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: 1N91Z

Calculation Name: 3F56-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F56

Chain ID: A

ChEMBL ID:

UniProt ID: Q7V2D3

Base Structure: X-ray

Registration Date: 2023-09-23

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2286412.552837
FMO2-HF: Nuclear repulsion 2207134.249144
FMO2-HF: Total energy -79278.303693
FMO2-MP2: Total energy -79506.918126


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:50:GLN)


Summations of interaction energy for fragment #1(A:50:GLN)
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.
-11.648-5.3140.317-2.682-3.97-0.009
Interaction energy analysis for fragmet #1(A:50:GLN)
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 : -0.042
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].
3A52GLU-1-0.853-0.9062.908-4.5790.1320.188-2.050-2.849-0.012
4A53GLN0-0.103-0.0423.8770.7651.3860.000-0.136-0.4850.000
5A54ILE0-0.062-0.0365.5640.5510.5510.0000.0000.0000.000
6A55GLU-1-0.848-0.9007.6750.1810.1810.0000.0000.0000.000
7A56LEU0-0.020-0.02311.3570.0380.0380.0000.0000.0000.000
8A57ARG10.9130.96113.680-0.152-0.1520.0000.0000.0000.000
9A58THR00.0060.00416.434-0.012-0.0120.0000.0000.0000.000
10A59TYR00.0140.01217.5530.0100.0100.0000.0000.0000.000
11A60VAL00.001-0.00419.560-0.011-0.0110.0000.0000.0000.000
12A61PHE00.0030.00423.0200.0060.0060.0000.0000.0000.000
13A62LEU0-0.049-0.02524.941-0.005-0.0050.0000.0000.0000.000
14A63ASP-1-0.794-0.88528.3310.0460.0460.0000.0000.0000.000
15A64SER0-0.021-0.00530.449-0.001-0.0010.0000.0000.0000.000
16A65LEU0-0.024-0.00329.6760.0000.0000.0000.0000.0000.000
17A66GLN00.0050.01533.061-0.005-0.0050.0000.0000.0000.000
18A67PRO00.0480.00835.9070.0040.0040.0000.0000.0000.000
19A68GLN0-0.008-0.01037.6190.0040.0040.0000.0000.0000.000
20A69LEU00.0020.00330.5410.0040.0040.0000.0000.0000.000
21A70ALA0-0.0110.00132.9190.0060.0060.0000.0000.0000.000
22A71ALA00.0100.01033.8080.0040.0040.0000.0000.0000.000
23A72TYR0-0.049-0.03430.4900.0040.0040.0000.0000.0000.000
24A73MET0-0.040-0.02325.9580.0050.0050.0000.0000.0000.000
25A74GLY00.003-0.00729.9100.0070.0070.0000.0000.0000.000
26A75THR0-0.077-0.03632.0840.0010.0010.0000.0000.0000.000
27A76VAL0-0.023-0.01228.4960.0030.0030.0000.0000.0000.000
28A77SER0-0.089-0.02426.3600.0120.0120.0000.0000.0000.000
29A78ARG10.9020.93524.694-0.132-0.1320.0000.0000.0000.000
30A79GLY0-0.0080.01825.3470.0060.0060.0000.0000.0000.000
31A80PHE0-0.087-0.05825.465-0.012-0.0120.0000.0000.0000.000
32A81LEU00.0160.00828.3830.0030.0030.0000.0000.0000.000
33A82PRO00.0050.01329.856-0.002-0.0020.0000.0000.0000.000
34A83ILE0-0.041-0.02931.460-0.003-0.0030.0000.0000.0000.000
35A84PRO00.016-0.01233.8800.0010.0010.0000.0000.0000.000
36A85GLY0-0.035-0.01535.184-0.003-0.0030.0000.0000.0000.000
37A86ASP-1-0.836-0.90930.2240.0610.0610.0000.0000.0000.000
38A87SER0-0.025-0.02327.625-0.001-0.0010.0000.0000.0000.000
39A88CYS0-0.043-0.04125.6900.0100.0100.0000.0000.0000.000
40A89LEU0-0.0230.01118.603-0.006-0.0060.0000.0000.0000.000
41A90TRP00.0360.00420.8700.0150.0150.0000.0000.0000.000
42A91MET0-0.023-0.01815.776-0.018-0.0180.0000.0000.0000.000
43A92GLU-1-0.806-0.90616.3110.1710.1710.0000.0000.0000.000
44A93VAL0-0.016-0.01510.813-0.020-0.0200.0000.0000.0000.000
45A94SER00.0000.01911.2850.0400.0400.0000.0000.0000.000
46A95PRO00.0970.0406.746-0.055-0.0550.0000.0000.0000.000
47A96GLY00.0680.0269.7990.0780.0780.0000.0000.0000.000
48A97MET0-0.003-0.0189.9230.0020.0020.0000.0000.0000.000
49A98ALA00.0110.0086.9900.2070.2070.0000.0000.0000.000
50A99VAL00.0270.0158.5190.0380.0380.0000.0000.0000.000
51A100HIS00.0150.02310.960-0.065-0.0650.0000.0000.0000.000
52A101ARG10.9270.9812.692-8.139-7.1370.129-0.496-0.6360.003
53A102VAL00.0280.01510.001-0.144-0.1440.0000.0000.0000.000
54A103THR00.003-0.02111.822-0.112-0.1120.0000.0000.0000.000
55A104ASP-1-0.878-0.93312.6790.3510.3510.0000.0000.0000.000
56A105ILE0-0.007-0.0089.005-0.060-0.0600.0000.0000.0000.000
57A106ALA00.0010.00113.515-0.070-0.0700.0000.0000.0000.000
58A107LEU0-0.012-0.01416.511-0.037-0.0370.0000.0000.0000.000
59A108LYS10.8190.90415.249-0.310-0.3100.0000.0000.0000.000
60A109ALA0-0.0120.01517.103-0.032-0.0320.0000.0000.0000.000
61A110SER0-0.027-0.04019.012-0.022-0.0220.0000.0000.0000.000
62A111ASN0-0.011-0.00222.4220.0130.0130.0000.0000.0000.000
63A112VAL0-0.0130.01621.033-0.002-0.0020.0000.0000.0000.000
64A113ARG10.9070.95623.772-0.087-0.0870.0000.0000.0000.000
65A114LEU00.0280.01319.3290.0010.0010.0000.0000.0000.000
66A115GLY00.0460.00622.958-0.006-0.0060.0000.0000.0000.000
67A116GLN00.0510.00721.850-0.001-0.0010.0000.0000.0000.000
68A117MET0-0.019-0.00616.8870.0260.0260.0000.0000.0000.000
69A118ILE0-0.041-0.00618.550-0.008-0.0080.0000.0000.0000.000
70A119VAL0-0.008-0.00914.5540.0190.0190.0000.0000.0000.000
71A120GLU-1-0.833-0.91017.1540.1600.1600.0000.0000.0000.000
72A121ARG10.9090.94517.649-0.141-0.1410.0000.0000.0000.000
73A122ALA0-0.036-0.01515.8340.0120.0120.0000.0000.0000.000
74A123PHE00.0160.00614.2940.0160.0160.0000.0000.0000.000
75A124GLY00.0170.01914.1470.0070.0070.0000.0000.0000.000
76A125SER0-0.0210.00215.063-0.022-0.0220.0000.0000.0000.000
77A126LEU0-0.037-0.02515.7290.0170.0170.0000.0000.0000.000
78A127ALA00.0270.01918.993-0.018-0.0180.0000.0000.0000.000
79A128LEU0-0.036-0.00818.2340.0080.0080.0000.0000.0000.000
80A129TYR00.0570.03422.664-0.009-0.0090.0000.0000.0000.000
81A130HIS0-0.008-0.01626.2520.0010.0010.0000.0000.0000.000
82A131LYS10.9901.01028.269-0.039-0.0390.0000.0000.0000.000
83A132ASP-1-0.896-0.94629.8110.0310.0310.0000.0000.0000.000
84A133GLN00.0590.00928.4430.0030.0030.0000.0000.0000.000
85A134SER0-0.011-0.01026.7910.0050.0050.0000.0000.0000.000
86A135THR00.0010.00625.139-0.003-0.0030.0000.0000.0000.000
87A136VAL0-0.006-0.00323.2100.0060.0060.0000.0000.0000.000
88A137LEU00.006-0.01221.8920.0080.0080.0000.0000.0000.000
89A138HIS00.0410.04320.873-0.001-0.0010.0000.0000.0000.000
90A139SER0-0.0070.00618.852-0.007-0.0070.0000.0000.0000.000
91A140GLY0-0.036-0.01917.0680.0190.0190.0000.0000.0000.000
92A141ASP-1-0.891-0.94116.3650.0130.0130.0000.0000.0000.000
93A142VAL00.0050.00414.473-0.015-0.0150.0000.0000.0000.000
94A143VAL0-0.055-0.02712.0520.0000.0000.0000.0000.0000.000
95A144LEU0-0.051-0.03511.539-0.006-0.0060.0000.0000.0000.000
96A145ASP-1-0.863-0.91711.986-0.131-0.1310.0000.0000.0000.000
97A146ALA0-0.069-0.0309.506-0.079-0.0790.0000.0000.0000.000
98A147ILE0-0.108-0.0667.110-0.037-0.0370.0000.0000.0000.000
99A148GLY00.0210.0278.143-0.131-0.1310.0000.0000.0000.000
100A149SER0-0.072-0.0529.9850.0630.0630.0000.0000.0000.000
101A150GLU-1-0.832-0.93712.427-0.004-0.0040.0000.0000.0000.000
102A151VAL00.0520.02816.2050.0140.0140.0000.0000.0000.000
103A152ARG10.8700.91719.043-0.015-0.0150.0000.0000.0000.000
104A153LYS10.8820.94912.0840.0010.0010.0000.0000.0000.000
105A154ARG10.8220.95116.108-0.057-0.0570.0000.0000.0000.000
106A155THR0-0.015-0.02416.834-0.003-0.0030.0000.0000.0000.000
107A156LYS10.9110.96618.777-0.072-0.0720.0000.0000.0000.000
108A157PRO0-0.0160.00622.5340.0050.0050.0000.0000.0000.000
109A158SER00.0120.00424.859-0.006-0.0060.0000.0000.0000.000
110A159THR00.004-0.01926.8760.0030.0030.0000.0000.0000.000
111A160SER0-0.034-0.02329.008-0.002-0.0020.0000.0000.0000.000
112A161TRP0-0.056-0.03430.833-0.002-0.0020.0000.0000.0000.000
113A162THR0-0.001-0.00833.7180.0010.0010.0000.0000.0000.000
114A163GLU-1-0.891-0.92736.3310.0510.0510.0000.0000.0000.000
115A164VAL00.0270.01139.9950.0010.0010.0000.0000.0000.000
116A165ILE0-0.0180.00842.204-0.001-0.0010.0000.0000.0000.000
117A166CYS00.005-0.00645.0020.0010.0010.0000.0000.0000.000
118A167ALA0-0.022-0.00148.3100.0000.0000.0000.0000.0000.000
119A168ILE00.0090.01644.7600.0000.0000.0000.0000.0000.000
120A169THR00.0510.00848.245-0.001-0.0010.0000.0000.0000.000
121A170PRO00.025-0.02248.9430.0010.0010.0000.0000.0000.000
122A171ASP-1-0.893-0.94049.0720.0420.0420.0000.0000.0000.000
123A172HIS00.0200.00541.9360.0020.0020.0000.0000.0000.000
124A173ALA00.0460.01944.4630.0020.0020.0000.0000.0000.000
125A174VAL0-0.022-0.00644.6910.0020.0020.0000.0000.0000.000
126A175LEU0-0.022-0.02542.4230.0020.0020.0000.0000.0000.000
127A176ILE00.0150.01839.5350.0030.0030.0000.0000.0000.000
128A177ASN0-0.035-0.02239.9920.0040.0040.0000.0000.0000.000
129A178ARG10.9330.96941.421-0.052-0.0520.0000.0000.0000.000
130A179GLN0-0.0120.00636.9100.0050.0050.0000.0000.0000.000
131A180ASN0-0.048-0.02131.3890.0010.0010.0000.0000.0000.000
132A181ARG10.8720.94734.448-0.056-0.0560.0000.0000.0000.000
133A182SER0-0.074-0.04033.3880.0010.0010.0000.0000.0000.000
134A183GLY00.0230.01935.544-0.001-0.0010.0000.0000.0000.000
135A184SER0-0.026-0.01137.352-0.002-0.0020.0000.0000.0000.000
136A185MET0-0.070-0.04340.9620.0010.0010.0000.0000.0000.000
137A186ILE00.0420.02842.677-0.001-0.0010.0000.0000.0000.000
138A187GLN0-0.050-0.05044.5530.0000.0000.0000.0000.0000.000
139A188SER00.0210.00548.3320.0000.0000.0000.0000.0000.000
140A189GLY0-0.021-0.00149.966-0.001-0.0010.0000.0000.0000.000
141A190MET0-0.0530.00246.6480.0000.0000.0000.0000.0000.000
142A191SER00.0320.02746.1680.0000.0000.0000.0000.0000.000
143A192MET0-0.022-0.01940.5580.0010.0010.0000.0000.0000.000
144A193PHE00.0490.01835.589-0.001-0.0010.0000.0000.0000.000
145A194ILE0-0.040-0.01636.1420.0020.0020.0000.0000.0000.000
146A195LEU00.030-0.00730.980-0.002-0.0020.0000.0000.0000.000
147A196GLU-1-0.831-0.87829.2010.0880.0880.0000.0000.0000.000
148A197THR0-0.025-0.02125.579-0.003-0.0030.0000.0000.0000.000
149A198GLU-1-0.919-0.95223.0300.1160.1160.0000.0000.0000.000
150A199PRO00.001-0.00919.544-0.003-0.0030.0000.0000.0000.000
151A200ALA00.0390.03621.513-0.008-0.0080.0000.0000.0000.000
152A201GLY00.041-0.00121.598-0.007-0.0070.0000.0000.0000.000
153A202TYR00.014-0.02420.434-0.008-0.0080.0000.0000.0000.000
154A203VAL0-0.0060.01425.207-0.007-0.0070.0000.0000.0000.000
155A204LEU00.0110.00125.171-0.005-0.0050.0000.0000.0000.000
156A205LYS10.9180.95927.088-0.061-0.0610.0000.0000.0000.000
157A206ALA00.0290.01028.937-0.005-0.0050.0000.0000.0000.000
158A207ALA00.0130.01431.247-0.004-0.0040.0000.0000.0000.000
159A208ASN00.004-0.00731.465-0.003-0.0030.0000.0000.0000.000
160A209GLU-1-0.885-0.93932.4250.0430.0430.0000.0000.0000.000
161A210ALA00.0160.00734.944-0.003-0.0030.0000.0000.0000.000
162A211GLU-1-0.795-0.90536.6000.0510.0510.0000.0000.0000.000
163A212LYS10.7750.87133.507-0.047-0.0470.0000.0000.0000.000
164A213SER0-0.048-0.02039.025-0.003-0.0030.0000.0000.0000.000
165A214ALA00.0100.02041.322-0.002-0.0020.0000.0000.0000.000
166A215ASN0-0.032-0.00242.6570.0020.0020.0000.0000.0000.000
167A216ILE00.0000.00739.1480.0000.0000.0000.0000.0000.000
168A217THR0-0.021-0.00641.7410.0000.0000.0000.0000.0000.000
169A218ILE00.004-0.00435.2870.0010.0010.0000.0000.0000.000
170A219ILE0-0.033-0.00937.9000.0000.0000.0000.0000.0000.000
171A220ASP-1-0.762-0.89033.1470.0800.0800.0000.0000.0000.000
172A221VAL00.0160.01129.083-0.002-0.0020.0000.0000.0000.000
173A222LYS10.8860.95828.327-0.081-0.0810.0000.0000.0000.000
174A223ALA00.0340.01624.603-0.001-0.0010.0000.0000.0000.000
175A224VAL00.000-0.00820.9310.0080.0080.0000.0000.0000.000
176A225GLY00.0260.00821.511-0.007-0.0070.0000.0000.0000.000
177A226ALA0-0.039-0.02321.5050.0040.0040.0000.0000.0000.000
178A227PHE00.0020.00722.626-0.001-0.0010.0000.0000.0000.000
179A228GLY0-0.0090.00625.5030.0040.0040.0000.0000.0000.000
180A229ARG10.7870.87626.631-0.099-0.0990.0000.0000.0000.000
181A230LEU0-0.0060.01330.3530.0020.0020.0000.0000.0000.000
182A231THR0-0.036-0.02032.814-0.002-0.0020.0000.0000.0000.000
183A232LEU00.0470.01436.2400.0010.0010.0000.0000.0000.000
184A233ALA00.0090.01339.076-0.001-0.0010.0000.0000.0000.000
185A234GLY00.0570.01842.8310.0000.0000.0000.0000.0000.000
186A235LYS10.9450.96746.205-0.032-0.0320.0000.0000.0000.000
187A236GLU-1-0.856-0.93547.4870.0350.0350.0000.0000.0000.000
188A237GLY00.0480.02647.2560.0010.0010.0000.0000.0000.000
189A238ASP-1-0.894-0.94545.8560.0340.0340.0000.0000.0000.000
190A239VAL0-0.050-0.03542.4000.0020.0020.0000.0000.0000.000
191A240GLU-1-0.926-0.96542.5270.0380.0380.0000.0000.0000.000
192A241GLU-1-0.932-0.96243.1140.0350.0350.0000.0000.0000.000
193A242ALA0-0.035-0.02339.6870.0010.0010.0000.0000.0000.000
194A243ALA0-0.009-0.00538.6190.0020.0020.0000.0000.0000.000
195A244ALA00.0030.00238.2100.0020.0020.0000.0000.0000.000
196A245ALA0-0.033-0.02737.7860.0010.0010.0000.0000.0000.000
197A246ALA0-0.0140.00634.4560.0020.0020.0000.0000.0000.000
198A247ILE00.0420.00833.4750.0030.0030.0000.0000.0000.000
199A248ARG10.9871.00633.808-0.038-0.0380.0000.0000.0000.000
200A249ALA0-0.026-0.00231.3370.0000.0000.0000.0000.0000.000
201A250ILE0-0.005-0.01128.7480.0020.0020.0000.0000.0000.000
202A251ASP-1-0.855-0.93329.1840.0540.0540.0000.0000.0000.000
203A252GLN0-0.074-0.04830.072-0.001-0.0010.0000.0000.0000.000
204A253ILE0-0.097-0.03924.499-0.002-0.0020.0000.0000.0000.000
205A254SER0-0.009-0.01025.6060.0020.0020.0000.0000.0000.000
206A255ASN0-0.055-0.01926.4240.0020.0020.0000.0000.0000.000
207A256TYR0-0.0120.00823.382-0.006-0.0060.0000.0000.0000.000