FMO DATABASE

FMODB ID: 17N6Z

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	OptH
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	-1032263.883446
FMO2-HF: Nuclear repulsion	984385.351737
FMO2-HF: Total energy	-47878.531709
FMO2-MP2: Total energy	-48020.119057

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.
-14.96	-4.41	12.017	-8.369	-14.195	-0.033

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 : -0.015 / q_NPA : -0.025

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	1.005	1.017	3.772	-8.025	0.208	-0.135	-4.484	-3.613	-0.017
4	B	116	SER	0	0.050	0.027	6.599	0.307	0.307	0.000	0.000	0.000	0.000
5	B	117	ALA	0	-0.022	0.006	8.611	-0.086	-0.086	0.000	0.000	0.000	0.000
6	B	118	PHE	0	0.013	0.009	12.192	0.035	0.035	0.000	0.000	0.000	0.000
7	B	119	SER	0	-0.004	0.007	15.821	-0.022	-0.022	0.000	0.000	0.000	0.000
8	B	120	VAL	0	-0.027	-0.013	19.196	0.007	0.007	0.000	0.000	0.000	0.000
9	B	121	GLY	0	0.061	0.005	22.083	-0.008	-0.008	0.000	0.000	0.000	0.000
10	B	122	LEU	0	-0.044	-0.012	25.667	0.005	0.005	0.000	0.000	0.000	0.000
11	B	123	GLU	-1	-0.756	-0.871	29.151	0.048	0.048	0.000	0.000	0.000	0.000
12	B	124	THR	0	-0.015	-0.003	32.766	-0.004	-0.004	0.000	0.000	0.000	0.000
13	B	125	ARG	1	0.834	0.900	33.310	-0.032	-0.032	0.000	0.000	0.000	0.000
14	B	126	VAL	0	0.007	0.014	34.640	-0.001	-0.001	0.000	0.000	0.000	0.000
15	B	127	THR	0	0.010	-0.003	30.021	0.004	0.004	0.000	0.000	0.000	0.000
16	B	128	VAL	0	-0.031	-0.020	29.544	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	129	PRO	0	0.004	-0.008	30.896	0.002	0.002	0.000	0.000	0.000	0.000
18	B	130	ASN	0	-0.060	-0.006	30.577	0.000	0.000	0.000	0.000	0.000	0.000
19	B	131	VAL	0	0.020	0.034	28.191	0.001	0.001	0.000	0.000	0.000	0.000
20	B	132	PRO	0	-0.016	-0.016	23.617	0.000	0.000	0.000	0.000	0.000	0.000
21	B	133	ILE	0	0.021	-0.001	25.538	-0.003	-0.003	0.000	0.000	0.000	0.000
22	B	134	ARG	1	0.877	0.940	24.814	-0.066	-0.066	0.000	0.000	0.000	0.000
23	B	135	PHE	0	0.007	0.015	23.065	-0.006	-0.006	0.000	0.000	0.000	0.000
24	B	136	THR	0	0.050	0.012	24.251	0.009	0.009	0.000	0.000	0.000	0.000
25	B	137	LYS	1	0.866	0.946	25.937	-0.050	-0.050	0.000	0.000	0.000	0.000
26	B	138	ILE	0	-0.005	-0.008	20.444	0.001	0.001	0.000	0.000	0.000	0.000
27	B	139	PHE	0	0.030	0.026	21.783	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	140	TYR	0	0.008	-0.014	12.456	0.002	0.002	0.000	0.000	0.000	0.000
29	B	141	ASN	0	0.049	-0.008	15.769	0.016	0.016	0.000	0.000	0.000	0.000
30	B	142	GLN	0	-0.006	0.021	12.792	0.012	0.012	0.000	0.000	0.000	0.000
31	B	143	GLN	0	-0.007	-0.001	8.481	-0.077	-0.077	0.000	0.000	0.000	0.000
32	B	144	ASN	0	-0.012	-0.004	11.727	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	145	HIS	0	-0.034	-0.034	7.725	0.009	0.009	0.000	0.000	0.000	0.000
34	B	146	TYR	0	-0.030	0.008	13.099	-0.017	-0.017	0.000	0.000	0.000	0.000
35	B	147	ASP	-1	-0.773	-0.867	16.535	0.136	0.136	0.000	0.000	0.000	0.000
36	B	148	GLY	0	0.049	0.011	19.040	-0.013	-0.013	0.000	0.000	0.000	0.000
37	B	149	SER	0	-0.083	-0.056	22.115	-0.015	-0.015	0.000	0.000	0.000	0.000
38	B	150	THR	0	0.002	-0.008	20.431	-0.009	-0.009	0.000	0.000	0.000	0.000
39	B	151	GLY	0	-0.010	-0.008	22.142	-0.008	-0.008	0.000	0.000	0.000	0.000
40	B	152	LYS	1	0.873	0.960	18.404	-0.095	-0.095	0.000	0.000	0.000	0.000
41	B	153	PHE	0	0.013	0.012	10.015	-0.003	-0.003	0.000	0.000	0.000	0.000
42	B	154	TYR	0	-0.014	-0.032	12.505	-0.023	-0.023	0.000	0.000	0.000	0.000
43	B	155	CYS	0	-0.060	-0.005	8.339	0.111	0.111	0.000	0.000	0.000	0.000
44	B	156	ASN	0	0.054	0.025	6.175	-0.151	-0.151	0.000	0.000	0.000	0.000
45	B	157	ILE	0	-0.037	-0.022	2.280	-0.998	-2.089	5.776	-1.130	-3.555	-0.001
46	B	158	PRO	0	0.035	0.046	2.877	-1.994	-1.319	1.623	-0.463	-1.835	0.003
47	B	159	GLY	0	0.079	0.033	4.689	0.754	1.172	0.008	-0.085	-0.342	0.000
48	B	160	LEU	0	-0.065	-0.015	6.925	-0.119	-0.119	0.000	0.000	0.000	0.000
49	B	161	TYR	0	0.002	-0.035	6.453	-0.252	-0.252	0.000	0.000	0.000	0.000
50	B	162	TYR	0	0.004	0.004	11.216	-0.016	-0.016	0.000	0.000	0.000	0.000
51	B	163	PHE	0	0.022	0.006	13.419	0.021	0.021	0.000	0.000	0.000	0.000
52	B	164	SER	0	0.006	0.001	17.092	-0.011	-0.011	0.000	0.000	0.000	0.000
53	B	165	TYR	0	0.004	-0.003	20.554	0.012	0.012	0.000	0.000	0.000	0.000
54	B	166	HIS	0	-0.007	-0.007	23.552	-0.007	-0.007	0.000	0.000	0.000	0.000
55	B	167	ILE	0	0.046	0.003	26.717	0.004	0.004	0.000	0.000	0.000	0.000
56	B	168	THR	0	-0.009	0.002	29.286	-0.004	-0.004	0.000	0.000	0.000	0.000
57	B	169	VAL	0	-0.038	-0.029	31.753	0.003	0.003	0.000	0.000	0.000	0.000
58	B	170	TYR	0	-0.004	0.011	34.247	0.001	0.001	0.000	0.000	0.000	0.000
59	B	171	MET	0	-0.011	0.012	34.141	0.001	0.001	0.000	0.000	0.000	0.000
60	B	172	LYS	1	0.839	0.896	38.451	-0.013	-0.013	0.000	0.000	0.000	0.000
61	B	173	ASP	-1	-0.786	-0.880	39.054	0.014	0.014	0.000	0.000	0.000	0.000
62	B	174	VAL	0	0.011	0.023	33.999	0.001	0.001	0.000	0.000	0.000	0.000
63	B	175	LYS	1	0.967	0.976	31.771	-0.016	-0.016	0.000	0.000	0.000	0.000
64	B	176	VAL	0	0.014	-0.004	27.138	0.003	0.003	0.000	0.000	0.000	0.000
65	B	177	SER	0	-0.034	-0.031	24.554	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	178	LEU	0	0.031	0.032	18.692	0.003	0.003	0.000	0.000	0.000	0.000
67	B	179	PHE	0	0.011	0.002	21.549	-0.011	-0.011	0.000	0.000	0.000	0.000
68	B	180	LYS	1	1.010	0.982	14.175	-0.142	-0.142	0.000	0.000	0.000	0.000
69	B	181	LYS	1	0.786	0.896	13.794	-0.113	-0.113	0.000	0.000	0.000	0.000
70	B	182	ASP	-1	-0.871	-0.936	19.224	0.054	0.054	0.000	0.000	0.000	0.000
71	B	183	LYS	1	0.800	0.924	22.786	-0.042	-0.042	0.000	0.000	0.000	0.000
72	B	185	VAL	0	-0.022	-0.005	19.789	0.000	0.000	0.000	0.000	0.000	0.000
73	B	186	LEU	0	0.032	0.035	22.750	-0.005	-0.005	0.000	0.000	0.000	0.000
74	B	187	PHE	0	-0.050	-0.033	25.799	0.002	0.002	0.000	0.000	0.000	0.000
75	B	188	THR	0	-0.002	0.004	29.114	-0.002	-0.002	0.000	0.000	0.000	0.000
76	B	189	TYR	0	-0.034	-0.023	30.833	0.002	0.002	0.000	0.000	0.000	0.000
77	B	190	ASP	-1	-0.872	-0.932	35.287	0.002	0.002	0.000	0.000	0.000	0.000
78	B	191	GLN	0	-0.024	-0.010	38.013	0.001	0.001	0.000	0.000	0.000	0.000
79	B	192	TYR	0	-0.085	-0.062	40.690	0.000	0.000	0.000	0.000	0.000	0.000
80	B	193	GLN	0	-0.003	-0.009	40.733	-0.002	-0.002	0.000	0.000	0.000	0.000
81	B	194	GLU	-1	-0.874	-0.929	41.390	0.011	0.011	0.000	0.000	0.000	0.000
82	B	195	LYS	1	0.849	0.928	40.285	-0.012	-0.012	0.000	0.000	0.000	0.000
83	B	197	VAL	0	0.008	0.013	33.946	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	198	ASP	-1	-0.817	-0.910	37.158	0.017	0.017	0.000	0.000	0.000	0.000
85	B	199	GLN	0	-0.016	0.000	33.004	0.004	0.004	0.000	0.000	0.000	0.000
86	B	200	ALA	0	-0.015	-0.011	29.923	-0.002	-0.002	0.000	0.000	0.000	0.000
87	B	201	SER	0	0.020	0.007	27.220	0.004	0.004	0.000	0.000	0.000	0.000
88	B	202	GLY	0	0.001	0.007	24.852	-0.002	-0.002	0.000	0.000	0.000	0.000
89	B	203	SER	0	-0.026	-0.020	20.771	0.000	0.000	0.000	0.000	0.000	0.000
90	B	204	VAL	0	-0.036	0.000	17.624	-0.004	-0.004	0.000	0.000	0.000	0.000
91	B	205	LEU	0	0.013	0.008	13.886	0.001	0.001	0.000	0.000	0.000	0.000
92	B	206	LEU	0	-0.021	-0.013	14.216	-0.003	-0.003	0.000	0.000	0.000	0.000
93	B	207	HIS	1	0.873	0.920	8.408	-0.414	-0.414	0.000	0.000	0.000	0.000
94	B	208	LEU	0	-0.138	-0.068	9.959	-0.078	-0.078	0.000	0.000	0.000	0.000
95	B	209	GLU	-1	-0.829	-0.936	7.992	0.503	0.503	0.000	0.000	0.000	0.000
96	B	210	VAL	0	0.030	0.003	4.903	0.030	0.030	0.000	0.000	0.000	0.000
97	B	211	GLY	0	-0.007	-0.002	7.733	-0.096	-0.096	0.000	0.000	0.000	0.000
98	B	212	ASP	-1	-0.840	-0.899	10.975	0.171	0.171	0.000	0.000	0.000	0.000
99	B	213	GLN	0	-0.020	-0.020	12.800	0.020	0.020	0.000	0.000	0.000	0.000
100	B	214	VAL	0	-0.034	-0.015	15.095	-0.018	-0.018	0.000	0.000	0.000	0.000
101	B	215	TRP	0	-0.025	-0.014	17.451	0.012	0.012	0.000	0.000	0.000	0.000
102	B	216	LEU	0	0.043	0.032	20.509	-0.007	-0.007	0.000	0.000	0.000	0.000
103	B	217	GLN	0	0.053	0.015	23.470	0.008	0.008	0.000	0.000	0.000	0.000
104	B	218	VAL	0	0.024	0.033	26.744	-0.003	-0.003	0.000	0.000	0.000	0.000
105	B	219	TYR	0	0.055	-0.022	29.043	0.002	0.002	0.000	0.000	0.000	0.000
106	B	234	ASP	-1	-0.862	-0.932	29.501	0.042	0.042	0.000	0.000	0.000	0.000
107	B	235	SER	0	-0.097	-0.019	28.396	-0.004	-0.004	0.000	0.000	0.000	0.000
108	B	236	THR	0	-0.010	-0.018	23.696	0.003	0.003	0.000	0.000	0.000	0.000
109	B	237	PHE	0	-0.007	-0.016	18.664	-0.002	-0.002	0.000	0.000	0.000	0.000
110	B	238	THR	0	0.017	0.013	16.909	0.010	0.010	0.000	0.000	0.000	0.000
111	B	239	GLY	0	0.027	0.007	14.921	-0.006	-0.006	0.000	0.000	0.000	0.000
112	B	240	PHE	0	-0.048	-0.035	11.550	0.013	0.013	0.000	0.000	0.000	0.000
113	B	241	LEU	0	-0.009	0.010	3.754	-0.211	-0.012	0.002	-0.040	-0.160	0.000
114	B	242	LEU	0	-0.056	-0.033	8.464	-0.132	-0.132	0.000	0.000	0.000	0.000
115	B	243	TYR	0	-0.003	-0.007	7.746	-0.189	-0.189	0.000	0.000	0.000	0.000
116	B	244	HIS	0	-0.008	0.010	2.309	-3.225	-1.872	3.522	-1.567	-3.307	-0.012
117	B	245	ASP	-1	-0.810	-0.895	3.407	-0.514	0.249	1.221	-0.600	-1.383	-0.006

Top

Graph

Manual

About

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