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: 1NK7Z

Calculation Name: 3GNL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GNL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-23

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2818242.649447
FMO2-HF: Nuclear repulsion 2727493.084781
FMO2-HF: Total energy -90749.564666
FMO2-MP2: Total energy -91018.45511


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:9:GLU)


Summations of interaction energy for fragment #1(A:9:GLU)
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.
-153.335-159.23140.644-19.104-15.6450.208
Interaction energy analysis for fragmet #1(A:9:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.815 / q_NPA : -0.890
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].
3A11GLN0-0.021-0.0133.7861.0062.560-0.005-0.661-0.8890.002
4A12LEU00.0060.0166.016-0.731-0.7310.0000.0000.0000.000
5A13SER0-0.018-0.0307.741-1.550-1.5500.0000.0000.0000.000
6A14LYS10.8730.90011.392-19.944-19.9440.0000.0000.0000.000
7A15ARG10.8600.94013.897-18.895-18.8950.0000.0000.0000.000
8A16LEU0-0.038-0.02110.072-0.367-0.3670.0000.0000.0000.000
9A17GLU-1-0.835-0.89710.75422.21322.2130.0000.0000.0000.000
10A18LYS10.8850.94311.589-16.044-16.0440.0000.0000.0000.000
11A19VAL00.0040.01413.903-0.589-0.5890.0000.0000.0000.000
12A20ALA00.0420.00910.650-0.508-0.5080.0000.0000.0000.000
13A21SER0-0.053-0.02912.598-0.595-0.5950.0000.0000.0000.000
14A22TYR00.000-0.00814.886-0.912-0.9120.0000.0000.0000.000
15A23ILE0-0.0340.00312.514-0.983-0.9830.0000.0000.0000.000
16A24THR0-0.010-0.02414.6400.5840.5840.0000.0000.0000.000
17A25LYS10.8980.95116.743-14.375-14.3750.0000.0000.0000.000
18A26ASN00.0370.01914.7750.4430.4430.0000.0000.0000.000
19A27GLU-1-0.726-0.81615.55916.83516.8350.0000.0000.0000.000
20A28ARG10.8800.94615.028-15.312-15.3120.0000.0000.0000.000
21A29ILE00.0180.00111.327-1.173-1.1730.0000.0000.0000.000
22A30ALA00.008-0.00215.4630.5160.5160.0000.0000.0000.000
23A31ASP-1-0.807-0.87312.54122.76022.7600.0000.0000.0000.000
24A32ILE0-0.003-0.01215.2720.2630.2630.0000.0000.0000.000
25A33GLY0-0.021-0.01817.771-0.377-0.3770.0000.0000.0000.000
26A34SER0-0.057-0.04011.9591.0741.0740.0000.0000.0000.000
27A35ASP-1-0.783-0.87811.52722.13722.1370.0000.0000.0000.000
28A36HIS0-0.039-0.0458.7641.3011.3010.0000.0000.0000.000
29A37ALA00.0340.0118.2993.0313.0310.0000.0000.0000.000
30A38TYR0-0.031-0.0234.7083.8233.911-0.001-0.005-0.0820.000
31A39LEU0-0.0010.0065.6915.2655.2650.0000.0000.0000.000
32A40PRO00.005-0.0047.9131.4281.4280.0000.0000.0000.000
33A41CYS0-0.0130.0032.984-6.130-4.7410.168-0.754-0.8030.008
34A42PHE00.0210.0074.2684.4124.8000.002-0.072-0.3180.000
35A43ALA00.015-0.0035.082-2.212-2.206-0.001-0.002-0.0030.000
36A44VAL00.0000.0096.924-2.474-2.4740.0000.0000.0000.000
37A45LYS10.7810.8911.787-145.540-150.33222.593-9.817-7.9840.129
38A46ASN0-0.0350.0045.792-5.728-5.735-0.0010.0000.0080.000
39A47GLN0-0.010-0.0058.360-4.027-4.0270.0000.0000.0000.000
40A48THR0-0.045-0.02310.519-2.660-2.6600.0000.0000.0000.000
41A49ALA0-0.053-0.03010.722-2.109-2.1090.0000.0000.0000.000
42A50SER0-0.005-0.00411.3101.7031.7030.0000.0000.0000.000
43A51PHE0-0.037-0.01812.9590.1210.1210.0000.0000.0000.000
44A52ALA00.0110.01010.934-0.372-0.3720.0000.0000.0000.000
45A53ILE0-0.0040.01512.9650.1770.1770.0000.0000.0000.000
46A54ALA00.0150.00211.7870.2100.2100.0000.0000.0000.000
47A55GLY0-0.001-0.00113.938-0.626-0.6260.0000.0000.0000.000
48A56GLH0-0.075-0.07714.128-0.031-0.0310.0000.0000.0000.000
49A57VAL00.0630.03918.558-0.516-0.5160.0000.0000.0000.000
50A58VAL00.001-0.00620.762-0.590-0.5900.0000.0000.0000.000
51A59ASP-1-0.781-0.90419.83915.16915.1690.0000.0000.0000.000
52A60GLY00.0030.02618.5110.7270.7270.0000.0000.0000.000
53A61PRO00.0810.02015.3270.9470.9470.0000.0000.0000.000
54A62PHE00.0080.01614.7161.4571.4570.0000.0000.0000.000
55A63GLN0-0.026-0.03715.0271.7171.7170.0000.0000.0000.000
56A64SER0-0.014-0.00911.9181.1781.1780.0000.0000.0000.000
57A65ALA00.0370.03210.4742.7212.7210.0000.0000.0000.000
58A66GLN00.0150.00210.2133.0703.0700.0000.0000.0000.000
59A67LYS10.8730.93510.633-20.552-20.5520.0000.0000.0000.000
60A68GLN00.0520.0493.223-7.421-6.5640.041-0.426-0.4720.001
61A69VAL00.0420.0155.5578.8408.928-0.0010.000-0.0870.000
62A70ARG10.8430.9096.989-21.914-21.9140.0000.0000.0000.000
63A71SER0-0.037-0.0105.558-2.716-2.7160.0000.0000.0000.000
64A72SER0-0.047-0.0351.653-18.793-24.72617.842-7.256-4.6530.066
65A73GLY0-0.005-0.0013.736-1.307-0.9900.008-0.099-0.2260.002
66A74LEU00.012-0.0054.515-2.316-2.167-0.001-0.012-0.1360.000
67A75THR0-0.010-0.0218.027-2.536-2.5360.0000.0000.0000.000
68A76GLU-1-0.972-0.97411.19320.60820.6080.0000.0000.0000.000
69A77GLN0-0.059-0.0369.9770.1550.1550.0000.0000.0000.000
70A78ILE0-0.016-0.0067.246-0.458-0.4580.0000.0000.0000.000
71A79ASP-1-0.806-0.86911.54919.21719.2170.0000.0000.0000.000
72A80VAL0-0.045-0.03212.1600.0000.0000.0000.0000.0000.000
73A81ARG10.6990.80114.912-17.930-17.9300.0000.0000.0000.000
74A82LYS10.8400.91518.501-14.134-14.1340.0000.0000.0000.000
75A83GLY00.010-0.01621.093-0.600-0.6000.0000.0000.0000.000
76A84ASN00.0100.00422.7010.7640.7640.0000.0000.0000.000
77A85GLY00.0650.03123.553-0.284-0.2840.0000.0000.0000.000
78A86LEU00.0350.00722.6210.6650.6650.0000.0000.0000.000
79A87ALA0-0.020-0.00224.179-0.077-0.0770.0000.0000.0000.000
80A88VAL0-0.035-0.00219.358-0.024-0.0240.0000.0000.0000.000
81A89ILE00.0280.02820.5910.6350.6350.0000.0000.0000.000
82A90GLU-1-0.844-0.93222.66011.02811.0280.0000.0000.0000.000
83A91LYS10.9190.95424.361-10.479-10.4790.0000.0000.0000.000
84A92LYS10.9450.97124.580-12.775-12.7750.0000.0000.0000.000
85A93ASP-1-0.781-0.84620.39915.36815.3680.0000.0000.0000.000
86A94ALA00.0030.01121.0120.6640.6640.0000.0000.0000.000
87A95ILE0-0.008-0.00517.9990.4310.4310.0000.0000.0000.000
88A96ASP-1-0.827-0.89419.38214.67714.6770.0000.0000.0000.000
89A97THR0-0.048-0.06517.532-1.053-1.0530.0000.0000.0000.000
90A98ILE0-0.0110.00018.2430.7740.7740.0000.0000.0000.000
91A99VAL0-0.017-0.00514.680-0.553-0.5530.0000.0000.0000.000
92A100ILE00.0440.01417.7140.1300.1300.0000.0000.0000.000
93A101ALA00.0190.00315.937-0.651-0.6510.0000.0000.0000.000
94A102GLY0-0.0010.01518.0960.2070.2070.0000.0000.0000.000
95A103MET00.0050.01618.976-0.566-0.5660.0000.0000.0000.000
96A104GLY0-0.009-0.01022.376-0.168-0.1680.0000.0000.0000.000
97A105GLY00.0470.01825.9150.1610.1610.0000.0000.0000.000
98A106THR00.0300.00327.5270.0060.0060.0000.0000.0000.000
99A107LEU0-0.0060.02324.696-0.125-0.1250.0000.0000.0000.000
100A108ILE00.0260.00622.4160.0570.0570.0000.0000.0000.000
101A109ARG10.7570.86025.873-9.096-9.0960.0000.0000.0000.000
102A110THR0-0.009-0.01429.264-0.201-0.2010.0000.0000.0000.000
103A111ILE0-0.021-0.00723.560-0.002-0.0020.0000.0000.0000.000
104A112LEU0-0.032-0.02225.0150.1110.1110.0000.0000.0000.000
105A113GLU-1-0.861-0.92228.1519.3239.3230.0000.0000.0000.000
106A114GLU-1-0.940-0.97630.18510.19310.1930.0000.0000.0000.000
107A115GLY0-0.038-0.01827.870-0.041-0.0410.0000.0000.0000.000
108A116ALA00.0760.03828.4490.2750.2750.0000.0000.0000.000
109A117ALA0-0.012-0.01430.4980.0520.0520.0000.0000.0000.000
110A118LYS10.7270.84125.555-12.019-12.0190.0000.0000.0000.000
111A119LEU00.0450.03425.7080.5090.5090.0000.0000.0000.000
112A120ALA0-0.052-0.02527.469-0.076-0.0760.0000.0000.0000.000
113A121GLY0-0.019-0.01227.1610.3170.3170.0000.0000.0000.000
114A122VAL0-0.0110.02422.6120.2810.2810.0000.0000.0000.000
115A123THR0-0.060-0.04223.521-0.447-0.4470.0000.0000.0000.000
116A124LYS10.7690.85918.562-16.453-16.4530.0000.0000.0000.000
117A125LEU0-0.0070.01921.7070.4780.4780.0000.0000.0000.000
118A126ILE0-0.015-0.00416.975-0.398-0.3980.0000.0000.0000.000
119A127LEU00.0060.00319.4470.5250.5250.0000.0000.0000.000
120A128GLN00.000-0.01518.0530.6440.6440.0000.0000.0000.000
121A129PRO0-0.0020.01720.6150.2580.2580.0000.0000.0000.000
122A130ASN0-0.005-0.01420.6200.2240.2240.0000.0000.0000.000
123A131ILE00.0220.00623.869-0.337-0.3370.0000.0000.0000.000
124A132ALA00.003-0.00527.6980.1680.1680.0000.0000.0000.000
125A133ALA00.1180.05327.2420.0200.0200.0000.0000.0000.000
126A134TRP00.0510.01928.5450.0810.0810.0000.0000.0000.000
127A135GLN0-0.0170.00930.615-0.123-0.1230.0000.0000.0000.000
128A136LEU00.0290.00625.487-0.084-0.0840.0000.0000.0000.000
129A137ARG10.7690.89727.997-10.411-10.4110.0000.0000.0000.000
130A138GLU-1-0.830-0.90231.6328.3328.3320.0000.0000.0000.000
131A139TRP0-0.0010.00928.698-0.040-0.0400.0000.0000.0000.000
132A140SER0-0.015-0.02830.425-0.126-0.1260.0000.0000.0000.000
133A141GLU-1-0.858-0.92932.1998.0688.0680.0000.0000.0000.000
134A142GLN0-0.034-0.02735.908-0.053-0.0530.0000.0000.0000.000
135A143ASN0-0.061-0.03232.931-0.186-0.1860.0000.0000.0000.000
136A144ASN00.0000.01334.1770.0620.0620.0000.0000.0000.000
137A145TRP00.0460.02225.8250.3540.3540.0000.0000.0000.000
138A146LEU0-0.0030.01730.957-0.141-0.1410.0000.0000.0000.000
139A147ILE00.0120.00227.3630.4340.4340.0000.0000.0000.000
140A148THR0-0.032-0.02425.904-0.191-0.1910.0000.0000.0000.000
141A149SER0-0.034-0.03423.5750.0930.0930.0000.0000.0000.000
142A150GLU-1-0.751-0.87324.08310.76110.7610.0000.0000.0000.000
143A151ALA0-0.0180.00121.046-0.008-0.0080.0000.0000.0000.000
144A152ILE00.0080.00923.155-0.015-0.0150.0000.0000.0000.000
145A153LEU00.0020.01217.8960.0130.0130.0000.0000.0000.000
146A154ARG10.9130.94521.897-11.049-11.0490.0000.0000.0000.000
147A155GLU-1-0.741-0.84215.01718.46318.4630.0000.0000.0000.000
148A156ASP-1-0.791-0.90018.10115.24315.2430.0000.0000.0000.000
149A157ASN0-0.061-0.03521.046-0.363-0.3630.0000.0000.0000.000
150A158LYS10.8540.93719.550-14.626-14.6260.0000.0000.0000.000
151A159VAL0-0.024-0.02522.7380.3390.3390.0000.0000.0000.000
152A160TYR0-0.005-0.00118.975-0.028-0.0280.0000.0000.0000.000
153A161GLU-1-0.845-0.92322.36010.80810.8080.0000.0000.0000.000
154A162ILE0-0.021-0.02017.6880.4360.4360.0000.0000.0000.000
155A163MET0-0.018-0.00121.676-0.587-0.5870.0000.0000.0000.000
156A164VAL00.0000.00120.8320.5350.5350.0000.0000.0000.000
157A165LEU0-0.005-0.01223.418-0.607-0.6070.0000.0000.0000.000
158A166ALA00.0180.00725.0830.5540.5540.0000.0000.0000.000
159A167PRO00.0030.01127.262-0.369-0.3690.0000.0000.0000.000
160A168SER0-0.049-0.03330.462-0.015-0.0150.0000.0000.0000.000
161A169GLU-1-0.948-0.97433.8288.3048.3040.0000.0000.0000.000
162A170LYS10.9010.95936.952-8.155-8.1550.0000.0000.0000.000
163A171PRO00.0170.00137.6600.2020.2020.0000.0000.0000.000
164A172VAL0-0.0320.00534.1440.0090.0090.0000.0000.0000.000
165A173THR0-0.028-0.01937.407-0.138-0.1380.0000.0000.0000.000
166A174TRP0-0.037-0.01732.2560.0170.0170.0000.0000.0000.000
167A175THR00.0400.02538.215-0.205-0.2050.0000.0000.0000.000
168A176LYS10.9210.93938.370-6.879-6.8790.0000.0000.0000.000
169A177GLN00.006-0.01838.0180.2310.2310.0000.0000.0000.000
170A178GLU-1-0.851-0.93235.0548.7728.7720.0000.0000.0000.000
171A179ILE00.0250.01133.6310.3560.3560.0000.0000.0000.000
172A180PHE0-0.082-0.04333.2980.2710.2710.0000.0000.0000.000
173A181PHE0-0.033-0.03432.5880.1720.1720.0000.0000.0000.000
174A182GLY00.0660.03530.2180.3160.3160.0000.0000.0000.000
175A183PRO00.0000.00530.676-0.170-0.1700.0000.0000.0000.000
176A184CYS0-0.059-0.02828.091-0.262-0.2620.0000.0000.0000.000
177A185LEU00.0090.00925.874-0.058-0.0580.0000.0000.0000.000
178A186LEU0-0.031-0.01229.813-0.182-0.1820.0000.0000.0000.000
179A187LYS10.8510.92332.775-9.217-9.2170.0000.0000.0000.000
180A188GLU-1-0.893-0.91626.61010.94410.9440.0000.0000.0000.000
181A189GLN0-0.060-0.02731.397-0.129-0.1290.0000.0000.0000.000
182A190SER00.015-0.00527.912-0.117-0.1170.0000.0000.0000.000
183A191ALA00.0350.00029.513-0.181-0.1810.0000.0000.0000.000
184A192ILE0-0.032-0.00924.232-0.203-0.2030.0000.0000.0000.000
185A193PHE00.0470.03528.426-0.117-0.1170.0000.0000.0000.000
186A194LYS10.9040.95030.188-8.308-8.3080.0000.0000.0000.000
187A195SER0-0.036-0.03030.726-0.086-0.0860.0000.0000.0000.000
188A196LYS10.8340.91328.346-10.271-10.2710.0000.0000.0000.000
189A197TRP00.0520.01130.982-0.233-0.2330.0000.0000.0000.000
190A198ARG10.8620.92334.510-7.632-7.6320.0000.0000.0000.000
191A199HIS0-0.066-0.03133.597-0.260-0.2600.0000.0000.0000.000
192A200GLU-1-0.817-0.89531.7379.2509.2500.0000.0000.0000.000
193A201ALA00.0250.01036.121-0.190-0.1900.0000.0000.0000.000
194A202ASN00.0120.00839.056-0.300-0.3000.0000.0000.0000.000
195A203THR0-0.0050.00337.329-0.193-0.1930.0000.0000.0000.000
196A204TRP00.007-0.01336.111-0.153-0.1530.0000.0000.0000.000
197A205GLN00.0670.03641.744-0.091-0.0910.0000.0000.0000.000
198A206ASN00.0250.00942.128-0.277-0.2770.0000.0000.0000.000
199A207ILE0-0.049-0.01340.385-0.135-0.1350.0000.0000.0000.000
200A208ILE00.0400.01644.818-0.121-0.1210.0000.0000.0000.000
201A209GLN0-0.0220.00847.749-0.110-0.1100.0000.0000.0000.000
202A210THR0-0.021-0.02546.715-0.115-0.1150.0000.0000.0000.000
203A211ILE0-0.034-0.01546.379-0.093-0.0930.0000.0000.0000.000
204A212SER0-0.019-0.01950.260-0.139-0.1390.0000.0000.0000.000
205A213ASN0-0.062-0.03452.642-0.065-0.0650.0000.0000.0000.000
206A214ASN0-0.072-0.02651.344-0.113-0.1130.0000.0000.0000.000
207A215GLN00.0060.03054.7200.0020.0020.0000.0000.0000.000
208A216PRO0-0.010-0.01457.703-0.046-0.0460.0000.0000.0000.000
209A217VAL00.0170.00552.8230.0810.0810.0000.0000.0000.000
210A218SER0-0.023-0.03452.750-0.034-0.0340.0000.0000.0000.000
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