FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 52Z6Z

Calculation Name: 4K51-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 4K51

Chain ID: A

ChEMBL ID:
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UniProt ID: P38249

Base Structure: X-ray

Registration Date: 2023-06-21

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2615627.048662
FMO2-HF: Nuclear repulsion 2529750.355613
FMO2-HF: Total energy -85876.693049
FMO2-MP2: Total energy -86132.222407


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:278:THR)


Summations of interaction energy for fragment #1(A:278:THR)
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.
-8.725-5.1336.573-3.563-6.6-0.029
Interaction energy analysis for fragmet #1(A:278:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.017
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].
3A280ALA00.0550.0271.892-1.342-0.6554.127-1.894-2.920-0.006
4A281ASN00.0390.0012.383-8.598-6.0312.445-1.644-3.368-0.023
5A282TYR00.0150.0213.8261.3531.6310.002-0.023-0.2560.000
6A283TYR00.0440.0015.8360.8650.8650.0000.0000.0000.000
7A284GLU-1-0.805-0.8846.875-2.621-2.6210.0000.0000.0000.000
8A285ASN0-0.028-0.0277.6150.4550.4550.0000.0000.0000.000
9A286LEU00.0010.0029.4820.2930.2930.0000.0000.0000.000
10A287VAL00.0000.01111.1730.1890.1890.0000.0000.0000.000
11A288LYS10.8660.92510.4391.6921.6920.0000.0000.0000.000
12A289VAL00.0200.01213.5850.1140.1140.0000.0000.0000.000
13A290PHE00.0250.00114.5540.0890.0890.0000.0000.0000.000
14A291PHE0-0.0370.00117.0810.0560.0560.0000.0000.0000.000
15A292VAL0-0.013-0.01718.1490.0450.0450.0000.0000.0000.000
16A293SER0-0.083-0.05019.2220.0450.0450.0000.0000.0000.000
17A294GLY00.0230.02921.7260.0340.0340.0000.0000.0000.000
18A295ASP-1-0.821-0.88620.882-0.221-0.2210.0000.0000.0000.000
19A296PRO00.033-0.00120.529-0.042-0.0420.0000.0000.0000.000
20A297LEU00.0520.02620.542-0.033-0.0330.0000.0000.0000.000
21A298LEU0-0.0050.00317.9200.0010.0010.0000.0000.0000.000
22A299HIS0-0.0100.02816.100-0.028-0.0280.0000.0000.0000.000
23A300THR00.0470.01715.754-0.067-0.0670.0000.0000.0000.000
24A301THR0-0.037-0.03615.7120.0050.0050.0000.0000.0000.000
25A302ALA0-0.016-0.02012.1370.0080.0080.0000.0000.0000.000
26A303TRP00.0120.00811.304-0.168-0.1680.0000.0000.0000.000
27A304LYS10.9010.94912.1690.2090.2090.0000.0000.0000.000
28A305LYS10.8430.93510.4150.1860.1860.0000.0000.0000.000
29A306PHE0-0.019-0.0026.1830.0140.0140.0000.0000.0000.000
30A307TYR00.014-0.0018.335-0.030-0.0300.0000.0000.0000.000
31A308LYS10.9010.95311.1500.2380.2380.0000.0000.0000.000
32A309LEU00.0010.0074.7030.0170.077-0.001-0.002-0.0560.000
33A310TYR00.0230.0257.8700.1750.1750.0000.0000.0000.000
34A311SER0-0.009-0.0188.7690.0570.0570.0000.0000.0000.000
35A312THR0-0.117-0.0628.8020.1280.1280.0000.0000.0000.000
36A313ASN0-0.044-0.0236.236-0.009-0.0090.0000.0000.0000.000
37A314PRO00.0580.0339.507-0.044-0.0440.0000.0000.0000.000
38A315ARG10.8370.9179.1470.2170.2170.0000.0000.0000.000
39A316ALA00.0330.02111.439-0.093-0.0930.0000.0000.0000.000
40A317THR00.0500.03713.1390.0730.0730.0000.0000.0000.000
41A318GLU-1-0.800-0.90315.580-0.251-0.2510.0000.0000.0000.000
42A319GLU-1-0.916-0.96717.635-0.392-0.3920.0000.0000.0000.000
43A320GLU-1-0.855-0.89713.021-0.869-0.8690.0000.0000.0000.000
44A321PHE00.0110.00913.234-0.030-0.0300.0000.0000.0000.000
45A322LYS10.9390.97516.4150.2550.2550.0000.0000.0000.000
46A323THR0-0.0090.01016.6490.0220.0220.0000.0000.0000.000
47A324TYR0-0.072-0.05610.713-0.070-0.0700.0000.0000.0000.000
48A325SER00.0200.01415.8270.0130.0130.0000.0000.0000.000
49A326SER0-0.011-0.01918.2560.0380.0380.0000.0000.0000.000
50A327THR0-0.027-0.03617.1190.0130.0130.0000.0000.0000.000
51A328ILE0-0.049-0.02214.4180.0160.0160.0000.0000.0000.000
52A329PHE00.015-0.00218.4830.0250.0250.0000.0000.0000.000
53A330LEU00.0460.03122.0740.0230.0230.0000.0000.0000.000
54A331SER00.0120.01819.9300.0030.0030.0000.0000.0000.000
55A332ALA0-0.044-0.00721.9020.0170.0170.0000.0000.0000.000
56A333ILE00.0210.01323.5650.0200.0200.0000.0000.0000.000
57A334SER0-0.083-0.04924.7570.0120.0120.0000.0000.0000.000
58A335THR0-0.038-0.02824.117-0.010-0.0100.0000.0000.0000.000
59A336GLN00.0310.01226.4450.0020.0020.0000.0000.0000.000
60A337LEU0-0.004-0.00829.1660.0000.0000.0000.0000.0000.000
61A338ASP-1-0.803-0.91629.212-0.148-0.1480.0000.0000.0000.000
62A339GLU-1-0.920-0.93730.960-0.129-0.1290.0000.0000.0000.000
63A340ILE00.005-0.01032.8500.0020.0020.0000.0000.0000.000
64A341PRO00.0080.02131.5990.0070.0070.0000.0000.0000.000
65A342SER0-0.028-0.03934.8940.0030.0030.0000.0000.0000.000
66A343ILE0-0.027-0.00936.4800.0050.0050.0000.0000.0000.000
67A344GLY00.0210.02535.1090.0040.0040.0000.0000.0000.000
68A345TYR0-0.043-0.02528.1830.0010.0010.0000.0000.0000.000
69A346ASP-1-0.715-0.85126.856-0.120-0.1200.0000.0000.0000.000
70A347PRO0-0.017-0.00225.8650.0130.0130.0000.0000.0000.000
71A348HIS10.8460.90522.6550.1680.1680.0000.0000.0000.000
72A349LEU00.0130.01621.913-0.002-0.0020.0000.0000.0000.000
73A350ARG10.9410.95319.0780.0180.0180.0000.0000.0000.000
74A351MET00.0430.03316.8940.0050.0050.0000.0000.0000.000
75A352TYR00.002-0.03517.813-0.025-0.0250.0000.0000.0000.000
76A353ARG10.9630.97818.864-0.098-0.0980.0000.0000.0000.000
77A354LEU0-0.033-0.00912.1180.0480.0480.0000.0000.0000.000
78A355LEU0-0.038-0.01413.380-0.005-0.0050.0000.0000.0000.000
79A356ASN0-0.114-0.06715.4720.0320.0320.0000.0000.0000.000
80A357LEU0-0.0020.02117.5960.0010.0010.0000.0000.0000.000
81A358ASP-1-0.892-0.94920.4250.0520.0520.0000.0000.0000.000
82A359ALA0-0.055-0.03223.7780.0060.0060.0000.0000.0000.000
83A360LYS10.9200.96624.2240.0860.0860.0000.0000.0000.000
84A361PRO0-0.0260.00522.0690.0050.0050.0000.0000.0000.000
85A362THR00.0300.00224.655-0.003-0.0030.0000.0000.0000.000
86A363ARG10.7610.84626.0080.1660.1660.0000.0000.0000.000
87A364LYS10.9210.95926.9390.0970.0970.0000.0000.0000.000
88A365GLU-1-0.871-0.93826.246-0.091-0.0910.0000.0000.0000.000
89A366MET0-0.0270.01320.780-0.007-0.0070.0000.0000.0000.000
90A367LEU00.0470.01823.318-0.009-0.0090.0000.0000.0000.000
91A368GLN0-0.031-0.01625.620-0.005-0.0050.0000.0000.0000.000
92A369SER0-0.052-0.04022.038-0.004-0.0040.0000.0000.0000.000
93A370ILE0-0.044-0.03220.031-0.005-0.0050.0000.0000.0000.000
94A371ILE0-0.0110.00322.332-0.001-0.0010.0000.0000.0000.000
95A372GLU-1-0.903-0.94325.472-0.079-0.0790.0000.0000.0000.000
96A373ASP-1-0.836-0.87218.810-0.142-0.1420.0000.0000.0000.000
97A374GLU-1-0.912-0.97221.984-0.145-0.1450.0000.0000.0000.000
98A375SER0-0.066-0.05117.675-0.021-0.0210.0000.0000.0000.000
99A376ILE0-0.019-0.00416.917-0.039-0.0390.0000.0000.0000.000
100A377TYR00.0850.02119.313-0.013-0.0130.0000.0000.0000.000
101A378GLY00.0400.03322.5500.0060.0060.0000.0000.0000.000
102A379LYS10.7350.84218.8700.2110.2110.0000.0000.0000.000
103A380VAL0-0.055-0.02121.807-0.028-0.0280.0000.0000.0000.000
104A381ASP-1-0.800-0.86023.295-0.262-0.2620.0000.0000.0000.000
105A382GLU-1-0.792-0.90125.875-0.162-0.1620.0000.0000.0000.000
106A383GLU-1-0.811-0.90028.894-0.209-0.2090.0000.0000.0000.000
107A384LEU0-0.005-0.00324.0620.0050.0050.0000.0000.0000.000
108A385LYS10.8080.91026.3390.1810.1810.0000.0000.0000.000
109A386GLU-1-0.813-0.90829.757-0.143-0.1430.0000.0000.0000.000
110A387LEU0-0.005-0.00728.8410.0060.0060.0000.0000.0000.000
111A388TYR0-0.003-0.01929.1990.0060.0060.0000.0000.0000.000
112A389ASP-1-0.863-0.92231.250-0.104-0.1040.0000.0000.0000.000
113A390ILE00.015-0.00534.6010.0060.0060.0000.0000.0000.000
114A391ILE0-0.047-0.03531.2820.0050.0050.0000.0000.0000.000
115A392GLU-1-0.844-0.87730.902-0.149-0.1490.0000.0000.0000.000
116A393VAL0-0.082-0.03034.2490.0070.0070.0000.0000.0000.000
117A394ASN0-0.093-0.04036.8050.0130.0130.0000.0000.0000.000
118A395PHE0-0.0040.00437.945-0.003-0.0030.0000.0000.0000.000
119A396ASP-1-0.803-0.91139.936-0.079-0.0790.0000.0000.0000.000
120A397VAL0-0.0040.00242.691-0.005-0.0050.0000.0000.0000.000
121A398ASP-1-0.901-0.94444.033-0.084-0.0840.0000.0000.0000.000
122A399THR0-0.031-0.04142.8290.0030.0030.0000.0000.0000.000
123A400VAL00.0020.01039.351-0.004-0.0040.0000.0000.0000.000
124A401LYS10.8100.90640.2870.1040.1040.0000.0000.0000.000
125A402GLN00.0540.02541.515-0.003-0.0030.0000.0000.0000.000
126A403GLN00.0030.02039.277-0.002-0.0020.0000.0000.0000.000
127A404LEU0-0.009-0.01434.906-0.006-0.0060.0000.0000.0000.000
128A405GLU-1-0.931-0.95736.929-0.130-0.1300.0000.0000.0000.000
129A406ASN00.021-0.01438.162-0.007-0.0070.0000.0000.0000.000
130A407LEU0-0.0260.00932.116-0.008-0.0080.0000.0000.0000.000
131A408LEU00.0530.01632.187-0.015-0.0150.0000.0000.0000.000
132A409VAL0-0.0150.01932.917-0.013-0.0130.0000.0000.0000.000
133A410LYS10.8380.92632.2130.1520.1520.0000.0000.0000.000
134A411LEU0-0.001-0.01527.819-0.015-0.0150.0000.0000.0000.000
135A412SER0-0.037-0.03228.240-0.024-0.0240.0000.0000.0000.000
136A413SER0-0.046-0.01428.7060.0010.0010.0000.0000.0000.000
137A414LYS10.7340.86824.4510.2440.2440.0000.0000.0000.000
138A415THR00.018-0.00420.5410.0050.0050.0000.0000.0000.000
139A416TYR0-0.032-0.04619.807-0.020-0.0200.0000.0000.0000.000
140A417PHE00.0280.00821.280-0.002-0.0020.0000.0000.0000.000
141A418SER00.0580.01924.5680.0010.0010.0000.0000.0000.000
142A419GLN0-0.046-0.01718.513-0.010-0.0100.0000.0000.0000.000
143A420TYR00.000-0.04218.732-0.016-0.0160.0000.0000.0000.000
144A421ILE00.0000.01825.1820.0240.0240.0000.0000.0000.000
145A422ALA0-0.019-0.01327.9370.0180.0180.0000.0000.0000.000
146A423PRO00.0290.02125.1660.0150.0150.0000.0000.0000.000
147A424LEU00.0310.00828.2570.0160.0160.0000.0000.0000.000
148A425ARG10.8580.92729.7320.2180.2180.0000.0000.0000.000
149A426ASP-1-0.854-0.92031.293-0.182-0.1820.0000.0000.0000.000
150A427VAL0-0.0280.00329.6740.0160.0160.0000.0000.0000.000
151A428ILE0-0.001-0.00232.9380.0140.0140.0000.0000.0000.000
152A429MET00.0330.02235.4820.0080.0080.0000.0000.0000.000
153A430ARG10.8090.89435.0150.1510.1510.0000.0000.0000.000
154A431ARG10.8640.91433.5620.1390.1390.0000.0000.0000.000
155A432VAL0-0.001-0.00938.3970.0080.0080.0000.0000.0000.000
156A433PHE00.0200.00239.8170.0080.0080.0000.0000.0000.000
157A434VAL00.0190.01940.0760.0060.0060.0000.0000.0000.000
158A435ALA00.0210.03442.4980.0060.0060.0000.0000.0000.000
159A436ALA0-0.001-0.00644.2980.0050.0050.0000.0000.0000.000
160A437SER0-0.116-0.08545.3610.0050.0050.0000.0000.0000.000
161A438GLN0-0.022-0.01243.9640.0050.0050.0000.0000.0000.000
162A439LYS10.8080.92548.7900.0810.0810.0000.0000.0000.000
163A440PHE0-0.018-0.02549.1140.0030.0030.0000.0000.0000.000
164A441THR00.0200.02952.0910.0010.0010.0000.0000.0000.000
165A442THR0-0.007-0.01653.956-0.001-0.0010.0000.0000.0000.000
166A443VAL0-0.0080.02051.1040.0020.0020.0000.0000.0000.000
167A444SER00.0110.01253.563-0.002-0.0020.0000.0000.0000.000
168A445GLN00.0670.01949.7820.0010.0010.0000.0000.0000.000
169A446SER0-0.0200.00049.926-0.004-0.0040.0000.0000.0000.000
170A447GLU-1-0.968-0.99550.615-0.076-0.0760.0000.0000.0000.000
171A448LEU00.0220.01446.889-0.003-0.0030.0000.0000.0000.000
172A449TYR0-0.016-0.07145.785-0.004-0.0040.0000.0000.0000.000
173A450LYS10.9531.00945.4010.0880.0880.0000.0000.0000.000
174A451LEU0-0.034-0.01445.606-0.004-0.0040.0000.0000.0000.000
175A452ALA00.0390.01742.246-0.003-0.0030.0000.0000.0000.000
176A453THR0-0.042-0.03341.238-0.007-0.0070.0000.0000.0000.000
177A454LEU0-0.051-0.01836.4870.0040.0040.0000.0000.0000.000
178A455PRO00.0130.01238.317-0.001-0.0010.0000.0000.0000.000
179A456ALA00.026-0.01636.391-0.008-0.0080.0000.0000.0000.000
180A457PRO00.0150.02932.3870.0020.0020.0000.0000.0000.000
181A458LEU0-0.089-0.04931.973-0.009-0.0090.0000.0000.0000.000
182A459ASP-1-0.926-0.94435.351-0.152-0.1520.0000.0000.0000.000
183A460LEU00.000-0.00836.000-0.007-0.0070.0000.0000.0000.000
184A461SER00.0330.01739.5040.0090.0090.0000.0000.0000.000
185A462ALA00.025-0.00742.459-0.001-0.0010.0000.0000.0000.000
186A463TRP00.0200.01241.2570.0070.0070.0000.0000.0000.000
187A464ASP-1-0.866-0.94338.673-0.151-0.1510.0000.0000.0000.000
188A465ILE0-0.034-0.00840.093-0.002-0.0020.0000.0000.0000.000
189A466GLU-1-0.788-0.85641.926-0.094-0.0940.0000.0000.0000.000
190A467LYS10.9520.96937.2660.1510.1510.0000.0000.0000.000
191A468SER00.003-0.00236.9550.0020.0020.0000.0000.0000.000
192A469LEU0-0.0040.00439.0580.0010.0010.0000.0000.0000.000
193A470LEU0-0.018-0.02442.0700.0040.0040.0000.0000.0000.000
194A471GLN0-0.082-0.03935.1480.0050.0050.0000.0000.0000.000
195A472ALA00.009-0.01038.5300.0010.0010.0000.0000.0000.000
196A473ALA0-0.044-0.01539.4630.0040.0040.0000.0000.0000.000
197A474VAL0-0.0130.00538.3580.0040.0040.0000.0000.0000.000
198A475GLU-1-0.847-0.87634.642-0.147-0.1470.0000.0000.0000.000
199A476ASP-1-0.965-0.98238.352-0.076-0.0760.0000.0000.0000.000
200A477TYR0-0.038-0.02134.6240.0000.0000.0000.0000.0000.000
201A478VAL0-0.001-0.01440.8730.0020.0020.0000.0000.0000.000
202A479SER0-0.0030.00544.1910.0020.0020.0000.0000.0000.000
203A480ILE00.0130.01045.6490.0020.0020.0000.0000.0000.000
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