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: QNNMY

Calculation Name: 4I2O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4I2O

Chain ID: A

ChEMBL ID:

UniProt ID: O69245

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2134773.706689
FMO2-HF: Nuclear repulsion 2057660.455658
FMO2-HF: Total energy -77113.251031
FMO2-MP2: Total energy -77337.992541


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:38:LEU)


Summations of interaction energy for fragment #1(A:38:LEU)
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.
-1.6910.7640.038-0.762-1.7330.002
Interaction energy analysis for fragmet #1(A:38:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.027
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].
3A40ALA0-0.010-0.0033.7070.8842.273-0.005-0.511-0.8740.001
4A41THR0-0.004-0.0015.991-0.221-0.2210.0000.0000.0000.000
5A42GLU-1-0.932-0.9709.727-0.117-0.1170.0000.0000.0000.000
6A43PHE0-0.043-0.01912.6700.0430.0430.0000.0000.0000.000
7A44SER0-0.009-0.01415.561-0.034-0.0340.0000.0000.0000.000
8A45TYR00.0040.01016.2500.0290.0290.0000.0000.0000.000
9A46ARG10.9170.94721.223-0.117-0.1170.0000.0000.0000.000
10A47LYS10.8480.88524.777-0.043-0.0430.0000.0000.0000.000
11A48ASP-1-0.876-0.90926.4370.0650.0650.0000.0000.0000.000
12A49GLU-1-0.854-0.89023.3290.1350.1350.0000.0000.0000.000
13A50GLU-1-0.909-0.96222.8510.1790.1790.0000.0000.0000.000
14A51ILE0-0.101-0.05216.8370.0070.0070.0000.0000.0000.000
15A52TYR0-0.034-0.01916.0150.0520.0520.0000.0000.0000.000
16A53GLY00.0780.04520.291-0.027-0.0270.0000.0000.0000.000
17A54GLU-1-0.843-0.93822.3890.1590.1590.0000.0000.0000.000
18A55ASP-1-0.963-0.97923.7610.1810.1810.0000.0000.0000.000
19A56GLU-1-0.863-0.92019.0820.3420.3420.0000.0000.0000.000
20A57PRO0-0.006-0.02318.6080.0180.0180.0000.0000.0000.000
21A58ALA0-0.0110.00515.5070.0180.0180.0000.0000.0000.000
22A59GLU-1-0.881-0.92012.5670.7670.7670.0000.0000.0000.000
23A60TYR0-0.057-0.04910.0440.3300.3300.0000.0000.0000.000
24A61VAL0-0.030-0.0098.454-0.147-0.1470.0000.0000.0000.000
25A62TYR00.0520.0169.2440.2090.2090.0000.0000.0000.000
26A63GLN0-0.030-0.0069.712-0.155-0.1550.0000.0000.0000.000
27A64VAL00.0110.01711.622-0.004-0.0040.0000.0000.0000.000
28A65VAL0-0.0260.00112.914-0.053-0.0530.0000.0000.0000.000
29A66THR00.005-0.00115.403-0.011-0.0110.0000.0000.0000.000
30A67GLY00.0570.02719.1260.0210.0210.0000.0000.0000.000
31A68ALA0-0.034-0.03221.009-0.011-0.0110.0000.0000.0000.000
32A69VAL00.0160.02818.1510.0060.0060.0000.0000.0000.000
33A70ARG10.7400.83921.307-0.097-0.0970.0000.0000.0000.000
34A71SER00.0480.00820.1600.0210.0210.0000.0000.0000.000
35A72TYR0-0.083-0.08522.962-0.017-0.0170.0000.0000.0000.000
36A73LYS10.8480.91826.003-0.128-0.1280.0000.0000.0000.000
37A74LEU00.001-0.00328.513-0.011-0.0110.0000.0000.0000.000
38A75LEU0-0.023-0.00631.7700.0020.0020.0000.0000.0000.000
39A76SER00.0550.00835.1130.0000.0000.0000.0000.0000.000
40A77ASP-1-0.883-0.90237.1830.0610.0610.0000.0000.0000.000
41A78GLY00.0210.00536.107-0.004-0.0040.0000.0000.0000.000
42A79ARG10.7810.86835.843-0.059-0.0590.0000.0000.0000.000
43A80ARG10.8410.90729.505-0.070-0.0700.0000.0000.0000.000
44A81GLN0-0.055-0.00929.763-0.009-0.0090.0000.0000.0000.000
45A82ILE0-0.040-0.03526.1400.0100.0100.0000.0000.0000.000
46A83GLY0-0.002-0.00725.478-0.009-0.0090.0000.0000.0000.000
47A84ALA00.0160.00321.901-0.008-0.0080.0000.0000.0000.000
48A85PHE00.0100.00823.1770.0080.0080.0000.0000.0000.000
49A86HIS00.0030.02817.5440.0040.0040.0000.0000.0000.000
50A87LEU00.008-0.01719.1830.0040.0040.0000.0000.0000.000
51A88PRO00.014-0.00217.3070.0030.0030.0000.0000.0000.000
52A89GLY00.0050.01014.097-0.017-0.0170.0000.0000.0000.000
53A90ASP-1-0.803-0.87413.662-0.020-0.0200.0000.0000.0000.000
54A91VAL0-0.049-0.0439.9440.0130.0130.0000.0000.0000.000
55A92PHE0-0.001-0.00412.684-0.016-0.0160.0000.0000.0000.000
56A93GLY00.0840.02812.9600.0810.0810.0000.0000.0000.000
57A94LEU0-0.060-0.02310.5060.0930.0930.0000.0000.0000.000
58A95GLU-1-0.783-0.88513.2820.2060.2060.0000.0000.0000.000
59A96SER0-0.053-0.01614.3610.0580.0580.0000.0000.0000.000
60A97GLY00.0270.00416.2090.0100.0100.0000.0000.0000.000
61A98PRO0-0.003-0.00817.0400.0440.0440.0000.0000.0000.000
62A99SER00.0290.00918.7850.0250.0250.0000.0000.0000.000
63A100HIS10.8760.96715.280-0.423-0.4230.0000.0000.0000.000
64A101ARG10.9360.97419.946-0.251-0.2510.0000.0000.0000.000
65A102LEU0-0.054-0.02421.716-0.028-0.0280.0000.0000.0000.000
66A103ALA00.0700.04621.7170.0260.0260.0000.0000.0000.000
67A104ALA00.005-0.00519.574-0.013-0.0130.0000.0000.0000.000
68A105GLU-1-0.750-0.83321.5740.1170.1170.0000.0000.0000.000
69A106ALA0-0.0050.00421.633-0.009-0.0090.0000.0000.0000.000
70A107ILE0-0.065-0.03122.891-0.008-0.0080.0000.0000.0000.000
71A108ILE0-0.075-0.04624.199-0.009-0.0090.0000.0000.0000.000
72A109ASP-1-0.805-0.89023.7680.0550.0550.0000.0000.0000.000
73A110THR0-0.070-0.05418.105-0.016-0.0160.0000.0000.0000.000
74A111SER00.0070.01116.7490.0100.0100.0000.0000.0000.000
75A112VAL00.0200.00413.192-0.015-0.0150.0000.0000.0000.000
76A113ARG10.9120.9518.2270.5430.5430.0000.0000.0000.000
77A114LEU0-0.008-0.0048.7230.0130.0130.0000.0000.0000.000
78A115VAL00.0150.0083.289-0.1220.2280.028-0.137-0.2420.001
79A116LYS10.9490.9726.154-1.751-1.7510.0000.0000.0000.000
80A117ARG10.8510.9006.9160.0150.0150.0000.0000.0000.000
81A118SER00.016-0.0078.6720.1080.1080.0000.0000.0000.000
82A119SER0-0.011-0.0153.364-0.764-0.4510.016-0.072-0.2570.000
83A120LEU0-0.0040.0013.957-0.553-0.2850.000-0.022-0.2460.000
84A121GLU-1-0.828-0.8885.761-0.014-0.0140.0000.0000.0000.000
85A122LYS10.9410.9765.797-0.768-0.7680.0000.0000.0000.000
86A123ALA0-0.005-0.0074.206-0.422-0.287-0.001-0.020-0.1140.000
87A124ALA00.000-0.0016.291-0.173-0.1730.0000.0000.0000.000
88A125GLY00.0140.0199.140-0.052-0.0520.0000.0000.0000.000
89A126ILE0-0.103-0.0446.428-0.022-0.0220.0000.0000.0000.000
90A127ASP-1-0.819-0.9268.945-0.403-0.4030.0000.0000.0000.000
91A128VAL00.0370.01310.8310.0240.0240.0000.0000.0000.000
92A129GLN0-0.008-0.01911.6090.0450.0450.0000.0000.0000.000
93A130VAL0-0.0080.0126.235-0.003-0.0030.0000.0000.0000.000
94A131ALA00.0350.0199.2010.0900.0900.0000.0000.0000.000
95A132ARG10.8980.96411.7050.0560.0560.0000.0000.0000.000
96A133LYS10.9410.97210.0200.2060.2060.0000.0000.0000.000
97A134LEU00.0470.0087.9930.0250.0250.0000.0000.0000.000
98A135TRP00.0260.01911.7750.0050.0050.0000.0000.0000.000
99A136ALA0-0.057-0.04115.012-0.001-0.0010.0000.0000.0000.000
100A137MET0-0.043-0.0149.695-0.045-0.0450.0000.0000.0000.000
101A138THR00.0850.05114.9180.0030.0030.0000.0000.0000.000
102A139ALA0-0.038-0.02017.210-0.010-0.0100.0000.0000.0000.000
103A140GLY0-0.064-0.02718.448-0.011-0.0110.0000.0000.0000.000
104A141GLU-1-0.906-0.96116.7160.1820.1820.0000.0000.0000.000
105A142LEU0-0.0050.00620.327-0.002-0.0020.0000.0000.0000.000
106A143ARG10.9670.98821.206-0.005-0.0050.0000.0000.0000.000
107A144HIS0-0.039-0.01223.0280.0020.0020.0000.0000.0000.000
108A145ALA00.0490.02424.586-0.003-0.0030.0000.0000.0000.000
109A146GLU-1-0.932-0.98526.3560.0410.0410.0000.0000.0000.000
110A147ASP-1-0.927-0.96028.1660.0120.0120.0000.0000.0000.000
111A148HIS0-0.048-0.03428.139-0.007-0.0070.0000.0000.0000.000
112A149MET0-0.019-0.01529.3160.0010.0010.0000.0000.0000.000
113A150LEU0-0.0100.01732.388-0.002-0.0020.0000.0000.0000.000
114A151LEU0-0.026-0.01332.167-0.003-0.0030.0000.0000.0000.000
115A152LEU0-0.025-0.01731.433-0.002-0.0020.0000.0000.0000.000
116A153GLY0-0.0130.00535.5190.0000.0000.0000.0000.0000.000
117A154ARG10.8580.90137.899-0.030-0.0300.0000.0000.0000.000
118A155LYS10.8450.95934.882-0.013-0.0130.0000.0000.0000.000
119A156THR0-0.015-0.03239.6410.0030.0030.0000.0000.0000.000
120A157ALA00.032-0.00540.2630.0000.0000.0000.0000.0000.000
121A158MET0-0.012-0.00139.8660.0000.0000.0000.0000.0000.000
122A159GLU-1-0.732-0.83139.0800.0120.0120.0000.0000.0000.000
123A160ARG10.7760.90636.016-0.032-0.0320.0000.0000.0000.000
124A161VAL00.006-0.00935.1500.0000.0000.0000.0000.0000.000
125A162ALA0-0.0020.00235.725-0.002-0.0020.0000.0000.0000.000
126A163THR00.030-0.00431.796-0.003-0.0030.0000.0000.0000.000
127A164PHE00.0260.01329.270-0.003-0.0030.0000.0000.0000.000
128A165LEU0-0.038-0.03131.032-0.003-0.0030.0000.0000.0000.000
129A166LEU00.0320.01532.081-0.005-0.0050.0000.0000.0000.000
130A167GLU-1-0.851-0.88425.3920.0130.0130.0000.0000.0000.000
131A168MET0-0.014-0.02025.805-0.004-0.0040.0000.0000.0000.000
132A169ASP-1-0.775-0.86827.906-0.036-0.0360.0000.0000.0000.000
133A170ARG10.9300.97324.2270.0160.0160.0000.0000.0000.000
134A171ARG10.7080.82320.488-0.023-0.0230.0000.0000.0000.000
135A172LEU00.0060.00323.477-0.004-0.0040.0000.0000.0000.000
136A173ALA0-0.061-0.00925.724-0.001-0.0010.0000.0000.0000.000
137A174VAL00.0280.00926.659-0.009-0.0090.0000.0000.0000.000
138A175ALA0-0.033-0.02229.2550.0050.0050.0000.0000.0000.000
139A176GLY00.0030.00431.9760.0040.0040.0000.0000.0000.000
140A177MET0-0.020-0.01132.6450.0050.0050.0000.0000.0000.000
141A178MET0-0.0060.02330.226-0.003-0.0030.0000.0000.0000.000
142A179ALA00.0380.02729.1180.0040.0040.0000.0000.0000.000
143A180LEU0-0.031-0.02928.6170.0010.0010.0000.0000.0000.000
144A181PRO00.0690.02525.3240.0010.0010.0000.0000.0000.000
145A182MET0-0.0120.01226.9870.0020.0020.0000.0000.0000.000
146A183SER0-0.093-0.06929.833-0.007-0.0070.0000.0000.0000.000
147A184ARG10.9330.93733.142-0.012-0.0120.0000.0000.0000.000
148A185ARG10.9861.00034.171-0.048-0.0480.0000.0000.0000.000
149A186ASP-1-0.737-0.83229.6590.0590.0590.0000.0000.0000.000
150A187ILE0-0.009-0.00831.3800.0010.0010.0000.0000.0000.000
151A188GLY0-0.019-0.01332.7340.0000.0000.0000.0000.0000.000
152A189ASP-1-0.769-0.88531.9540.0580.0580.0000.0000.0000.000
153A190TYR0-0.086-0.03626.4280.0050.0050.0000.0000.0000.000
154A191LEU00.008-0.00430.806-0.001-0.0010.0000.0000.0000.000
155A192GLY00.0710.04733.865-0.003-0.0030.0000.0000.0000.000
156A193LEU0-0.098-0.04536.007-0.004-0.0040.0000.0000.0000.000
157A194THR00.027-0.00537.7200.0020.0020.0000.0000.0000.000
158A195LEU00.0790.02838.127-0.002-0.0020.0000.0000.0000.000
159A196GLU-1-0.861-0.92539.3030.0260.0260.0000.0000.0000.000
160A197THR0-0.036-0.01741.442-0.003-0.0030.0000.0000.0000.000
161A198VAL00.0460.02836.491-0.003-0.0030.0000.0000.0000.000
162A199SER0-0.015-0.01439.737-0.003-0.0030.0000.0000.0000.000
163A200ARG10.9450.98241.735-0.020-0.0200.0000.0000.0000.000
164A201ALA00.0520.03940.979-0.002-0.0020.0000.0000.0000.000
165A202LEU00.0320.00037.170-0.003-0.0030.0000.0000.0000.000
166A203SER0-0.046-0.03741.350-0.002-0.0020.0000.0000.0000.000
167A204GLN0-0.0160.00044.839-0.001-0.0010.0000.0000.0000.000
168A205LEU00.010-0.00339.917-0.002-0.0020.0000.0000.0000.000
169A206HIS0-0.036-0.01743.348-0.003-0.0030.0000.0000.0000.000
170A207THR0-0.026-0.01344.590-0.001-0.0010.0000.0000.0000.000
171A208GLN0-0.0040.01046.1060.0000.0000.0000.0000.0000.000
172A209GLY00.0510.02946.345-0.001-0.0010.0000.0000.0000.000
173A210ILE0-0.072-0.03440.771-0.002-0.0020.0000.0000.0000.000
174A211LEU0-0.0020.00838.528-0.002-0.0020.0000.0000.0000.000
175A212GLY0-0.012-0.00639.9690.0010.0010.0000.0000.0000.000
176A213PHE00.0150.00038.4370.0010.0010.0000.0000.0000.000
177A214SER0-0.025-0.00938.197-0.002-0.0020.0000.0000.0000.000
178A215GLY00.0860.04438.6590.0000.0000.0000.0000.0000.000
179A216ALA0-0.010-0.01438.246-0.001-0.0010.0000.0000.0000.000
180A217ARG10.9400.96731.265-0.021-0.0210.0000.0000.0000.000
181A218GLN00.0500.05432.198-0.003-0.0030.0000.0000.0000.000
182A219ILE00.000-0.00234.3510.0010.0010.0000.0000.0000.000
183A220VAL00.0280.02834.833-0.003-0.0030.0000.0000.0000.000
184A221LEU00.0130.00534.4370.0030.0030.0000.0000.0000.000
185A222ARG10.9460.96037.6480.0130.0130.0000.0000.0000.000
186A223ASN0-0.004-0.00240.626-0.001-0.0010.0000.0000.0000.000
187A224ARG10.8570.88933.5790.0320.0320.0000.0000.0000.000
188A225GLN00.0360.02938.2410.0000.0000.0000.0000.0000.000
189A226ARG10.8510.90840.5890.0110.0110.0000.0000.0000.000
190A227LEU00.0040.00236.5730.0020.0020.0000.0000.0000.000
191A228HIS00.007-0.01734.642-0.001-0.0010.0000.0000.0000.000
192A229ASN0-0.047-0.02238.6420.0010.0010.0000.0000.0000.000
193A230LEU0-0.045-0.00641.1640.0010.0010.0000.0000.0000.000
194A231ASP-1-0.832-0.89836.6250.0030.0030.0000.0000.0000.000
195A232ALA0-0.031-0.00838.3020.0000.0000.0000.0000.0000.000
196A233ALA0-0.009-0.00738.269-0.001-0.0010.0000.0000.0000.000
197A234ALA00.0030.00036.4110.0020.0020.0000.0000.0000.000
198A235ALA00.0060.00538.533-0.002-0.0020.0000.0000.0000.000