Manual

About

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: 94Q42

Calculation Name: 1PKQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PKQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q63345

Base Structure: X-ray

Registration Date: 2023-06-26

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2203339.592921
FMO2-HF: Nuclear repulsion 2119810.350187
FMO2-HF: Total energy -83529.242734
FMO2-MP2: Total energy -83773.861173


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:1:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
7.29413.812.336-3.454-5.3980.026
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.919 / q_NPA : -0.967
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].
3A3GLU-1-0.942-0.9523.77634.57437.091-0.016-1.141-1.3600.006
4A4LEU00.003-0.0305.679-3.238-3.2380.0000.0000.0000.000
5A5THR00.0070.0049.102-0.601-0.6010.0000.0000.0000.000
6A6GLN00.0020.00112.2400.1640.1640.0000.0000.0000.000
7A7SER0-0.0140.00015.297-0.467-0.4670.0000.0000.0000.000
8A8PRO00.0730.01318.779-0.064-0.0640.0000.0000.0000.000
9A9SER00.0320.04819.1180.2000.2000.0000.0000.0000.000
10A10SER0-0.015-0.01520.121-0.001-0.0010.0000.0000.0000.000
11A11LEU0-0.0110.00223.301-0.208-0.2080.0000.0000.0000.000
12A12ALA00.0280.02026.5080.0140.0140.0000.0000.0000.000
13A13VAL0-0.026-0.00829.441-0.104-0.1040.0000.0000.0000.000
14A14SER00.0160.00532.188-0.077-0.0770.0000.0000.0000.000
15A15ALA0-0.009-0.02234.7160.1530.1530.0000.0000.0000.000
16A16GLY00.0200.00235.257-0.212-0.2120.0000.0000.0000.000
17A17GLU-1-0.874-0.92933.3978.7008.7000.0000.0000.0000.000
18A18LYS10.9701.00129.310-9.758-9.7580.0000.0000.0000.000
19A19VAL0-0.030-0.00425.8230.0130.0130.0000.0000.0000.000
20A20THR0-0.021-0.03323.804-0.097-0.0970.0000.0000.0000.000
21A21MET0-0.047-0.01920.1890.1890.1890.0000.0000.0000.000
22A22SER0-0.003-0.00317.9480.3130.3130.0000.0000.0000.000
23A23CYS0-0.063-0.01413.0290.3620.3620.0000.0000.0000.000
24A24LYS10.8760.95513.684-15.603-15.6030.0000.0000.0000.000
25A25SER00.008-0.0229.1531.8611.8610.0000.0000.0000.000
26A26SER00.0390.0195.574-1.249-1.2490.0000.0000.0000.000
27A27GLN00.0450.0233.902-5.296-4.9100.003-0.102-0.2860.000
28A28SER00.0020.0308.643-1.708-1.7080.0000.0000.0000.000
29A29LEU00.0550.0268.0861.4241.4240.0000.0000.0000.000
30A30LEU0-0.083-0.00811.224-1.407-1.4070.0000.0000.0000.000
31A30ASN00.0500.04213.853-0.106-0.1060.0000.0000.0000.000
32A30SER00.046-0.01715.349-0.528-0.5280.0000.0000.0000.000
33A30GLY00.0130.01818.159-0.751-0.7510.0000.0000.0000.000
34A30ASN0-0.079-0.03718.1960.1530.1530.0000.0000.0000.000
35A30GLN0-0.012-0.01119.366-0.681-0.6810.0000.0000.0000.000
36A30LYS10.9840.98118.289-13.705-13.7050.0000.0000.0000.000
37A31ASN00.027-0.00115.047-0.133-0.1330.0000.0000.0000.000
38A32TYR00.0130.00012.628-0.970-0.9700.0000.0000.0000.000
39A33LEU00.0090.01511.8871.6551.6550.0000.0000.0000.000
40A34ALA00.0240.01313.697-1.445-1.4450.0000.0000.0000.000
41A35TRP00.0130.00815.0610.9450.9450.0000.0000.0000.000
42A36TYR0-0.010-0.04014.834-1.224-1.2240.0000.0000.0000.000
43A37GLN0-0.050-0.02918.779-0.056-0.0560.0000.0000.0000.000
44A38GLN00.0300.00319.5540.3590.3590.0000.0000.0000.000
45A39LYS10.9010.95722.083-10.659-10.6590.0000.0000.0000.000
46A40PRO00.047-0.00224.9240.3240.3240.0000.0000.0000.000
47A41GLY00.0130.01625.647-0.404-0.4040.0000.0000.0000.000
48A42LEU0-0.0290.00125.942-0.048-0.0480.0000.0000.0000.000
49A43PRO00.010-0.00621.9500.4200.4200.0000.0000.0000.000
50A44PRO0-0.034-0.01517.758-0.454-0.4540.0000.0000.0000.000
51A45LYS10.9660.99320.579-11.506-11.5060.0000.0000.0000.000
52A46LEU00.0300.03618.4980.4680.4680.0000.0000.0000.000
53A47LEU0-0.064-0.03120.852-0.709-0.7090.0000.0000.0000.000
54A48ILE00.006-0.00919.645-0.572-0.5720.0000.0000.0000.000
55A49TYR00.0860.04317.8530.7650.7650.0000.0000.0000.000
56A50GLY0-0.003-0.00916.966-0.680-0.6800.0000.0000.0000.000
57A51ALA0-0.020-0.00416.813-0.514-0.5140.0000.0000.0000.000
58A52SER0-0.076-0.05218.091-0.331-0.3310.0000.0000.0000.000
59A53THR0-0.0260.00321.780-0.726-0.7260.0000.0000.0000.000
60A54ARG10.8590.95122.716-10.042-10.0420.0000.0000.0000.000
61A55GLU-1-0.842-0.90723.58912.36212.3620.0000.0000.0000.000
62A56SER00.002-0.01625.369-0.535-0.5350.0000.0000.0000.000
63A57GLY0-0.043-0.01428.5330.1700.1700.0000.0000.0000.000
64A58VAL0-0.077-0.03125.549-0.233-0.2330.0000.0000.0000.000
65A59PRO00.009-0.00628.883-0.108-0.1080.0000.0000.0000.000
66A60ASP-1-0.805-0.92229.6829.4939.4930.0000.0000.0000.000
67A61ARG10.7160.83130.146-9.602-9.6020.0000.0000.0000.000
68A62PHE0-0.0220.01025.0960.2040.2040.0000.0000.0000.000
69A63THR00.000-0.02025.906-0.204-0.2040.0000.0000.0000.000
70A64GLY00.0210.00521.7410.1380.1380.0000.0000.0000.000
71A65SER0-0.0330.00422.149-0.196-0.1960.0000.0000.0000.000
72A66GLY00.0670.01219.3710.5090.5090.0000.0000.0000.000
73A67SER0-0.038-0.01317.519-0.282-0.2820.0000.0000.0000.000
74A68GLY0-0.0060.01216.336-0.193-0.1930.0000.0000.0000.000
75A69THR0-0.024-0.01811.4120.6350.6350.0000.0000.0000.000
76A70ASP-1-0.891-0.93913.82517.58817.5880.0000.0000.0000.000
77A71PHE00.012-0.00613.458-0.746-0.7460.0000.0000.0000.000
78A72THR0-0.077-0.03617.911-0.194-0.1940.0000.0000.0000.000
79A73LEU00.0170.02120.396-0.263-0.2630.0000.0000.0000.000
80A74THR0-0.009-0.01621.984-0.320-0.3200.0000.0000.0000.000
81A75ILE0-0.0140.00125.714-0.066-0.0660.0000.0000.0000.000
82A76SER0-0.012-0.00928.272-0.159-0.1590.0000.0000.0000.000
83A77SER0-0.019-0.00531.676-0.188-0.1880.0000.0000.0000.000
84A78VAL0-0.014-0.00829.8350.0240.0240.0000.0000.0000.000
85A79GLN00.0100.01631.776-0.609-0.6090.0000.0000.0000.000
86A80ALA00.0520.02832.3100.2340.2340.0000.0000.0000.000
87A81GLU-1-0.910-0.96532.0269.2109.2100.0000.0000.0000.000
88A82ASP-1-0.787-0.85628.51310.42010.4200.0000.0000.0000.000
89A83LEU00.0040.03127.4160.4890.4890.0000.0000.0000.000
90A84ALA0-0.056-0.04524.143-0.016-0.0160.0000.0000.0000.000
91A85VAL0-0.0250.00818.755-0.140-0.1400.0000.0000.0000.000
92A86TYR0-0.003-0.01419.5080.0560.0560.0000.0000.0000.000
93A87TYR00.0320.03614.2430.3210.3210.0000.0000.0000.000
94A89GLN00.012-0.01010.197-0.538-0.5380.0000.0000.0000.000
95A90ASN00.0330.0265.176-5.325-5.3250.0000.0000.0000.000
96A91ASP-1-0.900-0.9718.87722.69822.6980.0000.0000.0000.000
97A92HIS0-0.031-0.0138.722-0.545-0.5450.0000.0000.0000.000
98A93SER00.0050.0075.108-0.647-0.6470.0000.0000.0000.000
99A94TYR0-0.079-0.0105.7081.0651.0650.0000.0000.0000.000
100A95PRO00.0140.0112.422-7.220-4.1062.331-2.134-3.3110.020
101A96LEU00.0450.0024.4542.1212.240-0.001-0.012-0.1070.000
102A97THR0-0.027-0.0233.256-0.0800.3000.019-0.065-0.3340.000
103A98PHE00.011-0.0026.646-3.044-3.0440.0000.0000.0000.000
104A99GLY00.0230.0138.8791.4571.4570.0000.0000.0000.000
105A100ALA0-0.032-0.02511.057-0.260-0.2600.0000.0000.0000.000
106A101GLY00.002-0.01113.265-0.930-0.9300.0000.0000.0000.000
107A102THR0-0.075-0.04816.2010.0410.0410.0000.0000.0000.000
108A103LYS10.8540.93919.511-11.843-11.8430.0000.0000.0000.000
109A104LEU0-0.022-0.01822.542-0.184-0.1840.0000.0000.0000.000
110A105GLU-1-0.845-0.93325.68810.63810.6380.0000.0000.0000.000
111A106ILE0-0.028-0.01028.997-0.054-0.0540.0000.0000.0000.000
112A107LYS10.9220.98032.331-9.117-9.1170.0000.0000.0000.000
113A108ARG10.8670.92235.023-7.706-7.7060.0000.0000.0000.000
114A109THR0-0.016-0.00638.706-0.010-0.0100.0000.0000.0000.000
115A110VAL0-0.012-0.00641.6250.1150.1150.0000.0000.0000.000
116A111ALA0-0.024-0.01142.998-0.122-0.1220.0000.0000.0000.000
117A112ALA0-0.0010.00444.1030.1300.1300.0000.0000.0000.000
118A113PRO00.0240.01443.958-0.024-0.0240.0000.0000.0000.000
119A114SER0-0.0130.01045.982-0.209-0.2090.0000.0000.0000.000
120A115VAL0-0.019-0.00747.2640.0890.0890.0000.0000.0000.000
121A116PHE0-0.011-0.01047.495-0.197-0.1970.0000.0000.0000.000
122A117ILE0-0.0180.01048.5640.1280.1280.0000.0000.0000.000
123A118PHE0-0.020-0.01247.308-0.091-0.0910.0000.0000.0000.000
124A119PRO0-0.017-0.01150.7540.0730.0730.0000.0000.0000.000
125A120PRO0-0.011-0.00150.9120.0390.0390.0000.0000.0000.000
126A121SER00.0330.02750.916-0.105-0.1050.0000.0000.0000.000
127A122ASP-1-0.860-0.94152.7105.5925.5920.0000.0000.0000.000
128A123GLU-1-0.973-1.00751.8975.9345.9340.0000.0000.0000.000
129A124GLN00.015-0.00246.652-0.053-0.0530.0000.0000.0000.000
130A125LEU00.0790.05051.0920.0030.0030.0000.0000.0000.000
131A126LYS10.8380.92454.006-5.727-5.7270.0000.0000.0000.000
132A127SER0-0.006-0.00850.213-0.040-0.0400.0000.0000.0000.000
133A128GLY0-0.0120.00950.7530.1130.1130.0000.0000.0000.000
134A129THR0-0.022-0.01247.321-0.070-0.0700.0000.0000.0000.000
135A130ALA00.0020.00049.878-0.070-0.0700.0000.0000.0000.000
136A131SER00.0080.01846.0840.1110.1110.0000.0000.0000.000
137A132VAL0-0.0120.00147.958-0.096-0.0960.0000.0000.0000.000
138A133VAL00.0350.02444.5910.1470.1470.0000.0000.0000.000
139A134CYS0-0.0620.00145.906-0.112-0.1120.0000.0000.0000.000
140A135LEU00.002-0.01542.6620.1620.1620.0000.0000.0000.000
141A136LEU0-0.049-0.01842.608-0.186-0.1860.0000.0000.0000.000
142A137ASN00.022-0.02242.3720.2970.2970.0000.0000.0000.000
143A138ASN00.040-0.00640.974-0.001-0.0010.0000.0000.0000.000
144A139PHE0-0.062-0.00939.301-0.143-0.1430.0000.0000.0000.000
145A140TYR00.0970.02935.6500.3300.3300.0000.0000.0000.000
146A141PRO00.004-0.01337.874-0.236-0.2360.0000.0000.0000.000
147A142ARG11.0451.03632.011-9.400-9.4000.0000.0000.0000.000
148A143GLU-1-0.934-0.97635.5988.5828.5820.0000.0000.0000.000
149A144ALA0-0.002-0.01338.570-0.219-0.2190.0000.0000.0000.000
150A145LYS10.9280.98941.393-6.840-6.8400.0000.0000.0000.000
151A146VAL00.0510.01743.043-0.150-0.1500.0000.0000.0000.000
152A147GLN00.0060.00445.0740.0890.0890.0000.0000.0000.000
153A148TRP00.0260.01845.320-0.233-0.2330.0000.0000.0000.000
154A149LYS10.8630.92149.815-5.780-5.7800.0000.0000.0000.000
155A150VAL00.0070.00353.079-0.033-0.0330.0000.0000.0000.000
156A151ASP-1-0.806-0.88855.6275.2835.2830.0000.0000.0000.000
157A152ASN0-0.063-0.04957.411-0.068-0.0680.0000.0000.0000.000
158A153ALA00.0280.02356.0080.0020.0020.0000.0000.0000.000
159A154LEU00.0010.01651.2710.0740.0740.0000.0000.0000.000
160A155GLN0-0.052-0.02048.8970.0130.0130.0000.0000.0000.000
161A156SER0-0.021-0.03146.3450.0430.0430.0000.0000.0000.000
162A157GLY0-0.0060.00743.052-0.035-0.0350.0000.0000.0000.000
163A158ASN00.0480.01544.0480.1200.1200.0000.0000.0000.000
164A159SER00.022-0.00343.673-0.137-0.1370.0000.0000.0000.000
165A160GLN0-0.0560.00037.4400.0360.0360.0000.0000.0000.000
166A161GLU-1-0.854-0.95138.3887.6967.6960.0000.0000.0000.000
167A162SER0-0.0370.00235.0800.3560.3560.0000.0000.0000.000
168A163VAL0-0.012-0.02233.700-0.257-0.2570.0000.0000.0000.000
169A164THR00.0010.01533.1630.1520.1520.0000.0000.0000.000
170A165GLU-1-0.899-0.95627.96410.71610.7160.0000.0000.0000.000
171A166GLN0-0.049-0.05831.2000.0270.0270.0000.0000.0000.000
172A167ASP-1-0.831-0.90632.7068.5558.5550.0000.0000.0000.000
173A168SER0-0.104-0.05032.8270.0670.0670.0000.0000.0000.000
174A169LYS10.9340.94534.087-8.103-8.1030.0000.0000.0000.000
175A170ASP-1-0.778-0.84637.6077.7747.7740.0000.0000.0000.000
176A171SER0-0.029-0.01335.053-0.134-0.1340.0000.0000.0000.000
177A172THR0-0.083-0.06836.2310.0190.0190.0000.0000.0000.000
178A173TYR00.008-0.00432.0670.1880.1880.0000.0000.0000.000
179A174SER00.0690.05237.415-0.364-0.3640.0000.0000.0000.000
180A175LEU0-0.0390.00837.9170.2090.2090.0000.0000.0000.000
181A176SER00.001-0.03339.253-0.181-0.1810.0000.0000.0000.000
182A177SER00.0150.03640.3820.1660.1660.0000.0000.0000.000
183A178THR00.011-0.00241.659-0.246-0.2460.0000.0000.0000.000
184A179LEU0-0.039-0.02543.7660.1010.1010.0000.0000.0000.000
185A180THR0-0.0060.00244.215-0.075-0.0750.0000.0000.0000.000
186A181LEU0-0.026-0.01846.798-0.051-0.0510.0000.0000.0000.000
187A182SER00.0580.05149.8520.0290.0290.0000.0000.0000.000
188A183LYS10.9650.97452.077-5.609-5.6090.0000.0000.0000.000
189A184ALA0-0.018-0.01854.897-0.096-0.0960.0000.0000.0000.000
190A185ASP-1-0.852-0.96553.7735.7605.7600.0000.0000.0000.000
191A186TYR00.0070.02554.183-0.054-0.0540.0000.0000.0000.000
192A187GLU-1-0.823-0.93955.8265.4185.4180.0000.0000.0000.000
193A188LYS10.8390.95957.706-5.628-5.6280.0000.0000.0000.000
194A189HIS10.8700.92857.142-5.612-5.6120.0000.0000.0000.000
195A190LYS10.9180.96660.055-5.040-5.0400.0000.0000.0000.000
196A191VAL00.0090.00258.3830.0190.0190.0000.0000.0000.000
197A192TYR0-0.022-0.02553.8530.0860.0860.0000.0000.0000.000
198A193ALA00.027-0.01353.565-0.050-0.0500.0000.0000.0000.000
199A195GLU-1-0.868-0.94950.1865.8635.8630.0000.0000.0000.000
200A196VAL0-0.0080.00345.8000.1510.1510.0000.0000.0000.000
201A197THR0-0.039-0.02146.544-0.166-0.1660.0000.0000.0000.000
202A198HIS00.0590.01141.449-0.040-0.0400.0000.0000.0000.000
203A199GLN00.0500.02142.710-0.008-0.0080.0000.0000.0000.000
204A200GLY0-0.009-0.01845.747-0.088-0.0880.0000.0000.0000.000
205A201LEU0-0.092-0.04047.450-0.124-0.1240.0000.0000.0000.000
206A202SER00.0050.00350.1690.0390.0390.0000.0000.0000.000
207A203SER00.0240.00653.111-0.051-0.0510.0000.0000.0000.000
208A204PRO0-0.027-0.00351.2530.0430.0430.0000.0000.0000.000
209A205VAL00.0320.03050.998-0.134-0.1340.0000.0000.0000.000
210A206THR0-0.018-0.01951.8320.0820.0820.0000.0000.0000.000
211A207LYS10.9030.96352.076-6.048-6.0480.0000.0000.0000.000
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