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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: ZVYLN

Calculation Name: 1F7C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1F7C

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZMW5

Base Structure: X-ray

Registration Date: 2023-09-21

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2185706.035288
FMO2-HF: Nuclear repulsion 2108569.32779
FMO2-HF: Total energy -77136.707498
FMO2-MP2: Total energy -77358.843372


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:191:ALA)


Summations of interaction energy for fragment #1(A:191:ALA)
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.
-11.445-3.6627.722-6.553-8.951-0.013
Interaction energy analysis for fragmet #1(A:191:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.023
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].
3A193LEU00.0200.0113.815-1.1211.598-0.013-1.605-1.1000.008
4A194ASP-1-0.795-0.9074.353-0.253-0.067-0.001-0.016-0.1690.000
5A195SER00.0340.0097.1400.0530.0530.0000.0000.0000.000
6A196ILE00.0120.0104.364-0.0480.058-0.001-0.010-0.0950.000
7A197GLY00.0200.0114.2740.1550.226-0.001-0.019-0.0510.000
8A198PHE0-0.011-0.0204.983-0.0280.003-0.001-0.002-0.0280.000
9A199SER0-0.019-0.0028.2870.0150.0150.0000.0000.0000.000
10A200ILE00.0280.0164.012-0.0970.0480.001-0.026-0.1200.000
11A201ILE00.004-0.0067.267-0.015-0.0150.0000.0000.0000.000
12A202LYS10.9720.9929.516-0.029-0.0290.0000.0000.0000.000
13A203LYS10.8110.90910.583-0.348-0.3480.0000.0000.0000.000
14A204CYS0-0.080-0.04910.1350.0310.0310.0000.0000.0000.000
15A205ILE0-0.037-0.01812.776-0.020-0.0200.0000.0000.0000.000
16A206HIS00.0190.00215.196-0.019-0.0190.0000.0000.0000.000
17A207ALA0-0.0060.01716.417-0.007-0.0070.0000.0000.0000.000
18A208VAL0-0.028-0.02016.481-0.009-0.0090.0000.0000.0000.000
19A209GLU-1-0.765-0.87418.9130.0020.0020.0000.0000.0000.000
20A210THR0-0.020-0.02220.760-0.003-0.0030.0000.0000.0000.000
21A211ARG10.8480.93119.205-0.216-0.2160.0000.0000.0000.000
22A212GLY00.001-0.00521.8710.0080.0080.0000.0000.0000.000
23A213ILE00.0120.01922.826-0.001-0.0010.0000.0000.0000.000
24A214ASN00.0420.00824.106-0.014-0.0140.0000.0000.0000.000
25A215GLU-1-0.937-0.94723.1290.1400.1400.0000.0000.0000.000
26A216GLN0-0.025-0.02324.713-0.005-0.0050.0000.0000.0000.000
27A217GLY0-0.024-0.01023.6190.0120.0120.0000.0000.0000.000
28A218LEU00.0450.03319.5670.0170.0170.0000.0000.0000.000
29A219TYR0-0.010-0.03413.847-0.003-0.0030.0000.0000.0000.000
30A220ARG10.9010.95717.262-0.052-0.0520.0000.0000.0000.000
31A221ILE0-0.022-0.01219.8220.0090.0090.0000.0000.0000.000
32A222VAL0-0.042-0.01315.7370.0210.0210.0000.0000.0000.000
33A223GLY00.0180.01016.575-0.019-0.0190.0000.0000.0000.000
34A224VAL00.012-0.00617.5340.0120.0120.0000.0000.0000.000
35A225ASN00.0800.02813.2960.1400.1400.0000.0000.0000.000
36A226SER00.0360.01514.2000.0980.0980.0000.0000.0000.000
37A227ARG10.8360.90615.064-0.288-0.2880.0000.0000.0000.000
38A228VAL00.0060.00710.7070.0280.0280.0000.0000.0000.000
39A229GLN00.0260.0079.2630.3780.3780.0000.0000.0000.000
40A230LYS10.9460.98210.090-0.322-0.3220.0000.0000.0000.000
41A231LEU00.0230.02011.076-0.012-0.0120.0000.0000.0000.000
42A232LEU00.015-0.0015.645-0.035-0.0350.0000.0000.0000.000
43A233SER0-0.031-0.0207.158-0.020-0.0200.0000.0000.0000.000
44A234ILE0-0.072-0.0528.668-0.094-0.0940.0000.0000.0000.000
45A235LEU00.0130.0197.636-0.085-0.0850.0000.0000.0000.000
46A236MET0-0.075-0.0242.374-0.676-0.1180.978-0.392-1.1440.001
47A237ASP-1-0.855-0.9406.3410.2720.2720.0000.0000.0000.000
48A238PRO0-0.050-0.0029.4760.0380.0380.0000.0000.0000.000
49A239LYS10.8950.94411.217-0.800-0.8000.0000.0000.0000.000
50A240THR0-0.027-0.02414.625-0.060-0.0600.0000.0000.0000.000
51A241ALA0-0.0180.00414.1910.0130.0130.0000.0000.0000.000
52A242THR0-0.005-0.03815.979-0.012-0.0120.0000.0000.0000.000
53A243GLU-1-0.857-0.90611.7350.4570.4570.0000.0000.0000.000
54A244THR0-0.018-0.01713.8200.0110.0110.0000.0000.0000.000
55A245GLU-1-0.841-0.90315.1190.1790.1790.0000.0000.0000.000
56A246THR0-0.0090.00415.3840.0000.0000.0000.0000.0000.000
57A247GLU-1-0.893-0.93616.5020.1410.1410.0000.0000.0000.000
58A248ILE0-0.050-0.02612.8890.0170.0170.0000.0000.0000.000
59A249CYS00.0110.00116.604-0.041-0.0410.0000.0000.0000.000
60A250ALA00.0630.00719.3900.0170.0170.0000.0000.0000.000
61A251GLU-1-0.866-0.92120.4740.2610.2610.0000.0000.0000.000
62A252TRP0-0.087-0.03515.5220.0420.0420.0000.0000.0000.000
63A253GLU-1-0.774-0.87318.8370.2550.2550.0000.0000.0000.000
64A254ILE00.1170.05818.0380.0450.0450.0000.0000.0000.000
65A255LYS10.9210.95617.603-0.215-0.2150.0000.0000.0000.000
66A256THR0-0.047-0.02914.5430.0230.0230.0000.0000.0000.000
67A257ILE00.0520.02613.6780.0960.0960.0000.0000.0000.000
68A258THR0-0.0070.00512.9130.0300.0300.0000.0000.0000.000
69A259SER0-0.013-0.02512.770-0.035-0.0350.0000.0000.0000.000
70A260ALA00.0000.0149.5430.0800.0800.0000.0000.0000.000
71A261LEU00.0380.0318.1160.2200.2200.0000.0000.0000.000
72A262LYS10.8880.9238.151-0.289-0.2890.0000.0000.0000.000
73A263THR0-0.061-0.0537.720-0.096-0.0960.0000.0000.0000.000
74A264TYR00.0830.0412.087-1.146-0.8482.701-1.118-1.881-0.008
75A265LEU00.0310.0153.329-2.474-1.8790.023-0.340-0.278-0.003
76A266ARG10.9010.9516.008-0.611-0.6110.0000.0000.0000.000
77A267MET0-0.035-0.0092.379-2.533-1.6562.465-1.278-2.0640.009
78A268LEU0-0.0360.0132.405-6.553-4.5551.571-1.718-1.850-0.020
79A269PRO00.0230.0223.9521.3291.5280.000-0.029-0.1710.000
80A270GLY00.0070.0046.2700.6490.6490.0000.0000.0000.000
81A271PRO0-0.053-0.0098.049-0.289-0.2890.0000.0000.0000.000
82A272LEU00.0500.0279.118-0.006-0.0060.0000.0000.0000.000
83A273MET00.0050.00910.4990.0580.0580.0000.0000.0000.000
84A274MET0-0.014-0.00712.8690.0790.0790.0000.0000.0000.000
85A275TYR00.0550.00711.8190.0390.0390.0000.0000.0000.000
86A276GLN0-0.028-0.01215.8120.0190.0190.0000.0000.0000.000
87A277PHE00.0250.01017.7980.0460.0460.0000.0000.0000.000
88A278GLN0-0.014-0.00315.201-0.009-0.0090.0000.0000.0000.000
89A279ARG10.8450.89219.2990.2670.2670.0000.0000.0000.000
90A280SER0-0.0020.00322.6590.0300.0300.0000.0000.0000.000
91A281PHE00.0580.01118.3600.0230.0230.0000.0000.0000.000
92A282ILE0-0.0150.00220.7750.0210.0210.0000.0000.0000.000
93A283LYS10.8660.92224.0950.1750.1750.0000.0000.0000.000
94A284ALA0-0.014-0.00725.7370.0150.0150.0000.0000.0000.000
95A285ALA00.0260.00425.0080.0130.0130.0000.0000.0000.000
96A286LYS10.7900.88527.0910.1410.1410.0000.0000.0000.000
97A287LEU0-0.061-0.00830.0740.0090.0090.0000.0000.0000.000
98A288GLU-1-0.850-0.93332.578-0.073-0.0730.0000.0000.0000.000
99A289ASN0-0.031-0.00635.3110.0070.0070.0000.0000.0000.000
100A290GLN00.0780.03230.821-0.010-0.0100.0000.0000.0000.000
101A291GLU-1-0.890-0.94632.308-0.077-0.0770.0000.0000.0000.000
102A292SER0-0.026-0.01732.739-0.004-0.0040.0000.0000.0000.000
103A293ARG10.8460.92428.7800.0820.0820.0000.0000.0000.000
104A294VAL00.0340.02127.782-0.014-0.0140.0000.0000.0000.000
105A295SER00.0100.01027.791-0.010-0.0100.0000.0000.0000.000
106A296GLU-1-0.844-0.92027.897-0.175-0.1750.0000.0000.0000.000
107A297ILE00.0060.00622.543-0.020-0.0200.0000.0000.0000.000
108A298HIS0-0.020-0.00723.694-0.016-0.0160.0000.0000.0000.000
109A299SER00.0440.00524.769-0.019-0.0190.0000.0000.0000.000
110A300LEU0-0.092-0.04022.190-0.014-0.0140.0000.0000.0000.000
111A301VAL00.0190.01119.544-0.035-0.0350.0000.0000.0000.000
112A302HIS0-0.035-0.03120.332-0.033-0.0330.0000.0000.0000.000
113A303ARG10.8580.94022.3660.2120.2120.0000.0000.0000.000
114A304LEU0-0.0530.00316.083-0.030-0.0300.0000.0000.0000.000
115A305PRO00.0380.01315.1780.0390.0390.0000.0000.0000.000
116A306GLU-1-0.766-0.87115.957-0.315-0.3150.0000.0000.0000.000
117A307LYS10.8770.9299.6310.8770.8770.0000.0000.0000.000
118A308ASN0-0.002-0.01611.663-0.029-0.0290.0000.0000.0000.000
119A309ARG10.8900.93913.0440.3330.3330.0000.0000.0000.000
120A310GLN0-0.035-0.03913.9620.0270.0270.0000.0000.0000.000
121A311MET0-0.035-0.0076.612-0.020-0.0200.0000.0000.0000.000
122A312LEU0-0.012-0.01112.1110.0530.0530.0000.0000.0000.000
123A313HIS00.0150.01414.4970.0450.0450.0000.0000.0000.000
124A314LEU0-0.012-0.00412.5990.0380.0380.0000.0000.0000.000
125A315LEU0-0.019-0.01710.6900.0410.0410.0000.0000.0000.000
126A316MET0-0.015-0.00315.0530.0400.0400.0000.0000.0000.000
127A317ASN00.0060.00618.4930.0350.0350.0000.0000.0000.000
128A318HIS0-0.001-0.00616.4450.0350.0350.0000.0000.0000.000
129A319LEU0-0.004-0.01716.2310.0210.0210.0000.0000.0000.000
130A320ALA00.0150.01719.8250.0120.0120.0000.0000.0000.000
131A321LYS10.8520.93220.4220.0190.0190.0000.0000.0000.000
132A322VAL0-0.042-0.02219.7880.0120.0120.0000.0000.0000.000
133A323ALA00.0080.00023.0600.0070.0070.0000.0000.0000.000
134A324ASP-1-0.927-0.94825.157-0.009-0.0090.0000.0000.0000.000
135A325ASN0-0.041-0.01826.7490.0000.0000.0000.0000.0000.000
136A326HIS00.0220.01027.6830.0090.0090.0000.0000.0000.000
137A327LYS10.8450.91928.5740.0030.0030.0000.0000.0000.000
138A328GLN00.0290.02129.7070.0070.0070.0000.0000.0000.000
139A329ASN00.0560.02125.0400.0000.0000.0000.0000.0000.000
140A330LEU0-0.031-0.02626.0810.0060.0060.0000.0000.0000.000
141A331MET0-0.072-0.01020.813-0.002-0.0020.0000.0000.0000.000
142A332THR00.0450.02824.961-0.006-0.0060.0000.0000.0000.000
143A333VAL00.0960.03824.1280.0020.0020.0000.0000.0000.000
144A334ALA00.0440.02923.499-0.007-0.0070.0000.0000.0000.000
145A335ASN0-0.084-0.05323.898-0.008-0.0080.0000.0000.0000.000
146A336LEU0-0.008-0.00119.1020.0060.0060.0000.0000.0000.000
147A337GLY00.0720.03319.064-0.014-0.0140.0000.0000.0000.000
148A338VAL0-0.037-0.02219.661-0.019-0.0190.0000.0000.0000.000
149A339VAL0-0.059-0.01715.803-0.001-0.0010.0000.0000.0000.000
150A340PHE00.006-0.02712.461-0.001-0.0010.0000.0000.0000.000
151A341GLY00.0590.04614.983-0.056-0.0560.0000.0000.0000.000
152A342PRO0-0.049-0.03215.908-0.048-0.0480.0000.0000.0000.000
153A343THR0-0.109-0.04910.244-0.009-0.0090.0000.0000.0000.000
154A344LEU0-0.019-0.01210.635-0.145-0.1450.0000.0000.0000.000
155A345LEU00.0010.01312.566-0.082-0.0820.0000.0000.0000.000
156A346ARG10.8660.9306.5561.4371.4370.0000.0000.0000.000
157A347PRO00.0520.01714.060-0.010-0.0100.0000.0000.0000.000
158A348GLN0-0.046-0.03716.580-0.023-0.0230.0000.0000.0000.000
159A349GLU-1-0.824-0.89417.629-0.255-0.2550.0000.0000.0000.000
160A350GLU-1-0.838-0.89819.181-0.181-0.1810.0000.0000.0000.000
161A351THR0-0.063-0.04121.2960.0160.0160.0000.0000.0000.000
162A352VAL00.0300.01123.6040.0110.0110.0000.0000.0000.000
163A353ALA00.0390.03227.3210.0100.0100.0000.0000.0000.000
164A354ALA00.0180.00724.2140.0050.0050.0000.0000.0000.000
165A355ILE00.0310.01224.337-0.008-0.0080.0000.0000.0000.000
166A356MET0-0.042-0.02625.9040.0080.0080.0000.0000.0000.000
167A357ASP-1-0.776-0.87624.924-0.130-0.1300.0000.0000.0000.000
168A358ILE00.0070.00220.702-0.012-0.0120.0000.0000.0000.000
169A359LYS10.9100.94722.4770.0800.0800.0000.0000.0000.000
170A360PHE00.0470.01124.4760.0030.0030.0000.0000.0000.000
171A361GLN0-0.030-0.01017.222-0.021-0.0210.0000.0000.0000.000
172A362ASN00.004-0.01620.181-0.028-0.0280.0000.0000.0000.000
173A363ILE00.0410.03621.7610.0010.0010.0000.0000.0000.000
174A364VAL00.0010.01119.8120.0010.0010.0000.0000.0000.000
175A365ILE0-0.037-0.01516.547-0.005-0.0050.0000.0000.0000.000
176A366GLU-1-0.868-0.94420.150-0.072-0.0720.0000.0000.0000.000
177A367ILE0-0.0090.00123.5620.0060.0060.0000.0000.0000.000
178A368LEU0-0.024-0.01618.4440.0010.0010.0000.0000.0000.000
179A369ILE0-0.007-0.00819.7070.0040.0040.0000.0000.0000.000
180A370GLU-1-0.926-0.97422.596-0.058-0.0580.0000.0000.0000.000
181A371ASN0-0.064-0.02525.3200.0120.0120.0000.0000.0000.000
182A372HIS00.0140.01121.968-0.005-0.0050.0000.0000.0000.000
183A373GLU-1-0.874-0.93023.895-0.084-0.0840.0000.0000.0000.000
184A374LYS10.8690.92726.2660.1060.1060.0000.0000.0000.000
185A375ILE0-0.015-0.00322.581-0.006-0.0060.0000.0000.0000.000
186A376PHE0-0.018-0.02618.482-0.021-0.0210.0000.0000.0000.000
187A377ASN0-0.0220.00323.004-0.014-0.0140.0000.0000.0000.000
188A378THR0-0.042-0.02125.6530.0100.0100.0000.0000.0000.000
189A379VAL00.0080.00426.965-0.013-0.0130.0000.0000.0000.000
190A380PRO0-0.0280.00727.0370.0080.0080.0000.0000.0000.000
191A381GLU-1-0.866-0.92429.858-0.106-0.1060.0000.0000.0000.000