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: 6NVJZ

Calculation Name: 4CTI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4CTI

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEJ4

Base Structure: X-ray

Registration Date: 2023-09-19

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2379557.083744
FMO2-HF: Nuclear repulsion 2290227.941463
FMO2-HF: Total energy -89329.142281
FMO2-MP2: Total energy -89586.12935


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:279:THR)


Summations of interaction energy for fragment #1(A:279:THR)
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.
-5.15-1.793-0.021-1.784-1.5520.001
Interaction energy analysis for fragmet #1(A:279:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.012
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].
3A281THR00.0360.0103.675-3.555-0.198-0.021-1.784-1.5520.001
4A282ARG10.8670.9215.316-1.848-1.8480.0000.0000.0000.000
5A283PRO00.0360.0105.576-0.221-0.2210.0000.0000.0000.000
6A284ILE00.0230.0237.118-0.174-0.1740.0000.0000.0000.000
7A285ILE00.0000.0229.629-0.215-0.2150.0000.0000.0000.000
8A286GLU-1-0.734-0.83710.2990.3320.3320.0000.0000.0000.000
9A287LEU0-0.0160.00212.565-0.092-0.0920.0000.0000.0000.000
10A288SER0-0.018-0.01513.597-0.064-0.0640.0000.0000.0000.000
11A289ASN0-0.037-0.02915.653-0.042-0.0420.0000.0000.0000.000
12A290THR0-0.051-0.03116.621-0.089-0.0890.0000.0000.0000.000
13A291PHE0-0.011-0.02616.922-0.045-0.0450.0000.0000.0000.000
14A292ASP-1-0.839-0.90419.6770.4200.4200.0000.0000.0000.000
15A293LYS10.9150.95119.951-0.301-0.3010.0000.0000.0000.000
16A294ILE0-0.027-0.01521.712-0.025-0.0250.0000.0000.0000.000
17A295ALA0-0.045-0.02124.435-0.018-0.0180.0000.0000.0000.000
18A296GLU-1-0.951-0.97226.0330.2200.2200.0000.0000.0000.000
19A297GLY00.0180.01927.964-0.016-0.0160.0000.0000.0000.000
20A298ASN0-0.0100.00026.202-0.028-0.0280.0000.0000.0000.000
21A299LEU0-0.026-0.03226.1340.0080.0080.0000.0000.0000.000
22A300GLU-1-0.799-0.89827.2940.0600.0600.0000.0000.0000.000
23A301ALA0-0.076-0.01622.815-0.012-0.0120.0000.0000.0000.000
24A302GLU-1-0.950-0.97718.918-0.007-0.0070.0000.0000.0000.000
25A303VAL0-0.0050.00217.8590.0360.0360.0000.0000.0000.000
26A304PRO00.0610.04014.404-0.048-0.0480.0000.0000.0000.000
27A305HIS0-0.044-0.0639.298-0.082-0.0820.0000.0000.0000.000
28A306GLN00.0430.00712.974-0.029-0.0290.0000.0000.0000.000
29A307ASN0-0.039-0.00114.7970.0070.0070.0000.0000.0000.000
30A308ARG10.8200.8965.7550.2810.2810.0000.0000.0000.000
31A309ALA00.004-0.01711.6310.1110.1110.0000.0000.0000.000
32A310ASP-1-0.737-0.8167.831-0.209-0.2090.0000.0000.0000.000
33A311GLU-1-0.851-0.9469.7570.2660.2660.0000.0000.0000.000
34A312ILE0-0.0070.0007.3810.0370.0370.0000.0000.0000.000
35A313GLY00.0560.01811.361-0.037-0.0370.0000.0000.0000.000
36A314ILE0-0.038-0.01113.279-0.017-0.0170.0000.0000.0000.000
37A315LEU00.0120.02013.588-0.010-0.0100.0000.0000.0000.000
38A316ALA00.0590.03414.382-0.017-0.0170.0000.0000.0000.000
39A317LYS10.8240.89015.6230.0830.0830.0000.0000.0000.000
40A318SER0-0.084-0.06318.948-0.025-0.0250.0000.0000.0000.000
41A319ILE00.0210.02316.790-0.007-0.0070.0000.0000.0000.000
42A320GLU-1-0.740-0.81920.5530.0460.0460.0000.0000.0000.000
43A321ARG10.8440.92121.327-0.093-0.0930.0000.0000.0000.000
44A322LEU0-0.0050.00523.647-0.007-0.0070.0000.0000.0000.000
45A323ARG10.8760.91423.512-0.085-0.0850.0000.0000.0000.000
46A324ARG10.8490.89724.625-0.027-0.0270.0000.0000.0000.000
47A325SER0-0.035-0.00928.526-0.007-0.0070.0000.0000.0000.000
48A326LEU00.010-0.01027.139-0.003-0.0030.0000.0000.0000.000
49A327LYS10.8510.93330.292-0.066-0.0660.0000.0000.0000.000
50A328GLN0-0.032-0.01531.984-0.006-0.0060.0000.0000.0000.000
51A329LEU0-0.021-0.01533.002-0.002-0.0020.0000.0000.0000.000
52A330ALA0-0.021-0.00933.9530.0050.0050.0000.0000.0000.000
53A331ASP-1-0.819-0.92735.6990.0570.0570.0000.0000.0000.000
54A332ASP-1-0.856-0.92137.9210.0420.0420.0000.0000.0000.000
55A333ARG10.7610.88733.856-0.098-0.0980.0000.0000.0000.000
56A334THR00.024-0.01140.3470.0010.0010.0000.0000.0000.000
57A335LEU0-0.022-0.00743.409-0.003-0.0030.0000.0000.0000.000
58A336LEU00.0160.00844.076-0.003-0.0030.0000.0000.0000.000
59A337MET00.0270.00646.229-0.003-0.0030.0000.0000.0000.000
60A338ALA00.0100.01347.948-0.002-0.0020.0000.0000.0000.000
61A339GLY00.0180.01149.139-0.003-0.0030.0000.0000.0000.000
62A340VAL00.0080.00050.354-0.002-0.0020.0000.0000.0000.000
63A341SER00.0170.01052.383-0.002-0.0020.0000.0000.0000.000
64A342HIS0-0.040-0.02153.807-0.001-0.0010.0000.0000.0000.000
65A343ASP-1-0.894-0.95754.3070.0290.0290.0000.0000.0000.000
66A344LEU0-0.021-0.01456.046-0.001-0.0010.0000.0000.0000.000
67A345ARG10.9490.98254.532-0.032-0.0320.0000.0000.0000.000
68A346THR00.0430.03460.149-0.001-0.0010.0000.0000.0000.000
69A347PRO0-0.083-0.02861.199-0.001-0.0010.0000.0000.0000.000
70A348LEU00.0840.04460.423-0.001-0.0010.0000.0000.0000.000
71A349THR0-0.005-0.01163.444-0.001-0.0010.0000.0000.0000.000
72A350ARG10.8650.91364.506-0.023-0.0230.0000.0000.0000.000
73A351ILE0-0.0030.00465.874-0.001-0.0010.0000.0000.0000.000
74A352ARG10.8290.88264.881-0.029-0.0290.0000.0000.0000.000
75A353LEU0-0.043-0.02469.605-0.001-0.0010.0000.0000.0000.000
76A354ALA0-0.021-0.01072.011-0.001-0.0010.0000.0000.0000.000
77A355THR0-0.006-0.03272.0720.0000.0000.0000.0000.0000.000
78A356GLU-1-0.884-0.91773.7540.0220.0220.0000.0000.0000.000
79A357MET0-0.091-0.03576.508-0.001-0.0010.0000.0000.0000.000
80A358MET0-0.070-0.00876.3000.0000.0000.0000.0000.0000.000
81A359SER0-0.064-0.05979.724-0.001-0.0010.0000.0000.0000.000
82A360GLU-1-0.881-0.95682.1070.0200.0200.0000.0000.0000.000
83A361GLN0-0.114-0.06083.3140.0000.0000.0000.0000.0000.000
84A362ASP-1-0.811-0.87879.7360.0210.0210.0000.0000.0000.000
85A363GLY00.0620.03478.7120.0010.0010.0000.0000.0000.000
86A364TYR00.010-0.00477.4030.0010.0010.0000.0000.0000.000
87A365LEU0-0.019-0.00575.2390.0010.0010.0000.0000.0000.000
88A366ALA00.0420.02073.8160.0010.0010.0000.0000.0000.000
89A367GLU-1-0.883-0.93272.9700.0290.0290.0000.0000.0000.000
90A368SER0-0.080-0.04570.5180.0010.0010.0000.0000.0000.000
91A369ILE00.0370.01769.1470.0010.0010.0000.0000.0000.000
92A370ASN0-0.034-0.01968.0810.0010.0010.0000.0000.0000.000
93A371LYS10.8690.93067.104-0.030-0.0300.0000.0000.0000.000
94A372ASP-1-0.825-0.91065.3930.0350.0350.0000.0000.0000.000
95A373ILE0-0.048-0.02463.4770.0010.0010.0000.0000.0000.000
96A374GLU-1-0.791-0.86562.2840.0330.0330.0000.0000.0000.000
97A375GLU-1-0.966-0.97260.2950.0450.0450.0000.0000.0000.000
98A376CYS0-0.067-0.04259.0330.0020.0020.0000.0000.0000.000
99A377ASN0-0.059-0.03857.5850.0020.0020.0000.0000.0000.000
100A378ALA00.0340.01756.5570.0020.0020.0000.0000.0000.000
101A379ILE0-0.008-0.00154.1110.0030.0030.0000.0000.0000.000
102A380ILE0-0.036-0.02052.9390.0030.0030.0000.0000.0000.000
103A381GLU-1-0.946-0.97551.7540.0410.0410.0000.0000.0000.000
104A382GLN0-0.003-0.00351.0440.0010.0010.0000.0000.0000.000
105A383PHE00.012-0.00245.6200.0040.0040.0000.0000.0000.000
106A384ILE0-0.028-0.01747.1330.0030.0030.0000.0000.0000.000
107A385ASP-1-0.826-0.91946.4580.0580.0580.0000.0000.0000.000
108A386TYR00.0140.00641.7830.0040.0040.0000.0000.0000.000
109A387LEU0-0.033-0.00242.6240.0050.0050.0000.0000.0000.000
110A388ARG10.9130.95041.520-0.048-0.0480.0000.0000.0000.000
111A389THR0-0.091-0.05941.3260.0020.0020.0000.0000.0000.000
112A390GLY00.0120.01937.8270.0060.0060.0000.0000.0000.000
113A391GLN0-0.080-0.03036.9320.0010.0010.0000.0000.0000.000
114A392GLU-1-0.784-0.85836.0610.0810.0810.0000.0000.0000.000
115A393MET00.0090.01135.8780.0030.0030.0000.0000.0000.000
116A394PRO00.005-0.00631.840-0.004-0.0040.0000.0000.0000.000
117A395MET0-0.0280.01134.4460.0000.0000.0000.0000.0000.000
118A396GLU-1-0.838-0.91736.0860.0520.0520.0000.0000.0000.000
119A397MET0-0.027-0.02538.0370.0080.0080.0000.0000.0000.000
120A398ALA00.0240.01439.841-0.005-0.0050.0000.0000.0000.000
121A399ASP-1-0.756-0.88043.5530.0450.0450.0000.0000.0000.000
122A400LEU00.0180.00445.1930.0000.0000.0000.0000.0000.000
123A401ASN00.0410.00547.726-0.002-0.0020.0000.0000.0000.000
124A402ALA0-0.0050.00249.554-0.002-0.0020.0000.0000.0000.000
125A403VAL0-0.025-0.01446.993-0.001-0.0010.0000.0000.0000.000
126A404LEU0-0.014-0.01750.2430.0000.0000.0000.0000.0000.000
127A405GLY00.0050.00352.478-0.001-0.0010.0000.0000.0000.000
128A406GLU-1-0.844-0.90550.6360.0360.0360.0000.0000.0000.000
129A407VAL0-0.045-0.02152.092-0.001-0.0010.0000.0000.0000.000
130A408ILE0-0.0200.00655.1450.0000.0000.0000.0000.0000.000
131A409ALA0-0.056-0.01258.096-0.001-0.0010.0000.0000.0000.000
132A417GLU-1-0.979-0.99266.0080.0330.0330.0000.0000.0000.000
133A418ILE00.0160.00359.9600.0020.0020.0000.0000.0000.000
134A419GLU-1-0.837-0.89262.4090.0370.0370.0000.0000.0000.000
135A420THR0-0.008-0.01959.3860.0010.0010.0000.0000.0000.000
136A421ALA0-0.032-0.00958.731-0.001-0.0010.0000.0000.0000.000
137A422LEU00.0150.00754.3210.0020.0020.0000.0000.0000.000
138A423TYR00.0090.00650.716-0.001-0.0010.0000.0000.0000.000
139A424PRO0-0.044-0.02752.976-0.001-0.0010.0000.0000.0000.000
140A425GLY00.0440.01949.8760.0030.0030.0000.0000.0000.000
141A426SER0-0.108-0.06749.151-0.003-0.0030.0000.0000.0000.000
142A427ILE0-0.054-0.02442.203-0.001-0.0010.0000.0000.0000.000
143A428GLU-1-0.855-0.91443.7470.0540.0540.0000.0000.0000.000
144A429VAL00.001-0.00839.9400.0040.0040.0000.0000.0000.000
145A430LYS10.8400.92033.713-0.079-0.0790.0000.0000.0000.000
146A431MET0-0.033-0.01937.8940.0060.0060.0000.0000.0000.000
147A432HIS00.0680.03938.482-0.005-0.0050.0000.0000.0000.000
148A433PRO00.0210.01941.1310.0010.0010.0000.0000.0000.000
149A434LEU0-0.022-0.01443.849-0.001-0.0010.0000.0000.0000.000
150A435SER0-0.046-0.05741.218-0.002-0.0020.0000.0000.0000.000
151A436ILE00.0400.02242.2840.0010.0010.0000.0000.0000.000
152A437LYS10.8010.88445.814-0.041-0.0410.0000.0000.0000.000
153A438ARG10.8830.97042.675-0.067-0.0670.0000.0000.0000.000
154A439ALA00.0220.00946.0450.0000.0000.0000.0000.0000.000
155A440VAL00.0480.01948.1450.0000.0000.0000.0000.0000.000
156A441ALA00.0130.01251.184-0.001-0.0010.0000.0000.0000.000
157A442ASN0-0.058-0.04650.1370.0000.0000.0000.0000.0000.000
158A443MET0-0.024-0.01148.447-0.001-0.0010.0000.0000.0000.000
159A444VAL00.0330.02053.208-0.001-0.0010.0000.0000.0000.000
160A445VAL0-0.020-0.00555.495-0.002-0.0020.0000.0000.0000.000
161A446ASN0-0.044-0.03254.7150.0000.0000.0000.0000.0000.000
162A447ALA00.000-0.00556.793-0.001-0.0010.0000.0000.0000.000
163A448ALA00.0270.00658.987-0.001-0.0010.0000.0000.0000.000
164A449ARG10.8770.94657.002-0.048-0.0480.0000.0000.0000.000
165A450TYR0-0.059-0.03559.6860.0000.0000.0000.0000.0000.000
166A451GLY00.0610.03362.1660.0010.0010.0000.0000.0000.000
167A452ASN0-0.120-0.08363.532-0.002-0.0020.0000.0000.0000.000
168A453GLY0-0.006-0.00165.817-0.002-0.0020.0000.0000.0000.000
169A454TRP0-0.046-0.01963.469-0.001-0.0010.0000.0000.0000.000
170A455ILE00.007-0.00458.9190.0020.0020.0000.0000.0000.000
171A456LYS10.8200.90659.672-0.042-0.0420.0000.0000.0000.000
172A457VAL00.0080.00254.8310.0030.0030.0000.0000.0000.000
173A458SER0-0.033-0.02655.050-0.001-0.0010.0000.0000.0000.000
174A459SER0-0.008-0.02351.2490.0030.0030.0000.0000.0000.000
175A460GLY0-0.002-0.00350.565-0.002-0.0020.0000.0000.0000.000
176A461THR0-0.055-0.02647.2510.0030.0030.0000.0000.0000.000
177A462GLU-1-0.836-0.90345.5660.0780.0780.0000.0000.0000.000
178A463PRO0-0.065-0.03942.1040.0020.0020.0000.0000.0000.000
179A464ASN0-0.016-0.01040.4430.0000.0000.0000.0000.0000.000
180A465ARG10.8040.92140.904-0.070-0.0700.0000.0000.0000.000
181A466ALA00.0560.01842.194-0.002-0.0020.0000.0000.0000.000
182A467TRP0-0.014-0.00244.4980.0000.0000.0000.0000.0000.000
183A468PHE00.0200.01145.496-0.003-0.0030.0000.0000.0000.000
184A469GLN00.0070.01249.7190.0060.0060.0000.0000.0000.000
185A470VAL0-0.016-0.00552.514-0.003-0.0030.0000.0000.0000.000
186A471GLU-1-0.858-0.90755.1900.0530.0530.0000.0000.0000.000
187A472ASP-1-0.750-0.87958.0840.0440.0440.0000.0000.0000.000
188A473ASP-1-0.851-0.89761.3330.0440.0440.0000.0000.0000.000
189A474GLY00.0250.03962.972-0.001-0.0010.0000.0000.0000.000
190A475PRO0-0.093-0.04161.5240.0020.0020.0000.0000.0000.000
191A499SER00.0270.00651.5340.0010.0010.0000.0000.0000.000
192A500GLY00.0550.00953.497-0.002-0.0020.0000.0000.0000.000
193A501THR00.0370.03253.4150.0010.0010.0000.0000.0000.000
194A502GLY00.0260.01651.1700.0020.0020.0000.0000.0000.000
195A503LEU0-0.041-0.01247.9660.0040.0040.0000.0000.0000.000
196A504GLY00.0900.03948.5420.0020.0020.0000.0000.0000.000
197A505LEU00.003-0.00349.0730.0010.0010.0000.0000.0000.000
198A506ALA0-0.0180.00245.0820.0040.0040.0000.0000.0000.000
199A507ILE0-0.031-0.01344.2610.0050.0050.0000.0000.0000.000
200A508VAL0-0.007-0.00344.4880.0020.0020.0000.0000.0000.000
201A509GLN0-0.038-0.03641.101-0.002-0.0020.0000.0000.0000.000
202A510ARG10.8100.89937.112-0.111-0.1110.0000.0000.0000.000
203A511ILE00.0110.00539.6040.0040.0040.0000.0000.0000.000
204A512VAL00.0030.00140.2810.0010.0010.0000.0000.0000.000
205A513ASP-1-0.780-0.85837.1050.1240.1240.0000.0000.0000.000
206A514ASN0-0.098-0.06535.6390.0140.0140.0000.0000.0000.000
207A515HIS0-0.050-0.02735.560-0.006-0.0060.0000.0000.0000.000
208A516ASN0-0.084-0.03932.5250.0080.0080.0000.0000.0000.000
209A517GLY00.0170.01635.6160.0000.0000.0000.0000.0000.000
210A518MET0-0.044-0.02239.1090.0080.0080.0000.0000.0000.000
211A519LEU0-0.006-0.00141.855-0.006-0.0060.0000.0000.0000.000
212A520GLU-1-0.829-0.89145.3440.0780.0780.0000.0000.0000.000
213A521LEU0-0.008-0.01448.236-0.003-0.0030.0000.0000.0000.000
214A522GLY00.009-0.00251.6830.0020.0020.0000.0000.0000.000
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