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: 4LVJN

Calculation Name: 3K1H-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K1H

Chain ID: A

ChEMBL ID:

UniProt ID: O25709

Base Structure: X-ray

Registration Date: 2025-07-09

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 224
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -919763.440369
FMO2-HF: Nuclear repulsion 873735.423093
FMO2-HF: Total energy -46028.017276
FMO2-MP2: Total energy -46160.303291


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:33:PHE)


Summations of interaction energy for fragment #1(A:33:PHE)
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.
-8.615-3.6581.814-3.031-3.741-0.019
Interaction energy analysis for fragmet #1(A:33:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.134 / q_NPA : 0.043
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].
4A34SER0-0.0350.0904.3370.1620.4970.001-0.166-0.1710.000
5A35ARG0-0.009-0.1143.806-1.7070.648-0.020-1.351-0.9840.006
6A35ARG10.7340.9964.5922.5612.599-0.001-0.004-0.0330.000
7A36ASP00.118-0.0766.712-0.006-0.0060.0000.0000.0000.000
8A36ASP-1-0.945-0.8159.607-0.958-0.9580.0000.0000.0000.000
9A37MET00.027-0.13910.4260.0470.0470.0000.0000.0000.000
10A37MET0-0.1230.1119.4790.0370.0370.0000.0000.0000.000
11A38LYS00.159-0.03812.7680.0860.0860.0000.0000.0000.000
12A38LYS10.7270.97015.1090.5200.5200.0000.0000.0000.000
13A39ASN00.093-0.03815.6390.0650.0650.0000.0000.0000.000
14A39ASN0-0.0900.02318.660-0.022-0.0220.0000.0000.0000.000
15A40ILE00.168-0.08217.389-0.085-0.0850.0000.0000.0000.000
16A40ILE0-0.0310.15420.8290.0000.0000.0000.0000.0000.000
17A41ASN00.083-0.07019.250-0.025-0.0250.0000.0000.0000.000
18A41ASN0-0.1200.04419.8910.0120.0120.0000.0000.0000.000
19A42GLU00.084-0.11715.1280.0160.0160.0000.0000.0000.000
20A42GLU-1-0.896-0.77614.057-0.710-0.7100.0000.0000.0000.000
21A43SER00.017-0.08514.637-0.116-0.1160.0000.0000.0000.000
22A43SER0-0.0080.07316.165-0.003-0.0030.0000.0000.0000.000
23A44VAL00.102-0.08615.684-0.072-0.0720.0000.0000.0000.000
24A44VAL0-0.0820.11919.8680.0070.0070.0000.0000.0000.000
25A45GLY0-0.039-0.12817.0330.0090.0090.0000.0000.0000.000
26A46ALA00.110-0.00312.5950.0700.0700.0000.0000.0000.000
27A46ALA0-0.0360.11111.700-0.044-0.0440.0000.0000.0000.000
28A47LEU00.031-0.12313.647-0.073-0.0730.0000.0000.0000.000
29A47LEU0-0.0480.12813.7570.0050.0050.0000.0000.0000.000
30A48GLN00.120-0.07015.4920.0270.0270.0000.0000.0000.000
31A48GLN0-0.0760.09918.6400.0080.0080.0000.0000.0000.000
32A49VAL00.054-0.13015.3850.0780.0780.0000.0000.0000.000
33A49VAL0-0.0790.11214.2890.0040.0040.0000.0000.0000.000
34A50LEU00.144-0.10513.2960.0790.0790.0000.0000.0000.000
35A50LEU0-0.0690.12510.833-0.015-0.0150.0000.0000.0000.000
36A51GLN00.125-0.07414.3680.0420.0420.0000.0000.0000.000
37A51GLN0-0.1100.07718.2020.0360.0360.0000.0000.0000.000
38A52ILE00.033-0.08817.5810.0520.0520.0000.0000.0000.000
39A52ILE0-0.1050.07618.9150.0140.0140.0000.0000.0000.000
40A53ALA00.072-0.11115.6590.0900.0900.0000.0000.0000.000
41A53ALA0-0.0010.12814.980-0.016-0.0160.0000.0000.0000.000
42A54CYS00.103-0.12716.4070.0640.0640.0000.0000.0000.000
43A54CYS0-0.1220.09814.552-0.016-0.0160.0000.0000.0000.000
44A55LYS00.145-0.05316.9700.0460.0460.0000.0000.0000.000
45A55LYS10.8151.03020.6690.3480.3480.0000.0000.0000.000
46A56LYS00.013-0.09320.1700.0420.0420.0000.0000.0000.000
47A56LYS10.8701.04619.7950.3250.3250.0000.0000.0000.000
48A57LEU00.067-0.10018.0880.0470.0470.0000.0000.0000.000
49A57LEU0-0.0810.10814.9920.0000.0000.0000.0000.0000.000
50A58PHE00.158-0.07319.5580.0380.0380.0000.0000.0000.000
51A58PHE0-0.1100.10620.621-0.006-0.0060.0000.0000.0000.000
52A59ASN00.091-0.05821.6480.0270.0270.0000.0000.0000.000
53A59ASN0-0.1240.04524.4690.0030.0030.0000.0000.0000.000
54A60LYS00.047-0.11523.4670.0200.0200.0000.0000.0000.000
55A60LYS10.7530.98422.6060.1550.1550.0000.0000.0000.000
56A61SER0-0.011-0.10623.1540.0230.0230.0000.0000.0000.000
57A61SER0-0.0200.07622.2300.0010.0010.0000.0000.0000.000
58A62MET00.111-0.08924.3600.0150.0150.0000.0000.0000.000
59A62MET0-0.1360.10626.9940.0010.0010.0000.0000.0000.000
60A63GLY00.042-0.08727.5260.0050.0050.0000.0000.0000.000
61A64LEU00.0720.00526.5810.0100.0100.0000.0000.0000.000
62A64LEU0-0.1200.07924.150-0.001-0.0010.0000.0000.0000.000
63A65GLU00.037-0.13828.1120.0090.0090.0000.0000.0000.000
64A65GLU-1-0.905-0.82028.707-0.082-0.0820.0000.0000.0000.000
65A66ASP00.046-0.12729.6660.0100.0100.0000.0000.0000.000
66A66ASP-1-1.010-0.85633.278-0.054-0.0540.0000.0000.0000.000
67A67LYS00.059-0.06831.2170.0050.0050.0000.0000.0000.000
68A67LYS10.7401.00428.4840.0900.0900.0000.0000.0000.000
69A68ASP00.052-0.08832.1540.0050.0050.0000.0000.0000.000
70A68ASP-1-0.883-0.84334.408-0.029-0.0290.0000.0000.0000.000
71A69ALA00.173-0.08331.453-0.006-0.0060.0000.0000.0000.000
72A69ALA0-0.0950.09932.4430.0020.0020.0000.0000.0000.000
73A70LEU00.078-0.09530.6800.0040.0040.0000.0000.0000.000
74A70LEU0-0.1130.09831.9200.0010.0010.0000.0000.0000.000
75A71GLN00.082-0.10930.4150.0000.0000.0000.0000.0000.000
76A71GLN0-0.0650.10931.261-0.007-0.0070.0000.0000.0000.000
77A72ALA00.126-0.08427.920-0.012-0.0120.0000.0000.0000.000
78A72ALA0-0.0540.11127.8120.0020.0020.0000.0000.0000.000
79A73SER0-0.036-0.10826.134-0.008-0.0080.0000.0000.0000.000
80A73SER0-0.0680.04727.6200.0040.0040.0000.0000.0000.000
81A74ILE00.068-0.08625.5860.0030.0030.0000.0000.0000.000
82A74ILE0-0.0950.08427.8700.0000.0000.0000.0000.0000.000
83A75ILE00.112-0.07625.247-0.007-0.0070.0000.0000.0000.000
84A75ILE0-0.0680.10324.091-0.001-0.0010.0000.0000.0000.000
85A76LYS00.104-0.09321.929-0.026-0.0260.0000.0000.0000.000
86A76LYS10.8541.05922.1340.0300.0300.0000.0000.0000.000
87A77GLN00.066-0.09720.644-0.007-0.0070.0000.0000.0000.000
88A77GLN0-0.1010.06920.8570.0190.0190.0000.0000.0000.000
89A78GLU00.051-0.12020.823-0.005-0.0050.0000.0000.0000.000
90A78GLU-1-0.865-0.79622.916-0.131-0.1310.0000.0000.0000.000
91A79LEU00.047-0.08019.279-0.036-0.0360.0000.0000.0000.000
92A79LEU0-0.0920.09118.672-0.001-0.0010.0000.0000.0000.000
93A80ARG00.099-0.12516.321-0.060-0.0600.0000.0000.0000.000
94A80ARG10.7160.96716.707-0.026-0.0260.0000.0000.0000.000
95A81GLU00.124-0.07815.820-0.029-0.0290.0000.0000.0000.000
96A81GLU-1-0.963-0.79419.589-0.089-0.0890.0000.0000.0000.000
97A82ILE00.069-0.07416.892-0.036-0.0360.0000.0000.0000.000
98A82ILE0-0.1210.06716.356-0.004-0.0040.0000.0000.0000.000
99A83VAL00.066-0.11613.209-0.100-0.1000.0000.0000.0000.000
100A83VAL0-0.0800.09911.154-0.002-0.0020.0000.0000.0000.000
101A84GLU00.048-0.10612.146-0.163-0.1630.0000.0000.0000.000
102A84GLU-1-0.891-0.79013.5500.0290.0290.0000.0000.0000.000
103A85ASN00.024-0.08612.947-0.041-0.0410.0000.0000.0000.000
104A85ASN0-0.1730.02716.4320.0150.0150.0000.0000.0000.000
105A86CYS00.157-0.09712.7580.0190.0190.0000.0000.0000.000
106A86CYS0-0.1680.10011.919-0.042-0.0420.0000.0000.0000.000
107A87GLN00.033-0.10210.518-0.185-0.1850.0000.0000.0000.000
108A87GLN0-0.0830.08811.2700.0130.0130.0000.0000.0000.000
109A88PHE00.078-0.11710.5980.1760.1760.0000.0000.0000.000
110A88PHE0-0.0540.12211.2470.0130.0130.0000.0000.0000.000
111A89LEU00.007-0.10110.779-0.192-0.1920.0000.0000.0000.000
112A89LEU0-0.0530.10311.9730.0070.0070.0000.0000.0000.000
113A90ALA00.138-0.07211.809-0.066-0.0660.0000.0000.0000.000
114A90ALA0-0.0960.09612.8770.0350.0350.0000.0000.0000.000
115A91SER00.064-0.1037.9710.1860.1860.0000.0000.0000.000
116A91SER0-0.0350.0826.275-0.283-0.2830.0000.0000.0000.000
117A92PRO00.033-0.0804.3020.2440.3140.000-0.016-0.0540.000
118A93LEU00.0620.0136.353-0.793-0.7930.0000.0000.0000.000
119A93LEU0-0.0810.0878.8100.0780.0780.0000.0000.0000.000
120A94PHE00.109-0.0717.436-0.322-0.3220.0000.0000.0000.000
121A94PHE0-0.0470.0918.3880.1000.1000.0000.0000.0000.000
122A95ASP00.016-0.1094.679-0.800-0.745-0.002-0.025-0.0290.000
123A95ASP-1-0.883-0.8064.122-0.172-0.083-0.001-0.016-0.0710.000
124A96THR00.067-0.0862.301-5.980-4.0571.827-1.871-1.879-0.025
125A96THR0-0.1170.0433.255-1.188-1.4630.0090.546-0.2800.000
126A97GLN00.154-0.0773.7551.2721.6390.001-0.128-0.2400.000
127A97GLN0-0.1390.0665.7110.1690.1690.0000.0000.0000.000
128A98LEU0-0.009-0.1186.140-0.505-0.5050.0000.0000.0000.000
129A98LEU0-0.0860.0867.1960.0710.0710.0000.0000.0000.000
130A99ASN00.118-0.0798.7790.2680.2680.0000.0000.0000.000
131A99ASN0-0.1040.0918.617-0.010-0.0100.0000.0000.0000.000
132A100ILE00.100-0.09611.054-0.030-0.0300.0000.0000.0000.000
133A100ILE0-0.0660.08912.8040.0020.0020.0000.0000.0000.000
134A101ALA00.164-0.07314.5300.0310.0310.0000.0000.0000.000
135A101ALA0-0.1100.10017.4910.0080.0080.0000.0000.0000.000
136A102ILE00.017-0.12917.762-0.011-0.0110.0000.0000.0000.000
137A102ILE0-0.0830.09218.740-0.003-0.0030.0000.0000.0000.000
138A103ASN0-0.010-0.04120.8820.0060.0060.0000.0000.0000.000
139A103ASN0-0.0760.03924.7620.0020.0020.0000.0000.0000.000
140A104ASP00.156-0.07522.5480.0050.0050.0000.0000.0000.000
141A104ASP-1-1.027-0.86824.350-0.235-0.2350.0000.0000.0000.000
142A105GLU00.077-0.16920.6050.0210.0210.0000.0000.0000.000
143A105GLU-1-0.996-0.81720.615-0.282-0.2820.0000.0000.0000.000
144A106ILE00.057-0.10115.923-0.021-0.0210.0000.0000.0000.000
145A106ILE0-0.0910.07813.843-0.002-0.0020.0000.0000.0000.000
146A107PHE00.052-0.09715.7920.0400.0400.0000.0000.0000.000
147A107PHE0-0.0760.09516.326-0.006-0.0060.0000.0000.0000.000
148A108SER00.030-0.10111.692-0.080-0.0800.0000.0000.0000.000
149A108SER0-0.0550.06410.6460.0630.0630.0000.0000.0000.000
150A109MET00.146-0.07710.9720.1730.1730.0000.0000.0000.000
151A109MET0-0.1300.09611.4660.0370.0370.0000.0000.0000.000
152A110ILE0-0.008-0.1117.927-0.355-0.3550.0000.0000.0000.000
153A110ILE0-0.0570.1165.0630.0410.0410.0000.0000.0000.000
154A111VAL00.102-0.1028.3800.2930.2930.0000.0000.0000.000
155A111VAL0-0.0780.10310.2470.0220.0220.0000.0000.0000.000
156A112VAL00.114-0.0957.576-0.362-0.3620.0000.0000.0000.000
157A112VAL0-0.0680.1127.6010.0170.0170.0000.0000.0000.000
158A113ASN00.092-0.1128.208-0.046-0.0460.0000.0000.0000.000
159A113ASN0-0.0610.0879.278-0.047-0.0470.0000.0000.0000.000
160A114PRO0-0.034-0.10310.1160.0980.0980.0000.0000.0000.000
161A115LEU00.041-0.00913.5690.0220.0220.0000.0000.0000.000
162A115LEU0-0.0770.09413.8370.0060.0060.0000.0000.0000.000
163A116ASP00.099-0.09514.4090.0080.0080.0000.0000.0000.000
164A116ASP-1-0.962-0.85313.0670.1950.1950.0000.0000.0000.000
165A117LEU00.042-0.13716.0760.0320.0320.0000.0000.0000.000
166A117LEU0-0.0480.12515.518-0.007-0.0070.0000.0000.0000.000
167A118LEU00.097-0.06118.116-0.011-0.0110.0000.0000.0000.000
168A118LEU0-0.1320.07518.8940.0020.0020.0000.0000.0000.000
169A119GLU0-0.029-0.16120.323-0.011-0.0110.0000.0000.0000.000
170A119GLU-1-1.012-0.85121.5510.0360.0360.0000.0000.0000.000
171A120ASN00.122-0.08422.0090.0040.0040.0000.0000.0000.000
172A120ASN0-0.1610.04922.858-0.007-0.0070.0000.0000.0000.000
173A121VAL00.089-0.10722.427-0.015-0.0150.0000.0000.0000.000
174A121VAL0-0.0770.11524.3650.0010.0010.0000.0000.0000.000
175A122GLY00.072-0.08323.278-0.020-0.0200.0000.0000.0000.000
176A123GLU00.080-0.02621.445-0.023-0.0230.0000.0000.0000.000
177A123GLU-1-0.949-0.80720.421-0.036-0.0360.0000.0000.0000.000
178A124PHE00.145-0.05918.565-0.030-0.0300.0000.0000.0000.000
179A124PHE0-0.1430.06217.089-0.008-0.0080.0000.0000.0000.000
180A125GLN00.038-0.13518.967-0.047-0.0470.0000.0000.0000.000
181A125GLN0-0.0940.09922.9750.0060.0060.0000.0000.0000.000
182A126ALA00.117-0.06921.190-0.033-0.0330.0000.0000.0000.000
183A126ALA0-0.0540.10721.7050.0050.0050.0000.0000.0000.000
184A127TYR00.110-0.07216.974-0.018-0.0180.0000.0000.0000.000
185A127TYR0-0.0750.09111.644-0.048-0.0480.0000.0000.0000.000
186A128LEU00.049-0.11916.720-0.062-0.0620.0000.0000.0000.000
187A128LEU0-0.1100.09415.560-0.009-0.0090.0000.0000.0000.000
188A129GLU00.089-0.12517.733-0.055-0.0550.0000.0000.0000.000
189A129GLU-1-1.013-0.83722.078-0.195-0.1950.0000.0000.0000.000
190A130GLU00.023-0.14518.915-0.010-0.0100.0000.0000.0000.000
191A130GLU-1-0.956-0.83318.141-0.255-0.2550.0000.0000.0000.000
192A131LYS00.081-0.08015.055-0.005-0.0050.0000.0000.0000.000
193A131LYS10.7340.99712.4340.5880.5880.0000.0000.0000.000
194A132LEU00.067-0.12616.292-0.071-0.0710.0000.0000.0000.000
195A132LEU0-0.1290.08818.0690.0040.0040.0000.0000.0000.000
196A133ASN00.092-0.06918.721-0.013-0.0130.0000.0000.0000.000
197A133ASN0-0.1450.04521.0550.0150.0150.0000.0000.0000.000
198A134GLU00.064-0.12616.9160.0390.0390.0000.0000.0000.000
199A134GLU-1-0.866-0.77914.792-0.600-0.6000.0000.0000.0000.000
200A135ILE00.125-0.06316.914-0.011-0.0110.0000.0000.0000.000
201A135ILE0-0.1010.07714.155-0.010-0.0100.0000.0000.0000.000
202A136LYS00.079-0.09417.537-0.009-0.0090.0000.0000.0000.000
203A136LYS10.7621.01921.8990.2910.2910.0000.0000.0000.000
204A137GLU00.047-0.10520.9270.0170.0170.0000.0000.0000.000
205A137GLU-1-0.915-0.81020.629-0.293-0.2930.0000.0000.0000.000
206A138LEU00.092-0.08918.0870.0430.0430.0000.0000.0000.000
207A138LEU0-0.0680.09815.472-0.021-0.0210.0000.0000.0000.000
208A139LEU00.044-0.12019.6220.0060.0060.0000.0000.0000.000
209A139LEU0-0.1070.09219.1530.0010.0010.0000.0000.0000.000
210A140GLY00.013-0.08221.2380.0270.0270.0000.0000.0000.000
211A141TYR00.1190.03423.1510.0290.0290.0000.0000.0000.000
212A141TYR0-0.0780.07621.235-0.006-0.0060.0000.0000.0000.000
213A142LEU00.080-0.09121.3430.0300.0300.0000.0000.0000.000
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