FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: R4NV8

Calculation Name: 1Z7C-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1Z7C

Chain ID: A

ChEMBL ID:

UniProt ID: P0DML2

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 186
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2174499.342483
FMO2-HF: Nuclear repulsion 2095981.910452
FMO2-HF: Total energy -78517.432032
FMO2-MP2: Total energy -78742.568707


3D Structure Molmil
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:2:GLN)


Summations of interaction energy for fragment #1(A:2:GLN)
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.
-139.305-136.150.155-1.368-1.94-0.006
Interaction energy analysis for fragmet #1(A:2:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.912
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].
3A4VAL00.0110.0083.1930.5743.2740.155-1.324-1.530-0.006
4A5PRO0-0.026-0.0194.4231.7441.949-0.001-0.008-0.1960.000
7A8ARG10.9650.9803.70237.64437.8940.001-0.036-0.2140.000
5A6LEU00.0710.0347.176-0.110-0.1100.0000.0000.0000.000
6A7SER00.0900.05710.3250.1220.1220.0000.0000.0000.000
8A9LEU0-0.052-0.0209.441-0.033-0.0330.0000.0000.0000.000
9A10PHE00.1040.04711.4470.6830.6830.0000.0000.0000.000
10A11ASP-1-0.894-0.94712.977-18.040-18.0400.0000.0000.0000.000
11A12HIS0-0.109-0.06412.6800.1910.1910.0000.0000.0000.000
12A13ALA00.0290.00914.6340.9070.9070.0000.0000.0000.000
13A14MET00.0210.03117.2100.8430.8430.0000.0000.0000.000
14A15LEU0-0.025-0.00917.2040.6960.6960.0000.0000.0000.000
15A16GLN0-0.013-0.00717.8671.2631.2630.0000.0000.0000.000
16A17ALA00.0310.00820.4530.5950.5950.0000.0000.0000.000
17A18HIS0-0.043-0.01922.5380.5360.5360.0000.0000.0000.000
18A19ARG10.8570.91919.84913.93613.9360.0000.0000.0000.000
19A20ALA0-0.003-0.01224.5420.4350.4350.0000.0000.0000.000
20A21HIS0-0.009-0.01026.4270.7210.7210.0000.0000.0000.000
21A22GLN0-0.029-0.02127.8280.2870.2870.0000.0000.0000.000
22A23LEU00.0000.01028.6560.3460.3460.0000.0000.0000.000
23A24ALA00.0160.02130.5070.3670.3670.0000.0000.0000.000
24A25ILE0-0.051-0.01931.2660.4200.4200.0000.0000.0000.000
25A26ASP-1-0.837-0.92632.255-8.830-8.8300.0000.0000.0000.000
26A27THR0-0.029-0.03333.8940.2940.2940.0000.0000.0000.000
27A28TYR0-0.044-0.04236.4530.2470.2470.0000.0000.0000.000
28A29GLN0-0.013-0.01136.7330.2880.2880.0000.0000.0000.000
29A30GLU-1-0.814-0.85938.042-7.791-7.7910.0000.0000.0000.000
30A31PHE00.0090.00640.6210.2070.2070.0000.0000.0000.000
31A32GLU-1-0.776-0.84842.465-6.765-6.7650.0000.0000.0000.000
32A33GLU-1-0.954-0.98743.634-6.581-6.5810.0000.0000.0000.000
33A34THR0-0.110-0.05143.9150.1590.1590.0000.0000.0000.000
34A35TYR0-0.048-0.03344.0550.1190.1190.0000.0000.0000.000
35A36ILE0-0.0360.00546.6170.1220.1220.0000.0000.0000.000
36A37PRO00.0070.02449.2510.0010.0010.0000.0000.0000.000
37A38LYS10.9310.94151.9835.5575.5570.0000.0000.0000.000
38A39ASP-1-0.954-0.98753.094-5.620-5.6200.0000.0000.0000.000
39A40GLN00.0060.01051.8180.0280.0280.0000.0000.0000.000
40A41LYS10.8760.95845.7026.5386.5380.0000.0000.0000.000
41A42TYR0-0.043-0.03343.8570.1560.1560.0000.0000.0000.000
42A43SER0-0.063-0.04447.542-0.008-0.0080.0000.0000.0000.000
43A44PHE0-0.0020.00443.6310.1080.1080.0000.0000.0000.000
44A45LEU0-0.061-0.02547.5790.0550.0550.0000.0000.0000.000
45A46HIS-1-0.812-0.88042.001-7.339-7.3390.0000.0000.0000.000
46A47ASP-1-0.885-0.91742.988-7.003-7.0030.0000.0000.0000.000
47A48SER0-0.026-0.01944.1710.2180.2180.0000.0000.0000.000
48A49GLN0-0.099-0.06146.991-0.053-0.0530.0000.0000.0000.000
49A50THR0-0.031-0.02549.3210.0180.0180.0000.0000.0000.000
50A51SER0-0.016-0.01145.200-0.027-0.0270.0000.0000.0000.000
51A52PHE0-0.0340.00340.8630.0230.0230.0000.0000.0000.000
52A53CYS0-0.0240.00237.446-0.073-0.0730.0000.0000.0000.000
53A54PHE0-0.059-0.03432.729-0.026-0.0260.0000.0000.0000.000
54A55SER00.004-0.04233.6060.0180.0180.0000.0000.0000.000
55A56ASP-1-0.780-0.88634.950-7.836-7.8360.0000.0000.0000.000
56A57SER0-0.104-0.05936.6810.1970.1970.0000.0000.0000.000
57A58ILE0-0.049-0.01632.6250.0730.0730.0000.0000.0000.000
58A59PRO0-0.011-0.00735.8090.0010.0010.0000.0000.0000.000
59A60THR-1-0.639-0.79732.714-9.238-9.2380.0000.0000.0000.000
60A61PRO0-0.125-0.05133.3150.2680.2680.0000.0000.0000.000
61A62SER0-0.009-0.01934.222-0.183-0.1830.0000.0000.0000.000
62A63ASN00.0550.00928.781-0.109-0.1090.0000.0000.0000.000
63A64MET0-0.088-0.03130.623-0.306-0.3060.0000.0000.0000.000
64A65GLU-1-0.910-0.95332.387-8.034-8.0340.0000.0000.0000.000
65A66GLU-1-0.847-0.89428.750-10.403-10.4030.0000.0000.0000.000
66A67THR0-0.060-0.05031.9310.0190.0190.0000.0000.0000.000
67A68GLN00.0040.00728.935-0.117-0.1170.0000.0000.0000.000
68A69GLN0-0.070-0.05827.132-0.291-0.2910.0000.0000.0000.000
69A70LYS0-0.067-0.02024.5050.0610.0610.0000.0000.0000.000
70A71SER-1-0.752-0.86421.780-12.393-12.3930.0000.0000.0000.000
71A72ASN0-0.103-0.05821.604-0.365-0.3650.0000.0000.0000.000
72A73LEU00.002-0.00221.6980.0430.0430.0000.0000.0000.000
73A74GLU-1-0.782-0.86724.028-9.973-9.9730.0000.0000.0000.000
74A75LEU00.0190.01625.3810.1090.1090.0000.0000.0000.000
75A76LEU00.0490.03219.255-0.013-0.0130.0000.0000.0000.000
76A77ARG10.8080.88623.7979.9869.9860.0000.0000.0000.000
77A78ILE0-0.023-0.00626.2830.1690.1690.0000.0000.0000.000
78A79SER00.018-0.00124.3400.2050.2050.0000.0000.0000.000
79A80LEU0-0.056-0.02022.5780.0550.0550.0000.0000.0000.000
80A81LEU0-0.048-0.03325.4230.1900.1900.0000.0000.0000.000
81A82LEU00.0360.03128.7820.2480.2480.0000.0000.0000.000
82A83ILE00.0360.03024.2950.2470.2470.0000.0000.0000.000
83A84GLU-1-0.867-0.94526.738-10.979-10.9790.0000.0000.0000.000
84A85SER0-0.112-0.05628.8790.3410.3410.0000.0000.0000.000
85A86TRP00.019-0.02430.4670.3430.3430.0000.0000.0000.000
86A87LEU0-0.030-0.01025.5270.1630.1630.0000.0000.0000.000
87A88GLU-1-0.856-0.91029.918-8.673-8.6730.0000.0000.0000.000
88A89PRO0-0.020-0.02633.1800.1030.1030.0000.0000.0000.000
89A90VAL00.0660.03729.3950.1950.1950.0000.0000.0000.000
90A91ARG10.8640.94332.3239.1099.1090.0000.0000.0000.000
91A92PHE0-0.031-0.02033.6530.2210.2210.0000.0000.0000.000
92A93LEU00.0110.04232.9520.2800.2800.0000.0000.0000.000
93A94ARG10.8560.87134.9628.4998.4990.0000.0000.0000.000
94A95SER0-0.110-0.06237.7450.2450.2450.0000.0000.0000.000
95A96MET0-0.0020.00238.9630.2120.2120.0000.0000.0000.000
96A97PHE0-0.040-0.00438.7530.1390.1390.0000.0000.0000.000
97A98ALA0-0.019-0.01642.7270.0580.0580.0000.0000.0000.000
98A99ASN00.0040.00145.6030.0330.0330.0000.0000.0000.000
99A100ASN0-0.048-0.02548.732-0.004-0.0040.0000.0000.0000.000
100A101LEU00.0060.02341.8040.0300.0300.0000.0000.0000.000
101A102VAL0-0.023-0.01843.080-0.082-0.0820.0000.0000.0000.000
102A103TYR00.024-0.00333.8270.0680.0680.0000.0000.0000.000
103A104ASP-1-0.835-0.88938.202-8.163-8.1630.0000.0000.0000.000
104A105THR0-0.139-0.07536.222-0.009-0.0090.0000.0000.0000.000
105A106SER0-0.059-0.04135.067-0.288-0.2880.0000.0000.0000.000
106A107ASP-1-0.886-0.96328.234-11.071-11.0710.0000.0000.0000.000
107A108SER0-0.075-0.01228.3980.1900.1900.0000.0000.0000.000
108A109ASP-1-0.828-0.93529.354-9.515-9.5150.0000.0000.0000.000
109A110ASP-1-0.935-0.95926.796-10.785-10.7850.0000.0000.0000.000
110A111TYR00.015-0.01725.954-0.309-0.3090.0000.0000.0000.000
111A112HIS00.0330.01325.346-0.102-0.1020.0000.0000.0000.000
112A113LEU0-0.0500.00321.611-0.562-0.5620.0000.0000.0000.000
113A114LEU00.0360.00322.302-0.501-0.5010.0000.0000.0000.000
114A115LYS10.8180.89022.68412.22612.2260.0000.0000.0000.000
115A116ASP-1-0.864-0.90417.581-17.046-17.0460.0000.0000.0000.000
116A117LEU00.0260.01318.394-0.689-0.6890.0000.0000.0000.000
117A118GLU-1-0.796-0.88520.118-12.659-12.6590.0000.0000.0000.000
118A119GLU-1-0.929-0.93415.406-19.723-19.7230.0000.0000.0000.000
119A120GLY00.0690.02415.446-0.605-0.6050.0000.0000.0000.000
120A121ILE00.0090.00716.319-0.496-0.4960.0000.0000.0000.000
121A122GLN0-0.032-0.02618.927-0.420-0.4200.0000.0000.0000.000
122A123THR0-0.116-0.07912.536-0.524-0.5240.0000.0000.0000.000
123A124LEU0-0.036-0.02514.246-0.954-0.9540.0000.0000.0000.000
124A125MET00.0150.01615.9210.0830.0830.0000.0000.0000.000
125A126GLY0-0.0140.00317.0520.2700.2700.0000.0000.0000.000
126A127ARG10.7720.8778.75725.11925.1190.0000.0000.0000.000
127A128LEU00.0110.00415.495-0.174-0.1740.0000.0000.0000.000
128A129GLU-1-0.940-0.95418.808-14.561-14.5610.0000.0000.0000.000
129A130ASP-1-0.720-0.82821.130-11.059-11.0590.0000.0000.0000.000
130A131GLY0-0.049-0.03121.555-0.688-0.6880.0000.0000.0000.000
131A132SER00.016-0.00320.2390.3110.3110.0000.0000.0000.000
132A133ARG10.7940.89321.76811.64611.6460.0000.0000.0000.000
133A134ARG0-0.022-0.01524.5660.5400.5400.0000.0000.0000.000
134A135THR0-0.066-0.06225.9980.6240.6240.0000.0000.0000.000
135A136GLY00.0570.02029.3470.0130.0130.0000.0000.0000.000
136A137GLN00.0000.01030.0300.2590.2590.0000.0000.0000.000
137A138ILE0-0.039-0.03233.1650.1470.1470.0000.0000.0000.000
138A139LEU00.0070.00836.0050.2920.2920.0000.0000.0000.000
139A140LYS10.8590.93430.9139.5659.5650.0000.0000.0000.000
140A141GLN00.0330.03335.5760.1990.1990.0000.0000.0000.000
141A142THR0-0.017-0.02235.345-0.245-0.2450.0000.0000.0000.000
142A143TYR00.002-0.00734.8610.4170.4170.0000.0000.0000.000
143A144SER0-0.054-0.03138.2730.0120.0120.0000.0000.0000.000
144A145LYS10.8430.92637.9018.0638.0630.0000.0000.0000.000
145A146PHE00.0920.03435.7240.2020.2020.0000.0000.0000.000
146A147ASP-1-0.901-0.94841.166-6.782-6.7820.0000.0000.0000.000
147A148THR00.0360.01143.6330.0130.0130.0000.0000.0000.000
148A149ASN0-0.020-0.00945.9430.1880.1880.0000.0000.0000.000
149A150SER0-0.001-0.01048.292-0.100-0.1000.0000.0000.0000.000
150A151HIS0-0.056-0.02450.7810.1540.1540.0000.0000.0000.000
151A152ASN0-0.058-0.03353.1390.0690.0690.0000.0000.0000.000
152A153HIS-1-0.782-0.90851.284-6.072-6.0720.0000.0000.0000.000
153A154ASP-1-0.849-0.90851.205-5.857-5.8570.0000.0000.0000.000
154A155ALA0-0.047-0.02448.795-0.120-0.1200.0000.0000.0000.000
155A156LEU0-0.0030.01747.243-0.177-0.1770.0000.0000.0000.000
156A157LEU00.0510.01146.650-0.177-0.1770.0000.0000.0000.000
157A158LYS10.8290.92743.9946.8356.8350.0000.0000.0000.000
158A159ASN0-0.003-0.02142.772-0.293-0.2930.0000.0000.0000.000
159A160TYR0-0.005-0.02741.858-0.133-0.1330.0000.0000.0000.000
160A161GLY00.0460.02342.107-0.132-0.1320.0000.0000.0000.000
161A162LEU0-0.054-0.02539.279-0.161-0.1610.0000.0000.0000.000
162A163LEU00.000-0.00237.582-0.260-0.2600.0000.0000.0000.000
163A164TYR0-0.034-0.04337.359-0.233-0.2330.0000.0000.0000.000
164A166PHE00.0110.00630.318-0.242-0.2420.0000.0000.0000.000
165A167ARG10.8810.93732.8027.8887.8880.0000.0000.0000.000
166A168LYS10.8500.89932.9667.5557.5550.0000.0000.0000.000
167A169ASP-1-0.705-0.79231.870-8.963-8.9630.0000.0000.0000.000
168A170MET0-0.083-0.02928.439-0.499-0.4990.0000.0000.0000.000
169A171ASP-1-0.894-0.93228.226-9.600-9.6000.0000.0000.0000.000
170A172LYS10.7750.88029.3268.6328.6320.0000.0000.0000.000
171A173VAL0-0.022-0.01424.507-0.301-0.3010.0000.0000.0000.000
172A174GLU-1-0.797-0.88024.292-11.627-11.6270.0000.0000.0000.000
173A175THR00.0320.01524.833-0.336-0.3360.0000.0000.0000.000
174A176PHE0-0.038-0.03426.198-0.128-0.1280.0000.0000.0000.000
175A177LEU0-0.052-0.03320.255-0.418-0.4180.0000.0000.0000.000
176A178ARG0-0.040-0.04221.262-0.259-0.2590.0000.0000.0000.000
177A179MET00.001-0.02022.901-0.072-0.0720.0000.0000.0000.000
178A180VAL0-0.019-0.01919.980-0.289-0.2890.0000.0000.0000.000
179A181GLN0-0.0050.00716.1170.0490.0490.0000.0000.0000.000
180A189CYS-1-0.989-0.96818.753-12.304-12.3040.0000.0000.0000.000
181A183ARG0-0.0130.00520.9360.1190.1190.0000.0000.0000.000
182A184SER0-0.017-0.00917.152-0.164-0.1640.0000.0000.0000.000
183A185VAL0-0.135-0.07213.762-1.309-1.3090.0000.0000.0000.000
184A186GLU-1-0.909-0.93616.309-12.851-12.8510.0000.0000.0000.000
185A187GLY0-0.043-0.02917.037-0.656-0.6560.0000.0000.0000.000
186A188SER0-0.084-0.06417.200-0.400-0.4000.0000.0000.0000.000