FMO DATABASE

FMODB ID: 228MR

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	OptAll
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	-805399.33503
FMO2-HF: Nuclear repulsion	758733.939923
FMO2-HF: Total energy	-46665.395106
FMO2-MP2: Total energy	-46800.802552

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.
-17.65	-12.909	10.201	-6.551	-8.389	-0.035

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 : 0.000

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	0.027	0.035	3.886	1.796	3.577	-0.017	-0.974	-0.790	0.002
4	A	133	TYR	0	0.066	0.021	5.443	-0.307	-0.307	0.000	0.000	0.000	0.000
5	A	134	LEU	0	-0.035	-0.005	2.476	-2.411	-1.334	2.564	-1.429	-2.212	0.011
6	A	135	GLU	-1	-0.790	-0.877	2.737	-7.901	-6.539	0.348	-0.520	-1.189	-0.002
7	A	136	GLU	-1	-0.930	-0.973	3.270	-0.028	0.018	0.035	0.098	-0.179	0.000
8	A	137	LEU	0	0.006	0.014	6.198	0.097	0.097	0.000	0.000	0.000	0.000
9	A	138	GLU	-1	-0.815	-0.908	2.097	-15.393	-15.076	7.272	-3.704	-3.885	-0.046
10	A	139	LYS	1	0.837	0.910	5.995	3.382	3.382	0.000	0.000	0.000	0.000
11	A	140	GLU	-1	-0.780	-0.859	8.467	-0.244	-0.244	0.000	0.000	0.000	0.000
12	A	141	ARG	1	0.867	0.904	9.525	0.754	0.754	0.000	0.000	0.000	0.000
13	A	142	SER	0	-0.034	-0.032	9.219	0.186	0.186	0.000	0.000	0.000	0.000
14	A	143	LEU	0	-0.016	0.005	11.907	0.119	0.119	0.000	0.000	0.000	0.000
15	A	144	LEU	0	0.013	-0.003	14.203	0.093	0.093	0.000	0.000	0.000	0.000
16	A	145	LEU	0	-0.016	-0.011	13.296	0.066	0.066	0.000	0.000	0.000	0.000
17	A	146	ALA	0	0.009	0.006	16.136	0.056	0.056	0.000	0.000	0.000	0.000
18	A	147	ASP	-1	-0.829	-0.901	18.011	-0.252	-0.252	0.000	0.000	0.000	0.000
19	A	148	LEU	0	-0.035	-0.014	19.062	0.037	0.037	0.000	0.000	0.000	0.000
20	A	149	ASP	-1	-0.845	-0.898	20.647	-0.214	-0.214	0.000	0.000	0.000	0.000
21	A	150	LYS	1	0.900	0.943	22.024	0.244	0.244	0.000	0.000	0.000	0.000
22	A	151	GLU	-1	-0.747	-0.846	23.929	-0.171	-0.171	0.000	0.000	0.000	0.000
23	A	152	GLU	-1	-0.826	-0.899	25.358	-0.135	-0.135	0.000	0.000	0.000	0.000
24	A	153	LYS	1	0.863	0.918	23.706	0.223	0.223	0.000	0.000	0.000	0.000
25	A	154	GLU	-1	-0.795	-0.861	28.140	-0.163	-0.163	0.000	0.000	0.000	0.000
26	A	155	LYS	1	0.797	0.864	28.824	0.152	0.152	0.000	0.000	0.000	0.000
27	A	156	ASP	-1	-0.899	-0.944	30.875	-0.111	-0.111	0.000	0.000	0.000	0.000
28	A	157	TRP	0	-0.062	-0.022	32.603	0.010	0.010	0.000	0.000	0.000	0.000
29	A	158	TYR	0	0.027	-0.021	32.523	0.012	0.012	0.000	0.000	0.000	0.000
30	A	159	TYR	0	0.012	-0.005	33.975	0.007	0.007	0.000	0.000	0.000	0.000
31	A	160	ALA	0	0.021	0.017	36.969	0.007	0.007	0.000	0.000	0.000	0.000
32	A	161	GLN	0	-0.005	0.001	38.117	0.007	0.007	0.000	0.000	0.000	0.000
33	A	162	LEU	0	0.001	-0.002	39.563	0.006	0.006	0.000	0.000	0.000	0.000
34	A	163	GLN	0	0.011	0.018	38.385	0.007	0.007	0.000	0.000	0.000	0.000
35	A	164	ASN	0	-0.024	-0.017	41.702	0.008	0.008	0.000	0.000	0.000	0.000
36	A	165	LEU	0	-0.032	-0.001	44.636	0.003	0.003	0.000	0.000	0.000	0.000
37	A	166	THR	0	-0.023	-0.020	45.589	0.003	0.003	0.000	0.000	0.000	0.000
38	A	167	LYS	1	0.947	0.961	44.707	0.062	0.062	0.000	0.000	0.000	0.000
39	A	168	ARG	1	0.841	0.930	47.983	0.062	0.062	0.000	0.000	0.000	0.000
40	A	169	ILE	0	-0.016	-0.013	50.294	0.002	0.002	0.000	0.000	0.000	0.000
41	A	170	ASP	-1	-0.903	-0.960	50.275	-0.046	-0.046	0.000	0.000	0.000	0.000
42	A	171	SER	0	-0.071	-0.038	52.536	0.002	0.002	0.000	0.000	0.000	0.000
43	A	172	LEU	0	-0.096	-0.036	55.058	0.001	0.001	0.000	0.000	0.000	0.000
44	A	173	PRO	0	-0.024	-0.017	57.753	0.001	0.001	0.000	0.000	0.000	0.000
45	A	174	LEU	0	-0.065	-0.021	61.309	0.001	0.001	0.000	0.000	0.000	0.000
46	A	175	THR	0	0.035	0.004	62.186	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	176	GLU	-1	-0.849	-0.927	63.752	-0.029	-0.029	0.000	0.000	0.000	0.000
48	A	177	ASN	0	-0.011	0.006	60.891	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	178	PHE	0	-0.007	0.020	63.532	0.000	0.000	0.000	0.000	0.000	0.000
50	A	179	SER	0	0.006	-0.019	64.477	0.000	0.000	0.000	0.000	0.000	0.000
51	A	180	LEU	0	0.045	0.019	64.191	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	181	GLN	0	0.059	0.030	60.283	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	182	THR	0	0.014	0.025	59.701	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	183	ASP	-1	-0.731	-0.851	59.082	-0.040	-0.040	0.000	0.000	0.000	0.000
55	A	184	MET	0	-0.071	-0.032	59.120	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	185	THR	0	-0.012	-0.021	55.392	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	186	ARG	1	0.917	0.952	54.667	0.039	0.039	0.000	0.000	0.000	0.000
58	A	187	ARG	1	0.844	0.900	53.858	0.039	0.039	0.000	0.000	0.000	0.000
59	A	188	GLN	0	-0.024	-0.013	51.403	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	189	LEU	0	0.003	-0.001	50.378	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	190	GLU	-1	-0.865	-0.931	49.148	-0.052	-0.052	0.000	0.000	0.000	0.000
62	A	191	TYR	0	-0.046	-0.019	48.979	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	192	GLU	-1	-0.782	-0.878	46.914	-0.065	-0.065	0.000	0.000	0.000	0.000
64	A	193	ALA	0	0.038	0.009	44.781	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	194	ARG	1	0.822	0.909	44.295	0.054	0.054	0.000	0.000	0.000	0.000
66	A	195	GLN	0	-0.027	-0.020	44.695	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	196	ILE	0	0.002	0.000	39.645	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	197	ARG	1	0.882	0.932	39.794	0.067	0.067	0.000	0.000	0.000	0.000
69	A	198	VAL	0	0.005	0.021	39.754	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	199	ALA	0	0.049	0.028	38.377	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	200	MET	0	-0.047	-0.011	34.022	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	201	GLU	-1	-0.938	-0.973	34.728	-0.097	-0.097	0.000	0.000	0.000	0.000
73	A	202	GLU	-1	-0.957	-0.990	35.253	-0.105	-0.105	0.000	0.000	0.000	0.000
74	A	203	GLN	0	-0.097	-0.048	30.718	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	204	LEU	0	-0.053	-0.025	29.066	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	205	GLY	0	0.031	0.040	31.334	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	206	THR	0	0.021	-0.008	33.279	0.005	0.005	0.000	0.000	0.000	0.000
78	A	207	CYS	0	0.000	-0.016	33.662	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	208	GLN	0	-0.022	-0.020	33.376	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	209	ASP	-1	-0.829	-0.879	31.240	-0.125	-0.125	0.000	0.000	0.000	0.000
81	A	210	MET	0	0.048	0.039	29.349	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	211	GLU	-1	-0.795	-0.888	28.362	-0.101	-0.101	0.000	0.000	0.000	0.000
83	A	212	LYS	1	0.809	0.868	28.128	0.087	0.087	0.000	0.000	0.000	0.000
84	A	213	ARG	1	0.713	0.850	24.492	0.157	0.157	0.000	0.000	0.000	0.000
85	A	214	ALA	0	0.053	0.027	23.748	-0.019	-0.019	0.000	0.000	0.000	0.000
86	A	215	GLN	0	-0.002	-0.004	22.986	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	216	ARG	1	0.903	0.946	22.398	0.157	0.157	0.000	0.000	0.000	0.000
88	A	217	ARG	1	0.741	0.838	19.177	0.234	0.234	0.000	0.000	0.000	0.000
89	A	218	ILE	0	0.031	0.017	18.149	-0.030	-0.030	0.000	0.000	0.000	0.000
90	A	219	ALA	0	0.004	0.002	18.610	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	220	ARG	1	0.757	0.844	12.193	0.353	0.353	0.000	0.000	0.000	0.000
92	A	221	ILE	0	0.016	0.007	14.075	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	222	GLN	0	0.053	0.024	13.903	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	223	GLN	0	-0.096	-0.029	15.050	0.051	0.051	0.000	0.000	0.000	0.000
95	A	224	ILE	0	0.028	0.018	9.365	0.039	0.039	0.000	0.000	0.000	0.000
96	A	225	GLU	-1	-0.830	-0.904	10.220	-0.353	-0.353	0.000	0.000	0.000	0.000
97	A	226	LYS	1	0.824	0.889	10.916	0.148	0.148	0.000	0.000	0.000	0.000
98	A	227	ASP	-1	-0.787	-0.876	10.492	-0.045	-0.045	0.000	0.000	0.000	0.000
99	A	228	ILE	0	0.011	-0.003	5.432	0.217	0.217	0.000	0.000	0.000	0.000
100	A	229	LEU	0	-0.030	-0.008	7.419	0.349	0.349	0.000	0.000	0.000	0.000
101	A	230	ARG	1	0.873	0.924	9.783	-0.114	-0.114	0.000	0.000	0.000	0.000
102	A	231	ILE	0	0.040	0.026	6.596	0.089	0.089	0.000	0.000	0.000	0.000
103	A	232	ARG	1	0.889	0.923	3.828	1.812	1.970	-0.001	-0.022	-0.134	0.000
104	A	233	GLN	0	0.046	0.037	7.482	0.009	0.009	0.000	0.000	0.000	0.000
105	A	234	LEU	0	-0.013	0.023	10.970	-0.030	-0.030	0.000	0.000	0.000	0.000
106	A	235	LEU	0	0.024	0.002	5.497	0.016	0.016	0.000	0.000	0.000	0.000
107	A	236	GLN	0	-0.042	-0.042	7.279	-0.051	-0.051	0.000	0.000	0.000	0.000
108	A	237	SER	0	-0.066	-0.037	11.058	-0.126	-0.126	0.000	0.000	0.000	0.000
109	A	238	GLN	0	-0.041	-0.007	11.653	0.022	0.022	0.000	0.000	0.000	0.000
110	A	239	ALA	0	-0.061	-0.019	10.548	-0.100	-0.100	0.000	0.000	0.000	0.000

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