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: 2238R

Calculation Name: 4N77-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N77

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WH0

Base Structure: X-ray

Registration Date: 2023-06-19

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2236999.717012
FMO2-HF: Nuclear repulsion 2162315.70599
FMO2-HF: Total energy -74684.011022
FMO2-MP2: Total energy -74908.532992


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:2:PRO)


Summations of interaction energy for fragment #1(A:2: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.
6.158-13.71554.461-11.905-22.688-0.087
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.080 / q_NPA : -0.004
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].
3A4LEU0-0.065-0.0173.805-1.3801.464-0.044-1.517-1.2840.007
4A5LEU0-0.016-0.0046.442-0.657-0.6570.0000.0000.0000.000
5A6ILE0-0.030-0.0239.676-0.007-0.0070.0000.0000.0000.000
6A7ARG10.9600.99213.047-0.382-0.3820.0000.0000.0000.000
7A8LEU0-0.046-0.03316.582-0.020-0.0200.0000.0000.0000.000
8A9GLN00.0440.02019.466-0.007-0.0070.0000.0000.0000.000
9A10GLY00.0510.02222.5420.0080.0080.0000.0000.0000.000
10A11PRO00.0060.02026.014-0.006-0.0060.0000.0000.0000.000
11A12LEU00.007-0.00128.865-0.008-0.0080.0000.0000.0000.000
12A13GLN00.0210.01622.8120.0110.0110.0000.0000.0000.000
13A14SER0-0.049-0.02426.476-0.013-0.0130.0000.0000.0000.000
14A15TRP00.0330.02320.7080.0070.0070.0000.0000.0000.000
15A16GLY00.0360.02425.173-0.009-0.0090.0000.0000.0000.000
16A17THR00.0100.03024.3600.0030.0030.0000.0000.0000.000
17A18ARG10.8440.89225.736-0.038-0.0380.0000.0000.0000.000
18A19SER00.0720.06327.829-0.006-0.0060.0000.0000.0000.000
19A20ARG10.7610.86128.860-0.009-0.0090.0000.0000.0000.000
20A21PHE00.0530.06529.457-0.001-0.0010.0000.0000.0000.000
21A22ASP-1-0.715-0.83431.5050.0300.0300.0000.0000.0000.000
22A23HIS0-0.043-0.03131.9020.0050.0050.0000.0000.0000.000
23A24ARG10.7750.86632.831-0.022-0.0220.0000.0000.0000.000
24A25ASP-1-0.826-0.90232.3480.0290.0290.0000.0000.0000.000
25A26THR0-0.047-0.05027.7560.0090.0090.0000.0000.0000.000
26A27TRP0-0.023-0.00323.357-0.007-0.0070.0000.0000.0000.000
27A28PRO00.0290.00525.2440.0080.0080.0000.0000.0000.000
28A29TYR0-0.058-0.06820.6110.0090.0090.0000.0000.0000.000
29A30PRO0-0.008-0.00418.411-0.011-0.0110.0000.0000.0000.000
30A31THR00.005-0.01319.648-0.005-0.0050.0000.0000.0000.000
31A32LYS10.8510.90013.7280.0900.0900.0000.0000.0000.000
32A33SER0-0.017-0.01318.0230.0120.0120.0000.0000.0000.000
33A34GLY0-0.065-0.02720.6270.0080.0080.0000.0000.0000.000
34A35VAL00.0550.02214.4220.0140.0140.0000.0000.0000.000
35A36VAL00.0300.01515.1970.0250.0250.0000.0000.0000.000
36A37GLY0-0.015-0.00916.9690.0050.0050.0000.0000.0000.000
37A38LEU0-0.035-0.00916.5080.0010.0010.0000.0000.0000.000
38A39LEU00.0330.00612.0810.0110.0110.0000.0000.0000.000
39A40ALA00.0230.01315.7100.0050.0050.0000.0000.0000.000
40A41ALA0-0.031-0.01318.263-0.005-0.0050.0000.0000.0000.000
41A42ALA00.010-0.00316.026-0.004-0.0040.0000.0000.0000.000
42A43LEU00.011-0.00113.5710.0040.0040.0000.0000.0000.000
43A44GLY0-0.062-0.02317.477-0.014-0.0140.0000.0000.0000.000
44A45ARG10.7760.86115.311-0.088-0.0880.0000.0000.0000.000
45A46ASP-1-0.842-0.93121.5800.0530.0530.0000.0000.0000.000
46A47ARG10.9160.93424.035-0.071-0.0710.0000.0000.0000.000
47A48ARG10.8850.93525.632-0.044-0.0440.0000.0000.0000.000
48A49GLU-1-0.876-0.91222.0640.0610.0610.0000.0000.0000.000
49A50ASP-1-0.826-0.87020.089-0.020-0.0200.0000.0000.0000.000
50A51VAL0-0.033-0.03318.1950.0150.0150.0000.0000.0000.000
51A52SER0-0.037-0.05817.149-0.003-0.0030.0000.0000.0000.000
52A53ASP-1-0.724-0.82713.3850.0110.0110.0000.0000.0000.000
53A54LEU0-0.020-0.02312.459-0.011-0.0110.0000.0000.0000.000
54A55ALA0-0.060-0.03213.150-0.002-0.0020.0000.0000.0000.000
55A56ALA0-0.0050.00312.417-0.012-0.0120.0000.0000.0000.000
56A57LEU0-0.0290.0097.751-0.059-0.0590.0000.0000.0000.000
57A58ARG10.9090.9358.8500.4180.4180.0000.0000.0000.000
58A59MET0-0.029-0.0049.6160.0470.0470.0000.0000.0000.000
59A60GLY0-0.005-0.00511.891-0.064-0.0640.0000.0000.0000.000
60A61VAL0-0.036-0.02113.1580.0730.0730.0000.0000.0000.000
61A62ARG10.8070.86614.063-0.243-0.2430.0000.0000.0000.000
62A63VAL0-0.053-0.04016.5090.0270.0270.0000.0000.0000.000
63A64ASP-1-0.730-0.82017.8310.1810.1810.0000.0000.0000.000
64A65ARG10.9540.98120.617-0.124-0.1240.0000.0000.0000.000
65A66LYS10.9860.97924.146-0.038-0.0380.0000.0000.0000.000
66A67GLY00.0210.02625.8810.0020.0020.0000.0000.0000.000
67A68VAL0-0.048-0.02228.421-0.007-0.0070.0000.0000.0000.000
68A69LEU00.0170.01831.7050.0040.0040.0000.0000.0000.000
69A70LYS10.9360.96833.077-0.059-0.0590.0000.0000.0000.000
70A71VAL00.0110.00035.1300.0010.0010.0000.0000.0000.000
71A72ASP-1-0.885-0.93535.4030.0620.0620.0000.0000.0000.000
72A73TYR0-0.016-0.02337.545-0.003-0.0030.0000.0000.0000.000
73A117LYS10.9420.96039.784-0.038-0.0380.0000.0000.0000.000
74A118ARG10.9500.97835.099-0.052-0.0520.0000.0000.0000.000
75A119TYR00.0790.05433.5790.0030.0030.0000.0000.0000.000
76A120PHE0-0.056-0.03030.7500.0030.0030.0000.0000.0000.000
77A121LEU00.0180.01925.648-0.005-0.0050.0000.0000.0000.000
78A122SER0-0.023-0.03129.1400.0070.0070.0000.0000.0000.000
79A123ASP-1-0.887-0.94328.4050.0870.0870.0000.0000.0000.000
80A124ALA00.0080.00724.772-0.001-0.0010.0000.0000.0000.000
81A125ALA0-0.033-0.03621.5000.0110.0110.0000.0000.0000.000
82A126PHE0-0.015-0.01318.581-0.015-0.0150.0000.0000.0000.000
83A127LEU00.0580.04412.0260.0290.0290.0000.0000.0000.000
84A128VAL0-0.037-0.02212.568-0.058-0.0580.0000.0000.0000.000
85A129GLY00.0550.0309.5210.1380.1380.0000.0000.0000.000
86A130LEU0-0.050-0.0378.016-0.211-0.2110.0000.0000.0000.000
87A131GLU-1-0.821-0.9093.876-1.561-1.1200.002-0.122-0.3200.000
88A132GLY00.0220.0004.0910.0560.226-0.001-0.038-0.1320.000
89A133GLU-1-0.917-0.9524.094-0.810-0.6300.000-0.028-0.1520.000
90A134ARG10.9090.9342.052-0.856-1.4764.789-1.480-2.6900.004
91A135ALA00.0270.0234.7750.3930.422-0.001-0.001-0.0270.000
92A136LEU00.0140.0148.1240.1430.1430.0000.0000.0000.000
93A137LEU00.0050.0032.955-0.2760.2490.061-0.120-0.4660.000
94A138GLU-1-0.904-0.9565.3540.9510.9510.0000.0000.0000.000
95A139ALA0-0.051-0.0267.447-0.031-0.0310.0000.0000.0000.000
96A140LEU0-0.020-0.0179.096-0.028-0.0280.0000.0000.0000.000
97A141HIS00.0060.0137.937-0.047-0.0470.0000.0000.0000.000
98A142ARG10.9310.95310.004-0.585-0.5850.0000.0000.0000.000
99A143ALA0-0.010-0.00512.996-0.054-0.0540.0000.0000.0000.000
100A144LEU00.000-0.01211.528-0.053-0.0530.0000.0000.0000.000
101A145LYS10.8950.97314.772-0.383-0.3830.0000.0000.0000.000
102A146ASN0-0.104-0.05316.488-0.050-0.0500.0000.0000.0000.000
103A147PRO0-0.0060.01118.540-0.011-0.0110.0000.0000.0000.000
104A148ARG10.9300.96519.532-0.177-0.1770.0000.0000.0000.000
105A149PHE0-0.043-0.00121.634-0.020-0.0200.0000.0000.0000.000
106A150PRO0-0.015-0.02022.2540.0150.0150.0000.0000.0000.000
107A151LEU00.0210.02518.171-0.006-0.0060.0000.0000.0000.000
108A152TYR00.008-0.01522.240-0.008-0.0080.0000.0000.0000.000
109A153LEU00.0030.01721.2990.0070.0070.0000.0000.0000.000
110A154GLY00.0720.03424.033-0.012-0.0120.0000.0000.0000.000
111A155ARG10.7390.86925.925-0.069-0.0690.0000.0000.0000.000
112A156LYS10.9660.96827.893-0.077-0.0770.0000.0000.0000.000
113A157SER0-0.051-0.02429.334-0.008-0.0080.0000.0000.0000.000
114A158TYR0-0.0260.01127.657-0.003-0.0030.0000.0000.0000.000
115A159VAL00.001-0.00826.5190.0090.0090.0000.0000.0000.000
116A160PRO0-0.014-0.00421.902-0.004-0.0040.0000.0000.0000.000
117A161SER0-0.052-0.01224.070-0.001-0.0010.0000.0000.0000.000
118A162PRO00.0560.01121.089-0.010-0.0100.0000.0000.0000.000
119A163PRO00.014-0.00319.501-0.002-0.0020.0000.0000.0000.000
120A164PRO00.0480.01216.7040.0140.0140.0000.0000.0000.000
121A165TYR0-0.0290.00212.230-0.002-0.0020.0000.0000.0000.000
122A166LEU00.0180.01712.273-0.081-0.0810.0000.0000.0000.000
123A167PRO0-0.012-0.01512.0060.1480.1480.0000.0000.0000.000
124A168ASP-1-0.843-0.89510.5380.7090.7090.0000.0000.0000.000
125A169GLY00.0150.0019.5170.0400.0400.0000.0000.0000.000
126A170LEU0-0.040-0.0143.569-0.524-0.0790.014-0.130-0.3300.001
127A171VAL00.0380.0154.474-0.786-0.235-0.001-0.180-0.3710.000
128A172GLU-1-0.742-0.8871.9828.673-10.49942.656-10.575-12.909-0.075
129A173ALA00.0050.0021.7854.587-1.6906.0582.953-2.734-0.014
130A174PRO00.0470.0332.867-0.9200.0420.929-0.663-1.228-0.010
131A175LEU0-0.036-0.0184.4210.4590.508-0.001-0.004-0.0450.000
132A176ALA0-0.027-0.0186.9940.1870.1870.0000.0000.0000.000
133A177GLU-1-0.860-0.9337.442-0.388-0.3880.0000.0000.0000.000
134A178ALA0-0.016-0.0065.1130.1550.1550.0000.0000.0000.000
135A179LEU0-0.049-0.0337.1280.1120.1120.0000.0000.0000.000
136A180GLU-1-0.943-0.97910.501-0.093-0.0930.0000.0000.0000.000
137A181GLY0-0.032-0.02510.7890.0010.0010.0000.0000.0000.000
138A182TYR0-0.046-0.03910.408-0.009-0.0090.0000.0000.0000.000
139A183PRO00.0480.03212.218-0.059-0.0590.0000.0000.0000.000
140A184TYR00.006-0.00315.8590.0220.0220.0000.0000.0000.000
141A185LEU0-0.007-0.02016.0920.0130.0130.0000.0000.0000.000
142A186LEU0-0.128-0.04819.275-0.002-0.0020.0000.0000.0000.000
143A187GLY00.0180.00222.1650.0060.0060.0000.0000.0000.000
144A188GLY00.0560.02624.064-0.009-0.0090.0000.0000.0000.000
145A189LYS10.8470.90520.156-0.054-0.0540.0000.0000.0000.000
146A190PRO00.0230.01520.559-0.001-0.0010.0000.0000.0000.000
147A191PRO0-0.0120.00523.438-0.009-0.0090.0000.0000.0000.000
148A192GLU-1-0.969-1.01225.6390.0370.0370.0000.0000.0000.000
149A193ASP-1-0.861-0.92623.0010.0170.0170.0000.0000.0000.000
150A194LEU0-0.052-0.01918.6350.0080.0080.0000.0000.0000.000
151A195LEU0-0.056-0.02020.856-0.012-0.0120.0000.0000.0000.000
152A196LEU00.0320.01113.7420.0280.0280.0000.0000.0000.000
153A197ALA0-0.015-0.00417.262-0.022-0.0220.0000.0000.0000.000
154A198LEU00.0040.00112.4580.0190.0190.0000.0000.0000.000
155A199GLU-1-0.813-0.88513.467-0.111-0.1110.0000.0000.0000.000
156A200ALA0-0.053-0.02514.284-0.046-0.0460.0000.0000.0000.000
157A201GLU-1-0.888-0.94616.370-0.237-0.2370.0000.0000.0000.000
158A202GLU-1-0.913-0.94318.777-0.107-0.1070.0000.0000.0000.000
159A203GLY0-0.020-0.01920.7730.0000.0000.0000.0000.0000.000
160A204ARG10.9150.95623.1600.0470.0470.0000.0000.0000.000
161A205LEU00.0160.01923.270-0.001-0.0010.0000.0000.0000.000
162A206VAL00.0110.01121.6270.0100.0100.0000.0000.0000.000
163A207TYR00.0210.00923.354-0.007-0.0070.0000.0000.0000.000
164A208ASP-1-0.751-0.86520.6890.0150.0150.0000.0000.0000.000
165A209GLN00.0950.05816.2890.0210.0210.0000.0000.0000.000
166A210PRO0-0.033-0.02918.235-0.002-0.0020.0000.0000.0000.000
167A211ALA00.015-0.00219.948-0.011-0.0110.0000.0000.0000.000
168A212GLY00.0170.00522.439-0.007-0.0070.0000.0000.0000.000
169A213PRO00.0580.05523.3190.0070.0070.0000.0000.0000.000
170A214PHE00.0310.00419.930-0.005-0.0050.0000.0000.0000.000
171A215SER0-0.057-0.03425.1770.0000.0000.0000.0000.0000.000
172A216GLU-1-0.936-0.96727.867-0.003-0.0030.0000.0000.0000.000
173A217ARG10.8420.92427.234-0.026-0.0260.0000.0000.0000.000
174A218ARG11.0461.03825.9380.0260.0260.0000.0000.0000.000
175A219PHE0-0.032-0.02322.6510.0050.0050.0000.0000.0000.000
176A220ALA00.0380.02522.595-0.002-0.0020.0000.0000.0000.000
177A221ALA0-0.019-0.02123.2770.0070.0070.0000.0000.0000.000
178A222ARG10.8490.91016.2250.0110.0110.0000.0000.0000.000
179A223PHE00.009-0.00119.9880.0180.0180.0000.0000.0000.000
180A224VAL0-0.014-0.00518.327-0.010-0.0100.0000.0000.0000.000
181A225ARG10.8380.88715.3550.1610.1610.0000.0000.0000.000
182A226GLU-1-0.881-0.91218.6080.0030.0030.0000.0000.0000.000
183A227GLU-1-0.813-0.89016.766-0.133-0.1330.0000.0000.0000.000
184A228VAL00.002-0.00920.3210.0160.0160.0000.0000.0000.000
185A229LEU0-0.0040.00415.718-0.011-0.0110.0000.0000.0000.000
186A230PRO00.0410.01819.1190.0140.0140.0000.0000.0000.000
187A231LYS10.9790.99519.964-0.020-0.0200.0000.0000.0000.000
188A232GLU-1-0.956-0.98921.0410.0220.0220.0000.0000.0000.000
189A233ARG10.8850.96611.7180.0320.0320.0000.0000.0000.000
190A234VAL00.0200.01716.2960.0090.0090.0000.0000.0000.000
191A235PRO0-0.0200.01514.647-0.017-0.0170.0000.0000.0000.000
192A236GLU-1-0.959-0.98217.8090.1160.1160.0000.0000.0000.000
193A237GLY00.0010.03519.3890.0230.0230.0000.0000.0000.000
194A238PRO0-0.068-0.04120.363-0.023-0.0230.0000.0000.0000.000
195A239PRO0-0.018-0.01015.975-0.010-0.0100.0000.0000.0000.000