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: 5NVJZ

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 OptAll
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 -924207.635248
FMO2-HF: Nuclear repulsion 878179.659311
FMO2-HF: Total energy -46027.975937
FMO2-MP2: Total energy -46160.231147


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.
-9.426-8.4538.239-4.996-4.215-0.035
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 : 0.148 / q_NPA : 0.048
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].
4A34SER0-0.0290.0864.3310.2270.5190.001-0.139-0.1540.000
5A35ARG0-0.023-0.1103.879-1.8630.513-0.015-1.440-0.9210.005
6A35ARG10.7450.9715.0632.4132.438-0.001-0.002-0.0210.000
7A36ASP00.086-0.0607.117-0.063-0.0630.0000.0000.0000.000
8A36ASP-1-0.926-0.8229.515-1.007-1.0070.0000.0000.0000.000
9A37MET00.043-0.13410.8130.0700.0700.0000.0000.0000.000
10A37MET0-0.1200.1229.8070.0350.0350.0000.0000.0000.000
11A38LYS00.161-0.05713.3330.0840.0840.0000.0000.0000.000
12A38LYS10.7060.97215.4990.5710.5710.0000.0000.0000.000
13A39ASN00.066-0.04416.2630.0690.0690.0000.0000.0000.000
14A39ASN0-0.1030.01518.570-0.010-0.0100.0000.0000.0000.000
15A40ILE00.190-0.05717.767-0.087-0.0870.0000.0000.0000.000
16A40ILE0-0.0420.15121.4580.0000.0000.0000.0000.0000.000
17A41ASN00.067-0.08019.567-0.027-0.0270.0000.0000.0000.000
18A41ASN0-0.1010.04520.1260.0140.0140.0000.0000.0000.000
19A42GLU00.112-0.08515.5930.0070.0070.0000.0000.0000.000
20A42GLU-1-0.893-0.79214.524-0.658-0.6580.0000.0000.0000.000
21A43SER00.021-0.09914.974-0.125-0.1250.0000.0000.0000.000
22A43SER0-0.0070.07216.601-0.002-0.0020.0000.0000.0000.000
23A44VAL00.099-0.08915.976-0.072-0.0720.0000.0000.0000.000
24A44VAL0-0.0890.11920.0280.0070.0070.0000.0000.0000.000
25A45GLY0-0.019-0.12217.1350.0100.0100.0000.0000.0000.000
26A46ALA00.120-0.00312.6220.0620.0620.0000.0000.0000.000
27A46ALA0-0.0440.10911.680-0.041-0.0410.0000.0000.0000.000
28A47LEU00.029-0.12713.619-0.088-0.0880.0000.0000.0000.000
29A47LEU0-0.0440.13113.8320.0040.0040.0000.0000.0000.000
30A48GLN00.145-0.06915.3750.0280.0280.0000.0000.0000.000
31A48GLN0-0.0910.10118.6090.0060.0060.0000.0000.0000.000
32A49VAL00.040-0.12415.4870.0810.0810.0000.0000.0000.000
33A49VAL0-0.0780.10814.4380.0050.0050.0000.0000.0000.000
34A50LEU00.151-0.09613.1270.0820.0820.0000.0000.0000.000
35A50LEU0-0.0680.13210.585-0.011-0.0110.0000.0000.0000.000
36A51GLN00.118-0.06314.2580.0420.0420.0000.0000.0000.000
37A51GLN0-0.1120.06718.2910.0390.0390.0000.0000.0000.000
38A52ILE00.059-0.09217.5810.0570.0570.0000.0000.0000.000
39A52ILE0-0.1190.06818.7110.0150.0150.0000.0000.0000.000
40A53ALA00.056-0.11815.4130.0960.0960.0000.0000.0000.000
41A53ALA0-0.0060.12214.790-0.021-0.0210.0000.0000.0000.000
42A54CYS00.105-0.13016.1650.0680.0680.0000.0000.0000.000
43A54CYS0-0.1180.10314.374-0.012-0.0120.0000.0000.0000.000
44A55LYS00.156-0.05016.8460.0500.0500.0000.0000.0000.000
45A55LYS10.8151.03020.5920.3490.3490.0000.0000.0000.000
46A56LYS00.023-0.09020.0820.0440.0440.0000.0000.0000.000
47A56LYS10.8471.04019.6660.3540.3540.0000.0000.0000.000
48A57LEU00.066-0.11517.9360.0470.0470.0000.0000.0000.000
49A57LEU0-0.0850.10514.7490.0000.0000.0000.0000.0000.000
50A58PHE00.176-0.06119.3940.0410.0410.0000.0000.0000.000
51A58PHE0-0.1190.10220.402-0.005-0.0050.0000.0000.0000.000
52A59ASN00.088-0.06721.4500.0280.0280.0000.0000.0000.000
53A59ASN0-0.1220.04824.3270.0030.0030.0000.0000.0000.000
54A60LYS00.047-0.10023.2420.0200.0200.0000.0000.0000.000
55A60LYS10.7300.97822.5270.1690.1690.0000.0000.0000.000
56A61SER00.032-0.09522.6180.0250.0250.0000.0000.0000.000
57A61SER0-0.0370.05921.735-0.003-0.0030.0000.0000.0000.000
58A62MET00.127-0.08823.8520.0170.0170.0000.0000.0000.000
59A62MET0-0.1300.11126.3940.0030.0030.0000.0000.0000.000
60A63GLY00.047-0.07527.0640.0040.0040.0000.0000.0000.000
61A64LEU00.004-0.02626.1490.0080.0080.0000.0000.0000.000
62A64LEU0-0.0950.09323.629-0.002-0.0020.0000.0000.0000.000
63A65GLU00.024-0.13927.6700.0090.0090.0000.0000.0000.000
64A65GLU-1-0.875-0.80428.135-0.082-0.0820.0000.0000.0000.000
65A66ASP00.038-0.12329.2090.0100.0100.0000.0000.0000.000
66A66ASP-1-0.985-0.85332.804-0.055-0.0550.0000.0000.0000.000
67A67LYS00.055-0.08830.9110.0040.0040.0000.0000.0000.000
68A67LYS10.7531.00728.0880.0930.0930.0000.0000.0000.000
69A68ASP00.060-0.08231.6520.0050.0050.0000.0000.0000.000
70A68ASP-1-0.886-0.83733.909-0.033-0.0330.0000.0000.0000.000
71A69ALA00.178-0.07730.893-0.006-0.0060.0000.0000.0000.000
72A69ALA0-0.0990.09731.8680.0020.0020.0000.0000.0000.000
73A70LEU00.073-0.08830.1320.0030.0030.0000.0000.0000.000
74A70LEU0-0.1180.09531.3680.0010.0010.0000.0000.0000.000
75A71GLN00.071-0.11729.903-0.002-0.0020.0000.0000.0000.000
76A71GLN0-0.0590.10931.050-0.007-0.0070.0000.0000.0000.000
77A72ALA00.148-0.08427.526-0.015-0.0150.0000.0000.0000.000
78A72ALA0-0.0570.11827.5150.0020.0020.0000.0000.0000.000
79A73SER0-0.034-0.10225.831-0.007-0.0070.0000.0000.0000.000
80A73SER0-0.0790.03927.1110.0040.0040.0000.0000.0000.000
81A74ILE00.083-0.08125.1230.0000.0000.0000.0000.0000.000
82A74ILE0-0.1000.08327.4760.0000.0000.0000.0000.0000.000
83A75ILE00.115-0.07824.826-0.010-0.0100.0000.0000.0000.000
84A75ILE0-0.0710.10523.969-0.002-0.0020.0000.0000.0000.000
85A76LYS00.103-0.09221.686-0.029-0.0290.0000.0000.0000.000
86A76LYS10.8311.05421.9170.0280.0280.0000.0000.0000.000
87A77GLN00.073-0.08920.390-0.006-0.0060.0000.0000.0000.000
88A77GLN0-0.1000.07620.7560.0210.0210.0000.0000.0000.000
89A78GLU00.062-0.11220.432-0.012-0.0120.0000.0000.0000.000
90A78GLU-1-0.862-0.80222.670-0.149-0.1490.0000.0000.0000.000
91A79LEU00.064-0.08118.992-0.044-0.0440.0000.0000.0000.000
92A79LEU0-0.1080.09618.548-0.001-0.0010.0000.0000.0000.000
93A80ARG00.093-0.10516.147-0.059-0.0590.0000.0000.0000.000
94A80ARG10.6800.93516.5630.0170.0170.0000.0000.0000.000
95A81GLU00.121-0.08915.715-0.051-0.0510.0000.0000.0000.000
96A81GLU-1-0.961-0.80019.535-0.123-0.1230.0000.0000.0000.000
97A82ILE00.062-0.08216.817-0.046-0.0460.0000.0000.0000.000
98A82ILE0-0.1130.07016.317-0.003-0.0030.0000.0000.0000.000
99A83VAL00.086-0.10512.980-0.112-0.1120.0000.0000.0000.000
100A83VAL0-0.0810.10110.902-0.001-0.0010.0000.0000.0000.000
101A84GLU00.063-0.10912.104-0.182-0.1820.0000.0000.0000.000
102A84GLU-1-0.891-0.78613.696-0.039-0.0390.0000.0000.0000.000
103A85ASN00.023-0.08412.885-0.050-0.0500.0000.0000.0000.000
104A85ASN0-0.1720.02316.1560.0150.0150.0000.0000.0000.000
105A86CYS00.152-0.10312.3200.0250.0250.0000.0000.0000.000
106A86CYS0-0.1750.10911.399-0.034-0.0340.0000.0000.0000.000
107A87GLN00.038-0.10610.344-0.287-0.2870.0000.0000.0000.000
108A87GLN0-0.0870.08511.006-0.005-0.0050.0000.0000.0000.000
109A88PHE00.082-0.11410.8780.1910.1910.0000.0000.0000.000
110A88PHE0-0.0490.12111.8050.0280.0280.0000.0000.0000.000
111A89LEU0-0.005-0.10211.268-0.185-0.1850.0000.0000.0000.000
112A89LEU0-0.0610.09812.6040.0110.0110.0000.0000.0000.000
113A90ALA00.161-0.06211.871-0.109-0.1090.0000.0000.0000.000
114A90ALA0-0.0970.09013.0350.0340.0340.0000.0000.0000.000
115A91SER00.074-0.0958.3880.1520.1520.0000.0000.0000.000
116A91SER0-0.0400.0806.772-0.240-0.2400.0000.0000.0000.000
117A92PRO00.013-0.0864.5030.3040.355-0.001-0.009-0.0410.000
118A93LEU00.0420.0097.001-0.507-0.5070.0000.0000.0000.000
119A93LEU0-0.0740.0819.2320.0860.0860.0000.0000.0000.000
120A94PHE00.113-0.0567.470-0.192-0.1920.0000.0000.0000.000
121A94PHE0-0.0340.0988.1040.1060.1060.0000.0000.0000.000
122A95ASP00.041-0.0824.283-1.303-1.097-0.002-0.121-0.0830.000
123A95ASP-1-0.883-0.8083.816-0.224-0.0900.001-0.048-0.0870.000
124A96THR00.058-0.0991.900-6.233-8.8528.249-3.210-2.420-0.039
125A96THR0-0.1050.0343.544-1.286-1.2220.0060.144-0.215-0.001
126A97GLN00.168-0.0593.7631.2551.6990.001-0.171-0.2730.000
127A97GLN0-0.1440.0655.4530.1440.1440.0000.0000.0000.000
128A98LEU00.002-0.1126.122-0.449-0.4490.0000.0000.0000.000
129A98LEU0-0.1100.0747.4810.0810.0810.0000.0000.0000.000
130A99ASN00.160-0.0728.9080.2740.2740.0000.0000.0000.000
131A99ASN0-0.0930.0949.1810.0030.0030.0000.0000.0000.000
132A100ILE00.051-0.10311.182-0.056-0.0560.0000.0000.0000.000
133A100ILE0-0.0750.08912.9640.0030.0030.0000.0000.0000.000
134A101ALA00.182-0.07314.6900.0320.0320.0000.0000.0000.000
135A101ALA0-0.1020.10417.7220.0070.0070.0000.0000.0000.000
136A102ILE00.000-0.13817.954-0.012-0.0120.0000.0000.0000.000
137A102ILE0-0.0830.08918.658-0.004-0.0040.0000.0000.0000.000
138A103ASN00.030-0.02721.0470.0100.0100.0000.0000.0000.000
139A103ASN0-0.0670.06224.9340.0000.0000.0000.0000.0000.000
140A104ASP00.102-0.09222.8960.0070.0070.0000.0000.0000.000
141A104ASP-1-1.021-0.87324.668-0.230-0.2300.0000.0000.0000.000
142A105GLU00.106-0.13221.1410.0170.0170.0000.0000.0000.000
143A105GLU-1-1.005-0.84320.825-0.267-0.2670.0000.0000.0000.000
144A106ILE00.035-0.10816.518-0.021-0.0210.0000.0000.0000.000
145A106ILE0-0.0830.07714.514-0.002-0.0020.0000.0000.0000.000
146A107PHE00.033-0.08815.7440.0450.0450.0000.0000.0000.000
147A107PHE0-0.0540.09316.101-0.007-0.0070.0000.0000.0000.000
148A108SER00.024-0.10811.428-0.078-0.0780.0000.0000.0000.000
149A108SER0-0.0490.06910.3490.0650.0650.0000.0000.0000.000
150A109MET00.167-0.06311.3880.1480.1480.0000.0000.0000.000
151A109MET0-0.1350.09011.1480.0410.0410.0000.0000.0000.000
152A110ILE0-0.018-0.1217.850-0.364-0.3640.0000.0000.0000.000
153A110ILE0-0.0490.1124.9440.0450.0450.0000.0000.0000.000
154A111VAL00.075-0.1087.8630.3250.3250.0000.0000.0000.000
155A111VAL0-0.0750.1029.7820.0210.0210.0000.0000.0000.000
156A112VAL00.120-0.0857.106-0.426-0.4260.0000.0000.0000.000
157A112VAL0-0.0600.1087.1780.0280.0280.0000.0000.0000.000
158A113ASN00.101-0.1117.893-0.083-0.0830.0000.0000.0000.000
159A113ASN0-0.0950.0718.887-0.079-0.0790.0000.0000.0000.000
160A114PRO0-0.023-0.0959.8090.1050.1050.0000.0000.0000.000
161A115LEU00.050-0.01113.2280.0310.0310.0000.0000.0000.000
162A115LEU0-0.0920.08813.2920.0080.0080.0000.0000.0000.000
163A116ASP00.096-0.08313.8090.0030.0030.0000.0000.0000.000
164A116ASP-1-0.956-0.83912.3090.2820.2820.0000.0000.0000.000
165A117LEU00.051-0.12615.3990.0350.0350.0000.0000.0000.000
166A117LEU0-0.0640.12215.021-0.008-0.0080.0000.0000.0000.000
167A118LEU00.051-0.08417.481-0.011-0.0110.0000.0000.0000.000
168A118LEU0-0.1370.07418.2390.0000.0000.0000.0000.0000.000
169A119GLU00.044-0.12819.677-0.010-0.0100.0000.0000.0000.000
170A119GLU-1-1.039-0.87120.9690.0480.0480.0000.0000.0000.000
171A120ASN00.177-0.07021.867-0.007-0.0070.0000.0000.0000.000
172A120ASN0-0.1600.04922.357-0.008-0.0080.0000.0000.0000.000
173A121VAL00.059-0.11722.047-0.015-0.0150.0000.0000.0000.000
174A121VAL0-0.0910.10923.7970.0000.0000.0000.0000.0000.000
175A122GLY00.084-0.07722.953-0.021-0.0210.0000.0000.0000.000
176A123GLU00.075-0.02620.785-0.024-0.0240.0000.0000.0000.000
177A123GLU-1-0.953-0.80919.758-0.008-0.0080.0000.0000.0000.000
178A124PHE00.135-0.06918.212-0.029-0.0290.0000.0000.0000.000
179A124PHE0-0.1310.06816.729-0.010-0.0100.0000.0000.0000.000
180A125GLN00.020-0.12318.788-0.047-0.0470.0000.0000.0000.000
181A125GLN0-0.1290.07823.0700.0030.0030.0000.0000.0000.000
182A126ALA00.156-0.06620.762-0.036-0.0360.0000.0000.0000.000
183A126ALA0-0.0620.10621.2220.0050.0050.0000.0000.0000.000
184A127TYR00.118-0.07816.490-0.020-0.0200.0000.0000.0000.000
185A127TYR0-0.0660.09411.219-0.055-0.0550.0000.0000.0000.000
186A128LEU00.046-0.11516.529-0.069-0.0690.0000.0000.0000.000
187A128LEU0-0.1180.10215.267-0.011-0.0110.0000.0000.0000.000
188A129GLU00.091-0.12817.521-0.055-0.0550.0000.0000.0000.000
189A129GLU-1-1.021-0.83921.749-0.187-0.1870.0000.0000.0000.000
190A130GLU00.029-0.14218.353-0.009-0.0090.0000.0000.0000.000
191A130GLU-1-0.967-0.83817.603-0.231-0.2310.0000.0000.0000.000
192A131LYS00.067-0.09214.617-0.001-0.0010.0000.0000.0000.000
193A131LYS10.7471.00411.9770.5740.5740.0000.0000.0000.000
194A132LEU00.080-0.12215.856-0.079-0.0790.0000.0000.0000.000
195A132LEU0-0.1160.09517.9240.0040.0040.0000.0000.0000.000
196A133ASN00.089-0.06118.403-0.009-0.0090.0000.0000.0000.000
197A133ASN0-0.1070.05520.6920.0150.0150.0000.0000.0000.000
198A134GLU00.074-0.12316.3630.0360.0360.0000.0000.0000.000
199A134GLU-1-0.885-0.78214.238-0.590-0.5900.0000.0000.0000.000
200A135ILE00.125-0.07216.557-0.012-0.0120.0000.0000.0000.000
201A135ILE0-0.1030.07913.809-0.011-0.0110.0000.0000.0000.000
202A136LYS00.072-0.08617.150-0.010-0.0100.0000.0000.0000.000
203A136LYS10.6960.98321.4140.2910.2910.0000.0000.0000.000
204A137GLU00.068-0.10720.6110.0150.0150.0000.0000.0000.000
205A137GLU-1-0.896-0.78820.357-0.287-0.2870.0000.0000.0000.000
206A138LEU00.081-0.08617.8210.0450.0450.0000.0000.0000.000
207A138LEU0-0.0610.10215.280-0.021-0.0210.0000.0000.0000.000
208A139LEU00.048-0.12319.3560.0020.0020.0000.0000.0000.000
209A139LEU0-0.1060.09518.9260.0010.0010.0000.0000.0000.000
210A140GLY00.024-0.07621.0760.0280.0280.0000.0000.0000.000
211A141TYR00.1200.03323.1590.0240.0240.0000.0000.0000.000
212A141TYR0-0.0920.05921.392-0.003-0.0030.0000.0000.0000.000
213A142LEU00.063-0.10221.4870.0280.0280.0000.0000.0000.000
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