FMO DATABASE

FMODB ID: N9L6Q

Calculation Name: 5H3C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5H3C

Chain ID: A

ChEMBL ID:

UniProt ID: O23530

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1643784.084059
FMO2-HF: Nuclear repulsion	1580020.521957
FMO2-HF: Total energy	-63763.562103
FMO2-MP2: Total energy	-63948.288979

3D Structure Molmil

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:17:GLY)

Summations of interaction energy for fragment #1(A:17: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.
0.304	1.42	-0.017	-0.523	-0.576	0.002

Interaction energy analysis for fragmet #1(A:17:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.017

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	19	ARG	1	0.929	0.971	3.808	1.271	2.387	-0.017	-0.523	-0.576	0.002
4	A	20	ARG	1	0.933	0.990	6.841	0.519	0.519	0.000	0.000	0.000	0.000
5	A	21	TYR	0	-0.004	-0.010	9.198	0.184	0.184	0.000	0.000	0.000	0.000
6	A	22	ASP	-1	-0.772	-0.880	11.860	-0.361	-0.361	0.000	0.000	0.000	0.000
7	A	23	VAL	0	-0.010	-0.017	13.792	-0.047	-0.047	0.000	0.000	0.000	0.000
8	A	24	PHE	0	-0.013	-0.016	16.204	0.010	0.010	0.000	0.000	0.000	0.000
9	A	25	PRO	0	-0.014	-0.011	17.849	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	26	SER	0	-0.005	0.005	21.677	0.005	0.005	0.000	0.000	0.000	0.000
11	A	27	PHE	0	0.005	-0.010	23.490	0.009	0.009	0.000	0.000	0.000	0.000
12	A	28	ARG	1	0.984	1.000	27.164	0.079	0.079	0.000	0.000	0.000	0.000
13	A	29	GLY	0	0.020	-0.005	30.101	0.005	0.005	0.000	0.000	0.000	0.000
14	A	30	GLU	-1	-0.871	-0.937	31.224	-0.071	-0.071	0.000	0.000	0.000	0.000
15	A	31	ASP	-1	-0.818	-0.888	33.391	-0.072	-0.072	0.000	0.000	0.000	0.000
16	A	32	VAL	0	-0.004	-0.015	29.791	0.002	0.002	0.000	0.000	0.000	0.000
17	A	33	ARG	1	0.801	0.889	26.619	0.081	0.081	0.000	0.000	0.000	0.000
18	A	34	ASP	-1	-0.869	-0.938	31.232	-0.045	-0.045	0.000	0.000	0.000	0.000
19	A	35	SER	0	-0.027	-0.004	33.957	0.003	0.003	0.000	0.000	0.000	0.000
20	A	36	PHE	0	0.022	0.012	28.884	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	37	LEU	0	-0.006	0.000	25.462	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	38	SER	0	-0.024	-0.008	28.073	0.000	0.000	0.000	0.000	0.000	0.000
23	A	39	HIS	0	0.003	-0.006	29.331	0.004	0.004	0.000	0.000	0.000	0.000
24	A	40	LEU	0	0.042	0.025	24.652	0.001	0.001	0.000	0.000	0.000	0.000
25	A	41	LEU	0	0.008	0.001	22.921	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	42	LYS	1	0.901	0.956	24.792	0.028	0.028	0.000	0.000	0.000	0.000
27	A	43	GLU	-1	-0.887	-0.941	26.455	-0.038	-0.038	0.000	0.000	0.000	0.000
28	A	44	LEU	0	-0.030	-0.027	20.522	0.002	0.002	0.000	0.000	0.000	0.000
29	A	45	ARG	1	0.968	0.975	22.011	0.052	0.052	0.000	0.000	0.000	0.000
30	A	46	GLY	0	-0.037	-0.003	22.882	0.013	0.013	0.000	0.000	0.000	0.000
31	A	47	LYS	1	0.902	0.957	22.196	0.050	0.050	0.000	0.000	0.000	0.000
32	A	48	ALA	0	-0.035	-0.018	18.715	0.000	0.000	0.000	0.000	0.000	0.000
33	A	49	ILE	0	-0.001	0.012	17.374	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	50	THR	0	-0.032	-0.021	14.070	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	51	PHE	0	-0.017	-0.032	16.325	-0.037	-0.037	0.000	0.000	0.000	0.000
36	A	52	ILE	0	-0.061	-0.018	16.029	0.021	0.021	0.000	0.000	0.000	0.000
37	A	53	ASP	-1	-0.954	-0.972	17.946	-0.058	-0.058	0.000	0.000	0.000	0.000
38	A	54	ASP	-1	-0.814	-0.893	21.115	-0.101	-0.101	0.000	0.000	0.000	0.000
39	A	66	LEU	0	0.057	0.020	19.684	0.000	0.000	0.000	0.000	0.000	0.000
40	A	67	LEU	0	0.066	0.021	18.664	-0.022	-0.022	0.000	0.000	0.000	0.000
41	A	68	SER	0	-0.084	-0.041	14.798	-0.041	-0.041	0.000	0.000	0.000	0.000
42	A	69	ALA	0	0.059	0.026	13.499	-0.061	-0.061	0.000	0.000	0.000	0.000
43	A	70	ILE	0	0.020	0.037	13.543	-0.070	-0.070	0.000	0.000	0.000	0.000
44	A	71	LYS	1	0.962	0.955	10.645	0.413	0.413	0.000	0.000	0.000	0.000
45	A	72	GLU	-1	-0.983	-1.000	7.721	-1.155	-1.155	0.000	0.000	0.000	0.000
46	A	73	SER	0	0.002	0.008	10.217	0.015	0.015	0.000	0.000	0.000	0.000
47	A	74	ARG	1	0.849	0.932	9.610	0.360	0.360	0.000	0.000	0.000	0.000
48	A	75	ILE	0	-0.009	-0.004	12.110	0.021	0.021	0.000	0.000	0.000	0.000
49	A	76	ALA	0	0.001	0.023	15.924	0.014	0.014	0.000	0.000	0.000	0.000
50	A	77	ILE	0	0.008	0.008	18.489	0.015	0.015	0.000	0.000	0.000	0.000
51	A	78	VAL	0	0.007	0.004	21.950	0.004	0.004	0.000	0.000	0.000	0.000
52	A	79	ILE	0	-0.012	-0.013	24.492	0.010	0.010	0.000	0.000	0.000	0.000
53	A	80	PHE	0	-0.019	-0.009	27.300	0.003	0.003	0.000	0.000	0.000	0.000
54	A	81	SER	0	0.023	-0.010	30.471	0.003	0.003	0.000	0.000	0.000	0.000
55	A	82	LYS	1	0.926	0.952	33.565	0.062	0.062	0.000	0.000	0.000	0.000
56	A	83	ASN	0	-0.045	-0.023	35.572	0.000	0.000	0.000	0.000	0.000	0.000
57	A	84	TYR	0	0.020	-0.006	25.183	0.000	0.000	0.000	0.000	0.000	0.000
58	A	85	ALA	0	-0.011	-0.005	31.707	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	86	SER	0	-0.013	-0.015	33.811	0.001	0.001	0.000	0.000	0.000	0.000
60	A	87	SER	0	-0.015	-0.006	29.550	0.003	0.003	0.000	0.000	0.000	0.000
61	A	88	THR	0	0.041	0.005	30.216	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	89	TRP	0	0.017	0.009	26.548	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	90	CYS	0	0.022	0.035	25.463	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	91	LEU	0	0.008	0.011	25.664	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	92	ASN	0	0.007	-0.007	24.428	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	93	GLU	-1	-0.836	-0.930	21.294	-0.191	-0.191	0.000	0.000	0.000	0.000
67	A	94	LEU	0	-0.031	0.000	21.300	-0.027	-0.027	0.000	0.000	0.000	0.000
68	A	95	VAL	0	0.008	-0.006	22.522	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	96	GLU	-1	-0.876	-0.942	16.422	-0.372	-0.372	0.000	0.000	0.000	0.000
70	A	97	ILE	0	0.016	-0.004	17.856	-0.043	-0.043	0.000	0.000	0.000	0.000
71	A	98	HIS	0	0.011	0.011	18.262	-0.046	-0.046	0.000	0.000	0.000	0.000
72	A	99	LYS	1	0.901	0.965	14.098	0.410	0.410	0.000	0.000	0.000	0.000
73	A	100	CYS	0	-0.084	-0.034	13.778	-0.059	-0.059	0.000	0.000	0.000	0.000
74	A	101	TYR	0	0.008	0.016	14.668	-0.064	-0.064	0.000	0.000	0.000	0.000
75	A	102	THR	0	-0.041	-0.018	16.948	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	103	ASN	0	-0.047	-0.021	14.563	0.003	0.003	0.000	0.000	0.000	0.000
77	A	104	LEU	0	-0.103	-0.065	9.413	-0.069	-0.069	0.000	0.000	0.000	0.000
78	A	105	ASN	0	-0.019	0.005	11.416	-0.031	-0.031	0.000	0.000	0.000	0.000
79	A	106	GLN	0	-0.035	-0.017	13.530	0.038	0.038	0.000	0.000	0.000	0.000
80	A	107	MET	0	-0.010	-0.004	13.589	0.097	0.097	0.000	0.000	0.000	0.000
81	A	108	VAL	0	0.016	0.002	17.052	0.002	0.002	0.000	0.000	0.000	0.000
82	A	109	ILE	0	-0.002	-0.005	20.092	0.017	0.017	0.000	0.000	0.000	0.000
83	A	110	PRO	0	-0.027	0.008	23.005	0.003	0.003	0.000	0.000	0.000	0.000
84	A	111	ILE	0	0.023	0.002	26.138	0.010	0.010	0.000	0.000	0.000	0.000
85	A	112	PHE	0	-0.036	-0.014	28.790	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	113	PHE	0	0.033	0.008	32.278	0.006	0.006	0.000	0.000	0.000	0.000
87	A	114	HIS	0	-0.012	-0.008	34.028	0.002	0.002	0.000	0.000	0.000	0.000
88	A	115	VAL	0	-0.036	-0.014	33.841	0.003	0.003	0.000	0.000	0.000	0.000
89	A	116	ASP	-1	-0.802	-0.912	36.367	-0.077	-0.077	0.000	0.000	0.000	0.000
90	A	117	ALA	0	0.054	0.022	33.372	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	118	SER	0	-0.108	-0.055	34.492	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	119	GLU	-1	-0.768	-0.892	36.820	-0.072	-0.072	0.000	0.000	0.000	0.000
93	A	120	VAL	0	0.001	0.012	30.912	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	121	LYS	1	0.931	0.957	32.488	0.104	0.104	0.000	0.000	0.000	0.000
95	A	122	LYS	1	0.890	0.927	33.529	0.081	0.081	0.000	0.000	0.000	0.000
96	A	123	GLN	0	-0.011	0.022	33.535	0.006	0.006	0.000	0.000	0.000	0.000
97	A	124	THR	0	-0.026	-0.019	37.076	0.005	0.005	0.000	0.000	0.000	0.000
98	A	125	GLY	0	0.042	0.022	39.934	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	126	GLU	-1	-0.922	-0.962	41.139	-0.057	-0.057	0.000	0.000	0.000	0.000
100	A	127	PHE	0	0.024	0.019	32.015	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	128	GLY	0	0.013	-0.009	37.777	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	129	LYS	1	0.917	0.972	39.054	0.057	0.057	0.000	0.000	0.000	0.000
103	A	130	VAL	0	0.027	0.023	37.625	0.001	0.001	0.000	0.000	0.000	0.000
104	A	131	PHE	0	-0.003	0.009	32.535	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	132	GLU	-1	-0.824	-0.923	36.799	-0.078	-0.078	0.000	0.000	0.000	0.000
106	A	133	GLU	-1	-0.998	-0.996	39.626	-0.056	-0.056	0.000	0.000	0.000	0.000
107	A	134	THR	0	-0.014	-0.007	34.359	0.001	0.001	0.000	0.000	0.000	0.000
108	A	135	CYS	0	-0.095	-0.061	35.923	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	136	LYS	1	0.945	0.988	37.283	0.062	0.062	0.000	0.000	0.000	0.000
110	A	137	ALA	0	-0.021	0.001	38.765	0.002	0.002	0.000	0.000	0.000	0.000
111	A	138	LYS	1	0.868	0.927	33.307	0.079	0.079	0.000	0.000	0.000	0.000
112	A	139	SER	0	0.025	0.025	32.677	0.005	0.005	0.000	0.000	0.000	0.000
113	A	140	GLU	-1	-0.883	-0.945	34.643	-0.081	-0.081	0.000	0.000	0.000	0.000
114	A	141	ASP	-1	-0.901	-0.951	31.406	-0.110	-0.110	0.000	0.000	0.000	0.000
115	A	142	GLU	-1	-0.906	-0.963	29.292	-0.117	-0.117	0.000	0.000	0.000	0.000
116	A	143	LYS	1	0.858	0.921	30.397	0.076	0.076	0.000	0.000	0.000	0.000
117	A	144	GLN	0	-0.028	-0.019	31.409	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	145	SER	0	0.015	0.009	26.971	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	146	TRP	0	-0.009	-0.016	27.664	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	147	LYS	1	0.888	0.945	29.380	0.096	0.096	0.000	0.000	0.000	0.000
121	A	148	GLN	0	-0.002	-0.001	27.732	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	149	ALA	0	0.006	0.014	24.953	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	150	LEU	0	-0.028	-0.012	26.432	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	151	ALA	0	-0.039	-0.017	29.131	0.002	0.002	0.000	0.000	0.000	0.000
125	A	152	ALA	0	-0.047	-0.017	25.489	0.003	0.003	0.000	0.000	0.000	0.000
126	A	153	VAL	0	0.066	0.015	23.423	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	154	ALA	0	-0.030	-0.006	25.994	0.005	0.005	0.000	0.000	0.000	0.000
128	A	155	VAL	0	-0.094	-0.050	28.464	0.012	0.012	0.000	0.000	0.000	0.000
129	A	156	MET	0	-0.046	-0.002	21.259	0.003	0.003	0.000	0.000	0.000	0.000
130	A	157	ALA	0	-0.020	-0.010	25.868	0.011	0.011	0.000	0.000	0.000	0.000
131	A	158	GLY	0	0.047	0.010	25.941	-0.014	-0.014	0.000	0.000	0.000	0.000
132	A	159	TYR	0	-0.061	-0.047	25.481	0.014	0.014	0.000	0.000	0.000	0.000
133	A	160	ASP	-1	-0.865	-0.945	30.081	-0.083	-0.083	0.000	0.000	0.000	0.000
134	A	161	LEU	0	0.087	0.026	33.516	0.004	0.004	0.000	0.000	0.000	0.000
135	A	162	ARG	1	0.881	0.954	35.410	0.075	0.075	0.000	0.000	0.000	0.000
136	A	163	LYS	1	0.843	0.914	34.537	0.089	0.089	0.000	0.000	0.000	0.000
137	A	164	TRP	0	0.061	0.028	31.426	0.001	0.001	0.000	0.000	0.000	0.000
138	A	165	PRO	0	-0.012	0.002	36.737	0.002	0.002	0.000	0.000	0.000	0.000
139	A	166	SER	0	0.004	-0.010	37.312	0.002	0.002	0.000	0.000	0.000	0.000
140	A	167	GLU	-1	-0.839	-0.937	34.412	-0.061	-0.061	0.000	0.000	0.000	0.000
141	A	168	ALA	0	0.001	0.011	33.173	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	169	ALA	0	0.038	0.019	32.774	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	170	MET	0	-0.048	-0.001	30.415	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	171	ILE	0	-0.015	-0.010	28.042	-0.009	-0.009	0.000	0.000	0.000	0.000
145	A	172	GLU	-1	-0.921	-0.950	27.859	-0.045	-0.045	0.000	0.000	0.000	0.000
146	A	173	GLU	-1	-0.930	-0.967	27.938	-0.083	-0.083	0.000	0.000	0.000	0.000
147	A	174	LEU	0	-0.030	-0.007	23.843	-0.010	-0.010	0.000	0.000	0.000	0.000
148	A	175	ALA	0	0.020	0.003	23.574	-0.016	-0.016	0.000	0.000	0.000	0.000
149	A	176	GLU	-1	-0.944	-0.973	22.892	-0.053	-0.053	0.000	0.000	0.000	0.000
150	A	177	ASP	-1	-0.837	-0.868	22.487	-0.168	-0.168	0.000	0.000	0.000	0.000
151	A	178	VAL	0	-0.011	-0.018	18.419	-0.021	-0.021	0.000	0.000	0.000	0.000
152	A	179	LEU	0	0.038	0.024	18.374	-0.022	-0.022	0.000	0.000	0.000	0.000
153	A	180	ARG	1	0.955	0.991	18.113	0.075	0.075	0.000	0.000	0.000	0.000
154	A	181	LYS	1	0.855	0.925	16.771	0.190	0.190	0.000	0.000	0.000	0.000
155	A	182	THR	0	-0.089	-0.063	13.920	-0.052	-0.052	0.000	0.000	0.000	0.000
156	A	183	MET	0	-0.025	-0.019	13.471	0.028	0.028	0.000	0.000	0.000	0.000
157	A	184	THR	0	-0.029	-0.013	12.223	0.045	0.045	0.000	0.000	0.000	0.000
158	A	185	PRO	0	-0.044	-0.009	8.457	-0.143	-0.143	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:17:GLY)