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: JMZK9

Calculation Name: 1P7N-A-Xray310

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: 2021-09-06

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 176
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1544769.925658
FMO2-HF: Nuclear repulsion 1479185.505412
FMO2-HF: Total energy -65584.420246
FMO2-MP2: Total energy -65776.006246


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.
-0.4480.9690.026-0.589-0.853-0.001
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 : 0.039 / q_NPA : 0.010
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-26THR 00.0430.0303.0130.6011.7150.024-0.434-0.7040.000
4A-25SER 0-0.034-0.0135.6710.6870.6870.0000.0000.0000.000
5A-24PRO 0-0.038-0.0137.6150.1780.1780.0000.0000.0000.000
6A-23GLY 00.0820.0319.1070.1740.1740.0000.0000.0000.000
7A-22PRO 0-0.030-0.0157.639-0.251-0.2510.0000.0000.0000.000
8A-21ALA 0-0.0140.0147.9610.2600.2600.0000.0000.0000.000
9A-20LEU 00.000-0.0018.3420.2080.2080.0000.0000.0000.000
10A-19THR 00.009-0.0039.100-0.241-0.2410.0000.0000.0000.000
11A-18ASP -1-0.788-0.9126.849-2.025-2.0250.0000.0000.0000.000
12A-17TRP 00.015-0.0188.8540.1730.1730.0000.0000.0000.000
13A-16ALA 0-0.032-0.0067.6510.1780.1780.0000.0000.0000.000
14A-15ARG 10.9760.9967.0471.5581.5580.0000.0000.0000.000
15A-14VAL 0-0.0080.01310.5680.1420.1420.0000.0000.0000.000
16A-13ARG 10.8910.94012.9860.4000.4000.0000.0000.0000.000
17A-12GLU -1-0.927-0.99010.346-0.377-0.3770.0000.0000.0000.000
18A-11GLU -1-0.923-0.94414.375-0.328-0.3280.0000.0000.0000.000
19A-10LEU 0-0.033-0.03316.5180.0460.0460.0000.0000.0000.000
20A-9ALA 00.0030.01817.5870.0310.0310.0000.0000.0000.000
21A-8SER 0-0.105-0.01618.3390.0310.0310.0000.0000.0000.000
22A-7THR 0-0.051-0.05920.2410.0060.0060.0000.0000.0000.000
23A-6GLY 00.0020.01322.934-0.004-0.0040.0000.0000.0000.000
24A-5PRO 00.016-0.01224.503-0.008-0.0080.0000.0000.0000.000
25A-4PRO 0-0.0220.00126.456-0.002-0.0020.0000.0000.0000.000
26A-3VAL 00.0190.02724.0980.0030.0030.0000.0000.0000.000
27A-2VAL 00.0350.00021.4760.0010.0010.0000.0000.0000.000
28A-1ALA 00.0060.03616.779-0.022-0.0220.0000.0000.0000.000
29A0MET 0-0.080-0.06318.3650.0000.0000.0000.0000.0000.000
30A1PRO 00.0220.03715.2550.0140.0140.0000.0000.0000.000
31A2VAL 00.013-0.02516.051-0.009-0.0090.0000.0000.0000.000
32A3VAL 0-0.048-0.01410.508-0.051-0.0510.0000.0000.0000.000
33A4ILE 0-0.001-0.00411.2920.0340.0340.0000.0000.0000.000
34A5LYS 10.9510.9826.7860.5150.5150.0000.0000.0000.000
35A6THR 00.0300.0338.2150.1160.1160.0000.0000.0000.000
36A7GLU -1-0.969-1.0103.814-2.626-2.3230.002-0.155-0.149-0.001
37A8GLY 0-0.006-0.0035.6890.1830.1830.0000.0000.0000.000
38A9PRO 0-0.018-0.0066.499-0.128-0.1280.0000.0000.0000.000
39A10ALA 00.0290.0179.7940.0810.0810.0000.0000.0000.000
40A11TRP 0-0.009-0.00512.239-0.001-0.0010.0000.0000.0000.000
41A12THR 0-0.008-0.01213.4060.0630.0630.0000.0000.0000.000
42A13PRO 0-0.0110.00714.056-0.034-0.0340.0000.0000.0000.000
43A14LEU 00.0430.01417.0190.0190.0190.0000.0000.0000.000
44A15GLU -1-0.828-0.91320.3020.0540.0540.0000.0000.0000.000
45A16PRO 00.0240.00221.431-0.002-0.0020.0000.0000.0000.000
46A17LYS 10.9840.98124.703-0.047-0.0470.0000.0000.0000.000
47A18LEU 00.0190.00322.621-0.002-0.0020.0000.0000.0000.000
48A19ILE 00.0310.01623.937-0.001-0.0010.0000.0000.0000.000
49A20THR 0-0.084-0.04627.295-0.005-0.0050.0000.0000.0000.000
50A21ARG 10.9701.00228.002-0.085-0.0850.0000.0000.0000.000
51A22LEU 00.0340.04628.793-0.001-0.0010.0000.0000.0000.000
52A23ALA 00.0150.00331.094-0.003-0.0030.0000.0000.0000.000
53A24ASP -1-0.934-0.97433.4560.0360.0360.0000.0000.0000.000
54A25THR 0-0.101-0.06033.204-0.004-0.0040.0000.0000.0000.000
55A26VAL 0-0.029-0.02733.843-0.001-0.0010.0000.0000.0000.000
56A27ARG 10.8960.95636.561-0.028-0.0280.0000.0000.0000.000
57A28THR 0-0.037-0.03738.6010.0000.0000.0000.0000.0000.000
58A29LYS 10.8530.94138.437-0.047-0.0470.0000.0000.0000.000
59A30GLY 00.0470.04640.4390.0010.0010.0000.0000.0000.000
60A31LEU 00.0450.02136.7540.0020.0020.0000.0000.0000.000
61A32ARG 10.8930.97138.591-0.037-0.0370.0000.0000.0000.000
62A33SER 0-0.028-0.00139.2580.0030.0030.0000.0000.0000.000
63A34PRO 00.0640.00638.0800.0030.0030.0000.0000.0000.000
64A35ILE 00.0110.01435.1490.0050.0050.0000.0000.0000.000
65A36THR 00.0360.02734.1780.0060.0060.0000.0000.0000.000
66A37MET 0-0.0230.01332.6340.0020.0020.0000.0000.0000.000
67A38ALA 00.0130.00232.1070.0060.0060.0000.0000.0000.000
68A39GLU -1-0.853-0.94329.3730.0860.0860.0000.0000.0000.000
69A40VAL 0-0.037-0.01528.4290.0060.0060.0000.0000.0000.000
70A41GLU -1-0.879-0.97927.5890.1100.1100.0000.0000.0000.000
71A42ALA 0-0.0110.01025.8880.0110.0110.0000.0000.0000.000
72A43LEU 0-0.0300.03422.7510.0180.0180.0000.0000.0000.000
73A44MET 0-0.088-0.03023.183-0.001-0.0010.0000.0000.0000.000
74A45SER 0-0.005-0.04322.4740.0040.0040.0000.0000.0000.000
75A46SER 0-0.048-0.02017.5240.0320.0320.0000.0000.0000.000
76A47PRO 0-0.028-0.02217.032-0.028-0.0280.0000.0000.0000.000
77A48LEU 00.0440.02317.9440.0080.0080.0000.0000.0000.000
78A49LEU 00.0110.01316.405-0.007-0.0070.0000.0000.0000.000
79A50PRO 00.0110.00220.1470.0010.0010.0000.0000.0000.000
80A51HIS 00.015-0.00521.954-0.001-0.0010.0000.0000.0000.000
81A52ASP -1-0.854-0.92619.6190.0520.0520.0000.0000.0000.000
82A53VAL 0-0.0410.00123.1140.0010.0010.0000.0000.0000.000
83A54THR 00.0000.00325.556-0.003-0.0030.0000.0000.0000.000
84A55ASN 0-0.023-0.02225.330-0.004-0.0040.0000.0000.0000.000
85A56LEU 0-0.0120.00825.747-0.001-0.0010.0000.0000.0000.000
86A57MET 00.009-0.01327.803-0.002-0.0020.0000.0000.0000.000
87A58ARG 10.9170.96430.775-0.007-0.0070.0000.0000.0000.000
88A59VAL 0-0.066-0.02829.452-0.003-0.0030.0000.0000.0000.000
89A60ILE 0-0.029-0.01230.709-0.001-0.0010.0000.0000.0000.000
90A61LEU 0-0.0120.00233.688-0.001-0.0010.0000.0000.0000.000
91A62GLY 00.0270.03635.883-0.002-0.0020.0000.0000.0000.000
92A63PRO 0-0.031-0.04937.9310.0000.0000.0000.0000.0000.000
93A64ALA 00.0330.01039.4790.0000.0000.0000.0000.0000.000
94A65PRO 00.0550.02938.638-0.001-0.0010.0000.0000.0000.000
95A66TYR 00.0180.01831.184-0.001-0.0010.0000.0000.0000.000
96A67ALA 00.0270.02136.2340.0010.0010.0000.0000.0000.000
97A68LEU 00.0570.03338.3370.0000.0000.0000.0000.0000.000
98A69TRP 0-0.009-0.00229.272-0.001-0.0010.0000.0000.0000.000
99A70MET 0-0.041-0.02933.0960.0020.0020.0000.0000.0000.000
100A71ASP -1-0.896-0.94935.0250.0170.0170.0000.0000.0000.000
101A72ALA 0-0.026-0.02136.4600.0010.0010.0000.0000.0000.000
102A73TRP 0-0.028-0.03326.7870.0000.0000.0000.0000.0000.000
103A74GLY 00.0100.00132.4320.0020.0020.0000.0000.0000.000
104A75VAL 00.0200.01334.1750.0000.0000.0000.0000.0000.000
105A76GLN 0-0.009-0.01932.3050.0040.0040.0000.0000.0000.000
106A77LEU 0-0.008-0.00727.8270.0020.0020.0000.0000.0000.000
107A78GLN 0-0.034-0.02231.394-0.001-0.0010.0000.0000.0000.000
108A79THR 0-0.056-0.00433.4600.0000.0000.0000.0000.0000.000
109A80VAL 00.0390.01127.5740.0030.0030.0000.0000.0000.000
110A81ILE 0-0.020-0.01229.617-0.001-0.0010.0000.0000.0000.000
111A82ALA 00.0080.03131.603-0.004-0.0040.0000.0000.0000.000
112A83ALA 00.0110.00630.414-0.001-0.0010.0000.0000.0000.000
113A84ALA 00.0120.02128.4750.0030.0030.0000.0000.0000.000
114A85THR 0-0.017-0.03129.427-0.005-0.0050.0000.0000.0000.000
115A86ARG 10.7510.86332.350-0.030-0.0300.0000.0000.0000.000
116A87ASP -1-0.710-0.84128.9710.0590.0590.0000.0000.0000.000
117A88PRO 0-0.081-0.05128.506-0.001-0.0010.0000.0000.0000.000
118A89ARG 10.9250.93925.314-0.057-0.0570.0000.0000.0000.000
119A90HIS 00.0370.05824.8990.0130.0130.0000.0000.0000.000
120A91PRO 00.0490.00721.116-0.004-0.0040.0000.0000.0000.000
121A92ALA 0-0.027-0.01521.1010.0000.0000.0000.0000.0000.000
122A93ASN 0-0.035-0.00923.113-0.020-0.0200.0000.0000.0000.000
123A94GLY 0-0.007-0.00920.6890.0090.0090.0000.0000.0000.000
124A95GLN 0-0.043-0.01519.2870.0070.0070.0000.0000.0000.000
125A96GLY 00.0090.00922.215-0.002-0.0020.0000.0000.0000.000
126A97ARG 10.9510.95724.3400.0250.0250.0000.0000.0000.000
127A98GLY 00.0300.01326.9070.0040.0040.0000.0000.0000.000
128A99GLU -1-0.891-0.91820.908-0.038-0.0380.0000.0000.0000.000
129A100ARG 10.9250.95924.1400.0010.0010.0000.0000.0000.000
130A101THR 00.013-0.00124.185-0.006-0.0060.0000.0000.0000.000
131A102ASN 00.0390.03026.4210.0000.0000.0000.0000.0000.000
132A103LEU 00.0850.02428.2510.0010.0010.0000.0000.0000.000
133A104ASN 00.0600.00429.3250.0040.0040.0000.0000.0000.000
134A105ARG 10.7130.84320.6010.0150.0150.0000.0000.0000.000
135A106LEU 00.0230.01224.6360.0010.0010.0000.0000.0000.000
136A107LYS 10.9670.99025.851-0.005-0.0050.0000.0000.0000.000
137A108GLY 0-0.003-0.00224.466-0.001-0.0010.0000.0000.0000.000
138A109LEU 0-0.038-0.04225.272-0.006-0.0060.0000.0000.0000.000
139A110ALA 0-0.040-0.02625.159-0.004-0.0040.0000.0000.0000.000
140A111ASP -1-0.865-0.93826.324-0.070-0.0700.0000.0000.0000.000
141A112GLY 00.0460.03023.865-0.006-0.0060.0000.0000.0000.000
142A113MET 0-0.092-0.01821.532-0.001-0.0010.0000.0000.0000.000
143A114VAL 00.0360.03123.7430.0050.0050.0000.0000.0000.000
144A115GLY 0-0.007-0.00126.315-0.007-0.0070.0000.0000.0000.000
145A116ASN 0-0.029-0.01720.936-0.012-0.0120.0000.0000.0000.000
146A117PRO 00.0400.01919.445-0.002-0.0020.0000.0000.0000.000
147A118GLN 00.0650.03414.6240.0340.0340.0000.0000.0000.000
148A119GLY 00.008-0.00116.587-0.013-0.0130.0000.0000.0000.000
149A120GLN 0-0.020-0.03918.4510.0120.0120.0000.0000.0000.000
150A121ALA 0-0.0060.00113.7610.0140.0140.0000.0000.0000.000
151A122ALA 0-0.0270.00014.0020.0030.0030.0000.0000.0000.000
152A123LEU 0-0.042-0.01715.049-0.004-0.0040.0000.0000.0000.000
153A124LEU 0-0.071-0.02918.0260.0110.0110.0000.0000.0000.000
154A125ARG 10.9380.96516.528-0.003-0.0030.0000.0000.0000.000
155A126PRO 00.0680.01614.0280.0060.0060.0000.0000.0000.000
156A127GLY 00.0190.00816.6920.0040.0040.0000.0000.0000.000
157A128GLU -1-0.753-0.84820.0460.0090.0090.0000.0000.0000.000
158A129LEU 00.0240.02715.893-0.004-0.0040.0000.0000.0000.000
159A130VAL 00.0160.02119.3810.0010.0010.0000.0000.0000.000
160A131ALA 0-0.0060.00621.757-0.007-0.0070.0000.0000.0000.000
161A132ILE 0-0.0130.00121.854-0.005-0.0050.0000.0000.0000.000
162A133THR 00.0550.00821.881-0.007-0.0070.0000.0000.0000.000
163A134ALA 00.0310.03324.461-0.003-0.0030.0000.0000.0000.000
164A135SER 0-0.015-0.02826.952-0.008-0.0080.0000.0000.0000.000
165A136ALA 0-0.025-0.00527.036-0.006-0.0060.0000.0000.0000.000
166A137LEU 00.0640.01927.267-0.005-0.0050.0000.0000.0000.000
167A138GLN 0-0.047-0.02629.764-0.008-0.0080.0000.0000.0000.000
168A139ALA 00.0170.00932.615-0.003-0.0030.0000.0000.0000.000
169A140PHE 00.0250.01032.032-0.004-0.0040.0000.0000.0000.000
170A141ARG 10.8960.95330.865-0.092-0.0920.0000.0000.0000.000
171A142GLU -1-0.941-0.97636.0320.0450.0450.0000.0000.0000.000
172A143VAL 0-0.020-0.01737.136-0.004-0.0040.0000.0000.0000.000
173A144ALA 0-0.0060.00637.045-0.002-0.0020.0000.0000.0000.000
174A145ARG 10.8740.92039.053-0.049-0.0490.0000.0000.0000.000
175A146LEU 0-0.110-0.04241.641-0.002-0.0020.0000.0000.0000.000
176A147ALA -1-0.866-0.94042.2470.0320.0320.0000.0000.0000.000