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: 16N4Z

Calculation Name: 1P9Q-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P9Q

Chain ID: C

ChEMBL ID:

UniProt ID: O29759

Base Structure: X-ray

Registration Date: 2023-09-27

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2579284.253647
FMO2-HF: Nuclear repulsion 2487384.763362
FMO2-HF: Total energy -91899.490285
FMO2-MP2: Total energy -92170.074665


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(C:2:VAL)


Summations of interaction energy for fragment #1(C:2:VAL)
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.
-19.513-12.2399.551-3.256-13.571-0.028
Interaction energy analysis for fragmet #1(C:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.001
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].
3C4LEU00.0750.0232.873-2.4440.1890.323-1.334-1.623-0.002
4C5ASP-1-0.845-0.8975.0460.9071.043-0.001-0.006-0.1290.000
5C6LYS10.8010.8852.813-5.031-4.0340.258-0.277-0.9770.002
6C7ALA0-0.0340.0062.707-1.0180.1330.306-0.413-1.045-0.001
7C8VAL0-0.016-0.0013.5550.1050.1640.0330.087-0.1790.000
8C9ILE00.0030.0106.882-0.309-0.3090.0000.0000.0000.000
9C10ALA0-0.0230.0079.5990.0970.0970.0000.0000.0000.000
10C11ARG10.7850.86311.0700.2950.2950.0000.0000.0000.000
11C12LEU00.0310.01414.5290.0290.0290.0000.0000.0000.000
12C13ARG10.8150.92117.5240.2180.2180.0000.0000.0000.000
13C14LYS10.9150.95221.0140.3130.3130.0000.0000.0000.000
14C15GLY00.0210.00422.8980.0010.0010.0000.0000.0000.000
15C16GLY0-0.025-0.01426.1460.0070.0070.0000.0000.0000.000
16C17GLU-1-0.849-0.89622.378-0.216-0.2160.0000.0000.0000.000
17C18GLU-1-0.788-0.86318.930-0.272-0.2720.0000.0000.0000.000
18C19PHE00.025-0.00116.2430.0000.0000.0000.0000.0000.000
19C20GLU-1-0.756-0.88712.444-0.399-0.3990.0000.0000.0000.000
20C21VAL00.0440.0318.5420.0010.0010.0000.0000.0000.000
21C22LEU00.0180.0105.5300.1470.1470.0000.0000.0000.000
22C23VAL00.009-0.0073.488-0.748-0.4700.009-0.059-0.2290.000
23C24ASP-1-0.754-0.8692.127-2.827-0.5264.481-2.699-4.083-0.009
24C25PRO0-0.012-0.0192.9021.9890.4170.1771.905-0.5110.000
25C26TYR0-0.107-0.0815.6890.1030.1030.0000.0000.0000.000
26C27LEU00.0210.0184.5690.0700.186-0.001-0.005-0.1100.000
27C28ALA00.0260.0056.9230.1570.1570.0000.0000.0000.000
28C29ARG10.7900.8758.5640.4810.4810.0000.0000.0000.000
29C30ASP-1-0.787-0.88310.664-0.349-0.3490.0000.0000.0000.000
30C31LEU00.0450.03110.7680.0950.0950.0000.0000.0000.000
31C32LYS10.8230.91412.6930.5540.5540.0000.0000.0000.000
32C33GLU-1-0.872-0.91714.763-0.205-0.2050.0000.0000.0000.000
33C34GLY0-0.056-0.02315.9990.0570.0570.0000.0000.0000.000
34C35LYS10.7270.87313.8920.3650.3650.0000.0000.0000.000
35C36GLU-1-0.903-0.95514.888-0.610-0.6100.0000.0000.0000.000
36C37VAL0-0.049-0.0288.675-0.019-0.0190.0000.0000.0000.000
37C38ASN0-0.011-0.0068.4770.0530.0530.0000.0000.0000.000
38C39PHE0-0.005-0.0357.662-0.414-0.4140.0000.0000.0000.000
39C40GLU-1-0.901-0.9406.626-1.490-1.4900.0000.0000.0000.000
40C41ASP-1-0.895-0.9344.062-1.986-1.852-0.001-0.023-0.1100.000
41C42LEU0-0.099-0.0432.747-5.545-3.7650.474-0.928-1.326-0.010
42C43LEU0-0.017-0.0133.129-1.808-0.6610.139-0.583-0.702-0.005
43C44ALA0-0.002-0.0012.228-2.447-1.8543.148-1.475-2.266-0.002
44C45ALA0-0.017-0.0232.7733.2860.8070.2062.554-0.281-0.001
45C46GLU-1-0.948-0.9616.558-1.028-1.0280.0000.0000.0000.000
46C47GLU-1-0.839-0.9169.336-0.389-0.3890.0000.0000.0000.000
47C48VAL00.0010.00810.631-0.105-0.1050.0000.0000.0000.000
48C49PHE0-0.019-0.0089.4130.1080.1080.0000.0000.0000.000
49C50LYS10.7930.87114.3810.2850.2850.0000.0000.0000.000
50C51ASP-1-0.820-0.91916.268-0.239-0.2390.0000.0000.0000.000
51C52ALA00.0010.00110.7360.0100.0100.0000.0000.0000.000
52C53LYS10.7940.89812.6760.3280.3280.0000.0000.0000.000
53C54LYS10.8040.89613.9070.2440.2440.0000.0000.0000.000
54C55GLY00.0150.02214.0030.0240.0240.0000.0000.0000.000
55C56GLU-1-0.932-0.96315.050-0.229-0.2290.0000.0000.0000.000
56C57ARG10.8850.92613.9920.3870.3870.0000.0000.0000.000
57C58ALA0-0.0160.00216.2480.0510.0510.0000.0000.0000.000
58C59SER00.0230.00518.152-0.017-0.0170.0000.0000.0000.000
59C60VAL00.0670.01919.884-0.009-0.0090.0000.0000.0000.000
60C61ASP-1-0.875-0.93821.488-0.224-0.2240.0000.0000.0000.000
61C62GLU-1-0.843-0.90322.094-0.250-0.2500.0000.0000.0000.000
62C63LEU0-0.008-0.00516.9500.0020.0020.0000.0000.0000.000
63C64ARG10.8570.91921.1130.2780.2780.0000.0000.0000.000
64C65LYS10.8310.92324.0140.2400.2400.0000.0000.0000.000
65C66ILE0-0.068-0.03521.8930.0150.0150.0000.0000.0000.000
66C67PHE0-0.035-0.04618.1030.0020.0020.0000.0000.0000.000
67C68GLY0-0.0020.02422.090-0.004-0.0040.0000.0000.0000.000
68C69THR0-0.032-0.02819.4850.0120.0120.0000.0000.0000.000
69C70ASP-1-0.842-0.93219.740-0.346-0.3460.0000.0000.0000.000
70C71ASP-1-0.847-0.89715.663-0.687-0.6870.0000.0000.0000.000
71C72VAL00.0580.01311.115-0.005-0.0050.0000.0000.0000.000
72C73PHE00.0360.0209.200-0.114-0.1140.0000.0000.0000.000
73C74GLU-1-0.906-0.94712.607-0.449-0.4490.0000.0000.0000.000
74C75ILE0-0.046-0.03614.7530.0180.0180.0000.0000.0000.000
75C76ALA00.0240.0089.7430.0240.0240.0000.0000.0000.000
76C77ARG10.9360.97211.8790.6780.6780.0000.0000.0000.000
77C78LYS10.8200.88413.3380.4450.4450.0000.0000.0000.000
78C79ILE0-0.022-0.00512.6620.0640.0640.0000.0000.0000.000
79C80ILE00.0150.0168.6650.0650.0650.0000.0000.0000.000
80C81LEU0-0.067-0.03712.6390.0870.0870.0000.0000.0000.000
81C82GLU-1-0.847-0.91615.900-0.323-0.3230.0000.0000.0000.000
82C83GLY0-0.0210.01616.1530.0460.0460.0000.0000.0000.000
83C84GLU-1-0.950-0.96515.557-0.252-0.2520.0000.0000.0000.000
84C85VAL00.031-0.0049.520-0.049-0.0490.0000.0000.0000.000
85C86GLN0-0.098-0.05911.4610.0790.0790.0000.0000.0000.000
86C87ILE0-0.0220.0069.2380.0250.0250.0000.0000.0000.000
87C88THR00.0600.0179.9110.0040.0040.0000.0000.0000.000
88C89ALA0-0.002-0.01512.391-0.015-0.0150.0000.0000.0000.000
89C90GLU-1-0.777-0.86713.5680.1730.1730.0000.0000.0000.000
90C91GLN00.1060.0617.055-0.146-0.1460.0000.0000.0000.000
91C92ARG10.9370.96312.0580.1150.1150.0000.0000.0000.000
92C93ARG10.8370.89314.800-0.153-0.1530.0000.0000.0000.000
93C94GLU-1-0.846-0.90411.6900.2740.2740.0000.0000.0000.000
94C95MET00.002-0.00411.369-0.028-0.0280.0000.0000.0000.000
95C96LEU0-0.033-0.00914.996-0.015-0.0150.0000.0000.0000.000
96C97GLU-1-0.868-0.91218.4870.0440.0440.0000.0000.0000.000
97C98ALA00.0150.00016.535-0.002-0.0020.0000.0000.0000.000
98C99LYS10.7810.88417.8750.1630.1630.0000.0000.0000.000
99C100ARG10.9890.99019.7740.0070.0070.0000.0000.0000.000
100C101LYS10.9080.93421.871-0.051-0.0510.0000.0000.0000.000
101C102GLN00.0150.01618.055-0.012-0.0120.0000.0000.0000.000
102C103ILE00.0240.01223.159-0.004-0.0040.0000.0000.0000.000
103C104ILE00.0070.01525.4960.0000.0000.0000.0000.0000.000
104C105ASN0-0.063-0.03725.8830.0060.0060.0000.0000.0000.000
105C106PHE00.0030.00926.4660.0020.0020.0000.0000.0000.000
106C107ILE00.019-0.00228.4440.0000.0000.0000.0000.0000.000
107C108SER0-0.072-0.02131.1510.0020.0020.0000.0000.0000.000
108C109ARG10.9770.97726.1550.0110.0110.0000.0000.0000.000
109C110ASN0-0.074-0.04429.997-0.001-0.0010.0000.0000.0000.000
110C111THR0-0.095-0.06333.880-0.004-0.0040.0000.0000.0000.000
111C112ILE00.011-0.01436.6200.0040.0040.0000.0000.0000.000
112C113ASP-1-0.870-0.97539.968-0.014-0.0140.0000.0000.0000.000
113C114PRO0-0.059-0.03642.3970.0020.0020.0000.0000.0000.000
114C115ARG10.9030.94345.7360.0090.0090.0000.0000.0000.000
115C116THR0-0.018-0.01846.1000.0010.0010.0000.0000.0000.000
116C117ASN0-0.0200.01445.6390.0000.0000.0000.0000.0000.000
117C118ALA00.0530.02042.4080.0020.0020.0000.0000.0000.000
118C119PRO00.0360.08137.250-0.003-0.0030.0000.0000.0000.000
119C120HIS00.0290.02536.4430.0060.0060.0000.0000.0000.000
120C121PRO00.0640.04135.694-0.001-0.0010.0000.0000.0000.000
121C122PRO00.0920.01730.328-0.003-0.0030.0000.0000.0000.000
122C123SER00.0250.02132.219-0.004-0.0040.0000.0000.0000.000
123C124ARG10.8000.91033.7190.0060.0060.0000.0000.0000.000
124C125ILE00.004-0.00230.974-0.004-0.0040.0000.0000.0000.000
125C126GLU-1-0.905-0.97427.8870.0120.0120.0000.0000.0000.000
126C127ARG10.9710.98931.265-0.010-0.0100.0000.0000.0000.000
127C128ALA0-0.0060.00334.242-0.002-0.0020.0000.0000.0000.000
128C129LEU0-0.018-0.01627.916-0.005-0.0050.0000.0000.0000.000
129C130GLU-1-0.931-0.95830.3390.0050.0050.0000.0000.0000.000
130C131GLU-1-0.838-0.92432.159-0.010-0.0100.0000.0000.0000.000
131C132ALA0-0.027-0.01034.205-0.001-0.0010.0000.0000.0000.000
132C133LYS10.8720.93631.4110.0290.0290.0000.0000.0000.000
133C134VAL0-0.0130.00028.170-0.007-0.0070.0000.0000.0000.000
134C135HIS0-0.0010.00722.8570.0140.0140.0000.0000.0000.000
135C136ILE0-0.032-0.02421.518-0.003-0.0030.0000.0000.0000.000
136C137ASP-1-0.838-0.91219.846-0.203-0.2030.0000.0000.0000.000
137C138ILE0-0.010-0.01215.0280.0020.0020.0000.0000.0000.000
138C139PHE00.0130.00412.327-0.012-0.0120.0000.0000.0000.000
139C140LYS10.9430.98616.9320.1720.1720.0000.0000.0000.000
140C141SER00.0800.04119.8950.0220.0220.0000.0000.0000.000
141C142VAL00.0420.01320.7430.0130.0130.0000.0000.0000.000
142C143GLU-1-0.880-0.96622.914-0.130-0.1300.0000.0000.0000.000
143C144ALA0-0.033-0.00223.3630.0080.0080.0000.0000.0000.000
144C145GLN0-0.024-0.02421.4590.0150.0150.0000.0000.0000.000
145C146VAL0-0.023-0.00726.4370.0120.0120.0000.0000.0000.000
146C147LYS10.9730.97128.5720.1050.1050.0000.0000.0000.000
147C148ASP-1-0.856-0.92629.851-0.088-0.0880.0000.0000.0000.000
148C149ILE00.0440.02726.1460.0070.0070.0000.0000.0000.000
149C150VAL00.0610.02830.7640.0080.0080.0000.0000.0000.000
150C151LYS10.7260.87333.6940.0880.0880.0000.0000.0000.000
151C152ALA00.0250.01732.9570.0000.0000.0000.0000.0000.000
152C153LEU0-0.0010.00432.2140.0040.0040.0000.0000.0000.000
153C154LYS10.8490.93836.1050.0480.0480.0000.0000.0000.000
154C155PRO0-0.006-0.01238.6080.0030.0030.0000.0000.0000.000
155C156ILE0-0.0010.01436.7960.0020.0020.0000.0000.0000.000
156C157LEU0-0.028-0.00336.0130.0040.0040.0000.0000.0000.000
157C158PRO0-0.0160.00939.354-0.004-0.0040.0000.0000.0000.000
158C159LEU00.022-0.00434.5570.0020.0020.0000.0000.0000.000
159C160LYS10.8270.91239.0210.0300.0300.0000.0000.0000.000
160C161PHE00.0290.01032.1650.0020.0020.0000.0000.0000.000
161C162GLU-1-0.861-0.93837.646-0.027-0.0270.0000.0000.0000.000
162C163GLU-1-0.749-0.81336.716-0.052-0.0520.0000.0000.0000.000
163C164MET0-0.056-0.02539.3580.0020.0020.0000.0000.0000.000
164C165GLU-1-0.806-0.87841.103-0.038-0.0380.0000.0000.0000.000
165C166ILE0-0.017-0.02142.1570.0020.0020.0000.0000.0000.000
166C167ALA0-0.0020.01044.581-0.001-0.0010.0000.0000.0000.000
167C168ILE00.026-0.00443.3590.0020.0020.0000.0000.0000.000
168C169LYS10.9190.96646.8510.0020.0020.0000.0000.0000.000
169C170ILE0-0.033-0.02444.7800.0020.0020.0000.0000.0000.000
170C171PRO00.0390.02048.326-0.001-0.0010.0000.0000.0000.000
171C172PRO00.020-0.00449.6770.0010.0010.0000.0000.0000.000
172C173GLU-1-0.871-0.94449.9150.0110.0110.0000.0000.0000.000
173C174HIS0-0.004-0.00446.4440.0030.0030.0000.0000.0000.000
174C175THR0-0.051-0.01545.1960.0010.0010.0000.0000.0000.000
175C176GLY00.0180.01443.589-0.001-0.0010.0000.0000.0000.000
176C177ARG10.8280.88840.138-0.029-0.0290.0000.0000.0000.000
177C178ALA00.0110.00540.7690.0010.0010.0000.0000.0000.000
178C179ILE00.0270.01840.077-0.001-0.0010.0000.0000.0000.000
179C180SER00.0000.00836.333-0.003-0.0030.0000.0000.0000.000
180C181ALA00.0360.01035.685-0.002-0.0020.0000.0000.0000.000
181C182LEU00.0160.00335.589-0.002-0.0020.0000.0000.0000.000
182C183TYR0-0.057-0.06434.419-0.003-0.0030.0000.0000.0000.000
183C184ASN0-0.068-0.02630.279-0.004-0.0040.0000.0000.0000.000
184C185PHE0-0.076-0.02931.348-0.001-0.0010.0000.0000.0000.000
185C186GLY00.0370.03432.465-0.004-0.0040.0000.0000.0000.000
186C187GLY00.032-0.00733.3250.0020.0020.0000.0000.0000.000
187C188VAL0-0.019-0.00636.0250.0000.0000.0000.0000.0000.000
188C189THR0-0.010-0.00738.005-0.005-0.0050.0000.0000.0000.000
189C190ARG10.8640.90840.6590.0360.0360.0000.0000.0000.000
190C191GLU-1-0.822-0.87239.528-0.026-0.0260.0000.0000.0000.000
191C192GLU-1-0.899-0.94843.920-0.019-0.0190.0000.0000.0000.000
192C193TRP0-0.001-0.01044.0880.0020.0020.0000.0000.0000.000
193C194GLN0-0.072-0.04048.609-0.001-0.0010.0000.0000.0000.000
194C195ARG10.9550.96452.2880.0070.0070.0000.0000.0000.000
195C196ASP-1-0.836-0.89954.534-0.001-0.0010.0000.0000.0000.000
196C197GLY00.0500.04251.7740.0020.0020.0000.0000.0000.000
197C198SER0-0.083-0.05650.4890.0010.0010.0000.0000.0000.000
198C199TRP00.0590.00241.385-0.001-0.0010.0000.0000.0000.000
199C200ILE0-0.0200.00347.4090.0020.0020.0000.0000.0000.000
200C201CYS00.0050.02341.985-0.001-0.0010.0000.0000.0000.000
201C202VAL0-0.051-0.02243.4550.0010.0010.0000.0000.0000.000
202C203MET0-0.0020.02837.365-0.003-0.0030.0000.0000.0000.000
203C204ARG10.7670.83637.9680.0490.0490.0000.0000.0000.000
204C205ILE00.0020.00736.341-0.001-0.0010.0000.0000.0000.000
205C206PRO00.0810.04733.207-0.001-0.0010.0000.0000.0000.000
206C207SER00.000-0.04536.3580.0040.0040.0000.0000.0000.000
207C208GLY0-0.0080.00936.5870.0040.0040.0000.0000.0000.000
208C209MET00.0000.00932.9730.0030.0030.0000.0000.0000.000
209C210TYR0-0.020-0.02136.7320.0030.0030.0000.0000.0000.000
210C211GLY0-0.004-0.01340.2070.0020.0020.0000.0000.0000.000
211C212ASP-1-0.825-0.90835.6410.0110.0110.0000.0000.0000.000
212C213LEU0-0.045-0.01938.1230.0020.0020.0000.0000.0000.000
213C214MET0-0.042-0.03439.6410.0010.0010.0000.0000.0000.000
214C215ASP-1-0.873-0.92340.0670.0190.0190.0000.0000.0000.000
215C216LEU0-0.062-0.02336.5250.0030.0030.0000.0000.0000.000
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