FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2J4VR

Calculation Name: 1HYN-P-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HYN

Chain ID: P

ChEMBL ID:

UniProt ID: P02730

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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 293
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4279413.916256
FMO2-HF: Nuclear repulsion 4165251.282772
FMO2-HF: Total energy -114162.633484
FMO2-MP2: Total energy -114499.921425


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(P:56:LYS)


Summations of interaction energy for fragment #1(P:56: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.
-276.49-271.79531.157-15.25-20.6-0.106
Interaction energy analysis for fragmet #1(P:56:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.806 / q_NPA : 0.902
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].
3P58TYR0-0.011-0.0063.881-6.773-5.346-0.015-0.664-0.7470.000
4P59VAL0-0.013-0.0126.5074.0144.0140.0000.0000.0000.000
5P60GLU-1-0.713-0.8239.017-21.872-21.8720.0000.0000.0000.000
6P61LEU0-0.0120.00112.6111.0321.0320.0000.0000.0000.000
7P62GLN0-0.021-0.02415.6961.0301.0300.0000.0000.0000.000
8P63GLU-1-0.738-0.83719.262-13.565-13.5650.0000.0000.0000.000
9P64LEU0-0.0180.00522.5830.1640.1640.0000.0000.0000.000
10P65VAL0-0.037-0.02225.0340.1870.1870.0000.0000.0000.000
11P66MET00.0290.01627.8200.3300.3300.0000.0000.0000.000
12P67ASP-1-0.763-0.87429.325-10.303-10.3030.0000.0000.0000.000
13P68GLU-1-0.890-0.92630.223-9.645-9.6450.0000.0000.0000.000
14P69LYS10.7410.87132.54210.13910.1390.0000.0000.0000.000
15P70ASN0-0.037-0.03332.7760.5080.5080.0000.0000.0000.000
16P71GLN0-0.0260.00234.6360.1570.1570.0000.0000.0000.000
17P72GLU-1-0.756-0.83432.184-9.819-9.8190.0000.0000.0000.000
18P73LEU0-0.025-0.01930.119-0.152-0.1520.0000.0000.0000.000
19P74ARG10.7990.86826.54111.41611.4160.0000.0000.0000.000
20P75TRP00.000-0.02422.645-0.202-0.2020.0000.0000.0000.000
21P76MET0-0.033-0.00620.1670.3010.3010.0000.0000.0000.000
22P77GLU-1-0.775-0.86715.872-19.478-19.4780.0000.0000.0000.000
23P78ALA00.0090.00617.4890.3850.3850.0000.0000.0000.000
24P79ALA0-0.037-0.02413.151-0.189-0.1890.0000.0000.0000.000
25P80ARG10.8080.8979.31327.79927.7990.0000.0000.0000.000
26P81TRP0-0.002-0.0117.015-0.658-0.6580.0000.0000.0000.000
27P82VAL00.0700.0372.310-1.940-0.7440.999-0.739-1.456-0.006
28P83GLN0-0.082-0.0471.790-51.954-50.35313.970-7.122-8.449-0.092
29P84LEU0-0.053-0.0213.3108.6579.2890.006-0.158-0.480-0.001
30P85GLU-1-0.675-0.7835.236-25.971-25.940-0.0010.001-0.0300.000
31P86GLU-1-0.751-0.8848.390-31.042-31.0420.0000.0000.0000.000
32P87ASN00.016-0.01210.847-0.147-0.1470.0000.0000.0000.000
33P88LEU00.0060.02014.544-0.012-0.0120.0000.0000.0000.000
34P89GLY00.0400.01117.1800.6690.6690.0000.0000.0000.000
35P90GLU-1-0.895-0.96520.064-13.464-13.4640.0000.0000.0000.000
36P91ASN0-0.047-0.02622.0750.2380.2380.0000.0000.0000.000
37P92GLY00.0180.00721.0850.2540.2540.0000.0000.0000.000
38P93ALA00.0070.02018.755-0.694-0.6940.0000.0000.0000.000
39P94TRP0-0.036-0.02713.335-0.319-0.3190.0000.0000.0000.000
40P95GLY00.0610.03315.2020.1200.1200.0000.0000.0000.000
41P96ARG10.8620.93511.43621.63921.6390.0000.0000.0000.000
42P97PRO00.0340.0187.4570.3350.3350.0000.0000.0000.000
43P98HIS10.7620.8699.12026.98026.9800.0000.0000.0000.000
44P99LEU00.0440.0138.093-3.285-3.2850.0000.0000.0000.000
45P100SER0-0.005-0.01310.0031.1651.1650.0000.0000.0000.000
46P101HIS0-0.053-0.01711.8500.9920.9920.0000.0000.0000.000
47P102LEU00.0600.03014.554-0.308-0.3080.0000.0000.0000.000
48P103THR00.0370.02917.9000.7280.7280.0000.0000.0000.000
49P104PHE00.0480.02621.386-0.121-0.1210.0000.0000.0000.000
50P105TRP00.0310.00023.4420.0720.0720.0000.0000.0000.000
51P106SER0-0.011-0.00219.808-0.062-0.0620.0000.0000.0000.000
52P107LEU00.0590.02716.649-0.078-0.0780.0000.0000.0000.000
53P108LEU0-0.050-0.01120.5300.3340.3340.0000.0000.0000.000
54P109GLU-1-0.842-0.92323.840-10.551-10.5510.0000.0000.0000.000
55P110LEU00.0410.02216.3660.2120.2120.0000.0000.0000.000
56P111ARG10.8300.88421.01211.68011.6800.0000.0000.0000.000
57P112ARG10.8250.91222.70310.69210.6920.0000.0000.0000.000
58P113VAL00.0030.00122.4360.2770.2770.0000.0000.0000.000
59P114PHE00.0410.02016.4940.1190.1190.0000.0000.0000.000
60P115THR0-0.026-0.04122.3220.1940.1940.0000.0000.0000.000
61P116LYS10.7630.87425.00810.34010.3400.0000.0000.0000.000
62P117GLY00.0310.03423.3870.1210.1210.0000.0000.0000.000
63P118THR0-0.008-0.02224.4480.2290.2290.0000.0000.0000.000
64P119VAL0-0.058-0.04020.918-0.517-0.5170.0000.0000.0000.000
65P120LEU0-0.033-0.00921.8030.4750.4750.0000.0000.0000.000
66P121LEU00.0210.00318.401-0.507-0.5070.0000.0000.0000.000
67P122ASP-1-0.823-0.88419.249-12.366-12.3660.0000.0000.0000.000
68P123LEU00.0370.02221.0880.4850.4850.0000.0000.0000.000
69P124GLN0-0.052-0.02622.235-0.159-0.1590.0000.0000.0000.000
70P125GLU-1-0.848-0.91923.189-10.255-10.2550.0000.0000.0000.000
71P126THR00.0110.00121.830-0.341-0.3410.0000.0000.0000.000
72P127SER00.0070.00622.895-0.054-0.0540.0000.0000.0000.000
73P128LEU00.0640.02721.0680.0960.0960.0000.0000.0000.000
74P129ALA00.0300.01123.5070.1980.1980.0000.0000.0000.000
75P130GLY00.0210.02626.7810.3220.3220.0000.0000.0000.000
76P131VAL00.020-0.00121.1580.1890.1890.0000.0000.0000.000
77P132ALA0-0.009-0.00324.4870.1270.1270.0000.0000.0000.000
78P133ASN0-0.024-0.01526.2140.5210.5210.0000.0000.0000.000
79P134GLN00.024-0.00426.8130.2610.2610.0000.0000.0000.000
80P135LEU0-0.0210.00023.1660.0890.0890.0000.0000.0000.000
81P136LEU0-0.0190.00126.3120.1300.1300.0000.0000.0000.000
82P137ASP-1-0.793-0.87429.441-8.656-8.6560.0000.0000.0000.000
83P138ARG10.8000.88927.1039.8019.8010.0000.0000.0000.000
84P139PHE00.024-0.01424.9480.0670.0670.0000.0000.0000.000
85P140ILE0-0.018-0.00629.8900.2110.2110.0000.0000.0000.000
86P141PHE0-0.091-0.03932.1800.2500.2500.0000.0000.0000.000
87P142GLU-1-0.813-0.87928.405-9.911-9.9110.0000.0000.0000.000
88P143ASP-1-0.945-0.96232.653-8.003-8.0030.0000.0000.0000.000
89P144GLN0-0.109-0.05527.4710.0690.0690.0000.0000.0000.000
90P145ILE0-0.053-0.02730.522-0.127-0.1270.0000.0000.0000.000
91P146ARG10.7200.82033.4238.1988.1980.0000.0000.0000.000
92P147PRO00.018-0.00636.379-0.114-0.1140.0000.0000.0000.000
93P148GLN00.0200.00237.792-0.087-0.0870.0000.0000.0000.000
94P149ASP-1-0.786-0.87034.648-8.267-8.2670.0000.0000.0000.000
95P150ARG10.7540.85233.1498.4778.4770.0000.0000.0000.000
96P151GLU-1-0.845-0.93633.486-8.440-8.4400.0000.0000.0000.000
97P152GLU-1-0.809-0.88834.683-8.293-8.2930.0000.0000.0000.000
98P153LEU00.0240.01029.736-0.293-0.2930.0000.0000.0000.000
99P154LEU0-0.030-0.01229.682-0.403-0.4030.0000.0000.0000.000
100P155ARG10.8090.87530.1418.1428.1420.0000.0000.0000.000
101P156ALA00.0220.01129.657-0.181-0.1810.0000.0000.0000.000
102P157LEU00.0070.00624.246-0.414-0.4140.0000.0000.0000.000
103P158LEU0-0.067-0.01225.682-0.511-0.5110.0000.0000.0000.000
104P159LEU0-0.0150.02028.0810.1900.1900.0000.0000.0000.000
105P160LYS10.8220.88726.7169.8139.8130.0000.0000.0000.000
106P161HIS10.8040.88521.37113.37313.3730.0000.0000.0000.000
107P162SER0-0.023-0.02321.978-0.185-0.1850.0000.0000.0000.000
108P163HIS10.8230.88317.05816.77716.7770.0000.0000.0000.000
109P164ALA00.0310.01017.5970.9030.9030.0000.0000.0000.000
110P165GLY00.0420.02719.7350.6040.6040.0000.0000.0000.000
111P166GLU-1-0.824-0.89122.560-12.432-12.4320.0000.0000.0000.000
112P167LEU0-0.0270.00022.6380.6750.6750.0000.0000.0000.000
113P168GLU-1-0.878-0.94523.100-13.234-13.2340.0000.0000.0000.000
114P169ALA0-0.060-0.02426.2320.5410.5410.0000.0000.0000.000
115P170LEU0-0.040-0.01926.7680.5270.5270.0000.0000.0000.000
116P171GLY0-0.0160.00628.9090.4590.4590.0000.0000.0000.000
117P172GLY00.0580.02327.1000.3690.3690.0000.0000.0000.000
118P173VAL0-0.046-0.04124.6330.2080.2080.0000.0000.0000.000
119P174LYS10.8510.91827.6409.4229.4220.0000.0000.0000.000
120P175PRO00.0170.00927.703-0.160-0.1600.0000.0000.0000.000
121P176ALA0-0.008-0.01128.7830.4140.4140.0000.0000.0000.000
122P177VAL0-0.031-0.00630.027-0.372-0.3720.0000.0000.0000.000
123P178LEU00.0140.01731.3100.2400.2400.0000.0000.0000.000
124P179THR00.004-0.01533.3880.1790.1790.0000.0000.0000.000
125P180ARG10.8360.88737.0287.6887.6880.0000.0000.0000.000
126P181SER0-0.047-0.04039.3020.0780.0780.0000.0000.0000.000
127P182GLY0-0.029-0.02235.9410.0240.0240.0000.0000.0000.000
128P183ASP-1-0.873-0.88635.704-8.159-8.1590.0000.0000.0000.000
129P184PRO00.0000.00433.823-0.104-0.1040.0000.0000.0000.000
130P185SER0-0.030-0.01734.9380.3190.3190.0000.0000.0000.000
131P186GLN00.002-0.01134.200-0.155-0.1550.0000.0000.0000.000
132P187PRO0-0.0180.00331.2380.1900.1900.0000.0000.0000.000
133P188LEU0-0.020-0.02334.3140.1800.1800.0000.0000.0000.000
134P189LEU0-0.063-0.02433.7930.2030.2030.0000.0000.0000.000
135P190PRO0-0.023-0.02233.702-0.147-0.1470.0000.0000.0000.000
136P191GLN0-0.012-0.01130.220-0.351-0.3510.0000.0000.0000.000
137P192HIS0-0.040-0.02226.7160.4920.4920.0000.0000.0000.000
138P193SER00.0730.04723.875-0.166-0.1660.0000.0000.0000.000
139P194SER0-0.010-0.00819.3550.2790.2790.0000.0000.0000.000
140P195LEU00.0550.01320.693-0.013-0.0130.0000.0000.0000.000
141P196GLU-1-0.785-0.86715.676-16.986-16.9860.0000.0000.0000.000
142P197THR0-0.006-0.02117.819-0.536-0.5360.0000.0000.0000.000
143P198GLN0-0.057-0.04820.0170.1510.1510.0000.0000.0000.000
144P199LEU0-0.0070.01718.8320.3340.3340.0000.0000.0000.000
145P200PHE0-0.088-0.05015.072-0.826-0.8260.0000.0000.0000.000
146P201CYS0-0.0360.00017.018-1.085-1.0850.0000.0000.0000.000
147P202GLU-1-0.950-0.95419.220-12.783-12.7830.0000.0000.0000.000
148P203GLN0-0.068-0.04217.656-0.301-0.3010.0000.0000.0000.000
149P204GLY0-0.017-0.00320.2370.8220.8220.0000.0000.0000.000
150P205ASP-1-0.958-0.96819.638-14.460-14.4600.0000.0000.0000.000
151P206GLY0-0.014-0.00716.874-0.114-0.1140.0000.0000.0000.000
152P207GLY00.005-0.00417.7770.4610.4610.0000.0000.0000.000
153P208THR0-0.077-0.02316.1410.9160.9160.0000.0000.0000.000
154P209GLU-1-0.828-0.91014.406-20.987-20.9870.0000.0000.0000.000
155P210GLY00.0360.02716.921-0.811-0.8110.0000.0000.0000.000
156P211HIS00.0410.01815.394-0.841-0.8410.0000.0000.0000.000
157P212SER0-0.031-0.04812.440-0.963-0.9630.0000.0000.0000.000
158P213PRO0-0.001-0.00310.801-2.794-2.7940.0000.0000.0000.000
159P214SER00.001-0.00510.043-2.647-2.6470.0000.0000.0000.000
160P215GLY00.0120.0128.816-1.371-1.3710.0000.0000.0000.000
161P216ILE0-0.046-0.0213.714-8.775-8.5260.003-0.052-0.1990.000
162P217LEU00.0440.0225.158-8.501-8.449-0.0010.001-0.0510.000
163P218GLU-1-0.920-0.9437.382-30.519-30.5190.0000.0000.0000.000
164P219LYS10.6990.8301.95339.11340.0432.121-1.125-1.928-0.016
165P220ILE00.0320.0222.631-17.362-14.9870.703-1.333-1.745-0.016
166P221PRO0-0.066-0.0292.5662.6713.5391.383-0.549-1.703-0.004
167P222PRO0-0.0060.0085.1671.2711.315-0.001-0.003-0.0390.000
168P223ASP-1-0.904-0.9438.231-19.508-19.5080.0000.0000.0000.000
169P224SER0-0.094-0.0605.508-1.858-1.8580.0000.0000.0000.000
170P225GLU-1-0.725-0.8167.571-17.869-17.8690.0000.0000.0000.000
171P226ALA0-0.001-0.0057.720-3.248-3.2480.0000.0000.0000.000
172P227THR0-0.042-0.0309.5652.2842.2840.0000.0000.0000.000
173P228LEU00.0170.01111.343-1.144-1.1440.0000.0000.0000.000
174P229VAL0-0.033-0.01513.2811.0341.0340.0000.0000.0000.000
175P230LEU00.0010.00916.018-0.030-0.0300.0000.0000.0000.000
176P231VAL00.0180.00619.3820.2760.2760.0000.0000.0000.000
177P232GLY00.017-0.00221.8790.0840.0840.0000.0000.0000.000
178P233ARG10.7600.86224.79812.13012.1300.0000.0000.0000.000
179P234ALA00.0170.00429.1470.0780.0780.0000.0000.0000.000
180P235ASP-1-0.792-0.89332.413-8.071-8.0710.0000.0000.0000.000
181P236PHE00.001-0.00333.9890.1750.1750.0000.0000.0000.000
182P237LEU0-0.0020.02930.1360.1700.1700.0000.0000.0000.000
183P238GLU-1-0.840-0.91734.130-7.898-7.8980.0000.0000.0000.000
184P239GLN00.0080.01431.285-0.092-0.0920.0000.0000.0000.000
185P240PRO00.0070.00526.976-0.074-0.0740.0000.0000.0000.000
186P241VAL0-0.0120.00426.6810.1770.1770.0000.0000.0000.000
187P242LEU0-0.0010.00419.166-0.381-0.3810.0000.0000.0000.000
188P243GLY00.0180.01922.3870.4640.4640.0000.0000.0000.000
189P244PHE0-0.039-0.03114.254-0.499-0.4990.0000.0000.0000.000
190P245VAL00.0130.00317.8780.7150.7150.0000.0000.0000.000
191P246ARG10.7690.84315.10813.07913.0790.0000.0000.0000.000
192P247LEU0-0.018-0.00316.9980.7470.7470.0000.0000.0000.000
193P248GLN0-0.042-0.02817.8540.0420.0420.0000.0000.0000.000
194P249GLU-1-0.862-0.93917.472-14.428-14.4280.0000.0000.0000.000
195P250ALA0-0.0470.00214.2570.1790.1790.0000.0000.0000.000
196P251ALA00.0140.00316.2280.4510.4510.0000.0000.0000.000
197P252GLU-1-0.933-0.96316.442-17.203-17.2030.0000.0000.0000.000
198P253LEU0-0.035-0.03017.2821.0481.0480.0000.0000.0000.000
199P254GLU-1-0.930-0.96818.241-12.928-12.9280.0000.0000.0000.000
200P255ALA0-0.016-0.00619.441-0.002-0.0020.0000.0000.0000.000
201P256VAL0-0.0100.00713.237-0.247-0.2470.0000.0000.0000.000
202P257GLU-1-0.827-0.90013.110-23.052-23.0520.0000.0000.0000.000
203P258LEU0-0.027-0.02510.7900.0990.0990.0000.0000.0000.000
204P259PRO0-0.0160.00614.2990.0290.0290.0000.0000.0000.000
205P260VAL00.0170.0019.006-1.008-1.0080.0000.0000.0000.000
206P261PRO00.003-0.00412.3510.5720.5720.0000.0000.0000.000
207P262ILE00.0020.01012.428-1.350-1.3500.0000.0000.0000.000
208P263ARG10.7780.87211.79117.38017.3800.0000.0000.0000.000
209P264PHE0-0.010-0.01610.6001.2161.2160.0000.0000.0000.000
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