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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: P8J4Y

Calculation Name: 4NYH-C-Xray13

Preferred Name:

Target Type:

Ligand Name: phosphate ion

ligand 3-letter code: PO4

PDB ID: 4NYH

Chain ID: C

ChEMBL ID:

UniProt ID: O75319

Base Structure: X-ray

Registration Date: 2018-03-01

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 180
LigandCharge CL-=-1,PO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2098864.311252
FMO2-HF: Nuclear repulsion 2025177.803078
FMO2-HF: Total energy -73686.508174
FMO2-MP2: Total energy -73901.154704


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:28:ACE)


Summations of interaction energy for fragment #1(C:28:ACE)
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.
-0.251-1.79115.512-8.673-5.297-0.022
Interaction energy analysis for fragmet #1(C:28:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : -0.007
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].
3C30HIS0-0.018-0.0013.8280.2771.135-0.012-0.352-0.494-0.001
4C31ILE00.0130.0085.7450.2470.2470.0000.0000.0000.000
5C32PRO0-0.014-0.0037.2380.0230.0230.0000.0000.0000.000
6C33GLU-1-0.758-0.8759.900-0.220-0.2200.0000.0000.0000.000
7C34ARG10.9730.98613.3880.0800.0800.0000.0000.0000.000
8C35TRP0-0.060-0.02810.440-0.014-0.0140.0000.0000.0000.000
9C36LYS10.9210.95212.4230.2760.2760.0000.0000.0000.000
10C37ASP-1-0.894-0.92514.506-0.074-0.0740.0000.0000.0000.000
11C38TYR0-0.131-0.08616.8180.0080.0080.0000.0000.0000.000
12C39LEU00.0540.02417.3260.0040.0040.0000.0000.0000.000
13C40PRO0-0.033-0.02615.7100.0110.0110.0000.0000.0000.000
14C41VAL0-0.003-0.01017.2330.0210.0210.0000.0000.0000.000
15C42GLY00.0080.01819.849-0.012-0.0120.0000.0000.0000.000
16C43GLN00.013-0.00123.2430.0050.0050.0000.0000.0000.000
17C44ARG10.7810.86526.436-0.061-0.0610.0000.0000.0000.000
18C45MET0-0.025-0.00827.775-0.004-0.0040.0000.0000.0000.000
19C46PRO00.0330.02130.0500.0010.0010.0000.0000.0000.000
20C47GLY0-0.0010.00333.569-0.001-0.0010.0000.0000.0000.000
21C48THR0-0.016-0.00330.4410.0030.0030.0000.0000.0000.000
22C49ARG10.8470.91129.616-0.075-0.0750.0000.0000.0000.000
23C50PHE00.0320.02125.9050.0090.0090.0000.0000.0000.000
24C51ILE00.0280.01922.236-0.006-0.0060.0000.0000.0000.000
25C52ALA00.0030.01421.2180.0120.0120.0000.0000.0000.000
26C53PHE00.0240.01215.590-0.006-0.0060.0000.0000.0000.000
27C54LYS10.7950.91113.030-0.027-0.0270.0000.0000.0000.000
28C55VAL0-0.042-0.0179.5190.0160.0160.0000.0000.0000.000
29C56PRO00.0400.02910.603-0.018-0.0180.0000.0000.0000.000
30C57LEU0-0.037-0.0185.5690.1760.1760.0000.0000.0000.000
31C58GLN00.020-0.0073.031-1.252-1.0650.058-0.143-0.1010.000
32C59LYS10.9710.9715.320-0.181-0.1810.0000.0000.0000.000
33C60SER0-0.048-0.0131.7820.550-2.2678.454-4.191-1.4460.004
34C61PHE0-0.0050.0002.569-1.359-1.5257.012-3.907-2.939-0.025
35C62GLU-1-0.769-0.9024.189-0.0370.0390.001-0.020-0.0570.000
36C63LYS10.8850.9497.1870.4490.4490.0000.0000.0000.000
37C64LYS10.8800.9447.3670.9880.9880.0000.0000.0000.000
38C65LEU0-0.039-0.0078.3630.0420.0420.0000.0000.0000.000
39C66ALA00.0380.03711.1940.0080.0080.0000.0000.0000.000
40C67PRO00.018-0.01014.0600.0130.0130.0000.0000.0000.000
41C68GLU-1-0.898-0.95415.540-0.061-0.0610.0000.0000.0000.000
42C69GLU-1-0.904-0.96013.208-0.168-0.1680.0000.0000.0000.000
43C70CYS0-0.097-0.03111.169-0.001-0.0010.0000.0000.0000.000
44C71PHE00.025-0.00110.7550.0080.0080.0000.0000.0000.000
45C72SER00.0070.0159.9180.0750.0750.0000.0000.0000.000
46C73PRO00.025-0.0159.605-0.044-0.0440.0000.0000.0000.000
47C74LEU00.0250.02412.829-0.037-0.0370.0000.0000.0000.000
48C75ASP-1-0.820-0.90313.5770.1040.1040.0000.0000.0000.000
49C76LEU0-0.034-0.01214.983-0.023-0.0230.0000.0000.0000.000
50C77PHE00.0340.00616.091-0.020-0.0200.0000.0000.0000.000
51C78ASN0-0.026-0.01718.606-0.015-0.0150.0000.0000.0000.000
52C79LYS10.9580.98117.542-0.084-0.0840.0000.0000.0000.000
53C80ILE0-0.0250.00120.440-0.008-0.0080.0000.0000.0000.000
54C81ARG10.9710.98021.567-0.115-0.1150.0000.0000.0000.000
55C82GLU-1-0.985-0.98223.8900.0450.0450.0000.0000.0000.000
56C83GLN0-0.060-0.04024.028-0.008-0.0080.0000.0000.0000.000
57C84ASN0-0.069-0.02927.383-0.002-0.0020.0000.0000.0000.000
58C85GLU-1-0.857-0.92326.1480.0660.0660.0000.0000.0000.000
59C86GLU-1-0.915-0.97325.3210.1010.1010.0000.0000.0000.000
60C87LEU0-0.057-0.01919.704-0.001-0.0010.0000.0000.0000.000
61C88GLY00.014-0.00523.8250.0000.0000.0000.0000.0000.000
62C89LEU0-0.032-0.01922.1650.0020.0020.0000.0000.0000.000
63C90ILE0-0.0250.00516.228-0.004-0.0040.0000.0000.0000.000
64C91ILE0-0.003-0.00619.5880.0080.0080.0000.0000.0000.000
65C92ASP-1-0.719-0.80313.3520.3890.3890.0000.0000.0000.000
66C93LEU00.0320.00316.548-0.005-0.0050.0000.0000.0000.000
67C94THR0-0.123-0.08111.8050.0010.0010.0000.0000.0000.000
68C95TYR00.0640.01012.9720.0200.0200.0000.0000.0000.000
69C96THR0-0.0340.00810.1190.0450.0450.0000.0000.0000.000
70C97GLN00.0370.0263.976-0.231-0.0950.000-0.043-0.0930.000
71C98ARG10.8960.9665.923-0.905-0.9050.0000.0000.0000.000
72C99TYR00.006-0.0154.6520.6050.791-0.001-0.017-0.1670.000
73C100TYR00.020-0.0195.7880.2510.2510.0000.0000.0000.000
74C101LYS10.9030.9567.936-0.774-0.7740.0000.0000.0000.000
75C102PRO00.0020.00610.586-0.038-0.0380.0000.0000.0000.000
76C103GLU-1-0.887-0.95613.4240.4260.4260.0000.0000.0000.000
77C104ASP-1-0.917-0.96110.3920.6210.6210.0000.0000.0000.000
78C105LEU0-0.103-0.04113.438-0.005-0.0050.0000.0000.0000.000
79C106PRO0-0.027-0.01814.394-0.021-0.0210.0000.0000.0000.000
80C107GLU-1-0.918-0.94817.2220.1150.1150.0000.0000.0000.000
81C108THR0-0.026-0.01719.0200.0290.0290.0000.0000.0000.000
82C109VAL00.0030.00019.756-0.019-0.0190.0000.0000.0000.000
83C110PRO0-0.028-0.00220.1480.0210.0210.0000.0000.0000.000
84C111TYR00.006-0.03113.9960.0050.0050.0000.0000.0000.000
85C112LEU00.0040.00019.476-0.011-0.0110.0000.0000.0000.000
86C113LYS10.7830.89612.082-0.375-0.3750.0000.0000.0000.000
87C114ILE00.0010.00018.018-0.021-0.0210.0000.0000.0000.000
88C115PHE0-0.049-0.02514.5050.0030.0030.0000.0000.0000.000
89C116THR00.0480.02617.821-0.020-0.0200.0000.0000.0000.000
90C117VAL0-0.004-0.01317.4880.0050.0050.0000.0000.0000.000
91C118GLY00.0000.00918.465-0.009-0.0090.0000.0000.0000.000
92C119HIS00.033-0.00318.9820.0160.0160.0000.0000.0000.000
93C120GLN00.0190.01822.697-0.003-0.0030.0000.0000.0000.000
94C121VAL0-0.014-0.00824.8710.0050.0050.0000.0000.0000.000
95C122PRO0-0.044-0.01923.6600.0020.0020.0000.0000.0000.000
96C123ASP-1-0.781-0.86425.6480.0650.0650.0000.0000.0000.000
97C124ASP-1-0.758-0.89827.8500.0480.0480.0000.0000.0000.000
98C125GLU-1-0.925-0.96127.5330.0600.0600.0000.0000.0000.000
99C126THR0-0.118-0.08323.1020.0120.0120.0000.0000.0000.000
100C127ILE0-0.0060.00325.7660.0080.0080.0000.0000.0000.000
101C128PHE00.0040.00828.2480.0030.0030.0000.0000.0000.000
102C129LYS10.9260.95023.102-0.105-0.1050.0000.0000.0000.000
103C130PHE00.0020.00223.3470.0070.0070.0000.0000.0000.000
104C131LYS10.8770.92126.313-0.051-0.0510.0000.0000.0000.000
105C132HIS0-0.041-0.00328.710-0.004-0.0040.0000.0000.0000.000
106C133ALA0-0.018-0.01025.4110.0000.0000.0000.0000.0000.000
107C134VAL00.0160.01327.0230.0020.0020.0000.0000.0000.000
108C135ASN00.0380.02528.881-0.002-0.0020.0000.0000.0000.000
109C136GLY0-0.058-0.02830.956-0.003-0.0030.0000.0000.0000.000
110C137PHE00.0470.02327.079-0.001-0.0010.0000.0000.0000.000
111C138LEU00.0330.01129.828-0.004-0.0040.0000.0000.0000.000
112C139LYS10.8530.93032.754-0.077-0.0770.0000.0000.0000.000
113C140GLU-1-0.929-0.95931.6740.0720.0720.0000.0000.0000.000
114C141ASN0-0.0470.00329.7780.0020.0020.0000.0000.0000.000
115C142LYS10.9040.94833.228-0.062-0.0620.0000.0000.0000.000
116C143ASP-1-0.912-0.93935.5860.0640.0640.0000.0000.0000.000
117C144ASN0-0.032-0.02931.6790.0020.0020.0000.0000.0000.000
118C145ASP-1-0.793-0.89232.6000.0610.0610.0000.0000.0000.000
119C146LYS10.9360.99227.495-0.096-0.0960.0000.0000.0000.000
120C147LEU00.005-0.00825.259-0.002-0.0020.0000.0000.0000.000
121C148ILE0-0.0110.00123.8670.0110.0110.0000.0000.0000.000
122C149GLY00.0290.00320.812-0.009-0.0090.0000.0000.0000.000
123C150VAL0-0.024-0.00420.1300.0150.0150.0000.0000.0000.000
124C151HIS00.0290.03712.6960.0190.0190.0000.0000.0000.000
125C152SER00.019-0.01515.7720.0010.0010.0000.0000.0000.000
126C153THR00.009-0.01611.4760.0310.0310.0000.0000.0000.000
127C154HIS00.023-0.01213.4990.0280.0280.0000.0000.0000.000
128C155GLY00.0230.03416.161-0.006-0.0060.0000.0000.0000.000
129C156LEU0-0.0090.01018.243-0.005-0.0050.0000.0000.0000.000
130C157ASN00.009-0.00120.451-0.001-0.0010.0000.0000.0000.000
131C158ARG10.9710.98114.585-0.111-0.1110.0000.0000.0000.000
132C159THR00.0140.01719.6490.0040.0040.0000.0000.0000.000
133C160GLY00.0750.03921.815-0.001-0.0010.0000.0000.0000.000
134C161TYR0-0.007-0.02624.6890.0000.0000.0000.0000.0000.000
135C162LEU00.0140.00222.525-0.002-0.0020.0000.0000.0000.000
136C163ILE0-0.014-0.00124.055-0.001-0.0010.0000.0000.0000.000
137C164CYS0-0.016-0.00727.429-0.004-0.0040.0000.0000.0000.000
138C165ARG10.8520.91829.311-0.043-0.0430.0000.0000.0000.000
139C166TYR0-0.025-0.03929.581-0.001-0.0010.0000.0000.0000.000
140C167LEU00.001-0.01631.241-0.002-0.0020.0000.0000.0000.000
141C168ILE0-0.0180.01133.373-0.003-0.0030.0000.0000.0000.000
142C169ASP-1-0.755-0.86534.4040.0420.0420.0000.0000.0000.000
143C170VAL0-0.108-0.05433.758-0.001-0.0010.0000.0000.0000.000
144C171GLU-1-0.949-0.97435.3480.0470.0470.0000.0000.0000.000
145C172GLY0-0.0270.01337.787-0.002-0.0020.0000.0000.0000.000
146C173VAL0-0.053-0.02235.887-0.003-0.0030.0000.0000.0000.000
147C174ARG10.9150.94138.055-0.022-0.0220.0000.0000.0000.000
148C175PRO00.0800.03035.6940.0010.0010.0000.0000.0000.000
149C176ASP-1-0.843-0.91035.1340.0210.0210.0000.0000.0000.000
150C177ASP-1-0.881-0.93236.0120.0250.0250.0000.0000.0000.000
151C178ALA0-0.029-0.01532.6420.0020.0020.0000.0000.0000.000
152C179ILE00.026-0.00230.6750.0030.0030.0000.0000.0000.000
153C180GLU-1-0.945-0.96231.0870.0200.0200.0000.0000.0000.000
154C181LEU0-0.025-0.01231.5860.0000.0000.0000.0000.0000.000
155C182PHE00.0250.00223.1590.0040.0040.0000.0000.0000.000
156C183ASN00.0690.02127.4290.0050.0050.0000.0000.0000.000
157C184ARG10.9310.97027.996-0.028-0.0280.0000.0000.0000.000
158C185CYS0-0.079-0.01727.874-0.001-0.0010.0000.0000.0000.000
159C186ARG10.7670.88618.426-0.061-0.0610.0000.0000.0000.000
160C187GLY00.0240.01323.5940.0020.0020.0000.0000.0000.000
161C188HIS00.0130.00821.755-0.003-0.0030.0000.0000.0000.000
162C189CYS0-0.012-0.00625.0820.0060.0060.0000.0000.0000.000
163C190LEU0-0.013-0.01525.096-0.001-0.0010.0000.0000.0000.000
164C191GLU-1-0.783-0.85822.314-0.002-0.0020.0000.0000.0000.000
165C192ARG10.8750.95219.513-0.023-0.0230.0000.0000.0000.000
166C193GLN00.0720.02126.4490.0030.0030.0000.0000.0000.000
167C194ASN00.0460.01726.6490.0010.0010.0000.0000.0000.000
168C195TYR0-0.066-0.04022.9210.0060.0060.0000.0000.0000.000
169C196ILE00.0200.01128.7790.0030.0030.0000.0000.0000.000
170C197GLU-1-0.828-0.89531.3680.0150.0150.0000.0000.0000.000
171C198ASP-1-0.770-0.86231.3170.0360.0360.0000.0000.0000.000
172C199LEU0-0.074-0.04529.2280.0020.0020.0000.0000.0000.000
173C200GLN0-0.100-0.07333.403-0.001-0.0010.0000.0000.0000.000
174C201ASN0-0.050-0.03136.5240.0000.0000.0000.0000.0000.000
175C202GLY0-0.0290.00135.775-0.001-0.0010.0000.0000.0000.000
176C203PRO0-0.068-0.02835.9630.0000.0000.0000.0000.0000.000
177C204ILE0-0.018-0.00936.0740.0020.0020.0000.0000.0000.000
178C205ARG0-0.148-0.08331.9000.0040.0040.0000.0000.0000.000
179C301PO4-2-2.000-2.00028.478-0.066-0.0660.0000.0000.0000.000
180C302CL--1-1.000-1.00027.321-0.017-0.0170.0000.0000.0000.000