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: X16GZ

Calculation Name: 4QXL-A-Xray40

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4QXL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2019-02-15

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1010428.263834
FMO2-HF: Nuclear repulsion 962168.192388
FMO2-HF: Total energy -48260.071445
FMO2-MP2: Total energy -48398.761677


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-41.335-39.76723.517-13.73-11.356-0.15
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.752 / q_NPA : 0.857
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].
3A3GLU-1-0.812-0.8841.706-128.059-125.80618.226-11.687-8.791-0.139
4A4GLY00.0610.0434.7004.0544.157-0.001-0.015-0.0860.000
5A5ALA00.0130.0088.397-0.203-0.2030.0000.0000.0000.000
6A6TRP0-0.0410.01611.7281.2391.2390.0000.0000.0000.000
7A7GLN0-0.068-0.03515.0750.4070.4070.0000.0000.0000.000
8A8ASP-1-0.757-0.88118.404-13.340-13.3400.0000.0000.0000.000
9A9SER0-0.043-0.02721.7930.1690.1690.0000.0000.0000.000
10A10GLY00.0530.02825.1550.0770.0770.0000.0000.0000.000
11A11MET0-0.025-0.00128.5190.0840.0840.0000.0000.0000.000
12A12GLY00.0380.03131.050-0.223-0.2230.0000.0000.0000.000
13A13VAL0-0.0100.00332.0360.2930.2930.0000.0000.0000.000
14A14THR0-0.001-0.00834.8500.0970.0970.0000.0000.0000.000
15A15LEU0-0.037-0.00436.4070.0810.0810.0000.0000.0000.000
16A16ASN00.028-0.01239.9080.1140.1140.0000.0000.0000.000
17A17TYR00.0070.00442.6750.2420.2420.0000.0000.0000.000
18A18ARG10.9110.95541.9117.0067.0060.0000.0000.0000.000
19A19GLY00.0330.02641.3740.1410.1410.0000.0000.0000.000
20A20VAL0-0.047-0.01038.8730.0420.0420.0000.0000.0000.000
21A21SER00.0520.03233.907-0.184-0.1840.0000.0000.0000.000
22A22ALA0-0.0040.00334.7440.0920.0920.0000.0000.0000.000
23A23SER00.0350.00029.463-0.330-0.3300.0000.0000.0000.000
24A24SER0-0.053-0.02228.3960.4230.4230.0000.0000.0000.000
25A25SER00.007-0.01428.918-0.065-0.0650.0000.0000.0000.000
26A26PRO0-0.036-0.01624.683-0.188-0.1880.0000.0000.0000.000
27A27LEU0-0.0400.01022.1100.1270.1270.0000.0000.0000.000
28A28SER0-0.033-0.03019.621-0.270-0.2700.0000.0000.0000.000
29A29ALA00.0400.02316.2580.2600.2600.0000.0000.0000.000
30A30ARG10.8800.95618.18615.13815.1380.0000.0000.0000.000
31A31GLN0-0.036-0.01413.2731.9981.9980.0000.0000.0000.000
32A32PRO00.0290.00215.674-0.159-0.1590.0000.0000.0000.000
33A33VAL0-0.0230.00012.131-1.537-1.5370.0000.0000.0000.000
34A34SER00.0160.00510.6870.5970.5970.0000.0000.0000.000
35A35GLY00.0000.0038.030-2.708-2.7080.0000.0000.0000.000
36A36VAL0-0.026-0.0117.3103.4063.4060.0000.0000.0000.000
37A37MET00.0110.0038.018-3.281-3.2810.0000.0000.0000.000
38A38THR0-0.052-0.0496.2630.7700.7700.0000.0000.0000.000
39A39LEU00.0350.0299.5782.2522.2520.0000.0000.0000.000
40A40VAL00.007-0.00212.477-0.799-0.7990.0000.0000.0000.000
41A41ALA0-0.012-0.00715.4370.7890.7890.0000.0000.0000.000
42A42TRP0-0.038-0.01318.2400.0610.0610.0000.0000.0000.000
43A43ARG10.9430.96521.61912.86212.8620.0000.0000.0000.000
44A44TYR00.006-0.00325.1110.0610.0610.0000.0000.0000.000
45A45GLU-1-0.889-0.92328.472-10.012-10.0120.0000.0000.0000.000
46A46LEU0-0.052-0.02131.9310.0520.0520.0000.0000.0000.000
47A47ASN0-0.0030.00435.3040.0040.0040.0000.0000.0000.000
48A48GLY00.0300.01138.6460.1280.1280.0000.0000.0000.000
49A49PRO00.0030.00639.150-0.192-0.1920.0000.0000.0000.000
50A50THR00.0700.02635.3740.0200.0200.0000.0000.0000.000
51A51PRO0-0.0160.00637.3850.2070.2070.0000.0000.0000.000
52A52ALA00.0820.04038.587-0.203-0.2030.0000.0000.0000.000
53A53GLY00.0210.02838.5680.1590.1590.0000.0000.0000.000
54A54LEU0-0.0430.00933.653-0.026-0.0260.0000.0000.0000.000
55A55ARG10.8600.91930.2549.5899.5890.0000.0000.0000.000
56A56VAL0-0.007-0.01427.9670.0710.0710.0000.0000.0000.000
57A57ARG10.8590.92226.5869.9869.9860.0000.0000.0000.000
58A58LEU00.0100.01820.3820.0610.0610.0000.0000.0000.000
59A64CYS00.001-0.00621.8680.0480.0480.0000.0000.0000.000
60A60SER00.0470.02918.948-0.004-0.0040.0000.0000.0000.000
61A61GLN00.0040.02320.5450.4380.4380.0000.0000.0000.000
62A62SER00.000-0.00921.1000.7300.7300.0000.0000.0000.000
63A63ARG10.8740.95215.45617.26117.2610.0000.0000.0000.000
64A65VAL00.0020.04619.836-0.045-0.0450.0000.0000.0000.000
65A66GLU-1-0.753-0.84323.225-10.298-10.2980.0000.0000.0000.000
66A67LEU0-0.0190.00523.244-0.389-0.3890.0000.0000.0000.000
67A68ASP-1-0.861-0.90326.388-10.689-10.6890.0000.0000.0000.000
68A69GLY00.0090.00327.606-0.316-0.3160.0000.0000.0000.000
69A70GLN00.001-0.03428.9510.1730.1730.0000.0000.0000.000
70A71SER0-0.029-0.03624.666-0.287-0.2870.0000.0000.0000.000
71A72GLY00.0380.03322.7790.3870.3870.0000.0000.0000.000
72A73THR0-0.015-0.01217.555-0.594-0.5940.0000.0000.0000.000
73A74THR00.0350.01317.4250.4020.4020.0000.0000.0000.000
74A75HIS00.0510.02610.980-1.375-1.3750.0000.0000.0000.000
75A76GLY00.0310.02015.079-0.414-0.4140.0000.0000.0000.000
76A77PHE00.001-0.01414.9330.6200.6200.0000.0000.0000.000
77A78ALA00.0080.01511.615-1.129-1.1290.0000.0000.0000.000
78A79HIS0-0.041-0.0479.8920.6480.6480.0000.0000.0000.000
79A80VAL0-0.0030.02411.7660.7970.7970.0000.0000.0000.000
80A81PRO00.0210.01512.395-1.967-1.9670.0000.0000.0000.000
81A82ALA00.025-0.00610.6110.9860.9860.0000.0000.0000.000
82A83VAL00.0270.00912.7110.6890.6890.0000.0000.0000.000
83A84GLU-1-0.760-0.85715.859-14.717-14.7170.0000.0000.0000.000
84A85PRO0-0.007-0.00117.843-0.405-0.4050.0000.0000.0000.000
85A86LEU0-0.017-0.01417.3000.0670.0670.0000.0000.0000.000
86A87ARG10.9290.95821.41612.08012.0800.0000.0000.0000.000
87A88PHE00.0260.02423.885-0.162-0.1620.0000.0000.0000.000
88A89VAL0-0.020-0.01326.9160.3540.3540.0000.0000.0000.000
89A90TRP0-0.019-0.01529.468-0.011-0.0110.0000.0000.0000.000
90A91GLU-1-0.856-0.93632.837-8.407-8.4070.0000.0000.0000.000
91A92VAL00.0090.01135.951-0.101-0.1010.0000.0000.0000.000
92A93PRO00.0390.03037.4790.2300.2300.0000.0000.0000.000
93A94GLY00.0100.00240.3320.1210.1210.0000.0000.0000.000
94A95GLY00.0330.00344.089-0.032-0.0320.0000.0000.0000.000
95A96GLY00.0170.01746.5830.0520.0520.0000.0000.0000.000
96A97ARG10.9650.97446.4446.0506.0500.0000.0000.0000.000
97A98LEU0-0.0260.00740.3200.0400.0400.0000.0000.0000.000
98A99ILE0-0.0500.01145.0260.0530.0530.0000.0000.0000.000
99A100PRO0-0.0030.00443.5150.0390.0390.0000.0000.0000.000
100A101ALA00.0480.00342.519-0.091-0.0910.0000.0000.0000.000
101A102LEU00.0470.04634.908-0.014-0.0140.0000.0000.0000.000
102A103LYS10.8530.92538.1227.5347.5340.0000.0000.0000.000
103A104VAL00.0450.03131.222-0.031-0.0310.0000.0000.0000.000
104A105ARG10.9410.98833.8828.9308.9300.0000.0000.0000.000
105A106SER0-0.013-0.00329.342-0.160-0.1600.0000.0000.0000.000
106A107ASN00.0450.02426.6970.3750.3750.0000.0000.0000.000
107A108GLN0-0.037-0.04822.5350.5380.5380.0000.0000.0000.000
108A109VAL00.0250.01318.7890.0640.0640.0000.0000.0000.000
109A110ILE0-0.002-0.00814.908-0.020-0.0200.0000.0000.0000.000
110A111VAL00.0040.00412.346-0.042-0.0420.0000.0000.0000.000
111A112ASN0-0.029-0.0089.257-2.090-2.0900.0000.0000.0000.000
112A113TYR00.0250.0087.7352.4962.4960.0000.0000.0000.000
113A114ARG10.9550.9902.51636.70537.4050.243-0.325-0.6180.001
114A115HIS0-0.016-0.0113.7399.3319.694-0.001-0.129-0.2340.000
115A0NME00.0370.0364.107-6.769-6.5280.002-0.054-0.1900.000
116A203HOH0-0.011-0.01513.6050.4180.4180.0000.0000.0000.000
117A204HOH00.010-0.00738.723-0.034-0.0340.0000.0000.0000.000
118A205HOH0-0.009-0.02039.047-0.004-0.0040.0000.0000.0000.000
119A206HOH0-0.003-0.00219.0060.1520.1520.0000.0000.0000.000
120A207HOH0-0.033-0.02134.809-0.112-0.1120.0000.0000.0000.000
121A209HOH00.020-0.00325.0810.0960.0960.0000.0000.0000.000
122A210HOH00.008-0.00227.847-0.062-0.0620.0000.0000.0000.000
123A211HOH0-0.034-0.03441.9470.0890.0890.0000.0000.0000.000
124A212HOH0-0.039-0.0317.7281.7581.7580.0000.0000.0000.000
125A213HOH0-0.030-0.02940.463-0.005-0.0050.0000.0000.0000.000
126A214HOH00.0320.01824.527-0.051-0.0510.0000.0000.0000.000
127A215HOH00.0030.0027.872-1.777-1.7770.0000.0000.0000.000
128A216HOH00.0230.02333.891-0.024-0.0240.0000.0000.0000.000
129A217HOH00.003-0.01042.852-0.072-0.0720.0000.0000.0000.000
130A218HOH00.0040.00312.3600.1080.1080.0000.0000.0000.000
131A219HOH00.0030.0165.9012.1752.1750.0000.0000.0000.000
132A220HOH00.0330.01934.359-0.072-0.0720.0000.0000.0000.000
133A221HOH00.012-0.00924.985-0.190-0.1900.0000.0000.0000.000
134A222HOH0-0.009-0.01217.0620.0160.0160.0000.0000.0000.000
135A223HOH0-0.021-0.02241.0830.0880.0880.0000.0000.0000.000
136A224HOH0-0.001-0.00320.231-0.170-0.1700.0000.0000.0000.000
137A225HOH0-0.014-0.01731.545-0.048-0.0480.0000.0000.0000.000
138A226HOH0-0.0080.00629.4810.1380.1380.0000.0000.0000.000
139A227HOH00.0300.01951.317-0.042-0.0420.0000.0000.0000.000
140A228HOH0-0.029-0.02319.1330.0620.0620.0000.0000.0000.000
141A229HOH00.000-0.00518.500-0.270-0.2700.0000.0000.0000.000
142A230HOH00.0440.02818.6660.0890.0890.0000.0000.0000.000
143A231HOH00.0290.03023.512-0.153-0.1530.0000.0000.0000.000
144A232HOH0-0.002-0.0121.8741.437-0.6665.049-1.519-1.428-0.012
145A233HOH0-0.038-0.0235.165-3.174-3.163-0.001-0.001-0.0090.000
146A234HOH00.0180.01518.074-0.049-0.0490.0000.0000.0000.000
147A236HOH0-0.020-0.03346.148-0.040-0.0400.0000.0000.0000.000
148A237HOH00.0340.02131.931-0.015-0.0150.0000.0000.0000.000
149A238HOH0-0.007-0.00521.912-0.159-0.1590.0000.0000.0000.000
150A239HOH0-0.021-0.01632.8050.1140.1140.0000.0000.0000.000
151A241HOH0-0.005-0.00929.8950.0680.0680.0000.0000.0000.000
152A242HOH0-0.039-0.02825.267-0.134-0.1340.0000.0000.0000.000
153A245HOH0-0.036-0.01918.463-0.093-0.0930.0000.0000.0000.000
154A246HOH0-0.067-0.07023.678-0.106-0.1060.0000.0000.0000.000
155A247HOH0-0.0060.00133.249-0.142-0.1420.0000.0000.0000.000
156A248HOH00.0270.03526.9690.2080.2080.0000.0000.0000.000
157A249HOH00.0160.01441.6460.0590.0590.0000.0000.0000.000
158A250HOH00.0280.02128.840-0.172-0.1720.0000.0000.0000.000
159A251HOH00.0530.03046.020-0.074-0.0740.0000.0000.0000.000
160A252HOH00.0460.03523.285-0.184-0.1840.0000.0000.0000.000
161A253HOH0-0.052-0.05228.0230.0430.0430.0000.0000.0000.000
162A254HOH0-0.026-0.02143.2920.0570.0570.0000.0000.0000.000
163A255HOH0-0.053-0.04018.4900.0570.0570.0000.0000.0000.000
164A257HOH0-0.018-0.02535.0990.1160.1160.0000.0000.0000.000
165A259HOH00.0380.03621.039-0.294-0.2940.0000.0000.0000.000
166A260HOH0-0.036-0.02336.361-0.023-0.0230.0000.0000.0000.000
167A262HOH0-0.042-0.03433.2520.1220.1220.0000.0000.0000.000
168A263HOH0-0.049-0.05919.860-0.188-0.1880.0000.0000.0000.000
169A264HOH0-0.040-0.02244.7340.0510.0510.0000.0000.0000.000
170A265HOH00.0260.01631.506-0.034-0.0340.0000.0000.0000.000
171A266HOH0-0.032-0.02736.3140.0720.0720.0000.0000.0000.000
172A267HOH00.001-0.00526.622-0.127-0.1270.0000.0000.0000.000
173A268HOH0-0.074-0.06724.3320.1390.1390.0000.0000.0000.000
174A269HOH0-0.035-0.03632.099-0.056-0.0560.0000.0000.0000.000
175A270HOH00.0060.00920.8460.3180.3180.0000.0000.0000.000
176A278HOH00.0240.02521.453-0.265-0.2650.0000.0000.0000.000
177A282HOH0-0.036-0.02948.5430.0620.0620.0000.0000.0000.000
178A283HOH0-0.037-0.02325.112-0.038-0.0380.0000.0000.0000.000
179A285HOH0-0.016-0.01327.415-0.053-0.0530.0000.0000.0000.000