FMO DATABASE

FMODB ID: V24Z1

Calculation Name: 1M5I-A-Xray315

Preferred Name: Adenomatous polyposis coli protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1M5I

Chain ID: A

ChEMBL ID: CHEMBL3233

UniProt ID: P25054

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	112
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-808004.098772
FMO2-HF: Nuclear repulsion	761169.386477
FMO2-HF: Total energy	-46834.712296
FMO2-MP2: Total energy	-46970.761113

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:129:ACE )

Summations of interaction energy for fragment #1(A:129: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.
13.337	-9.596	39.584	-8.42	-8.232	-0.041

Interaction energy analysis for fragmet #1(A:129:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.086 / q_NPA : -0.054

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 ES EX CT+mix DI(MP2)

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].
3	A	131	THR	0	0.036	0.019	3.419	2.079	2.301	0.021	0.561	-0.805	-0.004
4	A	132	GLY	0	0.046	0.017	6.199	-0.025	-0.025	0.000	0.000	0.000	0.000
5	A	133	TYR	0	0.063	0.028	8.103	0.023	0.023	0.000	0.000	0.000	0.000
6	A	134	LEU	0	-0.027	0.029	2.046	8.393	-3.008	12.391	1.233	-2.223	0.000
7	A	135	GLU	-1	-0.938	-0.954	4.526	-0.645	-0.457	0.000	-0.024	-0.164	0.000
8	A	136	GLU	-1	-0.907	-0.973	5.636	0.123	0.123	0.000	0.000	0.000	0.000
9	A	137	LEU	0	-0.012	0.002	6.369	0.168	0.168	0.000	0.000	0.000	0.000
10	A	138	GLU	-1	-0.831	-0.897	2.178	13.489	4.364	19.417	-7.207	-3.085	-0.035
11	A	139	LYS	1	0.936	0.961	6.542	0.346	0.346	0.000	0.000	0.000	0.000
12	A	140	GLU	-1	-0.765	-0.871	9.635	0.132	0.132	0.000	0.000	0.000	0.000
13	A	141	ARG	1	0.866	0.925	8.722	-0.688	-0.688	0.000	0.000	0.000	0.000
14	A	142	SER	0	-0.050	-0.032	9.565	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	143	LEU	0	-0.025	-0.002	12.156	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	144	LEU	0	0.004	-0.006	14.381	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	145	LEU	0	-0.064	-0.037	12.765	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	146	ALA	0	0.000	0.008	16.475	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	147	ASP	-1	-0.890	-0.953	18.227	0.067	0.067	0.000	0.000	0.000	0.000
20	A	148	LEU	0	-0.068	-0.041	18.850	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	149	ASP	-1	-0.827	-0.904	20.433	0.091	0.091	0.000	0.000	0.000	0.000
22	A	150	LYS	1	0.940	0.966	22.219	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	151	GLU	-1	-0.818	-0.916	24.223	0.060	0.060	0.000	0.000	0.000	0.000
24	A	152	GLU	-1	-0.902	-0.968	25.287	0.087	0.087	0.000	0.000	0.000	0.000
25	A	153	LYS	1	0.878	0.953	23.492	-0.081	-0.081	0.000	0.000	0.000	0.000
26	A	154	GLU	-1	-0.942	-0.967	28.286	0.032	0.032	0.000	0.000	0.000	0.000
27	A	155	LYS	1	0.933	0.948	29.936	-0.073	-0.073	0.000	0.000	0.000	0.000
28	A	156	ASP	-1	-0.916	-0.945	30.293	0.062	0.062	0.000	0.000	0.000	0.000
29	A	157	TRP	0	-0.082	-0.031	32.479	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	158	TYR	0	0.079	0.019	33.309	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	159	TYR	0	-0.005	-0.023	34.924	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	160	ALA	0	0.025	0.036	36.869	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	161	GLN	0	-0.042	-0.024	38.455	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	162	LEU	0	-0.017	-0.008	39.827	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	163	GLN	0	0.033	0.009	38.063	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	164	ASN	0	-0.005	-0.009	41.604	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	165	LEU	0	-0.023	-0.005	44.689	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	166	THR	0	0.001	0.005	45.751	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	167	LYS	1	0.974	0.980	44.737	-0.031	-0.031	0.000	0.000	0.000	0.000
40	A	168	ARG	1	0.900	0.971	48.491	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	169	ILE	0	-0.014	-0.008	50.620	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	170	ASP	-1	-0.922	-0.966	50.513	0.025	0.025	0.000	0.000	0.000	0.000
43	A	171	SER	0	-0.078	-0.044	52.228	0.000	0.000	0.000	0.000	0.000	0.000
44	A	172	LEU	0	-0.107	-0.039	54.764	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	173	PRO	0	0.055	0.034	57.526	0.000	0.000	0.000	0.000	0.000	0.000
46	A	174	LEU	0	-0.051	-0.021	59.555	0.000	0.000	0.000	0.000	0.000	0.000
47	A	175	THR	0	0.005	-0.015	61.872	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	176	GLU	-1	-0.924	-0.955	63.244	0.014	0.014	0.000	0.000	0.000	0.000
49	A	177	ASN	0	-0.025	-0.037	65.561	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	178	PHE	0	0.028	0.033	63.796	0.000	0.000	0.000	0.000	0.000	0.000
51	A	179	SER	0	0.005	0.019	63.985	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	180	LEU	0	0.052	0.008	64.423	0.000	0.000	0.000	0.000	0.000	0.000
53	A	181	GLN	0	0.062	0.022	60.644	0.000	0.000	0.000	0.000	0.000	0.000
54	A	182	THR	0	0.019	0.008	59.211	0.000	0.000	0.000	0.000	0.000	0.000
55	A	183	ASP	-1	-0.865	-0.927	59.097	0.015	0.015	0.000	0.000	0.000	0.000
56	A	184	MET	0	-0.099	-0.050	59.208	0.000	0.000	0.000	0.000	0.000	0.000
57	A	185	THR	0	0.010	-0.006	55.477	0.000	0.000	0.000	0.000	0.000	0.000
58	A	186	ARG	1	0.969	0.986	54.766	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	187	ARG	1	0.938	0.972	54.126	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	188	GLN	0	-0.043	-0.006	51.947	0.000	0.000	0.000	0.000	0.000	0.000
61	A	189	LEU	0	0.021	-0.002	50.373	0.000	0.000	0.000	0.000	0.000	0.000
62	A	190	GLU	-1	-0.920	-0.962	49.378	0.020	0.020	0.000	0.000	0.000	0.000
63	A	191	TYR	0	-0.062	-0.030	49.424	0.001	0.001	0.000	0.000	0.000	0.000
64	A	192	GLU	-1	-0.862	-0.942	47.490	0.016	0.016	0.000	0.000	0.000	0.000
65	A	193	ALA	0	0.032	0.010	45.197	0.001	0.001	0.000	0.000	0.000	0.000
66	A	194	ARG	1	0.882	0.944	44.652	-0.016	-0.016	0.000	0.000	0.000	0.000
67	A	195	GLN	0	-0.009	0.006	44.947	0.000	0.000	0.000	0.000	0.000	0.000
68	A	196	ILE	0	-0.003	-0.002	40.099	0.000	0.000	0.000	0.000	0.000	0.000
69	A	197	ARG	1	0.899	0.944	40.098	-0.025	-0.025	0.000	0.000	0.000	0.000
70	A	198	VAL	0	-0.005	0.007	40.149	0.001	0.001	0.000	0.000	0.000	0.000
71	A	199	ALA	0	0.039	0.017	38.830	0.000	0.000	0.000	0.000	0.000	0.000
72	A	200	MET	0	-0.026	0.004	34.254	0.000	0.000	0.000	0.000	0.000	0.000
73	A	201	GLU	-1	-0.928	-0.959	35.165	0.031	0.031	0.000	0.000	0.000	0.000
74	A	202	GLU	-1	-0.977	-0.987	35.929	0.015	0.015	0.000	0.000	0.000	0.000
75	A	203	GLN	0	-0.055	-0.020	32.408	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	204	LEU	0	-0.074	-0.045	29.614	0.003	0.003	0.000	0.000	0.000	0.000
77	A	205	GLY	0	0.018	0.023	31.925	0.005	0.005	0.000	0.000	0.000	0.000
78	A	206	THR	0	-0.005	-0.005	33.983	0.001	0.001	0.000	0.000	0.000	0.000
79	A	207	CYS	0	-0.003	-0.018	34.133	0.004	0.004	0.000	0.000	0.000	0.000
80	A	208	GLN	0	0.021	0.001	33.680	0.003	0.003	0.000	0.000	0.000	0.000
81	A	209	ASP	-1	-0.899	-0.950	31.330	0.048	0.048	0.000	0.000	0.000	0.000
82	A	210	MET	0	0.027	0.035	29.655	0.004	0.004	0.000	0.000	0.000	0.000
83	A	211	GLU	-1	-0.901	-0.957	28.574	0.073	0.073	0.000	0.000	0.000	0.000
84	A	212	LYS	1	0.921	0.946	27.939	-0.052	-0.052	0.000	0.000	0.000	0.000
85	A	213	ARG	1	0.781	0.864	24.781	-0.049	-0.049	0.000	0.000	0.000	0.000
86	A	214	ALA	0	0.054	0.022	23.485	0.008	0.008	0.000	0.000	0.000	0.000
87	A	215	GLN	0	0.004	0.002	22.745	0.021	0.021	0.000	0.000	0.000	0.000
88	A	216	ARG	1	0.952	1.012	22.075	-0.063	-0.063	0.000	0.000	0.000	0.000
89	A	217	ARG	1	0.949	0.995	19.061	-0.077	-0.077	0.000	0.000	0.000	0.000
90	A	218	ILE	0	0.031	0.026	17.722	0.029	0.029	0.000	0.000	0.000	0.000
91	A	219	ALA	0	0.010	0.013	17.884	0.029	0.029	0.000	0.000	0.000	0.000
92	A	220	ARG	1	0.817	0.904	13.092	-0.140	-0.140	0.000	0.000	0.000	0.000
93	A	221	ILE	0	0.037	0.015	13.004	0.041	0.041	0.000	0.000	0.000	0.000
94	A	222	GLN	0	0.059	0.023	12.809	0.063	0.063	0.000	0.000	0.000	0.000
95	A	223	GLN	0	-0.129	-0.067	13.812	0.022	0.022	0.000	0.000	0.000	0.000
96	A	224	ILE	0	0.018	0.010	8.985	0.039	0.039	0.000	0.000	0.000	0.000
97	A	225	GLU	-1	-0.882	-0.941	9.153	0.723	0.723	0.000	0.000	0.000	0.000
98	A	226	LYS	1	0.852	0.933	9.470	-0.179	-0.179	0.000	0.000	0.000	0.000
99	A	227	ASP	-1	-0.862	-0.928	9.642	0.319	0.319	0.000	0.000	0.000	0.000
100	A	228	ILE	0	0.018	0.002	3.858	-0.007	0.070	0.001	-0.028	-0.051	0.000
101	A	229	LEU	0	-0.023	-0.010	5.929	0.230	0.230	0.000	0.000	0.000	0.000
102	A	230	ARG	1	0.939	0.972	7.998	-0.403	-0.403	0.000	0.000	0.000	0.000
103	A	231	ILE	0	0.039	0.024	6.265	-0.111	-0.111	0.000	0.000	0.000	0.000
104	A	232	ARG	1	0.876	0.921	1.898	-10.112	-13.006	7.754	-2.955	-1.904	-0.002
105	A	233	GLN	0	0.006	0.010	6.089	-0.342	-0.342	0.000	0.000	0.000	0.000
106	A	234	LEU	0	-0.039	0.004	9.650	-0.106	-0.106	0.000	0.000	0.000	0.000
107	A	235	LEU	0	0.025	-0.007	5.926	-0.085	-0.085	0.000	0.000	0.000	0.000
108	A	236	GLN	0	-0.060	-0.044	6.671	-0.064	-0.064	0.000	0.000	0.000	0.000
109	A	237	SER	0	-0.088	-0.048	10.359	-0.023	-0.023	0.000	0.000	0.000	0.000
110	A	238	GLN	0	-0.034	-0.010	12.229	-0.051	-0.051	0.000	0.000	0.000	0.000
111	A	239	ALA	0	-0.014	0.019	11.724	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	240	NME	0	-0.013	-0.006	13.656	0.024	0.024	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:129:ACE )