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: GN8K1

Calculation Name: 1P7N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P7N

Chain ID: A

ChEMBL ID:

UniProt ID: P03322

Base Structure: X-ray

Registration Date: 2023-03-13

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1545299.217243
FMO2-HF: Nuclear repulsion 1479711.984646
FMO2-HF: Total energy -65587.232597
FMO2-MP2: Total energy -65778.355934


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:-28:GLY)


Summations of interaction energy for fragment #1(A:-28:GLY)
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.
-7.337-5.6263.426-2.314-2.823-0.027
Interaction energy analysis for fragmet #1(A:-28:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / 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].
3A-26THR00.0180.0163.6050.6021.5860.006-0.380-0.6110.001
4A-25SER00.015-0.0035.9210.3860.481-0.001-0.005-0.0880.000
5A-24PRO0-0.020-0.0087.8020.1530.1530.0000.0000.0000.000
6A-23GLY00.0430.0229.1910.1830.1830.0000.0000.0000.000
7A-22PRO0-0.048-0.0167.132-0.128-0.1280.0000.0000.0000.000
8A-21ALA00.0010.0147.5970.2280.2280.0000.0000.0000.000
9A-20LEU0-0.014-0.0017.9750.1910.1910.0000.0000.0000.000
10A-19THR00.006-0.0058.518-0.212-0.2120.0000.0000.0000.000
11A-18ASP-1-0.753-0.8656.891-2.020-2.0200.0000.0000.0000.000
12A-17TRP00.022-0.0178.7760.1640.1640.0000.0000.0000.000
13A-16ALA0-0.025-0.0057.1370.1580.1580.0000.0000.0000.000
14A-15ARG10.9110.9365.3321.7071.7070.0000.0000.0000.000
15A-14VAL0-0.0090.01010.3050.1390.1390.0000.0000.0000.000
16A-13ARG10.8220.89812.1180.4680.4680.0000.0000.0000.000
17A-12GLU-1-0.925-0.9789.306-0.503-0.5030.0000.0000.0000.000
18A-11GLU-1-0.911-0.94913.714-0.286-0.2860.0000.0000.0000.000
19A-10LEU0-0.014-0.01416.0640.0480.0480.0000.0000.0000.000
20A-9ALA0-0.048-0.02316.9120.0300.0300.0000.0000.0000.000
21A-8SER0-0.082-0.03517.8490.0360.0360.0000.0000.0000.000
22A-7THR0-0.025-0.01019.6760.0280.0280.0000.0000.0000.000
23A-6GLY00.0310.01622.414-0.007-0.0070.0000.0000.0000.000
24A-5PRO0-0.004-0.02324.814-0.007-0.0070.0000.0000.0000.000
25A-4PRO0-0.045-0.01626.214-0.002-0.0020.0000.0000.0000.000
26A-3VAL00.0090.00123.6460.0040.0040.0000.0000.0000.000
27A-2VAL00.0520.05420.965-0.006-0.0060.0000.0000.0000.000
28A-1ALA00.0200.00916.351-0.020-0.0200.0000.0000.0000.000
29A0MET0-0.056-0.01818.185-0.002-0.0020.0000.0000.0000.000
30A1PRO00.0430.03214.7510.0110.0110.0000.0000.0000.000
31A2VAL00.023-0.00515.444-0.010-0.0100.0000.0000.0000.000
32A3VAL0-0.048-0.0159.677-0.055-0.0550.0000.0000.0000.000
33A4ILE00.002-0.00211.4860.0050.0050.0000.0000.0000.000
34A5LYS10.8690.9315.1721.4491.4490.0000.0000.0000.000
35A6THR00.0300.0187.4310.0570.0570.0000.0000.0000.000
36A7GLU-1-0.870-0.9312.091-10.132-9.5003.421-1.929-2.124-0.028
37A8GLY00.0010.0045.8340.1280.1280.0000.0000.0000.000
38A9PRO0-0.006-0.0186.702-0.127-0.1270.0000.0000.0000.000
39A10ALA0-0.0050.0159.8190.0570.0570.0000.0000.0000.000
40A11TRP0-0.040-0.02912.131-0.025-0.0250.0000.0000.0000.000
41A12THR00.011-0.00413.5070.0540.0540.0000.0000.0000.000
42A13PRO0-0.028-0.00414.210-0.032-0.0320.0000.0000.0000.000
43A14LEU00.0310.01117.1030.0130.0130.0000.0000.0000.000
44A15GLU-1-0.787-0.88420.4860.0640.0640.0000.0000.0000.000
45A16PRO00.024-0.00621.591-0.003-0.0030.0000.0000.0000.000
46A17LYS10.9120.94624.255-0.069-0.0690.0000.0000.0000.000
47A18LEU00.0210.02222.936-0.003-0.0030.0000.0000.0000.000
48A19ILE00.0260.01624.049-0.003-0.0030.0000.0000.0000.000
49A20THR0-0.076-0.04027.556-0.005-0.0050.0000.0000.0000.000
50A21ARG10.8860.91828.375-0.082-0.0820.0000.0000.0000.000
51A22LEU00.0390.03828.729-0.002-0.0020.0000.0000.0000.000
52A23ALA00.0310.00431.304-0.003-0.0030.0000.0000.0000.000
53A24ASP-1-0.841-0.91133.5280.0350.0350.0000.0000.0000.000
54A25THR0-0.063-0.03533.429-0.004-0.0040.0000.0000.0000.000
55A26VAL0-0.014-0.00733.807-0.002-0.0020.0000.0000.0000.000
56A27ARG10.8090.89236.794-0.034-0.0340.0000.0000.0000.000
57A28THR0-0.056-0.03738.908-0.001-0.0010.0000.0000.0000.000
58A29LYS10.8630.93838.422-0.046-0.0460.0000.0000.0000.000
59A30GLY00.0650.05140.4360.0000.0000.0000.0000.0000.000
60A31LEU00.0220.01736.6610.0030.0030.0000.0000.0000.000
61A32ARG10.8640.91438.516-0.034-0.0340.0000.0000.0000.000
62A33SER0-0.0360.00238.6730.0020.0020.0000.0000.0000.000
63A34PRO00.0370.00137.8770.0030.0030.0000.0000.0000.000
64A35ILE00.0050.01135.5560.0050.0050.0000.0000.0000.000
65A36THR00.038-0.00234.3230.0050.0050.0000.0000.0000.000
66A37MET0-0.0380.00132.5440.0010.0010.0000.0000.0000.000
67A38ALA00.0340.01632.1210.0050.0050.0000.0000.0000.000
68A39GLU-1-0.800-0.86729.4130.0880.0880.0000.0000.0000.000
69A40VAL0-0.008-0.01228.4010.0070.0070.0000.0000.0000.000
70A41GLU-1-0.823-0.91627.6540.0930.0930.0000.0000.0000.000
71A42ALA0-0.016-0.00226.0380.0110.0110.0000.0000.0000.000
72A43LEU0-0.044-0.00722.9110.0150.0150.0000.0000.0000.000
73A44MET0-0.055-0.02123.1450.0000.0000.0000.0000.0000.000
74A45SER0-0.024-0.01522.4030.0070.0070.0000.0000.0000.000
75A46SER0-0.031-0.00517.6310.0270.0270.0000.0000.0000.000
76A47PRO0-0.022-0.01316.836-0.023-0.0230.0000.0000.0000.000
77A48LEU00.0120.01117.8130.0140.0140.0000.0000.0000.000
78A49LEU0-0.0030.00516.660-0.009-0.0090.0000.0000.0000.000
79A50PRO00.008-0.00520.5200.0010.0010.0000.0000.0000.000
80A51HIS00.0210.02322.366-0.004-0.0040.0000.0000.0000.000
81A52ASP-1-0.791-0.89119.7400.0650.0650.0000.0000.0000.000
82A53VAL0-0.0150.00223.3730.0000.0000.0000.0000.0000.000
83A54THR0-0.027-0.02825.930-0.004-0.0040.0000.0000.0000.000
84A55ASN0-0.078-0.05226.144-0.006-0.0060.0000.0000.0000.000
85A56LEU00.0240.01825.576-0.002-0.0020.0000.0000.0000.000
86A57MET00.0150.00728.186-0.001-0.0010.0000.0000.0000.000
87A58ARG10.9020.95131.110-0.015-0.0150.0000.0000.0000.000
88A59VAL0-0.057-0.02630.112-0.003-0.0030.0000.0000.0000.000
89A60ILE0-0.022-0.00830.761-0.001-0.0010.0000.0000.0000.000
90A61LEU0-0.045-0.01233.9530.0000.0000.0000.0000.0000.000
91A62GLY00.0410.03236.177-0.002-0.0020.0000.0000.0000.000
92A63PRO0-0.013-0.03438.1000.0010.0010.0000.0000.0000.000
93A64ALA00.0300.02339.5870.0000.0000.0000.0000.0000.000
94A65PRO00.0350.00438.8840.0000.0000.0000.0000.0000.000
95A66TYR00.022-0.00132.3000.0000.0000.0000.0000.0000.000
96A67ALA00.0190.01236.4580.0000.0000.0000.0000.0000.000
97A68LEU00.0310.01138.6980.0000.0000.0000.0000.0000.000
98A69TRP0-0.021-0.01729.353-0.001-0.0010.0000.0000.0000.000
99A70MET00.0180.02332.4310.0020.0020.0000.0000.0000.000
100A71ASP-1-0.921-0.94235.1520.0150.0150.0000.0000.0000.000
101A72ALA0-0.020-0.01236.5690.0010.0010.0000.0000.0000.000
102A73TRP00.005-0.00526.9580.0000.0000.0000.0000.0000.000
103A74GLY0-0.016-0.02032.6640.0010.0010.0000.0000.0000.000
104A75VAL00.0180.01634.5610.0000.0000.0000.0000.0000.000
105A76GLN0-0.002-0.00432.3530.0030.0030.0000.0000.0000.000
106A77LEU00.0060.01327.9600.0020.0020.0000.0000.0000.000
107A78GLN0-0.043-0.02931.369-0.002-0.0020.0000.0000.0000.000
108A79THR0-0.046-0.02533.2310.0000.0000.0000.0000.0000.000
109A80VAL00.0240.01827.0950.0010.0010.0000.0000.0000.000
110A81ILE0-0.0150.00429.429-0.002-0.0020.0000.0000.0000.000
111A82ALA00.0010.01831.462-0.003-0.0030.0000.0000.0000.000
112A83ALA00.004-0.00630.286-0.001-0.0010.0000.0000.0000.000
113A84ALA0-0.003-0.00327.7850.0010.0010.0000.0000.0000.000
114A85THR0-0.034-0.02529.128-0.006-0.0060.0000.0000.0000.000
115A86ARG10.8470.93032.297-0.023-0.0230.0000.0000.0000.000
116A87ASP-1-0.783-0.88728.1270.0460.0460.0000.0000.0000.000
117A88PRO0-0.034-0.02228.4060.0000.0000.0000.0000.0000.000
118A89ARG10.9200.94724.903-0.036-0.0360.0000.0000.0000.000
119A90HIS00.0720.05824.2430.0090.0090.0000.0000.0000.000
120A91PRO00.0320.00021.065-0.007-0.0070.0000.0000.0000.000
121A92ALA0-0.0150.01020.8700.0030.0030.0000.0000.0000.000
122A93ASN0-0.038-0.02722.486-0.017-0.0170.0000.0000.0000.000
123A94GLY00.0220.00420.4180.0080.0080.0000.0000.0000.000
124A95GLN0-0.050-0.02119.1960.0080.0080.0000.0000.0000.000
125A96GLY00.0460.02422.0660.0020.0020.0000.0000.0000.000
126A97ARG10.9410.94924.1830.0370.0370.0000.0000.0000.000
127A98GLY00.0500.02826.8080.0060.0060.0000.0000.0000.000
128A99GLU-1-0.860-0.89920.231-0.056-0.0560.0000.0000.0000.000
129A100ARG10.8060.89323.8090.0130.0130.0000.0000.0000.000
130A101THR0-0.005-0.02024.305-0.004-0.0040.0000.0000.0000.000
131A102ASN00.018-0.00326.5190.0010.0010.0000.0000.0000.000
132A103LEU00.0720.01928.1680.0020.0020.0000.0000.0000.000
133A104ASN00.0300.01829.3990.0060.0060.0000.0000.0000.000
134A105ARG10.7620.83920.3390.0180.0180.0000.0000.0000.000
135A106LEU00.0000.00024.7430.0030.0030.0000.0000.0000.000
136A107LYS10.9640.98026.167-0.009-0.0090.0000.0000.0000.000
137A108GLY0-0.0010.00424.5970.0000.0000.0000.0000.0000.000
138A109LEU0-0.041-0.03625.449-0.005-0.0050.0000.0000.0000.000
139A110ALA0-0.016-0.01225.311-0.003-0.0030.0000.0000.0000.000
140A111ASP-1-0.810-0.91226.517-0.066-0.0660.0000.0000.0000.000
141A112GLY0-0.014-0.00123.229-0.002-0.0020.0000.0000.0000.000
142A113MET0-0.081-0.02420.8790.0020.0020.0000.0000.0000.000
143A114VAL00.0350.03023.6240.0080.0080.0000.0000.0000.000
144A115GLY0-0.013-0.00326.357-0.006-0.0060.0000.0000.0000.000
145A116ASN0-0.026-0.01020.672-0.004-0.0040.0000.0000.0000.000
146A117PRO00.0340.01519.563-0.001-0.0010.0000.0000.0000.000
147A118GLN00.0580.02313.5000.0320.0320.0000.0000.0000.000
148A119GLY00.0110.01616.428-0.017-0.0170.0000.0000.0000.000
149A120GLN0-0.021-0.04218.1650.0120.0120.0000.0000.0000.000
150A121ALA00.017-0.00114.1830.0090.0090.0000.0000.0000.000
151A122ALA0-0.0140.00513.6780.0100.0100.0000.0000.0000.000
152A123LEU0-0.026-0.00114.699-0.021-0.0210.0000.0000.0000.000
153A124LEU0-0.055-0.01217.5610.0050.0050.0000.0000.0000.000
154A125ARG10.8940.93416.4700.0050.0050.0000.0000.0000.000
155A126PRO00.0590.00813.9400.0060.0060.0000.0000.0000.000
156A127GLY00.0340.01916.6970.0100.0100.0000.0000.0000.000
157A128GLU-1-0.749-0.81120.2400.0040.0040.0000.0000.0000.000
158A129LEU00.0500.02916.089-0.002-0.0020.0000.0000.0000.000
159A130VAL00.0030.01819.1160.0010.0010.0000.0000.0000.000
160A131ALA00.0160.00821.471-0.006-0.0060.0000.0000.0000.000
161A132ILE0-0.0030.00322.062-0.008-0.0080.0000.0000.0000.000
162A133THR00.0170.00221.772-0.007-0.0070.0000.0000.0000.000
163A134ALA00.0240.01424.376-0.004-0.0040.0000.0000.0000.000
164A135SER0-0.002-0.01926.782-0.007-0.0070.0000.0000.0000.000
165A136ALA0-0.024-0.00327.117-0.006-0.0060.0000.0000.0000.000
166A137LEU00.0610.03427.332-0.005-0.0050.0000.0000.0000.000
167A138GLN0-0.0020.00529.7640.0000.0000.0000.0000.0000.000
168A139ALA00.0280.01532.377-0.004-0.0040.0000.0000.0000.000
169A140PHE00.018-0.00732.182-0.004-0.0040.0000.0000.0000.000
170A141ARG10.8210.87931.439-0.085-0.0850.0000.0000.0000.000
171A142GLU-1-0.834-0.90035.7400.0420.0420.0000.0000.0000.000
172A143VAL0-0.0030.00637.389-0.003-0.0030.0000.0000.0000.000
173A144ALA00.0150.00937.135-0.002-0.0020.0000.0000.0000.000
174A145ARG10.8250.90338.274-0.047-0.0470.0000.0000.0000.000
175A146LEU0-0.028-0.01941.619-0.002-0.0020.0000.0000.0000.000
176A147ALA0-0.040-0.00541.792-0.003-0.0030.0000.0000.0000.000