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: VRV11

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 OptH
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 -1545035.967944
FMO2-HF: Nuclear repulsion 1479451.005899
FMO2-HF: Total energy -65584.962046
FMO2-MP2: Total energy -65776.552549


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.
-0.2631.140.007-0.591-0.82-0.001
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 : 0.042 / q_NPA : 0.011
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-26THR00.0410.0263.4820.8091.8880.006-0.421-0.6650.000
4A-25SER0-0.032-0.0115.6620.6570.6570.0000.0000.0000.000
5A-24PRO0-0.037-0.0137.6150.1850.1850.0000.0000.0000.000
6A-23GLY00.0810.0309.1060.1850.1850.0000.0000.0000.000
7A-22PRO0-0.028-0.0137.640-0.247-0.2470.0000.0000.0000.000
8A-21ALA0-0.0150.0127.9620.2590.2590.0000.0000.0000.000
9A-20LEU0-0.001-0.0028.3430.2110.2110.0000.0000.0000.000
10A-19THR00.009-0.0039.102-0.243-0.2430.0000.0000.0000.000
11A-18ASP-1-0.788-0.9116.876-2.069-2.0690.0000.0000.0000.000
12A-17TRP00.014-0.0188.8880.1620.1620.0000.0000.0000.000
13A-16ALA0-0.029-0.0057.6710.1810.1810.0000.0000.0000.000
14A-15ARG10.9760.9967.0051.6721.6720.0000.0000.0000.000
15A-14VAL0-0.0080.01310.5740.1410.1410.0000.0000.0000.000
16A-13ARG10.8890.93913.0040.4060.4060.0000.0000.0000.000
17A-12GLU-1-0.928-0.99010.338-0.415-0.4150.0000.0000.0000.000
18A-11GLU-1-0.922-0.94314.371-0.353-0.3530.0000.0000.0000.000
19A-10LEU0-0.034-0.03416.5150.0470.0470.0000.0000.0000.000
20A-9ALA00.0050.01917.5870.0310.0310.0000.0000.0000.000
21A-8SER0-0.105-0.01718.3240.0310.0310.0000.0000.0000.000
22A-7THR0-0.051-0.05920.2310.0060.0060.0000.0000.0000.000
23A-6GLY00.0030.01522.929-0.004-0.0040.0000.0000.0000.000
24A-5PRO00.015-0.01224.507-0.008-0.0080.0000.0000.0000.000
25A-4PRO0-0.0200.00226.467-0.001-0.0010.0000.0000.0000.000
26A-3VAL00.0210.02824.1230.0040.0040.0000.0000.0000.000
27A-2VAL00.033-0.00121.4890.0010.0010.0000.0000.0000.000
28A-1ALA00.0040.03616.795-0.021-0.0210.0000.0000.0000.000
29A0MET0-0.076-0.06318.3880.0010.0010.0000.0000.0000.000
30A1PRO00.0240.03915.2870.0160.0160.0000.0000.0000.000
31A2VAL00.011-0.02616.003-0.008-0.0080.0000.0000.0000.000
32A3VAL0-0.048-0.01410.549-0.049-0.0490.0000.0000.0000.000
33A4ILE00.000-0.00311.2520.0350.0350.0000.0000.0000.000
34A5LYS10.9500.9826.7560.5020.5020.0000.0000.0000.000
35A6THR00.0310.0338.1900.1180.1180.0000.0000.0000.000
36A7GLU-1-0.970-1.0113.785-2.567-2.2430.001-0.170-0.155-0.001
37A8GLY0-0.004-0.0025.6930.1660.1660.0000.0000.0000.000
38A9PRO0-0.018-0.0066.499-0.140-0.1400.0000.0000.0000.000
39A10ALA00.0290.0179.7940.0810.0810.0000.0000.0000.000
40A11TRP0-0.007-0.00412.239-0.004-0.0040.0000.0000.0000.000
41A12THR0-0.009-0.01313.4060.0660.0660.0000.0000.0000.000
42A13PRO0-0.0100.00814.055-0.034-0.0340.0000.0000.0000.000
43A14LEU00.0390.01217.0190.0190.0190.0000.0000.0000.000
44A15GLU-1-0.824-0.91020.3030.0590.0590.0000.0000.0000.000
45A16PRO00.0270.00221.432-0.002-0.0020.0000.0000.0000.000
46A17LYS10.9850.98224.703-0.050-0.0500.0000.0000.0000.000
47A18LEU00.0160.00222.622-0.002-0.0020.0000.0000.0000.000
48A19ILE00.0310.01623.936-0.001-0.0010.0000.0000.0000.000
49A20THR0-0.084-0.04527.296-0.005-0.0050.0000.0000.0000.000
50A21ARG10.9731.00428.004-0.091-0.0910.0000.0000.0000.000
51A22LEU00.0320.04528.794-0.001-0.0010.0000.0000.0000.000
52A23ALA00.0150.00231.095-0.003-0.0030.0000.0000.0000.000
53A24ASP-1-0.933-0.97233.4580.0390.0390.0000.0000.0000.000
54A25THR0-0.102-0.06033.205-0.005-0.0050.0000.0000.0000.000
55A26VAL0-0.025-0.02833.845-0.001-0.0010.0000.0000.0000.000
56A27ARG10.8910.95336.562-0.031-0.0310.0000.0000.0000.000
57A28THR0-0.031-0.03338.6030.0000.0000.0000.0000.0000.000
58A29LYS10.8620.94538.439-0.050-0.0500.0000.0000.0000.000
59A30GLY00.0430.04440.4410.0010.0010.0000.0000.0000.000
60A31LEU00.0500.02436.7520.0020.0020.0000.0000.0000.000
61A32ARG10.8840.96138.593-0.041-0.0410.0000.0000.0000.000
62A33SER0-0.0090.00939.2590.0030.0030.0000.0000.0000.000
63A34PRO00.0650.01038.0810.0030.0030.0000.0000.0000.000
64A35ILE00.0200.01935.1500.0050.0050.0000.0000.0000.000
65A36THR00.0340.02734.1790.0060.0060.0000.0000.0000.000
66A37MET0-0.0280.00932.6360.0020.0020.0000.0000.0000.000
67A38ALA00.0120.00232.1080.0060.0060.0000.0000.0000.000
68A39GLU-1-0.847-0.94029.3740.0920.0920.0000.0000.0000.000
69A40VAL0-0.040-0.01528.4310.0060.0060.0000.0000.0000.000
70A41GLU-1-0.876-0.97927.5910.1180.1180.0000.0000.0000.000
71A42ALA0-0.0090.01125.8890.0110.0110.0000.0000.0000.000
72A43LEU0-0.0270.03422.7520.0180.0180.0000.0000.0000.000
73A44MET0-0.090-0.03123.184-0.001-0.0010.0000.0000.0000.000
74A45SER0-0.005-0.04222.4750.0040.0040.0000.0000.0000.000
75A46SER0-0.045-0.01817.5250.0330.0330.0000.0000.0000.000
76A47PRO0-0.027-0.02217.033-0.030-0.0300.0000.0000.0000.000
77A48LEU00.0430.02317.9430.0100.0100.0000.0000.0000.000
78A49LEU00.0140.01516.405-0.006-0.0060.0000.0000.0000.000
79A50PRO00.0090.00020.1470.0000.0000.0000.0000.0000.000
80A51HIS00.015-0.00521.954-0.002-0.0020.0000.0000.0000.000
81A52ASP-1-0.848-0.92319.6190.0630.0630.0000.0000.0000.000
82A53VAL0-0.0420.00023.1140.0000.0000.0000.0000.0000.000
83A54THR00.0030.00325.556-0.003-0.0030.0000.0000.0000.000
84A55ASN0-0.024-0.02125.330-0.004-0.0040.0000.0000.0000.000
85A56LEU0-0.0130.00825.746-0.002-0.0020.0000.0000.0000.000
86A57MET00.011-0.01227.803-0.002-0.0020.0000.0000.0000.000
87A58ARG10.9160.96230.775-0.012-0.0120.0000.0000.0000.000
88A59VAL0-0.063-0.02729.451-0.004-0.0040.0000.0000.0000.000
89A60ILE0-0.029-0.01130.709-0.001-0.0010.0000.0000.0000.000
90A61LEU0-0.020-0.00133.688-0.001-0.0010.0000.0000.0000.000
91A62GLY00.0250.03435.882-0.002-0.0020.0000.0000.0000.000
92A63PRO0-0.021-0.04437.9310.0010.0010.0000.0000.0000.000
93A64ALA00.0340.01039.4790.0000.0000.0000.0000.0000.000
94A65PRO00.0370.02038.6380.0000.0000.0000.0000.0000.000
95A66TYR00.0230.02031.185-0.001-0.0010.0000.0000.0000.000
96A67ALA00.0340.02536.2340.0010.0010.0000.0000.0000.000
97A68LEU00.0450.02738.3370.0010.0010.0000.0000.0000.000
98A69TRP0-0.015-0.00529.272-0.001-0.0010.0000.0000.0000.000
99A70MET0-0.030-0.02433.0960.0020.0020.0000.0000.0000.000
100A71ASP-1-0.894-0.94835.0250.0220.0220.0000.0000.0000.000
101A72ALA0-0.033-0.02536.4600.0010.0010.0000.0000.0000.000
102A73TRP0-0.025-0.03226.7870.0010.0010.0000.0000.0000.000
103A74GLY00.0110.00232.4320.0020.0020.0000.0000.0000.000
104A75VAL00.0180.01334.1750.0000.0000.0000.0000.0000.000
105A76GLN0-0.007-0.01932.3050.0050.0050.0000.0000.0000.000
106A77LEU00.002-0.00327.8260.0030.0030.0000.0000.0000.000
107A78GLN0-0.043-0.02431.393-0.001-0.0010.0000.0000.0000.000
108A79THR0-0.056-0.00433.4700.0000.0000.0000.0000.0000.000
109A80VAL00.0380.01027.5890.0030.0030.0000.0000.0000.000
110A81ILE0-0.015-0.01029.6230.0000.0000.0000.0000.0000.000
111A82ALA00.0070.03131.612-0.004-0.0040.0000.0000.0000.000
112A83ALA00.0120.00630.432-0.002-0.0020.0000.0000.0000.000
113A84ALA00.0140.02128.4820.0030.0030.0000.0000.0000.000
114A85THR0-0.017-0.03129.438-0.005-0.0050.0000.0000.0000.000
115A86ARG10.7510.86232.357-0.036-0.0360.0000.0000.0000.000
116A87ASP-1-0.707-0.84028.9910.0690.0690.0000.0000.0000.000
117A88PRO0-0.082-0.05128.5130.0000.0000.0000.0000.0000.000
118A89ARG10.9240.93925.326-0.066-0.0660.0000.0000.0000.000
119A90HIS00.0410.05924.9170.0140.0140.0000.0000.0000.000
120A91PRO00.0470.00621.139-0.004-0.0040.0000.0000.0000.000
121A92ALA0-0.028-0.01521.1150.0020.0020.0000.0000.0000.000
122A93ASN0-0.035-0.01023.117-0.020-0.0200.0000.0000.0000.000
123A94GLY0-0.009-0.00920.6900.0110.0110.0000.0000.0000.000
124A95GLN0-0.041-0.01419.2820.0050.0050.0000.0000.0000.000
125A96GLY00.0100.00922.211-0.003-0.0030.0000.0000.0000.000
126A97ARG10.9510.95724.3280.0200.0200.0000.0000.0000.000
127A98GLY00.0300.01226.8920.0040.0040.0000.0000.0000.000
128A99GLU-1-0.890-0.91820.897-0.025-0.0250.0000.0000.0000.000
129A100ARG10.9220.95924.136-0.007-0.0070.0000.0000.0000.000
130A101THR00.017-0.00124.188-0.007-0.0070.0000.0000.0000.000
131A102ASN00.0390.03126.4200.0000.0000.0000.0000.0000.000
132A103LEU00.0880.02428.2510.0010.0010.0000.0000.0000.000
133A104ASN00.0560.00329.3250.0040.0040.0000.0000.0000.000
134A105ARG10.7160.84520.6020.0030.0030.0000.0000.0000.000
135A106LEU00.0210.01024.6360.0010.0010.0000.0000.0000.000
136A107LYS10.9640.98825.851-0.010-0.0100.0000.0000.0000.000
137A108GLY0-0.004-0.00124.467-0.001-0.0010.0000.0000.0000.000
138A109LEU0-0.040-0.04325.272-0.006-0.0060.0000.0000.0000.000
139A110ALA0-0.034-0.02325.159-0.004-0.0040.0000.0000.0000.000
140A111ASP-1-0.868-0.94026.324-0.065-0.0650.0000.0000.0000.000
141A112GLY00.0480.03123.865-0.005-0.0050.0000.0000.0000.000
142A113MET0-0.090-0.01721.533-0.001-0.0010.0000.0000.0000.000
143A114VAL00.0310.02923.7440.0050.0050.0000.0000.0000.000
144A115GLY0-0.010-0.00226.315-0.007-0.0070.0000.0000.0000.000
145A116ASN0-0.022-0.01520.936-0.012-0.0120.0000.0000.0000.000
146A117PRO00.0380.01819.445-0.001-0.0010.0000.0000.0000.000
147A118GLN00.0680.03514.6250.0380.0380.0000.0000.0000.000
148A119GLY00.004-0.00216.588-0.012-0.0120.0000.0000.0000.000
149A120GLN0-0.018-0.03818.4510.0130.0130.0000.0000.0000.000
150A121ALA0-0.0070.00013.7620.0150.0150.0000.0000.0000.000
151A122ALA0-0.0220.00114.0030.0080.0080.0000.0000.0000.000
152A123LEU0-0.042-0.01715.050-0.004-0.0040.0000.0000.0000.000
153A124LEU0-0.073-0.03018.0260.0100.0100.0000.0000.0000.000
154A125ARG10.9390.96616.528-0.015-0.0150.0000.0000.0000.000
155A126PRO00.0690.01614.0430.0030.0030.0000.0000.0000.000
156A127GLY00.0180.00716.7080.0030.0030.0000.0000.0000.000
157A128GLU-1-0.752-0.84720.0640.0220.0220.0000.0000.0000.000
158A129LEU00.0280.02815.892-0.006-0.0060.0000.0000.0000.000
159A130VAL00.0120.01919.398-0.001-0.0010.0000.0000.0000.000
160A131ALA0-0.0040.00821.757-0.008-0.0080.0000.0000.0000.000
161A132ILE0-0.0110.00221.854-0.006-0.0060.0000.0000.0000.000
162A133THR00.0520.00621.880-0.009-0.0090.0000.0000.0000.000
163A134ALA00.0300.03424.460-0.004-0.0040.0000.0000.0000.000
164A135SER0-0.012-0.02726.951-0.009-0.0090.0000.0000.0000.000
165A136ALA0-0.023-0.00527.035-0.007-0.0070.0000.0000.0000.000
166A137LEU00.0580.01827.269-0.007-0.0070.0000.0000.0000.000
167A138GLN0-0.041-0.02329.763-0.009-0.0090.0000.0000.0000.000
168A139ALA00.0220.01132.615-0.004-0.0040.0000.0000.0000.000
169A140PHE00.0220.01032.032-0.005-0.0050.0000.0000.0000.000
170A141ARG10.9000.95530.866-0.100-0.1000.0000.0000.0000.000
171A142GLU-1-0.929-0.96936.0340.0510.0510.0000.0000.0000.000
172A143VAL0-0.009-0.00937.136-0.004-0.0040.0000.0000.0000.000
173A144ALA0-0.0090.00437.044-0.003-0.0030.0000.0000.0000.000
174A145ARG10.8690.91339.052-0.055-0.0550.0000.0000.0000.000
175A146LEU0-0.072-0.02141.647-0.002-0.0020.0000.0000.0000.000
176A147ALA00.0150.00442.242-0.003-0.0030.0000.0000.0000.000