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: 4LYMN

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 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 237
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1015094.784313
FMO2-HF: Nuclear repulsion 965130.876691
FMO2-HF: Total energy -49963.907623
FMO2-MP2: Total energy -50108.702333


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.
2.8744.565-0.024-0.674-0.9920
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 : 0.150 / q_NPA : 0.055
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].
4A3ILE0-0.0430.1283.515-0.360-0.224-0.0030.090-0.2230.000
5A4LYS00.064-0.0933.8290.5792.005-0.017-0.734-0.6760.000
6A4LYS10.8771.0785.4210.2820.2820.0000.0000.0000.000
7A5HIS00.155-0.0695.776-0.080-0.0800.0000.0000.0000.000
8A5HIS0-0.0550.1208.5750.0910.0910.0000.0000.0000.000
9A6GLU00.068-0.1298.632-0.046-0.0460.0000.0000.0000.000
10A6GLU-1-0.925-0.8189.549-0.050-0.0500.0000.0000.0000.000
11A7HIS00.114-0.1199.3100.0680.0680.0000.0000.0000.000
12A7HIS0-0.0920.0938.466-0.198-0.1980.0000.0000.0000.000
13A8ILE00.058-0.1209.691-0.109-0.1090.0000.0000.0000.000
14A8ILE0-0.0520.1157.223-0.004-0.0040.0000.0000.0000.000
15A9ARG00.084-0.07510.8640.0070.0070.0000.0000.0000.000
16A9ARG10.7761.02513.658-0.048-0.0480.0000.0000.0000.000
17A10MET00.024-0.10313.6610.0270.0270.0000.0000.0000.000
18A10MET0-0.0910.09013.711-0.015-0.0150.0000.0000.0000.000
19A11ALA00.097-0.10713.7610.0310.0310.0000.0000.0000.000
20A11ALA0-0.0510.12213.332-0.016-0.0160.0000.0000.0000.000
21A12MET00.064-0.11314.765-0.002-0.0020.0000.0000.0000.000
22A12MET0-0.1230.09914.2670.0000.0000.0000.0000.0000.000
23A13ASN00.133-0.05716.5190.0150.0150.0000.0000.0000.000
24A13ASN0-0.1080.06218.4210.0140.0140.0000.0000.0000.000
25A14ALA00.110-0.08818.3680.0200.0200.0000.0000.0000.000
26A14ALA0-0.1070.08918.318-0.007-0.0070.0000.0000.0000.000
27A15TRP00.047-0.12318.8770.0040.0040.0000.0000.0000.000
28A15TRP0-0.0800.11016.759-0.008-0.0080.0000.0000.0000.000
29A16ALA00.104-0.10920.3040.0030.0030.0000.0000.0000.000
30A16ALA0-0.0830.12021.4710.0030.0030.0000.0000.0000.000
31A17HIS00.042-0.08122.6910.0110.0110.0000.0000.0000.000
32A17HIS0-0.1200.05324.0250.0010.0010.0000.0000.0000.000
33A18PRO0-0.098-0.13823.9970.0050.0050.0000.0000.0000.000
34A19ASP00.0730.02226.5690.0040.0040.0000.0000.0000.000
35A19ASP-1-0.985-0.85427.674-0.053-0.0530.0000.0000.0000.000
36A20GLY00.021-0.11226.8640.0080.0080.0000.0000.0000.000
37A21GLU00.115-0.07723.562-0.010-0.0100.0000.0000.0000.000
38A21GLU-1-0.965-0.80422.8180.0160.0160.0000.0000.0000.000
39A22LYS00.047-0.10823.8170.0060.0060.0000.0000.0000.000
40A22LYS10.8951.07027.8850.0020.0020.0000.0000.0000.000
41A23VAL00.034-0.09324.8800.0090.0090.0000.0000.0000.000
42A23VAL0-0.0270.12523.973-0.001-0.0010.0000.0000.0000.000
43A24PRO00.038-0.06919.4320.0010.0010.0000.0000.0000.000
44A25ALA00.1300.01620.6390.0010.0010.0000.0000.0000.000
45A25ALA0-0.0350.13522.6430.0020.0020.0000.0000.0000.000
46A26ALA00.096-0.05722.1510.0140.0140.0000.0000.0000.000
47A26ALA0-0.0620.11425.391-0.001-0.0010.0000.0000.0000.000
48A27GLU0-0.008-0.13821.5680.0100.0100.0000.0000.0000.000
49A27GLU-1-0.964-0.83320.864-0.058-0.0580.0000.0000.0000.000
50A28ILE00.104-0.09318.409-0.009-0.0090.0000.0000.0000.000
51A28ILE0-0.0950.08016.7440.0050.0050.0000.0000.0000.000
52A29THR00.034-0.09819.1130.0150.0150.0000.0000.0000.000
53A29THR0-0.100-0.01522.8030.0060.0060.0000.0000.0000.000
54A30ARG00.121-0.08221.8620.0130.0130.0000.0000.0000.000
55A30ARG10.8011.05122.9120.0350.0350.0000.0000.0000.000
56A31ALA00.104-0.08718.7140.0030.0030.0000.0000.0000.000
57A31ALA0-0.0930.10817.954-0.004-0.0040.0000.0000.0000.000
58A32TYR00.112-0.07818.4710.0000.0000.0000.0000.0000.000
59A32TYR0-0.1290.06618.060-0.003-0.0030.0000.0000.0000.000
60A33PHE00.023-0.13819.4650.0140.0140.0000.0000.0000.000
61A33PHE0-0.0850.10524.1840.0010.0010.0000.0000.0000.000
62A34GLU00.076-0.08722.0220.0050.0050.0000.0000.0000.000
63A34GLU-1-0.995-0.85421.247-0.039-0.0390.0000.0000.0000.000
64A35LEU00.000-0.13518.230-0.009-0.0090.0000.0000.0000.000
65A35LEU0-0.1010.09215.683-0.004-0.0040.0000.0000.0000.000
66A36GLY0-0.008-0.09019.7040.0100.0100.0000.0000.0000.000
67A37MET00.049-0.01218.3860.0080.0080.0000.0000.0000.000
68A37MET0-0.0950.09614.566-0.013-0.0130.0000.0000.0000.000
69A38THR0-0.008-0.07719.406-0.014-0.0140.0000.0000.0000.000
70A38THR0-0.0330.06020.8820.0090.0090.0000.0000.0000.000
71A39PHE00.126-0.07217.762-0.016-0.0160.0000.0000.0000.000
72A39PHE0-0.0890.10014.397-0.010-0.0100.0000.0000.0000.000
73A40PRO0-0.039-0.12815.4790.0250.0250.0000.0000.0000.000
74A41GLU00.1190.01918.324-0.011-0.0110.0000.0000.0000.000
75A41GLU-1-1.031-0.86322.8150.1230.1230.0000.0000.0000.000
76A42LEU00.078-0.13721.9990.0050.0050.0000.0000.0000.000
77A42LEU0-0.0860.12419.870-0.002-0.0020.0000.0000.0000.000
78A43TYR00.072-0.08923.164-0.001-0.0010.0000.0000.0000.000
79A43TYR0-0.1170.05927.4170.0010.0010.0000.0000.0000.000
80A44ASP00.124-0.06226.919-0.004-0.0040.0000.0000.0000.000
81A44ASP-1-0.855-0.80327.8530.0500.0500.0000.0000.0000.000
82A45ASP00.115-0.09928.2830.0030.0030.0000.0000.0000.000
83A45ASP-1-0.965-0.84429.2670.0200.0200.0000.0000.0000.000
84A46SER0-0.098-0.10331.104-0.004-0.0040.0000.0000.0000.000
85A46SER0-0.0340.07232.3400.0000.0000.0000.0000.0000.000
86A47HIS00.072-0.13231.7320.0020.0020.0000.0000.0000.000
87A47HIS0-0.1990.05230.5070.0030.0030.0000.0000.0000.000
88A48PRO00.008-0.09733.139-0.002-0.0020.0000.0000.0000.000
89A49GLU00.1790.02833.043-0.003-0.0030.0000.0000.0000.000
90A49GLU-1-1.047-0.87531.8830.0280.0280.0000.0000.0000.000
91A50ALA00.079-0.13629.4190.0030.0030.0000.0000.0000.000
92A50ALA0-0.0530.13828.952-0.001-0.0010.0000.0000.0000.000
93A51LEU00.139-0.08927.3400.0080.0080.0000.0000.0000.000
94A51LEU0-0.0800.12926.420-0.001-0.0010.0000.0000.0000.000
95A52ALA00.108-0.11527.1450.0020.0020.0000.0000.0000.000
96A52ALA0-0.0640.12530.7580.0000.0000.0000.0000.0000.000
97A53ARG00.056-0.10827.7940.0010.0010.0000.0000.0000.000
98A53ARG10.8311.05527.828-0.056-0.0560.0000.0000.0000.000
99A54ASN00.077-0.12024.0290.0120.0120.0000.0000.0000.000
100A54ASN0-0.0670.10523.4790.0100.0100.0000.0000.0000.000
101A55THR00.042-0.08122.7030.0140.0140.0000.0000.0000.000
102A55THR0-0.0320.08124.262-0.005-0.0050.0000.0000.0000.000
103A56GLN00.167-0.06723.0220.0010.0010.0000.0000.0000.000
104A56GLN0-0.1370.07925.2360.0020.0020.0000.0000.0000.000
105A57LYS0-0.028-0.13122.3160.0040.0040.0000.0000.0000.000
106A57LYS10.7911.03621.461-0.139-0.1390.0000.0000.0000.000
107A58ILE00.080-0.09118.5970.0250.0250.0000.0000.0000.000
108A58ILE0-0.0490.12217.5450.0000.0000.0000.0000.0000.000
109A59PHE00.075-0.12817.9960.0250.0250.0000.0000.0000.000
110A59PHE0-0.0060.15719.521-0.001-0.0010.0000.0000.0000.000
111A60ARG00.204-0.05419.710-0.007-0.0070.0000.0000.0000.000
112A60ARG10.8351.06020.985-0.106-0.1060.0000.0000.0000.000
113A61TRP0-0.001-0.15416.306-0.004-0.0040.0000.0000.0000.000
114A61TRP0-0.0830.09815.3180.0090.0090.0000.0000.0000.000
115A62VAL00.070-0.09214.7910.0400.0400.0000.0000.0000.000
116A62VAL0-0.0730.11715.084-0.005-0.0050.0000.0000.0000.000
117A63GLU00.087-0.12815.546-0.011-0.0110.0000.0000.0000.000
118A63GLU-1-1.004-0.83219.6600.0540.0540.0000.0000.0000.000
119A64LYS0-0.023-0.10917.060-0.019-0.0190.0000.0000.0000.000
120A64LYS10.8631.06017.122-0.093-0.0930.0000.0000.0000.000
121A65ASP00.125-0.09513.5940.0180.0180.0000.0000.0000.000
122A65ASP-1-0.934-0.81813.0660.1170.1170.0000.0000.0000.000
123A66THR00.012-0.07913.9350.0190.0190.0000.0000.0000.000
124A66THR0-0.0380.03916.8860.0040.0040.0000.0000.0000.000
125A67PRO00.059-0.08112.6680.0260.0260.0000.0000.0000.000
126A68ASP00.1630.06813.0130.0910.0910.0000.0000.0000.000
127A68ASP-1-0.936-0.84717.1450.2620.2620.0000.0000.0000.000
128A69ALA00.124-0.10414.7010.0380.0380.0000.0000.0000.000
129A69ALA0-0.1120.11214.845-0.013-0.0130.0000.0000.0000.000
130A70VAL00.070-0.11210.423-0.018-0.0180.0000.0000.0000.000
131A70VAL0-0.1020.0948.4990.0160.0160.0000.0000.0000.000
132A71GLU00.089-0.1309.9130.2210.2210.0000.0000.0000.000
133A71GLU-1-1.005-0.83411.7000.5170.5170.0000.0000.0000.000
134A72LYS00.091-0.08811.1690.0800.0800.0000.0000.0000.000
135A72LYS10.7591.02014.936-0.296-0.2960.0000.0000.0000.000
136A73ILE00.100-0.08611.701-0.035-0.0350.0000.0000.0000.000
137A73ILE0-0.0950.08910.383-0.013-0.0130.0000.0000.0000.000
138A74GLN00.015-0.1238.263-0.173-0.1730.0000.0000.0000.000
139A74GLN0-0.0910.0755.4061.1991.242-0.001-0.001-0.0400.000
140A75ALA00.121-0.0968.9440.0140.0140.0000.0000.0000.000
141A75ALA0-0.0790.11712.742-0.018-0.0180.0000.0000.0000.000
142A76LEU00.099-0.09811.786-0.075-0.0750.0000.0000.0000.000
143A76LEU0-0.1150.10113.593-0.010-0.0100.0000.0000.0000.000
144A77LEU00.048-0.1398.769-0.163-0.1630.0000.0000.0000.000
145A77LEU0-0.0990.1176.154-0.010-0.0100.0000.0000.0000.000
146A78PRO00.017-0.09410.133-0.176-0.1760.0000.0000.0000.000
147A79ALA00.1500.00811.817-0.079-0.0790.0000.0000.0000.000
148A79ALA0-0.0330.13115.6480.0060.0060.0000.0000.0000.000
149A80ILE00.047-0.10012.948-0.029-0.0290.0000.0000.0000.000
150A80ILE0-0.1170.07211.943-0.004-0.0040.0000.0000.0000.000
151A81GLU00.033-0.13611.309-0.015-0.0150.0000.0000.0000.000
152A81GLU-1-1.024-0.8697.947-0.796-0.7960.0000.0000.0000.000
153A82LYS00.052-0.10512.525-0.042-0.0420.0000.0000.0000.000
154A82LYS10.7951.04215.4450.0720.0720.0000.0000.0000.000
155A83SER0-0.031-0.11815.740-0.006-0.0060.0000.0000.0000.000
156A83SER0-0.0550.08317.1290.0060.0060.0000.0000.0000.000
157A84MET00.172-0.05615.5690.0200.0200.0000.0000.0000.000
158A84MET0-0.1370.08813.796-0.029-0.0290.0000.0000.0000.000
159A85PRO0-0.040-0.11416.910-0.025-0.0250.0000.0000.0000.000
160A86PRO00.1210.03616.103-0.035-0.0350.0000.0000.0000.000
161A87LEU00.120-0.00615.545-0.061-0.0610.0000.0000.0000.000
162A87LEU0-0.0880.10817.6630.0060.0060.0000.0000.0000.000
163A88LEU0-0.033-0.15016.043-0.039-0.0390.0000.0000.0000.000
164A88LEU0-0.0450.12016.0030.0000.0000.0000.0000.0000.000
165A89VAL00.175-0.08712.270-0.044-0.0440.0000.0000.0000.000
166A89VAL0-0.0660.12810.823-0.014-0.0140.0000.0000.0000.000
167A90ALA00.098-0.11511.140-0.191-0.1910.0000.0000.0000.000
168A90ALA0-0.0960.10614.2270.0150.0150.0000.0000.0000.000
169A91ARG00.105-0.08512.073-0.100-0.1000.0000.0000.0000.000
170A91ARG10.7881.01814.8230.2590.2590.0000.0000.0000.000
171A92MET00.144-0.04310.875-0.042-0.0420.0000.0000.0000.000
172A92MET0-0.0830.1178.8130.0550.0550.0000.0000.0000.000
173A93ARG0-0.019-0.1187.511-0.083-0.0830.0000.0000.0000.000
174A93ARG10.8331.0466.1871.4321.4320.0000.0000.0000.000
175A94SER00.038-0.1198.188-0.225-0.2250.0000.0000.0000.000
176A94SER0-0.0360.06712.0730.0600.0600.0000.0000.0000.000
177A95HIS00.033-0.1219.3060.0690.0690.0000.0000.0000.000
178A95HIS0-0.1090.0898.4400.1080.1080.0000.0000.0000.000
179A96SER00.007-0.0734.9750.2780.315-0.002-0.003-0.0310.000
180A96SER0-0.0580.0604.2490.1320.181-0.001-0.026-0.0220.000
181A97SER00.018-0.0756.4090.0960.0960.0000.0000.0000.000
182A97SER0-0.0410.0627.3920.0630.0630.0000.0000.0000.000
183A98ALA00.146-0.0858.6430.0150.0150.0000.0000.0000.000
184A98ALA0-0.0500.13012.7930.0160.0160.0000.0000.0000.000
185A99TYR00.136-0.06411.9540.0570.0570.0000.0000.0000.000
186A99TYR0-0.0840.09511.5650.0050.0050.0000.0000.0000.000
187A100PHE00.091-0.11411.1840.0970.0970.0000.0000.0000.000
188A100PHE0-0.1270.0988.607-0.055-0.0550.0000.0000.0000.000
189A101ARG00.223-0.06812.4410.0380.0380.0000.0000.0000.000
190A101ARG10.8101.05912.7750.3470.3470.0000.0000.0000.000
191A102GLU0-0.024-0.16214.2040.0440.0440.0000.0000.0000.000
192A102GLU-1-0.990-0.83916.298-0.295-0.2950.0000.0000.0000.000
193A103LEU00.061-0.09615.8820.0560.0560.0000.0000.0000.000
194A103LEU0-0.0800.12314.961-0.004-0.0040.0000.0000.0000.000
195A104VAL00.086-0.11716.2480.0450.0450.0000.0000.0000.000
196A104VAL0-0.0550.11414.969-0.001-0.0010.0000.0000.0000.000
197A105GLU00.086-0.09717.7870.0330.0330.0000.0000.0000.000
198A105GLU-1-0.966-0.82617.748-0.287-0.2870.0000.0000.0000.000
199A106THR00.000-0.12320.2120.0290.0290.0000.0000.0000.000
200A106THR0-0.0480.05020.4920.0070.0070.0000.0000.0000.000
201A107ARG00.087-0.06520.9860.0250.0250.0000.0000.0000.000
202A107ARG10.8421.06720.5580.1770.1770.0000.0000.0000.000
203A108GLU00.069-0.11422.1250.0170.0170.0000.0000.0000.000
204A108GLU-1-0.926-0.83621.267-0.204-0.2040.0000.0000.0000.000
205A109ARG00.025-0.08723.9270.0150.0150.0000.0000.0000.000
206A109ARG10.8831.05224.0600.1610.1610.0000.0000.0000.000
207A110LEU00.117-0.06425.8010.0130.0130.0000.0000.0000.000
208A110LEU0-0.1280.08625.711-0.002-0.0020.0000.0000.0000.000
209A111VAL00.124-0.08626.6730.0110.0110.0000.0000.0000.000
210A111VAL0-0.1050.07625.665-0.002-0.0020.0000.0000.0000.000
211A112ARG00.119-0.04628.1940.0090.0090.0000.0000.0000.000
212A112ARG10.8301.02125.6640.1320.1320.0000.0000.0000.000
213A113ASP00.159-0.07430.0680.0080.0080.0000.0000.0000.000
214A113ASP-1-1.033-0.86130.877-0.111-0.1110.0000.0000.0000.000
215A114ALA00.068-0.11431.2990.0080.0080.0000.0000.0000.000
216A114ALA0-0.0970.11331.449-0.001-0.0010.0000.0000.0000.000
217A115ASP00.068-0.12332.2750.0070.0070.0000.0000.0000.000
218A115ASP-1-0.994-0.85531.129-0.099-0.0990.0000.0000.0000.000
219A116ASP00.063-0.13933.9660.0070.0070.0000.0000.0000.000
220A116ASP-1-1.041-0.84934.537-0.085-0.0850.0000.0000.0000.000
221A117PHE00.154-0.07435.8460.0060.0060.0000.0000.0000.000
222A117PHE0-0.1480.07136.4910.0000.0000.0000.0000.0000.000
223A118VAL00.058-0.12537.0080.0050.0050.0000.0000.0000.000
224A118VAL0-0.0960.10236.4050.0000.0000.0000.0000.0000.000
225A119ALA00.105-0.07138.2630.0050.0050.0000.0000.0000.000
226A119ALA0-0.0670.09338.6110.0000.0000.0000.0000.0000.000
227A120VAL00.021-0.13140.0790.0040.0040.0000.0000.0000.000
228A120VAL0-0.0930.11140.1660.0000.0000.0000.0000.0000.000
229A121ALA00.115-0.10241.5770.0040.0040.0000.0000.0000.000
230A121ALA0-0.0890.09942.0050.0000.0000.0000.0000.0000.000
231A122ILE00.017-0.11242.7910.0030.0030.0000.0000.0000.000
232A122ILE0-0.1100.07441.5440.0000.0000.0000.0000.0000.000
233A123ALA00.046-0.12244.3400.0030.0030.0000.0000.0000.000
234A123ALA0-0.0930.09944.9780.0000.0000.0000.0000.0000.000
235A124GLY0-0.086-0.11146.1350.0020.0020.0000.0000.0000.000
236A125PHE0-0.0290.00747.6190.0030.0030.0000.0000.0000.000
237A125PHE0-0.024-0.02047.9320.0000.0000.0000.0000.0000.000