FMO DATABASE

FMODB ID: 7G5KK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-803437.282924
FMO2-HF: Nuclear repulsion	756772.25235
FMO2-HF: Total energy	-46665.030574
FMO2-MP2: Total energy	-46800.46206

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.
-11.689	-4.945	2.679	-4.169	-5.253	-0.008

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 : 0.023 / q_NPA : 0.003

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	0.036	0.018	3.835	1.426	3.301	-0.022	-1.043	-0.810	0.002
4	A	133	TYR	0	0.067	0.030	6.147	-0.426	-0.426	0.000	0.000	0.000	0.000
5	A	134	LEU	0	-0.023	-0.007	2.413	-1.845	-0.979	2.182	-1.129	-1.919	0.009
6	A	135	GLU	-1	-0.836	-0.892	3.189	-6.228	-5.375	0.040	-0.282	-0.610	-0.001
7	A	136	GLU	-1	-0.896	-0.970	3.757	-0.319	-0.137	0.003	-0.019	-0.166	0.000
8	A	137	LEU	0	-0.015	0.003	6.529	0.247	0.247	0.000	0.000	0.000	0.000
9	A	138	GLU	-1	-0.836	-0.914	2.732	-10.460	-7.612	0.477	-1.688	-1.638	-0.018
10	A	139	LYS	1	0.855	0.913	6.526	3.155	3.155	0.000	0.000	0.000	0.000
11	A	140	GLU	-1	-0.777	-0.849	8.947	-0.314	-0.314	0.000	0.000	0.000	0.000
12	A	141	ARG	1	0.857	0.899	9.951	0.723	0.723	0.000	0.000	0.000	0.000
13	A	142	SER	0	-0.045	-0.035	9.831	0.161	0.161	0.000	0.000	0.000	0.000
14	A	143	LEU	0	-0.004	0.012	12.490	0.104	0.104	0.000	0.000	0.000	0.000
15	A	144	LEU	0	0.003	-0.014	14.622	0.090	0.090	0.000	0.000	0.000	0.000
16	A	145	LEU	0	-0.030	-0.020	13.697	0.062	0.062	0.000	0.000	0.000	0.000
17	A	146	ALA	0	-0.002	0.004	16.812	0.052	0.052	0.000	0.000	0.000	0.000
18	A	147	ASP	-1	-0.840	-0.905	18.613	-0.271	-0.271	0.000	0.000	0.000	0.000
19	A	148	LEU	0	-0.041	-0.020	19.632	0.033	0.033	0.000	0.000	0.000	0.000
20	A	149	ASP	-1	-0.815	-0.885	21.277	-0.194	-0.194	0.000	0.000	0.000	0.000
21	A	150	LYS	1	0.906	0.940	22.646	0.236	0.236	0.000	0.000	0.000	0.000
22	A	151	GLU	-1	-0.758	-0.868	24.599	-0.174	-0.174	0.000	0.000	0.000	0.000
23	A	152	GLU	-1	-0.818	-0.894	25.900	-0.132	-0.132	0.000	0.000	0.000	0.000
24	A	153	LYS	1	0.848	0.917	24.053	0.204	0.204	0.000	0.000	0.000	0.000
25	A	154	GLU	-1	-0.814	-0.882	28.743	-0.160	-0.160	0.000	0.000	0.000	0.000
26	A	155	LYS	1	0.816	0.874	29.520	0.147	0.147	0.000	0.000	0.000	0.000
27	A	156	ASP	-1	-0.908	-0.943	31.506	-0.104	-0.104	0.000	0.000	0.000	0.000
28	A	157	TRP	0	-0.084	-0.035	33.096	0.009	0.009	0.000	0.000	0.000	0.000
29	A	158	TYR	0	0.026	-0.017	33.039	0.011	0.011	0.000	0.000	0.000	0.000
30	A	159	TYR	0	0.002	-0.012	34.829	0.007	0.007	0.000	0.000	0.000	0.000
31	A	160	ALA	0	0.021	0.029	37.589	0.007	0.007	0.000	0.000	0.000	0.000
32	A	161	GLN	0	-0.027	-0.021	39.147	0.005	0.005	0.000	0.000	0.000	0.000
33	A	162	LEU	0	0.006	0.002	40.089	0.005	0.005	0.000	0.000	0.000	0.000
34	A	163	GLN	0	0.031	0.025	38.991	0.006	0.006	0.000	0.000	0.000	0.000
35	A	164	ASN	0	0.002	-0.003	42.356	0.008	0.008	0.000	0.000	0.000	0.000
36	A	165	LEU	0	-0.020	0.008	45.466	0.004	0.004	0.000	0.000	0.000	0.000
37	A	166	THR	0	-0.019	-0.021	46.151	0.003	0.003	0.000	0.000	0.000	0.000
38	A	167	LYS	1	0.942	0.959	45.054	0.058	0.058	0.000	0.000	0.000	0.000
39	A	168	ARG	1	0.893	0.960	49.230	0.058	0.058	0.000	0.000	0.000	0.000
40	A	169	ILE	0	-0.017	-0.014	50.742	0.002	0.002	0.000	0.000	0.000	0.000
41	A	170	ASP	-1	-0.916	-0.956	51.307	-0.044	-0.044	0.000	0.000	0.000	0.000
42	A	171	SER	0	-0.080	-0.041	53.172	0.002	0.002	0.000	0.000	0.000	0.000
43	A	172	LEU	0	-0.097	-0.035	55.699	0.001	0.001	0.000	0.000	0.000	0.000
44	A	173	PRO	0	-0.011	-0.008	58.334	0.001	0.001	0.000	0.000	0.000	0.000
45	A	174	LEU	0	-0.075	-0.031	62.006	0.001	0.001	0.000	0.000	0.000	0.000
46	A	175	THR	0	0.058	0.014	62.970	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	176	GLU	-1	-0.864	-0.928	64.473	-0.028	-0.028	0.000	0.000	0.000	0.000
48	A	177	ASN	0	-0.046	-0.016	61.060	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	178	PHE	0	0.005	0.022	63.822	0.000	0.000	0.000	0.000	0.000	0.000
50	A	179	SER	0	-0.033	-0.031	64.742	0.000	0.000	0.000	0.000	0.000	0.000
51	A	180	LEU	0	0.076	0.027	64.946	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	181	GLN	0	0.055	0.025	61.021	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	182	THR	0	0.022	0.014	59.972	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	183	ASP	-1	-0.755	-0.869	59.613	-0.038	-0.038	0.000	0.000	0.000	0.000
55	A	184	MET	0	-0.079	-0.036	59.571	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	185	THR	0	-0.013	-0.022	55.966	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	186	ARG	1	0.965	0.990	55.287	0.037	0.037	0.000	0.000	0.000	0.000
58	A	187	ARG	1	0.854	0.914	54.514	0.038	0.038	0.000	0.000	0.000	0.000
59	A	188	GLN	0	-0.048	-0.023	52.083	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	189	LEU	0	0.010	0.000	50.853	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	190	GLU	-1	-0.890	-0.951	49.706	-0.051	-0.051	0.000	0.000	0.000	0.000
62	A	191	TYR	0	-0.045	-0.029	49.625	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	192	GLU	-1	-0.838	-0.913	47.654	-0.063	-0.063	0.000	0.000	0.000	0.000
64	A	193	ALA	0	0.019	0.004	45.471	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	194	ARG	1	0.887	0.955	44.843	0.054	0.054	0.000	0.000	0.000	0.000
66	A	195	GLN	0	-0.025	-0.013	44.991	-0.004	-0.004	0.000	0.000	0.000	0.000
67	A	196	ILE	0	-0.007	-0.006	40.310	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	197	ARG	1	0.903	0.947	40.183	0.067	0.067	0.000	0.000	0.000	0.000
69	A	198	VAL	0	-0.014	0.000	40.251	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	199	ALA	0	0.044	0.022	38.709	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	200	MET	0	-0.023	0.004	34.537	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	201	GLU	-1	-0.926	-0.960	35.191	-0.099	-0.099	0.000	0.000	0.000	0.000
73	A	202	GLU	-1	-0.966	-0.980	35.889	-0.105	-0.105	0.000	0.000	0.000	0.000
74	A	203	GLN	0	-0.094	-0.046	31.295	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	204	LEU	0	-0.072	-0.041	29.620	-0.012	-0.012	0.000	0.000	0.000	0.000
76	A	205	GLY	0	0.027	0.040	32.030	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	206	THR	0	0.000	-0.024	34.094	0.006	0.006	0.000	0.000	0.000	0.000
78	A	207	CYS	0	0.016	-0.009	34.555	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	208	GLN	0	-0.029	-0.020	34.388	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	209	ASP	-1	-0.846	-0.912	31.614	-0.129	-0.129	0.000	0.000	0.000	0.000
81	A	210	MET	0	0.042	0.041	30.112	-0.013	-0.013	0.000	0.000	0.000	0.000
82	A	211	GLU	-1	-0.854	-0.936	29.209	-0.102	-0.102	0.000	0.000	0.000	0.000
83	A	212	LYS	1	0.839	0.915	28.855	0.095	0.095	0.000	0.000	0.000	0.000
84	A	213	ARG	1	0.721	0.847	25.137	0.155	0.155	0.000	0.000	0.000	0.000
85	A	214	ALA	0	0.053	0.017	24.219	-0.020	-0.020	0.000	0.000	0.000	0.000
86	A	215	GLN	0	0.007	0.005	23.726	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	216	ARG	1	0.967	0.987	22.753	0.176	0.176	0.000	0.000	0.000	0.000
88	A	217	ARG	1	0.773	0.879	19.710	0.234	0.234	0.000	0.000	0.000	0.000
89	A	218	ILE	0	0.040	0.024	18.644	-0.030	-0.030	0.000	0.000	0.000	0.000
90	A	219	ALA	0	0.001	0.008	19.244	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	220	ARG	1	0.786	0.864	12.598	0.421	0.421	0.000	0.000	0.000	0.000
92	A	221	ILE	0	0.025	0.012	14.508	-0.034	-0.034	0.000	0.000	0.000	0.000
93	A	222	GLN	0	0.048	0.023	14.260	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	223	GLN	0	-0.106	-0.058	15.477	0.040	0.040	0.000	0.000	0.000	0.000
95	A	224	ILE	0	0.003	0.009	9.902	0.030	0.030	0.000	0.000	0.000	0.000
96	A	225	GLU	-1	-0.841	-0.909	10.700	-0.357	-0.357	0.000	0.000	0.000	0.000
97	A	226	LYS	1	0.818	0.905	11.513	0.181	0.181	0.000	0.000	0.000	0.000
98	A	227	ASP	-1	-0.818	-0.904	10.773	-0.125	-0.125	0.000	0.000	0.000	0.000
99	A	228	ILE	0	0.026	0.005	5.872	0.179	0.179	0.000	0.000	0.000	0.000
100	A	229	LEU	0	-0.022	-0.006	7.683	0.299	0.299	0.000	0.000	0.000	0.000
101	A	230	ARG	1	0.916	0.956	9.847	-0.035	-0.035	0.000	0.000	0.000	0.000
102	A	231	ILE	0	0.040	0.023	6.618	0.094	0.094	0.000	0.000	0.000	0.000
103	A	232	ARG	1	0.882	0.927	4.059	1.503	1.623	-0.001	-0.008	-0.110	0.000
104	A	233	GLN	0	0.038	0.028	7.345	0.032	0.032	0.000	0.000	0.000	0.000
105	A	234	LEU	0	-0.031	0.018	10.702	-0.016	-0.016	0.000	0.000	0.000	0.000
106	A	235	LEU	0	0.015	-0.008	5.795	0.022	0.022	0.000	0.000	0.000	0.000
107	A	236	GLN	0	-0.052	-0.036	7.451	-0.022	-0.022	0.000	0.000	0.000	0.000
108	A	237	SER	0	-0.085	-0.057	11.287	-0.114	-0.114	0.000	0.000	0.000	0.000
109	A	238	GLN	0	-0.040	-0.009	11.712	0.041	0.041	0.000	0.000	0.000	0.000
110	A	239	ALA	0	-0.031	0.000	10.744	-0.077	-0.077	0.000	0.000	0.000	0.000

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