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: NNY5Q

Calculation Name: 1S7H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1S7H

Chain ID: A

ChEMBL ID:

UniProt ID: O34911

Base Structure: X-ray

Registration Date: 2023-09-24

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1965837.901783
FMO2-HF: Nuclear repulsion 1893138.087731
FMO2-HF: Total energy -72699.814052
FMO2-MP2: Total energy -72908.307795


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:8:SER)


Summations of interaction energy for fragment #1(A:8: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.
-7.744-4.8746.357-4.314-4.912-0.027
Interaction energy analysis for fragmet #1(A:8:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.021
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].
3A10ILE0-0.029-0.0012.842-0.6911.7390.199-1.148-1.4810.004
4A11ALA00.0470.0325.286-0.709-0.686-0.001-0.004-0.0180.000
5A12GLY00.012-0.0169.113-0.070-0.0700.0000.0000.0000.000
6A13PHE0-0.004-0.00211.7140.0010.0010.0000.0000.0000.000
7A14ARG10.8300.89215.5080.0610.0610.0000.0000.0000.000
8A15PHE0-0.004-0.00517.7990.0050.0050.0000.0000.0000.000
9A16SER00.022-0.00721.414-0.017-0.0170.0000.0000.0000.000
10A17LEU0-0.016-0.00424.8850.0130.0130.0000.0000.0000.000
11A18TYR0-0.007-0.01927.541-0.012-0.0120.0000.0000.0000.000
12A19PRO0-0.0010.00830.9800.0040.0040.0000.0000.0000.000
13A20MET0-0.044-0.02233.736-0.010-0.0100.0000.0000.0000.000
14A21THR0-0.001-0.01436.777-0.001-0.0010.0000.0000.0000.000
15A22ASP-1-0.881-0.94338.0080.0240.0240.0000.0000.0000.000
16A23ASP-1-0.876-0.91238.4090.0380.0380.0000.0000.0000.000
17A24PHE00.015-0.00433.2040.0040.0040.0000.0000.0000.000
18A25ILE0-0.003-0.00632.6420.0050.0050.0000.0000.0000.000
19A26SER0-0.053-0.05132.2660.0030.0030.0000.0000.0000.000
20A27VAL00.0240.02032.0880.0070.0070.0000.0000.0000.000
21A28ILE00.0070.01027.3460.0110.0110.0000.0000.0000.000
22A29LYS10.9300.96328.184-0.023-0.0230.0000.0000.0000.000
23A30SER0-0.032-0.02328.9250.0070.0070.0000.0000.0000.000
24A31ALA00.0340.02127.4590.0090.0090.0000.0000.0000.000
25A32LEU00.0120.00222.6380.0170.0170.0000.0000.0000.000
26A33LYS10.8640.93924.598-0.079-0.0790.0000.0000.0000.000
27A34LYS10.9120.95827.184-0.107-0.1070.0000.0000.0000.000
28A35THR0-0.021-0.00421.5160.0180.0180.0000.0000.0000.000
29A36ASP-1-0.838-0.88821.0300.2510.2510.0000.0000.0000.000
30A37THR00.009-0.01518.3580.0340.0340.0000.0000.0000.000
31A38SER0-0.067-0.05617.1150.0280.0280.0000.0000.0000.000
32A39LYS10.8060.89114.698-0.402-0.4020.0000.0000.0000.000
33A40VAL0-0.021-0.01412.4650.1420.1420.0000.0000.0000.000
34A41TRP0-0.0200.02411.256-0.087-0.0870.0000.0000.0000.000
35A42THR0-0.015-0.02413.0880.0250.0250.0000.0000.0000.000
36A43LYS10.9400.97916.1330.1140.1140.0000.0000.0000.000
37A44THR00.003-0.00918.0530.0210.0210.0000.0000.0000.000
38A45ASP-1-0.825-0.89220.726-0.098-0.0980.0000.0000.0000.000
39A46HIS0-0.003-0.00923.5360.0150.0150.0000.0000.0000.000
40A47ILE0-0.0110.00924.7690.0050.0050.0000.0000.0000.000
41A48SER0-0.0210.00421.6280.0100.0100.0000.0000.0000.000
42A49THR00.0130.01619.423-0.025-0.0250.0000.0000.0000.000
43A50VAL0-0.047-0.01414.1360.0040.0040.0000.0000.0000.000
44A51LEU00.0180.01014.645-0.013-0.0130.0000.0000.0000.000
45A52ARG10.7780.8476.3150.8120.8120.0000.0000.0000.000
46A53GLY00.0470.0238.622-0.116-0.1160.0000.0000.0000.000
47A54SER0-0.029-0.0248.2700.3550.3550.0000.0000.0000.000
48A55ILE00.0630.0189.537-0.280-0.2800.0000.0000.0000.000
49A56ASP-1-0.820-0.89311.7480.9230.9230.0000.0000.0000.000
50A57HIS00.0080.01912.771-0.011-0.0110.0000.0000.0000.000
51A58VAL0-0.0110.00411.670-0.126-0.1260.0000.0000.0000.000
52A59PHE00.0440.01514.663-0.093-0.0930.0000.0000.0000.000
53A60ASP-1-0.833-0.90417.3910.3410.3410.0000.0000.0000.000
54A61ALA00.0370.01417.527-0.055-0.0550.0000.0000.0000.000
55A62ALA0-0.0040.00218.673-0.048-0.0480.0000.0000.0000.000
56A63LYS10.8990.95620.391-0.356-0.3560.0000.0000.0000.000
57A64ALA0-0.025-0.00622.575-0.030-0.0300.0000.0000.0000.000
58A65ILE0-0.007-0.00720.852-0.029-0.0290.0000.0000.0000.000
59A66TYR0-0.015-0.03124.677-0.021-0.0210.0000.0000.0000.000
60A67LEU00.0250.01326.692-0.017-0.0170.0000.0000.0000.000
61A68HIS00.001-0.00526.094-0.027-0.0270.0000.0000.0000.000
62A69ALA0-0.023-0.00728.779-0.014-0.0140.0000.0000.0000.000
63A70ALA00.0270.03330.493-0.011-0.0110.0000.0000.0000.000
64A71ASN0-0.052-0.03132.187-0.012-0.0120.0000.0000.0000.000
65A72SER0-0.091-0.07034.184-0.005-0.0050.0000.0000.0000.000
66A73GLU-1-0.939-0.97236.1070.0700.0700.0000.0000.0000.000
67A74GLN0-0.0200.00236.156-0.008-0.0080.0000.0000.0000.000
68A75HIS00.0230.03735.4030.0020.0020.0000.0000.0000.000
69A76ILE0-0.050-0.02329.808-0.007-0.0070.0000.0000.0000.000
70A77VAL00.0230.02029.5910.0060.0060.0000.0000.0000.000
71A78MET0-0.049-0.00323.7340.0010.0010.0000.0000.0000.000
72A79ASN0-0.025-0.01725.6350.0020.0020.0000.0000.0000.000
73A80GLY00.0400.01021.559-0.010-0.0100.0000.0000.0000.000
74A81THR0-0.036-0.00917.4420.0010.0010.0000.0000.0000.000
75A82PHE00.0150.02015.510-0.012-0.0120.0000.0000.0000.000
76A83SER0-0.030-0.02912.734-0.051-0.0510.0000.0000.0000.000
77A84ILE00.0450.0177.9460.0950.0950.0000.0000.0000.000
78A85GLY00.0400.0237.2950.0080.0080.0000.0000.0000.000
79A86CYS0-0.030-0.0018.333-0.011-0.0110.0000.0000.0000.000
80A87PRO00.021-0.0068.994-0.360-0.3600.0000.0000.0000.000
81A88GLY0-0.013-0.0049.3040.0870.0870.0000.0000.0000.000
82A89ASP-1-0.851-0.8946.569-1.191-1.1910.0000.0000.0000.000
83A90THR0-0.0030.0066.495-0.917-0.9170.0000.0000.0000.000
84A91GLN0-0.005-0.0182.186-6.759-6.6616.152-3.080-3.169-0.031
85A92GLY00.0020.0124.5450.4810.558-0.001-0.002-0.0740.000
86A93ASP-1-0.885-0.9527.139-0.445-0.4450.0000.0000.0000.000
87A94THR00.011-0.0085.1870.1180.1180.0000.0000.0000.000
88A95TYR0-0.018-0.0158.530-0.180-0.1800.0000.0000.0000.000
89A96LEU0-0.015-0.0154.0200.1570.3990.008-0.080-0.1700.000
90A97SER00.007-0.0178.367-0.225-0.2250.0000.0000.0000.000
91A98LYS10.8870.9349.145-1.262-1.2620.0000.0000.0000.000
92A99GLY00.0120.01211.137-0.070-0.0700.0000.0000.0000.000
93A100ASP-1-0.777-0.82914.2940.4390.4390.0000.0000.0000.000
94A101LYS10.8100.89415.550-0.275-0.2750.0000.0000.0000.000
95A102ARG10.7570.84316.108-0.634-0.6340.0000.0000.0000.000
96A103VAL0-0.013-0.00718.740-0.031-0.0310.0000.0000.0000.000
97A104ASN0-0.053-0.04520.405-0.075-0.0750.0000.0000.0000.000
98A105GLU-1-0.843-0.92521.4950.3830.3830.0000.0000.0000.000
99A106ASP-1-0.825-0.90123.8870.2540.2540.0000.0000.0000.000
100A107ALA0-0.038-0.01226.636-0.019-0.0190.0000.0000.0000.000
101A108VAL00.003-0.00125.542-0.017-0.0170.0000.0000.0000.000
102A109ARG10.8800.93428.269-0.219-0.2190.0000.0000.0000.000
103A110GLY0-0.044-0.01629.325-0.005-0.0050.0000.0000.0000.000
104A111LEU0-0.044-0.00529.950-0.013-0.0130.0000.0000.0000.000
105A112LYS10.8570.92031.344-0.174-0.1740.0000.0000.0000.000
106A113ALA00.009-0.01231.325-0.010-0.0100.0000.0000.0000.000
107A114GLU-1-0.886-0.93231.8970.1530.1530.0000.0000.0000.000
108A115ALA0-0.022-0.01128.978-0.004-0.0040.0000.0000.0000.000
109A116PRO00.0450.04630.5220.0090.0090.0000.0000.0000.000
110A117CYS0-0.065-0.03326.431-0.004-0.0040.0000.0000.0000.000
111A118GLN0-0.032-0.00729.407-0.001-0.0010.0000.0000.0000.000
112A119PHE00.009-0.02123.9760.0050.0050.0000.0000.0000.000
113A120ALA00.0180.01124.352-0.012-0.0120.0000.0000.0000.000
114A121LEU0-0.013-0.00918.6610.0130.0130.0000.0000.0000.000
115A122TYR0-0.002-0.00619.892-0.022-0.0220.0000.0000.0000.000
116A123PRO00.0500.02317.136-0.007-0.0070.0000.0000.0000.000
117A124MET0-0.044-0.02115.925-0.034-0.0340.0000.0000.0000.000
118A125ASN0-0.084-0.05416.565-0.019-0.0190.0000.0000.0000.000
119A126GLU-1-0.794-0.87917.8700.2000.2000.0000.0000.0000.000
120A127PRO0-0.038-0.03319.766-0.007-0.0070.0000.0000.0000.000
121A128ASP-1-0.866-0.93221.9970.1480.1480.0000.0000.0000.000
122A129TYR0-0.010-0.00521.7890.0170.0170.0000.0000.0000.000
123A130MET0-0.021-0.01222.7300.0100.0100.0000.0000.0000.000
124A131GLY00.0480.04025.2520.0040.0040.0000.0000.0000.000
125A132LEU00.0230.00118.0150.0120.0120.0000.0000.0000.000
126A133ILE0-0.037-0.02222.4460.0160.0160.0000.0000.0000.000
127A134MET0-0.020-0.01324.864-0.002-0.0020.0000.0000.0000.000
128A135GLU-1-0.822-0.90122.2260.3060.3060.0000.0000.0000.000
129A136ALA0-0.006-0.00822.6420.0130.0130.0000.0000.0000.000
130A137VAL0-0.035-0.01624.171-0.001-0.0010.0000.0000.0000.000
131A138ASP-1-0.818-0.90527.7320.1700.1700.0000.0000.0000.000
132A139ILE0-0.020-0.00921.7290.0010.0010.0000.0000.0000.000
133A140ALA00.0200.00425.974-0.001-0.0010.0000.0000.0000.000
134A141LYS10.8030.90227.704-0.167-0.1670.0000.0000.0000.000
135A142ALA0-0.037-0.01027.883-0.008-0.0080.0000.0000.0000.000
136A143GLN0-0.052-0.03824.0930.0190.0190.0000.0000.0000.000
137A144GLY0-0.033-0.01128.915-0.004-0.0040.0000.0000.0000.000
138A145THR00.0290.02228.811-0.004-0.0040.0000.0000.0000.000
139A146PHE0-0.033-0.02330.229-0.009-0.0090.0000.0000.0000.000
140A147VAL0-0.020-0.00231.635-0.006-0.0060.0000.0000.0000.000
141A148GLN0-0.077-0.04833.818-0.012-0.0120.0000.0000.0000.000
142A149GLY00.0110.01032.9100.0110.0110.0000.0000.0000.000
143A150VAL0-0.020-0.01233.100-0.008-0.0080.0000.0000.0000.000
144A151HIS0-0.004-0.01633.2860.0040.0040.0000.0000.0000.000
145A152TYR0-0.036-0.02529.994-0.003-0.0030.0000.0000.0000.000
146A153ALA0-0.0090.01228.6890.0030.0030.0000.0000.0000.000
147A154SER0-0.007-0.00328.080-0.002-0.0020.0000.0000.0000.000
148A155GLU-1-0.864-0.91929.3880.1020.1020.0000.0000.0000.000
149A156LEU0-0.020-0.01126.1510.0060.0060.0000.0000.0000.000
150A157ASP-1-0.844-0.93230.8830.1160.1160.0000.0000.0000.000
151A158GLY00.0300.02732.2430.0110.0110.0000.0000.0000.000
152A159ASP-1-0.709-0.86530.5140.1930.1930.0000.0000.0000.000
153A160ALA00.0150.01027.5490.0140.0140.0000.0000.0000.000
154A161HIS0-0.030-0.01926.0050.0490.0490.0000.0000.0000.000
155A162ASP-1-0.872-0.93825.5490.2450.2450.0000.0000.0000.000
156A163VAL00.0150.01526.3880.0210.0210.0000.0000.0000.000
157A164PHE0-0.018-0.03721.3850.0170.0170.0000.0000.0000.000
158A165SER0-0.0500.00121.5370.0370.0370.0000.0000.0000.000
159A166THR00.0260.00521.6940.0420.0420.0000.0000.0000.000
160A167LEU0-0.013-0.01021.2660.0180.0180.0000.0000.0000.000
161A168GLU-1-0.720-0.81115.9800.7320.7320.0000.0000.0000.000
162A169ALA0-0.017-0.00317.3140.0760.0760.0000.0000.0000.000
163A170VAL00.0060.00718.8400.0300.0300.0000.0000.0000.000
164A171PHE00.001-0.01312.3380.0250.0250.0000.0000.0000.000
165A172ARG10.8000.85911.859-0.955-0.9550.0000.0000.0000.000
166A173MET0-0.0350.01814.7570.0630.0630.0000.0000.0000.000
167A174ALA00.0550.02116.5290.0090.0090.0000.0000.0000.000
168A175GLU-1-0.886-0.9209.5011.6391.6390.0000.0000.0000.000
169A176GLN0-0.095-0.05710.3330.0550.0550.0000.0000.0000.000
170A177GLN0-0.081-0.04113.068-0.003-0.0030.0000.0000.0000.000
171A178THR0-0.004-0.01614.117-0.062-0.0620.0000.0000.0000.000
172A179ASN0-0.031-0.0209.5850.1730.1730.0000.0000.0000.000
173A180HIS00.0130.02210.0440.0140.0140.0000.0000.0000.000
174A181ILE00.0210.02412.519-0.022-0.0220.0000.0000.0000.000
175A182THR0-0.039-0.02614.026-0.025-0.0250.0000.0000.0000.000
176A183MET00.0000.00916.7430.0280.0280.0000.0000.0000.000
177A184THR0-0.0140.00719.4740.0100.0100.0000.0000.0000.000
178A185VAL00.021-0.00121.6770.0180.0180.0000.0000.0000.000
179A186ASN0-0.014-0.00324.156-0.020-0.0200.0000.0000.0000.000
180A187LEU00.0460.02424.6000.0030.0030.0000.0000.0000.000
181A188SER00.000-0.00528.923-0.012-0.0120.0000.0000.0000.000
182A189ALA00.0580.04232.2030.0020.0020.0000.0000.0000.000
183A190ASN0-0.041-0.05433.762-0.004-0.0040.0000.0000.0000.000
184A191SER0-0.0020.01136.924-0.005-0.0050.0000.0000.0000.000
185A192PRO00.0170.01138.4870.0010.0010.0000.0000.0000.000
186A193SER0-0.053-0.02140.2770.0020.0020.0000.0000.0000.000