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: 6NJQZ

Calculation Name: 1M3S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1M3S

Chain ID: A

ChEMBL ID:

UniProt ID: P42404

Base Structure: X-ray

Registration Date: 2023-09-20

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1837031.864577
FMO2-HF: Nuclear repulsion 1765847.965914
FMO2-HF: Total energy -71183.898663
FMO2-MP2: Total energy -71388.157276


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
-1.5851.035-0.009-1.538-1.0750.001
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.027
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].
3A2LYS10.8750.9173.9012.2034.445-0.017-1.378-0.8480.002
4A3THR00.0280.0097.419-0.096-0.0960.0000.0000.0000.000
5A4THR00.0250.0009.394-0.040-0.0400.0000.0000.0000.000
6A5GLU-1-0.774-0.8707.549-2.812-2.8120.0000.0000.0000.000
7A6TYR00.0660.0233.655-0.815-0.4370.008-0.160-0.227-0.001
8A7VAL0-0.039-0.0128.7930.2530.2530.0000.0000.0000.000
9A8ALA00.0100.01111.5190.1260.1260.0000.0000.0000.000
10A9GLU-1-0.863-0.9318.361-0.896-0.8960.0000.0000.0000.000
11A10ILE0-0.019-0.00410.8390.1810.1810.0000.0000.0000.000
12A11LEU0-0.0020.00213.3160.0990.0990.0000.0000.0000.000
13A12ASN0-0.011-0.01212.2110.1520.1520.0000.0000.0000.000
14A13GLU-1-0.773-0.84811.945-0.262-0.2620.0000.0000.0000.000
15A14LEU0-0.030-0.02815.6090.0670.0670.0000.0000.0000.000
16A15HIS0-0.0210.00518.3470.0360.0360.0000.0000.0000.000
17A16ASN0-0.017-0.02218.1260.0650.0650.0000.0000.0000.000
18A17SER00.0090.00319.3340.0420.0420.0000.0000.0000.000
19A18ALA00.0470.00121.0960.0270.0270.0000.0000.0000.000
20A19ALA0-0.0180.00523.4530.0190.0190.0000.0000.0000.000
21A20TYR0-0.083-0.03321.5340.0210.0210.0000.0000.0000.000
22A21ILE0-0.048-0.02725.8170.0170.0170.0000.0000.0000.000
23A22SER0-0.042-0.00628.886-0.005-0.0050.0000.0000.0000.000
24A23ASN00.034-0.00532.609-0.005-0.0050.0000.0000.0000.000
25A24GLU-1-0.906-0.94234.862-0.060-0.0600.0000.0000.0000.000
26A25GLU-1-0.942-0.98235.238-0.048-0.0480.0000.0000.0000.000
27A26ALA0-0.003-0.01733.6360.0020.0020.0000.0000.0000.000
28A27ASP-1-0.809-0.91835.638-0.080-0.0800.0000.0000.0000.000
29A28GLN00.0390.02238.6770.0060.0060.0000.0000.0000.000
30A29LEU0-0.0100.00235.1460.0040.0040.0000.0000.0000.000
31A30ALA0-0.015-0.00638.4060.0020.0020.0000.0000.0000.000
32A31ASP-1-0.809-0.90039.872-0.058-0.0580.0000.0000.0000.000
33A32HIS0-0.007-0.00641.6280.0030.0030.0000.0000.0000.000
34A33ILE0-0.037-0.02337.7810.0020.0020.0000.0000.0000.000
35A34LEU0-0.085-0.04642.3950.0010.0010.0000.0000.0000.000
36A35SER0-0.062-0.02645.0970.0020.0020.0000.0000.0000.000
37A36SER0-0.025-0.00245.0810.0020.0020.0000.0000.0000.000
38A37HIS0-0.042-0.00546.948-0.003-0.0030.0000.0000.0000.000
39A38GLN0-0.075-0.05346.031-0.002-0.0020.0000.0000.0000.000
40A39ILE0-0.0020.00539.7930.0000.0000.0000.0000.0000.000
41A40PHE0-0.038-0.01540.598-0.001-0.0010.0000.0000.0000.000
42A41THR0-0.005-0.00834.9220.0010.0010.0000.0000.0000.000
43A42ALA00.015-0.00535.1310.0050.0050.0000.0000.0000.000
44A43GLY00.0430.01531.250-0.004-0.0040.0000.0000.0000.000
45A44ALA0-0.005-0.00230.2030.0030.0030.0000.0000.0000.000
46A45GLY00.0240.00627.207-0.003-0.0030.0000.0000.0000.000
47A46ARG10.9080.92019.0050.0730.0730.0000.0000.0000.000
48A47SER00.0320.02025.425-0.015-0.0150.0000.0000.0000.000
49A48GLY0-0.0110.01027.164-0.005-0.0050.0000.0000.0000.000
50A49LEU0-0.015-0.01225.554-0.003-0.0030.0000.0000.0000.000
51A50MET0-0.0070.01023.033-0.009-0.0090.0000.0000.0000.000
52A51ALA00.0060.00428.236-0.004-0.0040.0000.0000.0000.000
53A52LYS10.8770.94431.6210.0300.0300.0000.0000.0000.000
54A53SER0-0.008-0.00528.6380.0010.0010.0000.0000.0000.000
55A54PHE00.0360.01531.349-0.003-0.0030.0000.0000.0000.000
56A55ALA00.011-0.00733.1480.0010.0010.0000.0000.0000.000
57A56MET0-0.014-0.00333.360-0.001-0.0010.0000.0000.0000.000
58A57ARG10.9530.98731.2920.1120.1120.0000.0000.0000.000
59A58LEU00.012-0.00336.1000.0010.0010.0000.0000.0000.000
60A59MET00.0110.01938.8100.0020.0020.0000.0000.0000.000
61A60HIS0-0.022-0.00735.689-0.004-0.0040.0000.0000.0000.000
62A61MET00.0100.01838.852-0.001-0.0010.0000.0000.0000.000
63A62GLY0-0.019-0.00941.7080.0020.0020.0000.0000.0000.000
64A63PHE0-0.024-0.01941.3290.0030.0030.0000.0000.0000.000
65A64ASN00.0050.01543.9430.0000.0000.0000.0000.0000.000
66A65ALA0-0.0040.00039.9000.0020.0020.0000.0000.0000.000
67A66HIS00.011-0.00241.0950.0020.0020.0000.0000.0000.000
68A67ILE00.0080.00635.953-0.002-0.0020.0000.0000.0000.000
69A68VAL0-0.008-0.00738.1350.0040.0040.0000.0000.0000.000
70A69GLY0-0.032-0.02537.8160.0000.0000.0000.0000.0000.000
71A70GLU-1-0.849-0.90036.568-0.023-0.0230.0000.0000.0000.000
72A71ILE0-0.017-0.01540.3880.0010.0010.0000.0000.0000.000
73A72LEU0-0.033-0.02443.4010.0010.0010.0000.0000.0000.000
74A73THR0-0.047-0.01541.608-0.001-0.0010.0000.0000.0000.000
75A74PRO00.0090.02244.4500.0030.0030.0000.0000.0000.000
76A75PRO0-0.039-0.03246.7270.0000.0000.0000.0000.0000.000
77A76LEU0-0.0070.00044.916-0.002-0.0020.0000.0000.0000.000
78A77ALA0-0.048-0.03148.1360.0020.0020.0000.0000.0000.000
79A78GLU-1-0.923-0.97549.816-0.017-0.0170.0000.0000.0000.000
80A79GLY0-0.005-0.00549.598-0.001-0.0010.0000.0000.0000.000
81A80ASP-1-0.762-0.86246.111-0.029-0.0290.0000.0000.0000.000
82A81LEU0-0.0080.00340.3080.0010.0010.0000.0000.0000.000
83A82VAL0-0.029-0.02039.0810.0000.0000.0000.0000.0000.000
84A83ILE00.0110.01034.6510.0000.0000.0000.0000.0000.000
85A84ILE0-0.039-0.03133.8380.0010.0010.0000.0000.0000.000
86A85GLY00.0670.04830.461-0.002-0.0020.0000.0000.0000.000
87A86SER0-0.075-0.06629.2610.0090.0090.0000.0000.0000.000
88A87GLY00.0690.05226.006-0.001-0.0010.0000.0000.0000.000
89A88SER0-0.013-0.02126.961-0.002-0.0020.0000.0000.0000.000
90A89GLY00.0830.03828.7430.0010.0010.0000.0000.0000.000
91A90GLU-1-0.767-0.88231.5880.0280.0280.0000.0000.0000.000
92A91THR0-0.0260.00131.1810.0060.0060.0000.0000.0000.000
93A92LYS10.9400.95633.403-0.039-0.0390.0000.0000.0000.000
94A93SER00.0350.01935.342-0.003-0.0030.0000.0000.0000.000
95A94LEU00.0180.01432.328-0.003-0.0030.0000.0000.0000.000
96A95ILE0-0.0130.00336.342-0.003-0.0030.0000.0000.0000.000
97A96HIS00.002-0.00338.750-0.001-0.0010.0000.0000.0000.000
98A97THR0-0.013-0.01539.133-0.002-0.0020.0000.0000.0000.000
99A98ALA00.0230.02339.298-0.002-0.0020.0000.0000.0000.000
100A99ALA00.0530.02841.304-0.002-0.0020.0000.0000.0000.000
101A100LYS10.8680.93644.3260.0030.0030.0000.0000.0000.000
102A101ALA00.0590.03843.633-0.001-0.0010.0000.0000.0000.000
103A102LYS10.8300.89544.1970.0160.0160.0000.0000.0000.000
104A103SER0-0.109-0.05946.9110.0000.0000.0000.0000.0000.000
105A104LEU0-0.069-0.04948.1470.0010.0010.0000.0000.0000.000
106A105HIS00.0310.03250.062-0.001-0.0010.0000.0000.0000.000
107A106GLY00.0560.04746.634-0.002-0.0020.0000.0000.0000.000
108A107ILE0-0.0140.00143.2500.0020.0020.0000.0000.0000.000
109A108VAL0-0.034-0.03139.351-0.001-0.0010.0000.0000.0000.000
110A109ALA00.0580.03937.4660.0000.0000.0000.0000.0000.000
111A110ALA0-0.029-0.01634.7080.0010.0010.0000.0000.0000.000
112A111LEU00.0160.01930.254-0.003-0.0030.0000.0000.0000.000
113A112THR0-0.025-0.04029.3350.0060.0060.0000.0000.0000.000
114A113ILE0-0.0160.00923.916-0.004-0.0040.0000.0000.0000.000
115A114ASN0-0.002-0.00228.118-0.003-0.0030.0000.0000.0000.000
116A115PRO00.0370.02531.0650.0020.0020.0000.0000.0000.000
117A116GLU-1-0.884-0.92734.4400.0050.0050.0000.0000.0000.000
118A117SER0-0.030-0.01732.9430.0050.0050.0000.0000.0000.000
119A118SER0-0.014-0.04935.069-0.003-0.0030.0000.0000.0000.000
120A119ILE0-0.079-0.03133.653-0.002-0.0020.0000.0000.0000.000
121A120GLY00.0170.01435.692-0.004-0.0040.0000.0000.0000.000
122A121LYS10.8350.89736.670-0.008-0.0080.0000.0000.0000.000
123A122GLN0-0.073-0.03739.8590.0000.0000.0000.0000.0000.000
124A123ALA0-0.046-0.01238.277-0.001-0.0010.0000.0000.0000.000
125A124ASP-1-0.792-0.86340.377-0.019-0.0190.0000.0000.0000.000
126A125LEU0-0.0140.01037.952-0.001-0.0010.0000.0000.0000.000
127A126ILE0-0.022-0.01434.1130.0010.0010.0000.0000.0000.000
128A127ILE00.0460.02630.958-0.003-0.0030.0000.0000.0000.000
129A128ARG10.8710.93727.6200.0630.0630.0000.0000.0000.000
130A129MET0-0.040-0.01025.801-0.014-0.0140.0000.0000.0000.000
131A130PRO0-0.032-0.02022.8660.0150.0150.0000.0000.0000.000
132A131GLY00.037-0.01421.965-0.001-0.0010.0000.0000.0000.000
133A132SER0-0.035-0.01922.8710.0210.0210.0000.0000.0000.000
134A133PRO00.024-0.01924.013-0.003-0.0030.0000.0000.0000.000
135A134LYS10.9641.00524.7970.0390.0390.0000.0000.0000.000
136A135ASP-1-0.769-0.86523.064-0.043-0.0430.0000.0000.0000.000
137A136GLN0-0.031-0.01919.0170.0090.0090.0000.0000.0000.000
138A137SER0-0.061-0.01619.3530.0230.0230.0000.0000.0000.000
139A138ASN0-0.065-0.03720.6060.0250.0250.0000.0000.0000.000
140A139GLY0-0.015-0.01117.504-0.007-0.0070.0000.0000.0000.000
141A140SER0-0.020-0.00217.878-0.032-0.0320.0000.0000.0000.000
142A141TYR00.0410.02218.659-0.031-0.0310.0000.0000.0000.000
143A142LYS10.9320.96912.8760.2650.2650.0000.0000.0000.000
144A143THR0-0.023-0.05113.280-0.027-0.0270.0000.0000.0000.000
145A144ILE0-0.0120.0016.7600.0940.0940.0000.0000.0000.000
146A145GLN0-0.066-0.04110.0660.0780.0780.0000.0000.0000.000
147A146PRO00.004-0.00212.2070.0630.0630.0000.0000.0000.000
148A147MET0-0.004-0.00514.896-0.057-0.0570.0000.0000.0000.000
149A148GLY00.0600.03318.253-0.013-0.0130.0000.0000.0000.000
150A149SER0-0.044-0.03116.009-0.019-0.0190.0000.0000.0000.000
151A150LEU00.0650.04516.312-0.017-0.0170.0000.0000.0000.000
152A151PHE00.0210.02218.203-0.010-0.0100.0000.0000.0000.000
153A152GLU-1-0.795-0.89121.239-0.044-0.0440.0000.0000.0000.000
154A153GLN00.010-0.00615.590-0.007-0.0070.0000.0000.0000.000
155A154THR0-0.003-0.02321.128-0.012-0.0120.0000.0000.0000.000
156A155LEU0-0.044-0.01623.0960.0040.0040.0000.0000.0000.000
157A156LEU0-0.0050.00823.5130.0040.0040.0000.0000.0000.000
158A157LEU00.004-0.00121.5830.0000.0000.0000.0000.0000.000
159A158PHE00.0290.01425.8480.0050.0050.0000.0000.0000.000
160A159TYR0-0.025-0.03128.4440.0100.0100.0000.0000.0000.000
161A160ASP-1-0.850-0.93428.427-0.130-0.1300.0000.0000.0000.000
162A161ALA0-0.042-0.00729.6410.0000.0000.0000.0000.0000.000
163A162VAL0-0.001-0.00331.4270.0060.0060.0000.0000.0000.000
164A163ILE00.007-0.00333.4860.0060.0060.0000.0000.0000.000
165A164LEU00.0010.00031.3350.0030.0030.0000.0000.0000.000
166A165LYS10.8030.90335.3050.0920.0920.0000.0000.0000.000
167A166LEU0-0.027-0.01237.5150.0060.0060.0000.0000.0000.000
168A167MET0-0.032-0.01537.1180.0020.0020.0000.0000.0000.000
169A168GLU-1-0.852-0.90139.269-0.086-0.0860.0000.0000.0000.000
170A169LYS10.8220.89841.0360.0730.0730.0000.0000.0000.000
171A170LYS10.8470.93243.1560.0640.0640.0000.0000.0000.000
172A171GLY0-0.0230.00444.3100.0020.0020.0000.0000.0000.000
173A172LEU0-0.058-0.03441.6970.0010.0010.0000.0000.0000.000
174A173ASP-1-0.774-0.88740.105-0.108-0.1080.0000.0000.0000.000
175A174SER0-0.044-0.03535.9890.0000.0000.0000.0000.0000.000
176A175GLU-1-1.013-0.99038.191-0.108-0.1080.0000.0000.0000.000
177A176THR0-0.071-0.06340.0010.0050.0050.0000.0000.0000.000
178A177MET0-0.051-0.00138.7140.0050.0050.0000.0000.0000.000
179A178PHE0-0.024-0.00742.183-0.001-0.0010.0000.0000.0000.000
180A179THR00.012-0.00238.8790.0000.0000.0000.0000.0000.000
181A180HIS0-0.036-0.01542.2110.0030.0030.0000.0000.0000.000
182A181HIS0-0.061-0.03639.6620.0010.0010.0000.0000.0000.000
183A182ALA00.0130.00440.1330.0030.0030.0000.0000.0000.000
184A183ASN00.012-0.01441.656-0.002-0.0020.0000.0000.0000.000
185A184LEU00.0020.00343.5570.0010.0010.0000.0000.0000.000
186A185GLU-1-1.000-0.97839.255-0.047-0.0470.0000.0000.0000.000