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: 3QZQL

Calculation Name: 1X1P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1X1P

Chain ID: A

ChEMBL ID:

UniProt ID: O74035

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2353600.711553
FMO2-HF: Nuclear repulsion 2273447.194594
FMO2-HF: Total energy -80153.516959
FMO2-MP2: Total energy -80392.774633


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-11.108-1.51512.24-8.081-13.753-0.054
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.013
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].
3A3ILE00.0510.0313.104-1.5300.4841.870-1.149-2.7360.003
4A4ALA00.0250.0045.728-0.498-0.500-0.001-0.0050.0090.000
5A5GLY0-0.0230.0069.284-0.082-0.0820.0000.0000.0000.000
6A6ILE0-0.053-0.02612.4710.0150.0150.0000.0000.0000.000
7A7ASP-1-0.797-0.88415.7080.1240.1240.0000.0000.0000.000
8A8GLH0-0.067-0.08419.2580.0130.0130.0000.0000.0000.000
9A9ALA0-0.0130.02822.838-0.017-0.0170.0000.0000.0000.000
10A10GLY0-0.071-0.03725.684-0.004-0.0040.0000.0000.0000.000
11A11ARG10.9920.98627.084-0.070-0.0700.0000.0000.0000.000
12A12GLY00.1040.04928.9860.0050.0050.0000.0000.0000.000
13A13PRO0-0.080-0.03030.930-0.008-0.0080.0000.0000.0000.000
14A14VAL00.006-0.01333.9740.0010.0010.0000.0000.0000.000
15A15ILE00.0110.00637.0230.0000.0000.0000.0000.0000.000
16A16GLY00.0120.00434.7120.0010.0010.0000.0000.0000.000
17A17PRO00.0100.01230.130-0.002-0.0020.0000.0000.0000.000
18A18MET0-0.017-0.00325.9050.0000.0000.0000.0000.0000.000
19A19VAL0-0.010-0.00724.0890.0090.0090.0000.0000.0000.000
20A20ILE00.0110.00620.101-0.007-0.0070.0000.0000.0000.000
21A21ALA0-0.048-0.01519.4950.0090.0090.0000.0000.0000.000
22A22ALA00.0390.02315.066-0.005-0.0050.0000.0000.0000.000
23A23VAL0-0.028-0.01912.429-0.012-0.0120.0000.0000.0000.000
24A24VAL00.0310.0097.8410.0570.0570.0000.0000.0000.000
25A25VAL00.0070.0147.135-0.095-0.0950.0000.0000.0000.000
26A26ASP-1-0.766-0.8613.109-2.283-1.0110.071-0.636-0.708-0.006
27A27GLU-1-0.876-0.9632.119-9.961-7.4056.665-3.688-5.533-0.029
28A28ASN0-0.129-0.0733.7970.6770.9880.005-0.031-0.2850.000
29A29SER0-0.022-0.0226.8450.2520.2520.0000.0000.0000.000
30A30LEU0-0.0070.0156.2110.2070.2070.0000.0000.0000.000
31A31PRO00.0290.0078.2780.1450.1450.0000.0000.0000.000
32A32LYS10.8780.92811.4180.2730.2730.0000.0000.0000.000
33A33LEU00.0320.01911.1980.0440.0440.0000.0000.0000.000
34A34GLU-1-0.780-0.86313.640-0.045-0.0450.0000.0000.0000.000
35A35GLU-1-0.871-0.91814.778-0.191-0.1910.0000.0000.0000.000
36A36LEU0-0.027-0.00916.6370.0120.0120.0000.0000.0000.000
37A37LYS10.7890.88818.6440.1020.1020.0000.0000.0000.000
38A38VAL00.0360.02015.7790.0110.0110.0000.0000.0000.000
39A39ARG10.8280.90515.5200.0490.0490.0000.0000.0000.000
40A40ASP-1-0.915-0.93519.937-0.024-0.0240.0000.0000.0000.000
41A41SER00.022-0.01021.6430.0000.0000.0000.0000.0000.000
42A42LYS10.7520.85223.114-0.052-0.0520.0000.0000.0000.000
43A43LYS10.8350.89625.5300.0030.0030.0000.0000.0000.000
44A44LEU0-0.0030.02324.6940.0000.0000.0000.0000.0000.000
45A45THR00.0210.01228.6900.0040.0040.0000.0000.0000.000
46A46PRO00.0990.04129.8620.0020.0020.0000.0000.0000.000
47A47LYS11.0090.99129.617-0.039-0.0390.0000.0000.0000.000
48A48ARG10.9130.95028.655-0.017-0.0170.0000.0000.0000.000
49A49ARG10.9030.95424.614-0.065-0.0650.0000.0000.0000.000
50A50GLU-1-0.816-0.88624.8510.0950.0950.0000.0000.0000.000
51A51LYS10.8810.94325.491-0.043-0.0430.0000.0000.0000.000
52A52LEU00.0990.05820.3230.0050.0050.0000.0000.0000.000
53A53PHE00.0000.00320.8800.0090.0090.0000.0000.0000.000
54A54ASN0-0.052-0.03720.8180.0270.0270.0000.0000.0000.000
55A55GLU-1-0.908-0.96119.9800.0430.0430.0000.0000.0000.000
56A56ILE0-0.024-0.02415.802-0.006-0.0060.0000.0000.0000.000
57A57LEU0-0.041-0.01515.8800.0200.0200.0000.0000.0000.000
58A58GLY0-0.0340.00016.5660.0260.0260.0000.0000.0000.000
59A59VAL0-0.040-0.03312.7850.0000.0000.0000.0000.0000.000
60A60LEU0-0.095-0.02811.361-0.011-0.0110.0000.0000.0000.000
61A61ASP-1-0.781-0.8807.1520.9140.9140.0000.0000.0000.000
62A62ASP-1-0.821-0.92510.4850.7920.7920.0000.0000.0000.000
63A63TYR0-0.036-0.03012.979-0.054-0.0540.0000.0000.0000.000
64A64VAL0-0.0130.00115.680-0.015-0.0150.0000.0000.0000.000
65A65ILE0-0.027-0.01018.657-0.013-0.0130.0000.0000.0000.000
66A66LEU00.000-0.00721.881-0.009-0.0090.0000.0000.0000.000
67A67GLU-1-0.919-0.96324.0840.1400.1400.0000.0000.0000.000
68A68LEU0-0.020-0.01125.852-0.003-0.0030.0000.0000.0000.000
69A69PRO0-0.022-0.01729.467-0.008-0.0080.0000.0000.0000.000
70A70PRO00.0040.01332.1060.0020.0020.0000.0000.0000.000
71A71ASP-1-0.793-0.87932.5140.0900.0900.0000.0000.0000.000
72A72VAL0-0.071-0.03835.094-0.003-0.0030.0000.0000.0000.000
73A73ILE0-0.035-0.03938.435-0.002-0.0020.0000.0000.0000.000
74A74GLY00.0030.01839.862-0.002-0.0020.0000.0000.0000.000
75A75SER0-0.089-0.04235.345-0.003-0.0030.0000.0000.0000.000
76A76ARG10.8760.93230.860-0.071-0.0710.0000.0000.0000.000
77A77GLU-1-0.887-0.95334.7690.0530.0530.0000.0000.0000.000
78A78GLY0-0.057-0.01834.772-0.001-0.0010.0000.0000.0000.000
79A79THR00.0410.01429.8910.0010.0010.0000.0000.0000.000
80A80LEU00.0260.02230.9890.0030.0030.0000.0000.0000.000
81A81ASN00.002-0.00925.9530.0070.0070.0000.0000.0000.000
82A82GLU-1-0.881-0.95625.8260.0730.0730.0000.0000.0000.000
83A83PHE0-0.020-0.01526.3760.0040.0040.0000.0000.0000.000
84A84GLU-1-0.862-0.86922.2110.1430.1430.0000.0000.0000.000
85A85VAL00.0580.03419.3960.0220.0220.0000.0000.0000.000
86A86GLU-1-0.841-0.89220.3200.1650.1650.0000.0000.0000.000
87A87ASN0-0.007-0.03522.0020.0210.0210.0000.0000.0000.000
88A88PHE00.0290.01117.2150.0280.0280.0000.0000.0000.000
89A89ALA00.0330.02817.1450.0420.0420.0000.0000.0000.000
90A90LYS10.8150.90218.012-0.137-0.1370.0000.0000.0000.000
91A91ALA00.0380.02718.6680.0240.0240.0000.0000.0000.000
92A92LEU00.0870.04312.3600.0460.0460.0000.0000.0000.000
93A93ASN0-0.046-0.03115.1900.1090.1090.0000.0000.0000.000
94A94SER0-0.107-0.06717.094-0.016-0.0160.0000.0000.0000.000
95A95LEU0-0.068-0.01012.259-0.016-0.0160.0000.0000.0000.000
96A96LYS10.8980.95714.472-0.525-0.5250.0000.0000.0000.000
97A97VAL0-0.015-0.0168.3830.0430.0430.0000.0000.0000.000
98A98LYS10.8240.9229.917-0.764-0.7640.0000.0000.0000.000
99A99PRO0-0.029-0.0106.5410.4670.4670.0000.0000.0000.000
100A100ASP-1-0.822-0.9142.4762.3115.0562.865-2.310-3.301-0.020
101A101VAL0-0.003-0.0062.345-1.890-1.2310.766-0.261-1.164-0.002
102A102ILE0-0.044-0.0295.0520.4210.459-0.001-0.001-0.0350.000
103A103TYR00.0090.0046.630-0.124-0.1240.0000.0000.0000.000
104A104ALA0-0.002-0.03211.1900.0090.0090.0000.0000.0000.000
105A105ASP-1-0.814-0.92314.7300.0790.0790.0000.0000.0000.000
106A106ALA0-0.039-0.00918.2160.0030.0030.0000.0000.0000.000
107A107ALA00.020-0.00420.238-0.007-0.0070.0000.0000.0000.000
108A108ASP-1-0.972-1.00123.9800.0430.0430.0000.0000.0000.000
109A109VAL0-0.0220.00822.254-0.007-0.0070.0000.0000.0000.000
110A110ASP-1-0.907-0.97722.2500.0010.0010.0000.0000.0000.000
111A111GLU-1-0.808-0.89718.3360.0110.0110.0000.0000.0000.000
112A112GLU-1-0.904-0.95617.010-0.044-0.0440.0000.0000.0000.000
113A113ARG10.8200.89217.795-0.042-0.0420.0000.0000.0000.000
114A114PHE0-0.013-0.00917.5150.0110.0110.0000.0000.0000.000
115A115ALA00.004-0.00413.6460.0220.0220.0000.0000.0000.000
116A116ARG10.8350.92214.799-0.025-0.0250.0000.0000.0000.000
117A117GLU-1-0.799-0.88816.6070.0730.0730.0000.0000.0000.000
118A118LEU0-0.037-0.02614.8090.0160.0160.0000.0000.0000.000
119A119GLY00.0420.01613.4940.0330.0330.0000.0000.0000.000
120A120GLU-1-0.886-0.93314.2390.0810.0810.0000.0000.0000.000
121A121ARG10.8120.90017.313-0.145-0.1450.0000.0000.0000.000
122A122LEU0-0.0200.00512.0540.0190.0190.0000.0000.0000.000
123A123ASN0-0.067-0.03815.9150.0070.0070.0000.0000.0000.000
124A124PHE0-0.021-0.0379.5990.0260.0260.0000.0000.0000.000
125A125GLU-1-0.969-0.9809.105-0.066-0.0660.0000.0000.0000.000
126A126ALA00.0550.0247.2130.1340.1340.0000.0000.0000.000
127A127GLU-1-0.939-0.9465.521-0.578-0.5780.0000.0000.0000.000
128A128VAL0-0.024-0.0167.3940.2000.2000.0000.0000.0000.000
129A129VAL00.0100.0108.995-0.076-0.0760.0000.0000.0000.000
130A130ALA0-0.001-0.00111.6780.0670.0670.0000.0000.0000.000
131A131LYS10.8320.88914.948-0.035-0.0350.0000.0000.0000.000
132A132HIS00.0150.03318.0800.0260.0260.0000.0000.0000.000
133A133LYS10.8990.96520.749-0.036-0.0360.0000.0000.0000.000
134A134ALA00.0740.03816.058-0.014-0.0140.0000.0000.0000.000
135A135ASP-1-0.799-0.88516.9890.0790.0790.0000.0000.0000.000
136A136ASP-1-0.869-0.91718.8290.0210.0210.0000.0000.0000.000
137A137ILE0-0.070-0.02415.367-0.028-0.0280.0000.0000.0000.000
138A138PHE00.0750.01811.712-0.023-0.0230.0000.0000.0000.000
139A139PRO00.0450.01812.0850.0280.0280.0000.0000.0000.000
140A140VAL00.0400.0329.689-0.032-0.0320.0000.0000.0000.000
141A141VAL00.0370.01812.2560.0240.0240.0000.0000.0000.000
142A142SER0-0.031-0.02114.908-0.019-0.0190.0000.0000.0000.000
143A143ALA0-0.036-0.03814.660-0.007-0.0070.0000.0000.0000.000
144A144ALA00.0080.01115.335-0.004-0.0040.0000.0000.0000.000
145A145SER00.014-0.00817.229-0.016-0.0160.0000.0000.0000.000
146A146ILE0-0.100-0.04919.383-0.021-0.0210.0000.0000.0000.000
147A147LEU00.001-0.00117.828-0.014-0.0140.0000.0000.0000.000
148A148ALA00.0410.03721.567-0.009-0.0090.0000.0000.0000.000
149A149LYS10.8230.88023.527-0.094-0.0940.0000.0000.0000.000
150A150VAL0-0.030-0.01225.091-0.009-0.0090.0000.0000.0000.000
151A151THR00.0110.00024.688-0.008-0.0080.0000.0000.0000.000
152A152ARG10.8630.93627.448-0.101-0.1010.0000.0000.0000.000
153A153ASP-1-0.863-0.92529.4390.0740.0740.0000.0000.0000.000
154A154ARG10.8260.89626.610-0.125-0.1250.0000.0000.0000.000
155A155ALA00.0380.02931.822-0.006-0.0060.0000.0000.0000.000
156A156VAL0-0.017-0.01833.685-0.005-0.0050.0000.0000.0000.000
157A157GLU-1-0.966-0.98235.0450.0530.0530.0000.0000.0000.000
158A158LYS10.8260.87636.069-0.079-0.0790.0000.0000.0000.000
159A159LEU00.0100.01137.333-0.003-0.0030.0000.0000.0000.000
160A160LYS10.8610.94238.015-0.059-0.0590.0000.0000.0000.000
161A161GLU-1-0.892-0.92239.3520.0650.0650.0000.0000.0000.000
162A162GLU-1-0.915-0.93242.8520.0640.0640.0000.0000.0000.000
163A163TYR0-0.117-0.07943.102-0.003-0.0030.0000.0000.0000.000
164A164GLY00.0070.01245.341-0.003-0.0030.0000.0000.0000.000
165A165GLU-1-0.843-0.92542.1730.0480.0480.0000.0000.0000.000
166A166ILE00.0780.04139.295-0.001-0.0010.0000.0000.0000.000
167A167GLY0-0.043-0.00640.9390.0010.0010.0000.0000.0000.000
168A168SER0-0.058-0.06935.3890.0030.0030.0000.0000.0000.000
169A169GLY00.0560.03335.7190.0060.0060.0000.0000.0000.000
170A170TYR00.0080.00931.2280.0050.0050.0000.0000.0000.000
171A171PRO00.0920.05036.570-0.004-0.0040.0000.0000.0000.000
172A172SER00.0090.00137.393-0.003-0.0030.0000.0000.0000.000
173A173ASP-1-0.782-0.83538.7010.0410.0410.0000.0000.0000.000
174A174PRO00.038-0.00340.5660.0010.0010.0000.0000.0000.000
175A175ARG10.8320.88639.790-0.042-0.0420.0000.0000.0000.000
176A176THR0-0.014-0.00740.2010.0010.0010.0000.0000.0000.000
177A177ARG10.8330.90842.952-0.038-0.0380.0000.0000.0000.000
178A178ALA00.0160.01045.2290.0000.0000.0000.0000.0000.000
179A179PHE0-0.0130.00043.8530.0000.0000.0000.0000.0000.000
180A180LEU00.007-0.01042.4830.0000.0000.0000.0000.0000.000
181A181GLU-1-0.905-0.93046.9220.0320.0320.0000.0000.0000.000
182A182ASN0-0.054-0.03050.405-0.002-0.0020.0000.0000.0000.000
183A183TYR00.0200.02048.879-0.001-0.0010.0000.0000.0000.000
184A184TYR00.0340.01850.0790.0000.0000.0000.0000.0000.000
185A185ARG10.7800.86252.250-0.032-0.0320.0000.0000.0000.000
186A186GLU-1-0.904-0.93854.3700.0370.0370.0000.0000.0000.000
187A187HIS10.8020.89852.023-0.041-0.0410.0000.0000.0000.000
188A188GLY0-0.032-0.00254.8520.0010.0010.0000.0000.0000.000
189A189GLU-1-0.908-0.95350.8210.0510.0510.0000.0000.0000.000
190A190PHE0-0.015-0.03546.233-0.001-0.0010.0000.0000.0000.000
191A191PRO00.0360.03344.5550.0010.0010.0000.0000.0000.000
192A192PRO00.0570.02144.3440.0010.0010.0000.0000.0000.000
193A193ILE0-0.040-0.00940.2840.0040.0040.0000.0000.0000.000
194A194VAL0-0.036-0.01839.8600.0020.0020.0000.0000.0000.000
195A195ARG10.9290.97234.855-0.093-0.0930.0000.0000.0000.000
196A196LYS10.8900.93741.327-0.048-0.0480.0000.0000.0000.000
197A197GLY00.020-0.00942.4280.0020.0020.0000.0000.0000.000
198A198ALA0-0.032-0.00441.443-0.003-0.0030.0000.0000.0000.000
199A199GLY00.0920.04842.0990.0020.0020.0000.0000.0000.000
200A200ALA0-0.081-0.07742.824-0.002-0.0020.0000.0000.0000.000
201A201ILE0-0.0100.00442.203-0.002-0.0020.0000.0000.0000.000
202A202ILE00.0680.02244.8440.0000.0000.0000.0000.0000.000
203A203GLY00.0880.01046.6270.0020.0020.0000.0000.0000.000
204A204LEU0-0.0350.00448.9630.0000.0000.0000.0000.0000.000
205A205ALA00.0260.00852.7100.0000.0000.0000.0000.0000.000
206A206VAL0-0.055-0.02454.7770.0000.0000.0000.0000.0000.000
207A207GLY00.0690.03758.3870.0000.0000.0000.0000.0000.000
208A208GLY00.0010.01356.776-0.001-0.0010.0000.0000.0000.000
209A209VAL0-0.034-0.02850.5520.0000.0000.0000.0000.0000.000
210A210VAL00.0190.03550.0010.0010.0010.0000.0000.0000.000
211A211ILE0-0.012-0.00944.8260.0020.0020.0000.0000.0000.000
212A212ALA00.0280.05943.952-0.002-0.0020.0000.0000.0000.000