FMO DATABASE

FMODB ID: M3JLZ

Calculation Name: 1M5I-A-Xray372

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: 2023-06-19

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	110
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-802916.650974
FMO2-HF: Nuclear repulsion	756252.684061
FMO2-HF: Total energy	-46663.966912
FMO2-MP2: Total energy	-46799.472656

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:130:SER)

Summations of interaction energy for fragment #1(A:130:SER)

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.
-8.665	-5.669	7.177	-4.673	-5.5	-0.003

Interaction energy analysis for fragmet #1(A:130:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.004

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	132	GLY	0	0.048	0.018	3.835	0.184	2.043	-0.024	-1.040	-0.795	0.002
4	A	133	TYR	0	0.062	0.028	6.067	-0.403	-0.403	0.000	0.000	0.000	0.000
5	A	134	LEU	0	-0.013	-0.006	2.397	0.248	-2.248	6.932	-1.922	-2.514	0.009
6	A	135	GLU	-1	-0.938	-0.955	3.187	-3.653	-2.718	0.044	-0.331	-0.648	-0.002
7	A	136	GLU	-1	-0.908	-0.973	3.721	0.277	0.466	0.004	-0.023	-0.170	0.000
8	A	137	LEU	0	-0.015	0.001	6.531	0.143	0.143	0.000	0.000	0.000	0.000
9	A	138	GLU	-1	-0.875	-0.934	2.957	-8.348	-5.986	0.222	-1.341	-1.243	-0.012
10	A	139	LYS	1	0.935	0.960	6.760	1.017	1.017	0.000	0.000	0.000	0.000
11	A	140	GLU	-1	-0.769	-0.871	8.971	-0.101	-0.101	0.000	0.000	0.000	0.000
12	A	141	ARG	1	0.872	0.926	10.005	0.496	0.496	0.000	0.000	0.000	0.000
13	A	142	SER	0	-0.052	-0.032	10.006	0.103	0.103	0.000	0.000	0.000	0.000
14	A	143	LEU	0	-0.026	-0.002	12.546	0.062	0.062	0.000	0.000	0.000	0.000
15	A	144	LEU	0	0.002	-0.005	14.687	0.045	0.045	0.000	0.000	0.000	0.000
16	A	145	LEU	0	-0.058	-0.035	13.845	0.032	0.032	0.000	0.000	0.000	0.000
17	A	146	ALA	0	-0.005	0.006	16.877	0.027	0.027	0.000	0.000	0.000	0.000
18	A	147	ASP	-1	-0.890	-0.953	18.667	-0.143	-0.143	0.000	0.000	0.000	0.000
19	A	148	LEU	0	-0.065	-0.040	19.844	0.016	0.016	0.000	0.000	0.000	0.000
20	A	149	ASP	-1	-0.828	-0.904	21.338	-0.086	-0.086	0.000	0.000	0.000	0.000
21	A	150	LYS	1	0.939	0.966	22.705	0.094	0.094	0.000	0.000	0.000	0.000
22	A	151	GLU	-1	-0.819	-0.916	24.651	-0.068	-0.068	0.000	0.000	0.000	0.000
23	A	152	GLU	-1	-0.900	-0.967	26.034	-0.069	-0.069	0.000	0.000	0.000	0.000
24	A	153	LYS	1	0.877	0.952	24.107	0.086	0.086	0.000	0.000	0.000	0.000
25	A	154	GLU	-1	-0.942	-0.967	28.798	-0.058	-0.058	0.000	0.000	0.000	0.000
26	A	155	LYS	1	0.930	0.947	30.538	0.058	0.058	0.000	0.000	0.000	0.000
27	A	156	ASP	-1	-0.913	-0.944	31.358	-0.048	-0.048	0.000	0.000	0.000	0.000
28	A	157	TRP	0	-0.082	-0.032	33.151	0.004	0.004	0.000	0.000	0.000	0.000
29	A	158	TYR	0	0.080	0.019	33.394	0.003	0.003	0.000	0.000	0.000	0.000
30	A	159	TYR	0	-0.004	-0.022	35.704	0.002	0.002	0.000	0.000	0.000	0.000
31	A	160	ALA	0	0.023	0.035	37.646	0.003	0.003	0.000	0.000	0.000	0.000
32	A	161	GLN	0	-0.039	-0.024	38.818	0.001	0.001	0.000	0.000	0.000	0.000
33	A	162	LEU	0	-0.020	-0.008	40.256	0.002	0.002	0.000	0.000	0.000	0.000
34	A	163	GLN	0	0.035	0.010	39.106	0.002	0.002	0.000	0.000	0.000	0.000
35	A	164	ASN	0	-0.007	-0.010	42.351	0.002	0.002	0.000	0.000	0.000	0.000
36	A	165	LEU	0	-0.026	-0.007	45.478	0.001	0.001	0.000	0.000	0.000	0.000
37	A	166	THR	0	0.007	0.008	46.606	0.001	0.001	0.000	0.000	0.000	0.000
38	A	167	LYS	1	0.973	0.980	45.826	0.024	0.024	0.000	0.000	0.000	0.000
39	A	168	ARG	1	0.896	0.968	49.209	0.020	0.020	0.000	0.000	0.000	0.000
40	A	169	ILE	0	-0.010	-0.006	51.311	0.001	0.001	0.000	0.000	0.000	0.000
41	A	170	ASP	-1	-0.912	-0.960	51.529	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	171	SER	0	-0.085	-0.047	53.211	0.000	0.000	0.000	0.000	0.000	0.000
43	A	172	LEU	0	-0.104	-0.038	55.750	0.001	0.001	0.000	0.000	0.000	0.000
44	A	173	PRO	0	-0.021	-0.009	58.396	0.000	0.000	0.000	0.000	0.000	0.000
45	A	174	LEU	0	-0.063	-0.024	62.069	0.000	0.000	0.000	0.000	0.000	0.000
46	A	175	THR	0	0.056	0.015	63.264	0.000	0.000	0.000	0.000	0.000	0.000
47	A	176	GLU	-1	-0.874	-0.932	64.646	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	177	ASN	0	-0.061	-0.024	60.807	0.000	0.000	0.000	0.000	0.000	0.000
49	A	178	PHE	0	0.012	0.025	63.781	0.000	0.000	0.000	0.000	0.000	0.000
50	A	179	SER	0	-0.033	-0.036	64.631	0.000	0.000	0.000	0.000	0.000	0.000
51	A	180	LEU	0	0.074	0.030	64.999	0.000	0.000	0.000	0.000	0.000	0.000
52	A	181	GLN	0	0.061	0.022	61.102	0.000	0.000	0.000	0.000	0.000	0.000
53	A	182	THR	0	0.024	0.009	59.909	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	183	ASP	-1	-0.821	-0.909	59.666	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	184	MET	0	-0.105	-0.054	59.620	0.000	0.000	0.000	0.000	0.000	0.000
56	A	185	THR	0	0.005	-0.009	55.998	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	186	ARG	1	0.986	0.996	55.345	0.014	0.014	0.000	0.000	0.000	0.000
58	A	187	ARG	1	0.936	0.970	54.564	0.012	0.012	0.000	0.000	0.000	0.000
59	A	188	GLN	0	-0.047	-0.008	52.135	0.000	0.000	0.000	0.000	0.000	0.000
60	A	189	LEU	0	0.019	-0.003	50.899	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	190	GLU	-1	-0.915	-0.959	49.754	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	191	TYR	0	-0.065	-0.032	49.669	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	192	GLU	-1	-0.865	-0.943	47.753	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	193	ALA	0	0.034	0.011	45.518	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	194	ARG	1	0.881	0.943	44.887	0.018	0.018	0.000	0.000	0.000	0.000
66	A	195	GLN	0	-0.007	0.006	45.026	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	196	ILE	0	-0.008	-0.004	40.344	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	197	ARG	1	0.903	0.946	40.224	0.024	0.024	0.000	0.000	0.000	0.000
69	A	198	VAL	0	-0.006	0.007	40.286	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	199	ALA	0	0.038	0.017	38.657	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	200	MET	0	-0.024	0.004	34.621	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	201	GLU	-1	-0.928	-0.959	35.224	-0.034	-0.034	0.000	0.000	0.000	0.000
73	A	202	GLU	-1	-0.978	-0.988	35.914	-0.032	-0.032	0.000	0.000	0.000	0.000
74	A	203	GLN	0	-0.058	-0.022	32.051	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	204	LEU	0	-0.072	-0.043	29.827	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	205	GLY	0	0.018	0.022	32.062	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	206	THR	0	-0.008	-0.005	34.121	0.002	0.002	0.000	0.000	0.000	0.000
78	A	207	CYS	0	-0.001	-0.018	34.592	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	208	GLN	0	0.022	0.001	34.431	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	209	ASP	-1	-0.900	-0.951	31.679	-0.046	-0.046	0.000	0.000	0.000	0.000
81	A	210	MET	0	0.026	0.034	30.144	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	211	GLU	-1	-0.902	-0.958	29.252	-0.045	-0.045	0.000	0.000	0.000	0.000
83	A	212	LYS	1	0.921	0.947	28.901	0.035	0.035	0.000	0.000	0.000	0.000
84	A	213	ARG	1	0.781	0.865	25.209	0.060	0.060	0.000	0.000	0.000	0.000
85	A	214	ALA	0	0.054	0.022	24.262	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	215	GLN	0	0.004	0.002	23.776	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	216	ARG	1	0.953	1.012	22.748	0.068	0.068	0.000	0.000	0.000	0.000
88	A	217	ARG	1	0.946	0.994	19.738	0.104	0.104	0.000	0.000	0.000	0.000
89	A	218	ILE	0	0.035	0.027	18.689	-0.019	-0.019	0.000	0.000	0.000	0.000
90	A	219	ALA	0	0.007	0.012	19.297	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	220	ARG	1	0.816	0.904	13.375	0.172	0.172	0.000	0.000	0.000	0.000
92	A	221	ILE	0	0.042	0.018	14.340	-0.020	-0.020	0.000	0.000	0.000	0.000
93	A	222	GLN	0	0.059	0.022	14.315	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	223	GLN	0	-0.133	-0.069	15.093	0.017	0.017	0.000	0.000	0.000	0.000
95	A	224	ILE	0	0.018	0.010	9.956	0.024	0.024	0.000	0.000	0.000	0.000
96	A	225	GLU	-1	-0.878	-0.940	10.738	-0.239	-0.239	0.000	0.000	0.000	0.000
97	A	226	LYS	1	0.850	0.933	11.489	0.087	0.087	0.000	0.000	0.000	0.000
98	A	227	ASP	-1	-0.865	-0.930	10.862	0.017	0.017	0.000	0.000	0.000	0.000
99	A	228	ILE	0	0.025	0.005	5.857	0.153	0.153	0.000	0.000	0.000	0.000
100	A	229	LEU	0	-0.025	-0.010	7.706	0.252	0.252	0.000	0.000	0.000	0.000
101	A	230	ARG	1	0.938	0.972	9.868	-0.039	-0.039	0.000	0.000	0.000	0.000
102	A	231	ILE	0	0.041	0.025	6.883	0.039	0.039	0.000	0.000	0.000	0.000
103	A	232	ARG	1	0.897	0.936	3.846	1.355	1.502	-0.001	-0.016	-0.130	0.000
104	A	233	GLN	0	0.004	0.010	7.422	-0.074	-0.074	0.000	0.000	0.000	0.000
105	A	234	LEU	0	-0.037	0.004	10.723	-0.053	-0.053	0.000	0.000	0.000	0.000
106	A	235	LEU	0	0.022	-0.008	5.812	0.034	0.034	0.000	0.000	0.000	0.000
107	A	236	GLN	0	-0.063	-0.045	7.634	-0.259	-0.259	0.000	0.000	0.000	0.000
108	A	237	SER	0	-0.095	-0.053	11.130	-0.092	-0.092	0.000	0.000	0.000	0.000
109	A	238	GLN	0	-0.048	-0.014	11.535	0.044	0.044	0.000	0.000	0.000	0.000
110	A	239	ALA	0	0.001	0.024	10.773	-0.075	-0.075	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:130:SER)