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: QNL9Y

Calculation Name: 3C4R-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C4R

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2025-07-08

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 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 237
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1014948.837741
FMO2-HF: Nuclear repulsion 964982.616059
FMO2-HF: Total energy -49966.221681
FMO2-MP2: Total energy -50110.996216


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:2:LYS)


Summations of interaction energy for fragment #1(A:2: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.
-1.6160.867-0.021-1.211-1.250.003
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.172 / q_NPA : 0.075
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].
4A3ILE0-0.0470.1263.554-0.394-0.157-0.0010.026-0.2620.000
5A4LYS00.109-0.1223.829-1.0350.877-0.017-1.062-0.8330.002
6A4LYS10.7941.0665.5650.5190.5190.0000.0000.0000.000
7A5HIS00.153-0.0695.912-0.061-0.0610.0000.0000.0000.000
8A5HIS0-0.0750.1288.620-0.091-0.0910.0000.0000.0000.000
9A6GLU00.073-0.1088.7490.0100.0100.0000.0000.0000.000
10A6GLU-1-0.861-0.8009.494-0.581-0.5810.0000.0000.0000.000
11A7HIS00.098-0.1149.4410.2160.2160.0000.0000.0000.000
12A7HIS0-0.0870.0828.465-0.256-0.2560.0000.0000.0000.000
13A8ILE00.054-0.1069.6640.0290.0290.0000.0000.0000.000
14A8ILE0-0.0580.1096.418-0.004-0.0040.0000.0000.0000.000
15A9ARG00.102-0.06810.5900.0880.0880.0000.0000.0000.000
16A9ARG10.7290.97313.5500.4190.4190.0000.0000.0000.000
17A10MET00.041-0.10513.7270.0860.0860.0000.0000.0000.000
18A10MET0-0.0850.09213.717-0.012-0.0120.0000.0000.0000.000
19A11ALA00.084-0.09213.7610.1190.1190.0000.0000.0000.000
20A11ALA0-0.0480.10913.277-0.030-0.0300.0000.0000.0000.000
21A12MET00.077-0.11314.5760.0590.0590.0000.0000.0000.000
22A12MET0-0.1260.09713.806-0.008-0.0080.0000.0000.0000.000
23A13ASN00.150-0.05016.2020.0510.0510.0000.0000.0000.000
24A13ASN0-0.1310.05518.660-0.004-0.0040.0000.0000.0000.000
25A14ALA00.104-0.07818.3660.0570.0570.0000.0000.0000.000
26A14ALA0-0.1070.07618.281-0.006-0.0060.0000.0000.0000.000
27A15TRP00.052-0.10518.8710.0460.0460.0000.0000.0000.000
28A15TRP0-0.0790.09616.742-0.026-0.0260.0000.0000.0000.000
29A16ALA00.097-0.09820.3390.0220.0220.0000.0000.0000.000
30A16ALA0-0.0840.09921.0110.0000.0000.0000.0000.0000.000
31A17HIS00.051-0.07022.4050.0290.0290.0000.0000.0000.000
32A17HIS0-0.1280.05023.9860.0050.0050.0000.0000.0000.000
33A18PRO0-0.093-0.14624.0460.0200.0200.0000.0000.0000.000
34A19ASP00.0510.02726.5340.0160.0160.0000.0000.0000.000
35A19ASP-1-0.977-0.85827.608-0.218-0.2180.0000.0000.0000.000
36A20GLY00.028-0.11226.4260.0140.0140.0000.0000.0000.000
37A21GLU00.120-0.06722.927-0.019-0.0190.0000.0000.0000.000
38A21GLU-1-0.967-0.82422.499-0.243-0.2430.0000.0000.0000.000
39A22LYS00.022-0.10323.136-0.018-0.0180.0000.0000.0000.000
40A22LYS10.8991.07027.1660.1740.1740.0000.0000.0000.000
41A23VAL00.073-0.08624.6430.0070.0070.0000.0000.0000.000
42A23VAL0-0.0460.14123.5160.0000.0000.0000.0000.0000.000
43A24PRO00.049-0.09319.000-0.007-0.0070.0000.0000.0000.000
44A25ALA00.1080.03320.302-0.028-0.0280.0000.0000.0000.000
45A25ALA0-0.0440.11321.7400.0050.0050.0000.0000.0000.000
46A26ALA00.093-0.08721.5050.0020.0020.0000.0000.0000.000
47A26ALA0-0.0510.11025.2200.0040.0040.0000.0000.0000.000
48A27GLU00.006-0.11921.7160.0230.0230.0000.0000.0000.000
49A27GLU-1-0.936-0.82521.059-0.282-0.2820.0000.0000.0000.000
50A28ILE00.118-0.09917.9470.0000.0000.0000.0000.0000.000
51A28ILE0-0.1100.07916.294-0.008-0.0080.0000.0000.0000.000
52A29THR00.028-0.10118.820-0.008-0.0080.0000.0000.0000.000
53A29THR0-0.0640.03022.1070.0090.0090.0000.0000.0000.000
54A30ARG00.091-0.08421.3420.0180.0180.0000.0000.0000.000
55A30ARG10.7671.02723.0280.2530.2530.0000.0000.0000.000
56A31ALA00.102-0.08418.7770.0340.0340.0000.0000.0000.000
57A31ALA0-0.0910.09818.013-0.013-0.0130.0000.0000.0000.000
58A32TYR00.132-0.05418.136-0.001-0.0010.0000.0000.0000.000
59A32TYR0-0.1280.05417.081-0.005-0.0050.0000.0000.0000.000
60A33PHE00.010-0.14819.0970.0120.0120.0000.0000.0000.000
61A33PHE0-0.0910.10123.8210.0010.0010.0000.0000.0000.000
62A34GLU00.072-0.10021.9840.0280.0280.0000.0000.0000.000
63A34GLU-1-0.949-0.81521.329-0.272-0.2720.0000.0000.0000.000
64A35LEU0-0.012-0.12818.2630.0270.0270.0000.0000.0000.000
65A35LEU0-0.0830.08515.604-0.010-0.0100.0000.0000.0000.000
66A36GLY0-0.009-0.08719.7330.0180.0180.0000.0000.0000.000
67A37MET00.055-0.01117.7740.0320.0320.0000.0000.0000.000
68A37MET0-0.0980.09613.906-0.025-0.0250.0000.0000.0000.000
69A38THR0-0.028-0.09418.4010.0000.0000.0000.0000.0000.000
70A38THR0-0.0280.06719.9610.0040.0040.0000.0000.0000.000
71A39PHE00.127-0.06816.8140.0130.0130.0000.0000.0000.000
72A39PHE0-0.0940.09613.7070.0040.0040.0000.0000.0000.000
73A40PRO0-0.021-0.12214.447-0.027-0.0270.0000.0000.0000.000
74A41GLU00.1490.05217.327-0.013-0.0130.0000.0000.0000.000
75A41GLU-1-1.053-0.88121.649-0.094-0.0940.0000.0000.0000.000
76A42LEU00.117-0.09420.994-0.008-0.0080.0000.0000.0000.000
77A42LEU0-0.0860.12419.122-0.004-0.0040.0000.0000.0000.000
78A43TYR00.082-0.06622.1510.0100.0100.0000.0000.0000.000
79A43TYR0-0.1010.06526.2080.0000.0000.0000.0000.0000.000
80A44ASP00.140-0.05225.908-0.019-0.0190.0000.0000.0000.000
81A44ASP-1-0.808-0.76626.958-0.097-0.0970.0000.0000.0000.000
82A45ASP00.110-0.08727.4100.0060.0060.0000.0000.0000.000
83A45ASP-1-0.976-0.84728.623-0.147-0.1470.0000.0000.0000.000
84A46SER0-0.029-0.09630.3800.0030.0030.0000.0000.0000.000
85A46SER0-0.0870.03531.4020.0040.0040.0000.0000.0000.000
86A47HIS00.024-0.15830.7760.0090.0090.0000.0000.0000.000
87A47HIS0-0.1780.05729.5020.0060.0060.0000.0000.0000.000
88A48PRO00.029-0.09632.131-0.006-0.0060.0000.0000.0000.000
89A49GLU00.1900.05632.068-0.004-0.0040.0000.0000.0000.000
90A49GLU-1-1.078-0.89531.001-0.111-0.1110.0000.0000.0000.000
91A50ALA00.067-0.13128.429-0.006-0.0060.0000.0000.0000.000
92A50ALA0-0.0500.13428.0310.0000.0000.0000.0000.0000.000
93A51LEU00.129-0.08926.439-0.007-0.0070.0000.0000.0000.000
94A51LEU0-0.0640.13025.4770.0020.0020.0000.0000.0000.000
95A52ALA00.126-0.10026.210-0.021-0.0210.0000.0000.0000.000
96A52ALA0-0.0450.14329.9160.0020.0020.0000.0000.0000.000
97A53ARG00.038-0.12126.911-0.008-0.0080.0000.0000.0000.000
98A53ARG10.7891.02926.8900.1050.1050.0000.0000.0000.000
99A54ASN00.059-0.10623.0750.0020.0020.0000.0000.0000.000
100A54ASN0-0.0750.08622.5150.0100.0100.0000.0000.0000.000
101A55THR00.057-0.09221.817-0.026-0.0260.0000.0000.0000.000
102A55THR0-0.0540.05823.497-0.003-0.0030.0000.0000.0000.000
103A56GLN00.146-0.05022.319-0.022-0.0220.0000.0000.0000.000
104A56GLN0-0.0990.09224.7740.0090.0090.0000.0000.0000.000
105A57LYS0-0.042-0.13621.574-0.001-0.0010.0000.0000.0000.000
106A57LYS10.7610.98320.5720.1400.1400.0000.0000.0000.000
107A58ILE00.064-0.06117.8150.0070.0070.0000.0000.0000.000
108A58ILE0-0.0450.11316.688-0.005-0.0050.0000.0000.0000.000
109A59PHE00.098-0.11517.376-0.041-0.0410.0000.0000.0000.000
110A59PHE0-0.0240.14118.990-0.004-0.0040.0000.0000.0000.000
111A60ARG00.195-0.04819.341-0.009-0.0090.0000.0000.0000.000
112A60ARG10.8011.03020.7070.1500.1500.0000.0000.0000.000
113A61TRP0-0.007-0.15015.8140.0250.0250.0000.0000.0000.000
114A61TRP0-0.0870.09514.8400.0020.0020.0000.0000.0000.000
115A62VAL00.089-0.09514.475-0.017-0.0170.0000.0000.0000.000
116A62VAL0-0.0930.11114.470-0.008-0.0080.0000.0000.0000.000
117A63GLU00.097-0.14415.465-0.046-0.0460.0000.0000.0000.000
118A63GLU-1-0.863-0.78719.483-0.186-0.1860.0000.0000.0000.000
119A64LYS0-0.058-0.04717.1380.0080.0080.0000.0000.0000.000
120A64LYS10.7350.98117.1900.1760.1760.0000.0000.0000.000
121A65ASP00.142-0.08913.738-0.064-0.0640.0000.0000.0000.000
122A65ASP-1-0.905-0.78213.548-0.332-0.3320.0000.0000.0000.000
123A66THR00.027-0.08214.0450.0390.0390.0000.0000.0000.000
124A66THR0-0.0250.04217.000-0.010-0.0100.0000.0000.0000.000
125A67PRO00.063-0.08212.764-0.045-0.0450.0000.0000.0000.000
126A68ASP00.1590.08112.8270.0030.0030.0000.0000.0000.000
127A68ASP-1-0.915-0.83916.889-0.062-0.0620.0000.0000.0000.000
128A69ALA00.133-0.08614.245-0.011-0.0110.0000.0000.0000.000
129A69ALA0-0.1150.09714.7900.0000.0000.0000.0000.0000.000
130A70VAL00.073-0.10410.411-0.085-0.0850.0000.0000.0000.000
131A70VAL0-0.1220.0858.433-0.005-0.0050.0000.0000.0000.000
132A71GLU00.092-0.1189.390-0.166-0.1660.0000.0000.0000.000
133A71GLU-1-1.001-0.85311.1030.1310.1310.0000.0000.0000.000
134A72LYS00.114-0.07510.590-0.018-0.0180.0000.0000.0000.000
135A72LYS10.7360.99514.2610.0800.0800.0000.0000.0000.000
136A73ILE00.079-0.09611.0480.0130.0130.0000.0000.0000.000
137A73ILE0-0.1110.0929.350-0.012-0.0120.0000.0000.0000.000
138A74GLN00.048-0.1087.154-0.204-0.2040.0000.0000.0000.000
139A74GLN0-0.1220.0654.252-0.331-0.255-0.001-0.025-0.0490.000
140A75ALA00.122-0.1007.945-0.134-0.1340.0000.0000.0000.000
141A75ALA0-0.0830.11311.7300.0240.0240.0000.0000.0000.000
142A76LEU00.121-0.08410.7850.0110.0110.0000.0000.0000.000
143A76LEU0-0.1230.09612.4840.0090.0090.0000.0000.0000.000
144A77LEU00.027-0.1288.2640.1180.1180.0000.0000.0000.000
145A77LEU0-0.0980.1035.707-0.143-0.1430.0000.0000.0000.000
146A78PRO00.021-0.1089.605-0.057-0.0570.0000.0000.0000.000
147A79ALA00.1380.01711.8570.0070.0070.0000.0000.0000.000
148A79ALA0-0.0260.12415.1930.0150.0150.0000.0000.0000.000
149A80ILE00.039-0.09412.8600.0960.0960.0000.0000.0000.000
150A80ILE0-0.1010.07511.260-0.011-0.0110.0000.0000.0000.000
151A81GLU00.051-0.11611.3100.0820.0820.0000.0000.0000.000
152A81GLU-1-0.920-0.8128.508-1.944-1.9440.0000.0000.0000.000
153A82LYS00.070-0.08912.5840.0200.0200.0000.0000.0000.000
154A82LYS10.7460.99915.3690.3310.3310.0000.0000.0000.000
155A83SER0-0.035-0.12315.7940.0490.0490.0000.0000.0000.000
156A83SER0-0.0460.07817.1750.0060.0060.0000.0000.0000.000
157A84MET00.167-0.06315.6740.0790.0790.0000.0000.0000.000
158A84MET0-0.1290.09313.843-0.050-0.0500.0000.0000.0000.000
159A85PRO0-0.038-0.11216.997-0.009-0.0090.0000.0000.0000.000
160A86PRO00.1080.03116.162-0.063-0.0630.0000.0000.0000.000
161A87LEU00.1200.00815.611-0.085-0.0850.0000.0000.0000.000
162A87LEU0-0.0890.10217.8370.0080.0080.0000.0000.0000.000
163A88LEU0-0.002-0.13316.114-0.027-0.0270.0000.0000.0000.000
164A88LEU0-0.0530.11916.0770.0010.0010.0000.0000.0000.000
165A89VAL00.171-0.10012.346-0.097-0.0970.0000.0000.0000.000
166A89VAL0-0.0850.12710.961-0.010-0.0100.0000.0000.0000.000
167A90ALA00.102-0.11511.208-0.266-0.2660.0000.0000.0000.000
168A90ALA0-0.1120.10314.3270.0280.0280.0000.0000.0000.000
169A91ARG00.104-0.08212.135-0.084-0.0840.0000.0000.0000.000
170A91ARG10.7650.99814.9740.4610.4610.0000.0000.0000.000
171A92MET00.135-0.06210.9550.0290.0290.0000.0000.0000.000
172A92MET0-0.0840.1168.8350.0230.0230.0000.0000.0000.000
173A93ARG0-0.007-0.1017.579-0.142-0.1420.0000.0000.0000.000
174A93ARG10.7390.9906.6701.7151.7150.0000.0000.0000.000
175A94SER00.028-0.1358.252-0.111-0.1110.0000.0000.0000.000
176A94SER0-0.0310.06712.1180.0830.0830.0000.0000.0000.000
177A95HIS00.037-0.1109.3260.1730.1730.0000.0000.0000.000
178A95HIS0-0.1280.0738.3900.1650.1650.0000.0000.0000.000
179A96SER00.003-0.0504.9970.3080.341-0.002-0.002-0.0290.000
180A96SER0-0.0870.0433.951-0.0670.1580.000-0.148-0.0770.001
181A97SER00.045-0.1036.4450.3090.3090.0000.0000.0000.000
182A97SER0-0.0390.0707.3590.0080.0080.0000.0000.0000.000
183A98ALA00.135-0.0748.685-0.072-0.0720.0000.0000.0000.000
184A98ALA0-0.0550.12812.6940.0230.0230.0000.0000.0000.000
185A99TYR00.124-0.06212.0100.0210.0210.0000.0000.0000.000
186A99TYR0-0.0770.08711.6470.0210.0210.0000.0000.0000.000
187A100PHE00.101-0.11011.2220.0950.0950.0000.0000.0000.000
188A100PHE0-0.1160.0989.165-0.086-0.0860.0000.0000.0000.000
189A101ARG00.219-0.06512.486-0.008-0.0080.0000.0000.0000.000
190A101ARG10.6970.98912.7620.3110.3110.0000.0000.0000.000
191A102GLU00.043-0.14214.2450.0280.0280.0000.0000.0000.000
192A102GLU-1-0.931-0.80216.413-0.237-0.2370.0000.0000.0000.000
193A103LEU00.022-0.09715.9220.0660.0660.0000.0000.0000.000
194A103LEU0-0.0890.09615.114-0.010-0.0100.0000.0000.0000.000
195A104VAL00.111-0.09616.2990.0490.0490.0000.0000.0000.000
196A104VAL0-0.0820.10815.181-0.005-0.0050.0000.0000.0000.000
197A105GLU00.086-0.12417.8420.0260.0260.0000.0000.0000.000
198A105GLU-1-0.917-0.79317.944-0.294-0.2940.0000.0000.0000.000
199A106THR00.033-0.10620.2580.0330.0330.0000.0000.0000.000
200A106THR0-0.0740.06420.7800.0140.0140.0000.0000.0000.000
201A107ARG00.092-0.05021.0380.0330.0330.0000.0000.0000.000
202A107ARG10.7450.99420.4660.2970.2970.0000.0000.0000.000
203A108GLU00.054-0.11022.1880.0170.0170.0000.0000.0000.000
204A108GLU-1-0.827-0.77620.971-0.344-0.3440.0000.0000.0000.000
205A109ARG00.025-0.09423.9850.0150.0150.0000.0000.0000.000
206A109ARG10.8821.04523.9710.1900.1900.0000.0000.0000.000
207A110LEU00.138-0.02625.8590.0170.0170.0000.0000.0000.000
208A110LEU0-0.1190.07225.821-0.003-0.0030.0000.0000.0000.000
209A111VAL00.136-0.09326.7320.0160.0160.0000.0000.0000.000
210A111VAL0-0.1230.08326.139-0.005-0.0050.0000.0000.0000.000
211A112ARG00.136-0.05428.2600.0080.0080.0000.0000.0000.000
212A112ARG10.8381.02825.3520.1850.1850.0000.0000.0000.000
213A113ASP00.121-0.07530.1260.0100.0100.0000.0000.0000.000
214A113ASP-1-1.038-0.87330.485-0.150-0.1500.0000.0000.0000.000
215A114ALA00.066-0.08831.3550.0130.0130.0000.0000.0000.000
216A114ALA0-0.0870.08831.460-0.002-0.0020.0000.0000.0000.000
217A115ASP00.058-0.12432.3370.0100.0100.0000.0000.0000.000
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