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: 1NM8Z

Calculation Name: 1GPP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GPP

Chain ID: A

ChEMBL ID:

UniProt ID: P17255

Base Structure: X-ray

Registration Date: 2023-09-23

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2477703.065649
FMO2-HF: Nuclear repulsion 2390858.793824
FMO2-HF: Total energy -86844.271825
FMO2-MP2: Total energy -87095.466301


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:SER)


Summations of interaction energy for fragment #1(A:-2: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.
-29.508-21.5418.988-7.606-9.3530.02
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.002
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].
3A1CYS0-0.044-0.0103.2780.2732.0620.060-0.847-1.0020.003
4A2PHE00.021-0.0075.7610.1600.1600.0000.0000.0000.000
5A3ALA00.0790.0359.4050.1320.1320.0000.0000.0000.000
6A4LYS10.9760.99412.5980.0690.0690.0000.0000.0000.000
7A5GLY00.0130.01014.135-0.016-0.0160.0000.0000.0000.000
8A6THR0-0.095-0.05312.193-0.003-0.0030.0000.0000.0000.000
9A7ASN00.0020.00713.5680.0670.0670.0000.0000.0000.000
10A8VAL00.0130.00510.398-0.103-0.1030.0000.0000.0000.000
11A9LEU0-0.030-0.00513.5720.0590.0590.0000.0000.0000.000
12A10MET00.0480.03212.9550.0150.0150.0000.0000.0000.000
13A11ALA0-0.033-0.03615.353-0.043-0.0430.0000.0000.0000.000
14A12ASP-1-0.854-0.90516.9010.0870.0870.0000.0000.0000.000
15A13GLY0-0.049-0.02319.335-0.014-0.0140.0000.0000.0000.000
16A14SER0-0.072-0.04219.748-0.028-0.0280.0000.0000.0000.000
17A15ILE0-0.023-0.03417.409-0.013-0.0130.0000.0000.0000.000
18A16GLU-1-0.782-0.87914.5470.1060.1060.0000.0000.0000.000
19A17CYS0-0.066-0.03014.619-0.070-0.0700.0000.0000.0000.000
20A18ILE00.0290.0057.2870.0850.0850.0000.0000.0000.000
21A19GLU-1-0.864-0.94410.704-0.017-0.0170.0000.0000.0000.000
22A20ASN0-0.080-0.04912.6150.0930.0930.0000.0000.0000.000
23A21ILE0-0.0300.0089.7400.0580.0580.0000.0000.0000.000
24A22GLU-1-0.923-0.96811.3190.5450.5450.0000.0000.0000.000
25A23VAL0-0.038-0.0319.6050.1000.1000.0000.0000.0000.000
26A24GLY00.0120.01211.447-0.170-0.1700.0000.0000.0000.000
27A25ASN0-0.0230.00012.121-0.175-0.1750.0000.0000.0000.000
28A26LYS10.8260.88312.211-0.430-0.4300.0000.0000.0000.000
29A27VAL00.0480.0359.206-0.093-0.0930.0000.0000.0000.000
30A28MET0-0.039-0.00812.5300.0070.0070.0000.0000.0000.000
31A29GLY00.0740.02611.727-0.080-0.0800.0000.0000.0000.000
32A30LYS10.8460.91211.8780.5010.5010.0000.0000.0000.000
33A31ASP-1-0.826-0.90014.209-0.129-0.1290.0000.0000.0000.000
34A32GLY0-0.048-0.03616.2450.0270.0270.0000.0000.0000.000
35A33ARG10.8590.93316.1420.0860.0860.0000.0000.0000.000
36A34PRO00.0360.00714.470-0.025-0.0250.0000.0000.0000.000
37A35ARG10.7540.8748.9630.0670.0670.0000.0000.0000.000
38A36GLU-1-0.793-0.86610.3830.7060.7060.0000.0000.0000.000
39A37VAL00.0120.0106.8680.3940.3940.0000.0000.0000.000
40A38ILE00.0310.0036.577-0.290-0.2900.0000.0000.0000.000
41A39LYS10.8890.9294.655-9.207-9.083-0.001-0.027-0.0950.000
42A40LEU00.0070.0155.4830.3660.3660.0000.0000.0000.000
43A41PRO0-0.037-0.0012.301-1.471-0.9691.596-0.850-1.2480.002
44A42ARG10.9240.9495.273-1.175-1.198-0.001-0.0010.0250.000
45A43GLY00.0150.0207.8200.2160.2160.0000.0000.0000.000
46A44SER00.0270.03510.131-0.072-0.0720.0000.0000.0000.000
47A45GLU-1-0.841-0.9168.980-1.147-1.1470.0000.0000.0000.000
48A46THR00.0210.01412.3880.0160.0160.0000.0000.0000.000
49A47MET0-0.0070.02610.764-0.199-0.1990.0000.0000.0000.000
50A48TYR0-0.042-0.06013.5390.0820.0820.0000.0000.0000.000
51A49SER0-0.0060.00814.659-0.077-0.0770.0000.0000.0000.000
52A50VAL00.0170.01314.1290.0250.0250.0000.0000.0000.000
53A51VAL0-0.006-0.01417.3710.0360.0360.0000.0000.0000.000
54A52GLN00.0450.02620.794-0.004-0.0040.0000.0000.0000.000
55A53LYS10.7910.88322.1240.3600.3600.0000.0000.0000.000
56A54SER00.006-0.00425.199-0.002-0.0020.0000.0000.0000.000
57A67MET0-0.011-0.01930.7990.0030.0030.0000.0000.0000.000
58A68PRO0-0.023-0.00927.5210.0060.0060.0000.0000.0000.000
59A69GLU-1-0.851-0.93325.733-0.232-0.2320.0000.0000.0000.000
60A70LEU0-0.054-0.01424.150-0.013-0.0130.0000.0000.0000.000
61A71LEU00.0120.00519.291-0.003-0.0030.0000.0000.0000.000
62A72LYS10.8660.92218.7280.2900.2900.0000.0000.0000.000
63A73PHE0-0.014-0.00411.3000.0250.0250.0000.0000.0000.000
64A74THR00.0190.01214.2840.0300.0300.0000.0000.0000.000
65A75CYS0-0.0220.0039.2210.0140.0140.0000.0000.0000.000
66A76ASN00.0910.0296.387-0.162-0.1620.0000.0000.0000.000
67A77ALA0-0.018-0.0149.811-0.158-0.1580.0000.0000.0000.000
68A78THR0-0.039-0.0447.181-0.085-0.0850.0000.0000.0000.000
69A79HIS00.0090.0245.679-1.241-1.2410.0000.0000.0000.000
70A80GLU-1-0.846-0.8935.709-1.773-1.7730.0000.0000.0000.000
71A81LEU0-0.049-0.0267.499-0.086-0.0860.0000.0000.0000.000
72A82VAL00.0320.0168.8250.0380.0380.0000.0000.0000.000
73A83VAL0-0.047-0.02811.0900.1660.1660.0000.0000.0000.000
74A84ARG10.8760.92714.6200.4880.4880.0000.0000.0000.000
75A85THR00.001-0.00117.838-0.002-0.0020.0000.0000.0000.000
76A86PRO0-0.0030.01620.9180.0080.0080.0000.0000.0000.000
77A87ARG10.8990.95524.0940.2500.2500.0000.0000.0000.000
78A88SER0-0.060-0.02825.8730.0250.0250.0000.0000.0000.000
79A89VAL00.0100.00828.5860.0020.0020.0000.0000.0000.000
80A90ARG10.8450.92431.4680.2090.2090.0000.0000.0000.000
81A91ARG10.8980.94434.6050.1260.1260.0000.0000.0000.000
82A92LEU0-0.043-0.02236.591-0.002-0.0020.0000.0000.0000.000
83A93SER00.0620.04040.1120.0010.0010.0000.0000.0000.000
84A94ARG10.8040.88936.8750.1450.1450.0000.0000.0000.000
85A95THR00.0530.02344.1960.0020.0020.0000.0000.0000.000
86A96ILE0-0.015-0.00543.292-0.001-0.0010.0000.0000.0000.000
87A97LYS10.9500.96046.5470.0920.0920.0000.0000.0000.000
88A98GLY00.0250.01450.2170.0030.0030.0000.0000.0000.000
89A99VAL00.0020.02548.5590.0020.0020.0000.0000.0000.000
90A100GLU-1-0.883-0.94747.338-0.097-0.0970.0000.0000.0000.000
91A101TYR0-0.023-0.01543.3810.0010.0010.0000.0000.0000.000
92A102PHE00.0660.03042.310-0.003-0.0030.0000.0000.0000.000
93A103GLU-1-0.781-0.85236.894-0.149-0.1490.0000.0000.0000.000
94A104VAL0-0.048-0.04434.763-0.002-0.0020.0000.0000.0000.000
95A105ILE0-0.023-0.00531.117-0.003-0.0030.0000.0000.0000.000
96A106THR0-0.020-0.03129.3290.0010.0010.0000.0000.0000.000
97A107PHE0-0.024-0.00124.348-0.006-0.0060.0000.0000.0000.000
98A108GLU-1-0.850-0.90924.582-0.209-0.2090.0000.0000.0000.000
99A109MET00.0210.02217.408-0.024-0.0240.0000.0000.0000.000
100A110GLY00.011-0.00420.9190.0420.0420.0000.0000.0000.000
101A111GLN00.0340.02419.794-0.020-0.0200.0000.0000.0000.000
102A112LYS10.8380.90520.0710.3910.3910.0000.0000.0000.000
103A113LYS10.9180.99920.0220.1960.1960.0000.0000.0000.000
104A114ALA00.0380.02318.1420.0090.0090.0000.0000.0000.000
105A115PRO00.007-0.01820.2410.0370.0370.0000.0000.0000.000
106A116ASP-1-0.788-0.87817.116-0.358-0.3580.0000.0000.0000.000
107A117GLY0-0.074-0.05620.7470.0300.0300.0000.0000.0000.000
108A118ARG10.7600.83912.9380.6110.6110.0000.0000.0000.000
109A119ILE0-0.024-0.01117.911-0.012-0.0120.0000.0000.0000.000
110A120VAL00.0250.01814.567-0.031-0.0310.0000.0000.0000.000
111A121GLU-1-0.908-0.95215.041-0.417-0.4170.0000.0000.0000.000
112A122LEU0-0.027-0.02715.627-0.074-0.0740.0000.0000.0000.000
113A123VAL0-0.0020.00517.9910.0580.0580.0000.0000.0000.000
114A124LYS10.8710.92420.8150.2850.2850.0000.0000.0000.000
115A125GLU-1-0.820-0.90324.235-0.227-0.2270.0000.0000.0000.000
116A126VAL0-0.0210.00327.6990.0050.0050.0000.0000.0000.000
117A127SER0-0.042-0.05230.2800.0040.0040.0000.0000.0000.000
118A128LYS10.9390.97434.0140.1360.1360.0000.0000.0000.000
119A129SER00.0140.00336.933-0.001-0.0010.0000.0000.0000.000
120A130TYR00.0240.01538.6210.0000.0000.0000.0000.0000.000
121A131PRO00.0380.01343.488-0.002-0.0020.0000.0000.0000.000
122A132VAL00.0130.00547.0360.0010.0010.0000.0000.0000.000
123A133SER0-0.051-0.04448.6100.0010.0010.0000.0000.0000.000
124A134GLU-1-0.943-0.95448.114-0.070-0.0700.0000.0000.0000.000
125A135GLY00.0220.03649.5320.0010.0010.0000.0000.0000.000
126A136PRO0-0.054-0.03945.853-0.004-0.0040.0000.0000.0000.000
127A137GLU-1-0.862-0.93744.381-0.086-0.0860.0000.0000.0000.000
128A138ARG10.9200.94443.0020.0810.0810.0000.0000.0000.000
129A139ALA00.003-0.00240.378-0.006-0.0060.0000.0000.0000.000
130A140ASN00.010-0.00139.351-0.012-0.0120.0000.0000.0000.000
131A141GLU-1-0.745-0.84939.442-0.098-0.0980.0000.0000.0000.000
132A142LEU0-0.0470.00234.180-0.005-0.0050.0000.0000.0000.000
133A143VAL0-0.034-0.02335.041-0.010-0.0100.0000.0000.0000.000
134A144GLU-1-0.939-0.96434.534-0.119-0.1190.0000.0000.0000.000
135A145SER0-0.025-0.04034.605-0.006-0.0060.0000.0000.0000.000
136A146TYR0-0.044-0.06026.752-0.006-0.0060.0000.0000.0000.000
137A147ARG10.9280.95930.0400.1390.1390.0000.0000.0000.000
138A148LYS10.9601.00530.9460.1380.1380.0000.0000.0000.000
139A149ALA0-0.105-0.04228.8020.0040.0040.0000.0000.0000.000
140A150SER0-0.029-0.02124.523-0.013-0.0130.0000.0000.0000.000
141A151ASN00.0410.02023.326-0.008-0.0080.0000.0000.0000.000
142A152LYS10.9030.96418.2590.4050.4050.0000.0000.0000.000
143A153ALA00.0490.01524.4140.0010.0010.0000.0000.0000.000
144A154TYR0-0.049-0.03218.8520.0230.0230.0000.0000.0000.000
145A155PHE00.0040.00218.7750.0160.0160.0000.0000.0000.000
146A156GLU-1-0.797-0.90214.693-0.497-0.4970.0000.0000.0000.000
147A157TRP0-0.015-0.02313.3470.0220.0220.0000.0000.0000.000
148A158THR0-0.003-0.0188.4670.1340.1340.0000.0000.0000.000
149A159ILE0-0.0160.00010.7980.1480.1480.0000.0000.0000.000
150A160GLU-1-0.737-0.8358.888-1.227-1.2270.0000.0000.0000.000
151A161ALA00.0200.01110.4430.2720.2720.0000.0000.0000.000
152A162ARG10.8420.89010.9660.9640.9640.0000.0000.0000.000
153A163ASP-1-0.797-0.86813.495-0.621-0.6210.0000.0000.0000.000
154A164LEU00.0040.00515.5320.0860.0860.0000.0000.0000.000
155A165SER0-0.023-0.01417.0790.0610.0610.0000.0000.0000.000
156A166LEU0-0.037-0.00817.6570.0750.0750.0000.0000.0000.000
157A167LEU00.0090.02118.4110.0490.0490.0000.0000.0000.000
158A168GLY00.0320.02021.6600.0250.0250.0000.0000.0000.000
159A169SER00.0370.00924.718-0.020-0.0200.0000.0000.0000.000
160A170HIS0-0.064-0.05626.6030.0000.0000.0000.0000.0000.000
161A171VAL00.0310.01721.693-0.001-0.0010.0000.0000.0000.000
162A172ARG10.8680.93120.8020.4480.4480.0000.0000.0000.000
163A173LYS10.9360.97022.4470.2270.2270.0000.0000.0000.000
164A174ALA0-0.021-0.01824.4190.0030.0030.0000.0000.0000.000
165A175THR0-0.008-0.00617.812-0.004-0.0040.0000.0000.0000.000
166A176TYR0-0.091-0.02819.3440.0080.0080.0000.0000.0000.000
167A177GLN00.0720.03913.876-0.121-0.1210.0000.0000.0000.000
168A178THR0-0.001-0.02815.5310.0940.0940.0000.0000.0000.000
169A179TYR00.0490.03016.111-0.044-0.0440.0000.0000.0000.000
170A180ALA00.0060.00017.5100.0220.0220.0000.0000.0000.000
171A181PRO0-0.0180.01419.3210.0250.0250.0000.0000.0000.000
172A182ILE00.009-0.01522.491-0.001-0.0010.0000.0000.0000.000
173A183GLY00.0140.03324.339-0.002-0.0020.0000.0000.0000.000
174A410ALA0-0.008-0.01027.2230.0140.0140.0000.0000.0000.000
175A411ALA0-0.030-0.04228.867-0.004-0.0040.0000.0000.0000.000
176A412PHE0-0.027-0.01227.1460.0040.0040.0000.0000.0000.000
177A413ALA00.0390.05023.8110.0040.0040.0000.0000.0000.000
178A414ARG10.8970.93918.8560.1740.1740.0000.0000.0000.000
179A415GLU-1-0.838-0.89521.873-0.185-0.1850.0000.0000.0000.000
180A416CYS0-0.046-0.02918.221-0.032-0.0320.0000.0000.0000.000
181A417ARG10.8380.90320.6910.2310.2310.0000.0000.0000.000
182A418GLY00.0430.01720.397-0.040-0.0400.0000.0000.0000.000
183A419PHE0-0.032-0.01916.5990.0470.0470.0000.0000.0000.000
184A420TYR00.0430.03020.211-0.037-0.0370.0000.0000.0000.000
185A421PHE00.0070.00716.7850.0050.0050.0000.0000.0000.000
186A422GLU-1-0.802-0.87720.981-0.393-0.3930.0000.0000.0000.000
187A423LEU00.0110.01614.676-0.030-0.0300.0000.0000.0000.000
188A424GLN0-0.051-0.01818.8180.0500.0500.0000.0000.0000.000
189A425GLU-1-0.830-0.88717.707-0.474-0.4740.0000.0000.0000.000
190A426LEU0-0.054-0.02416.9600.0670.0670.0000.0000.0000.000
191A427LYS10.8770.92219.0580.3430.3430.0000.0000.0000.000
192A428GLU-1-0.924-0.97015.768-0.320-0.3200.0000.0000.0000.000
193A429ASP-1-0.884-0.92714.586-0.254-0.2540.0000.0000.0000.000
194A430ASP-1-0.867-0.93312.826-0.143-0.1430.0000.0000.0000.000
195A431TYR0-0.073-0.0535.317-0.081-0.0810.0000.0000.0000.000
196A432TYR0-0.067-0.0618.1760.2600.2600.0000.0000.0000.000
197A433GLY00.0520.0034.010-0.561-0.534-0.001-0.019-0.0080.000
198A434ILE0-0.057-0.0153.7760.7691.2060.000-0.133-0.3050.000
199A435THR0-0.037-0.0181.999-13.401-9.1207.252-5.788-5.7460.013
200A436LEU0-0.002-0.0033.249-3.601-3.3460.0680.254-0.5780.003
201A437SER0-0.049-0.0535.0110.0210.089-0.0010.000-0.0670.000
202A438ASP-1-0.849-0.9176.9440.3190.3190.0000.0000.0000.000
203A439ASP-1-0.902-0.9178.6940.4580.4580.0000.0000.0000.000
204A440SER0-0.103-0.05810.018-0.082-0.0820.0000.0000.0000.000
205A441ASP-1-0.800-0.8738.970-0.481-0.4810.0000.0000.0000.000
206A442HIS00.026-0.0053.933-0.820-0.621-0.001-0.045-0.1540.000
207A443GLN0-0.048-0.0296.0080.1590.1590.0000.0000.0000.000
208A444PHE0-0.007-0.0095.7770.2390.2390.0000.0000.0000.000
209A445LEU0-0.035-0.00110.440-0.161-0.1610.0000.0000.0000.000
210A446LEU00.0440.02911.1150.0780.0780.0000.0000.0000.000
211A447ALA00.0250.01114.2460.0490.0490.0000.0000.0000.000
212A448ASN0-0.042-0.02917.0130.0070.0070.0000.0000.0000.000
213A449GLN00.003-0.02017.5200.0170.0170.0000.0000.0000.000
214A450VAL00.0030.00813.5790.0040.0040.0000.0000.0000.000
215A451VAL0-0.0010.00311.5690.0070.0070.0000.0000.0000.000
216A452VAL0-0.053-0.0178.574-0.140-0.1400.0000.0000.0000.000
217A453HIS00.0420.0063.523-0.1090.1990.017-0.150-0.175-0.001