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: 1NJMZ

Calculation Name: 4DEJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DEJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5R0K1

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2444415.174937
FMO2-HF: Nuclear repulsion 2362001.692191
FMO2-HF: Total energy -82413.482746
FMO2-MP2: Total energy -82652.95701


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:7:LYS)


Summations of interaction energy for fragment #1(A:7:LYS)
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.
-167.566-165.93-0.004-0.61-1.0230.002
Interaction energy analysis for fragmet #1(A:7:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.022 / q_NPA : 1.001
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].
3A9SER0-0.016-0.0203.7152.5083.890-0.002-0.599-0.7820.002
4A10VAL0-0.0120.0056.1813.5393.5390.0000.0000.0000.000
5A11MET00.0100.0176.577-2.165-2.1650.0000.0000.0000.000
6A12THR0-0.019-0.0157.105-1.651-1.6510.0000.0000.0000.000
7A13LEU00.0010.0119.1331.0651.0650.0000.0000.0000.000
8A14TYR00.0200.0058.872-0.821-0.8210.0000.0000.0000.000
9A15SER00.025-0.00214.3261.4011.4010.0000.0000.0000.000
10A16GLY00.0590.03017.781-0.366-0.3660.0000.0000.0000.000
11A17LYS10.9360.96019.75714.62114.6210.0000.0000.0000.000
12A18ASP-1-0.758-0.88722.742-10.729-10.7290.0000.0000.0000.000
13A19ASP-1-0.828-0.88422.898-12.405-12.4050.0000.0000.0000.000
14A20LEU00.0280.01624.982-0.172-0.1720.0000.0000.0000.000
15A21LYS10.9050.92123.29011.11211.1120.0000.0000.0000.000
16A22SER0-0.040-0.04020.567-0.613-0.6130.0000.0000.0000.000
17A23HIS00.0350.03521.050-0.275-0.2750.0000.0000.0000.000
18A24GLN00.000-0.00223.560-0.224-0.2240.0000.0000.0000.000
19A25VAL0-0.031-0.01417.205-0.023-0.0230.0000.0000.0000.000
20A26ARG10.7880.86919.11513.62613.6260.0000.0000.0000.000
21A27LEU00.0090.00820.433-0.017-0.0170.0000.0000.0000.000
22A28VAL00.0060.00420.5130.1410.1410.0000.0000.0000.000
23A29LEU0-0.020-0.01915.243-0.022-0.0220.0000.0000.0000.000
24A30ALA00.0150.02419.156-0.197-0.1970.0000.0000.0000.000
25A31GLU-1-0.843-0.90121.933-10.386-10.3860.0000.0000.0000.000
26A32LYS10.6980.82319.79012.15412.1540.0000.0000.0000.000
27A33GLY0-0.0020.01821.128-0.018-0.0180.0000.0000.0000.000
28A34VAL0-0.063-0.02315.602-0.419-0.4190.0000.0000.0000.000
29A35GLY00.0020.00415.4520.0940.0940.0000.0000.0000.000
30A36VAL0-0.043-0.03711.642-1.014-1.0140.0000.0000.0000.000
31A37GLU-1-0.851-0.9177.157-39.618-39.6180.0000.0000.0000.000
32A38ILE0-0.007-0.01211.312-0.288-0.2880.0000.0000.0000.000
33A39THR0-0.0110.00210.466-0.683-0.6830.0000.0000.0000.000
34A40TYR0-0.018-0.02613.0281.0191.0190.0000.0000.0000.000
35A41VAL0-0.017-0.00515.687-0.551-0.5510.0000.0000.0000.000
36A42THR0-0.018-0.02018.0500.5730.5730.0000.0000.0000.000
37A43ASP-1-0.894-0.95721.007-13.024-13.0240.0000.0000.0000.000
38A44GLU-1-0.990-0.98622.546-11.852-11.8520.0000.0000.0000.000
39A45SER0-0.057-0.03018.266-0.176-0.1760.0000.0000.0000.000
40A46THR00.0040.00917.316-0.105-0.1050.0000.0000.0000.000
41A47PRO0-0.001-0.00912.1060.2010.2010.0000.0000.0000.000
42A48GLU-1-0.908-0.95611.058-23.344-23.3440.0000.0000.0000.000
43A49ASP-1-0.901-0.9567.448-33.684-33.6840.0000.0000.0000.000
44A50LEU0-0.071-0.03910.1710.7160.7160.0000.0000.0000.000
45A51LEU0-0.012-0.01013.1151.1501.1500.0000.0000.0000.000
46A52GLN0-0.039-0.00810.7650.2470.2470.0000.0000.0000.000
47A53LEU0-0.051-0.0168.5630.5980.5980.0000.0000.0000.000
48A54ASN0-0.009-0.01612.8371.5961.5960.0000.0000.0000.000
49A55PRO00.0030.02016.264-0.003-0.0030.0000.0000.0000.000
50A56TYR0-0.066-0.03319.4070.8740.8740.0000.0000.0000.000
51A57PRO0-0.014-0.02621.190-0.381-0.3810.0000.0000.0000.000
52A58GLU-1-0.873-0.92622.990-13.303-13.3030.0000.0000.0000.000
53A59ALA0-0.0150.00117.556-0.074-0.0740.0000.0000.0000.000
54A60LYS10.8880.96117.34312.75512.7550.0000.0000.0000.000
55A61PRO0-0.0070.01117.7540.5930.5930.0000.0000.0000.000
56A62THR0-0.009-0.02112.3420.5300.5300.0000.0000.0000.000
57A63LEU0-0.0180.00411.499-1.024-1.0240.0000.0000.0000.000
58A64VAL00.0210.0016.2910.4260.4260.0000.0000.0000.000
59A65ASP-1-0.851-0.9497.059-24.663-24.6630.0000.0000.0000.000
60A66ARG10.8770.9304.36329.01929.112-0.001-0.007-0.0850.000
61A67GLU-1-0.883-0.9364.825-31.115-30.954-0.001-0.004-0.1560.000
62A68LEU0-0.073-0.0157.5351.6371.6370.0000.0000.0000.000
63A69VAL00.0140.0099.419-1.122-1.1220.0000.0000.0000.000
64A70LEU0-0.033-0.01611.2621.3131.3130.0000.0000.0000.000
65A71TYR00.0810.02914.564-0.041-0.0410.0000.0000.0000.000
66A72ASN00.020-0.00417.3320.5690.5690.0000.0000.0000.000
67A73ALA00.0740.03819.984-0.292-0.2920.0000.0000.0000.000
68A74GLN0-0.0030.00421.405-0.021-0.0210.0000.0000.0000.000
69A75ILE00.0140.01018.5100.1070.1070.0000.0000.0000.000
70A76ILE0-0.025-0.00615.923-0.210-0.2100.0000.0000.0000.000
71A77MET0-0.005-0.01118.256-0.133-0.1330.0000.0000.0000.000
72A78GLU-1-0.794-0.88321.062-10.424-10.4240.0000.0000.0000.000
73A79TYR00.0200.02012.1770.1120.1120.0000.0000.0000.000
74A80LEU0-0.034-0.02715.299-0.208-0.2080.0000.0000.0000.000
75A81ASP-1-0.813-0.90018.535-11.006-11.0060.0000.0000.0000.000
76A82GLU-1-0.980-0.97620.684-11.410-11.4100.0000.0000.0000.000
77A83ARG10.8580.93811.57917.93917.9390.0000.0000.0000.000
78A84PHE0-0.046-0.03013.976-0.415-0.4150.0000.0000.0000.000
79A85PRO00.0250.01619.9170.3100.3100.0000.0000.0000.000
80A86HIS0-0.067-0.00123.2380.5990.5990.0000.0000.0000.000
81A87PRO00.0630.02423.704-0.396-0.3960.0000.0000.0000.000
82A88PRO00.0270.01625.849-0.320-0.3200.0000.0000.0000.000
83A89LEU00.0380.02624.2790.2280.2280.0000.0000.0000.000
84A90MET0-0.032-0.01127.0020.3140.3140.0000.0000.0000.000
85A91PRO00.0180.01229.3740.0760.0760.0000.0000.0000.000
86A92VAL00.0450.01531.477-0.168-0.1680.0000.0000.0000.000
87A93TYR0-0.002-0.00233.262-0.017-0.0170.0000.0000.0000.000
88A94PRO00.044-0.00134.513-0.067-0.0670.0000.0000.0000.000
89A95VAL00.0380.02235.594-0.089-0.0890.0000.0000.0000.000
90A96ALA00.0490.02636.266-0.011-0.0110.0000.0000.0000.000
91A97ARG10.9370.97427.1949.5469.5460.0000.0000.0000.000
92A98GLY00.0020.00832.737-0.198-0.1980.0000.0000.0000.000
93A99THR00.003-0.00234.9780.0320.0320.0000.0000.0000.000
94A100SER00.0210.00132.242-0.022-0.0220.0000.0000.0000.000
95A101ARG10.8490.90627.1559.6919.6910.0000.0000.0000.000
96A102LEU0-0.0140.00631.920-0.094-0.0940.0000.0000.0000.000
97A103MET0-0.023-0.01835.0590.0940.0940.0000.0000.0000.000
98A104MET00.0120.00828.771-0.093-0.0930.0000.0000.0000.000
99A105TYR0-0.0050.01931.3980.0280.0280.0000.0000.0000.000
100A106ARG10.9160.94632.7107.3867.3860.0000.0000.0000.000
101A107ILE00.0250.04332.3610.0660.0660.0000.0000.0000.000
102A108GLU-1-0.837-0.92128.103-10.407-10.4070.0000.0000.0000.000
103A109ARG10.8910.94132.1227.9627.9620.0000.0000.0000.000
104A110ASP-1-0.897-0.93834.875-7.645-7.6450.0000.0000.0000.000
105A111TRP0-0.011-0.01535.7400.0190.0190.0000.0000.0000.000
106A112TYR0-0.009-0.02727.970-0.136-0.1360.0000.0000.0000.000
107A113SER0-0.022-0.01533.135-0.106-0.1060.0000.0000.0000.000
108A114LEU0-0.033-0.01134.9650.0180.0180.0000.0000.0000.000
109A115ALA00.0210.00033.6930.0940.0940.0000.0000.0000.000
110A116GLU-1-0.931-0.95030.891-10.096-10.0960.0000.0000.0000.000
111A117LYS10.8850.93234.1457.8227.8220.0000.0000.0000.000
112A118ILE0-0.029-0.01337.5500.1290.1290.0000.0000.0000.000
113A119GLN00.0070.00431.349-0.004-0.0040.0000.0000.0000.000
114A120LYS10.9060.98234.7378.8248.8240.0000.0000.0000.000
115A121ASN0-0.021-0.01937.6500.0340.0340.0000.0000.0000.000
116A122ASP-1-0.904-0.95941.251-7.160-7.1600.0000.0000.0000.000
117A123ALA00.008-0.00342.647-0.071-0.0710.0000.0000.0000.000
118A124GLN0-0.010-0.01045.4360.2060.2060.0000.0000.0000.000
119A125ALA00.0540.02740.3790.0350.0350.0000.0000.0000.000
120A126ARG10.9020.95541.7447.3967.3960.0000.0000.0000.000
121A127GLN0-0.055-0.03242.9750.0460.0460.0000.0000.0000.000
122A128GLU-1-0.897-0.94943.101-7.043-7.0430.0000.0000.0000.000
123A129LEU00.0160.01337.475-0.016-0.0160.0000.0000.0000.000
124A130LYS10.8690.94741.6606.6576.6570.0000.0000.0000.000
125A131GLU-1-0.908-0.96744.271-6.302-6.3020.0000.0000.0000.000
126A132GLY0-0.0120.01542.6900.0820.0820.0000.0000.0000.000
127A133ILE00.006-0.00938.8150.0060.0060.0000.0000.0000.000
128A134LEU0-0.033-0.02342.4980.0220.0220.0000.0000.0000.000
129A135SER0-0.038-0.01745.9000.1000.1000.0000.0000.0000.000
130A136LEU0-0.025-0.02241.3160.0700.0700.0000.0000.0000.000
131A137ALA00.005-0.00144.035-0.070-0.0700.0000.0000.0000.000
132A138PRO0-0.029-0.01845.8370.0030.0030.0000.0000.0000.000
133A139ILE00.0210.02040.5370.0270.0270.0000.0000.0000.000
134A140PHE0-0.042-0.02338.804-0.103-0.1030.0000.0000.0000.000
135A141ALA0-0.053-0.01743.579-0.017-0.0170.0000.0000.0000.000
136A142ASP-1-0.958-0.96044.983-6.369-6.3690.0000.0000.0000.000
137A143THR0-0.033-0.00640.7460.0330.0330.0000.0000.0000.000
138A144PRO0-0.059-0.02139.496-0.043-0.0430.0000.0000.0000.000
139A145TYR0-0.018-0.02434.666-0.241-0.2410.0000.0000.0000.000
140A146PHE00.018-0.00735.8840.2070.2070.0000.0000.0000.000
141A147MET0-0.044-0.02336.754-0.166-0.1660.0000.0000.0000.000
142A148SER0-0.042-0.03035.179-0.008-0.0080.0000.0000.0000.000
143A149GLU-1-0.871-0.94737.859-7.141-7.1410.0000.0000.0000.000
144A150GLU-1-0.977-0.98933.930-8.576-8.5760.0000.0000.0000.000
145A151PHE0-0.034-0.00527.7800.0580.0580.0000.0000.0000.000
146A152SER00.0380.01630.132-0.205-0.2050.0000.0000.0000.000
147A153LEU00.040-0.02124.453-0.090-0.0900.0000.0000.0000.000
148A154VAL0-0.011-0.00128.413-0.115-0.1150.0000.0000.0000.000
149A155ASP-1-0.693-0.84231.429-8.683-8.6830.0000.0000.0000.000
150A156CYS0-0.067-0.01426.278-0.173-0.1730.0000.0000.0000.000
151A157TYR00.0170.00226.990-0.396-0.3960.0000.0000.0000.000
152A158LEU00.0020.00829.8830.0300.0300.0000.0000.0000.000
153A159ALA00.0050.00829.7120.1190.1190.0000.0000.0000.000
154A160PRO00.0070.00427.2160.0860.0860.0000.0000.0000.000
155A161LEU0-0.025-0.00129.8240.0380.0380.0000.0000.0000.000
156A162LEU00.017-0.02132.9860.1690.1690.0000.0000.0000.000
157A163TRP0-0.035-0.01731.2170.3200.3200.0000.0000.0000.000
158A164ARG10.8080.89627.02810.96910.9690.0000.0000.0000.000
159A165LEU00.0150.00734.5370.1270.1270.0000.0000.0000.000
160A166PRO00.0150.00537.4980.1800.1800.0000.0000.0000.000
161A167ALA00.0140.01435.5410.1300.1300.0000.0000.0000.000
162A168TYR0-0.024-0.00732.945-0.031-0.0310.0000.0000.0000.000
163A169GLY00.0040.01738.8190.1740.1740.0000.0000.0000.000
164A170ILE0-0.072-0.04240.1210.2320.2320.0000.0000.0000.000
165A171ASP-1-0.846-0.92242.543-7.123-7.1230.0000.0000.0000.000
166A172LEU0-0.099-0.06044.6200.0640.0640.0000.0000.0000.000
167A173GLU-1-0.906-0.95546.356-6.123-6.1230.0000.0000.0000.000
168A174GLY00.0120.01049.5960.0090.0090.0000.0000.0000.000
169A175GLN0-0.049-0.03451.454-0.100-0.1000.0000.0000.0000.000
170A176GLY00.0780.04349.204-0.046-0.0460.0000.0000.0000.000
171A177ALA00.0770.01446.472-0.143-0.1430.0000.0000.0000.000
172A178LYS10.8910.96046.3056.1416.1410.0000.0000.0000.000
173A179GLU-1-0.868-0.94945.650-6.440-6.4400.0000.0000.0000.000
174A180ILE00.0020.01841.369-0.173-0.1730.0000.0000.0000.000
175A181LYS10.9980.99541.3487.2357.2350.0000.0000.0000.000
176A182GLN0-0.012-0.00841.869-0.045-0.0450.0000.0000.0000.000
177A183TYR0-0.046-0.03535.061-0.139-0.1390.0000.0000.0000.000
178A184MET0-0.014-0.00237.481-0.138-0.1380.0000.0000.0000.000
179A185VAL0-0.062-0.02037.061-0.211-0.2110.0000.0000.0000.000
180A186ARG10.9410.98437.7977.4867.4860.0000.0000.0000.000
181A187LEU0-0.040-0.01932.789-0.220-0.2200.0000.0000.0000.000
182A188PHE0-0.034-0.03232.873-0.257-0.2570.0000.0000.0000.000
183A189GLU-1-0.935-0.95733.393-8.248-8.2480.0000.0000.0000.000
184A190ARG10.8100.91729.4259.7529.7520.0000.0000.0000.000
185A191LYS10.9680.95229.5059.3949.3940.0000.0000.0000.000
186A192THR00.009-0.00725.587-0.131-0.1310.0000.0000.0000.000
187A193PHE00.0340.01925.911-0.431-0.4310.0000.0000.0000.000
188A194GLN0-0.014-0.01027.630-0.063-0.0630.0000.0000.0000.000
189A195ASP-1-0.928-0.95524.140-12.194-12.1940.0000.0000.0000.000
190A196SER0-0.104-0.05622.893-0.517-0.5170.0000.0000.0000.000
191A197LEU0-0.078-0.02023.518-0.329-0.3290.0000.0000.0000.000
192A198THR00.006-0.01221.695-0.150-0.1500.0000.0000.0000.000
193A199GLU-1-0.911-0.98723.468-12.526-12.5260.0000.0000.0000.000
194A200GLU-1-0.861-0.93824.150-12.700-12.7000.0000.0000.0000.000
195A201GLU-1-0.687-0.82825.595-11.958-11.9580.0000.0000.0000.000
196A202LYS10.8930.96026.41712.19412.1940.0000.0000.0000.000
197A203GLU-1-1.042-1.02229.988-10.081-10.0810.0000.0000.0000.000
198A204LEU0-0.0220.00730.4630.4000.4000.0000.0000.0000.000
199A205ALA0-0.031-0.00333.7420.3140.3140.0000.0000.0000.000
200A206ARG10.8810.92830.9999.9559.9550.0000.0000.0000.000
201A207ASN0-0.0080.00734.6340.3640.3640.0000.0000.0000.000
202A208ALA00.0030.02037.9870.1580.1580.0000.0000.0000.000