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: 2JMLR

Calculation Name: 4PK1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PK1

Chain ID: A

ChEMBL ID:

UniProt ID: P0A940

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 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 494
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -8854247.705245
FMO2-HF: Nuclear repulsion 8667404.69442
FMO2-HF: Total energy -186843.010825
FMO2-MP2: Total energy -187394.409245


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:176:GLU)


Summations of interaction energy for fragment #1(A:176:GLU)
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.
99.19885.84845.847-16.123-16.3730.06
Interaction energy analysis for fragmet #1(A:176:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.907 / q_NPA : -0.956
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].
3A178GLN00.0160.0031.847-21.972-20.6078.099-4.708-4.7550.048
4A179GLN0-0.021-0.0044.814-3.686-3.558-0.001-0.005-0.1220.000
5A180ILE0-0.014-0.0038.076-0.310-0.3100.0000.0000.0000.000
6A181ASN0-0.078-0.05810.725-0.655-0.6550.0000.0000.0000.000
7A182ILE00.0160.01414.191-0.358-0.3580.0000.0000.0000.000
8A183VAL0-0.0160.00117.733-0.272-0.2720.0000.0000.0000.000
9A184GLY00.0140.00020.581-0.349-0.3490.0000.0000.0000.000
10A185ASN0-0.068-0.03820.212-0.019-0.0190.0000.0000.0000.000
11A186HIS00.0420.00623.6100.3110.3110.0000.0000.0000.000
12A187ALA0-0.057-0.01526.492-0.212-0.2120.0000.0000.0000.000
13A188PHE0-0.024-0.02423.558-0.286-0.2860.0000.0000.0000.000
14A189THR00.0350.02820.6990.2610.2610.0000.0000.0000.000
15A190THR00.0840.02116.1990.0750.0750.0000.0000.0000.000
16A191ASP-1-0.956-0.98815.11118.83418.8340.0000.0000.0000.000
17A192GLU-1-0.940-0.96816.40213.72413.7240.0000.0000.0000.000
18A193LEU0-0.0150.01418.897-0.064-0.0640.0000.0000.0000.000
19A194ILE00.0060.00512.4600.1750.1750.0000.0000.0000.000
20A195SER0-0.036-0.02014.6500.2940.2940.0000.0000.0000.000
21A196HIS0-0.068-0.04315.700-0.687-0.6870.0000.0000.0000.000
22A197PHE0-0.031-0.01612.635-0.286-0.2860.0000.0000.0000.000
23A198GLN0-0.055-0.03612.3000.2660.2660.0000.0000.0000.000
24A199LEU00.006-0.0158.6040.5770.5770.0000.0000.0000.000
25A200ARG10.8260.9334.949-36.113-36.1130.0000.0000.0000.000
26A201ASP-1-0.903-0.9535.19130.08730.229-0.001-0.005-0.1360.000
27A202GLU-1-0.979-0.9701.99940.93435.72513.040-3.699-4.132-0.029
28A215GLN00.037-0.0034.938-2.134-2.1340.0000.0000.0000.000
29A216LYS10.9500.9739.170-17.103-17.1030.0000.0000.0000.000
30A217GLN00.0210.00911.959-0.140-0.1400.0000.0000.0000.000
31A218LYS10.8440.90311.109-17.721-17.7210.0000.0000.0000.000
32A219LEU00.0580.04610.637-0.325-0.3250.0000.0000.0000.000
33A220ALA00.0250.01113.176-0.540-0.5400.0000.0000.0000.000
34A221GLY00.0030.00416.000-0.608-0.6080.0000.0000.0000.000
35A222ASP-1-0.725-0.86514.34416.79416.7940.0000.0000.0000.000
36A223LEU00.0020.01016.449-0.302-0.3020.0000.0000.0000.000
37A224GLU-1-0.882-0.93018.37710.94810.9480.0000.0000.0000.000
38A225THR0-0.0120.00518.416-0.533-0.5330.0000.0000.0000.000
39A226LEU0-0.0040.00118.343-0.418-0.4180.0000.0000.0000.000
40A227ARG10.8920.92620.797-12.244-12.2440.0000.0000.0000.000
41A228SER0-0.0310.00223.807-0.480-0.4800.0000.0000.0000.000
42A229TYR0-0.010-0.00222.529-0.629-0.6290.0000.0000.0000.000
43A230TYR00.011-0.03823.037-0.220-0.2200.0000.0000.0000.000
44A231LEU0-0.0030.00127.139-0.478-0.4780.0000.0000.0000.000
45A232ASP-1-0.807-0.85627.4329.8539.8530.0000.0000.0000.000
46A233ARG10.8110.90525.868-11.193-11.1930.0000.0000.0000.000
47A234GLY00.0190.01031.165-0.118-0.1180.0000.0000.0000.000
48A235TYR00.0020.01529.786-0.215-0.2150.0000.0000.0000.000
49A236ALA0-0.017-0.01030.8680.2230.2230.0000.0000.0000.000
50A237ARG10.8520.89232.819-8.049-8.0490.0000.0000.0000.000
51A238PHE00.0250.02923.2830.0190.0190.0000.0000.0000.000
52A239ASN0-0.045-0.03127.314-0.129-0.1290.0000.0000.0000.000
53A240ILE0-0.018-0.00920.5060.2930.2930.0000.0000.0000.000
54A241ASP-1-0.839-0.86923.81410.98310.9830.0000.0000.0000.000
55A242SER0-0.016-0.02520.489-0.216-0.2160.0000.0000.0000.000
56A243THR0-0.035-0.01615.1820.4250.4250.0000.0000.0000.000
57A244GLN00.0200.02115.425-0.025-0.0250.0000.0000.0000.000
58A245VAL0-0.018-0.0139.5260.8800.8800.0000.0000.0000.000
59A246SER00.004-0.00410.568-1.128-1.1280.0000.0000.0000.000
60A247LEU0-0.025-0.0056.5462.1932.1930.0000.0000.0000.000
61A248THR00.003-0.0027.236-2.046-2.0460.0000.0000.0000.000
62A249PRO00.0470.0169.5970.0690.0690.0000.0000.0000.000
63A250ASP-1-0.849-0.8957.24037.90637.9060.0000.0000.0000.000
64A251LYS10.9010.9458.757-19.819-19.8190.0000.0000.0000.000
65A252LYS10.8480.8921.868-82.486-93.51424.698-7.390-6.2810.041
66A253GLY00.1220.0733.5558.0708.6680.007-0.165-0.4390.000
67A254ILE0-0.085-0.0373.682-5.230-4.5760.005-0.151-0.5080.000
68A255TYR00.041-0.0015.7233.7323.7320.0000.0000.0000.000
69A256VAL0-0.025-0.0018.860-1.910-1.9100.0000.0000.0000.000
70A257THR00.000-0.00911.4320.6050.6050.0000.0000.0000.000
71A258VAL0-0.040-0.02814.857-0.654-0.6540.0000.0000.0000.000
72A259ASN0-0.043-0.02617.671-0.402-0.4020.0000.0000.0000.000
73A260ILE0-0.010-0.00721.029-0.286-0.2860.0000.0000.0000.000
74A261THR0-0.002-0.04223.631-0.154-0.1540.0000.0000.0000.000
75A262GLU-1-0.798-0.85725.93511.19711.1970.0000.0000.0000.000
76A263GLY00.0260.02828.265-0.277-0.2770.0000.0000.0000.000
77A264ASP-1-0.794-0.89131.6388.4548.4540.0000.0000.0000.000
78A265GLN0-0.081-0.04733.079-0.129-0.1290.0000.0000.0000.000
79A266TYR0-0.049-0.05135.177-0.240-0.2400.0000.0000.0000.000
80A267LYS10.9230.96137.341-7.534-7.5340.0000.0000.0000.000
81A268LEU0-0.006-0.00539.053-0.014-0.0140.0000.0000.0000.000
82A269SER00.002-0.00641.471-0.121-0.1210.0000.0000.0000.000
83A270GLY0-0.019-0.01644.120-0.183-0.1830.0000.0000.0000.000
84A271VAL0-0.020-0.01142.8810.1700.1700.0000.0000.0000.000
85A272GLU-1-0.857-0.91344.9676.1596.1590.0000.0000.0000.000
86A273VAL00.0390.00944.9670.1480.1480.0000.0000.0000.000
87A274SER0-0.049-0.02246.168-0.148-0.1480.0000.0000.0000.000
88A275GLY00.0690.03046.6490.1090.1090.0000.0000.0000.000
89A276ASN0-0.098-0.04648.175-0.157-0.1570.0000.0000.0000.000
90A277LEU00.0160.03546.5830.0590.0590.0000.0000.0000.000
91A278ALA00.012-0.02449.4200.0180.0180.0000.0000.0000.000
92A279GLY0-0.012-0.01152.375-0.073-0.0730.0000.0000.0000.000
93A280HIS00.0000.00850.049-0.043-0.0430.0000.0000.0000.000
94A281SER0-0.023-0.02150.5280.0730.0730.0000.0000.0000.000
95A282ALA00.0590.04051.3010.0350.0350.0000.0000.0000.000
96A283GLU-1-0.920-0.97950.3285.8895.8890.0000.0000.0000.000
97A284ILE0-0.055-0.03544.9670.1070.1070.0000.0000.0000.000
98A285GLU-1-0.955-0.96046.2466.0186.0180.0000.0000.0000.000
99A286GLN0-0.075-0.02046.8230.0600.0600.0000.0000.0000.000
100A294GLU-1-0.910-0.96839.9377.2257.2250.0000.0000.0000.000
101A295LEU0-0.069-0.02934.307-0.074-0.0740.0000.0000.0000.000
102A296TYR00.0530.03232.8000.0710.0710.0000.0000.0000.000
103A297ASN00.0170.00932.7550.2850.2850.0000.0000.0000.000
104A298GLY00.0680.01230.825-0.177-0.1770.0000.0000.0000.000
105A299THR0-0.002-0.02028.193-0.223-0.2230.0000.0000.0000.000
106A300LYS10.8900.93430.877-8.921-8.9210.0000.0000.0000.000
107A301VAL00.0370.03134.467-0.223-0.2230.0000.0000.0000.000
108A302THR00.0310.01130.642-0.120-0.1200.0000.0000.0000.000
109A303LYS10.8450.91833.334-8.080-8.0800.0000.0000.0000.000
110A304MET0-0.044-0.03234.437-0.192-0.1920.0000.0000.0000.000
111A305GLU-1-0.812-0.90034.7698.0828.0820.0000.0000.0000.000
112A306ASP-1-0.825-0.90732.6438.5318.5310.0000.0000.0000.000
113A307ASP-1-0.876-0.92036.2757.6097.6090.0000.0000.0000.000
114A308ILE0-0.018-0.00639.463-0.211-0.2110.0000.0000.0000.000
115A309LYS10.8040.89433.699-8.509-8.5090.0000.0000.0000.000
116A310LYS10.9190.96237.188-7.816-7.8160.0000.0000.0000.000
117A311LEU0-0.062-0.02340.295-0.134-0.1340.0000.0000.0000.000
118A312LEU00.0440.00443.756-0.153-0.1530.0000.0000.0000.000
119A313GLY00.0490.02442.209-0.092-0.0920.0000.0000.0000.000
120A314ARG10.8770.93643.196-6.668-6.6680.0000.0000.0000.000
121A315TYR0-0.076-0.02745.820-0.120-0.1200.0000.0000.0000.000
122A316GLY00.0250.02246.570-0.108-0.1080.0000.0000.0000.000
123A317TYR0-0.054-0.03345.0680.0470.0470.0000.0000.0000.000
124A318ALA0-0.019-0.00841.8100.1260.1260.0000.0000.0000.000
125A319TYR0-0.037-0.03037.2350.0810.0810.0000.0000.0000.000
126A320PRO0-0.0150.01540.283-0.076-0.0760.0000.0000.0000.000
127A321ARG10.8950.94037.447-7.127-7.1270.0000.0000.0000.000
128A322VAL00.0210.01337.844-0.156-0.1560.0000.0000.0000.000
129A323GLN0-0.006-0.00834.7510.3200.3200.0000.0000.0000.000
130A324SER0-0.034-0.03537.227-0.275-0.2750.0000.0000.0000.000
131A325MET0-0.072-0.01536.7510.1810.1810.0000.0000.0000.000
132A326PRO00.009-0.01935.208-0.194-0.1940.0000.0000.0000.000
133A327GLU-1-0.853-0.90838.5516.6826.6820.0000.0000.0000.000
134A328ILE0-0.034-0.01536.432-0.017-0.0170.0000.0000.0000.000
135A329ASN0-0.0010.00041.031-0.068-0.0680.0000.0000.0000.000
136A330ASP-1-0.793-0.88138.9727.8377.8370.0000.0000.0000.000
137A331ALA0-0.059-0.01241.8340.0220.0220.0000.0000.0000.000
138A332ASP-1-0.843-0.90845.2856.7236.7230.0000.0000.0000.000
139A333LYS10.8000.91038.027-7.943-7.9430.0000.0000.0000.000
140A334THR0-0.053-0.04141.5290.0510.0510.0000.0000.0000.000
141A335VAL0-0.014-0.01637.4150.0090.0090.0000.0000.0000.000
142A336LYS10.8770.94440.898-6.445-6.4450.0000.0000.0000.000
143A337LEU00.0140.01038.1050.1010.1010.0000.0000.0000.000
144A338ARG10.8560.92141.494-6.727-6.7270.0000.0000.0000.000
145A339VAL00.008-0.00640.7010.1670.1670.0000.0000.0000.000
146A340ASN00.0160.01142.582-0.223-0.2230.0000.0000.0000.000
147A341VAL00.0280.00942.3770.1750.1750.0000.0000.0000.000
148A342ASP-1-0.903-0.94442.4986.7196.7190.0000.0000.0000.000
149A343ALA00.0350.02644.0110.1080.1080.0000.0000.0000.000
150A344GLY0-0.002-0.01344.9920.0420.0420.0000.0000.0000.000
151A345ASN0-0.054-0.04545.714-0.126-0.1260.0000.0000.0000.000
152A346ARG10.9971.02444.040-6.587-6.5870.0000.0000.0000.000
153A1032MET0-0.0240.00013.2430.0570.0570.0000.0000.0000.000
154A1033SER0-0.082-0.05015.298-0.678-0.6780.0000.0000.0000.000
155A1034PRO0-0.021-0.02218.9550.3100.3100.0000.0000.0000.000
156A1035LEU00.0280.02220.713-0.081-0.0810.0000.0000.0000.000
157A1036PRO00.0150.03922.676-0.280-0.2800.0000.0000.0000.000
158A1037THR0-0.002-0.02026.244-0.009-0.0090.0000.0000.0000.000
159A1038VAL0-0.022-0.02428.665-0.105-0.1050.0000.0000.0000.000
160A1039GLU-1-0.974-0.96331.3958.6408.6400.0000.0000.0000.000
161A1040ASN0-0.063-0.03232.6980.0580.0580.0000.0000.0000.000
162A1041GLN0-0.0090.01234.814-0.028-0.0280.0000.0000.0000.000
163A1042PHE0-0.012-0.01832.506-0.136-0.1360.0000.0000.0000.000
164A1043THR00.0240.00633.7970.2060.2060.0000.0000.0000.000
165A1044PRO0-0.0510.00030.136-0.202-0.2020.0000.0000.0000.000
166A1045THR00.003-0.01631.4620.1710.1710.0000.0000.0000.000
167A1046THR00.0320.01627.806-0.022-0.0220.0000.0000.0000.000
168A1047ALA0-0.039-0.00630.499-0.248-0.2480.0000.0000.0000.000
169A1048TRP0-0.021-0.01627.964-0.068-0.0680.0000.0000.0000.000
170A1049SER0-0.001-0.01526.2080.3160.3160.0000.0000.0000.000
171A1050THR0-0.043-0.03626.751-0.313-0.3130.0000.0000.0000.000
172A1051SER00.0110.01322.7480.3070.3070.0000.0000.0000.000
173A1052VAL00.029-0.00222.088-0.692-0.6920.0000.0000.0000.000
174A1053GLY0-0.0020.00620.7860.5450.5450.0000.0000.0000.000
175A1054SER0-0.066-0.03915.1440.0570.0570.0000.0000.0000.000
176A1055GLY00.0560.04015.3741.1751.1750.0000.0000.0000.000
177A1056ILE0-0.052-0.01712.6620.0980.0980.0000.0000.0000.000
178A1057GLY00.0330.02310.8601.7491.7490.0000.0000.0000.000
179A1058ASN0-0.012-0.0305.979-3.785-3.7850.0000.0000.0000.000
180A1059PHE0-0.048-0.0097.7802.2402.2400.0000.0000.0000.000
181A1060TYR00.0500.0129.110-2.038-2.0380.0000.0000.0000.000
182A1061SER00.0020.01610.974-1.717-1.7170.0000.0000.0000.000
183A1062ASN0-0.018-0.02814.421-0.163-0.1630.0000.0000.0000.000
184A1063LEU0-0.0580.00417.778-0.860-0.8600.0000.0000.0000.000
185A1064HIS10.8300.89519.132-13.021-13.0210.0000.0000.0000.000
186A1065PRO00.0190.00421.818-0.420-0.4200.0000.0000.0000.000
187A1066ALA00.0240.03025.1750.0210.0210.0000.0000.0000.000
188A1067LEU0-0.0070.00428.435-0.036-0.0360.0000.0000.0000.000
189A1068ALA00.0190.00631.944-0.021-0.0210.0000.0000.0000.000
190A1069ASP-1-0.945-0.96835.2818.0548.0540.0000.0000.0000.000
191A1070ASN0-0.058-0.04936.729-0.152-0.1520.0000.0000.0000.000
192A1071VAL0-0.028-0.01133.5070.0030.0030.0000.0000.0000.000
193A1072VAL0-0.003-0.02127.9690.1210.1210.0000.0000.0000.000
194A1073TYR00.0330.01228.585-0.070-0.0700.0000.0000.0000.000
195A1074ALA00.0000.00823.4940.2950.2950.0000.0000.0000.000
196A1075ALA00.019-0.00522.260-0.454-0.4540.0000.0000.0000.000
197A1076ASP-1-0.811-0.90217.98617.34917.3490.0000.0000.0000.000
198A1077ARG10.8440.90012.003-23.345-23.3450.0000.0000.0000.000
199A1078ALA0-0.019-0.01617.215-0.198-0.1980.0000.0000.0000.000
200A1079GLY00.0450.00218.858-0.488-0.4880.0000.0000.0000.000
201A1080LEU0-0.073-0.01922.157-0.584-0.5840.0000.0000.0000.000
202A1081VAL00.0230.01523.4060.4360.4360.0000.0000.0000.000
203A1082LYS10.8170.89325.788-12.094-12.0940.0000.0000.0000.000
204A1083ALA00.0390.03028.1920.1620.1620.0000.0000.0000.000
205A1084LEU0-0.018-0.02527.617-0.223-0.2230.0000.0000.0000.000
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