FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: N1K3Q

Calculation Name: 2NRA-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NRA

Chain ID: C

ChEMBL ID:

UniProt ID: P03067

Base Structure: X-ray

Registration Date: 2023-06-19

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 252
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3428489.505992
FMO2-HF: Nuclear repulsion 3328945.030951
FMO2-HF: Total energy -99544.475042
FMO2-MP2: Total energy -99842.783016


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:9:VAL)


Summations of interaction energy for fragment #1(C:9: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.
-3.6832.2570.742-3.225-3.4550.011
Interaction energy analysis for fragmet #1(C:9:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.118 / q_NPA : 0.068
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].
3C11LYS10.9770.9753.454-3.826-0.845-0.001-1.854-1.1250.008
4C12LYS10.9280.9676.2010.8040.8040.0000.0000.0000.000
5C13THR00.005-0.0092.298-0.6921.1310.697-1.113-1.4070.003
6C14LYS10.8490.9265.4341.1871.1870.0000.0000.0000.000
7C15ILE00.0220.0406.823-0.143-0.1430.0000.0000.0000.000
8C16ARG10.8460.9028.8600.3360.3360.0000.0000.0000.000
9C17HIS10.8960.96512.3010.1180.1180.0000.0000.0000.000
10C18ARG10.7790.88315.2930.0560.0560.0000.0000.0000.000
11C19ASN00.0100.02519.0880.0090.0090.0000.0000.0000.000
12C20GLU-1-0.800-0.90321.110-0.063-0.0630.0000.0000.0000.000
13C21LEU00.0000.00816.5050.0130.0130.0000.0000.0000.000
14C22ASN0-0.062-0.05219.2800.0170.0170.0000.0000.0000.000
15C23HIS00.1260.05220.4230.0130.0130.0000.0000.0000.000
16C24THR00.0730.05820.3230.0120.0120.0000.0000.0000.000
17C25LEU0-0.023-0.00915.3040.0210.0210.0000.0000.0000.000
18C26ALA0-0.021-0.01118.7640.0200.0200.0000.0000.0000.000
19C27GLN00.006-0.02320.9820.0120.0120.0000.0000.0000.000
20C28LEU0-0.0200.03317.1510.0110.0110.0000.0000.0000.000
21C29PRO00.0670.03420.055-0.002-0.0020.0000.0000.0000.000
22C30LEU00.0140.00716.9570.0250.0250.0000.0000.0000.000
23C31PRO0-0.011-0.00816.2650.0320.0320.0000.0000.0000.000
24C32ALA00.1010.04915.5130.0580.0580.0000.0000.0000.000
25C33LYS10.7690.89415.053-0.073-0.0730.0000.0000.0000.000
26C34ARG10.8200.88311.966-0.306-0.3060.0000.0000.0000.000
27C35VAL0-0.0060.01110.8690.1280.1280.0000.0000.0000.000
28C36MET00.0470.02011.1940.1340.1340.0000.0000.0000.000
29C37TYR00.013-0.0079.070-0.035-0.0350.0000.0000.0000.000
30C38MET0-0.008-0.0025.001-0.149-0.1490.0000.0000.0000.000
31C39ALA00.0500.0276.7770.4260.4260.0000.0000.0000.000
32C40LEU00.005-0.0088.476-0.086-0.0860.0000.0000.0000.000
33C41ALA0-0.073-0.0403.357-0.613-0.3620.019-0.061-0.2080.000
34C42LEU0-0.061-0.0244.010-1.131-0.7110.002-0.106-0.3160.000
35C43ILE0-0.0120.0025.557-0.308-0.3080.0000.0000.0000.000
36C44ASP-1-0.794-0.8767.612-0.842-0.8420.0000.0000.0000.000
37C45SER0-0.027-0.0258.9260.1240.1240.0000.0000.0000.000
38C46LYS10.7150.82711.3160.5740.5740.0000.0000.0000.000
39C47GLU-1-0.826-0.87312.716-0.306-0.3060.0000.0000.0000.000
40C48PRO00.002-0.01014.5010.0150.0150.0000.0000.0000.000
41C49LEU00.0630.04312.326-0.012-0.0120.0000.0000.0000.000
42C50GLU-1-0.798-0.89213.154-0.074-0.0740.0000.0000.0000.000
43C51ARG10.9350.97616.9040.0500.0500.0000.0000.0000.000
44C52GLY0-0.034-0.02219.2850.0220.0220.0000.0000.0000.000
45C53ARG10.7630.8809.1050.0230.0230.0000.0000.0000.000
46C54VAL00.0320.00914.5590.0280.0280.0000.0000.0000.000
47C55PHE0-0.030-0.0159.4010.0100.0100.0000.0000.0000.000
48C56LYS10.9090.96910.644-0.489-0.4890.0000.0000.0000.000
49C57ILE0-0.007-0.0089.0070.2700.2700.0000.0000.0000.000
50C58ARG10.9550.9778.513-1.253-1.2530.0000.0000.0000.000
51C59ALA0-0.002-0.0039.9960.1940.1940.0000.0000.0000.000
52C60GLU-1-0.880-0.93510.0320.8520.8520.0000.0000.0000.000
53C61ASP-1-0.810-0.9145.7572.5622.5620.0000.0000.0000.000
54C62LEU00.003-0.0177.573-0.113-0.1130.0000.0000.0000.000
55C63ALA0-0.0260.0019.125-0.193-0.1930.0000.0000.0000.000
56C64ALA00.0230.0117.966-0.149-0.1490.0000.0000.0000.000
57C65LEU0-0.048-0.0313.063-0.655-0.3210.026-0.081-0.2800.000
58C66ALA0-0.058-0.0367.611-0.257-0.2570.0000.0000.0000.000
59C67LYS10.8810.95010.742-0.254-0.2540.0000.0000.0000.000
60C68ILE0-0.0140.00913.128-0.063-0.0630.0000.0000.0000.000
61C69THR00.0460.01114.8500.0510.0510.0000.0000.0000.000
62C70PRO00.1220.03514.7900.0080.0080.0000.0000.0000.000
63C71SER0-0.0010.01516.3010.0150.0150.0000.0000.0000.000
64C72LEU0-0.012-0.01017.219-0.003-0.0030.0000.0000.0000.000
65C73ALA00.0310.02713.380-0.004-0.0040.0000.0000.0000.000
66C74TYR00.0410.02015.3650.0230.0230.0000.0000.0000.000
67C75ARG10.9550.98717.491-0.251-0.2510.0000.0000.0000.000
68C76GLN00.0150.00416.1740.0160.0160.0000.0000.0000.000
69C77LEU00.0480.03412.122-0.020-0.0200.0000.0000.0000.000
70C78LYS10.9250.98215.845-0.298-0.2980.0000.0000.0000.000
71C79GLU-1-0.828-0.91619.3220.1970.1970.0000.0000.0000.000
72C80GLY0-0.019-0.01217.174-0.028-0.0280.0000.0000.0000.000
73C81GLY00.0190.00018.001-0.015-0.0150.0000.0000.0000.000
74C82LYS10.8740.92018.681-0.230-0.2300.0000.0000.0000.000
75C83LEU0-0.017-0.01720.689-0.018-0.0180.0000.0000.0000.000
76C84LEU00.000-0.00615.353-0.020-0.0200.0000.0000.0000.000
77C85GLY0-0.0060.01319.905-0.019-0.0190.0000.0000.0000.000
78C86ALA0-0.0100.00422.389-0.019-0.0190.0000.0000.0000.000
79C87SER0-0.062-0.02521.323-0.019-0.0190.0000.0000.0000.000
80C88LYS10.8720.91223.369-0.097-0.0970.0000.0000.0000.000
81C89ILE0-0.045-0.03721.7680.0020.0020.0000.0000.0000.000
82C90SER0-0.0170.00223.978-0.003-0.0030.0000.0000.0000.000
83C91LEU0-0.020-0.01424.858-0.007-0.0070.0000.0000.0000.000
84C92ARG10.9550.97227.6830.0040.0040.0000.0000.0000.000
85C93GLY00.0820.01230.694-0.003-0.0030.0000.0000.0000.000
86C94ASP-1-0.895-0.94232.691-0.020-0.0200.0000.0000.0000.000
87C95ASP-1-0.912-0.96027.820-0.033-0.0330.0000.0000.0000.000
88C96ILE0-0.073-0.03628.799-0.001-0.0010.0000.0000.0000.000
89C97ILE0-0.013-0.00430.8050.0000.0000.0000.0000.0000.000
90C98ALA0-0.046-0.02028.287-0.002-0.0020.0000.0000.0000.000
91C99LEU00.0190.01925.000-0.001-0.0010.0000.0000.0000.000
92C100ALA00.0520.02627.959-0.001-0.0010.0000.0000.0000.000
93C101LYS10.9310.98330.8970.0290.0290.0000.0000.0000.000
94C102GLU-1-0.859-0.91624.772-0.068-0.0680.0000.0000.0000.000
95C103LEU0-0.051-0.02824.204-0.003-0.0030.0000.0000.0000.000
96C104ASN0-0.080-0.02027.5440.0040.0040.0000.0000.0000.000
97C113SER0-0.052-0.03536.598-0.002-0.0020.0000.0000.0000.000
98C114GLU-1-0.943-0.98332.7320.0260.0260.0000.0000.0000.000
99C115GLU-1-0.934-0.95033.6880.0200.0200.0000.0000.0000.000
100C116LEU0-0.034-0.01428.7300.0000.0000.0000.0000.0000.000
101C117ASP-1-0.796-0.88126.6590.0740.0740.0000.0000.0000.000
102C118LEU00.0070.00726.135-0.002-0.0020.0000.0000.0000.000
103C119ASN00.0180.01524.0360.0130.0130.0000.0000.0000.000
104C120ILE0-0.020-0.00917.830-0.005-0.0050.0000.0000.0000.000
105C121ILE0-0.060-0.04616.8750.0120.0120.0000.0000.0000.000
106C122GLU-1-0.787-0.86720.6360.0960.0960.0000.0000.0000.000
107C123TRP00.0490.01518.0110.0080.0080.0000.0000.0000.000
108C124ILE0-0.036-0.02717.5040.0350.0350.0000.0000.0000.000
109C125ALA00.0290.03318.850-0.029-0.0290.0000.0000.0000.000
110C126TYR0-0.014-0.00917.0480.0640.0640.0000.0000.0000.000
111C127SER00.0320.01818.339-0.046-0.0460.0000.0000.0000.000
112C128PRO0-0.090-0.07419.9720.0260.0260.0000.0000.0000.000
113C129ASP-1-0.847-0.93222.2240.2370.2370.0000.0000.0000.000
114C130GLU-1-0.891-0.93017.7920.3360.3360.0000.0000.0000.000
115C131GLY0-0.062-0.01716.0670.0510.0510.0000.0000.0000.000
116C132TYR0-0.036-0.04213.0390.1390.1390.0000.0000.0000.000
117C133LEU0-0.045-0.01713.763-0.100-0.1000.0000.0000.0000.000
118C134SER0-0.005-0.00713.7110.0980.0980.0000.0000.0000.000
119C135LEU00.0060.00113.652-0.027-0.0270.0000.0000.0000.000
120C136LYS10.8650.92415.524-0.100-0.1000.0000.0000.0000.000
121C137PHE00.0120.00112.5620.0040.0040.0000.0000.0000.000
122C138THR00.0390.01918.136-0.016-0.0160.0000.0000.0000.000
123C139ARG10.9870.95520.475-0.004-0.0040.0000.0000.0000.000
124C140THR00.0140.00322.020-0.013-0.0130.0000.0000.0000.000
125C141ILE0-0.021-0.01317.640-0.012-0.0120.0000.0000.0000.000
126C142GLU-1-0.774-0.87517.698-0.017-0.0170.0000.0000.0000.000
127C143PRO00.0240.02117.764-0.025-0.0250.0000.0000.0000.000
128C144TYR0-0.077-0.05818.415-0.019-0.0190.0000.0000.0000.000
129C145ILE0-0.103-0.07312.141-0.014-0.0140.0000.0000.0000.000
130C146SER00.0260.01514.3180.0040.0040.0000.0000.0000.000
131C147SER0-0.0270.01615.4900.0130.0130.0000.0000.0000.000
132C148LEU00.0900.04517.357-0.028-0.0280.0000.0000.0000.000
133C149ILE00.034-0.00215.1150.0090.0090.0000.0000.0000.000
134C150GLY0-0.068-0.00518.642-0.007-0.0070.0000.0000.0000.000
135C151LYS11.0160.99722.0430.1300.1300.0000.0000.0000.000
136C152LYS10.9770.95420.0470.2210.2210.0000.0000.0000.000
137C153ASN0-0.019-0.01320.790-0.012-0.0120.0000.0000.0000.000
138C154LYS10.9971.01021.9890.1040.1040.0000.0000.0000.000
139C155PHE00.0030.01017.1900.0010.0010.0000.0000.0000.000
140C156THR00.0340.01315.7210.0060.0060.0000.0000.0000.000
141C157THR0-0.043-0.02611.815-0.023-0.0230.0000.0000.0000.000
142C158GLN0-0.006-0.01611.4340.0570.0570.0000.0000.0000.000
143C159LEU00.0440.0249.192-0.139-0.1390.0000.0000.0000.000
144C160LEU00.0110.0344.075-0.0010.130-0.001-0.010-0.1190.000
145C161THR00.0380.0016.6450.2880.2880.0000.0000.0000.000
146C162ALA00.0300.0197.9210.1270.1270.0000.0000.0000.000
147C163SER0-0.005-0.0219.9180.0710.0710.0000.0000.0000.000
148C164LEU00.0130.0226.9560.0380.0380.0000.0000.0000.000
149C165ARG10.9310.9759.5110.0650.0650.0000.0000.0000.000
150C166LEU0-0.0110.00913.332-0.004-0.0040.0000.0000.0000.000
151C167SER0-0.047-0.03316.171-0.008-0.0080.0000.0000.0000.000
152C168SER00.0540.02418.334-0.004-0.0040.0000.0000.0000.000
153C169GLN00.0670.03520.442-0.002-0.0020.0000.0000.0000.000
154C170TYR00.0170.01021.740-0.008-0.0080.0000.0000.0000.000
155C171SER00.016-0.03820.050-0.014-0.0140.0000.0000.0000.000
156C172SER0-0.030-0.01317.081-0.011-0.0110.0000.0000.0000.000
157C173SER00.0350.02318.380-0.020-0.0200.0000.0000.0000.000
158C174LEU00.0120.00720.909-0.016-0.0160.0000.0000.0000.000
159C175TYR0-0.040-0.04113.092-0.023-0.0230.0000.0000.0000.000
160C176GLN0-0.007-0.00617.159-0.030-0.0300.0000.0000.0000.000
161C177LEU0-0.0100.02118.239-0.024-0.0240.0000.0000.0000.000
162C178ILE00.012-0.01620.210-0.010-0.0100.0000.0000.0000.000
163C179ARG10.8340.88815.1390.2750.2750.0000.0000.0000.000
164C180LYS10.8520.91918.6370.0410.0410.0000.0000.0000.000
165C181HIS10.8020.91920.4300.0760.0760.0000.0000.0000.000
166C182TYR00.0140.01417.6880.0120.0120.0000.0000.0000.000
167C183SER0-0.013-0.00720.476-0.021-0.0210.0000.0000.0000.000
168C184ASN00.013-0.01022.969-0.018-0.0180.0000.0000.0000.000
169C185PHE0-0.027-0.00317.1490.0030.0030.0000.0000.0000.000
170C186LYS10.9570.99921.8120.1460.1460.0000.0000.0000.000
171C187LYS10.9830.96224.5930.1190.1190.0000.0000.0000.000
172C188LYS10.8740.92925.1650.0710.0710.0000.0000.0000.000
173C189ASN0-0.0200.00623.895-0.004-0.0040.0000.0000.0000.000
174C190TYR00.020-0.00426.5350.0080.0080.0000.0000.0000.000
175C191PHE0-0.014-0.00425.069-0.005-0.0050.0000.0000.0000.000
176C192ILE00.0100.00429.6270.0040.0040.0000.0000.0000.000
177C193ILE0-0.0040.00228.712-0.002-0.0020.0000.0000.0000.000
178C194SER00.0450.02432.3930.0010.0010.0000.0000.0000.000
179C195VAL00.0000.00033.3260.0000.0000.0000.0000.0000.000
180C196ASP-1-0.764-0.87833.2100.0010.0010.0000.0000.0000.000
181C197GLU-1-0.849-0.91630.371-0.019-0.0190.0000.0000.0000.000
182C198LEU0-0.046-0.02727.5870.0000.0000.0000.0000.0000.000
183C199LYS10.8440.91228.683-0.002-0.0020.0000.0000.0000.000
184C200GLU-1-0.833-0.89229.6630.0080.0080.0000.0000.0000.000
185C201GLU-1-0.878-0.94724.907-0.030-0.0300.0000.0000.0000.000
186C202LEU0-0.137-0.07824.4750.0040.0040.0000.0000.0000.000
187C203ILE0-0.0090.00224.7860.0100.0100.0000.0000.0000.000
188C204ALA0-0.050-0.02827.5750.0070.0070.0000.0000.0000.000
189C205TYR0-0.009-0.03029.229-0.006-0.0060.0000.0000.0000.000
190C206THR0-0.037-0.01031.5570.0080.0080.0000.0000.0000.000
191C207PHE00.0280.01432.063-0.004-0.0040.0000.0000.0000.000
192C208ASP-1-0.849-0.94636.7110.0440.0440.0000.0000.0000.000
193C209LYS10.8770.94739.014-0.033-0.0330.0000.0000.0000.000
194C210ASP-1-0.900-0.94241.3520.0230.0230.0000.0000.0000.000
195C211GLY0-0.0160.00440.414-0.003-0.0030.0000.0000.0000.000
196C212ASN0-0.058-0.03738.8680.0010.0010.0000.0000.0000.000
197C213ILE0-0.0080.00235.2840.0030.0030.0000.0000.0000.000
198C214GLU-1-0.858-0.91536.4830.0280.0280.0000.0000.0000.000
199C215TYR0-0.102-0.08934.0520.0030.0030.0000.0000.0000.000
200C216LYS10.9010.96429.411-0.048-0.0480.0000.0000.0000.000
201C217TYR0-0.042-0.02231.1320.0020.0020.0000.0000.0000.000
202C218PRO00.0280.01636.143-0.004-0.0040.0000.0000.0000.000
203C219ASP-1-0.878-0.92939.3320.0100.0100.0000.0000.0000.000
204C220PHE00.0740.01334.7490.0010.0010.0000.0000.0000.000
205C221PRO00.000-0.00336.9340.0000.0000.0000.0000.0000.000
206C222ILE00.0430.02636.8440.0010.0010.0000.0000.0000.000
207C223PHE00.0440.02330.6530.0020.0020.0000.0000.0000.000
208C224LYS10.8670.93532.6280.0120.0120.0000.0000.0000.000
209C225ARG10.9120.95332.263-0.020-0.0200.0000.0000.0000.000
210C226ASP-1-0.813-0.89132.0550.0290.0290.0000.0000.0000.000
211C227VAL00.0000.00527.6980.0050.0050.0000.0000.0000.000
212C228LEU0-0.0190.00027.837-0.001-0.0010.0000.0000.0000.000
213C229ASN00.0150.00327.687-0.007-0.0070.0000.0000.0000.000
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215C231ALA00.0130.01424.0310.0010.0010.0000.0000.0000.000
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