FMO DATABASE

FMODB ID: 859NY

Calculation Name: 1C28-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1C28

Chain ID: B

ChEMBL ID:

UniProt ID: Q60994

Base Structure: X-ray

Registration Date: 2023-06-22

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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1029422.656036
FMO2-HF: Nuclear repulsion	981542.6166
FMO2-HF: Total energy	-47880.039436
FMO2-MP2: Total energy	-48021.445867

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(B:113:MET)

Summations of interaction energy for fragment #1(B:113:MET)

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.
-11.821	-5.516	12.385	-6.4	-12.29	-0.011

Interaction energy analysis for fragmet #1(B:113:MET)

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 : -0.007

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	B	115	ARG	1	0.948	0.964	3.881	-3.745	-0.055	-0.036	-2.076	-1.578	-0.004
4	B	116	SER	0	0.028	0.001	5.857	0.226	0.226	0.000	0.000	0.000	0.000
5	B	117	ALA	0	0.008	0.008	7.928	-0.068	-0.068	0.000	0.000	0.000	0.000
6	B	118	PHE	0	-0.016	0.000	11.636	0.011	0.011	0.000	0.000	0.000	0.000
7	B	119	SER	0	-0.010	-0.012	15.233	-0.021	-0.021	0.000	0.000	0.000	0.000
8	B	120	VAL	0	0.002	0.007	18.809	0.000	0.000	0.000	0.000	0.000	0.000
9	B	121	GLY	0	0.079	0.023	21.858	-0.006	-0.006	0.000	0.000	0.000	0.000
10	B	122	LEU	0	-0.018	-0.003	25.623	0.002	0.002	0.000	0.000	0.000	0.000
11	B	123	GLU	-1	-0.790	-0.896	29.120	0.102	0.102	0.000	0.000	0.000	0.000
12	B	124	THR	0	0.026	0.010	32.701	-0.005	-0.005	0.000	0.000	0.000	0.000
13	B	125	ARG	1	0.838	0.899	33.470	-0.088	-0.088	0.000	0.000	0.000	0.000
14	B	126	VAL	0	-0.009	0.011	34.951	0.000	0.000	0.000	0.000	0.000	0.000
15	B	127	THR	0	-0.014	-0.035	29.788	0.006	0.006	0.000	0.000	0.000	0.000
16	B	128	VAL	0	-0.021	-0.006	29.701	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	129	PRO	0	0.021	0.013	30.862	0.005	0.005	0.000	0.000	0.000	0.000
18	B	130	ASN	0	-0.033	-0.006	31.094	0.000	0.000	0.000	0.000	0.000	0.000
19	B	131	VAL	0	0.020	0.019	28.343	-0.002	-0.002	0.000	0.000	0.000	0.000
20	B	132	PRO	0	-0.023	-0.013	23.626	0.002	0.002	0.000	0.000	0.000	0.000
21	B	133	ILE	0	0.000	0.001	25.561	-0.007	-0.007	0.000	0.000	0.000	0.000
22	B	134	ARG	1	0.884	0.940	24.774	-0.097	-0.097	0.000	0.000	0.000	0.000
23	B	135	PHE	0	-0.015	-0.001	23.152	-0.008	-0.008	0.000	0.000	0.000	0.000
24	B	136	THR	0	0.017	0.008	24.251	0.011	0.011	0.000	0.000	0.000	0.000
25	B	137	LYS	1	0.786	0.887	25.375	-0.109	-0.109	0.000	0.000	0.000	0.000
26	B	138	ILE	0	-0.012	-0.015	19.699	0.009	0.009	0.000	0.000	0.000	0.000
27	B	139	PHE	0	0.000	0.010	21.140	-0.008	-0.008	0.000	0.000	0.000	0.000
28	B	140	TYR	0	-0.040	-0.033	11.505	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	141	ASN	0	0.034	-0.009	15.125	0.036	0.036	0.000	0.000	0.000	0.000
30	B	142	GLN	0	0.013	0.024	12.825	-0.015	-0.015	0.000	0.000	0.000	0.000
31	B	143	GLN	0	0.010	0.008	8.254	-0.060	-0.060	0.000	0.000	0.000	0.000
32	B	144	ASN	0	-0.034	-0.019	11.134	-0.028	-0.028	0.000	0.000	0.000	0.000
33	B	145	HIS	0	0.003	0.007	6.969	-0.037	-0.037	0.000	0.000	0.000	0.000
34	B	146	TYR	0	-0.023	-0.003	12.774	-0.022	-0.022	0.000	0.000	0.000	0.000
35	B	147	ASP	-1	-0.712	-0.792	16.273	0.172	0.172	0.000	0.000	0.000	0.000
36	B	148	GLY	0	0.031	0.009	19.248	-0.012	-0.012	0.000	0.000	0.000	0.000
37	B	149	SER	0	-0.084	-0.064	22.689	-0.020	-0.020	0.000	0.000	0.000	0.000
38	B	150	THR	0	-0.019	-0.040	21.042	-0.011	-0.011	0.000	0.000	0.000	0.000
39	B	151	GLY	0	-0.009	0.000	22.673	-0.009	-0.009	0.000	0.000	0.000	0.000
40	B	152	LYS	1	0.822	0.924	18.600	-0.143	-0.143	0.000	0.000	0.000	0.000
41	B	153	PHE	0	0.011	0.005	9.760	-0.003	-0.003	0.000	0.000	0.000	0.000
42	B	154	TYR	0	-0.019	-0.033	13.031	-0.046	-0.046	0.000	0.000	0.000	0.000
43	B	155	CYS	0	-0.057	-0.012	8.660	0.161	0.161	0.000	0.000	0.000	0.000
44	B	156	ASN	0	0.032	0.008	7.354	-0.173	-0.173	0.000	0.000	0.000	0.000
45	B	157	ILE	0	-0.037	-0.015	2.420	-1.603	-1.249	3.690	-0.864	-3.180	-0.002
46	B	158	PRO	0	0.014	0.035	2.727	-1.653	-1.320	2.523	-0.641	-2.216	0.002
47	B	159	GLY	0	0.070	0.032	4.136	1.530	2.472	0.081	-0.331	-0.692	-0.002
48	B	160	LEU	0	-0.037	-0.007	6.812	-0.363	-0.363	0.000	0.000	0.000	0.000
49	B	161	TYR	0	0.014	-0.014	6.580	-0.195	-0.195	0.000	0.000	0.000	0.000
50	B	162	TYR	0	0.007	0.003	11.017	-0.068	-0.068	0.000	0.000	0.000	0.000
51	B	163	PHE	0	0.014	-0.005	13.351	0.029	0.029	0.000	0.000	0.000	0.000
52	B	164	SER	0	0.005	-0.008	16.960	-0.024	-0.024	0.000	0.000	0.000	0.000
53	B	165	TYR	0	-0.015	-0.016	20.439	0.012	0.012	0.000	0.000	0.000	0.000
54	B	166	HIS	0	-0.018	-0.013	23.574	-0.012	-0.012	0.000	0.000	0.000	0.000
55	B	167	ILE	0	0.027	0.002	26.842	0.004	0.004	0.000	0.000	0.000	0.000
56	B	168	THR	0	0.034	0.020	29.534	-0.005	-0.005	0.000	0.000	0.000	0.000
57	B	169	VAL	0	-0.045	-0.017	31.931	0.005	0.005	0.000	0.000	0.000	0.000
58	B	170	TYR	0	-0.006	-0.011	34.480	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	171	MET	0	-0.002	0.021	34.363	-0.002	-0.002	0.000	0.000	0.000	0.000
60	B	172	LYS	1	0.825	0.886	38.716	-0.039	-0.039	0.000	0.000	0.000	0.000
61	B	173	ASP	-1	-0.786	-0.865	39.390	0.043	0.043	0.000	0.000	0.000	0.000
62	B	174	VAL	0	0.008	0.019	33.905	0.001	0.001	0.000	0.000	0.000	0.000
63	B	175	LYS	1	0.892	0.934	31.863	-0.055	-0.055	0.000	0.000	0.000	0.000
64	B	176	VAL	0	0.019	-0.001	27.283	0.002	0.002	0.000	0.000	0.000	0.000
65	B	177	SER	0	-0.042	-0.041	24.410	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	178	LEU	0	0.040	0.028	19.228	0.003	0.003	0.000	0.000	0.000	0.000
67	B	179	PHE	0	0.007	0.012	21.266	-0.019	-0.019	0.000	0.000	0.000	0.000
68	B	180	LYS	1	0.863	0.910	13.555	-0.269	-0.269	0.000	0.000	0.000	0.000
69	B	181	LYS	1	0.823	0.895	13.769	-0.151	-0.151	0.000	0.000	0.000	0.000
70	B	182	ASP	-1	-0.802	-0.907	19.123	0.087	0.087	0.000	0.000	0.000	0.000
71	B	183	LYS	1	0.771	0.924	21.834	-0.098	-0.098	0.000	0.000	0.000	0.000
72	B	185	VAL	0	-0.015	0.004	19.772	0.016	0.016	0.000	0.000	0.000	0.000
73	B	186	LEU	0	0.036	0.020	22.493	-0.006	-0.006	0.000	0.000	0.000	0.000
74	B	187	PHE	0	-0.003	-0.012	25.897	0.001	0.001	0.000	0.000	0.000	0.000
75	B	188	THR	0	-0.002	0.005	29.279	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	189	TYR	0	0.005	-0.003	30.306	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	190	ASP	-1	-0.820	-0.896	34.860	0.043	0.043	0.000	0.000	0.000	0.000
78	B	191	GLN	0	-0.040	-0.016	37.916	-0.002	-0.002	0.000	0.000	0.000	0.000
79	B	192	TYR	0	-0.065	-0.060	40.455	0.002	0.002	0.000	0.000	0.000	0.000
80	B	193	GLN	0	-0.012	-0.007	40.194	-0.003	-0.003	0.000	0.000	0.000	0.000
81	B	194	GLU	-1	-0.883	-0.935	40.841	0.039	0.039	0.000	0.000	0.000	0.000
82	B	195	LYS	1	0.820	0.904	39.915	-0.049	-0.049	0.000	0.000	0.000	0.000
83	B	197	VAL	0	-0.005	0.002	33.659	0.001	0.001	0.000	0.000	0.000	0.000
84	B	198	ASP	-1	-0.804	-0.878	37.147	0.054	0.054	0.000	0.000	0.000	0.000
85	B	199	GLN	0	0.022	0.004	33.205	0.002	0.002	0.000	0.000	0.000	0.000
86	B	200	ALA	0	-0.003	0.010	30.206	-0.003	-0.003	0.000	0.000	0.000	0.000
87	B	201	SER	0	0.020	0.005	27.415	0.005	0.005	0.000	0.000	0.000	0.000
88	B	202	GLY	0	0.006	0.008	25.097	-0.006	-0.006	0.000	0.000	0.000	0.000
89	B	203	SER	0	-0.054	-0.018	20.310	0.008	0.008	0.000	0.000	0.000	0.000
90	B	204	VAL	0	-0.001	0.006	17.804	-0.014	-0.014	0.000	0.000	0.000	0.000
91	B	205	LEU	0	0.016	0.011	14.630	0.019	0.019	0.000	0.000	0.000	0.000
92	B	206	LEU	0	-0.002	-0.006	14.120	-0.030	-0.030	0.000	0.000	0.000	0.000
93	B	207	HIS	1	0.797	0.871	7.983	-0.602	-0.602	0.000	0.000	0.000	0.000
94	B	208	LEU	0	-0.068	-0.021	9.815	-0.144	-0.144	0.000	0.000	0.000	0.000
95	B	209	GLU	-1	-0.780	-0.890	7.926	0.621	0.621	0.000	0.000	0.000	0.000
96	B	210	VAL	0	0.022	-0.002	5.237	0.068	0.068	0.000	0.000	0.000	0.000
97	B	211	GLY	0	0.021	0.014	7.876	-0.115	-0.115	0.000	0.000	0.000	0.000
98	B	212	ASP	-1	-0.816	-0.894	10.973	0.247	0.247	0.000	0.000	0.000	0.000
99	B	213	GLN	0	0.021	0.024	12.932	0.052	0.052	0.000	0.000	0.000	0.000
100	B	214	VAL	0	-0.015	-0.018	14.701	-0.018	-0.018	0.000	0.000	0.000	0.000
101	B	215	TRP	0	-0.014	-0.004	17.174	0.017	0.017	0.000	0.000	0.000	0.000
102	B	216	LEU	0	0.000	0.011	20.253	-0.005	-0.005	0.000	0.000	0.000	0.000
103	B	217	GLN	0	0.041	0.022	23.228	0.004	0.004	0.000	0.000	0.000	0.000
104	B	218	VAL	0	0.028	0.022	26.620	-0.002	-0.002	0.000	0.000	0.000	0.000
105	B	219	TYR	0	-0.015	-0.059	29.067	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	234	ASP	-1	-0.822	-0.897	29.352	0.109	0.109	0.000	0.000	0.000	0.000
107	B	235	SER	0	-0.031	0.011	28.707	-0.004	-0.004	0.000	0.000	0.000	0.000
108	B	236	THR	0	-0.014	-0.023	23.956	0.006	0.006	0.000	0.000	0.000	0.000
109	B	237	PHE	0	0.035	0.012	18.583	-0.003	-0.003	0.000	0.000	0.000	0.000
110	B	238	THR	0	-0.026	-0.008	17.243	0.005	0.005	0.000	0.000	0.000	0.000
111	B	239	GLY	0	0.041	0.023	14.865	-0.018	-0.018	0.000	0.000	0.000	0.000
112	B	240	PHE	0	-0.034	-0.020	11.265	0.024	0.024	0.000	0.000	0.000	0.000
113	B	241	LEU	0	-0.013	0.005	3.616	-0.275	-0.027	0.004	-0.052	-0.200	0.000
114	B	242	LEU	0	-0.047	-0.018	8.320	-0.119	-0.119	0.000	0.000	0.000	0.000
115	B	243	TYR	0	0.022	-0.007	7.528	-0.168	-0.168	0.000	0.000	0.000	0.000
116	B	244	HIS	0	-0.029	0.001	2.279	-2.319	-1.234	2.585	-1.341	-2.328	-0.004
117	B	245	ASP	-1	-0.830	-0.905	2.713	-2.398	-2.745	3.538	-1.095	-2.096	-0.001

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Interactive mode: IFIE and PIEDA for fragment #1(B:113:MET)