FMO DATABASE

FMODB ID: NNYQQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-2053984.77561
FMO2-HF: Nuclear repulsion	1979216.809997
FMO2-HF: Total energy	-74767.965613
FMO2-MP2: Total energy	-74983.712032

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.
-8.11	-4.12	7.409	-5.688	-5.708	-0.029

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 : 0.008 / q_NPA : 0.005

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	-0.038	-0.005	3.869	0.813	2.272	-0.010	-0.781	-0.667	0.002
4	A	4	THR	0	0.030	0.010	6.782	-0.133	-0.133	0.000	0.000	0.000	0.000
5	A	5	PHE	0	0.029	-0.005	9.863	0.213	0.213	0.000	0.000	0.000	0.000
6	A	6	TYR	0	0.036	0.000	13.280	-0.030	-0.030	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.752	-0.860	16.889	-0.297	-0.297	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.816	-0.890	20.096	-0.231	-0.231	0.000	0.000	0.000	0.000
9	A	9	ARG	0	0.094	0.081	20.476	-0.020	-0.020	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.033	-0.023	21.044	0.003	0.003	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.045	-0.022	15.624	0.005	0.005	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.034	-0.010	18.794	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.048	0.029	20.869	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.837	0.926	19.730	0.393	0.393	0.000	0.000	0.000	0.000
15	A	15	HIS	0	-0.013	-0.007	15.732	-0.049	-0.049	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.026	-0.031	11.998	0.024	0.024	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.799	-0.881	8.893	-1.922	-1.922	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.061	-0.011	8.417	0.140	0.140	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.048	0.012	4.186	-0.614	-0.473	-0.001	-0.058	-0.083	0.000
20	A	20	SER	0	-0.015	-0.012	3.940	-0.530	-0.314	0.000	-0.097	-0.119	0.000
21	A	21	ASP	-1	-0.782	-0.890	5.993	0.045	0.045	0.000	0.000	0.000	0.000
22	A	22	HIS	0	-0.010	0.008	8.994	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.008	0.007	12.022	0.041	0.041	0.000	0.000	0.000	0.000
24	A	24	ASN	0	0.071	0.010	15.423	0.057	0.057	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.025	0.012	12.118	-0.031	-0.031	0.000	0.000	0.000	0.000
26	A	26	GLN	0	0.016	0.008	16.292	0.002	0.002	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.043	-0.014	18.518	0.014	0.014	0.000	0.000	0.000	0.000
28	A	28	TYR	0	-0.021	-0.007	15.140	0.026	0.026	0.000	0.000	0.000	0.000
29	A	29	PHE	0	-0.046	-0.023	13.896	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.062	-0.048	19.308	0.027	0.027	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.792	0.889	20.971	0.304	0.304	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.102	-0.045	15.899	-0.064	-0.064	0.000	0.000	0.000	0.000
33	A	33	ASN	0	-0.024	-0.033	18.529	0.048	0.048	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.053	-0.020	17.322	0.023	0.023	0.000	0.000	0.000	0.000
35	A	35	ILE	0	0.012	0.005	10.890	-0.055	-0.055	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.820	0.900	10.424	0.669	0.669	0.000	0.000	0.000	0.000
37	A	37	VAL	0	-0.019	-0.003	6.210	-0.275	-0.275	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.826	-0.923	6.161	-1.132	-1.132	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.056	-0.047	2.481	-1.906	-1.269	2.040	-1.498	-1.178	-0.013
40	A	40	GLY	0	0.068	0.046	2.825	-1.715	-0.537	1.391	-1.521	-1.047	-0.013
41	A	41	CYS	0	-0.092	-0.015	3.670	-1.551	-1.649	0.015	0.037	0.046	0.000
42	A	42	TRP	0	0.013	-0.013	3.142	0.034	0.754	0.108	-0.266	-0.562	-0.001
43	A	43	MET	0	-0.058	0.000	7.467	0.072	0.072	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.012	-0.002	10.697	-0.135	-0.135	0.000	0.000	0.000	0.000
45	A	45	TYR	0	0.059	0.014	12.896	0.092	0.092	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.781	-0.887	16.383	-0.159	-0.159	0.000	0.000	0.000	0.000
47	A	47	GLN	0	-0.016	-0.006	19.607	-0.023	-0.023	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.043	0.019	18.647	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.057	-0.041	17.821	0.016	0.016	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.004	0.001	12.658	0.063	0.063	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.025	0.005	17.142	0.048	0.048	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.022	0.004	20.059	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.016	-0.008	20.783	0.019	0.019	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.052	0.032	16.325	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	TYR	0	-0.007	0.002	15.310	0.027	0.027	0.000	0.000	0.000	0.000
56	A	56	PHE	0	0.004	-0.007	10.711	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.042	-0.011	9.444	-0.039	-0.039	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.851	0.908	8.657	-0.498	-0.498	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.848	0.894	5.838	-1.746	-1.746	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.008	0.012	8.987	0.082	0.082	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.797	-0.867	11.682	-0.497	-0.497	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.010	-0.014	11.601	0.090	0.090	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.009	0.000	15.976	-0.037	-0.037	0.000	0.000	0.000	0.000
64	A	64	ASH	0	-0.001	-0.054	19.130	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.049	0.041	18.450	0.007	0.007	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.012	0.006	19.216	0.006	0.006	0.000	0.000	0.000	0.000
67	A	67	GLN	0	-0.031	-0.005	17.479	0.036	0.036	0.000	0.000	0.000	0.000
68	A	68	TRP	0	-0.023	0.001	15.045	0.017	0.017	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.080	-0.051	16.935	0.027	0.027	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.016	0.018	19.674	0.009	0.009	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.006	-0.012	20.470	0.009	0.009	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.052	-0.055	22.375	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.807	-0.886	20.431	-0.210	-0.210	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.009	-0.004	20.404	-0.034	-0.034	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.011	0.001	14.458	0.019	0.019	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.863	0.919	17.417	0.167	0.167	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.047	-0.015	14.617	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	CYS	0	0.001	0.010	9.235	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.816	0.913	9.236	-0.186	-0.186	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.028	0.032	2.149	-0.838	-1.101	3.866	-1.504	-2.098	-0.004
81	A	81	ILE	0	-0.056	-0.042	5.838	0.179	0.179	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.041	-0.019	7.118	0.666	0.666	0.000	0.000	0.000	0.000
83	A	83	HIS	0	0.034	0.025	8.050	-0.055	-0.055	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.034	-0.033	9.727	-0.204	-0.204	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.018	-0.008	13.431	0.053	0.053	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.054	-0.044	16.081	-0.029	-0.029	0.000	0.000	0.000	0.000
87	A	88	HIS	0	0.005	-0.001	13.479	0.010	0.010	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.779	0.863	18.739	-0.374	-0.374	0.000	0.000	0.000	0.000
89	A	90	LEU	0	-0.026	0.006	20.984	0.003	0.003	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.839	0.902	23.708	-0.228	-0.228	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.011	0.003	26.138	0.002	0.002	0.000	0.000	0.000	0.000
92	A	93	TYR	0	-0.003	-0.006	28.993	0.001	0.001	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.755	-0.864	32.405	0.091	0.091	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.850	0.918	35.378	-0.096	-0.096	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.779	-0.873	33.552	0.091	0.091	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.867	-0.933	33.672	0.098	0.098	0.000	0.000	0.000	0.000
97	A	98	TYR	0	-0.111	-0.081	28.456	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.885	0.957	33.990	-0.102	-0.102	0.000	0.000	0.000	0.000
99	A	100	GLY	0	0.020	-0.006	36.614	0.000	0.000	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.050	-0.026	37.189	0.007	0.007	0.000	0.000	0.000	0.000
101	A	102	MET	0	-0.016	0.002	32.097	0.007	0.007	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.009	0.000	29.463	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.765	-0.874	27.061	0.258	0.258	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.056	-0.016	23.941	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	106	THR	0	0.039	-0.005	22.200	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.841	-0.894	20.784	0.448	0.448	0.000	0.000	0.000	0.000
107	A	108	ASP	-1	-0.819	-0.895	18.043	0.427	0.427	0.000	0.000	0.000	0.000
108	A	109	CYS	0	-0.042	-0.017	21.205	-0.032	-0.032	0.000	0.000	0.000	0.000
109	A	110	SER	0	0.024	0.014	24.003	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	111	SER	0	0.004	-0.058	25.284	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.016	-0.014	25.369	0.001	0.001	0.000	0.000	0.000	0.000
112	A	113	HIS	1	0.804	0.871	28.936	-0.102	-0.102	0.000	0.000	0.000	0.000
113	A	114	GLU	-1	-0.827	-0.866	31.890	0.089	0.089	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.861	0.936	28.714	-0.146	-0.146	0.000	0.000	0.000	0.000
115	A	116	PHE	0	0.030	0.010	27.839	0.009	0.009	0.000	0.000	0.000	0.000
116	A	117	HIS	0	0.037	0.022	33.986	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	118	PHE	0	-0.013	-0.013	32.402	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	119	SER	0	0.026	0.011	35.120	0.005	0.005	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.877	-0.894	34.819	0.081	0.081	0.000	0.000	0.000	0.000
120	A	121	ILE	0	-0.032	-0.031	28.692	0.008	0.008	0.000	0.000	0.000	0.000
121	A	122	HIS	0	-0.051	-0.027	31.327	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	123	SER	0	-0.050	-0.024	29.368	0.000	0.000	0.000	0.000	0.000	0.000
123	A	124	PHE	0	-0.011	-0.013	25.093	0.005	0.005	0.000	0.000	0.000	0.000
124	A	125	HIS	0	0.013	0.007	25.802	0.006	0.006	0.000	0.000	0.000	0.000
125	A	126	VAL	0	-0.015	0.010	19.040	0.007	0.007	0.000	0.000	0.000	0.000
126	A	127	LEU	0	0.016	0.008	22.015	0.009	0.009	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.776	-0.849	19.442	0.452	0.452	0.000	0.000	0.000	0.000
128	A	129	GLY	0	0.066	0.036	15.484	-0.016	-0.016	0.000	0.000	0.000	0.000
129	A	130	TRP	0	0.015	0.003	12.393	-0.123	-0.123	0.000	0.000	0.000	0.000
130	A	131	TRP	0	0.002	-0.019	14.372	0.065	0.065	0.000	0.000	0.000	0.000
131	A	132	VAL	0	-0.012	-0.005	14.094	-0.017	-0.017	0.000	0.000	0.000	0.000
132	A	133	LEU	0	0.023	0.022	17.026	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	134	TYR	0	-0.010	-0.018	16.698	0.000	0.000	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.709	-0.825	22.343	0.044	0.044	0.000	0.000	0.000	0.000
135	A	136	MET	0	-0.038	-0.018	25.229	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	137	PRO	0	0.047	0.031	25.368	0.014	0.014	0.000	0.000	0.000	0.000
137	A	138	ASN	0	-0.073	-0.053	24.559	0.000	0.000	0.000	0.000	0.000	0.000
138	A	139	TYR	0	-0.038	-0.018	19.855	-0.008	-0.008	0.000	0.000	0.000	0.000
139	A	140	ARG	1	0.984	0.988	21.229	-0.074	-0.074	0.000	0.000	0.000	0.000
140	A	141	GLY	0	0.022	0.012	23.422	0.009	0.009	0.000	0.000	0.000	0.000
141	A	142	ARG	1	0.789	0.846	22.333	-0.038	-0.038	0.000	0.000	0.000	0.000
142	A	143	GLN	0	0.041	0.025	17.008	0.044	0.044	0.000	0.000	0.000	0.000
143	A	144	TYR	0	0.028	0.007	19.422	-0.027	-0.027	0.000	0.000	0.000	0.000
144	A	145	LEU	0	-0.031	-0.011	12.711	0.038	0.038	0.000	0.000	0.000	0.000
145	A	146	LEU	0	-0.022	0.000	16.531	-0.027	-0.027	0.000	0.000	0.000	0.000
146	A	147	ARG	1	0.975	0.995	16.122	-0.255	-0.255	0.000	0.000	0.000	0.000
147	A	148	PRO	0	0.023	0.006	16.266	-0.048	-0.048	0.000	0.000	0.000	0.000
148	A	149	GLY	0	-0.012	-0.006	19.452	-0.018	-0.018	0.000	0.000	0.000	0.000
149	A	150	ASP	-1	-0.754	-0.839	22.866	0.174	0.174	0.000	0.000	0.000	0.000
150	A	151	TYR	0	-0.031	-0.040	19.937	-0.012	-0.012	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.853	0.907	26.516	-0.143	-0.143	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.854	0.898	29.386	-0.095	-0.095	0.000	0.000	0.000	0.000
153	A	154	TYR	0	0.046	0.010	28.332	0.008	0.008	0.000	0.000	0.000	0.000
154	A	155	HIS	0	-0.026	0.004	27.489	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	156	GLU	-1	-0.886	-0.946	26.637	0.102	0.102	0.000	0.000	0.000	0.000
156	A	157	TRP	0	-0.057	-0.018	22.753	0.019	0.019	0.000	0.000	0.000	0.000
157	A	158	GLY	0	-0.016	-0.006	22.756	0.001	0.001	0.000	0.000	0.000	0.000
158	A	159	ALA	0	-0.039	-0.009	24.412	-0.015	-0.015	0.000	0.000	0.000	0.000
159	A	160	VAL	0	-0.013	-0.012	26.638	-0.001	-0.001	0.000	0.000	0.000	0.000
160	A	161	ASP	-1	-0.818	-0.905	29.255	0.045	0.045	0.000	0.000	0.000	0.000
161	A	162	ALA	0	0.050	0.028	29.120	0.008	0.008	0.000	0.000	0.000	0.000
162	A	163	ARG	1	0.829	0.910	29.573	-0.045	-0.045	0.000	0.000	0.000	0.000
163	A	164	VAL	0	0.015	0.021	26.034	0.003	0.003	0.000	0.000	0.000	0.000
164	A	165	GLY	0	0.000	-0.002	26.188	-0.009	-0.009	0.000	0.000	0.000	0.000
165	A	166	SER	0	-0.082	-0.040	23.477	0.007	0.007	0.000	0.000	0.000	0.000
166	A	167	LEU	0	0.008	0.012	20.059	-0.005	-0.005	0.000	0.000	0.000	0.000
167	A	168	ARG	1	0.889	0.960	15.670	-0.254	-0.254	0.000	0.000	0.000	0.000
168	A	169	ARG	1	0.828	0.905	15.321	-0.464	-0.464	0.000	0.000	0.000	0.000
169	A	170	ALA	0	-0.037	-0.019	10.275	-0.013	-0.013	0.000	0.000	0.000	0.000
170	A	171	VAL	0	0.033	0.014	11.039	0.115	0.115	0.000	0.000	0.000	0.000
171	A	172	ASP	-1	-0.727	-0.862	5.746	2.343	2.343	0.000	0.000	0.000	0.000
172	A	173	PHE	0	-0.021	0.000	8.847	-0.014	-0.014	0.000	0.000	0.000	0.000
173	A	174	TYR	0	0.033	0.023	7.872	0.395	0.395	0.000	0.000	0.000	0.000

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