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: GNL71

Calculation Name: 4N77-A-Xray319

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 199
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2255323.134209
FMO2-HF: Nuclear repulsion 2180297.382787
FMO2-HF: Total energy -75025.751422
FMO2-MP2: Total energy -75251.369256


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:1:ACE )


Summations of interaction energy for fragment #1(A:1:ACE )
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.
-0.110.18211.14-6.086-5.343-0.02
Interaction energy analysis for fragmet #1(A:1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.071 / q_NPA : -0.003
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].
3A3THR 00.0830.0143.8110.0731.4140.000-0.644-0.696-0.002
4A4LEU 0-0.055-0.0134.8470.4030.5120.000-0.009-0.0990.000
5A5LEU 0-0.020-0.0056.220-0.089-0.0890.0000.0000.0000.000
6A6ILE 0-0.028-0.0229.3350.1140.1140.0000.0000.0000.000
7A7ARG 10.9600.99212.419-0.159-0.1590.0000.0000.0000.000
8A8LEU 0-0.046-0.03215.9350.0060.0060.0000.0000.0000.000
9A9GLN 00.0440.02019.014-0.007-0.0070.0000.0000.0000.000
10A10GLY 00.0530.02321.9440.0090.0090.0000.0000.0000.000
11A11PRO 00.0030.01925.291-0.006-0.0060.0000.0000.0000.000
12A12LEU 00.0090.00028.247-0.005-0.0050.0000.0000.0000.000
13A13GLN 00.0220.01622.627-0.003-0.0030.0000.0000.0000.000
14A14SER 0-0.047-0.02326.415-0.003-0.0030.0000.0000.0000.000
15A15TRP 00.0330.02220.661-0.004-0.0040.0000.0000.0000.000
16A16GLY 00.0340.02225.8700.0000.0000.0000.0000.0000.000
17A17THR 00.0160.03225.714-0.005-0.0050.0000.0000.0000.000
18A18ARG 10.8350.89026.9720.0550.0550.0000.0000.0000.000
19A19SER 00.0720.06329.407-0.003-0.0030.0000.0000.0000.000
20A20ARG 10.7590.86030.3020.0530.0530.0000.0000.0000.000
21A21PHE 00.0540.06630.5760.0010.0010.0000.0000.0000.000
22A22ASP -1-0.714-0.83532.747-0.019-0.0190.0000.0000.0000.000
23A23HIS 0-0.042-0.02932.4710.0020.0020.0000.0000.0000.000
24A24ARG 10.7820.87033.2200.0200.0200.0000.0000.0000.000
25A25ASP -1-0.829-0.90333.399-0.026-0.0260.0000.0000.0000.000
26A26THR 0-0.049-0.05128.4800.0020.0020.0000.0000.0000.000
27A27TRP 0-0.019-0.00324.8010.0030.0030.0000.0000.0000.000
28A28PRO 00.0250.00526.7510.0060.0060.0000.0000.0000.000
29A29TYR 0-0.056-0.06822.0400.0010.0010.0000.0000.0000.000
30A30PRO 0-0.008-0.00419.213-0.003-0.0030.0000.0000.0000.000
31A31THR 00.001-0.01420.900-0.012-0.0120.0000.0000.0000.000
32A32LYS 10.8500.89915.7700.2660.2660.0000.0000.0000.000
33A33SER 0-0.016-0.01219.0690.0020.0020.0000.0000.0000.000
34A34GLY 0-0.063-0.02521.3260.0100.0100.0000.0000.0000.000
35A35VAL 00.0570.02114.9730.0170.0170.0000.0000.0000.000
36A36VAL 00.0290.01516.1430.0160.0160.0000.0000.0000.000
37A37GLY 0-0.016-0.00917.6360.0150.0150.0000.0000.0000.000
38A38LEU 0-0.031-0.00816.2980.0150.0150.0000.0000.0000.000
39A39LEU 00.0300.00512.6300.0260.0260.0000.0000.0000.000
40A40ALA 00.0240.01315.6700.0210.0210.0000.0000.0000.000
41A41ALA 0-0.032-0.01318.0830.0140.0140.0000.0000.0000.000
42A42ALA 00.008-0.00415.3960.0120.0120.0000.0000.0000.000
43A43LEU 00.0130.00012.6460.0250.0250.0000.0000.0000.000
44A44GLY 0-0.061-0.02216.5820.0050.0050.0000.0000.0000.000
45A45ARG 10.7770.86115.0470.0580.0580.0000.0000.0000.000
46A46ASP -1-0.844-0.93321.012-0.006-0.0060.0000.0000.0000.000
47A47ARG 10.9160.93523.8100.0030.0030.0000.0000.0000.000
48A48ARG 10.8860.93625.5850.0020.0020.0000.0000.0000.000
49A49GLU -1-0.876-0.91221.519-0.010-0.0100.0000.0000.0000.000
50A50ASP -1-0.825-0.86920.615-0.109-0.1090.0000.0000.0000.000
51A51VAL 0-0.030-0.03218.4910.0060.0060.0000.0000.0000.000
52A52SER 0-0.042-0.05917.972-0.025-0.0250.0000.0000.0000.000
53A53ASP -1-0.722-0.82513.738-0.159-0.1590.0000.0000.0000.000
54A54LEU 0-0.020-0.02312.931-0.052-0.0520.0000.0000.0000.000
55A55ALA 0-0.062-0.03314.546-0.033-0.0330.0000.0000.0000.000
56A56ALA 0-0.0010.00514.394-0.004-0.0040.0000.0000.0000.000
57A57LEU 0-0.0300.0109.476-0.055-0.0550.0000.0000.0000.000
58A58ARG 10.9070.93411.8360.4860.4860.0000.0000.0000.000
59A59MET 0-0.026-0.00412.075-0.042-0.0420.0000.0000.0000.000
60A60GLY 0-0.008-0.00713.7640.0130.0130.0000.0000.0000.000
61A61VAL 0-0.035-0.02114.8570.0150.0150.0000.0000.0000.000
62A62ARG 10.8040.86416.0640.0280.0280.0000.0000.0000.000
63A63VAL 0-0.049-0.03818.2980.0170.0170.0000.0000.0000.000
64A64ASP -1-0.733-0.82019.067-0.010-0.0100.0000.0000.0000.000
65A65ARG 10.9540.98121.833-0.012-0.0120.0000.0000.0000.000
66A66LYS 10.9880.98024.9400.0390.0390.0000.0000.0000.000
67A67GLY 00.0220.02726.9880.0000.0000.0000.0000.0000.000
68A68VAL 0-0.049-0.02329.048-0.004-0.0040.0000.0000.0000.000
69A69LEU 00.0170.01932.4480.0020.0020.0000.0000.0000.000
70A70LYS 10.9330.96733.6740.0020.0020.0000.0000.0000.000
71A71VAL 0-0.008-0.00835.410-0.002-0.0020.0000.0000.0000.000
72A72ASP -1-0.886-0.93735.1420.0060.0060.0000.0000.0000.000
73A73TYR 0-0.036-0.03537.379-0.002-0.0020.0000.0000.0000.000
74A74NME 00.0290.01839.7270.0000.0000.0000.0000.0000.000
75A116ACE 00.0590.02642.5820.0000.0000.0000.0000.0000.000
76A117LYS 10.9030.93339.7920.0060.0060.0000.0000.0000.000
77A118ARG 10.9420.98535.2090.0010.0010.0000.0000.0000.000
78A119TYR 00.0700.04934.1830.0020.0020.0000.0000.0000.000
79A120PHE 0-0.055-0.02830.766-0.001-0.0010.0000.0000.0000.000
80A121LEU 00.0210.01926.0700.0000.0000.0000.0000.0000.000
81A122SER 0-0.023-0.03129.0420.0040.0040.0000.0000.0000.000
82A123ASP -1-0.887-0.94328.1490.0120.0120.0000.0000.0000.000
83A124ALA 00.0060.00625.2450.0000.0000.0000.0000.0000.000
84A125ALA 0-0.030-0.03521.6100.0090.0090.0000.0000.0000.000
85A126PHE 0-0.012-0.01319.191-0.009-0.0090.0000.0000.0000.000
86A127LEU 00.0550.04312.7920.0200.0200.0000.0000.0000.000
87A128VAL 0-0.037-0.02113.246-0.027-0.0270.0000.0000.0000.000
88A129GLY 00.0520.02710.2820.0340.0340.0000.0000.0000.000
89A130LEU 0-0.045-0.0359.0240.0280.0280.0000.0000.0000.000
90A131GLU -1-0.822-0.9117.494-1.151-1.1510.0000.0000.0000.000
91A132GLY 00.016-0.0037.1030.3860.3860.0000.0000.0000.000
92A133GLU -1-0.917-0.9536.596-1.020-1.0200.0000.0000.0000.000
93A134ARG 00.1400.0712.386-0.327-1.8466.071-2.444-2.108-0.013
94A135ALA 00.0270.0224.4860.5600.6910.000-0.013-0.1170.000
95A136LEU 00.0100.0126.9540.2030.2030.0000.0000.0000.000
96A137LEU 0-0.003-0.0013.9250.2620.3800.003-0.048-0.0730.000
97A138GLU -1-0.902-0.9563.2851.9322.6080.032-0.305-0.403-0.002
98A139ALA 0-0.049-0.0245.620-0.046-0.0460.0000.0000.0000.000
99A140LEU 0-0.022-0.0188.5620.0020.0020.0000.0000.0000.000
100A141HIS 0-0.0010.0106.6360.0920.0920.0000.0000.0000.000
101A142ARG 10.9330.9538.451-0.800-0.8000.0000.0000.0000.000
102A143ALA 0-0.009-0.00511.207-0.058-0.0580.0000.0000.0000.000
103A144LEU 0-0.004-0.01310.700-0.041-0.0410.0000.0000.0000.000
104A145LYS 10.8910.97213.387-0.327-0.3270.0000.0000.0000.000
105A146ASN 0-0.099-0.05115.011-0.042-0.0420.0000.0000.0000.000
106A147PRO 0-0.0050.01017.388-0.007-0.0070.0000.0000.0000.000
107A148ARG 10.9290.96518.378-0.108-0.1080.0000.0000.0000.000
108A149PHE 0-0.045-0.00220.571-0.011-0.0110.0000.0000.0000.000
109A150PRO 0-0.015-0.01921.4540.0050.0050.0000.0000.0000.000
110A151LEU 00.0240.02617.383-0.010-0.0100.0000.0000.0000.000
111A152TYR 00.008-0.01621.6680.0020.0020.0000.0000.0000.000
112A153LEU 00.0020.01720.764-0.006-0.0060.0000.0000.0000.000
113A154GLY 00.0700.03423.751-0.005-0.0050.0000.0000.0000.000
114A155ARG 10.7400.86925.9300.0090.0090.0000.0000.0000.000
115A156LYS 10.9660.96927.866-0.004-0.0040.0000.0000.0000.000
116A157SER 0-0.049-0.02328.854-0.002-0.0020.0000.0000.0000.000
117A158TYR 0-0.0290.01027.234-0.001-0.0010.0000.0000.0000.000
118A159VAL 00.003-0.00725.5730.0000.0000.0000.0000.0000.000
119A160PRO 0-0.017-0.00521.074-0.003-0.0030.0000.0000.0000.000
120A161SER 0-0.050-0.01223.2120.0090.0090.0000.0000.0000.000
121A162PRO 00.0570.01119.827-0.008-0.0080.0000.0000.0000.000
122A163PRO 00.013-0.00218.131-0.010-0.0100.0000.0000.0000.000
123A164PRO 00.0490.01215.8570.0080.0080.0000.0000.0000.000
124A165TYR 0-0.0250.00510.540-0.044-0.0440.0000.0000.0000.000
125A166LEU 00.0190.01711.005-0.030-0.0300.0000.0000.0000.000
126A167PRO 0-0.011-0.01310.2980.0950.0950.0000.0000.0000.000
127A168ASP -1-0.843-0.8959.2710.4820.4820.0000.0000.0000.000
128A169GLY 00.0120.0008.227-0.028-0.0280.0000.0000.0000.000
129A170LEU 0-0.033-0.0032.0180.215-1.0364.491-2.012-1.227-0.004
130A171VAL 00.0460.0184.1680.3210.5600.002-0.047-0.1950.000
131A172GLH 0-0.010-0.0372.441-1.213-0.8130.541-0.557-0.3840.001
132A173ALA 00.0090.0064.9330.1220.1700.000-0.007-0.0410.000
133A174PRO 00.0550.0377.111-0.330-0.3300.0000.0000.0000.000
134A175LEU 0-0.034-0.0179.5530.1560.1560.0000.0000.0000.000
135A176ALA 0-0.024-0.01610.8060.0840.0840.0000.0000.0000.000
136A177GLU -1-0.859-0.93311.569-0.233-0.2330.0000.0000.0000.000
137A178ALA 0-0.020-0.0088.2160.0810.0810.0000.0000.0000.000
138A179LEU 0-0.047-0.03210.0640.1040.1040.0000.0000.0000.000
139A180GLU -1-0.944-0.97812.947-0.109-0.1090.0000.0000.0000.000
140A181GLY 0-0.031-0.02413.6120.0310.0310.0000.0000.0000.000
141A182TYR 0-0.047-0.04010.9210.0130.0130.0000.0000.0000.000
142A183PRO 00.0430.03013.597-0.021-0.0210.0000.0000.0000.000
143A184TYR 00.001-0.00416.784-0.004-0.0040.0000.0000.0000.000
144A185LEU 0-0.007-0.01915.9880.0190.0190.0000.0000.0000.000
145A186LEU 0-0.126-0.04819.5020.0100.0100.0000.0000.0000.000
146A187GLY 00.0240.00522.5740.0030.0030.0000.0000.0000.000
147A188GLY 00.0550.02524.579-0.008-0.0080.0000.0000.0000.000
148A189LYS 10.8480.90522.3180.0040.0040.0000.0000.0000.000
149A190PRO 00.0180.01322.2850.0010.0010.0000.0000.0000.000
150A191PRO 0-0.0100.00625.147-0.002-0.0020.0000.0000.0000.000
151A192GLU -1-0.968-1.01227.608-0.017-0.0170.0000.0000.0000.000
152A193ASP -1-0.861-0.92625.628-0.043-0.0430.0000.0000.0000.000
153A194LEU 0-0.053-0.02020.7450.0030.0030.0000.0000.0000.000
154A195LEU 0-0.056-0.02023.530-0.006-0.0060.0000.0000.0000.000
155A196LEU 00.0320.01216.4460.0030.0030.0000.0000.0000.000
156A197ALA 0-0.016-0.00419.571-0.001-0.0010.0000.0000.0000.000
157A198LEU 00.0020.00015.778-0.019-0.0190.0000.0000.0000.000
158A199GLU -1-0.811-0.88316.658-0.251-0.2510.0000.0000.0000.000
159A200ALA 0-0.054-0.02418.150-0.030-0.0300.0000.0000.0000.000
160A201GLU -1-0.889-0.94720.647-0.218-0.2180.0000.0000.0000.000
161A202GLU -1-0.912-0.94323.112-0.110-0.1100.0000.0000.0000.000
162A203GLY 0-0.021-0.02024.911-0.006-0.0060.0000.0000.0000.000
163A204ARG 10.9160.95526.7100.0910.0910.0000.0000.0000.000
164A205LEU 00.0180.02026.420-0.008-0.0080.0000.0000.0000.000
165A206VAL 00.0150.01223.8640.0110.0110.0000.0000.0000.000
166A207TYR 00.0220.00925.849-0.009-0.0090.0000.0000.0000.000
167A208ASP -1-0.760-0.86722.473-0.113-0.1130.0000.0000.0000.000
168A209GLN 00.0980.05918.825-0.005-0.0050.0000.0000.0000.000
169A210PRO 0-0.030-0.02819.7160.0140.0140.0000.0000.0000.000
170A211ALA 00.012-0.00221.752-0.013-0.0130.0000.0000.0000.000
171A212GLY 00.0190.00524.2660.0030.0030.0000.0000.0000.000
172A213PRO 00.0600.05623.896-0.003-0.0030.0000.0000.0000.000
173A214PHE 00.0290.00420.3570.0050.0050.0000.0000.0000.000
174A215SER 0-0.057-0.03425.6500.0040.0040.0000.0000.0000.000
175A216GLU -1-0.935-0.96628.430-0.052-0.0520.0000.0000.0000.000
176A217ARG 10.8400.92328.2150.0330.0330.0000.0000.0000.000
177A218ARG 11.0481.04027.5550.0790.0790.0000.0000.0000.000
178A219PHE 0-0.030-0.02223.912-0.001-0.0010.0000.0000.0000.000
179A220ALA 00.0350.02325.2580.0060.0060.0000.0000.0000.000
180A221ALA 0-0.020-0.02125.789-0.001-0.0010.0000.0000.0000.000
181A222ARG 10.8490.90918.4950.1620.1620.0000.0000.0000.000
182A223PHE 00.011-0.00123.2670.0180.0180.0000.0000.0000.000
183A224VAL 0-0.012-0.00420.956-0.020-0.0200.0000.0000.0000.000
184A225ARG 10.8390.88720.0410.1980.1980.0000.0000.0000.000
185A226GLU -1-0.883-0.91322.056-0.090-0.0900.0000.0000.0000.000
186A227GLU -1-0.813-0.89020.820-0.167-0.1670.0000.0000.0000.000
187A228VAL 00.002-0.00923.5680.0050.0050.0000.0000.0000.000
188A229LEU 0-0.0020.00418.516-0.006-0.0060.0000.0000.0000.000
189A230PRO 00.0420.01822.4810.0100.0100.0000.0000.0000.000
190A231LYS 10.9750.99422.8920.0190.0190.0000.0000.0000.000
191A232GLU -1-0.950-0.98723.491-0.026-0.0260.0000.0000.0000.000
192A233ARG 10.8830.96514.9090.1020.1020.0000.0000.0000.000
193A234VAL 00.0170.01518.2570.0020.0020.0000.0000.0000.000
194A235PRO 0-0.0190.01516.3060.0070.0070.0000.0000.0000.000
195A236GLU -1-0.959-0.98219.5030.0430.0430.0000.0000.0000.000
196A237GLY 00.0020.03419.8350.0120.0120.0000.0000.0000.000
197A238PRO 0-0.063-0.04220.451-0.007-0.0070.0000.0000.0000.000
198A239PRO 0-0.028-0.03215.2400.0050.0050.0000.0000.0000.000
199A240NME 00.0040.02315.831-0.004-0.0040.0000.0000.0000.000