104A110LEU00.007-0.01435.744-0.114-0.1140.0000.0000.0000.000
105A111SER0-0.022-0.01139.6960.1500.1500.0000.0000.0000.000
106A112ALA00.0210.01140.134-0.123-0.1230.0000.0000.0000.000
107A113GLN0-0.0100.03441.0500.2560.2560.0000.0000.0000.000
108A114PRO00.038-0.00541.621-0.149-0.1490.0000.0000.0000.000
109A115GLY00.046-0.00143.2350.1390.1390.0000.0000.0000.000
110A116PRO0-0.027-0.01140.702-0.118-0.1180.0000.0000.0000.000
111A117THR0-0.0040.00540.235-0.184-0.1840.0000.0000.0000.000
112A118VAL0-0.0100.00737.9990.1180.1180.0000.0000.0000.000
113A119GLN00.0610.04140.619-0.008-0.0080.0000.0000.0000.000
114A120ALA00.043-0.01137.555-0.097-0.0970.0000.0000.0000.000
115A121GLY0-0.030-0.02036.6320.1390.1390.0000.0000.0000.000
116A122GLU-1-0.921-0.95437.632-6.708-6.7080.0000.0000.0000.000
117A123ASN0-0.026-0.01736.555-0.358-0.3580.0000.0000.0000.000
118A124VAL00.0120.01837.0130.1630.1630.0000.0000.0000.000
119A125THR0-0.011-0.01136.793-0.247-0.2470.0000.0000.0000.000
120A126LEU0-0.0060.01134.2120.1580.1580.0000.0000.0000.000
121A127SER0-0.010-0.02537.011-0.119-0.1190.0000.0000.0000.000
122A128CYS0-0.080-0.02932.080-0.164-0.1640.0000.0000.0000.000
123A129SER00.041-0.00738.4220.0950.0950.0000.0000.0000.000
124A130SER00.0620.02941.170-0.028-0.0280.0000.0000.0000.000
125A131ARG10.8870.93943.0476.1476.1470.0000.0000.0000.000
126A132SER00.005-0.01141.7960.0600.0600.0000.0000.0000.000
127A133SER0-0.034-0.03242.1250.0250.0250.0000.0000.0000.000
128A134TYR0-0.067-0.03136.908-0.148-0.1480.0000.0000.0000.000
129A135ASP-1-0.775-0.88535.471-7.947-7.9470.0000.0000.0000.000
130A136MET0-0.119-0.03830.553-0.126-0.1260.0000.0000.0000.000
131A137TYR00.013-0.01233.2710.0630.0630.0000.0000.0000.000
132A138HIS10.8600.91527.5549.6019.6010.0000.0000.0000.000
133A139LEU00.0050.00529.4800.1830.1830.0000.0000.0000.000
134A140SER0-0.011-0.01327.020-0.268-0.2680.0000.0000.0000.000
135A141ARG10.8310.90726.5449.9859.9850.0000.0000.0000.000
136A142GLU-1-0.814-0.90326.976-9.112-9.1120.0000.0000.0000.000
137A143GLY00.0100.00525.3170.0610.0610.0000.0000.0000.000
138A144GLU-1-0.883-0.91722.412-10.858-10.8580.0000.0000.0000.000
139A145ALA0-0.017-0.01718.7700.0590.0590.0000.0000.0000.000
140A146HIS0-0.005-0.00116.3260.0190.0190.0000.0000.0000.000
141A147GLU-1-0.771-0.87921.689-11.023-11.0230.0000.0000.0000.000
142A148ARG10.8650.94425.1569.1609.1600.0000.0000.0000.000
143A149ARG10.9570.96923.82711.01411.0140.0000.0000.0000.000
144A150LEU0-0.0100.00529.028-0.062-0.0620.0000.0000.0000.000
145A151PRO00.021-0.00432.228-0.007-0.0070.0000.0000.0000.000
146A152ALA0-0.047-0.01234.6990.1420.1420.0000.0000.0000.000
147A153VAL00.0220.02237.8270.0500.0500.0000.0000.0000.000
148A154ARG10.9610.98540.9146.3666.3660.0000.0000.0000.000
149A155SER0-0.001-0.00444.2500.1330.1330.0000.0000.0000.000
150A156ILE00.0480.01547.3240.0140.0140.0000.0000.0000.000
151A157ASN00.0140.00350.2050.1270.1270.0000.0000.0000.000
152A158GLY0-0.055-0.02849.1270.0550.0550.0000.0000.0000.000
153A159THR0-0.058-0.02044.541-0.028-0.0280.0000.0000.0000.000
154A160PHE00.0460.03441.0680.0290.0290.0000.0000.0000.000
155A161GLN00.018-0.00340.2980.0230.0230.0000.0000.0000.000
156A162ALA0-0.0080.01135.690-0.056-0.0560.0000.0000.0000.000
157A163ASP-1-0.808-0.87937.517-7.102-7.1020.0000.0000.0000.000
158A164PHE0-0.017-0.02330.597-0.179-0.1790.0000.0000.0000.000
159A165PRO00.0110.02533.8130.0780.0780.0000.0000.0000.000
160A166LEU0-0.041-0.04231.989-0.307-0.3070.0000.0000.0000.000
161A167GLY00.0000.01332.074-0.213-0.2130.0000.0000.0000.000
162A168PRO00.003-0.00332.4900.1330.1330.0000.0000.0000.000
163A169ALA00.0020.00433.301-0.235-0.2350.0000.0000.0000.000
164A170THR00.0160.01230.2660.0620.0620.0000.0000.0000.000
165A171HIS0-0.010-0.01129.256-0.005-0.0050.0000.0000.0000.000
166A172GLY00.0420.02532.534-0.004-0.0040.0000.0000.0000.000
167A173GLY00.0120.00531.701-0.325-0.3250.0000.0000.0000.000
168A174THR00.004-0.00431.9220.3230.3230.0000.0000.0000.000
169A175TYR0-0.008-0.01730.635-0.392-0.3920.0000.0000.0000.000
170A176ARG10.8620.91131.7628.9758.9750.0000.0000.0000.000
171A178PHE00.0290.01729.8030.1340.1340.0000.0000.0000.000
172A179GLY00.0570.01933.309-0.059-0.0590.0000.0000.0000.000
173A180SER0-0.002-0.00231.775-0.215-0.2150.0000.0000.0000.000
174A181PHE00.0500.03133.9340.1450.1450.0000.0000.0000.000
175A182ARG10.8940.94232.1218.5988.5980.0000.0000.0000.000
176A183ASP-1-0.954-0.97632.265-8.824-8.8240.0000.0000.0000.000
177A184ALA00.0350.02630.917-0.295-0.2950.0000.0000.0000.000
178A185PRO0-0.028-0.01227.1690.0190.0190.0000.0000.0000.000
179A186TYR0-0.060-0.02821.7040.0920.0920.0000.0000.0000.000
180A187GLU-1-0.869-0.93827.608-9.592-9.5920.0000.0000.0000.000
181A188TRP0-0.072-0.06726.0320.2640.2640.0000.0000.0000.000
182A189SER00.0400.01132.2980.0360.0360.0000.0000.0000.000
183A190ASN0-0.053-0.02234.176-0.351-0.3510.0000.0000.0000.000
184A191SER00.0170.00333.494-0.049-0.0490.0000.0000.0000.000
185A192SER00.0110.01435.1080.1120.1120.0000.0000.0000.000
186A193ASP-1-0.840-0.90036.948-7.253-7.2530.0000.0000.0000.000
187A194PRO0-0.013-0.01635.586-0.044-0.0440.0000.0000.0000.000
188A195LEU00.0110.02736.4720.2060.2060.0000.0000.0000.000
189A196LEU0-0.013-0.00236.063-0.230-0.2300.0000.0000.0000.000
190A197VAL00.004-0.00335.5200.1800.1800.0000.0000.0000.000
191A198SER0-0.044-0.01736.485-0.166-0.1660.0000.0000.0000.000
192A199VAL00.0060.00635.1380.1240.1240.0000.0000.0000.000
193A200THR0-0.032-0.00138.3140.0140.0140.0000.0000.0000.000