FMO DATABASE

FMODB ID: 89YMY

Calculation Name: 1M8U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1M8U

Chain ID: A

ChEMBL ID:

UniProt ID: P23005

Base Structure: X-ray

Registration Date: 2023-09-24

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	173
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-2050878.488131
FMO2-HF: Nuclear repulsion	1976110.652107
FMO2-HF: Total energy	-74767.836024
FMO2-MP2: Total energy	-74983.528062

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:1:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-7.738	-2.72	5.209	-5.134	-5.092	-0.027

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.006

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	3	ILE	0	-0.042	-0.007	3.796	0.819	2.413	-0.016	-0.846	-0.731	0.002
4	A	4	THR	0	0.059	0.035	6.835	-0.079	-0.079	0.000	0.000	0.000	0.000
5	A	5	PHE	0	-0.001	-0.021	9.724	0.200	0.200	0.000	0.000	0.000	0.000
6	A	6	TYR	0	0.040	0.013	13.340	-0.042	-0.042	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.766	-0.891	16.944	-0.271	-0.271	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.835	-0.893	20.183	-0.220	-0.220	0.000	0.000	0.000	0.000
9	A	9	ARG	0	0.098	0.084	20.371	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.033	-0.021	20.652	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.046	-0.029	14.993	0.003	0.003	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.034	-0.004	18.503	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.051	0.024	20.755	-0.010	-0.010	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.862	0.935	19.345	0.359	0.359	0.000	0.000	0.000	0.000
15	A	15	HIS	0	0.002	-0.006	15.274	-0.047	-0.047	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.032	-0.026	11.833	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.816	-0.892	8.540	-2.154	-2.154	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.057	-0.017	7.889	0.154	0.154	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.061	0.021	3.992	-0.745	-0.588	0.000	-0.069	-0.087	0.000
20	A	20	SER	0	-0.012	-0.006	3.910	-0.460	-0.263	0.000	-0.098	-0.099	0.000
21	A	21	ASP	-1	-0.810	-0.897	6.325	0.288	0.288	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.029	-0.008	8.893	-0.019	-0.019	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.013	0.008	11.904	0.035	0.035	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.072	0.008	15.175	0.040	0.040	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.017	0.008	11.747	-0.035	-0.035	0.000	0.000	0.000	0.000
26	A	26	GLN	0	0.007	-0.001	15.916	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.042	-0.015	18.058	0.008	0.008	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.020	-0.006	15.243	-0.005	-0.005	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.048	-0.020	13.723	-0.031	-0.031	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.080	-0.032	19.200	0.026	0.026	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.814	0.901	20.818	0.285	0.285	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.091	-0.030	15.794	-0.055	-0.055	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.037	-0.047	18.380	0.058	0.058	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.041	-0.017	17.207	0.019	0.019	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.017	-0.008	10.924	-0.053	-0.053	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.861	0.923	10.395	0.674	0.674	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.050	-0.013	5.849	-0.289	-0.289	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.844	-0.930	5.920	-1.279	-1.279	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.063	-0.052	2.624	-1.596	-0.638	1.355	-1.248	-1.066	-0.011
40	A	40	GLY	0	0.059	0.034	2.622	-1.302	-0.445	1.913	-1.620	-1.150	-0.013
41	A	41	CYS	0	-0.078	-0.015	3.604	-1.646	-1.776	0.014	0.069	0.046	0.000
42	A	42	TRP	0	0.027	-0.006	2.890	0.096	0.849	0.258	-0.291	-0.719	-0.002
43	A	43	MET	0	-0.047	0.004	7.577	-0.007	-0.007	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.010	-0.002	10.523	-0.081	-0.081	0.000	0.000	0.000	0.000
45	A	45	TYR	0	0.030	-0.002	12.643	0.085	0.085	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.830	-0.901	16.103	-0.118	-0.118	0.000	0.000	0.000	0.000
47	A	47	GLN	0	-0.002	0.004	19.350	-0.034	-0.034	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.029	0.013	18.037	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.053	-0.043	17.372	0.018	0.018	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.022	-0.012	11.914	0.058	0.058	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.013	0.011	16.544	0.041	0.041	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.021	0.004	19.616	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.016	-0.013	20.221	0.022	0.022	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.072	0.035	15.897	0.016	0.016	0.000	0.000	0.000	0.000
55	A	55	TYR	0	-0.009	-0.006	15.137	0.012	0.012	0.000	0.000	0.000	0.000
56	A	56	PHE	0	0.010	0.000	10.892	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.051	-0.010	9.683	-0.068	-0.068	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.884	0.927	8.830	-0.446	-0.446	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.868	0.900	6.295	-1.275	-1.275	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.007	0.008	8.658	0.090	0.090	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.811	-0.889	11.501	-0.481	-0.481	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.003	0.005	11.644	0.106	0.106	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.001	-0.009	15.708	-0.041	-0.041	0.000	0.000	0.000	0.000
64	A	64	ASH	0	0.007	-0.047	18.822	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.079	0.045	18.639	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.011	0.003	19.663	0.011	0.011	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.040	-0.005	17.519	0.031	0.031	0.000	0.000	0.000	0.000
68	A	68	TRP	0	-0.029	-0.001	15.382	0.019	0.019	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.100	-0.058	17.213	0.031	0.031	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.023	0.017	19.926	0.014	0.014	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.018	-0.018	20.512	0.003	0.003	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.046	-0.047	22.146	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.815	-0.893	20.535	-0.184	-0.184	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.014	-0.005	20.589	-0.030	-0.030	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.004	-0.005	14.019	0.023	0.023	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.894	0.941	17.015	0.108	0.108	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.040	-0.013	13.944	0.008	0.008	0.000	0.000	0.000	0.000
78	A	78	CYS	0	0.002	0.012	8.776	-0.037	-0.037	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.882	0.961	8.992	-0.369	-0.369	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.005	0.010	2.564	-0.790	-0.158	1.685	-1.031	-1.286	-0.003
81	A	81	ILE	0	-0.061	-0.050	5.742	0.053	0.053	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.034	-0.015	7.129	0.618	0.618	0.000	0.000	0.000	0.000
83	A	83	HIS	0	0.039	0.033	8.339	0.056	0.056	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.033	-0.026	9.982	-0.185	-0.185	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.001	0.000	13.777	0.048	0.048	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.071	-0.061	16.153	-0.040	-0.040	0.000	0.000	0.000	0.000
87	A	88	HIS	0	-0.001	-0.007	13.920	0.010	0.010	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.812	0.882	19.162	-0.375	-0.375	0.000	0.000	0.000	0.000
89	A	90	LEU	0	-0.044	-0.004	21.364	0.007	0.007	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.846	0.913	24.228	-0.236	-0.236	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.005	-0.001	26.408	0.001	0.001	0.000	0.000	0.000	0.000
92	A	93	TYR	0	0.007	-0.001	29.176	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.762	-0.859	32.461	0.101	0.101	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.878	0.923	35.315	-0.104	-0.104	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.793	-0.877	33.616	0.109	0.109	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.888	-0.938	33.462	0.111	0.111	0.000	0.000	0.000	0.000
97	A	98	TYR	0	-0.113	-0.081	28.124	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.909	0.970	33.754	-0.114	-0.114	0.000	0.000	0.000	0.000
99	A	100	GLY	0	-0.002	-0.013	36.340	0.002	0.002	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.055	-0.035	37.479	0.007	0.007	0.000	0.000	0.000	0.000
101	A	102	MET	0	-0.012	-0.003	31.936	0.008	0.008	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.010	0.005	29.956	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.759	-0.864	27.671	0.258	0.258	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.056	-0.018	24.200	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	106	THR	0	0.055	0.000	22.773	0.006	0.006	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.870	-0.925	21.290	0.422	0.422	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.821	-0.878	18.738	0.422	0.422	0.000	0.000	0.000	0.000
108	A	109	CYS	0	-0.033	-0.005	21.647	-0.033	-0.033	0.000	0.000	0.000	0.000
109	A	110	SER	0	0.013	0.007	24.283	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	SER	0	0.010	-0.057	25.463	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.026	-0.024	25.453	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	113	HIS	1	0.808	0.888	29.263	-0.114	-0.114	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.849	-0.876	32.207	0.094	0.094	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.878	0.944	29.288	-0.148	-0.148	0.000	0.000	0.000	0.000
115	A	116	PHE	0	0.027	0.011	28.194	0.007	0.007	0.000	0.000	0.000	0.000
116	A	117	HIS	0	0.042	0.018	34.331	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	118	PHE	0	-0.023	0.008	32.817	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	119	SER	0	0.067	0.022	35.485	0.005	0.005	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.912	-0.924	34.955	0.091	0.091	0.000	0.000	0.000	0.000
120	A	121	ILE	0	-0.038	-0.042	29.180	0.007	0.007	0.000	0.000	0.000	0.000
121	A	122	HIS	0	-0.068	-0.040	31.746	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	123	SER	0	-0.032	-0.010	29.476	0.000	0.000	0.000	0.000	0.000	0.000
123	A	124	PHE	0	-0.018	-0.008	25.202	0.004	0.004	0.000	0.000	0.000	0.000
124	A	125	HIS	0	0.040	0.021	26.139	0.008	0.008	0.000	0.000	0.000	0.000
125	A	126	VAL	0	-0.019	0.005	19.357	0.005	0.005	0.000	0.000	0.000	0.000
126	A	127	LEU	0	0.009	0.005	22.455	0.006	0.006	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.786	-0.855	19.767	0.447	0.447	0.000	0.000	0.000	0.000
128	A	129	GLY	0	0.069	0.031	15.693	-0.012	-0.012	0.000	0.000	0.000	0.000
129	A	130	TRP	0	0.014	-0.001	12.769	-0.096	-0.096	0.000	0.000	0.000	0.000
130	A	131	TRP	0	0.009	-0.011	14.850	0.056	0.056	0.000	0.000	0.000	0.000
131	A	132	VAL	0	-0.006	0.002	14.281	-0.013	-0.013	0.000	0.000	0.000	0.000
132	A	133	LEU	0	0.017	0.016	17.218	-0.013	-0.013	0.000	0.000	0.000	0.000
133	A	134	TYR	0	-0.017	-0.013	16.714	0.002	0.002	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.721	-0.837	22.413	0.065	0.065	0.000	0.000	0.000	0.000
135	A	136	MET	0	-0.027	-0.017	25.358	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	137	PRO	0	0.042	0.023	25.488	0.014	0.014	0.000	0.000	0.000	0.000
137	A	138	ASN	0	-0.079	-0.054	24.610	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	139	TYR	0	-0.037	-0.025	19.899	-0.009	-0.009	0.000	0.000	0.000	0.000
139	A	140	ARG	1	1.005	1.005	21.316	-0.081	-0.081	0.000	0.000	0.000	0.000
140	A	141	GLY	0	0.018	0.012	23.429	0.010	0.010	0.000	0.000	0.000	0.000
141	A	142	ARG	1	0.784	0.844	22.367	-0.056	-0.056	0.000	0.000	0.000	0.000
142	A	143	GLN	0	0.056	0.023	16.901	0.049	0.049	0.000	0.000	0.000	0.000
143	A	144	TYR	0	0.022	0.003	19.391	-0.026	-0.026	0.000	0.000	0.000	0.000
144	A	145	LEU	0	-0.036	-0.009	12.592	0.035	0.035	0.000	0.000	0.000	0.000
145	A	146	LEU	0	-0.008	0.002	16.656	-0.030	-0.030	0.000	0.000	0.000	0.000
146	A	147	ARG	1	0.971	0.997	15.944	-0.341	-0.341	0.000	0.000	0.000	0.000
147	A	148	PRO	0	0.013	0.001	16.476	-0.051	-0.051	0.000	0.000	0.000	0.000
148	A	149	GLY	0	-0.007	0.001	19.627	-0.010	-0.010	0.000	0.000	0.000	0.000
149	A	150	ASP	-1	-0.778	-0.859	22.907	0.197	0.197	0.000	0.000	0.000	0.000
150	A	151	TYR	0	-0.020	-0.033	20.114	-0.008	-0.008	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.851	0.907	26.673	-0.164	-0.164	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.898	0.904	29.403	-0.115	-0.115	0.000	0.000	0.000	0.000
153	A	154	TYR	0	0.046	0.009	28.066	0.009	0.009	0.000	0.000	0.000	0.000
154	A	155	HIS	0	-0.020	0.011	27.267	0.001	0.001	0.000	0.000	0.000	0.000
155	A	156	GLU	-1	-0.912	-0.959	26.371	0.133	0.133	0.000	0.000	0.000	0.000
156	A	157	TRP	0	-0.058	-0.026	22.583	0.021	0.021	0.000	0.000	0.000	0.000
157	A	158	GLY	0	-0.020	-0.010	22.622	0.005	0.005	0.000	0.000	0.000	0.000
158	A	159	ALA	0	-0.045	-0.002	24.337	-0.014	-0.014	0.000	0.000	0.000	0.000
159	A	160	VAL	0	0.008	-0.002	26.460	-0.002	-0.002	0.000	0.000	0.000	0.000
160	A	161	ASP	-1	-0.837	-0.914	29.026	0.061	0.061	0.000	0.000	0.000	0.000
161	A	162	ALA	0	0.052	0.022	29.302	0.009	0.009	0.000	0.000	0.000	0.000
162	A	163	ARG	1	0.833	0.927	29.581	-0.064	-0.064	0.000	0.000	0.000	0.000
163	A	164	VAL	0	0.011	0.010	26.475	0.007	0.007	0.000	0.000	0.000	0.000
164	A	165	GLY	0	0.016	-0.001	26.193	-0.012	-0.012	0.000	0.000	0.000	0.000
165	A	166	SER	0	-0.084	-0.033	23.585	0.004	0.004	0.000	0.000	0.000	0.000
166	A	167	LEU	0	0.014	0.019	20.317	0.000	0.000	0.000	0.000	0.000	0.000
167	A	168	ARG	1	0.893	0.961	15.896	-0.288	-0.288	0.000	0.000	0.000	0.000
168	A	169	ARG	1	0.834	0.901	16.072	-0.442	-0.442	0.000	0.000	0.000	0.000
169	A	170	ALA	0	-0.059	-0.023	10.965	-0.012	-0.012	0.000	0.000	0.000	0.000
170	A	171	VAL	0	0.022	0.008	11.087	0.142	0.142	0.000	0.000	0.000	0.000
171	A	172	ASP	-1	-0.738	-0.861	5.615	2.046	2.046	0.000	0.000	0.000	0.000
172	A	173	PHE	0	-0.031	-0.007	8.871	-0.012	-0.012	0.000	0.000	0.000	0.000
173	A	174	TYR	0	0.033	0.024	8.372	0.383	0.383	0.000	0.000	0.000	0.000

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