FMO DATABASE

FMODB ID: 76KLK

Calculation Name: 3HCY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HCY

Chain ID: A

ChEMBL ID:

UniProt ID: Q92UP1

Base Structure: X-ray

Registration Date: 2023-09-23

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	148
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1376822.873188
FMO2-HF: Nuclear repulsion	1318522.718621
FMO2-HF: Total energy	-58300.154568
FMO2-MP2: Total energy	-58469.846762

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:-2:SER)

Summations of interaction energy for fragment #1(A:-2: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.
1.946	3.887	0.002	-0.837	-1.104	0.002

Interaction energy analysis for fragmet #1(A:-2:SER)

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 : -0.015

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	0	ALA	0	-0.009	0.009	3.654	1.035	2.798	0.004	-0.822	-0.944	0.002
4	A	1	ILE	0	0.002	-0.023	5.172	-0.013	0.062	-0.001	-0.006	-0.067	0.000
5	A	2	GLU	-1	-0.909	-0.937	8.281	0.437	0.437	0.000	0.000	0.000	0.000
6	A	3	GLU	-1	-0.821	-0.929	8.177	-0.784	-0.784	0.000	0.000	0.000	0.000
7	A	4	VAL	0	-0.049	-0.025	10.852	0.056	0.056	0.000	0.000	0.000	0.000
8	A	5	TYR	0	0.000	0.012	11.805	0.018	0.018	0.000	0.000	0.000	0.000
9	A	6	GLU	-1	-0.781	-0.897	14.262	-0.036	-0.036	0.000	0.000	0.000	0.000
10	A	7	ALA	0	0.010	0.013	15.351	0.029	0.029	0.000	0.000	0.000	0.000
11	A	8	THR	0	-0.071	-0.058	17.038	0.025	0.025	0.000	0.000	0.000	0.000
12	A	9	LEU	0	-0.003	-0.003	18.037	0.026	0.026	0.000	0.000	0.000	0.000
13	A	10	ASP	-1	-0.850	-0.905	18.891	-0.122	-0.122	0.000	0.000	0.000	0.000
14	A	11	ALA	0	-0.048	-0.020	21.216	0.017	0.017	0.000	0.000	0.000	0.000
15	A	12	ILE	0	-0.007	-0.007	22.003	0.014	0.014	0.000	0.000	0.000	0.000
16	A	13	GLN	0	0.015	0.015	23.929	0.013	0.013	0.000	0.000	0.000	0.000
17	A	14	GLY	0	-0.031	-0.014	25.663	0.008	0.008	0.000	0.000	0.000	0.000
18	A	15	ALA	0	-0.048	-0.023	27.251	0.005	0.005	0.000	0.000	0.000	0.000
19	A	16	LEU	0	-0.038	-0.033	27.474	0.004	0.004	0.000	0.000	0.000	0.000
20	A	17	ASN	0	-0.071	-0.020	30.124	0.007	0.007	0.000	0.000	0.000	0.000
21	A	18	CYS	0	-0.017	0.004	28.285	0.002	0.002	0.000	0.000	0.000	0.000
22	A	19	ASP	-1	-0.795	-0.865	29.678	-0.023	-0.023	0.000	0.000	0.000	0.000
23	A	20	ARG	1	0.735	0.848	27.064	0.002	0.002	0.000	0.000	0.000	0.000
24	A	21	ALA	0	0.016	0.001	24.092	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	22	SER	0	0.020	0.013	21.525	0.013	0.013	0.000	0.000	0.000	0.000
26	A	23	ILE	0	-0.017	-0.006	17.660	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	24	LEU	0	0.001	0.004	19.448	0.021	0.021	0.000	0.000	0.000	0.000
28	A	25	LEU	0	0.008	-0.005	15.115	-0.032	-0.032	0.000	0.000	0.000	0.000
29	A	26	PHE	0	0.001	0.001	19.215	0.019	0.019	0.000	0.000	0.000	0.000
30	A	27	ASP	-1	-0.753	-0.840	18.121	0.048	0.048	0.000	0.000	0.000	0.000
31	A	28	GLU	-1	-0.920	-0.972	17.288	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	29	ALA	0	-0.076	-0.023	20.058	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	30	GLY	0	-0.023	-0.007	22.561	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	31	THR	0	-0.099	-0.076	22.821	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	32	MET	0	-0.061	-0.018	22.092	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	33	ARG	1	0.857	0.916	18.798	-0.053	-0.053	0.000	0.000	0.000	0.000
37	A	34	PHE	0	-0.011	-0.011	19.445	-0.021	-0.021	0.000	0.000	0.000	0.000
38	A	35	VAL	0	-0.063	-0.025	14.435	0.027	0.027	0.000	0.000	0.000	0.000
39	A	36	ALA	0	0.031	0.023	14.820	0.001	0.001	0.000	0.000	0.000	0.000
40	A	37	ALA	0	0.005	-0.011	17.156	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	38	ARG	1	0.760	0.867	18.693	0.098	0.098	0.000	0.000	0.000	0.000
42	A	39	GLY	0	0.018	0.019	22.808	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	40	LEU	0	-0.003	-0.006	23.731	0.001	0.001	0.000	0.000	0.000	0.000
44	A	41	SER	0	-0.031	-0.054	24.463	0.011	0.011	0.000	0.000	0.000	0.000
45	A	42	GLU	-1	-0.825	-0.907	21.606	0.114	0.114	0.000	0.000	0.000	0.000
46	A	43	HIS	0	-0.060	-0.024	24.448	0.006	0.006	0.000	0.000	0.000	0.000
47	A	44	TYR	0	0.069	0.021	26.471	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	45	GLN	0	-0.036	-0.035	21.215	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	46	ARG	1	0.828	0.884	23.383	-0.093	-0.093	0.000	0.000	0.000	0.000
50	A	47	ALA	0	-0.038	0.004	25.842	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	48	VAL	0	-0.046	-0.023	27.364	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	49	ASP	-1	-0.798	-0.896	22.743	0.046	0.046	0.000	0.000	0.000	0.000
53	A	50	GLY	0	-0.043	-0.020	24.940	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	51	HIS	0	0.009	-0.002	26.633	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	52	SER	0	0.028	0.010	27.128	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	53	PRO	0	-0.061	-0.020	28.874	0.001	0.001	0.000	0.000	0.000	0.000
57	A	54	TRP	0	-0.021	-0.019	27.244	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	55	ILE	0	0.027	-0.002	30.435	0.002	0.002	0.000	0.000	0.000	0.000
59	A	56	THR	0	-0.008	-0.010	31.873	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	57	GLY	0	0.069	0.027	34.229	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	58	ALA	0	-0.012	0.006	28.775	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	59	ASN	0	-0.071	-0.041	29.315	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	60	GLU	-1	-0.913	-0.956	31.379	-0.090	-0.090	0.000	0.000	0.000	0.000
64	A	61	PRO	0	-0.086	-0.023	28.335	0.006	0.006	0.000	0.000	0.000	0.000
65	A	62	GLU	-1	-0.858	-0.929	31.232	-0.074	-0.074	0.000	0.000	0.000	0.000
66	A	63	PRO	0	-0.055	-0.043	31.180	0.002	0.002	0.000	0.000	0.000	0.000
67	A	64	ILE	0	-0.023	0.012	32.343	0.005	0.005	0.000	0.000	0.000	0.000
68	A	65	PHE	0	-0.002	-0.012	33.177	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	66	VAL	0	0.020	0.014	35.797	0.003	0.003	0.000	0.000	0.000	0.000
70	A	67	GLU	-1	-0.824	-0.914	37.053	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	68	ASN	0	-0.010	-0.039	39.339	0.002	0.002	0.000	0.000	0.000	0.000
72	A	69	VAL	0	0.009	0.015	36.718	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	70	ASP	-1	-0.899	-0.948	39.276	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	71	ASP	-1	-0.886	-0.922	42.897	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	72	ALA	0	-0.025	-0.001	38.907	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	73	GLU	-1	-0.956	-0.978	40.137	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	74	PHE	0	-0.049	-0.026	34.874	0.001	0.001	0.000	0.000	0.000	0.000
78	A	75	SER	0	-0.005	-0.019	37.686	0.000	0.000	0.000	0.000	0.000	0.000
79	A	76	ARG	1	0.839	0.896	39.098	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	77	GLU	-1	-0.803	-0.901	36.436	0.009	0.009	0.000	0.000	0.000	0.000
81	A	78	LEU	0	0.002	0.028	32.234	0.002	0.002	0.000	0.000	0.000	0.000
82	A	79	LYS	1	0.836	0.904	35.203	0.005	0.005	0.000	0.000	0.000	0.000
83	A	80	GLU	-1	-0.866	-0.913	37.649	0.010	0.010	0.000	0.000	0.000	0.000
84	A	81	SER	0	-0.029	-0.028	32.354	0.003	0.003	0.000	0.000	0.000	0.000
85	A	82	ILE	0	-0.027	-0.010	32.525	0.001	0.001	0.000	0.000	0.000	0.000
86	A	83	VAL	0	0.017	0.007	34.032	0.000	0.000	0.000	0.000	0.000	0.000
87	A	84	GLY	0	-0.010	-0.002	36.256	0.000	0.000	0.000	0.000	0.000	0.000
88	A	85	GLU	-1	-0.800	-0.858	28.830	0.026	0.026	0.000	0.000	0.000	0.000
89	A	86	GLY	0	-0.012	-0.001	32.782	0.000	0.000	0.000	0.000	0.000	0.000
90	A	87	ILE	0	-0.046	-0.007	29.801	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	88	ALA	0	0.000	-0.008	34.347	0.001	0.001	0.000	0.000	0.000	0.000
92	A	89	ALA	0	-0.039	-0.020	35.441	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	90	LEU	0	0.011	-0.003	31.233	0.000	0.000	0.000	0.000	0.000	0.000
94	A	91	GLY	0	-0.004	0.001	31.153	0.000	0.000	0.000	0.000	0.000	0.000
95	A	92	PHE	0	-0.017	-0.009	28.854	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	93	PHE	0	0.056	0.006	26.714	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	94	PRO	0	0.009	0.011	25.786	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	95	LEU	0	-0.031	0.005	19.864	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	96	VAL	0	0.037	0.012	23.101	0.008	0.008	0.000	0.000	0.000	0.000
100	A	97	THR	0	-0.032	-0.020	18.656	-0.030	-0.030	0.000	0.000	0.000	0.000
101	A	98	GLU	-1	-0.801	-0.885	20.304	-0.237	-0.237	0.000	0.000	0.000	0.000
102	A	99	GLY	0	0.004	0.022	23.844	0.012	0.012	0.000	0.000	0.000	0.000
103	A	100	ARG	1	0.956	0.979	20.144	0.153	0.153	0.000	0.000	0.000	0.000
104	A	101	LEU	0	0.033	0.014	23.878	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	102	ILE	0	-0.067	-0.019	18.627	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	103	GLY	0	0.043	0.002	20.380	0.010	0.010	0.000	0.000	0.000	0.000
107	A	104	LYS	1	0.864	0.947	21.904	0.027	0.027	0.000	0.000	0.000	0.000
108	A	105	PHE	0	-0.002	-0.003	22.376	0.000	0.000	0.000	0.000	0.000	0.000
109	A	106	MET	0	-0.049	0.001	23.681	0.004	0.004	0.000	0.000	0.000	0.000
110	A	107	THR	0	0.021	0.012	25.790	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	108	TYR	0	0.019	-0.021	25.499	0.006	0.006	0.000	0.000	0.000	0.000
112	A	109	TYR	0	-0.016	-0.026	30.602	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	110	ASP	-1	-0.785	-0.875	32.896	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	111	ARG	1	0.797	0.863	35.452	0.023	0.023	0.000	0.000	0.000	0.000
115	A	112	PRO	0	0.033	0.016	37.996	-0.003	-0.003	0.000	0.000	0.000	0.000
116	A	113	HIS	1	0.752	0.876	35.257	0.042	0.042	0.000	0.000	0.000	0.000
117	A	114	ARG	1	0.923	0.973	38.503	0.027	0.027	0.000	0.000	0.000	0.000
118	A	115	PHE	0	0.004	-0.017	32.835	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	116	ALA	0	0.026	0.023	37.823	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	117	ASP	-1	-0.847	-0.935	36.857	-0.055	-0.055	0.000	0.000	0.000	0.000
121	A	118	SER	0	-0.039	-0.021	35.938	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	119	GLU	-1	-0.796	-0.881	32.905	-0.057	-0.057	0.000	0.000	0.000	0.000
123	A	120	ILE	0	0.027	0.021	31.839	-0.008	-0.008	0.000	0.000	0.000	0.000
124	A	121	GLY	0	0.016	0.010	31.822	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	122	MET	0	-0.026	-0.003	29.353	-0.012	-0.012	0.000	0.000	0.000	0.000
126	A	123	ALA	0	0.044	0.030	27.626	-0.014	-0.014	0.000	0.000	0.000	0.000
127	A	124	LEU	0	0.016	-0.001	26.914	-0.013	-0.013	0.000	0.000	0.000	0.000
128	A	125	THR	0	-0.092	-0.050	25.965	-0.013	-0.013	0.000	0.000	0.000	0.000
129	A	126	ILE	0	0.018	0.005	22.233	-0.021	-0.021	0.000	0.000	0.000	0.000
130	A	127	ALA	0	0.021	0.015	22.315	-0.025	-0.025	0.000	0.000	0.000	0.000
131	A	128	ARG	1	0.930	0.965	22.688	0.117	0.117	0.000	0.000	0.000	0.000
132	A	129	GLN	0	-0.012	0.007	19.016	0.002	0.002	0.000	0.000	0.000	0.000
133	A	130	LEU	0	0.042	0.037	16.278	-0.054	-0.054	0.000	0.000	0.000	0.000
134	A	131	GLY	0	0.059	0.033	17.778	-0.037	-0.037	0.000	0.000	0.000	0.000
135	A	132	PHE	0	-0.020	-0.030	18.695	-0.025	-0.025	0.000	0.000	0.000	0.000
136	A	133	SER	0	-0.042	-0.028	14.679	-0.054	-0.054	0.000	0.000	0.000	0.000
137	A	134	ILE	0	0.039	0.018	13.922	-0.112	-0.112	0.000	0.000	0.000	0.000
138	A	135	GLN	0	-0.038	-0.033	14.124	-0.050	-0.050	0.000	0.000	0.000	0.000
139	A	136	ARG	1	0.942	0.965	15.071	0.368	0.368	0.000	0.000	0.000	0.000
140	A	137	MET	0	0.013	0.022	10.248	-0.121	-0.121	0.000	0.000	0.000	0.000
141	A	138	ARG	1	0.808	0.876	10.275	0.185	0.185	0.000	0.000	0.000	0.000
142	A	139	ALA	0	-0.023	-0.003	11.515	0.033	0.033	0.000	0.000	0.000	0.000
143	A	140	GLU	-1	-0.775	-0.856	9.926	-0.715	-0.715	0.000	0.000	0.000	0.000
144	A	141	TYR	0	-0.012	0.005	4.210	0.198	0.301	-0.001	-0.009	-0.093	0.000
145	A	142	ALA	0	0.044	0.021	8.737	0.082	0.082	0.000	0.000	0.000	0.000
146	A	143	ARG	1	0.846	0.900	11.642	0.598	0.598	0.000	0.000	0.000	0.000
147	A	144	ARG	1	0.750	0.867	7.193	1.114	1.114	0.000	0.000	0.000	0.000
148	A	145	GLN	0	-0.035	-0.014	10.503	0.037	0.037	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:SER)