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: YNGZ2

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 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 224
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -918977.163861
FMO2-HF: Nuclear repulsion 872950.698716
FMO2-HF: Total energy -46026.465145
FMO2-MP2: Total energy -46158.732097


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.
-6.539-3.0641.599-2.032-3.041-0.02
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 : 0.129 / q_NPA : 0.042
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].
4A34SER0-0.0320.0944.3530.3830.6230.000-0.111-0.1290.000
5A35ARG0-0.019-0.1233.806-0.9040.306-0.017-0.627-0.5650.000
6A35ARG10.7511.0134.7502.6752.702-0.001-0.004-0.0230.000
7A36ASP00.113-0.0966.6990.0850.0850.0000.0000.0000.000
8A36ASP-1-0.961-0.8129.786-0.503-0.5030.0000.0000.0000.000
9A37MET00.055-0.11910.413-0.026-0.0260.0000.0000.0000.000
10A37MET0-0.1360.1069.4230.0120.0120.0000.0000.0000.000
11A38LYS00.154-0.04212.7550.1170.1170.0000.0000.0000.000
12A38LYS10.7861.02315.1740.4640.4640.0000.0000.0000.000
13A39ASN00.097-0.03815.6260.0770.0770.0000.0000.0000.000
14A39ASN0-0.0930.02818.557-0.031-0.0310.0000.0000.0000.000
15A40ILE00.155-0.08817.378-0.082-0.0820.0000.0000.0000.000
16A40ILE0-0.0280.14720.8450.0000.0000.0000.0000.0000.000
17A41ASN00.091-0.07319.239-0.025-0.0250.0000.0000.0000.000
18A41ASN0-0.1310.05419.9590.0140.0140.0000.0000.0000.000
19A42GLU00.046-0.13115.0930.0050.0050.0000.0000.0000.000
20A42GLU-1-0.927-0.83013.762-0.796-0.7960.0000.0000.0000.000
21A43SER00.069-0.07114.625-0.135-0.1350.0000.0000.0000.000
22A43SER0-0.0110.08915.8790.0070.0070.0000.0000.0000.000
23A44VAL00.057-0.09415.674-0.070-0.0700.0000.0000.0000.000
24A44VAL0-0.0640.11419.8860.0070.0070.0000.0000.0000.000
25A45GLY0-0.029-0.12317.0220.0010.0010.0000.0000.0000.000
26A46ALA00.102-0.00312.5600.0410.0410.0000.0000.0000.000
27A46ALA0-0.0240.10811.678-0.042-0.0420.0000.0000.0000.000
28A47LEU00.051-0.11813.640-0.099-0.0990.0000.0000.0000.000
29A47LEU0-0.0490.13213.7710.0080.0080.0000.0000.0000.000
30A48GLN00.097-0.08415.4860.0280.0280.0000.0000.0000.000
31A48GLN0-0.0830.08818.5230.0160.0160.0000.0000.0000.000
32A49VAL00.032-0.12615.2870.0890.0890.0000.0000.0000.000
33A49VAL0-0.0480.10414.2000.0000.0000.0000.0000.0000.000
34A50LEU00.141-0.10613.3830.0420.0420.0000.0000.0000.000
35A50LEU0-0.0810.13011.101-0.018-0.0180.0000.0000.0000.000
36A51GLN00.140-0.09514.4080.0420.0420.0000.0000.0000.000
37A51GLN0-0.1480.08718.1450.0380.0380.0000.0000.0000.000
38A52ILE00.026-0.10217.6320.0580.0580.0000.0000.0000.000
39A52ILE0-0.0960.09619.0160.0090.0090.0000.0000.0000.000
40A53ALA00.031-0.11515.8330.1000.1000.0000.0000.0000.000
41A53ALA00.0230.12015.107-0.025-0.0250.0000.0000.0000.000
42A54CYS00.092-0.12516.4420.0480.0480.0000.0000.0000.000
43A54CYS0-0.1020.11614.442-0.004-0.0040.0000.0000.0000.000
44A55LYS00.167-0.05417.0630.0530.0530.0000.0000.0000.000
45A55LYS10.8421.05820.8810.3400.3400.0000.0000.0000.000
46A56LYS00.006-0.11920.3070.0510.0510.0000.0000.0000.000
47A56LYS10.8661.05019.9670.4570.4570.0000.0000.0000.000
48A57LEU00.063-0.10518.2510.0470.0470.0000.0000.0000.000
49A57LEU0-0.0800.11815.1360.0020.0020.0000.0000.0000.000
50A58PHE00.158-0.07219.7090.0350.0350.0000.0000.0000.000
51A58PHE0-0.1020.10920.725-0.007-0.0070.0000.0000.0000.000
52A59ASN00.105-0.05921.7360.0280.0280.0000.0000.0000.000
53A59ASN0-0.1280.04624.6600.0130.0130.0000.0000.0000.000
54A60LYS00.060-0.10123.6140.0280.0280.0000.0000.0000.000
55A60LYS10.8771.06722.6090.2790.2790.0000.0000.0000.000
56A61SER0-0.008-0.10223.2720.0160.0160.0000.0000.0000.000
57A61SER0-0.0170.08122.3600.0050.0050.0000.0000.0000.000
58A62MET00.103-0.10924.4960.0190.0190.0000.0000.0000.000
59A62MET0-0.1580.10527.3090.0010.0010.0000.0000.0000.000
60A63GLY00.024-0.08927.6310.0000.0000.0000.0000.0000.000
61A64LEU00.068-0.01626.7420.0090.0090.0000.0000.0000.000
62A64LEU0-0.1140.08724.351-0.003-0.0030.0000.0000.0000.000
63A65GLU00.011-0.12928.2530.0020.0020.0000.0000.0000.000
64A65GLU-1-0.919-0.82928.793-0.096-0.0960.0000.0000.0000.000
65A66ASP00.062-0.11729.7760.0100.0100.0000.0000.0000.000
66A66ASP-1-1.025-0.85333.422-0.072-0.0720.0000.0000.0000.000
67A67LYS00.050-0.08531.3690.0060.0060.0000.0000.0000.000
68A67LYS10.8181.03529.5870.1350.1350.0000.0000.0000.000
69A68ASP00.065-0.07632.3310.0040.0040.0000.0000.0000.000
70A68ASP-1-0.900-0.84234.525-0.086-0.0860.0000.0000.0000.000
71A69ALA00.186-0.11131.668-0.010-0.0100.0000.0000.0000.000
72A69ALA0-0.1010.11732.5310.0020.0020.0000.0000.0000.000
73A70LEU00.076-0.09030.889-0.004-0.0040.0000.0000.0000.000
74A70LEU0-0.1180.09732.0550.0010.0010.0000.0000.0000.000
75A71GLN00.062-0.09330.654-0.010-0.0100.0000.0000.0000.000
76A71GLN0-0.0380.09231.419-0.010-0.0100.0000.0000.0000.000
77A72ALA00.129-0.07828.133-0.018-0.0180.0000.0000.0000.000
78A72ALA0-0.0480.10627.9390.0020.0020.0000.0000.0000.000
79A73SER0-0.038-0.10926.368-0.016-0.0160.0000.0000.0000.000
80A73SER0-0.0810.03927.7510.0020.0020.0000.0000.0000.000
81A74ILE00.050-0.09925.765-0.013-0.0130.0000.0000.0000.000
82A74ILE0-0.0730.09528.0510.0020.0020.0000.0000.0000.000
83A75ILE00.126-0.06325.508-0.021-0.0210.0000.0000.0000.000
84A75ILE0-0.0710.09724.2360.0010.0010.0000.0000.0000.000
85A76LYS00.088-0.10122.165-0.034-0.0340.0000.0000.0000.000
86A76LYS10.8681.06922.3290.1130.1130.0000.0000.0000.000
87A77GLN00.055-0.10120.912-0.029-0.0290.0000.0000.0000.000
88A77GLN0-0.0640.10720.3290.0270.0270.0000.0000.0000.000
89A78GLU00.094-0.10421.007-0.033-0.0330.0000.0000.0000.000
90A78GLU-1-1.020-0.86723.277-0.220-0.2200.0000.0000.0000.000
91A79LEU00.024-0.12219.522-0.052-0.0520.0000.0000.0000.000
92A79LEU0-0.0790.09318.8470.0000.0000.0000.0000.0000.000
93A80ARG00.122-0.09416.581-0.076-0.0760.0000.0000.0000.000
94A80ARG10.8281.05516.9420.2600.2600.0000.0000.0000.000
95A81GLU00.121-0.10216.021-0.088-0.0880.0000.0000.0000.000
96A81GLU-1-1.017-0.83419.730-0.294-0.2940.0000.0000.0000.000
97A82ILE00.037-0.09916.922-0.066-0.0660.0000.0000.0000.000
98A82ILE0-0.1180.05816.4030.0060.0060.0000.0000.0000.000
99A83VAL00.036-0.10213.458-0.089-0.0890.0000.0000.0000.000
100A83VAL0-0.0670.09111.379-0.001-0.0010.0000.0000.0000.000
101A84GLU00.036-0.13212.284-0.243-0.2430.0000.0000.0000.000
102A84GLU-1-1.016-0.85113.347-0.407-0.4070.0000.0000.0000.000
103A85ASN00.046-0.10112.952-0.109-0.1090.0000.0000.0000.000
104A85ASN0-0.1320.06416.4180.0040.0040.0000.0000.0000.000
105A86CYS00.136-0.09312.8040.0560.0560.0000.0000.0000.000
106A86CYS0-0.1550.10411.974-0.024-0.0240.0000.0000.0000.000
107A87GLN00.017-0.10510.519-0.273-0.2730.0000.0000.0000.000
108A87GLN0-0.0840.08411.1910.0950.0950.0000.0000.0000.000
109A88PHE00.074-0.11210.5940.2300.2300.0000.0000.0000.000
110A88PHE0-0.0410.11811.2730.0200.0200.0000.0000.0000.000
111A89LEU00.006-0.10410.772-0.234-0.2340.0000.0000.0000.000
112A89LEU0-0.0540.10411.9250.0060.0060.0000.0000.0000.000
113A90ALA00.107-0.08611.801-0.075-0.0750.0000.0000.0000.000
114A90ALA0-0.0710.09912.7150.0410.0410.0000.0000.0000.000
115A91SER00.071-0.0887.8790.1200.1200.0000.0000.0000.000
116A91SER0-0.0030.0816.019-0.030-0.0300.0000.0000.0000.000
117A92PRO00.003-0.0884.4710.3600.420-0.001-0.015-0.0440.000
118A93LEU00.0620.0086.349-0.728-0.7280.0000.0000.0000.000
119A93LEU0-0.0810.0928.6040.0940.0940.0000.0000.0000.000
120A94PHE00.101-0.0707.526-0.141-0.1410.0000.0000.0000.000
121A94PHE0-0.0480.0838.5560.1090.1090.0000.0000.0000.000
122A95ASP00.042-0.1184.775-0.894-0.854-0.002-0.017-0.0210.000
123A95ASP-1-0.892-0.8004.197-0.907-0.822-0.001-0.015-0.0680.000
124A96THR00.054-0.0852.367-5.224-3.4511.615-1.630-1.757-0.020
125A96THR0-0.1060.0373.255-1.119-1.4040.0050.494-0.2150.000
126A97GLN00.143-0.0773.7131.0411.3660.001-0.107-0.2190.000
127A97GLN0-0.1360.0825.6890.5180.5180.0000.0000.0000.000
128A98LEU0-0.039-0.1425.855-0.594-0.5940.0000.0000.0000.000
129A98LEU0-0.0720.0977.1770.0180.0180.0000.0000.0000.000
130A99ASN00.139-0.0688.7790.2850.2850.0000.0000.0000.000
131A99ASN0-0.0970.0948.5610.0850.0850.0000.0000.0000.000
132A100ILE00.091-0.10111.054-0.095-0.0950.0000.0000.0000.000
133A100ILE0-0.0550.09112.814-0.009-0.0090.0000.0000.0000.000
134A101ALA00.141-0.06614.5300.0590.0590.0000.0000.0000.000
135A101ALA0-0.0860.09417.5980.0050.0050.0000.0000.0000.000
136A102ILE00.019-0.13317.762-0.036-0.0360.0000.0000.0000.000
137A102ILE0-0.0870.09818.669-0.005-0.0050.0000.0000.0000.000
138A103ASN0-0.017-0.07420.8820.0160.0160.0000.0000.0000.000
139A103ASN0-0.0710.05724.737-0.001-0.0010.0000.0000.0000.000
140A104ASP00.115-0.07322.5920.0080.0080.0000.0000.0000.000
141A104ASP-1-1.013-0.87024.356-0.118-0.1180.0000.0000.0000.000
142A105GLU00.107-0.16220.6050.0290.0290.0000.0000.0000.000
143A105GLU-1-1.015-0.80720.686-0.100-0.1000.0000.0000.0000.000
144A106ILE00.044-0.10515.895-0.047-0.0470.0000.0000.0000.000
145A106ILE0-0.0850.07413.8020.0010.0010.0000.0000.0000.000
146A107PHE00.050-0.09915.7370.0720.0720.0000.0000.0000.000
147A107PHE0-0.0560.10216.030-0.008-0.0080.0000.0000.0000.000
148A108SER00.034-0.09411.556-0.113-0.1130.0000.0000.0000.000
149A108SER0-0.0600.06010.4700.0790.0790.0000.0000.0000.000
150A109MET00.154-0.08910.7260.1690.1690.0000.0000.0000.000
151A109MET0-0.1310.10411.1890.0130.0130.0000.0000.0000.000
152A110ILE0-0.013-0.1047.668-0.361-0.3610.0000.0000.0000.000
153A110ILE0-0.0300.1074.8970.0830.0830.0000.0000.0000.000
154A111VAL00.071-0.0948.2740.3120.3120.0000.0000.0000.000
155A111VAL0-0.0580.09510.2420.0110.0110.0000.0000.0000.000
156A112VAL00.105-0.0867.569-0.468-0.4680.0000.0000.0000.000
157A112VAL0-0.0520.1097.5660.0460.0460.0000.0000.0000.000
158A113ASN00.127-0.1128.317-0.037-0.0370.0000.0000.0000.000
159A113ASN0-0.0760.0939.1640.0190.0190.0000.0000.0000.000
160A114PRO0-0.039-0.10110.2520.1340.1340.0000.0000.0000.000
161A115LEU00.029-0.01313.7210.0660.0660.0000.0000.0000.000
162A115LEU0-0.0740.09614.1430.0030.0030.0000.0000.0000.000
163A116ASP00.112-0.10914.5370.0050.0050.0000.0000.0000.000
164A116ASP-1-0.979-0.85012.9750.0210.0210.0000.0000.0000.000
165A117LEU00.029-0.12516.1780.0420.0420.0000.0000.0000.000
166A117LEU0-0.0530.12815.436-0.005-0.0050.0000.0000.0000.000
167A118LEU00.088-0.09818.1610.0050.0050.0000.0000.0000.000
168A118LEU0-0.1190.08819.078-0.002-0.0020.0000.0000.0000.000
169A119GLU0-0.028-0.15820.431-0.013-0.0130.0000.0000.0000.000
170A119GLU-1-1.003-0.83921.6210.0170.0170.0000.0000.0000.000
171A120ASN00.114-0.09322.0610.0050.0050.0000.0000.0000.000
172A120ASN0-0.1160.08622.774-0.012-0.0120.0000.0000.0000.000
173A121VAL00.076-0.09822.456-0.008-0.0080.0000.0000.0000.000
174A121VAL0-0.0490.11724.293-0.001-0.0010.0000.0000.0000.000
175A122GLY00.063-0.08723.311-0.019-0.0190.0000.0000.0000.000
176A123GLU00.075-0.03921.408-0.016-0.0160.0000.0000.0000.000
177A123GLU-1-0.992-0.82820.4730.0110.0110.0000.0000.0000.000
178A124PHE00.137-0.06418.585-0.010-0.0100.0000.0000.0000.000
179A124PHE0-0.1310.06317.036-0.014-0.0140.0000.0000.0000.000
180A125GLN00.029-0.13318.978-0.044-0.0440.0000.0000.0000.000
181A125GLN0-0.1010.10023.1320.0120.0120.0000.0000.0000.000
182A126ALA00.125-0.07721.163-0.033-0.0330.0000.0000.0000.000
183A126ALA0-0.0440.11521.6130.0060.0060.0000.0000.0000.000
184A127TYR00.135-0.07316.929-0.004-0.0040.0000.0000.0000.000
185A127TYR0-0.0690.10611.402-0.051-0.0510.0000.0000.0000.000
186A128LEU00.045-0.11616.697-0.035-0.0350.0000.0000.0000.000
187A128LEU0-0.1070.09115.386-0.016-0.0160.0000.0000.0000.000
188A129GLU00.086-0.12917.711-0.052-0.0520.0000.0000.0000.000
189A129GLU-1-1.024-0.84021.984-0.151-0.1510.0000.0000.0000.000
190A130GLU0-0.002-0.15818.842-0.017-0.0170.0000.0000.0000.000
191A130GLU-1-0.983-0.83217.992-0.097-0.0970.0000.0000.0000.000
192A131LYS00.091-0.08714.9670.0130.0130.0000.0000.0000.000
193A131LYS10.7921.04212.0030.3070.3070.0000.0000.0000.000
194A132LEU00.066-0.12116.177-0.060-0.0600.0000.0000.0000.000
195A132LEU0-0.1380.07718.224-0.002-0.0020.0000.0000.0000.000
196A133ASN00.067-0.07218.655-0.019-0.0190.0000.0000.0000.000
197A133ASN0-0.1060.06620.796-0.001-0.0010.0000.0000.0000.000
198A134GLU00.106-0.12516.7550.0240.0240.0000.0000.0000.000
199A134GLU-1-0.970-0.82014.901-0.296-0.2960.0000.0000.0000.000
200A135ILE00.123-0.07416.7730.0000.0000.0000.0000.0000.000
201A135ILE0-0.1150.07314.178-0.018-0.0180.0000.0000.0000.000
202A136LYS00.086-0.08917.425-0.015-0.0150.0000.0000.0000.000
203A136LYS10.8421.05722.0240.2200.2200.0000.0000.0000.000
204A137GLU00.036-0.11520.7940.0020.0020.0000.0000.0000.000
205A137GLU-1-1.008-0.85320.371-0.190-0.1900.0000.0000.0000.000
206A138LEU00.080-0.09917.9230.0350.0350.0000.0000.0000.000
207A138LEU0-0.0590.10815.248-0.020-0.0200.0000.0000.0000.000
208A139LEU00.035-0.12119.4460.0050.0050.0000.0000.0000.000
209A139LEU0-0.1250.08519.135-0.003-0.0030.0000.0000.0000.000
210A140GLY00.023-0.09021.1290.0160.0160.0000.0000.0000.000
211A141TYR00.1120.00522.8770.0180.0180.0000.0000.0000.000
212A141TYR0-0.0160.11220.859-0.001-0.0010.0000.0000.0000.000
213A142LEU00.066-0.08321.3420.0290.0290.0000.0000.0000.000
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