Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 72M4K

Calculation Name: 3ZLA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ZLA

Chain ID: A

ChEMBL ID:

UniProt ID: P16495

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 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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2847516.691719
FMO2-HF: Nuclear repulsion 2754871.548851
FMO2-HF: Total energy -92645.142867
FMO2-MP2: Total energy -92918.284232


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:GLY)


Summations of interaction energy for fragment #1(A:-1:GLY)
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.
0.5721.795-0.016-0.571-0.6370
Interaction energy analysis for fragmet #1(A:-1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.015
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].
3A1MET00.022-0.0053.8200.8612.084-0.016-0.571-0.6370.000
4A2ILE0-0.029-0.0066.901-0.042-0.0420.0000.0000.0000.000
5A3GLU-1-0.937-0.95810.332-0.135-0.1350.0000.0000.0000.000
6A4LEU0-0.050-0.02313.635-0.029-0.0290.0000.0000.0000.000
7A5GLU-1-0.911-0.94616.771-0.213-0.2130.0000.0000.0000.000
8A6PHE0-0.063-0.05019.9980.0060.0060.0000.0000.0000.000
9A7HIS00.0160.00123.8140.0030.0030.0000.0000.0000.000
10A8ASP-1-0.937-0.95227.335-0.048-0.0480.0000.0000.0000.000
11A9VAL0-0.021-0.01530.939-0.005-0.0050.0000.0000.0000.000
12A10ALA0-0.028-0.01833.7760.0040.0040.0000.0000.0000.000
13A11ALA00.0310.01137.5070.0030.0030.0000.0000.0000.000
14A12ASN0-0.056-0.01838.5880.0030.0030.0000.0000.0000.000
15A13THR00.0290.02238.405-0.001-0.0010.0000.0000.0000.000
16A14SER0-0.010-0.02041.3930.0020.0020.0000.0000.0000.000
17A15SER0-0.044-0.02043.708-0.002-0.0020.0000.0000.0000.000
18A16THR0-0.022-0.00642.1540.0000.0000.0000.0000.0000.000
19A17PHE00.0620.05044.6220.0000.0000.0000.0000.0000.000
20A18ASP-1-0.913-0.98046.428-0.029-0.0290.0000.0000.0000.000
21A19PRO00.0110.02550.023-0.002-0.0020.0000.0000.0000.000
22A20GLU-1-0.859-0.96451.159-0.026-0.0260.0000.0000.0000.000
23A21VAL00.0350.03651.2790.0000.0000.0000.0000.0000.000
24A22ALA00.0290.01648.422-0.001-0.0010.0000.0000.0000.000
25A23TYR0-0.096-0.06950.217-0.001-0.0010.0000.0000.0000.000
26A24ALA0-0.0090.00552.9310.0000.0000.0000.0000.0000.000
27A25ASN00.009-0.00448.7050.0000.0000.0000.0000.0000.000
28A26PHE00.0110.00249.911-0.001-0.0010.0000.0000.0000.000
29A27LYS10.9060.95451.7720.0270.0270.0000.0000.0000.000
30A28ARG10.9230.98452.6400.0390.0390.0000.0000.0000.000
31A29VAL0-0.021-0.00550.2810.0000.0000.0000.0000.0000.000
32A30HIS00.0280.00647.6930.0000.0000.0000.0000.0000.000
33A31THR0-0.103-0.06352.7260.0010.0010.0000.0000.0000.000
34A32THR00.0240.02255.7330.0010.0010.0000.0000.0000.000
35A33GLY00.0110.01356.2800.0010.0010.0000.0000.0000.000
36A34LEU0-0.032-0.01454.113-0.001-0.0010.0000.0000.0000.000
37A35SER00.018-0.00957.1510.0020.0020.0000.0000.0000.000
38A36TYR00.020-0.01857.858-0.001-0.0010.0000.0000.0000.000
39A37ASP-1-0.876-0.93858.413-0.025-0.0250.0000.0000.0000.000
40A38HIS00.0090.01053.9760.0000.0000.0000.0000.0000.000
41A39ILE00.0350.02653.590-0.001-0.0010.0000.0000.0000.000
42A40ARG10.9070.94754.0580.0230.0230.0000.0000.0000.000
43A41ILE0-0.045-0.01350.8110.0000.0000.0000.0000.0000.000
44A42PHE0-0.024-0.00246.7110.0000.0000.0000.0000.0000.000
45A43TYR00.010-0.02349.8140.0000.0000.0000.0000.0000.000
46A44ILE0-0.027-0.00351.5570.0010.0010.0000.0000.0000.000
47A45LYS10.9350.96748.1390.0310.0310.0000.0000.0000.000
48A46GLY00.0740.04647.123-0.002-0.0020.0000.0000.0000.000
49A47ARG10.9310.95645.4980.0210.0210.0000.0000.0000.000
50A48GLU-1-0.901-0.96343.911-0.033-0.0330.0000.0000.0000.000
51A49ILE00.0270.02042.440-0.003-0.0030.0000.0000.0000.000
52A50LYS10.9820.99840.1650.0290.0290.0000.0000.0000.000
53A51THR0-0.046-0.02538.944-0.003-0.0030.0000.0000.0000.000
54A52SER0-0.054-0.03737.609-0.004-0.0040.0000.0000.0000.000
55A53LEU00.0540.01737.087-0.004-0.0040.0000.0000.0000.000
56A54ALA0-0.0080.00135.075-0.004-0.0040.0000.0000.0000.000
57A55LYS10.8810.94633.1650.0490.0490.0000.0000.0000.000
58A56ARG10.9350.97531.7240.0620.0620.0000.0000.0000.000
59A57SER00.0700.03128.0530.0020.0020.0000.0000.0000.000
60A58GLU-1-0.883-0.93729.920-0.100-0.1000.0000.0000.0000.000
61A59TRP00.0540.01531.1280.0090.0090.0000.0000.0000.000
62A60GLU-1-0.920-0.95432.813-0.073-0.0730.0000.0000.0000.000
63A61VAL0-0.008-0.00335.888-0.002-0.0020.0000.0000.0000.000
64A62THR00.0010.00638.3370.0020.0020.0000.0000.0000.000
65A63LEU0-0.073-0.03941.9840.0010.0010.0000.0000.0000.000
66A64ASN00.0410.01044.6100.0000.0000.0000.0000.0000.000
67A65LEU0-0.050-0.01747.4270.0010.0010.0000.0000.0000.000
68A66GLY00.0260.00050.1780.0020.0020.0000.0000.0000.000
69A67GLY0-0.025-0.01951.697-0.001-0.0010.0000.0000.0000.000
70A68TRP00.0310.02851.585-0.002-0.0020.0000.0000.0000.000
71A69LYS10.9990.99545.3710.0530.0530.0000.0000.0000.000
72A70ILE0-0.033-0.01045.7050.0000.0000.0000.0000.0000.000
73A71THR00.0230.01740.7270.0000.0000.0000.0000.0000.000
74A72VAL0-0.077-0.04040.8100.0030.0030.0000.0000.0000.000
75A73TYR00.0910.05136.5030.0000.0000.0000.0000.0000.000
76A74ASN0-0.039-0.02434.0020.0110.0110.0000.0000.0000.000
77A75THR00.014-0.01434.378-0.004-0.0040.0000.0000.0000.000
78A76ASN0-0.095-0.04635.5630.0020.0020.0000.0000.0000.000
79A77PHE00.0190.02127.2480.0040.0040.0000.0000.0000.000
80A78PRO0-0.039-0.03629.189-0.001-0.0010.0000.0000.0000.000
81A79GLY00.0250.00527.2710.0020.0020.0000.0000.0000.000
82A80ASN0-0.0020.01227.896-0.010-0.0100.0000.0000.0000.000
83A81ARG10.8640.95730.5010.0490.0490.0000.0000.0000.000
84A82ASN0-0.055-0.03230.6960.0000.0000.0000.0000.0000.000
85A83ASN00.1010.05730.133-0.007-0.0070.0000.0000.0000.000
86A84PRO0-0.025-0.01432.1240.0030.0030.0000.0000.0000.000
87A85VAL0-0.024-0.01335.348-0.003-0.0030.0000.0000.0000.000
88A86PRO00.0480.03637.9900.0030.0030.0000.0000.0000.000
89A87ASP-1-0.833-0.94340.733-0.044-0.0440.0000.0000.0000.000
90A88ASP-1-0.952-0.97643.640-0.053-0.0530.0000.0000.0000.000
91A89GLY00.0220.01842.070-0.001-0.0010.0000.0000.0000.000
92A90LEU0-0.041-0.02542.7860.0040.0040.0000.0000.0000.000
93A91THR00.0750.02639.937-0.002-0.0020.0000.0000.0000.000
94A92LEU00.0440.00441.1880.0030.0030.0000.0000.0000.000
95A93HIS0-0.078-0.03043.2290.0010.0010.0000.0000.0000.000
96A94ARG10.8890.95342.3930.0480.0480.0000.0000.0000.000
97A95LEU00.0140.02746.1830.0020.0020.0000.0000.0000.000
98A96SER0-0.002-0.02447.7480.0020.0020.0000.0000.0000.000
99A97GLY00.0400.03049.3930.0020.0020.0000.0000.0000.000
100A98PHE0-0.006-0.01048.3290.0020.0020.0000.0000.0000.000
101A99LEU0-0.007-0.00551.1500.0010.0010.0000.0000.0000.000
102A100ALA00.0380.03053.8670.0010.0010.0000.0000.0000.000
103A101ARG10.9060.97255.4220.0270.0270.0000.0000.0000.000
104A102TYR00.005-0.00756.4970.0010.0010.0000.0000.0000.000
105A103LEU0-0.036-0.02257.6540.0010.0010.0000.0000.0000.000
106A104LEU00.0210.01959.9220.0010.0010.0000.0000.0000.000
107A105GLU-1-0.800-0.90460.610-0.025-0.0250.0000.0000.0000.000
108A106LYS10.8770.93261.5960.0260.0260.0000.0000.0000.000
109A107MET0-0.055-0.03363.8650.0000.0000.0000.0000.0000.000
110A108LEU00.0020.02465.4820.0010.0010.0000.0000.0000.000
111A109LYS10.9020.96464.4690.0240.0240.0000.0000.0000.000
112A110VAL0-0.068-0.01966.9990.0000.0000.0000.0000.0000.000
113A111SER00.0390.00969.9440.0010.0010.0000.0000.0000.000
114A112GLU-1-0.840-0.93871.591-0.015-0.0150.0000.0000.0000.000
115A113PRO00.0070.00672.9200.0000.0000.0000.0000.0000.000
116A114GLU-1-0.847-0.94367.161-0.022-0.0220.0000.0000.0000.000
117A115LYS10.9500.96667.9320.0160.0160.0000.0000.0000.000
118A116LEU0-0.0100.00567.7800.0000.0000.0000.0000.0000.000
119A117ILE00.0020.00965.0570.0000.0000.0000.0000.0000.000
120A118ILE0-0.045-0.01762.582-0.001-0.0010.0000.0000.0000.000
121A119LYS10.9560.97463.4820.0150.0150.0000.0000.0000.000
122A120SER0-0.0330.00964.9020.0000.0000.0000.0000.0000.000
123A121LYS10.8950.96361.2100.0230.0230.0000.0000.0000.000
124A122ILE0-0.013-0.00857.951-0.001-0.0010.0000.0000.0000.000
125A123ILE00.0350.02557.4490.0010.0010.0000.0000.0000.000
126A124ASN00.004-0.01555.241-0.002-0.0020.0000.0000.0000.000
127A125PRO0-0.019-0.01252.3540.0010.0010.0000.0000.0000.000
128A126LEU0-0.009-0.01249.9130.0010.0010.0000.0000.0000.000
129A127ALA00.0130.02154.2190.0010.0010.0000.0000.0000.000
130A128GLU-1-0.795-0.89957.823-0.015-0.0150.0000.0000.0000.000
131A129LYS10.8570.94453.9490.0120.0120.0000.0000.0000.000
132A130ASN0-0.091-0.05854.7670.0020.0020.0000.0000.0000.000
133A131GLY0-0.039-0.02158.5840.0010.0010.0000.0000.0000.000
134A132ILE00.0520.05260.1270.0000.0000.0000.0000.0000.000
135A133THR00.001-0.01361.708-0.001-0.0010.0000.0000.0000.000
136A134TRP00.026-0.02661.3200.0000.0000.0000.0000.0000.000
137A135ASN0-0.059-0.03165.2690.0000.0000.0000.0000.0000.000
138A136ASP-1-0.835-0.90365.269-0.011-0.0110.0000.0000.0000.000
139A137GLY00.0240.01566.6710.0000.0000.0000.0000.0000.000
140A138GLU-1-0.938-0.98864.563-0.017-0.0170.0000.0000.0000.000
141A139GLU-1-0.883-0.96362.682-0.017-0.0170.0000.0000.0000.000
142A140VAL00.0410.03161.208-0.001-0.0010.0000.0000.0000.000
143A141TYR0-0.0130.00760.082-0.001-0.0010.0000.0000.0000.000
144A142LEU0-0.002-0.00758.332-0.001-0.0010.0000.0000.0000.000
145A143SER0-0.032-0.02656.688-0.001-0.0010.0000.0000.0000.000
146A144PHE00.0030.00455.3420.0000.0000.0000.0000.0000.000
147A145PHE0-0.077-0.01252.7680.0000.0000.0000.0000.0000.000
148A146PRO0-0.0030.00147.8380.0000.0000.0000.0000.0000.000
149A147GLY00.0270.01849.023-0.002-0.0020.0000.0000.0000.000
150A148SER0-0.008-0.01449.8040.0000.0000.0000.0000.0000.000
151A149GLU-1-0.799-0.92148.786-0.026-0.0260.0000.0000.0000.000
152A150MET0-0.081-0.02648.801-0.001-0.0010.0000.0000.0000.000
153A151PHE0-0.0040.00051.6460.0000.0000.0000.0000.0000.000
154A152LEU00.0200.00454.0430.0010.0010.0000.0000.0000.000
155A153GLY00.0190.01657.1160.0010.0010.0000.0000.0000.000
156A154THR00.011-0.00258.6190.0010.0010.0000.0000.0000.000
157A155PHE0-0.020-0.00956.0140.0000.0000.0000.0000.0000.000
158A156ARG10.9130.96260.3320.0150.0150.0000.0000.0000.000
159A157PHE00.0300.00558.1920.0010.0010.0000.0000.0000.000
160A158TYR00.0630.03759.4180.0010.0010.0000.0000.0000.000
161A159PRO0-0.029-0.00254.3160.0010.0010.0000.0000.0000.000
162A160LEU0-0.016-0.00354.3860.0000.0000.0000.0000.0000.000
163A161ALA00.0270.02455.9670.0010.0010.0000.0000.0000.000
164A162ILE00.0100.00555.3940.0010.0010.0000.0000.0000.000
165A163GLY0-0.004-0.01153.6640.0010.0010.0000.0000.0000.000
166A164ILE00.004-0.00754.2890.0010.0010.0000.0000.0000.000
167A165TYR00.0190.00456.3400.0010.0010.0000.0000.0000.000
168A166LYS10.9430.96951.7640.0150.0150.0000.0000.0000.000
169A167VAL0-0.038-0.01351.2530.0010.0010.0000.0000.0000.000
170A168GLN00.0030.00853.6960.0010.0010.0000.0000.0000.000
171A169ARG10.8610.95156.7060.0080.0080.0000.0000.0000.000
172A170LYS10.9310.95053.466-0.001-0.0010.0000.0000.0000.000
173A171GLU-1-0.933-0.94652.220-0.009-0.0090.0000.0000.0000.000
174A172MET0-0.068-0.02848.938-0.001-0.0010.0000.0000.0000.000
175A173GLU-1-0.875-0.95043.974-0.006-0.0060.0000.0000.0000.000
176A174PRO00.045-0.00847.677-0.002-0.0020.0000.0000.0000.000
177A175LYS10.9961.01640.3820.0110.0110.0000.0000.0000.000
178A176TYR0-0.057-0.02942.146-0.001-0.0010.0000.0000.0000.000
179A177LEU0-0.021-0.00146.623-0.002-0.0020.0000.0000.0000.000
180A178GLU-1-0.880-0.94142.880-0.015-0.0150.0000.0000.0000.000
181A179LYS10.8700.92844.3500.0290.0290.0000.0000.0000.000
182A180THR00.023-0.00446.742-0.001-0.0010.0000.0000.0000.000
183A181MET00.0320.01649.7940.0000.0000.0000.0000.0000.000
184A182ARG10.9080.97943.2740.0250.0250.0000.0000.0000.000
185A183GLN0-0.022-0.00448.058-0.002-0.0020.0000.0000.0000.000
186A184ARG10.9741.00049.1300.0290.0290.0000.0000.0000.000
187A185TYR0-0.006-0.00654.8470.0000.0000.0000.0000.0000.000
188A186MET0-0.016-0.01658.3810.0010.0010.0000.0000.0000.000
189A187GLY00.0160.00858.501-0.001-0.0010.0000.0000.0000.000
190A188LEU0-0.036-0.00657.6470.0000.0000.0000.0000.0000.000
191A189GLU-1-0.793-0.90652.966-0.022-0.0220.0000.0000.0000.000
192A190ALA00.0600.03952.4160.0010.0010.0000.0000.0000.000
193A191ALA00.0330.05354.5350.0010.0010.0000.0000.0000.000
194A192THR0-0.053-0.03756.3870.0010.0010.0000.0000.0000.000
195A193TRP0-0.032-0.04654.4160.0020.0020.0000.0000.0000.000
196A194THR0-0.042-0.05556.8790.0000.0000.0000.0000.0000.000
197A195VAL00.0280.00859.0600.0010.0010.0000.0000.0000.000
198A196SER0-0.050-0.00362.6090.0000.0000.0000.0000.0000.000
199A197LYS10.9220.96462.5690.0120.0120.0000.0000.0000.000
200A198LEU00.0310.03162.5270.0000.0000.0000.0000.0000.000
201A199THR00.040-0.00863.9360.0000.0000.0000.0000.0000.000
202A200GLU-1-0.863-0.93364.487-0.011-0.0110.0000.0000.0000.000
203A201VAL00.0200.01860.0130.0000.0000.0000.0000.0000.000
204A202GLN0-0.031-0.00662.9490.0000.0000.0000.0000.0000.000
205A203SER0-0.0250.00865.4820.0000.0000.0000.0000.0000.000
206A204ALA00.0300.01162.6870.0000.0000.0000.0000.0000.000
207A205LEU00.024-0.00661.0540.0000.0000.0000.0000.0000.000
208A206THR0-0.010-0.01463.4830.0000.0000.0000.0000.0000.000
209A207VAL0-0.0030.01365.8090.0000.0000.0000.0000.0000.000
210A208VAL0-0.0210.00660.9240.0000.0000.0000.0000.0000.000
211A209SER0-0.074-0.06363.8160.0000.0000.0000.0000.0000.000
212A210SER0-0.085-0.05264.9320.0000.0000.0000.0000.0000.000
213A211LEU0-0.018-0.00363.1860.0000.0000.0000.0000.0000.000
214A212GLY00.0090.02265.3130.0000.0000.0000.0000.0000.000
215A213TRP00.0060.00257.3680.0000.0000.0000.0000.0000.000
216A214LYS10.9150.96460.2640.0110.0110.0000.0000.0000.000
217A215LYS10.9340.98055.1490.0040.0040.0000.0000.0000.000
218A216THR0-0.033-0.02957.2990.0000.0000.0000.0000.0000.000
219A217ASN00.0480.01855.8970.0000.0000.0000.0000.0000.000
220A218VAL0-0.0060.00659.7960.0000.0000.0000.0000.0000.000
221A219SER00.0500.01063.1660.0000.0000.0000.0000.0000.000
222A220ALA00.0630.02066.8540.0000.0000.0000.0000.0000.000
223A221ALA00.0800.02769.4790.0000.0000.0000.0000.0000.000
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