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: YVVM2

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2483585.221875
FMO2-HF: Nuclear repulsion 2397362.572312
FMO2-HF: Total energy -86222.649563
FMO2-MP2: Total energy -86476.438793


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.
-1.6263.0341.825-2.237-4.246-0.01
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 : -0.012 / q_NPA : -0.009
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].
3A220ILE0-0.117-0.0472.4590.0782.1760.634-0.961-1.7710.002
4A221SER00.0670.0425.722-0.023-0.0230.0000.0000.0000.000
5A222GLN00.0230.0157.6750.4540.4540.0000.0000.0000.000
6A223SER0-0.0070.00011.1850.1090.1090.0000.0000.0000.000
7A224TYR0-0.007-0.01014.9250.0110.0110.0000.0000.0000.000
8A225TRP00.0690.04517.8180.0200.0200.0000.0000.0000.000
9A226THR0-0.010-0.03721.256-0.001-0.0010.0000.0000.0000.000
10A227VAL0-0.067-0.03324.3520.0130.0130.0000.0000.0000.000
11A228TRP0-0.010-0.01826.3120.0140.0140.0000.0000.0000.000
12A229GLY0-0.0030.00729.253-0.004-0.0040.0000.0000.0000.000
13A230MET00.0250.04728.1520.0050.0050.0000.0000.0000.000
14A231ARG10.9490.96529.0210.1190.1190.0000.0000.0000.000
15A232LYS10.9170.95223.2030.2300.2300.0000.0000.0000.000
16A233ASN00.0300.02924.880-0.013-0.0130.0000.0000.0000.000
17A234GLU-1-0.877-0.95726.160-0.134-0.1340.0000.0000.0000.000
18A235ALA00.0370.00624.556-0.002-0.0020.0000.0000.0000.000
19A236LEU0-0.025-0.01319.650-0.018-0.0180.0000.0000.0000.000
20A237VAL00.0150.01322.218-0.009-0.0090.0000.0000.0000.000
21A238ARG10.8290.90724.3240.1580.1580.0000.0000.0000.000
22A239PHE00.016-0.02519.297-0.003-0.0030.0000.0000.0000.000
23A240LEU0-0.066-0.01518.397-0.017-0.0170.0000.0000.0000.000
24A241GLU-1-0.755-0.85120.706-0.116-0.1160.0000.0000.0000.000
25A242ALA0-0.047-0.01621.5300.0140.0140.0000.0000.0000.000
26A243GLU-1-0.944-0.97715.633-0.394-0.3940.0000.0000.0000.000
27A244ASP-1-0.851-0.91917.601-0.124-0.1240.0000.0000.0000.000
28A245PHE0-0.074-0.04915.074-0.053-0.0530.0000.0000.0000.000
29A246ASP-1-0.852-0.92214.2480.0030.0030.0000.0000.0000.000
30A247ALA00.0300.02614.6280.0120.0120.0000.0000.0000.000
31A248ALA0-0.036-0.02313.860-0.057-0.0570.0000.0000.0000.000
32A249ILE0-0.022-0.00912.5370.0470.0470.0000.0000.0000.000
33A250ILE0-0.008-0.01114.823-0.055-0.0550.0000.0000.0000.000
34A251PHE00.021-0.00112.4280.0370.0370.0000.0000.0000.000
35A252VAL00.005-0.00417.620-0.009-0.0090.0000.0000.0000.000
36A253ARG10.9040.95021.0200.2090.2090.0000.0000.0000.000
37A254THR0-0.056-0.06923.2410.0100.0100.0000.0000.0000.000
38A255LYS11.0120.97424.6180.1130.1130.0000.0000.0000.000
39A256ASN00.1090.08426.8890.0020.0020.0000.0000.0000.000
40A257ALA00.0120.01125.5660.0040.0040.0000.0000.0000.000
41A258THR0-0.036-0.01723.104-0.004-0.0040.0000.0000.0000.000
42A259LEU0-0.006-0.01825.0160.0020.0020.0000.0000.0000.000
43A260GLU-1-1.001-0.96428.200-0.130-0.1300.0000.0000.0000.000
44A261VAL00.0440.00222.9120.0010.0010.0000.0000.0000.000
45A262ALA0-0.024-0.01425.4090.0000.0000.0000.0000.0000.000
46A263GLU-1-0.786-0.92426.369-0.078-0.0780.0000.0000.0000.000
47A264ALA0-0.037-0.01027.4830.0030.0030.0000.0000.0000.000
48A265LEU0-0.056-0.03622.051-0.002-0.0020.0000.0000.0000.000
49A266GLU-1-0.901-0.92226.305-0.072-0.0720.0000.0000.0000.000
50A267ARG10.9310.99428.7770.1030.1030.0000.0000.0000.000
51A268ASN0-0.146-0.08527.8070.0020.0020.0000.0000.0000.000
52A269GLY0-0.021-0.01728.281-0.004-0.0040.0000.0000.0000.000
53A270TYR0-0.060-0.03222.494-0.001-0.0010.0000.0000.0000.000
54A271ASN00.0910.05724.5410.0060.0060.0000.0000.0000.000
55A272SER0-0.012-0.02123.034-0.005-0.0050.0000.0000.0000.000
56A273ALA00.0380.02422.9620.0110.0110.0000.0000.0000.000
57A274ALA0-0.006-0.00622.754-0.014-0.0140.0000.0000.0000.000
58A275LEU00.0450.01618.9350.0120.0120.0000.0000.0000.000
59A276ASN0-0.005-0.02422.024-0.011-0.0110.0000.0000.0000.000
60A277GLY0-0.009-0.03024.5900.0070.0070.0000.0000.0000.000
61A278ASP-1-0.937-0.95126.190-0.066-0.0660.0000.0000.0000.000
62A279MET0-0.0280.00025.0720.0010.0010.0000.0000.0000.000
63A280ASN0-0.051-0.00525.913-0.002-0.0020.0000.0000.0000.000
64A281GLN00.0330.00723.138-0.010-0.0100.0000.0000.0000.000
65A282ALA00.0630.02026.2160.0010.0010.0000.0000.0000.000
66A283LEU00.0250.01927.2630.0020.0020.0000.0000.0000.000
67A284ARG10.8790.92722.0140.0450.0450.0000.0000.0000.000
68A285GLU-1-0.828-0.91122.2860.0140.0140.0000.0000.0000.000
69A286GLN00.0040.00823.3290.0040.0040.0000.0000.0000.000
70A287THR0-0.032-0.02821.9360.0000.0000.0000.0000.0000.000
71A288LEU00.0110.00117.496-0.006-0.0060.0000.0000.0000.000
72A289GLU-1-0.895-0.93519.9130.0650.0650.0000.0000.0000.000
73A290ARG10.9060.96222.0310.0360.0360.0000.0000.0000.000
74A291LEU0-0.0160.00616.088-0.004-0.0040.0000.0000.0000.000
75A292LYS10.9340.96817.633-0.109-0.1090.0000.0000.0000.000
76A293ASP-1-0.838-0.89818.8990.0260.0260.0000.0000.0000.000
77A294GLY00.0330.01421.2610.0030.0030.0000.0000.0000.000
78A295ARG10.7650.85522.249-0.016-0.0160.0000.0000.0000.000
79A296LEU0-0.090-0.03722.020-0.007-0.0070.0000.0000.0000.000
80A297ASP-1-0.787-0.87419.581-0.063-0.0630.0000.0000.0000.000
81A298ILE0-0.040-0.02218.330-0.027-0.0270.0000.0000.0000.000
82A299LEU0-0.0010.01117.3240.0210.0210.0000.0000.0000.000
83A300ILE00.0120.03318.299-0.034-0.0340.0000.0000.0000.000
84A301ALA00.0140.01417.5300.0260.0260.0000.0000.0000.000
85A302THR00.007-0.00319.549-0.010-0.0100.0000.0000.0000.000
86A303ASP-1-0.764-0.86616.808-0.279-0.2790.0000.0000.0000.000
87A304VAL0-0.028-0.01518.6680.0120.0120.0000.0000.0000.000
88A305ALA0-0.057-0.02520.4200.0110.0110.0000.0000.0000.000
89A306ALA00.0700.03915.9850.0100.0100.0000.0000.0000.000
90A307ARG10.9040.95415.7620.0890.0890.0000.0000.0000.000
91A308GLY0-0.0210.00015.0990.0030.0030.0000.0000.0000.000
92A309LEU00.0220.0549.672-0.034-0.0340.0000.0000.0000.000
93A310ASP-1-0.905-1.01710.2380.1210.1210.0000.0000.0000.000
94A311VAL0-0.060-0.01912.4440.0230.0230.0000.0000.0000.000
95A312GLU-1-0.925-0.9529.9600.3250.3250.0000.0000.0000.000
96A313ARG10.8050.86611.9520.0640.0640.0000.0000.0000.000
97A314ILE0-0.065-0.03810.515-0.037-0.0370.0000.0000.0000.000
98A315SER00.0520.0449.585-0.062-0.0620.0000.0000.0000.000
99A316LEU0-0.015-0.00210.350-0.134-0.1340.0000.0000.0000.000
100A317VAL00.0080.0109.1970.0930.0930.0000.0000.0000.000
101A318VAL00.0220.00511.933-0.052-0.0520.0000.0000.0000.000
102A319ASN0-0.009-0.00512.8780.0990.0990.0000.0000.0000.000
103A320TYR00.0740.04316.2240.0110.0110.0000.0000.0000.000
104A321ASP-1-0.849-0.93219.772-0.193-0.1930.0000.0000.0000.000
105A322ILE00.0080.01518.742-0.026-0.0260.0000.0000.0000.000
106A323PRO0-0.020-0.01715.3870.0360.0360.0000.0000.0000.000
107A324MET0-0.031-0.02418.5340.0050.0050.0000.0000.0000.000
108A325ASP-1-0.857-0.93317.122-0.279-0.2790.0000.0000.0000.000
109A326SER00.0180.00113.964-0.051-0.0510.0000.0000.0000.000
110A327GLU-1-0.900-0.93612.980-0.311-0.3110.0000.0000.0000.000
111A328SER0-0.017-0.00512.705-0.039-0.0390.0000.0000.0000.000
112A329TYR0-0.030-0.05710.8290.0360.0360.0000.0000.0000.000
113A330VAL00.0260.0137.437-0.102-0.1020.0000.0000.0000.000
114A331HIS0-0.009-0.0068.524-0.116-0.1160.0000.0000.0000.000
115A332ARG10.6950.80810.0110.3510.3510.0000.0000.0000.000
116A333ILE0-0.0010.0006.0960.0380.0380.0000.0000.0000.000
117A334GLY00.0300.0155.291-0.177-0.1770.0000.0000.0000.000
118A335ARG10.8270.9176.2120.4790.4790.0000.0000.0000.000
119A336THR0-0.026-0.0166.1460.1690.1690.0000.0000.0000.000
120A337GLY00.0270.0122.995-0.907-0.5990.076-0.117-0.2670.000
121A338ARG00.0160.0432.645-0.8170.8611.088-1.036-1.730-0.012
122A339ALA00.017-0.0094.8420.0800.107-0.001-0.003-0.0220.000
123A340GLY0-0.036-0.0183.155-0.0750.2250.030-0.085-0.2450.000
124A341ARG10.9220.9744.177-1.041-0.921-0.001-0.028-0.0900.000
125A342ALA00.0060.0114.676-0.480-0.351-0.001-0.007-0.1210.000
126A343GLY00.0130.0046.3450.1880.1880.0000.0000.0000.000
127A344ARG10.9230.9837.5180.1740.1740.0000.0000.0000.000
128A345ALA00.0120.0029.0770.0700.0700.0000.0000.0000.000
129A346LEU00.0010.00810.7140.0140.0140.0000.0000.0000.000
130A347LEU0-0.046-0.02614.4420.0360.0360.0000.0000.0000.000
131A348PHE0-0.012-0.00516.5920.0280.0280.0000.0000.0000.000
132A349VAL0-0.014-0.01020.0140.0010.0010.0000.0000.0000.000
133A350GLU-1-0.811-0.91422.521-0.166-0.1660.0000.0000.0000.000
134A351ASN00.0290.00726.097-0.012-0.0120.0000.0000.0000.000
135A352ARG10.8410.91728.3540.1660.1660.0000.0000.0000.000
136A353GLU-1-0.893-0.94024.181-0.233-0.2330.0000.0000.0000.000
137A354ARG10.9800.98623.9790.2400.2400.0000.0000.0000.000
138A355ARG10.9460.98223.7170.1710.1710.0000.0000.0000.000
139A356LEU0-0.010-0.00421.697-0.007-0.0070.0000.0000.0000.000
140A357LEU00.1000.05918.010-0.014-0.0140.0000.0000.0000.000
141A358ARG10.9490.96419.0620.2690.2690.0000.0000.0000.000
142A359ASN0-0.068-0.04320.220-0.001-0.0010.0000.0000.0000.000
143A360ILE00.0100.00714.549-0.001-0.0010.0000.0000.0000.000
144A361GLU-1-0.798-0.89815.588-0.470-0.4700.0000.0000.0000.000
145A362ARG10.8620.93016.4250.2440.2440.0000.0000.0000.000
146A363THR0-0.046-0.02015.4070.0040.0040.0000.0000.0000.000
147A364MET00.0120.0119.0580.0290.0290.0000.0000.0000.000
148A365LYS10.9000.97611.3490.6120.6120.0000.0000.0000.000
149A366LEU0-0.035-0.02710.4330.0140.0140.0000.0000.0000.000
150A367THR0-0.013-0.00614.3140.0360.0360.0000.0000.0000.000
151A368ILE0-0.036-0.02313.371-0.082-0.0820.0000.0000.0000.000
152A369PRO0-0.015-0.00914.5230.0830.0830.0000.0000.0000.000
153A370GLU-1-0.862-0.91017.507-0.303-0.3030.0000.0000.0000.000
154A371VAL0-0.026-0.01118.0850.0000.0000.0000.0000.0000.000
155A372GLU-1-0.914-0.96420.935-0.204-0.2040.0000.0000.0000.000
156A373LEU0-0.038-0.01622.835-0.017-0.0170.0000.0000.0000.000
157A374PRO00.0160.01222.1320.0150.0150.0000.0000.0000.000
158A375ASN00.0660.03824.9160.0160.0160.0000.0000.0000.000
159A376ALA00.0520.01328.6020.0010.0010.0000.0000.0000.000
160A377GLU-1-0.930-0.95931.331-0.106-0.1060.0000.0000.0000.000
161A378LEU00.0100.00923.6670.0060.0060.0000.0000.0000.000
162A379LEU0-0.016-0.01026.9550.0020.0020.0000.0000.0000.000
163A380GLY00.0370.01328.6350.0070.0070.0000.0000.0000.000
164A381LYS10.9270.97126.9590.1110.1110.0000.0000.0000.000
165A382ARG10.8100.89921.5470.1650.1650.0000.0000.0000.000
166A383ARG10.7550.84027.5860.1140.1140.0000.0000.0000.000
167A384LEU00.0180.00730.3010.0080.0080.0000.0000.0000.000
168A385GLU-1-0.915-0.95926.529-0.089-0.0890.0000.0000.0000.000
169A386LYS10.9040.95323.4440.1070.1070.0000.0000.0000.000
170A387PHE0-0.0100.00629.2390.0080.0080.0000.0000.0000.000
171A388ALA00.0320.00832.9510.0070.0070.0000.0000.0000.000
172A389ALA00.0160.01530.0930.0060.0060.0000.0000.0000.000
173A390LYS10.9500.96631.6060.0440.0440.0000.0000.0000.000
174A391VAL0-0.021-0.01233.7620.0040.0040.0000.0000.0000.000
175A392GLN00.0170.00633.3650.0020.0020.0000.0000.0000.000
176A393GLN00.0120.00132.656-0.001-0.0010.0000.0000.0000.000
177A394GLN0-0.021-0.00936.3020.0040.0040.0000.0000.0000.000
178A395LEU0-0.055-0.02539.2570.0010.0010.0000.0000.0000.000
179A396GLU-1-0.979-0.97636.9570.0030.0030.0000.0000.0000.000
180A397SER0-0.063-0.01840.6430.0030.0030.0000.0000.0000.000
181A398SER00.008-0.01741.949-0.001-0.0010.0000.0000.0000.000
182A399ASP-1-0.875-0.93744.955-0.002-0.0020.0000.0000.0000.000
183A400LEU00.0180.02344.082-0.002-0.0020.0000.0000.0000.000
184A401ASP-1-0.907-0.97147.037-0.006-0.0060.0000.0000.0000.000
185A402GLN00.000-0.01350.3940.0000.0000.0000.0000.0000.000
186A403TYR0-0.025-0.00546.213-0.002-0.0020.0000.0000.0000.000
187A404ARG10.9040.96148.8220.0070.0070.0000.0000.0000.000
188A405ALA0-0.005-0.00551.443-0.001-0.0010.0000.0000.0000.000
189A406LEU0-0.049-0.03351.1460.0000.0000.0000.0000.0000.000
190A407LEU00.0070.01549.579-0.001-0.0010.0000.0000.0000.000
191A408SER0-0.020-0.01753.628-0.001-0.0010.0000.0000.0000.000
192A409LYS10.9190.96156.5780.0090.0090.0000.0000.0000.000
193A410ILE00.0090.03051.7600.0000.0000.0000.0000.0000.000
194A411GLN0-0.043-0.01656.0450.0010.0010.0000.0000.0000.000
195A420ASP-1-0.825-0.90754.547-0.025-0.0250.0000.0000.0000.000
196A421LEU0-0.009-0.01750.826-0.001-0.0010.0000.0000.0000.000
197A422GLU-1-0.920-0.93949.121-0.032-0.0320.0000.0000.0000.000
198A423THR0-0.011-0.03449.479-0.003-0.0030.0000.0000.0000.000
199A424LEU0-0.028-0.01050.238-0.001-0.0010.0000.0000.0000.000
200A425ALA00.0240.00046.563-0.001-0.0010.0000.0000.0000.000
201A426ALA00.0240.02745.483-0.002-0.0020.0000.0000.0000.000
202A427ALA0-0.016-0.01245.163-0.003-0.0030.0000.0000.0000.000
203A428LEU00.008-0.01145.420-0.001-0.0010.0000.0000.0000.000
204A429LEU0-0.0040.01439.192-0.001-0.0010.0000.0000.0000.000
205A430LYS10.9340.95040.9290.0450.0450.0000.0000.0000.000
206A431MET0-0.052-0.02641.364-0.002-0.0020.0000.0000.0000.000
207A432ALA0-0.0070.00440.0160.0000.0000.0000.0000.0000.000
208A433GLN0-0.040-0.00336.695-0.003-0.0030.0000.0000.0000.000
209A434GLY0-0.0080.00435.416-0.003-0.0030.0000.0000.0000.000
210A435GLU-1-0.885-0.95733.645-0.062-0.0620.0000.0000.0000.000
211A436ARG10.8530.93926.4260.0980.0980.0000.0000.0000.000
212A437THR0-0.030-0.01132.8250.0040.0040.0000.0000.0000.000
213A438LEU00.0710.01133.932-0.007-0.0070.0000.0000.0000.000
214A439ILE0-0.057-0.00935.727-0.002-0.0020.0000.0000.0000.000
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