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: 145GZ

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1545024.564983
FMO2-HF: Nuclear repulsion 1479438.375251
FMO2-HF: Total energy -65586.189732
FMO2-MP2: Total energy -65777.553479


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.
-0.950.6780.016-0.682-0.962-0.002
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 : 0.038 / q_NPA : 0.014
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-26THR00.0320.0283.5770.7301.7480.001-0.386-0.6330.000
4A-25SER0-0.023-0.0035.7710.5360.5360.0000.0000.0000.000
5A-24PRO0-0.036-0.0107.6060.1280.1280.0000.0000.0000.000
6A-23GLY00.0800.0309.1100.1540.1540.0000.0000.0000.000
7A-22PRO0-0.033-0.0157.642-0.232-0.2320.0000.0000.0000.000
8A-21ALA0-0.0190.0097.9530.2240.2240.0000.0000.0000.000
9A-20LEU0-0.004-0.0018.3350.1870.1870.0000.0000.0000.000
10A-19THR00.011-0.0029.096-0.196-0.1960.0000.0000.0000.000
11A-18ASP-1-0.772-0.8857.031-1.619-1.6190.0000.0000.0000.000
12A-17TRP00.014-0.0188.7620.1700.1700.0000.0000.0000.000
13A-16ALA0-0.026-0.0077.5680.1580.1580.0000.0000.0000.000
14A-15ARG10.9340.9505.8711.2091.2090.0000.0000.0000.000
15A-14VAL0-0.0080.01010.5810.1120.1120.0000.0000.0000.000
16A-13ARG10.8500.91412.7710.3480.3480.0000.0000.0000.000
17A-12GLU-1-0.905-0.97610.166-0.238-0.2380.0000.0000.0000.000
18A-11GLU-1-0.930-0.95114.465-0.223-0.2230.0000.0000.0000.000
19A-10LEU0-0.018-0.02516.5600.0340.0340.0000.0000.0000.000
20A-9ALA00.0110.02317.6320.0220.0220.0000.0000.0000.000
21A-8SER0-0.112-0.02618.3880.0240.0240.0000.0000.0000.000
22A-7THR0-0.043-0.05420.3010.0090.0090.0000.0000.0000.000
23A-6GLY00.0030.01622.983-0.006-0.0060.0000.0000.0000.000
24A-5PRO00.017-0.00824.510-0.007-0.0070.0000.0000.0000.000
25A-4PRO0-0.028-0.00726.427-0.003-0.0030.0000.0000.0000.000
26A-3VAL00.0160.02623.9760.0020.0020.0000.0000.0000.000
27A-2VAL00.030-0.00221.5530.0030.0030.0000.0000.0000.000
28A-1ALA00.0330.04416.861-0.019-0.0190.0000.0000.0000.000
29A0MET0-0.095-0.06518.285-0.002-0.0020.0000.0000.0000.000
30A1PRO00.0390.04615.0350.0100.0100.0000.0000.0000.000
31A2VAL00.016-0.01916.082-0.008-0.0080.0000.0000.0000.000
32A3VAL0-0.043-0.01010.276-0.046-0.0460.0000.0000.0000.000
33A4ILE00.0040.00111.9730.0290.0290.0000.0000.0000.000
34A5LYS10.8720.9326.2360.8050.8050.0000.0000.0000.000
35A6THR00.0310.0278.3570.0760.0760.0000.0000.0000.000
36A7GLU-1-0.906-0.9623.417-3.492-2.8820.015-0.296-0.329-0.002
37A8GLY00.0050.0005.7030.1520.1520.0000.0000.0000.000
38A9PRO0-0.011-0.0016.532-0.075-0.0750.0000.0000.0000.000
39A10ALA00.0240.0129.7970.0700.0700.0000.0000.0000.000
40A11TRP0-0.017-0.00112.1180.0100.0100.0000.0000.0000.000
41A12THR0-0.009-0.01213.4110.0460.0460.0000.0000.0000.000
42A13PRO0-0.0080.00914.000-0.025-0.0250.0000.0000.0000.000
43A14LEU00.0320.00817.0230.0170.0170.0000.0000.0000.000
44A15GLU-1-0.814-0.91120.0830.0360.0360.0000.0000.0000.000
45A16PRO00.0400.00521.4270.0000.0000.0000.0000.0000.000
46A17LYS10.9560.97524.546-0.032-0.0320.0000.0000.0000.000
47A18LEU00.0250.00722.671-0.001-0.0010.0000.0000.0000.000
48A19ILE00.0150.00923.578-0.001-0.0010.0000.0000.0000.000
49A20THR0-0.071-0.03327.290-0.003-0.0030.0000.0000.0000.000
50A21ARG10.8800.93127.842-0.061-0.0610.0000.0000.0000.000
51A22LEU00.0240.03628.5930.0000.0000.0000.0000.0000.000
52A23ALA00.0290.01331.090-0.002-0.0020.0000.0000.0000.000
53A24ASP-1-0.878-0.95133.4520.0210.0210.0000.0000.0000.000
54A25THR0-0.093-0.06433.267-0.003-0.0030.0000.0000.0000.000
55A26VAL0-0.040-0.03533.671-0.001-0.0010.0000.0000.0000.000
56A27ARG10.8440.93036.557-0.017-0.0170.0000.0000.0000.000
57A28THR0-0.033-0.02838.6690.0000.0000.0000.0000.0000.000
58A29LYS10.8860.95438.287-0.033-0.0330.0000.0000.0000.000
59A30GLY00.0590.05540.4350.0010.0010.0000.0000.0000.000
60A31LEU00.0400.01736.7320.0010.0010.0000.0000.0000.000
61A32ARG10.8930.94038.587-0.023-0.0230.0000.0000.0000.000
62A33SER0-0.038-0.01638.7470.0020.0020.0000.0000.0000.000
63A34PRO00.0520.01138.0760.0010.0010.0000.0000.0000.000
64A35ILE00.0120.01535.3380.0040.0040.0000.0000.0000.000
65A36THR00.0400.02734.1740.0040.0040.0000.0000.0000.000
66A37MET0-0.0200.01132.5280.0010.0010.0000.0000.0000.000
67A38ALA00.0050.00032.1040.0040.0040.0000.0000.0000.000
68A39GLU-1-0.787-0.87629.4530.0630.0630.0000.0000.0000.000
69A40VAL0-0.032-0.01828.4260.0040.0040.0000.0000.0000.000
70A41GLU-1-0.823-0.92827.5860.0710.0710.0000.0000.0000.000
71A42ALA0-0.0200.00125.9590.0070.0070.0000.0000.0000.000
72A43LEU0-0.0310.00322.8050.0120.0120.0000.0000.0000.000
73A44MET0-0.083-0.03023.179-0.002-0.0020.0000.0000.0000.000
74A45SER00.004-0.00622.2500.0030.0030.0000.0000.0000.000
75A46SER0-0.041-0.01417.5570.0230.0230.0000.0000.0000.000
76A47PRO0-0.021-0.01816.882-0.021-0.0210.0000.0000.0000.000
77A48LEU00.0250.01417.9480.0060.0060.0000.0000.0000.000
78A49LEU00.0030.01216.297-0.006-0.0060.0000.0000.0000.000
79A50PRO00.008-0.00320.1500.0030.0030.0000.0000.0000.000
80A51HIS00.0140.01121.9260.0000.0000.0000.0000.0000.000
81A52ASP-1-0.800-0.90519.5190.0130.0130.0000.0000.0000.000
82A53VAL0-0.0190.01023.1170.0030.0030.0000.0000.0000.000
83A54THR0-0.007-0.01325.5600.0000.0000.0000.0000.0000.000
84A55ASN0-0.076-0.05025.509-0.001-0.0010.0000.0000.0000.000
85A56LEU00.0050.01425.4610.0000.0000.0000.0000.0000.000
86A57MET00.010-0.00727.8070.0010.0010.0000.0000.0000.000
87A58ARG10.8950.95230.7760.0080.0080.0000.0000.0000.000
88A59VAL0-0.060-0.02529.945-0.002-0.0020.0000.0000.0000.000
89A60ILE0-0.026-0.01130.6300.0000.0000.0000.0000.0000.000
90A61LEU0-0.020-0.00433.6920.0000.0000.0000.0000.0000.000
91A62GLY00.0340.03735.887-0.001-0.0010.0000.0000.0000.000
92A63PRO0-0.021-0.04737.9350.0000.0000.0000.0000.0000.000
93A64ALA00.0220.01039.4820.0000.0000.0000.0000.0000.000
94A65PRO00.0520.02538.633-0.001-0.0010.0000.0000.0000.000
95A66TYR00.0300.01931.861-0.001-0.0010.0000.0000.0000.000
96A67ALA00.0260.02236.2380.0000.0000.0000.0000.0000.000
97A68LEU00.0490.02838.3400.0000.0000.0000.0000.0000.000
98A69TRP0-0.016-0.01129.136-0.001-0.0010.0000.0000.0000.000
99A70MET0-0.004-0.00132.4610.0010.0010.0000.0000.0000.000
100A71ASP-1-0.909-0.94935.0280.0020.0020.0000.0000.0000.000
101A72ALA0-0.036-0.02836.5190.0010.0010.0000.0000.0000.000
102A73TRP0-0.016-0.03026.8230.0000.0000.0000.0000.0000.000
103A74GLY00.003-0.00432.4350.0000.0000.0000.0000.0000.000
104A75VAL00.0170.01034.1780.0000.0000.0000.0000.0000.000
105A76GLN0-0.003-0.01332.3790.0030.0030.0000.0000.0000.000
106A77LEU00.0030.00727.9030.0010.0010.0000.0000.0000.000
107A78GLN0-0.034-0.02131.397-0.001-0.0010.0000.0000.0000.000
108A79THR0-0.067-0.02033.5570.0000.0000.0000.0000.0000.000
109A80VAL00.0350.00627.4070.0020.0020.0000.0000.0000.000
110A81ILE0-0.021-0.00929.402-0.001-0.0010.0000.0000.0000.000
111A82ALA00.0000.02431.607-0.003-0.0030.0000.0000.0000.000
112A83ALA00.0040.00230.493-0.001-0.0010.0000.0000.0000.000
113A84ALA00.0260.02728.3110.0020.0020.0000.0000.0000.000
114A85THR0-0.023-0.02229.421-0.004-0.0040.0000.0000.0000.000
115A86ARG10.8120.89532.360-0.009-0.0090.0000.0000.0000.000
116A87ASP-1-0.763-0.87828.6120.0300.0300.0000.0000.0000.000
117A88PRO0-0.048-0.02728.523-0.002-0.0020.0000.0000.0000.000
118A89ARG10.9170.93825.425-0.026-0.0260.0000.0000.0000.000
119A90HIS00.0560.05524.8620.0060.0060.0000.0000.0000.000
120A91PRO00.0390.00521.023-0.006-0.0060.0000.0000.0000.000
121A92ALA0-0.0060.00921.084-0.003-0.0030.0000.0000.0000.000
122A93ASN0-0.053-0.03623.134-0.017-0.0170.0000.0000.0000.000
123A94GLY0-0.014-0.01320.7240.0050.0050.0000.0000.0000.000
124A95GLN0-0.050-0.02019.4070.0110.0110.0000.0000.0000.000
125A96GLY00.0260.02122.2690.0030.0030.0000.0000.0000.000
126A97ARG10.9250.94224.4280.0390.0390.0000.0000.0000.000
127A98GLY00.0360.01927.0080.0040.0040.0000.0000.0000.000
128A99GLU-1-0.876-0.91520.914-0.066-0.0660.0000.0000.0000.000
129A100ARG10.9220.96324.1980.0210.0210.0000.0000.0000.000
130A101THR0-0.0070.00224.568-0.004-0.0040.0000.0000.0000.000
131A102ASN00.019-0.00526.4670.0010.0010.0000.0000.0000.000
132A103LEU00.0650.02528.2540.0000.0000.0000.0000.0000.000
133A104ASN00.0440.01029.3270.0040.0040.0000.0000.0000.000
134A105ARG10.7660.84820.3300.0490.0490.0000.0000.0000.000
135A106LEU00.0180.00924.6830.0000.0000.0000.0000.0000.000
136A107LYS10.9710.98925.8540.0110.0110.0000.0000.0000.000
137A108GLY00.0010.00024.4700.0000.0000.0000.0000.0000.000
138A109LEU0-0.049-0.04425.274-0.004-0.0040.0000.0000.0000.000
139A110ALA0-0.041-0.02225.229-0.003-0.0030.0000.0000.0000.000
140A111ASP-1-0.856-0.93826.325-0.079-0.0790.0000.0000.0000.000
141A112GLY00.0390.03023.865-0.006-0.0060.0000.0000.0000.000
142A113MET0-0.089-0.01921.239-0.003-0.0030.0000.0000.0000.000
143A114VAL00.0400.03523.7450.0050.0050.0000.0000.0000.000
144A115GLY0-0.017-0.00426.316-0.005-0.0050.0000.0000.0000.000
145A116ASN0-0.020-0.01420.974-0.010-0.0100.0000.0000.0000.000
146A117PRO00.0430.02019.397-0.004-0.0040.0000.0000.0000.000
147A118GLN00.0530.03113.9190.0220.0220.0000.0000.0000.000
148A119GLY00.0160.00516.588-0.015-0.0150.0000.0000.0000.000
149A120GLN0-0.034-0.05118.4520.0070.0070.0000.0000.0000.000
150A121ALA0-0.0020.00213.8060.0090.0090.0000.0000.0000.000
151A122ALA0-0.0240.00014.000-0.004-0.0040.0000.0000.0000.000
152A123LEU0-0.024-0.00715.050-0.005-0.0050.0000.0000.0000.000
153A124LEU0-0.061-0.01718.0490.0100.0100.0000.0000.0000.000
154A125ARG10.9300.95916.5300.0270.0270.0000.0000.0000.000
155A126PRO00.0700.01313.8850.0090.0090.0000.0000.0000.000
156A127GLY00.0140.00516.6660.0080.0080.0000.0000.0000.000
157A128GLU-1-0.749-0.84320.009-0.024-0.0240.0000.0000.0000.000
158A129LEU00.0390.02816.1470.0010.0010.0000.0000.0000.000
159A130VAL00.0070.02319.2870.0040.0040.0000.0000.0000.000
160A131ALA0-0.0020.00821.761-0.002-0.0020.0000.0000.0000.000
161A132ILE0-0.007-0.00521.893-0.002-0.0020.0000.0000.0000.000
162A133THR00.034-0.00421.897-0.004-0.0040.0000.0000.0000.000
163A134ALA00.0270.03424.4650.0000.0000.0000.0000.0000.000
164A135SER0-0.012-0.02026.956-0.004-0.0040.0000.0000.0000.000
165A136ALA0-0.026-0.00827.006-0.003-0.0030.0000.0000.0000.000
166A137LEU00.0660.02727.525-0.003-0.0030.0000.0000.0000.000
167A138GLN0-0.014-0.00729.7680.0000.0000.0000.0000.0000.000
168A139ALA00.0110.00632.621-0.002-0.0020.0000.0000.0000.000
169A140PHE00.0290.00932.059-0.003-0.0030.0000.0000.0000.000
170A141ARG10.8600.91431.119-0.062-0.0620.0000.0000.0000.000
171A142GLU-1-0.889-0.93736.0290.0270.0270.0000.0000.0000.000
172A143VAL0-0.006-0.01037.152-0.002-0.0020.0000.0000.0000.000
173A144ALA0-0.0070.00637.016-0.001-0.0010.0000.0000.0000.000
174A145ARG10.8310.89938.795-0.032-0.0320.0000.0000.0000.000
175A146LEU0-0.057-0.00541.666-0.001-0.0010.0000.0000.0000.000
176A147ALA0-0.017-0.00742.256-0.002-0.0020.0000.0000.0000.000