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: ZY37N

Calculation Name: 3R8C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R8C

Chain ID: A

ChEMBL ID:

UniProt ID: B1MB31

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptHSide
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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2011915.693477
FMO2-HF: Nuclear repulsion 1938528.46344
FMO2-HF: Total energy -73387.230037
FMO2-MP2: Total energy -73602.458446


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:SER)


Summations of interaction energy for fragment #1(A:-1:SER)
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.
-7.488-4.1581.71-1.526-3.516-0.004
Interaction energy analysis for fragmet #1(A:-1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.048
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].
3A1VAL00.0350.0203.8421.5452.812-0.016-0.549-0.702-0.001
4A2VAL0-0.027-0.0126.6050.3030.3030.0000.0000.0000.000
5A3ALA00.0260.0349.8570.1960.1960.0000.0000.0000.000
6A4VAL00.007-0.01112.9570.0690.0690.0000.0000.0000.000
7A5ASP-1-0.769-0.87515.995-0.489-0.4890.0000.0000.0000.000
8A6GLY00.0840.02819.2690.0230.0230.0000.0000.0000.000
9A7PRO0-0.096-0.04422.9000.0120.0120.0000.0000.0000.000
10A8SER00.0050.00425.1160.0020.0020.0000.0000.0000.000
11A9GLY00.016-0.01227.0730.0010.0010.0000.0000.0000.000
12A10THR00.0330.00424.4280.0170.0170.0000.0000.0000.000
13A11GLY0-0.0150.00124.9210.0030.0030.0000.0000.0000.000
14A12LYS10.8280.92419.4760.2610.2610.0000.0000.0000.000
15A13SER0-0.016-0.03419.4400.0030.0030.0000.0000.0000.000
16A14SER0-0.061-0.05119.0530.0220.0220.0000.0000.0000.000
17A15VAL00.0220.01218.1520.0240.0240.0000.0000.0000.000
18A16ALA00.0130.00815.0220.0070.0070.0000.0000.0000.000
19A17LYS10.9050.95914.3250.0080.0080.0000.0000.0000.000
20A18GLU-1-0.805-0.87714.9910.2330.2330.0000.0000.0000.000
21A19LEU0-0.009-0.01512.2700.0430.0430.0000.0000.0000.000
22A20ALA00.002-0.00210.7680.0200.0200.0000.0000.0000.000
23A21ARG10.8110.87410.986-0.076-0.0760.0000.0000.0000.000
24A22GLN0-0.112-0.06413.0830.1100.1100.0000.0000.0000.000
25A23LEU0-0.073-0.0428.4250.0090.0090.0000.0000.0000.000
26A24GLY0-0.0380.0028.4600.2080.2080.0000.0000.0000.000
27A25ALA0-0.077-0.0326.9560.4010.4010.0000.0000.0000.000
28A26SER00.0530.0217.122-0.251-0.2510.0000.0000.0000.000
29A27TYR0-0.071-0.0669.061-0.247-0.2470.0000.0000.0000.000
30A28LEU00.0440.02711.8600.0450.0450.0000.0000.0000.000
31A29ASP-1-0.782-0.87313.813-0.165-0.1650.0000.0000.0000.000
32A30THR00.018-0.03915.6640.0260.0260.0000.0000.0000.000
33A31GLY0-0.025-0.01018.2210.0120.0120.0000.0000.0000.000
34A32ALA0-0.026-0.02520.8360.0130.0130.0000.0000.0000.000
35A33MET00.0230.02217.2490.0040.0040.0000.0000.0000.000
36A34TYR00.0360.01020.3930.0130.0130.0000.0000.0000.000
37A35ARG10.8260.89224.1220.0850.0850.0000.0000.0000.000
38A36ILE00.0230.02222.7320.0100.0100.0000.0000.0000.000
39A37VAL00.0200.01024.5510.0090.0090.0000.0000.0000.000
40A38THR0-0.034-0.02127.3120.0020.0020.0000.0000.0000.000
41A39LEU00.0000.00629.7680.0050.0050.0000.0000.0000.000
42A40TRP0-0.013-0.01229.9270.0100.0100.0000.0000.0000.000
43A41VAL00.0320.00631.0050.0030.0030.0000.0000.0000.000
44A42LEU0-0.035-0.03033.4410.0030.0030.0000.0000.0000.000
45A43ARG10.7370.82633.653-0.002-0.0020.0000.0000.0000.000
46A44ALA0-0.0140.00835.6790.0040.0040.0000.0000.0000.000
47A45GLY0-0.037-0.00637.4550.0000.0000.0000.0000.0000.000
48A46VAL0-0.030-0.01735.530-0.001-0.0010.0000.0000.0000.000
49A47ASP-1-0.829-0.88938.484-0.063-0.0630.0000.0000.0000.000
50A48LEU0-0.008-0.02635.080-0.006-0.0060.0000.0000.0000.000
51A49THR0-0.096-0.06537.122-0.008-0.0080.0000.0000.0000.000
52A50ASP-1-0.835-0.91738.867-0.082-0.0820.0000.0000.0000.000
53A51PRO0-0.005-0.02034.131-0.001-0.0010.0000.0000.0000.000
54A52ALA00.0070.00934.143-0.005-0.0050.0000.0000.0000.000
55A53ALA00.0070.02035.5860.0020.0020.0000.0000.0000.000
56A54ILE0-0.008-0.00831.2580.0020.0020.0000.0000.0000.000
57A55ALA0-0.038-0.02230.777-0.001-0.0010.0000.0000.0000.000
58A56ALA00.0330.02831.077-0.001-0.0010.0000.0000.0000.000
59A57ALA0-0.0040.01333.3360.0060.0060.0000.0000.0000.000
60A58THR0-0.064-0.05127.9480.0020.0020.0000.0000.0000.000
61A59ASP-1-0.835-0.90827.591-0.107-0.1070.0000.0000.0000.000
62A60GLN0-0.064-0.02627.0990.0050.0050.0000.0000.0000.000
63A61VAL00.0020.00725.4670.0120.0120.0000.0000.0000.000
64A62PRO0-0.0040.02625.1420.0010.0010.0000.0000.0000.000
65A63MET0-0.026-0.01621.5260.0100.0100.0000.0000.0000.000
66A64SER0-0.037-0.01620.7360.0040.0040.0000.0000.0000.000
67A65VAL00.0320.00517.047-0.011-0.0110.0000.0000.0000.000
68A66SER00.0210.02216.6300.0460.0460.0000.0000.0000.000
69A67SER00.0320.01811.146-0.085-0.0850.0000.0000.0000.000
70A68ASP-1-0.780-0.88511.8850.5740.5740.0000.0000.0000.000
71A69PRO0-0.027-0.01212.488-0.106-0.1060.0000.0000.0000.000
72A70ASP-1-0.869-0.91115.4530.2550.2550.0000.0000.0000.000
73A71ALA0-0.057-0.02317.682-0.028-0.0280.0000.0000.0000.000
74A72GLN0-0.098-0.07016.036-0.059-0.0590.0000.0000.0000.000
75A73THR00.0090.01319.966-0.011-0.0110.0000.0000.0000.000
76A74ALA0-0.038-0.01821.5990.0010.0010.0000.0000.0000.000
77A75LEU00.0020.00223.039-0.001-0.0010.0000.0000.0000.000
78A76LEU0-0.009-0.01325.114-0.016-0.0160.0000.0000.0000.000
79A77ALA00.019-0.00427.7950.0040.0040.0000.0000.0000.000
80A78GLY0-0.040-0.01227.8160.0030.0030.0000.0000.0000.000
81A79GLU-1-0.796-0.84928.8360.0330.0330.0000.0000.0000.000
82A80ASP-1-0.804-0.88127.0870.0760.0760.0000.0000.0000.000
83A81VAL0-0.013-0.01127.194-0.008-0.0080.0000.0000.0000.000
84A82SER0-0.027-0.06025.539-0.014-0.0140.0000.0000.0000.000
85A83VAL0-0.017-0.00827.037-0.010-0.0100.0000.0000.0000.000
86A84PRO00.0400.01630.475-0.009-0.0090.0000.0000.0000.000
87A85ILE00.0000.02024.780-0.011-0.0110.0000.0000.0000.000
88A86ARG10.8270.90022.0940.0140.0140.0000.0000.0000.000
89A87GLY00.0370.04129.651-0.003-0.0030.0000.0000.0000.000
90A88ASN00.011-0.01332.941-0.012-0.0120.0000.0000.0000.000
91A89GLU-1-0.866-0.93635.515-0.034-0.0340.0000.0000.0000.000
92A90VAL00.0310.01729.845-0.008-0.0080.0000.0000.0000.000
93A91THR0-0.069-0.03731.282-0.013-0.0130.0000.0000.0000.000
94A92GLY0-0.048-0.01932.347-0.010-0.0100.0000.0000.0000.000
95A93ALA00.0300.02733.860-0.006-0.0060.0000.0000.0000.000
96A94VAL0-0.0030.00327.258-0.008-0.0080.0000.0000.0000.000
97A95SER0-0.042-0.01829.278-0.009-0.0090.0000.0000.0000.000
98A96ALA00.0390.02230.512-0.010-0.0100.0000.0000.0000.000
99A97VAL00.0380.02128.503-0.004-0.0040.0000.0000.0000.000
100A98SER0-0.012-0.02525.975-0.010-0.0100.0000.0000.0000.000
101A99ALA0-0.049-0.01326.920-0.022-0.0220.0000.0000.0000.000
102A100VAL00.0180.01429.451-0.005-0.0050.0000.0000.0000.000
103A101PRO0-0.019-0.02026.984-0.009-0.0090.0000.0000.0000.000
104A102ALA00.0490.03025.852-0.015-0.0150.0000.0000.0000.000
105A103VAL00.0180.01225.457-0.006-0.0060.0000.0000.0000.000
106A104ARG10.9170.94922.2540.2400.2400.0000.0000.0000.000
107A105GLU-1-0.879-0.91121.264-0.255-0.2550.0000.0000.0000.000
108A106ARG10.8320.88520.5320.1010.1010.0000.0000.0000.000
109A107LEU00.0170.01319.618-0.006-0.0060.0000.0000.0000.000
110A108VAL0-0.008-0.00616.615-0.020-0.0200.0000.0000.0000.000
111A109ARG10.8480.91715.4740.1830.1830.0000.0000.0000.000
112A110GLN00.0270.01314.929-0.032-0.0320.0000.0000.0000.000
113A111GLN0-0.020-0.01913.959-0.032-0.0320.0000.0000.0000.000
114A112ARG10.8410.90210.9930.6550.6550.0000.0000.0000.000
115A113GLU-1-0.871-0.9239.821-0.390-0.3900.0000.0000.0000.000
116A114LEU0-0.020-0.01510.3030.0860.0860.0000.0000.0000.000
117A115ALA0-0.041-0.0087.8670.2060.2060.0000.0000.0000.000
118A116GLU-1-0.966-0.9795.918-0.546-0.5460.0000.0000.0000.000
119A117SER0-0.064-0.0435.7360.3480.3480.0000.0000.0000.000
120A118SER0-0.041-0.0337.1560.3070.3070.0000.0000.0000.000
121A119GLY0-0.0200.0032.942-1.0300.0350.389-0.655-0.8000.006
122A120ALA0-0.001-0.0052.734-3.661-2.4111.254-0.775-1.729-0.008
123A121VAL0-0.0010.0123.1440.5160.2640.0830.453-0.285-0.001
124A122VAL0-0.0080.0006.628-0.595-0.5950.0000.0000.0000.000
125A123VAL00.011-0.0139.7240.1840.1840.0000.0000.0000.000
126A124GLU-1-0.714-0.80212.364-0.203-0.2030.0000.0000.0000.000
127A125GLY00.0170.00615.9980.0230.0230.0000.0000.0000.000
128A126ARG10.8600.92118.5630.2450.2450.0000.0000.0000.000
129A127ASP-1-0.866-0.93519.479-0.376-0.3760.0000.0000.0000.000
130A128ILE0-0.0080.01013.035-0.039-0.0390.0000.0000.0000.000
131A129GLY00.0520.02514.551-0.096-0.0960.0000.0000.0000.000
132A130THR0-0.056-0.04715.600-0.047-0.0470.0000.0000.0000.000
133A131VAL0-0.026-0.01417.8520.0070.0070.0000.0000.0000.000
134A132VAL0-0.025-0.00513.409-0.036-0.0360.0000.0000.0000.000
135A133LEU00.017-0.0078.947-0.024-0.0240.0000.0000.0000.000
136A134PRO00.0040.01512.013-0.102-0.1020.0000.0000.0000.000
137A135ASP-1-0.907-0.9529.926-1.211-1.2110.0000.0000.0000.000
138A136ALA0-0.048-0.0248.612-0.371-0.3710.0000.0000.0000.000
139A137ASP-1-0.815-0.8806.124-4.850-4.8500.0000.0000.0000.000
140A138VAL0-0.029-0.0179.2430.5150.5150.0000.0000.0000.000
141A139LYS10.8130.90811.8560.9840.9840.0000.0000.0000.000
142A140ILE0-0.0090.00714.5420.1010.1010.0000.0000.0000.000
143A141TYR0-0.001-0.01617.0700.0220.0220.0000.0000.0000.000
144A142LEU0-0.020-0.00719.4450.0350.0350.0000.0000.0000.000
145A143THR00.005-0.01522.2940.0150.0150.0000.0000.0000.000
146A144ALA00.0070.00926.0030.0130.0130.0000.0000.0000.000
147A145SER00.0630.03629.2660.0010.0010.0000.0000.0000.000
148A146ALA00.008-0.00732.8580.0030.0030.0000.0000.0000.000
149A147GLN00.010-0.00734.8690.0000.0000.0000.0000.0000.000
150A148ALA00.0710.04431.7490.0070.0070.0000.0000.0000.000
151A149ARG10.7520.83928.8110.1470.1470.0000.0000.0000.000
152A150ALA0-0.063-0.03732.1000.0070.0070.0000.0000.0000.000
153A151GLN0-0.021-0.00835.1880.0080.0080.0000.0000.0000.000
154A152ARG10.9020.97328.4040.0940.0940.0000.0000.0000.000
155A153ARG10.8390.89132.1950.0770.0770.0000.0000.0000.000
156A154ASN0-0.0220.00634.5310.0070.0070.0000.0000.0000.000
157A170LEU00.0760.02438.3040.0010.0010.0000.0000.0000.000
158A171ALA00.0920.03638.799-0.007-0.0070.0000.0000.0000.000
159A172ASP-1-0.822-0.87036.363-0.081-0.0810.0000.0000.0000.000
160A173VAL0-0.024-0.00333.075-0.005-0.0050.0000.0000.0000.000
161A174GLN00.0600.02435.134-0.005-0.0050.0000.0000.0000.000
162A175ARG10.9140.94337.5710.0720.0720.0000.0000.0000.000
163A176ARG10.8740.93431.6450.0990.0990.0000.0000.0000.000
164A177ASP-1-0.819-0.85831.974-0.157-0.1570.0000.0000.0000.000
165A178HIS0-0.045-0.01433.374-0.010-0.0100.0000.0000.0000.000
166A179LEU0-0.062-0.03333.034-0.009-0.0090.0000.0000.0000.000
167A187PRO00.0250.00622.6880.0100.0100.0000.0000.0000.000
168A188LEU00.0090.01222.251-0.021-0.0210.0000.0000.0000.000
169A189ARG10.9090.97024.3550.2380.2380.0000.0000.0000.000
170A190PRO00.0440.03921.558-0.023-0.0230.0000.0000.0000.000
171A191ALA00.022-0.00418.1600.0170.0170.0000.0000.0000.000
172A192GLU-1-0.919-0.95920.218-0.382-0.3820.0000.0000.0000.000
173A193ASP-1-0.849-0.90415.508-0.838-0.8380.0000.0000.0000.000
174A194ALA0-0.076-0.03817.519-0.062-0.0620.0000.0000.0000.000
175A195LEU0-0.019-0.00816.5190.0570.0570.0000.0000.0000.000
176A196GLU-1-0.927-0.97519.820-0.278-0.2780.0000.0000.0000.000
177A197VAL0-0.017-0.01220.5230.0190.0190.0000.0000.0000.000
178A198ASP-1-0.785-0.86723.426-0.142-0.1420.0000.0000.0000.000
179A199THR00.002-0.02523.8960.0170.0170.0000.0000.0000.000
180A200SER0-0.107-0.09226.7850.0170.0170.0000.0000.0000.000
181A201ASP-1-0.949-0.96230.350-0.071-0.0710.0000.0000.0000.000
182A202MET0-0.062-0.01123.8930.0000.0000.0000.0000.0000.000
183A203THR0-0.028-0.04727.374-0.004-0.0040.0000.0000.0000.000
184A204GLN00.0220.02222.497-0.004-0.0040.0000.0000.0000.000
185A205GLU-1-0.795-0.89322.524-0.001-0.0010.0000.0000.0000.000
186A206GLN00.0290.03422.448-0.008-0.0080.0000.0000.0000.000
187A207VAL00.0170.00420.396-0.017-0.0170.0000.0000.0000.000
188A208VAL0-0.003-0.00117.228-0.029-0.0290.0000.0000.0000.000
189A209ALA0-0.014-0.00817.841-0.011-0.0110.0000.0000.0000.000
190A210HIS00.0060.00219.0270.0060.0060.0000.0000.0000.000
191A211LEU00.007-0.01115.644-0.033-0.0330.0000.0000.0000.000
192A212LEU0-0.0100.00113.258-0.058-0.0580.0000.0000.0000.000
193A213ASP-1-0.918-0.93914.453-0.171-0.1710.0000.0000.0000.000
194A214LEU0-0.028-0.00416.091-0.037-0.0370.0000.0000.0000.000
195A215VAL0-0.017-0.0209.773-0.077-0.0770.0000.0000.0000.000
196A216ARG10.9080.95111.329-0.192-0.1920.0000.0000.0000.000
197A217THR0-0.041-0.01512.770-0.028-0.0280.0000.0000.0000.000
198A218ARG10.8180.91310.7770.7490.7490.0000.0000.0000.000