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: 1NN3Z

Calculation Name: 5GI4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GI4

Chain ID: A

ChEMBL ID:

UniProt ID: P0A9P6

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2490082.581004
FMO2-HF: Nuclear repulsion 2403857.178218
FMO2-HF: Total energy -86225.402787
FMO2-MP2: Total energy -86478.86058


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:218:PRO)


Summations of interaction energy for fragment #1(A:218:PRO)
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.
-2.0341.9182.713-2.126-4.538-0.012
Interaction energy analysis for fragmet #1(A:218:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.021
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].
3A220ILE0-0.044-0.0192.478-0.4121.7530.594-0.938-1.821-0.001
4A221SER00.0910.0515.5910.2530.2530.0000.0000.0000.000
5A222GLN0-0.024-0.0147.7960.4000.4000.0000.0000.0000.000
6A223SER0-0.013-0.00511.2220.1450.1450.0000.0000.0000.000
7A224TYR0-0.111-0.10614.991-0.029-0.0290.0000.0000.0000.000
8A225TRP00.0880.05118.0340.0220.0220.0000.0000.0000.000
9A226THR0-0.049-0.06121.5300.0020.0020.0000.0000.0000.000
10A227VAL0-0.069-0.02524.4780.0110.0110.0000.0000.0000.000
11A228TRP0-0.005-0.01026.4490.0140.0140.0000.0000.0000.000
12A229GLY00.0050.01429.352-0.004-0.0040.0000.0000.0000.000
13A230MET0-0.0050.01928.3330.0020.0020.0000.0000.0000.000
14A231ARG10.9530.97129.4200.1360.1360.0000.0000.0000.000
15A232LYS10.8470.92923.8460.2440.2440.0000.0000.0000.000
16A233ASN0-0.017-0.01124.803-0.011-0.0110.0000.0000.0000.000
17A234GLU-1-0.880-0.94426.226-0.142-0.1420.0000.0000.0000.000
18A235ALA00.0490.01224.475-0.001-0.0010.0000.0000.0000.000
19A236LEU0-0.029-0.01119.573-0.015-0.0150.0000.0000.0000.000
20A237VAL00.0230.01622.154-0.010-0.0100.0000.0000.0000.000
21A238ARG10.8520.90824.2410.1500.1500.0000.0000.0000.000
22A239PHE00.019-0.02019.3330.0010.0010.0000.0000.0000.000
23A240LEU0-0.050-0.01118.450-0.014-0.0140.0000.0000.0000.000
24A241GLU-1-0.764-0.84520.687-0.128-0.1280.0000.0000.0000.000
25A242ALA0-0.030-0.00521.3220.0140.0140.0000.0000.0000.000
26A243GLU-1-0.873-0.93715.638-0.361-0.3610.0000.0000.0000.000
27A244ASP-1-0.757-0.83218.140-0.172-0.1720.0000.0000.0000.000
28A245PHE0-0.055-0.01714.771-0.047-0.0470.0000.0000.0000.000
29A246ASP-1-0.880-0.90814.201-0.147-0.1470.0000.0000.0000.000
30A247ALA00.0280.00914.4930.0280.0280.0000.0000.0000.000
31A248ALA0-0.037-0.01913.809-0.063-0.0630.0000.0000.0000.000
32A249ILE0-0.033-0.01312.5300.0430.0430.0000.0000.0000.000
33A250ILE00.0130.00514.907-0.046-0.0460.0000.0000.0000.000
34A251PHE00.0160.00112.6630.0410.0410.0000.0000.0000.000
35A252VAL00.0160.00217.7480.0020.0020.0000.0000.0000.000
36A253ARG10.7470.82921.1510.2480.2480.0000.0000.0000.000
37A254THR0-0.043-0.02623.5430.0100.0100.0000.0000.0000.000
38A255LYS10.8850.90326.0190.1500.1500.0000.0000.0000.000
39A256ASN00.0560.03427.374-0.003-0.0030.0000.0000.0000.000
40A257ALA00.0320.03225.5820.0050.0050.0000.0000.0000.000
41A258THR0-0.034-0.04722.977-0.006-0.0060.0000.0000.0000.000
42A259LEU0-0.029-0.01325.1450.0030.0030.0000.0000.0000.000
43A260GLU-1-0.868-0.92227.944-0.174-0.1740.0000.0000.0000.000
44A261VAL00.011-0.00322.9740.0030.0030.0000.0000.0000.000
45A262ALA00.0130.01125.387-0.002-0.0020.0000.0000.0000.000
46A263GLU-1-0.845-0.92426.305-0.117-0.1170.0000.0000.0000.000
47A264ALA0-0.042-0.02727.6030.0050.0050.0000.0000.0000.000
48A265LEU0-0.029-0.00822.288-0.002-0.0020.0000.0000.0000.000
49A266GLU-1-0.775-0.87226.510-0.134-0.1340.0000.0000.0000.000
50A267ARG10.8790.94328.9850.1290.1290.0000.0000.0000.000
51A268ASN0-0.102-0.06228.1020.0110.0110.0000.0000.0000.000
52A269GLY00.0020.01728.633-0.001-0.0010.0000.0000.0000.000
53A270TYR0-0.013-0.02422.978-0.001-0.0010.0000.0000.0000.000
54A271ASN00.0000.00824.1480.0060.0060.0000.0000.0000.000
55A272SER0-0.029-0.02623.002-0.021-0.0210.0000.0000.0000.000
56A273ALA00.0240.00222.9470.0170.0170.0000.0000.0000.000
57A274ALA00.0130.00822.776-0.020-0.0200.0000.0000.0000.000
58A275LEU00.0370.00718.9500.0050.0050.0000.0000.0000.000
59A276ASN00.025-0.01522.443-0.009-0.0090.0000.0000.0000.000
60A277GLY00.012-0.00724.9070.0000.0000.0000.0000.0000.000
61A278ASP-1-0.838-0.89926.407-0.138-0.1380.0000.0000.0000.000
62A279MET0-0.0070.02725.4320.0050.0050.0000.0000.0000.000
63A280ASN0-0.0110.01625.663-0.009-0.0090.0000.0000.0000.000
64A281GLN0-0.003-0.00522.9280.0040.0040.0000.0000.0000.000
65A282ALA00.0690.00926.064-0.009-0.0090.0000.0000.0000.000
66A283LEU00.0130.02326.930-0.003-0.0030.0000.0000.0000.000
67A284ARG10.8610.90720.3370.1800.1800.0000.0000.0000.000
68A285GLU-1-0.835-0.90022.314-0.127-0.1270.0000.0000.0000.000
69A286GLN0-0.004-0.00723.081-0.004-0.0040.0000.0000.0000.000
70A287THR0-0.041-0.02921.8350.0030.0030.0000.0000.0000.000
71A288LEU00.021-0.00717.304-0.011-0.0110.0000.0000.0000.000
72A289GLU-1-0.826-0.88319.531-0.110-0.1100.0000.0000.0000.000
73A290ARG10.8620.92121.8110.1340.1340.0000.0000.0000.000
74A291LEU0-0.0270.00015.8860.0010.0010.0000.0000.0000.000
75A292LYS10.8180.88817.0210.0980.0980.0000.0000.0000.000
76A293ASP-1-0.826-0.89718.683-0.096-0.0960.0000.0000.0000.000
77A294GLY00.0520.03721.3920.0120.0120.0000.0000.0000.000
78A295ARG10.7760.86622.2730.0940.0940.0000.0000.0000.000
79A296LEU0-0.061-0.01821.7440.0030.0030.0000.0000.0000.000
80A297ASP-1-0.773-0.85819.451-0.172-0.1720.0000.0000.0000.000
81A298ILE0-0.008-0.00518.172-0.035-0.0350.0000.0000.0000.000
82A299LEU00.0090.01317.6090.0260.0260.0000.0000.0000.000
83A300ILE00.0140.02118.560-0.035-0.0350.0000.0000.0000.000
84A301ALA0-0.0050.01417.7730.0280.0280.0000.0000.0000.000
85A302THR00.0000.00019.779-0.007-0.0070.0000.0000.0000.000
86A303ASP-1-0.767-0.89015.904-0.432-0.4320.0000.0000.0000.000
87A304VAL0-0.043-0.03118.400-0.001-0.0010.0000.0000.0000.000
88A305ALA0-0.0150.01020.8860.0120.0120.0000.0000.0000.000
89A306ALA00.0540.03715.9900.0090.0090.0000.0000.0000.000
90A307ARG10.9310.98715.2510.2300.2300.0000.0000.0000.000
91A308GLY0-0.0450.00115.217-0.002-0.0020.0000.0000.0000.000
92A309LEU00.0090.0089.899-0.020-0.0200.0000.0000.0000.000
93A310ASP-1-0.862-0.9599.810-0.431-0.4310.0000.0000.0000.000
94A311VAL0-0.056-0.03412.3730.0610.0610.0000.0000.0000.000
95A312GLU-1-0.868-0.9338.855-0.156-0.1560.0000.0000.0000.000
96A313ARG10.7830.86912.1010.2320.2320.0000.0000.0000.000
97A314ILE0-0.0310.00510.5340.0140.0140.0000.0000.0000.000
98A315SER00.0730.0539.298-0.139-0.1390.0000.0000.0000.000
99A316LEU0-0.036-0.00710.331-0.070-0.0700.0000.0000.0000.000
100A317VAL00.0130.0109.2140.0710.0710.0000.0000.0000.000
101A318VAL00.0160.00011.968-0.011-0.0110.0000.0000.0000.000
102A319ASN0-0.009-0.00913.3500.0790.0790.0000.0000.0000.000
103A320TYR00.0410.00916.8210.0210.0210.0000.0000.0000.000
104A321ASP-1-0.814-0.91320.338-0.223-0.2230.0000.0000.0000.000
105A322ILE0-0.0180.00518.577-0.030-0.0300.0000.0000.0000.000
106A323PRO00.0320.01815.4300.0400.0400.0000.0000.0000.000
107A324MET0-0.013-0.01318.6180.0160.0160.0000.0000.0000.000
108A325ASP-1-0.845-0.92017.279-0.342-0.3420.0000.0000.0000.000
109A326SER00.031-0.00713.690-0.027-0.0270.0000.0000.0000.000
110A327GLU-1-0.868-0.90113.216-0.432-0.4320.0000.0000.0000.000
111A328SER0-0.043-0.02012.754-0.076-0.0760.0000.0000.0000.000
112A329TYR0-0.006-0.03710.5520.0390.0390.0000.0000.0000.000
113A330VAL00.0380.0197.507-0.101-0.1010.0000.0000.0000.000
114A331HIS0-0.049-0.0398.469-0.210-0.2100.0000.0000.0000.000
115A332ARG10.7020.84210.4040.4400.4400.0000.0000.0000.000
116A333ILE0-0.001-0.0036.2250.0160.0160.0000.0000.0000.000
117A334GLY00.0190.0115.665-0.240-0.2400.0000.0000.0000.000
118A335ARG10.7530.8636.7460.6880.6880.0000.0000.0000.000
119A336THR00.006-0.0255.9230.1390.1390.0000.0000.0000.000
120A337GLY00.0050.0092.392-1.000-0.6980.829-0.547-0.5840.000
121A338ARG00.0090.0032.652-0.8500.1261.225-0.517-1.684-0.011
122A339ALA00.014-0.0065.0380.0960.146-0.001-0.004-0.0440.000
123A340GLY0-0.032-0.0082.916-0.0150.3580.067-0.126-0.3140.000
124A341ARG10.8890.9623.9480.2320.318-0.0010.006-0.0910.000
125A342ALA00.0150.0105.275-0.357-0.3570.0000.0000.0000.000
126A343GLY0-0.0010.0056.4490.1400.1400.0000.0000.0000.000
127A344ARG10.8180.8977.4910.1650.1650.0000.0000.0000.000
128A345ALA00.0220.0009.022-0.006-0.0060.0000.0000.0000.000
129A346LEU00.0130.02310.8310.0570.0570.0000.0000.0000.000
130A347LEU0-0.031-0.02214.572-0.017-0.0170.0000.0000.0000.000
131A348PHE0-0.0010.01417.1240.0310.0310.0000.0000.0000.000
132A349VAL0-0.009-0.01120.562-0.001-0.0010.0000.0000.0000.000
133A350GLU-1-0.752-0.86223.059-0.176-0.1760.0000.0000.0000.000
134A351ASN00.0460.01626.529-0.013-0.0130.0000.0000.0000.000
135A352ARG10.7950.87027.8080.1890.1890.0000.0000.0000.000
136A353GLU-1-0.785-0.87124.568-0.231-0.2310.0000.0000.0000.000
137A354ARG10.8900.94224.0110.1960.1960.0000.0000.0000.000
138A355ARG10.9610.97723.9400.1720.1720.0000.0000.0000.000
139A356LEU0-0.028-0.01221.5790.0020.0020.0000.0000.0000.000
140A357LEU00.0720.04518.121-0.019-0.0190.0000.0000.0000.000
141A358ARG10.8840.92519.3180.2230.2230.0000.0000.0000.000
142A359ASN0-0.023-0.00420.8870.0210.0210.0000.0000.0000.000
143A360ILE00.0360.03814.5970.0060.0060.0000.0000.0000.000
144A361GLU-1-0.744-0.85116.049-0.351-0.3510.0000.0000.0000.000
145A362ARG10.8200.89516.8050.2160.2160.0000.0000.0000.000
146A363THR0-0.031-0.02515.8150.0310.0310.0000.0000.0000.000
147A364MET0-0.0140.0009.6450.0280.0280.0000.0000.0000.000
148A365LYS10.8780.94012.5150.2340.2340.0000.0000.0000.000
149A366LEU0-0.023-0.00510.2700.0540.0540.0000.0000.0000.000
150A367THR0-0.019-0.00814.421-0.012-0.0120.0000.0000.0000.000
151A368ILE0-0.010-0.00613.622-0.035-0.0350.0000.0000.0000.000
152A369PRO00.001-0.00714.5120.0630.0630.0000.0000.0000.000
153A370GLU-1-0.708-0.78917.440-0.274-0.2740.0000.0000.0000.000
154A371VAL0-0.038-0.02517.7900.0120.0120.0000.0000.0000.000
155A372GLU-1-0.884-0.95620.881-0.166-0.1660.0000.0000.0000.000
156A373LEU0-0.053-0.01122.789-0.020-0.0200.0000.0000.0000.000
157A374PRO0-0.002-0.00322.2800.0180.0180.0000.0000.0000.000
158A375ASN00.0290.01325.0990.0020.0020.0000.0000.0000.000
159A376ALA00.0440.01628.757-0.002-0.0020.0000.0000.0000.000
160A377GLU-1-0.884-0.93231.131-0.086-0.0860.0000.0000.0000.000
161A378LEU00.0040.00123.5910.0050.0050.0000.0000.0000.000
162A379LEU0-0.0060.00326.894-0.001-0.0010.0000.0000.0000.000
163A380GLY00.0500.01828.5150.0030.0030.0000.0000.0000.000
164A381LYS10.8420.90526.6190.0860.0860.0000.0000.0000.000
165A382ARG10.7840.85621.3050.1670.1670.0000.0000.0000.000
166A383ARG10.7520.84527.2300.1170.1170.0000.0000.0000.000
167A384LEU00.0210.00329.7640.0060.0060.0000.0000.0000.000
168A385GLU-1-0.862-0.91726.820-0.080-0.0800.0000.0000.0000.000
169A386LYS10.8530.90722.3680.1350.1350.0000.0000.0000.000
170A387PHE0-0.026-0.00328.8580.0050.0050.0000.0000.0000.000
171A388ALA00.0200.00232.5960.0050.0050.0000.0000.0000.000
172A389ALA00.0250.01630.2280.0050.0050.0000.0000.0000.000
173A390LYS10.9490.96930.9370.0660.0660.0000.0000.0000.000
174A391VAL00.0020.00733.8080.0030.0030.0000.0000.0000.000
175A392GLN0-0.040-0.02034.7180.0010.0010.0000.0000.0000.000
176A393GLN00.0240.00131.636-0.001-0.0010.0000.0000.0000.000
177A394GLN0-0.081-0.03436.5120.0000.0000.0000.0000.0000.000
178A395LEU0-0.030-0.01039.8440.0020.0020.0000.0000.0000.000
179A396GLU-1-0.882-0.92936.911-0.012-0.0120.0000.0000.0000.000
180A397SER0-0.066-0.03341.0160.0020.0020.0000.0000.0000.000
181A398SER0-0.006-0.02342.3910.0010.0010.0000.0000.0000.000
182A399ASP-1-0.853-0.90945.081-0.020-0.0200.0000.0000.0000.000
183A400LEU00.0200.02744.449-0.001-0.0010.0000.0000.0000.000
184A401ASP-1-0.806-0.89047.014-0.014-0.0140.0000.0000.0000.000
185A402GLN0-0.037-0.01949.6970.0010.0010.0000.0000.0000.000
186A403TYR0-0.016-0.02445.833-0.001-0.0010.0000.0000.0000.000
187A404ARG10.8390.89449.9480.0140.0140.0000.0000.0000.000
188A405ALA0-0.022-0.00851.5600.0000.0000.0000.0000.0000.000
189A406LEU0-0.018-0.01551.2500.0000.0000.0000.0000.0000.000
190A407LEU00.0360.02749.206-0.001-0.0010.0000.0000.0000.000
191A408SER0-0.021-0.01653.272-0.001-0.0010.0000.0000.0000.000
192A409LYS10.8670.92856.1720.0190.0190.0000.0000.0000.000
193A410ILE0-0.0140.01551.1110.0000.0000.0000.0000.0000.000
194A411GLN0-0.048-0.01755.4040.0000.0000.0000.0000.0000.000
195A420ASP-1-0.771-0.85753.898-0.027-0.0270.0000.0000.0000.000
196A421LEU0-0.028-0.03350.594-0.001-0.0010.0000.0000.0000.000
197A422GLU-1-0.921-0.94748.837-0.030-0.0300.0000.0000.0000.000
198A423THR0-0.030-0.05649.182-0.003-0.0030.0000.0000.0000.000
199A424LEU0-0.034-0.01249.847-0.002-0.0020.0000.0000.0000.000
200A425ALA00.0130.00146.440-0.002-0.0020.0000.0000.0000.000
201A426ALA00.0150.01145.197-0.003-0.0030.0000.0000.0000.000
202A427ALA0-0.038-0.01944.962-0.003-0.0030.0000.0000.0000.000
203A428LEU00.016-0.00945.320-0.002-0.0020.0000.0000.0000.000
204A429LEU0-0.0010.01239.065-0.002-0.0020.0000.0000.0000.000
205A430LYS10.9260.95940.5460.0500.0500.0000.0000.0000.000
206A431MET0-0.051-0.02441.276-0.002-0.0020.0000.0000.0000.000
207A432ALA00.0040.00139.616-0.002-0.0020.0000.0000.0000.000
208A433GLN0-0.040-0.01136.156-0.002-0.0020.0000.0000.0000.000
209A434GLY00.0130.01835.006-0.005-0.0050.0000.0000.0000.000
210A435GLU-1-0.900-0.96733.214-0.082-0.0820.0000.0000.0000.000
211A436ARG10.7400.88525.9430.1350.1350.0000.0000.0000.000
212A437THR0-0.037-0.02832.4320.0050.0050.0000.0000.0000.000
213A438LEU00.0640.02333.564-0.006-0.0060.0000.0000.0000.000
214A439ILE0-0.035-0.00835.315-0.001-0.0010.0000.0000.0000.000
215A440VAL00.0040.01331.987-0.003-0.0030.0000.0000.0000.000
216A441PRO0-0.020-0.00435.1380.0040.0040.0000.0000.0000.000
217A442PRO00.0450.00335.116-0.005-0.0050.0000.0000.0000.000
218A443ASP-1-0.945-0.94431.466-0.117-0.1170.0000.0000.0000.000