FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: Z7R9N

Calculation Name: 4U3Q-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U3Q

Chain ID: A

ChEMBL ID:

UniProt ID: P29722

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 192
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -745827.063688
FMO2-HF: Nuclear repulsion 705694.167143
FMO2-HF: Total energy -40132.896545
FMO2-MP2: Total energy -40247.490861


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:10:LYS)


Summations of interaction energy for fragment #1(A:10: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.
-11.293-6.3891.932-3.356-3.483-0.013
Interaction energy analysis for fragmet #1(A:10:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.208 / q_NPA : 0.039
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].
4A11ALA0-0.0990.0684.658-0.0140.163-0.001-0.070-0.1060.000
5A12LYS00.072-0.1373.687-2.528-1.282-0.002-0.637-0.6070.003
6A12LYS10.9031.1164.240-0.587-0.525-0.001-0.006-0.0550.000
7A13ALA00.112-0.1173.524-0.461-0.2560.0160.014-0.2360.000
8A13ALA0-0.0580.1402.915-0.0780.1240.192-0.212-0.1830.001
9A14GLU00.120-0.1044.1330.3270.467-0.001-0.065-0.0750.000
10A14GLU-1-0.965-0.8274.752-2.758-2.648-0.001-0.026-0.0830.000
11A15LYS00.038-0.0956.0440.1250.1250.0000.0000.0000.000
12A15LYS10.8441.0457.397-0.788-0.7880.0000.0000.0000.000
13A16VAL00.045-0.1077.8710.0340.0340.0000.0000.0000.000
14A16VAL0-0.0620.1048.3540.0190.0190.0000.0000.0000.000
15A17GLU00.130-0.1098.3680.0970.0970.0000.0000.0000.000
16A17GLU-1-0.991-0.8278.201-0.890-0.8900.0000.0000.0000.000
17A18CYS00.012-0.1559.9770.0430.0430.0000.0000.0000.000
18A18CYS0-0.1470.0759.7620.0010.0010.0000.0000.0000.000
19A19ALA00.104-0.08712.0400.0110.0110.0000.0000.0000.000
20A19ALA0-0.0790.10913.3180.0140.0140.0000.0000.0000.000
21A20LEU00.000-0.13513.3680.0330.0330.0000.0000.0000.000
22A20LEU0-0.0670.12112.4480.0030.0030.0000.0000.0000.000
23A21LYS00.120-0.07314.3750.0300.0300.0000.0000.0000.000
24A21LYS10.7921.04912.4710.4460.4460.0000.0000.0000.000
25A22GLY0-0.085-0.13816.128-0.001-0.0010.0000.0000.0000.000
26A23GLY0-0.048-0.02418.7670.0180.0180.0000.0000.0000.000
27A24ILE00.104-0.00620.328-0.007-0.0070.0000.0000.0000.000
28A24ILE0-0.0820.11424.2800.0000.0000.0000.0000.0000.000
29A25PHE00.061-0.10721.8140.0060.0060.0000.0000.0000.000
30A25PHE0-0.1050.09217.8620.0030.0030.0000.0000.0000.000
31A26ARG00.157-0.08423.097-0.004-0.0040.0000.0000.0000.000
32A26ARG10.7440.97627.4090.0000.0000.0000.0000.0000.000
33A27GLY0-0.033-0.12026.3190.0080.0080.0000.0000.0000.000
34A28THR00.0420.01527.970-0.005-0.0050.0000.0000.0000.000
35A28THR0-0.0420.08232.1220.0000.0000.0000.0000.0000.000
36A29LEU00.046-0.09428.4960.0060.0060.0000.0000.0000.000
37A29LEU0-0.0740.10925.6050.0010.0010.0000.0000.0000.000
38A30PRO0-0.007-0.10928.912-0.004-0.0040.0000.0000.0000.000
39A31ALA00.1270.01131.734-0.001-0.0010.0000.0000.0000.000
40A31ALA0-0.0770.11434.453-0.001-0.0010.0000.0000.0000.000
41A32ALA00.078-0.10234.3900.0030.0030.0000.0000.0000.000
42A32ALA0-0.0980.08935.3240.0000.0000.0000.0000.0000.000
43A33ASP00.075-0.10736.4460.0010.0010.0000.0000.0000.000
44A33ASP-1-1.000-0.85539.1230.0150.0150.0000.0000.0000.000
45A34CYS00.019-0.09637.9450.0000.0000.0000.0000.0000.000
46A34CYS0-0.1400.07539.9700.0010.0010.0000.0000.0000.000
47A35PRO00.008-0.11637.8270.0020.0020.0000.0000.0000.000
48A36GLY00.0300.00534.3580.0030.0030.0000.0000.0000.000
49A37ILE00.090-0.02532.798-0.002-0.0020.0000.0000.0000.000
50A37ILE0-0.0740.12631.8560.0000.0000.0000.0000.0000.000
51A38ASP00.101-0.09831.1980.0040.0040.0000.0000.0000.000
52A38ASP-1-0.909-0.77331.5940.0040.0040.0000.0000.0000.000
53A39THR0-0.008-0.09827.996-0.006-0.0060.0000.0000.0000.000
54A39THR0-0.0320.07426.1530.0000.0000.0000.0000.0000.000
55A40THR00.022-0.08526.3560.0060.0060.0000.0000.0000.000
56A40THR0-0.0570.05825.949-0.001-0.0010.0000.0000.0000.000
57A41VAL00.061-0.11822.188-0.004-0.0040.0000.0000.0000.000
58A41VAL0-0.0610.13220.3580.0010.0010.0000.0000.0000.000
59A42THR00.050-0.09021.9190.0060.0060.0000.0000.0000.000
60A42THR0-0.0390.06722.2370.0020.0020.0000.0000.0000.000
61A43PHE00.079-0.06517.389-0.001-0.0010.0000.0000.0000.000
62A43PHE0-0.0880.09516.3200.0050.0050.0000.0000.0000.000
63A44ASN00.168-0.07718.440-0.009-0.0090.0000.0000.0000.000
64A44ASN0-0.1160.06420.3860.0100.0100.0000.0000.0000.000
65A45ALA00.133-0.09916.783-0.015-0.0150.0000.0000.0000.000
66A45ALA0-0.0610.10917.5220.0010.0010.0000.0000.0000.000
67A46ASP0-0.042-0.15716.784-0.048-0.0480.0000.0000.0000.000
68A46ASP-1-0.834-0.74420.229-0.176-0.1760.0000.0000.0000.000
69A47GLY0-0.014-0.09015.794-0.020-0.0200.0000.0000.0000.000
70A48THR00.0340.00416.6890.0090.0090.0000.0000.0000.000
71A48THR0-0.0730.04220.7430.0110.0110.0000.0000.0000.000
72A49ALA00.094-0.11119.372-0.008-0.0080.0000.0000.0000.000
73A49ALA0-0.0830.10619.0850.0010.0010.0000.0000.0000.000
74A50GLN00.098-0.09020.9730.0010.0010.0000.0000.0000.000
75A50GLN0-0.1310.08124.876-0.003-0.0030.0000.0000.0000.000
76A51LYS00.091-0.10623.9740.0010.0010.0000.0000.0000.000
77A51LYS10.7821.05324.1510.0080.0080.0000.0000.0000.000
78A52VAL00.061-0.10625.732-0.003-0.0030.0000.0000.0000.000
79A52VAL0-0.0920.09128.266-0.001-0.0010.0000.0000.0000.000
80A53GLU00.068-0.11829.1200.0040.0040.0000.0000.0000.000
81A53GLU-1-0.910-0.80829.027-0.005-0.0050.0000.0000.0000.000
82A54LEU0-0.047-0.11331.487-0.002-0.0020.0000.0000.0000.000
83A54LEU00.0610.03333.8850.0000.0000.0000.0000.0000.000
84A63SER00.0510.01139.130-0.001-0.0010.0000.0000.0000.000
85A63SER0-0.0680.06138.0800.0010.0010.0000.0000.0000.000
86A64PRO0-0.018-0.10634.8450.0010.0010.0000.0000.0000.000
87A65LEU00.079-0.01533.368-0.004-0.0040.0000.0000.0000.000
88A65LEU0-0.0380.13832.7390.0000.0000.0000.0000.0000.000
89A66THR00.022-0.08330.2470.0020.0020.0000.0000.0000.000
90A66THR0-0.0640.04329.524-0.002-0.0020.0000.0000.0000.000
91A67TYR00.047-0.10427.151-0.001-0.0010.0000.0000.0000.000
92A67TYR0-0.0950.11026.4070.0000.0000.0000.0000.0000.000
93A68ARG00.106-0.09325.223-0.001-0.0010.0000.0000.0000.000
94A68ARG10.8441.05126.0730.0680.0680.0000.0000.0000.000
95A69GLY00.042-0.07822.4930.0060.0060.0000.0000.0000.000
96A70THR00.0090.03718.566-0.003-0.0030.0000.0000.0000.000
97A70THR0-0.0160.06417.5790.0060.0060.0000.0000.0000.000
98A71TRP00.091-0.08215.8380.0240.0240.0000.0000.0000.000
99A71TRP0-0.1130.08311.766-0.005-0.0050.0000.0000.0000.000
100A72MET00.064-0.11112.064-0.042-0.0420.0000.0000.0000.000
101A72MET0-0.0880.09711.763-0.016-0.0160.0000.0000.0000.000
102A73VAL00.071-0.1198.5180.0790.0790.0000.0000.0000.000
103A73VAL0-0.0710.1297.168-0.007-0.0070.0000.0000.0000.000
104A74ARG00.059-0.0747.683-0.121-0.1210.0000.0000.0000.000
105A74ARG10.7471.0018.617-0.100-0.1000.0000.0000.0000.000
106A75GLU00.158-0.1164.064-0.0640.022-0.001-0.021-0.0650.000
107A75GLU-1-1.004-0.8192.264-4.504-1.9831.732-2.252-2.000-0.017
108A76ASP0-0.039-0.1613.9870.1360.291-0.001-0.081-0.0730.000
109A76ASP-1-0.823-0.7877.9710.3040.3040.0000.0000.0000.000
110A77GLY0-0.061-0.1406.7170.1050.1050.0000.0000.0000.000
111A78ILE00.0760.0057.905-0.084-0.0840.0000.0000.0000.000
112A78ILE0-0.0730.09810.919-0.006-0.0060.0000.0000.0000.000
113A79VAL00.020-0.12510.465-0.033-0.0330.0000.0000.0000.000
114A79VAL0-0.0750.10711.510-0.006-0.0060.0000.0000.0000.000
115A80GLU00.119-0.11612.7260.0290.0290.0000.0000.0000.000
116A80GLU-1-1.001-0.84713.719-0.051-0.0510.0000.0000.0000.000
117A81LEU00.106-0.09614.964-0.037-0.0370.0000.0000.0000.000
118A81LEU0-0.1320.10417.9470.0010.0010.0000.0000.0000.000
119A82SER00.018-0.08718.0810.0200.0200.0000.0000.0000.000
120A82SER0-0.0400.07618.3200.0000.0000.0000.0000.0000.000
121A83LEU00.051-0.09220.579-0.016-0.0160.0000.0000.0000.000
122A83LEU0-0.0650.08922.3700.0010.0010.0000.0000.0000.000
123A84VAL0-0.032-0.11323.8450.0050.0050.0000.0000.0000.000
124A84VAL00.0650.04425.835-0.001-0.0010.0000.0000.0000.000
125A94GLU00.150-0.01824.8520.0050.0050.0000.0000.0000.000
126A94GLU-1-1.048-0.85424.374-0.045-0.0450.0000.0000.0000.000
127A95LYS00.037-0.09820.257-0.012-0.0120.0000.0000.0000.000
128A95LYS10.8171.03916.9150.0670.0670.0000.0000.0000.000
129A96GLU00.039-0.14420.0820.0140.0140.0000.0000.0000.000
130A96GLU-1-0.870-0.76620.715-0.007-0.0070.0000.0000.0000.000
131A97LEU00.142-0.09816.660-0.022-0.0220.0000.0000.0000.000
132A97LEU0-0.1240.09015.5870.0060.0060.0000.0000.0000.000
133A98TYR00.027-0.11915.5900.0080.0080.0000.0000.0000.000
134A98TYR0-0.1180.07416.008-0.002-0.0020.0000.0000.0000.000
135A99GLU00.200-0.09913.886-0.002-0.0020.0000.0000.0000.000
136A99GLU-1-0.988-0.84013.5210.2770.2770.0000.0000.0000.000
137A100LEU00.101-0.11113.251-0.033-0.0330.0000.0000.0000.000
138A100LEU0-0.1240.11612.2760.0030.0030.0000.0000.0000.000
139A101ILE00.038-0.08114.1180.0630.0630.0000.0000.0000.000
140A101ILE0-0.1180.05018.267-0.002-0.0020.0000.0000.0000.000
141A102ASP00.036-0.09916.1840.0480.0480.0000.0000.0000.000
142A102ASP-1-0.890-0.82218.4910.1120.1120.0000.0000.0000.000
143A103SER00.058-0.06616.150-0.012-0.0120.0000.0000.0000.000
144A103SER0-0.0490.05416.8840.0080.0080.0000.0000.0000.000
145A104ASN00.065-0.06817.183-0.032-0.0320.0000.0000.0000.000
146A104ASN0-0.1300.04421.1540.0090.0090.0000.0000.0000.000
147A105SER00.071-0.04019.045-0.020-0.0200.0000.0000.0000.000
148A105SER0-0.0560.02820.040-0.002-0.0020.0000.0000.0000.000
149A106VAL00.032-0.10217.8880.0220.0220.0000.0000.0000.000
150A106VAL0-0.0550.12816.234-0.002-0.0020.0000.0000.0000.000
151A107ARG00.214-0.07318.104-0.015-0.0150.0000.0000.0000.000
152A107ARG10.7821.04317.811-0.171-0.1710.0000.0000.0000.000
153A108TYR00.099-0.09218.7910.0080.0080.0000.0000.0000.000
154A108TYR0-0.0670.11821.743-0.002-0.0020.0000.0000.0000.000
155A109MET0-0.003-0.14318.9560.0020.0020.0000.0000.0000.000
156A109MET0-0.0950.12216.0240.0060.0060.0000.0000.0000.000
157A110GLY00.001-0.09020.3660.0040.0040.0000.0000.0000.000
158A111ALA00.1270.00320.8730.0000.0000.0000.0000.0000.000
159A111ALA0-0.0450.12823.567-0.001-0.0010.0000.0000.0000.000
160A112PRO0-0.074-0.12918.3940.0160.0160.0000.0000.0000.000
161A113GLY00.0090.00319.657-0.006-0.0060.0000.0000.0000.000
162A114ALA00.146-0.01721.107-0.003-0.0030.0000.0000.0000.000
163A114ALA0-0.0230.17222.285-0.001-0.0010.0000.0000.0000.000
164A115GLY0-0.072-0.13920.1690.0020.0020.0000.0000.0000.000
165A116LYS00.127-0.00120.9850.0190.0190.0000.0000.0000.000
166A116LYS10.7441.05325.479-0.101-0.1010.0000.0000.0000.000
167A117PRO00.034-0.07422.448-0.005-0.0050.0000.0000.0000.000
168A118SER00.0480.01124.217-0.011-0.0110.0000.0000.0000.000
169A118SER0-0.0300.09727.3620.0000.0000.0000.0000.0000.000
170A119LYS00.194-0.06727.065-0.010-0.0100.0000.0000.0000.000
171A119LYS10.7861.02223.154-0.109-0.1090.0000.0000.0000.000
172A120GLU00.022-0.13826.8100.0060.0060.0000.0000.0000.000
173A120GLU-1-0.946-0.81029.4230.0910.0910.0000.0000.0000.000
174A121MET00.090-0.11028.1900.0010.0010.0000.0000.0000.000
175A121MET0-0.0690.11628.652-0.001-0.0010.0000.0000.0000.000
176A122ALA00.142-0.10224.075-0.011-0.0110.0000.0000.0000.000
177A122ALA0-0.0830.09623.1090.0040.0040.0000.0000.0000.000
178A123PRO0-0.051-0.13124.800-0.002-0.0020.0000.0000.0000.000
179A124PHE00.066-0.00226.303-0.003-0.0030.0000.0000.0000.000
180A124PHE0-0.0710.12129.0590.0000.0000.0000.0000.0000.000
181A125TYR00.126-0.06924.525-0.011-0.0110.0000.0000.0000.000
182A125TYR0-0.1150.08023.7300.0020.0020.0000.0000.0000.000
183A126VAL00.103-0.09522.7080.0010.0010.0000.0000.0000.000
184A126VAL0-0.1200.07422.2790.0030.0030.0000.0000.0000.000
185A127LEU00.028-0.12222.305-0.004-0.0040.0000.0000.0000.000
186A127LEU0-0.0840.12921.618-0.003-0.0030.0000.0000.0000.000
187A128LYS00.157-0.09221.9610.0040.0040.0000.0000.0000.000
188A128LYS10.8551.07524.428-0.066-0.0660.0000.0000.0000.000
189A129LYS00.150-0.07622.254-0.008-0.0080.0000.0000.0000.000
190A129LYS10.8031.06218.6110.0540.0540.0000.0000.0000.000
191A130THR0-0.192-0.18123.1510.0030.0030.0000.0000.0000.000
192A130THR00.0810.05926.2780.0000.0000.0000.0000.0000.000