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: J3Y39

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 OptH
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 -2354250.748982
FMO2-HF: Nuclear repulsion 2274099.164314
FMO2-HF: Total energy -80151.584668
FMO2-MP2: Total energy -80391.028221


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.
-12.074-11.03225.712-10.287-16.467-0.069
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 : -0.040 / q_NPA : -0.021
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].
3A3ILE00.0590.0362.850-0.460-0.0174.163-1.380-3.2260.003
4A4ALA00.021-0.0015.633-0.706-0.702-0.001-0.0120.0080.000
5A5GLY0-0.032-0.0079.243-0.002-0.0020.0000.0000.0000.000
6A6ILE0-0.055-0.02212.365-0.017-0.0170.0000.0000.0000.000
7A7ASP-1-0.800-0.90615.6570.1640.1640.0000.0000.0000.000
8A8GLH0-0.076-0.06519.1750.0020.0020.0000.0000.0000.000
9A9ALA0-0.0220.02622.767-0.013-0.0130.0000.0000.0000.000
10A10GLY0-0.066-0.06025.572-0.006-0.0060.0000.0000.0000.000
11A11ARG10.9790.98227.157-0.078-0.0780.0000.0000.0000.000
12A12GLY00.1070.05329.0300.0040.0040.0000.0000.0000.000
13A13PRO0-0.093-0.03830.921-0.008-0.0080.0000.0000.0000.000
14A14VAL00.0230.00233.9570.0010.0010.0000.0000.0000.000
15A15ILE00.003-0.00336.957-0.001-0.0010.0000.0000.0000.000
16A16GLY0-0.009-0.01434.6520.0010.0010.0000.0000.0000.000
17A17PRO00.0040.00330.187-0.001-0.0010.0000.0000.0000.000
18A18MET00.0050.00725.660-0.003-0.0030.0000.0000.0000.000
19A19VAL0-0.0170.00223.8820.0060.0060.0000.0000.0000.000
20A20ILE00.0090.00320.022-0.003-0.0030.0000.0000.0000.000
21A21ALA0-0.046-0.01919.3310.0010.0010.0000.0000.0000.000
22A22ALA00.0410.02314.9070.0070.0070.0000.0000.0000.000
23A23VAL0-0.040-0.02212.382-0.027-0.0270.0000.0000.0000.000
24A24VAL00.0310.0087.9510.0810.0810.0000.0000.0000.000
25A25VAL0-0.0020.0046.919-0.101-0.1010.0000.0000.0000.000
26A26ASP-1-0.846-0.9163.180-4.157-2.7710.056-0.673-0.768-0.006
27A27GLU-1-0.858-0.9451.990-8.621-11.62515.963-5.352-7.607-0.040
28A28ASN0-0.059-0.0263.5410.4000.6800.0150.047-0.3410.000
29A29SER0-0.035-0.0376.5430.3390.3390.0000.0000.0000.000
30A30LEU00.0020.0236.2430.2640.2640.0000.0000.0000.000
31A31PRO00.0310.0078.0170.1920.1920.0000.0000.0000.000
32A32LYS11.0031.00511.2300.4020.4020.0000.0000.0000.000
33A33LEU00.0320.02010.7890.0600.0600.0000.0000.0000.000
34A34GLU-1-0.798-0.88213.482-0.006-0.0060.0000.0000.0000.000
35A35GLU-1-0.978-0.98314.935-0.259-0.2590.0000.0000.0000.000
36A36LEU0-0.046-0.01716.4610.0200.0200.0000.0000.0000.000
37A37LYS10.7840.89018.4640.1260.1260.0000.0000.0000.000
38A38VAL00.0330.01815.6180.0140.0140.0000.0000.0000.000
39A39ARG10.8400.91215.5700.0050.0050.0000.0000.0000.000
40A40ASP-1-0.921-0.94119.867-0.019-0.0190.0000.0000.0000.000
41A41SER00.024-0.00921.520-0.002-0.0020.0000.0000.0000.000
42A42LYS10.8410.91023.323-0.072-0.0720.0000.0000.0000.000
43A43LYS10.8300.90125.411-0.001-0.0010.0000.0000.0000.000
44A44LEU00.0150.02724.507-0.001-0.0010.0000.0000.0000.000
45A45THR00.0320.03128.5430.0040.0040.0000.0000.0000.000
46A46PRO00.0740.03729.6860.0000.0000.0000.0000.0000.000
47A47LYS11.0270.98829.427-0.020-0.0200.0000.0000.0000.000
48A48ARG10.9070.94728.467-0.001-0.0010.0000.0000.0000.000
49A49ARG10.8890.94624.465-0.052-0.0520.0000.0000.0000.000
50A50GLU-1-0.863-0.92924.6490.0620.0620.0000.0000.0000.000
51A51LYS10.8810.94025.248-0.009-0.0090.0000.0000.0000.000
52A52LEU00.1110.05519.6970.0010.0010.0000.0000.0000.000
53A53PHE0-0.0110.00920.6390.0000.0000.0000.0000.0000.000
54A54ASN0-0.016-0.01520.5740.0190.0190.0000.0000.0000.000
55A55GLU-1-0.933-0.96819.804-0.021-0.0210.0000.0000.0000.000
56A56ILE0-0.015-0.01915.493-0.017-0.0170.0000.0000.0000.000
57A57LEU0-0.039-0.02115.7130.0030.0030.0000.0000.0000.000
58A58GLY0-0.0360.00116.4640.0150.0150.0000.0000.0000.000
59A59VAL0-0.052-0.03612.599-0.018-0.0180.0000.0000.0000.000
60A60LEU0-0.095-0.03111.283-0.047-0.0470.0000.0000.0000.000
61A61ASP-1-0.782-0.8857.1920.1450.1450.0000.0000.0000.000
62A62ASP-1-0.817-0.92610.3600.6030.6030.0000.0000.0000.000
63A63TYR0-0.046-0.03712.841-0.031-0.0310.0000.0000.0000.000
64A64VAL0-0.0050.00915.680-0.013-0.0130.0000.0000.0000.000
65A65ILE0-0.022-0.01018.657-0.004-0.0040.0000.0000.0000.000
66A66LEU00.005-0.00621.881-0.009-0.0090.0000.0000.0000.000
67A67GLU-1-0.927-0.96724.0160.1160.1160.0000.0000.0000.000
68A68LEU0-0.032-0.01425.529-0.002-0.0020.0000.0000.0000.000
69A69PRO0-0.040-0.02429.332-0.007-0.0070.0000.0000.0000.000
70A70PRO0-0.017-0.00332.0290.0030.0030.0000.0000.0000.000
71A71ASP-1-0.837-0.91532.3520.0950.0950.0000.0000.0000.000
72A72VAL0-0.082-0.04535.083-0.004-0.0040.0000.0000.0000.000
73A73ILE0-0.014-0.03838.4570.0000.0000.0000.0000.0000.000
74A74GLY00.0200.02639.947-0.001-0.0010.0000.0000.0000.000
75A75SER0-0.038-0.00635.650-0.002-0.0020.0000.0000.0000.000
76A76ARG10.8480.94730.970-0.082-0.0820.0000.0000.0000.000
77A77GLU-1-0.890-0.96034.8940.0580.0580.0000.0000.0000.000
78A78GLY0-0.059-0.01634.9220.0000.0000.0000.0000.0000.000
79A79THR00.0580.02429.9360.0010.0010.0000.0000.0000.000
80A80LEU00.007-0.00431.1410.0040.0040.0000.0000.0000.000
81A81ASN00.006-0.00325.9930.0030.0030.0000.0000.0000.000
82A82GLU-1-0.880-0.95825.9790.0910.0910.0000.0000.0000.000
83A83PHE0-0.042-0.01526.4490.0030.0030.0000.0000.0000.000
84A84GLU-1-0.893-0.91222.4950.1610.1610.0000.0000.0000.000
85A85VAL00.0810.04519.6070.0190.0190.0000.0000.0000.000
86A86GLU-1-0.903-0.94520.3840.1610.1610.0000.0000.0000.000
87A87ASN0-0.035-0.04821.9930.0140.0140.0000.0000.0000.000
88A88PHE00.0320.01017.2480.0190.0190.0000.0000.0000.000
89A89ALA00.0380.03317.1330.0320.0320.0000.0000.0000.000
90A90LYS10.8240.91517.925-0.142-0.1420.0000.0000.0000.000
91A91ALA00.0330.01918.4700.0140.0140.0000.0000.0000.000
92A92LEU00.0810.04112.2030.0300.0300.0000.0000.0000.000
93A93ASN0-0.065-0.02914.9830.0740.0740.0000.0000.0000.000
94A94SER0-0.105-0.06116.922-0.016-0.0160.0000.0000.0000.000
95A95LEU0-0.064-0.01112.263-0.017-0.0170.0000.0000.0000.000
96A96LYS10.8790.94414.246-0.398-0.3980.0000.0000.0000.000
97A97VAL0-0.029-0.0278.3520.0490.0490.0000.0000.0000.000
98A98LYS10.8810.9579.661-0.636-0.6360.0000.0000.0000.000
99A99PRO0-0.029-0.0106.5930.3580.3580.0000.0000.0000.000
100A100ASP-1-0.816-0.9172.2280.5001.6095.138-2.735-3.513-0.024
101A101VAL00.0100.0042.546-1.313-0.5200.379-0.181-0.991-0.002
102A102ILE0-0.029-0.0235.1520.2980.329-0.001-0.001-0.0290.000
103A103TYR0-0.001-0.0086.558-0.027-0.0270.0000.0000.0000.000
104A104ALA0-0.005-0.03811.319-0.028-0.0280.0000.0000.0000.000
105A105ASP-1-0.866-0.94814.8550.1390.1390.0000.0000.0000.000
106A106ALA0-0.031-0.00718.358-0.003-0.0030.0000.0000.0000.000
107A107ALA00.027-0.00120.451-0.012-0.0120.0000.0000.0000.000
108A108ASP-1-0.978-1.00224.1810.0730.0730.0000.0000.0000.000
109A109VAL0-0.0250.00922.443-0.008-0.0080.0000.0000.0000.000
110A110ASP-1-0.910-0.98222.7980.0760.0760.0000.0000.0000.000
111A111GLU-1-0.869-0.94418.6860.1040.1040.0000.0000.0000.000
112A112GLU-1-0.904-0.95517.5420.0760.0760.0000.0000.0000.000
113A113ARG10.9090.96018.183-0.083-0.0830.0000.0000.0000.000
114A114PHE0-0.002-0.00517.4990.0060.0060.0000.0000.0000.000
115A115ALA00.014-0.00414.0020.0150.0150.0000.0000.0000.000
116A116ARG10.9350.99715.078-0.085-0.0850.0000.0000.0000.000
117A117GLU-1-0.921-0.98816.9350.1200.1200.0000.0000.0000.000
118A118LEU0-0.057-0.03014.4840.0060.0060.0000.0000.0000.000
119A119GLY00.0310.01113.6560.0210.0210.0000.0000.0000.000
120A120GLU-1-0.963-0.98314.4320.1300.1300.0000.0000.0000.000
121A121ARG10.8760.93917.493-0.169-0.1690.0000.0000.0000.000
122A122LEU0-0.044-0.00511.9560.0070.0070.0000.0000.0000.000
123A123ASN0-0.039-0.02215.9260.0090.0090.0000.0000.0000.000
124A124PHE0-0.032-0.0439.6190.0210.0210.0000.0000.0000.000
125A125GLU-1-0.980-0.9798.8090.0890.0890.0000.0000.0000.000
126A126ALA00.0800.0277.3170.0810.0810.0000.0000.0000.000
127A127GLU-1-0.960-0.9555.9570.1250.1250.0000.0000.0000.000
128A128VAL0-0.017-0.0077.7140.1790.1790.0000.0000.0000.000
129A129VAL0-0.0030.0059.797-0.085-0.0850.0000.0000.0000.000
130A130ALA00.002-0.00612.0140.0550.0550.0000.0000.0000.000
131A131LYS10.9160.95415.223-0.135-0.1350.0000.0000.0000.000
132A132HIS00.0250.03118.3650.0160.0160.0000.0000.0000.000
133A133LYS10.9080.96920.804-0.065-0.0650.0000.0000.0000.000
134A134ALA00.0750.05015.887-0.011-0.0110.0000.0000.0000.000
135A135ASP-1-0.829-0.91016.7330.1180.1180.0000.0000.0000.000
136A136ASP-1-0.890-0.94818.5860.0470.0470.0000.0000.0000.000
137A137ILE0-0.087-0.02915.085-0.028-0.0280.0000.0000.0000.000
138A138PHE00.0500.00011.126-0.027-0.0270.0000.0000.0000.000
139A139PRO00.0480.02211.9180.0110.0110.0000.0000.0000.000
140A140VAL00.0580.0499.664-0.055-0.0550.0000.0000.0000.000
141A141VAL00.0420.02012.1840.0070.0070.0000.0000.0000.000
142A142SER0-0.027-0.00414.705-0.036-0.0360.0000.0000.0000.000
143A143ALA0-0.018-0.03314.518-0.013-0.0130.0000.0000.0000.000
144A144ALA00.0120.01415.203-0.013-0.0130.0000.0000.0000.000
145A145SER00.0240.01717.132-0.020-0.0200.0000.0000.0000.000
146A146ILE0-0.066-0.03619.350-0.022-0.0220.0000.0000.0000.000
147A147LEU00.003-0.00317.625-0.014-0.0140.0000.0000.0000.000
148A148ALA00.0390.01921.415-0.008-0.0080.0000.0000.0000.000
149A149LYS10.8970.94323.424-0.081-0.0810.0000.0000.0000.000
150A150VAL0-0.049-0.01824.313-0.009-0.0090.0000.0000.0000.000
151A151THR00.0470.02924.618-0.008-0.0080.0000.0000.0000.000
152A152ARG10.9030.96227.296-0.090-0.0900.0000.0000.0000.000
153A153ASP-1-0.907-0.98029.3120.0630.0630.0000.0000.0000.000
154A154ARG10.8580.92926.854-0.082-0.0820.0000.0000.0000.000
155A155ALA00.0410.02831.673-0.005-0.0050.0000.0000.0000.000
156A156VAL0-0.010-0.00833.536-0.004-0.0040.0000.0000.0000.000
157A157GLU-1-0.975-0.98534.8950.0400.0400.0000.0000.0000.000
158A158LYS10.9610.96735.806-0.062-0.0620.0000.0000.0000.000
159A159LEU00.0010.00937.062-0.002-0.0020.0000.0000.0000.000
160A160LYS10.8960.96838.316-0.048-0.0480.0000.0000.0000.000
161A161GLU-1-0.986-0.99039.3680.0450.0450.0000.0000.0000.000
162A162GLU-1-0.979-0.97842.6900.0490.0490.0000.0000.0000.000
163A163TYR0-0.064-0.04043.050-0.002-0.0020.0000.0000.0000.000
164A164GLY00.0050.01045.172-0.002-0.0020.0000.0000.0000.000
165A165GLU-1-0.902-0.96042.0640.0410.0410.0000.0000.0000.000
166A166ILE00.0590.03239.3250.0000.0000.0000.0000.0000.000
167A167GLY0-0.049-0.03740.7970.0020.0020.0000.0000.0000.000
168A168SER0-0.085-0.07235.2880.0030.0030.0000.0000.0000.000
169A169GLY00.0470.02935.6020.0050.0050.0000.0000.0000.000
170A170TYR0-0.0020.01930.7540.0060.0060.0000.0000.0000.000
171A171PRO00.0800.04636.562-0.005-0.0050.0000.0000.0000.000
172A172SER00.007-0.00837.503-0.002-0.0020.0000.0000.0000.000
173A173ASP-1-0.819-0.88138.5340.0390.0390.0000.0000.0000.000
174A174PRO00.0350.00940.4270.0000.0000.0000.0000.0000.000
175A175ARG10.9080.94039.347-0.039-0.0390.0000.0000.0000.000
176A176THR00.0020.01340.0470.0000.0000.0000.0000.0000.000
177A177ARG10.8220.90642.838-0.041-0.0410.0000.0000.0000.000
178A178ALA00.0320.02045.1300.0000.0000.0000.0000.0000.000
179A179PHE0-0.023-0.00643.5770.0000.0000.0000.0000.0000.000
180A180LEU00.006-0.00942.6060.0000.0000.0000.0000.0000.000
181A181GLU-1-0.913-0.95646.8520.0330.0330.0000.0000.0000.000
182A182ASN0-0.059-0.04249.877-0.002-0.0020.0000.0000.0000.000
183A183TYR00.0480.03748.558-0.001-0.0010.0000.0000.0000.000
184A184TYR00.0410.02150.2260.0000.0000.0000.0000.0000.000
185A185ARG10.8540.92252.187-0.030-0.0300.0000.0000.0000.000
186A186GLU-1-1.000-0.99454.3650.0300.0300.0000.0000.0000.000
187A187HIS10.8780.94551.783-0.036-0.0360.0000.0000.0000.000
188A188GLY0-0.0190.00654.8240.0000.0000.0000.0000.0000.000
189A189GLU-1-0.961-0.98250.6400.0440.0440.0000.0000.0000.000
190A190PHE0-0.038-0.03546.208-0.001-0.0010.0000.0000.0000.000
191A191PRO00.0190.02344.5390.0000.0000.0000.0000.0000.000
192A192PRO00.0720.02344.3160.0020.0020.0000.0000.0000.000
193A193ILE0-0.039-0.01040.3290.0040.0040.0000.0000.0000.000
194A194VAL0-0.029-0.00939.7820.0030.0030.0000.0000.0000.000
195A195ARG10.9891.00035.885-0.086-0.0860.0000.0000.0000.000
196A196LYS10.9000.95341.266-0.047-0.0470.0000.0000.0000.000
197A197GLY00.020-0.01842.4460.0010.0010.0000.0000.0000.000
198A198ALA0-0.029-0.00241.501-0.003-0.0030.0000.0000.0000.000
199A199GLY00.0860.04442.1540.0020.0020.0000.0000.0000.000
200A200ALA0-0.077-0.07942.913-0.002-0.0020.0000.0000.0000.000
201A201ILE0-0.0140.01042.488-0.001-0.0010.0000.0000.0000.000
202A202ILE00.0550.01544.936-0.001-0.0010.0000.0000.0000.000
203A203GLY00.092-0.01746.6890.0020.0020.0000.0000.0000.000
204A204LEU0-0.0050.00049.0090.0000.0000.0000.0000.0000.000
205A205ALA00.0340.02052.7500.0000.0000.0000.0000.0000.000
206A206VAL0-0.053-0.03154.7850.0000.0000.0000.0000.0000.000
207A207GLY00.0710.03658.4140.0000.0000.0000.0000.0000.000
208A208GLY00.0030.01456.8180.0000.0000.0000.0000.0000.000
209A209VAL0-0.023-0.02250.5810.0000.0000.0000.0000.0000.000
210A210VAL0-0.0110.02549.7860.0010.0010.0000.0000.0000.000
211A211ILE0-0.0420.01745.0420.0020.0020.0000.0000.0000.000
212A212ALA00.0180.05544.022-0.001-0.0010.0000.0000.0000.000