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: R85M8

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 OptAll
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 -2195981.823042
FMO2-HF: Nuclear repulsion 2118844.752293
FMO2-HF: Total energy -77137.070749
FMO2-MP2: Total energy -77359.268869


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.
-10.96-3.087.776-6.489-9.163-0.021
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 : 0.054 / q_NPA : 0.029
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].
3A193LEU00.0300.0313.889-0.8811.364-0.016-1.357-0.8730.005
4A194ASP-1-0.785-0.8954.980-0.1160.009-0.001-0.003-0.1200.000
5A195SER00.0080.0097.5330.0680.0680.0000.0000.0000.000
6A196ILE00.0050.0054.351-0.0370.064-0.001-0.008-0.0920.000
7A197GLY0-0.002-0.0024.3580.1330.188-0.001-0.013-0.0400.000
8A198PHE0-0.001-0.0225.0550.0150.055-0.001-0.001-0.0370.000
9A199SER0-0.013-0.0078.3180.0190.0190.0000.0000.0000.000
10A200ILE00.0120.0073.882-0.0690.0700.001-0.022-0.1170.000
11A201ILE0-0.004-0.0047.802-0.017-0.0170.0000.0000.0000.000
12A202LYS10.9470.9799.954-0.064-0.0640.0000.0000.0000.000
13A203LYS10.7820.88410.587-0.389-0.3890.0000.0000.0000.000
14A204CYS0-0.070-0.04010.4650.0290.0290.0000.0000.0000.000
15A205ILE0-0.018-0.00712.849-0.025-0.0250.0000.0000.0000.000
16A206HIS00.0230.00415.691-0.022-0.0220.0000.0000.0000.000
17A207ALA0-0.0130.00816.533-0.010-0.0100.0000.0000.0000.000
18A208VAL0-0.049-0.02616.636-0.009-0.0090.0000.0000.0000.000
19A209GLU-1-0.756-0.87519.2420.0250.0250.0000.0000.0000.000
20A210THR0-0.024-0.02520.811-0.004-0.0040.0000.0000.0000.000
21A211ARG10.8220.90719.106-0.256-0.2560.0000.0000.0000.000
22A212GLY00.015-0.00621.6990.0110.0110.0000.0000.0000.000
23A213ILE00.0270.02922.525-0.001-0.0010.0000.0000.0000.000
24A214ASN00.0510.02023.908-0.014-0.0140.0000.0000.0000.000
25A215GLU-1-0.923-0.96022.5870.1690.1690.0000.0000.0000.000
26A216GLN0-0.040-0.03324.210-0.004-0.0040.0000.0000.0000.000
27A217GLY0-0.011-0.00623.4190.0090.0090.0000.0000.0000.000
28A218LEU00.0220.01719.2570.0210.0210.0000.0000.0000.000
29A219TYR0-0.005-0.02813.4860.0000.0000.0000.0000.0000.000
30A220ARG10.9250.96017.119-0.069-0.0690.0000.0000.0000.000
31A221ILE0-0.0070.00219.4860.0130.0130.0000.0000.0000.000
32A222VAL0-0.018-0.01015.7450.0260.0260.0000.0000.0000.000
33A223GLY00.0240.01916.393-0.029-0.0290.0000.0000.0000.000
34A224VAL00.0210.00017.5900.0060.0060.0000.0000.0000.000
35A225ASN00.0810.03513.1550.1390.1390.0000.0000.0000.000
36A226SER00.0390.01314.1140.1070.1070.0000.0000.0000.000
37A227ARG10.8010.88915.104-0.330-0.3300.0000.0000.0000.000
38A228VAL0-0.0030.01010.8140.0240.0240.0000.0000.0000.000
39A229GLN00.0280.0039.0220.4340.4340.0000.0000.0000.000
40A230LYS10.9490.99110.173-0.349-0.3490.0000.0000.0000.000
41A231LEU00.0370.02911.4570.0040.0040.0000.0000.0000.000
42A232LEU00.0080.0045.870-0.038-0.0380.0000.0000.0000.000
43A233SER0-0.068-0.0537.2700.0140.0140.0000.0000.0000.000
44A234ILE0-0.086-0.0518.803-0.152-0.1520.0000.0000.0000.000
45A235LEU00.0240.0108.143-0.047-0.0470.0000.0000.0000.000
46A236MET0-0.047-0.0192.298-0.633-0.6672.410-0.726-1.650-0.001
47A237ASP-1-0.867-0.9486.3130.2230.2230.0000.0000.0000.000
48A238PRO0-0.0290.0039.4590.0270.0270.0000.0000.0000.000
49A239LYS10.9000.95711.432-0.762-0.7620.0000.0000.0000.000
50A240THR0-0.026-0.02914.714-0.056-0.0560.0000.0000.0000.000
51A241ALA0-0.0350.00314.3790.0120.0120.0000.0000.0000.000
52A242THR00.033-0.01716.459-0.014-0.0140.0000.0000.0000.000
53A243GLU-1-0.845-0.89112.0360.4780.4780.0000.0000.0000.000
54A244THR0-0.014-0.01813.7980.0160.0160.0000.0000.0000.000
55A245GLU-1-0.857-0.90614.9440.1750.1750.0000.0000.0000.000
56A246THR00.0150.00915.354-0.002-0.0020.0000.0000.0000.000
57A247GLU-1-0.881-0.92215.6200.1890.1890.0000.0000.0000.000
58A248ILE0-0.028-0.01812.8470.0240.0240.0000.0000.0000.000
59A249CYS00.006-0.00116.707-0.041-0.0410.0000.0000.0000.000
60A250ALA00.0720.00919.7570.0230.0230.0000.0000.0000.000
61A251GLU-1-0.873-0.91720.4420.2870.2870.0000.0000.0000.000
62A252TRP0-0.054-0.01115.8650.0480.0480.0000.0000.0000.000
63A253GLU-1-0.734-0.84719.0530.3150.3150.0000.0000.0000.000
64A254ILE00.0850.05818.2280.0520.0520.0000.0000.0000.000
65A255LYS10.9280.97417.376-0.244-0.2440.0000.0000.0000.000
66A256THR0-0.063-0.04115.1110.0310.0310.0000.0000.0000.000
67A257ILE00.0320.02213.7190.1060.1060.0000.0000.0000.000
68A258THR0-0.011-0.02612.5620.0650.0650.0000.0000.0000.000
69A259SER0-0.004-0.02312.706-0.039-0.0390.0000.0000.0000.000
70A260ALA00.0090.0249.5830.1050.1050.0000.0000.0000.000
71A261LEU00.0440.0297.8340.3240.3240.0000.0000.0000.000
72A262LYS10.8190.8937.866-0.341-0.3410.0000.0000.0000.000
73A263THR0-0.059-0.0457.844-0.054-0.0540.0000.0000.0000.000
74A264TYR00.0730.0202.353-2.453-0.8541.430-0.994-2.036-0.006
75A265LEU00.0190.0013.467-2.143-1.6760.020-0.239-0.247-0.002
76A266ARG10.9040.9536.047-0.610-0.6100.0000.0000.0000.000
77A267MET0-0.029-0.0042.462-1.843-0.6041.614-1.185-1.6670.005
78A268LEU0-0.0240.0182.378-6.430-4.7212.314-1.955-2.068-0.022
79A269PRO00.0080.0103.5191.4831.6780.0070.014-0.2160.000
80A270GLY0-0.006-0.0016.2910.6030.6030.0000.0000.0000.000
81A271PRO0-0.0450.0027.890-0.252-0.2520.0000.0000.0000.000
82A272LEU00.0300.0239.134-0.053-0.0530.0000.0000.0000.000
83A273MET00.0080.00610.5950.0430.0430.0000.0000.0000.000
84A274MET0-0.009-0.00512.8900.0640.0640.0000.0000.0000.000
85A275TYR00.0490.00411.8470.0350.0350.0000.0000.0000.000
86A276GLN0-0.029-0.00715.8710.0140.0140.0000.0000.0000.000
87A277PHE00.0260.01017.6480.0430.0430.0000.0000.0000.000
88A278GLN00.0160.01115.088-0.004-0.0040.0000.0000.0000.000
89A279ARG10.8410.89319.1320.2540.2540.0000.0000.0000.000
90A280SER00.0120.00922.5500.0270.0270.0000.0000.0000.000
91A281PHE00.0580.01218.3900.0200.0200.0000.0000.0000.000
92A282ILE0-0.0120.00321.0970.0210.0210.0000.0000.0000.000
93A283LYS10.8550.91424.0830.1650.1650.0000.0000.0000.000
94A284ALA0-0.015-0.00525.4300.0130.0130.0000.0000.0000.000
95A285ALA00.027-0.00524.8380.0130.0130.0000.0000.0000.000
96A286LYS10.7830.87926.9170.1250.1250.0000.0000.0000.000
97A287LEU0-0.053-0.00129.9550.0080.0080.0000.0000.0000.000
98A288GLU-1-0.857-0.93332.368-0.063-0.0630.0000.0000.0000.000
99A289ASN0-0.061-0.03535.3190.0050.0050.0000.0000.0000.000
100A290GLN00.1070.04630.172-0.009-0.0090.0000.0000.0000.000
101A291GLU-1-0.835-0.91131.658-0.069-0.0690.0000.0000.0000.000
102A292SER0-0.0150.00132.074-0.005-0.0050.0000.0000.0000.000
103A293ARG10.8170.92328.4280.0680.0680.0000.0000.0000.000
104A294VAL00.0130.00927.488-0.014-0.0140.0000.0000.0000.000
105A295SER0-0.011-0.01327.492-0.010-0.0100.0000.0000.0000.000
106A296GLU-1-0.814-0.89927.517-0.168-0.1680.0000.0000.0000.000
107A297ILE0-0.0020.00022.265-0.020-0.0200.0000.0000.0000.000
108A298HIS0-0.0040.00923.209-0.015-0.0150.0000.0000.0000.000
109A299SER00.0540.01924.344-0.019-0.0190.0000.0000.0000.000
110A300LEU0-0.096-0.02121.975-0.012-0.0120.0000.0000.0000.000
111A301VAL00.0300.01319.164-0.033-0.0330.0000.0000.0000.000
112A302HIS0-0.033-0.02120.146-0.028-0.0280.0000.0000.0000.000
113A303ARG10.8100.88322.3370.1940.1940.0000.0000.0000.000
114A304LEU0-0.0370.01115.831-0.028-0.0280.0000.0000.0000.000
115A305PRO00.0220.00314.8450.0370.0370.0000.0000.0000.000
116A306GLU-1-0.756-0.85816.075-0.288-0.2880.0000.0000.0000.000
117A307LYS10.8780.93210.0480.8670.8670.0000.0000.0000.000
118A308ASN0-0.001-0.01711.570-0.027-0.0270.0000.0000.0000.000
119A309ARG10.8630.91712.9320.3180.3180.0000.0000.0000.000
120A310GLN0-0.029-0.02914.6300.0270.0270.0000.0000.0000.000
121A311MET0-0.027-0.0117.207-0.020-0.0200.0000.0000.0000.000
122A312LEU0-0.009-0.00712.3230.0510.0510.0000.0000.0000.000
123A313HIS00.0070.00714.3260.0460.0460.0000.0000.0000.000
124A314LEU0-0.007-0.00313.0840.0360.0360.0000.0000.0000.000
125A315LEU0-0.017-0.01010.4610.0470.0470.0000.0000.0000.000
126A316MET0-0.035-0.01214.8440.0400.0400.0000.0000.0000.000
127A317ASN00.0340.00318.2720.0330.0330.0000.0000.0000.000
128A318HIS0-0.036-0.01516.1910.0420.0420.0000.0000.0000.000
129A319LEU0-0.014-0.02315.5020.0190.0190.0000.0000.0000.000
130A320ALA00.0280.01819.4300.0090.0090.0000.0000.0000.000
131A321LYS10.8380.92720.541-0.002-0.0020.0000.0000.0000.000
132A322VAL0-0.062-0.03119.5760.0110.0110.0000.0000.0000.000
133A323ALA00.0110.01522.8800.0050.0050.0000.0000.0000.000
134A324ASP-1-0.905-0.93624.9020.0080.0080.0000.0000.0000.000
135A325ASN0-0.037-0.02726.412-0.002-0.0020.0000.0000.0000.000
136A326HIS00.0180.01027.2980.0080.0080.0000.0000.0000.000
137A327LYS10.8490.90628.180-0.012-0.0120.0000.0000.0000.000
138A328GLN00.0010.01429.1830.0060.0060.0000.0000.0000.000
139A329ASN00.0430.01424.3920.0000.0000.0000.0000.0000.000
140A330LEU0-0.0050.00025.5040.0070.0070.0000.0000.0000.000
141A331MET0-0.113-0.01220.693-0.002-0.0020.0000.0000.0000.000
142A332THR00.0840.03524.261-0.004-0.0040.0000.0000.0000.000
143A333VAL00.0720.03723.6860.0040.0040.0000.0000.0000.000
144A334ALA00.0540.03322.956-0.005-0.0050.0000.0000.0000.000
145A335ASN0-0.085-0.04623.343-0.007-0.0070.0000.0000.0000.000
146A336LEU0-0.012-0.00218.8300.0120.0120.0000.0000.0000.000
147A337GLY00.0620.02618.703-0.010-0.0100.0000.0000.0000.000
148A338VAL0-0.018-0.01719.350-0.018-0.0180.0000.0000.0000.000
149A339VAL0-0.049-0.00915.4800.0000.0000.0000.0000.0000.000
150A340PHE00.001-0.01912.1920.0030.0030.0000.0000.0000.000
151A341GLY00.0690.04114.568-0.056-0.0560.0000.0000.0000.000
152A342PRO0-0.039-0.02215.455-0.054-0.0540.0000.0000.0000.000
153A343THR0-0.099-0.04410.0080.0060.0060.0000.0000.0000.000
154A344LEU0-0.021-0.01510.233-0.146-0.1460.0000.0000.0000.000
155A345LEU0-0.0210.00212.216-0.089-0.0890.0000.0000.0000.000
156A346ARG10.8560.9206.3241.2801.2800.0000.0000.0000.000
157A347PRO00.0370.00713.793-0.010-0.0100.0000.0000.0000.000
158A348GLN0-0.031-0.02516.526-0.017-0.0170.0000.0000.0000.000
159A349GLU-1-0.824-0.88817.504-0.246-0.2460.0000.0000.0000.000
160A350GLU-1-0.840-0.89819.165-0.170-0.1700.0000.0000.0000.000
161A351THR0-0.060-0.03521.2580.0170.0170.0000.0000.0000.000
162A352VAL00.0300.01523.5680.0130.0130.0000.0000.0000.000
163A353ALA00.0210.00026.8950.0030.0030.0000.0000.0000.000
164A354ALA00.0400.02624.2200.0050.0050.0000.0000.0000.000
165A355ILE00.0220.01424.220-0.006-0.0060.0000.0000.0000.000
166A356MET0-0.022-0.01325.6360.0080.0080.0000.0000.0000.000
167A357ASP-1-0.802-0.88724.681-0.114-0.1140.0000.0000.0000.000
168A358ILE00.0090.00720.414-0.008-0.0080.0000.0000.0000.000
169A359LYS10.9090.94622.1490.0670.0670.0000.0000.0000.000
170A360PHE00.0380.00224.3490.0050.0050.0000.0000.0000.000
171A361GLN0-0.030-0.02016.723-0.024-0.0240.0000.0000.0000.000
172A362ASN00.0000.00419.869-0.021-0.0210.0000.0000.0000.000
173A363ILE00.0510.03121.535-0.003-0.0030.0000.0000.0000.000
174A364VAL0-0.0070.00219.439-0.001-0.0010.0000.0000.0000.000
175A365ILE0-0.023-0.00916.085-0.005-0.0050.0000.0000.0000.000
176A366GLU-1-0.866-0.95319.819-0.053-0.0530.0000.0000.0000.000
177A367ILE00.0130.01223.1660.0060.0060.0000.0000.0000.000
178A368LEU0-0.014-0.01318.2130.0000.0000.0000.0000.0000.000
179A369ILE00.007-0.00319.3410.0030.0030.0000.0000.0000.000
180A370GLU-1-0.939-0.96922.062-0.045-0.0450.0000.0000.0000.000
181A371ASN0-0.047-0.03124.9520.0080.0080.0000.0000.0000.000
182A372HIS0-0.009-0.00121.607-0.002-0.0020.0000.0000.0000.000
183A373GLU-1-0.842-0.90623.420-0.073-0.0730.0000.0000.0000.000
184A374LYS10.8270.89726.2050.0970.0970.0000.0000.0000.000
185A375ILE0-0.0030.00121.858-0.008-0.0080.0000.0000.0000.000
186A376PHE0-0.026-0.02718.137-0.024-0.0240.0000.0000.0000.000
187A377ASN0-0.019-0.00222.742-0.014-0.0140.0000.0000.0000.000
188A378THR0-0.050-0.03425.7160.0100.0100.0000.0000.0000.000
189A379VAL00.0180.00926.640-0.014-0.0140.0000.0000.0000.000
190A380PRO0-0.0350.00726.7020.0080.0080.0000.0000.0000.000
191A381GLU-1-0.853-0.91829.467-0.097-0.0970.0000.0000.0000.000