FMO DATABASE

FMODB ID: JLVK9

Calculation Name: 5H3C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1645838.311623
FMO2-HF: Nuclear repulsion	1582073.501807
FMO2-HF: Total energy	-63764.809815
FMO2-MP2: Total energy	-63949.578393

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: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.
-0.05	1.089	-0.017	-0.539	-0.583	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 : -0.006 / q_NPA : -0.019

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	0.878	0.947	3.808	1.171	2.310	-0.017	-0.539	-0.583	0.002
4	A	20	ARG	1	0.925	0.981	6.841	0.532	0.532	0.000	0.000	0.000	0.000
5	A	21	TYR	0	0.000	-0.001	9.197	0.184	0.184	0.000	0.000	0.000	0.000
6	A	22	ASP	-1	-0.738	-0.837	11.860	-0.339	-0.339	0.000	0.000	0.000	0.000
7	A	23	VAL	0	0.004	-0.007	13.792	-0.044	-0.044	0.000	0.000	0.000	0.000
8	A	24	PHE	0	-0.008	-0.017	16.157	0.011	0.011	0.000	0.000	0.000	0.000
9	A	25	PRO	0	-0.012	-0.011	17.848	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	26	SER	0	-0.005	-0.013	21.675	0.005	0.005	0.000	0.000	0.000	0.000
11	A	27	PHE	0	-0.006	-0.017	23.488	0.009	0.009	0.000	0.000	0.000	0.000
12	A	28	ARG	1	0.884	0.932	27.163	0.077	0.077	0.000	0.000	0.000	0.000
13	A	29	GLY	0	0.014	-0.006	30.074	0.005	0.005	0.000	0.000	0.000	0.000
14	A	30	GLU	-1	-0.813	-0.908	31.223	-0.069	-0.069	0.000	0.000	0.000	0.000
15	A	31	ASP	-1	-0.792	-0.845	33.402	-0.070	-0.070	0.000	0.000	0.000	0.000
16	A	32	VAL	0	-0.027	-0.025	29.877	0.002	0.002	0.000	0.000	0.000	0.000
17	A	33	ARG	1	0.790	0.864	26.464	0.079	0.079	0.000	0.000	0.000	0.000
18	A	34	ASP	-1	-0.874	-0.947	31.231	-0.045	-0.045	0.000	0.000	0.000	0.000
19	A	35	SER	0	-0.011	0.007	33.919	0.003	0.003	0.000	0.000	0.000	0.000
20	A	36	PHE	0	0.008	0.002	28.907	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	37	LEU	0	-0.003	0.003	25.403	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	38	SER	0	-0.026	-0.008	28.073	0.000	0.000	0.000	0.000	0.000	0.000
23	A	39	HIS	0	-0.002	-0.008	29.330	0.004	0.004	0.000	0.000	0.000	0.000
24	A	40	LEU	0	0.026	0.018	25.008	0.002	0.002	0.000	0.000	0.000	0.000
25	A	41	LEU	0	0.020	0.007	22.856	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	42	LYS	1	0.915	0.963	24.792	0.025	0.025	0.000	0.000	0.000	0.000
27	A	43	GLU	-1	-0.840	-0.909	26.305	-0.031	-0.031	0.000	0.000	0.000	0.000
28	A	44	LEU	0	-0.017	-0.022	20.672	0.002	0.002	0.000	0.000	0.000	0.000
29	A	45	ARG	1	0.939	0.966	22.000	0.050	0.050	0.000	0.000	0.000	0.000
30	A	46	GLY	0	-0.033	-0.004	22.883	0.013	0.013	0.000	0.000	0.000	0.000
31	A	47	LYS	1	0.840	0.920	22.098	0.048	0.048	0.000	0.000	0.000	0.000
32	A	48	ALA	0	-0.040	-0.024	18.822	0.001	0.001	0.000	0.000	0.000	0.000
33	A	49	ILE	0	-0.020	0.009	17.368	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	50	THR	0	-0.024	-0.033	14.034	-0.014	-0.014	0.000	0.000	0.000	0.000
35	A	51	PHE	0	-0.016	-0.033	16.325	-0.038	-0.038	0.000	0.000	0.000	0.000
36	A	52	ILE	0	-0.065	-0.018	16.410	0.020	0.020	0.000	0.000	0.000	0.000
37	A	53	ASP	-1	-0.920	-0.965	17.945	-0.058	-0.058	0.000	0.000	0.000	0.000
38	A	54	ASP	-1	-0.819	-0.866	21.113	-0.095	-0.095	0.000	0.000	0.000	0.000
39	A	66	LEU	0	0.054	0.016	19.374	0.000	0.000	0.000	0.000	0.000	0.000
40	A	67	LEU	0	0.072	0.024	18.664	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	68	SER	0	-0.075	-0.041	14.804	-0.040	-0.040	0.000	0.000	0.000	0.000
42	A	69	ALA	0	0.055	0.024	13.498	-0.059	-0.059	0.000	0.000	0.000	0.000
43	A	70	ILE	0	-0.002	0.034	13.542	-0.065	-0.065	0.000	0.000	0.000	0.000
44	A	71	LYS	1	0.883	0.913	10.756	0.399	0.399	0.000	0.000	0.000	0.000
45	A	72	GLU	-1	-0.911	-0.960	7.302	-1.390	-1.390	0.000	0.000	0.000	0.000
46	A	73	SER	0	-0.007	-0.002	10.216	0.019	0.019	0.000	0.000	0.000	0.000
47	A	74	ARG	1	0.829	0.919	9.363	0.310	0.310	0.000	0.000	0.000	0.000
48	A	75	ILE	0	-0.001	-0.003	12.110	0.024	0.024	0.000	0.000	0.000	0.000
49	A	76	ALA	0	0.001	0.020	15.924	0.014	0.014	0.000	0.000	0.000	0.000
50	A	77	ILE	0	0.009	0.009	18.487	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	-0.014	24.490	0.010	0.010	0.000	0.000	0.000	0.000
53	A	80	PHE	0	-0.007	-0.006	27.358	0.003	0.003	0.000	0.000	0.000	0.000
54	A	81	SER	0	0.001	-0.038	30.469	0.003	0.003	0.000	0.000	0.000	0.000
55	A	82	LYS	1	0.898	0.933	33.564	0.060	0.060	0.000	0.000	0.000	0.000
56	A	83	ASN	0	-0.033	-0.025	35.546	0.001	0.001	0.000	0.000	0.000	0.000
57	A	84	TYR	0	0.036	0.004	25.176	0.001	0.001	0.000	0.000	0.000	0.000
58	A	85	ALA	0	-0.013	-0.009	31.705	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	86	SER	0	-0.010	-0.005	33.809	0.001	0.001	0.000	0.000	0.000	0.000
60	A	87	SER	0	-0.010	-0.015	29.623	0.003	0.003	0.000	0.000	0.000	0.000
61	A	88	THR	0	0.085	0.020	30.205	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	89	TRP	0	-0.037	-0.010	26.599	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	90	CYS	0	0.045	0.058	25.462	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	91	LEU	0	0.013	0.014	25.663	-0.015	-0.015	0.000	0.000	0.000	0.000
65	A	92	ASN	0	0.014	-0.001	24.475	-0.013	-0.013	0.000	0.000	0.000	0.000
66	A	93	GLU	-1	-0.840	-0.907	21.628	-0.183	-0.183	0.000	0.000	0.000	0.000
67	A	94	LEU	0	-0.027	0.003	21.299	-0.026	-0.026	0.000	0.000	0.000	0.000
68	A	95	VAL	0	0.005	-0.007	22.520	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	96	GLU	-1	-0.766	-0.860	16.243	-0.372	-0.372	0.000	0.000	0.000	0.000
70	A	97	ILE	0	0.038	0.012	17.852	-0.042	-0.042	0.000	0.000	0.000	0.000
71	A	98	HIS	0	0.015	0.012	18.260	-0.044	-0.044	0.000	0.000	0.000	0.000
72	A	99	LYS	1	0.838	0.918	15.704	0.334	0.334	0.000	0.000	0.000	0.000
73	A	100	CYS	0	-0.057	-0.026	13.805	-0.048	-0.048	0.000	0.000	0.000	0.000
74	A	101	TYR	0	-0.004	0.009	14.666	-0.059	-0.059	0.000	0.000	0.000	0.000
75	A	102	THR	0	-0.038	-0.018	16.946	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	103	ASN	0	-0.095	-0.054	14.638	0.000	0.000	0.000	0.000	0.000	0.000
77	A	104	LEU	0	-0.074	-0.046	9.541	-0.067	-0.067	0.000	0.000	0.000	0.000
78	A	105	ASN	0	-0.030	-0.001	11.413	-0.044	-0.044	0.000	0.000	0.000	0.000
79	A	106	GLN	0	-0.036	-0.019	13.370	0.045	0.045	0.000	0.000	0.000	0.000
80	A	107	MET	0	0.002	0.002	13.671	0.095	0.095	0.000	0.000	0.000	0.000
81	A	108	VAL	0	0.009	-0.004	17.069	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	109	ILE	0	-0.007	-0.002	20.090	0.017	0.017	0.000	0.000	0.000	0.000
83	A	110	PRO	0	-0.022	0.008	23.003	0.003	0.003	0.000	0.000	0.000	0.000
84	A	111	ILE	0	0.016	-0.001	26.070	0.010	0.010	0.000	0.000	0.000	0.000
85	A	112	PHE	0	-0.036	-0.015	28.787	0.000	0.000	0.000	0.000	0.000	0.000
86	A	113	PHE	0	0.040	0.010	32.255	0.006	0.006	0.000	0.000	0.000	0.000
87	A	114	HIS	0	-0.003	0.000	34.026	0.001	0.001	0.000	0.000	0.000	0.000
88	A	115	VAL	0	-0.020	0.001	33.866	0.003	0.003	0.000	0.000	0.000	0.000
89	A	116	ASP	-1	-0.752	-0.877	36.365	-0.076	-0.076	0.000	0.000	0.000	0.000
90	A	117	ALA	0	0.043	0.021	33.358	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	118	SER	0	-0.066	-0.037	34.489	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	119	GLU	-1	-0.816	-0.913	36.818	-0.070	-0.070	0.000	0.000	0.000	0.000
93	A	120	VAL	0	0.010	0.017	30.953	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	121	LYS	1	0.906	0.958	32.375	0.107	0.107	0.000	0.000	0.000	0.000
95	A	122	LYS	1	0.896	0.939	33.527	0.075	0.075	0.000	0.000	0.000	0.000
96	A	123	GLN	0	-0.021	0.015	33.326	0.005	0.005	0.000	0.000	0.000	0.000
97	A	124	THR	0	0.025	0.004	37.074	0.003	0.003	0.000	0.000	0.000	0.000
98	A	125	GLY	0	0.016	0.014	39.932	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	126	GLU	-1	-0.835	-0.909	41.161	-0.055	-0.055	0.000	0.000	0.000	0.000
100	A	127	PHE	0	0.031	0.018	31.952	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	128	GLY	0	0.022	-0.004	37.775	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	129	LYS	1	0.823	0.907	39.052	0.054	0.054	0.000	0.000	0.000	0.000
103	A	130	VAL	0	0.017	0.020	37.159	0.001	0.001	0.000	0.000	0.000	0.000
104	A	131	PHE	0	0.008	0.019	32.443	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	132	GLU	-1	-0.820	-0.911	36.797	-0.078	-0.078	0.000	0.000	0.000	0.000
106	A	133	GLU	-1	-0.904	-0.935	39.625	-0.055	-0.055	0.000	0.000	0.000	0.000
107	A	134	THR	0	-0.021	-0.017	34.337	0.001	0.001	0.000	0.000	0.000	0.000
108	A	135	CYS	0	-0.098	-0.057	35.835	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	136	LYS	1	0.837	0.920	37.282	0.061	0.061	0.000	0.000	0.000	0.000
110	A	137	ALA	0	-0.023	-0.001	38.828	0.002	0.002	0.000	0.000	0.000	0.000
111	A	138	LYS	1	0.848	0.917	33.136	0.078	0.078	0.000	0.000	0.000	0.000
112	A	139	SER	0	0.023	-0.003	33.009	0.004	0.004	0.000	0.000	0.000	0.000
113	A	140	GLU	-1	-0.875	-0.939	34.642	-0.080	-0.080	0.000	0.000	0.000	0.000
114	A	141	ASP	-1	-0.906	-0.951	31.421	-0.108	-0.108	0.000	0.000	0.000	0.000
115	A	142	GLU	-1	-0.856	-0.919	29.518	-0.113	-0.113	0.000	0.000	0.000	0.000
116	A	143	LYS	1	0.864	0.914	30.395	0.074	0.074	0.000	0.000	0.000	0.000
117	A	144	GLN	0	-0.011	-0.006	31.344	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	145	SER	0	0.005	-0.001	26.685	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	146	TRP	0	-0.007	-0.026	27.741	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	147	LYS	1	0.879	0.932	29.378	0.093	0.093	0.000	0.000	0.000	0.000
121	A	148	GLN	0	-0.031	-0.012	27.889	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	149	ALA	0	0.006	0.008	24.913	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	150	LEU	0	-0.034	-0.012	26.430	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	151	ALA	0	-0.035	-0.014	29.128	0.002	0.002	0.000	0.000	0.000	0.000
125	A	152	ALA	0	-0.043	-0.017	25.457	0.003	0.003	0.000	0.000	0.000	0.000
126	A	153	VAL	0	0.070	0.015	23.358	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	154	ALA	0	-0.032	-0.007	25.992	0.005	0.005	0.000	0.000	0.000	0.000
128	A	155	VAL	0	-0.089	-0.053	28.602	0.012	0.012	0.000	0.000	0.000	0.000
129	A	156	MET	0	-0.036	0.004	21.216	0.004	0.004	0.000	0.000	0.000	0.000
130	A	157	ALA	0	-0.012	-0.007	25.905	0.010	0.010	0.000	0.000	0.000	0.000
131	A	158	GLY	0	0.049	0.011	25.966	-0.014	-0.014	0.000	0.000	0.000	0.000
132	A	159	TYR	0	-0.047	-0.028	25.309	0.014	0.014	0.000	0.000	0.000	0.000
133	A	160	ASP	-1	-0.777	-0.864	30.081	-0.078	-0.078	0.000	0.000	0.000	0.000
134	A	161	LEU	0	0.086	0.022	33.516	0.004	0.004	0.000	0.000	0.000	0.000
135	A	162	ARG	1	0.801	0.882	35.410	0.073	0.073	0.000	0.000	0.000	0.000
136	A	163	LYS	1	0.781	0.873	34.832	0.084	0.084	0.000	0.000	0.000	0.000
137	A	164	TRP	0	0.049	0.020	31.565	0.001	0.001	0.000	0.000	0.000	0.000
138	A	165	PRO	0	-0.009	0.006	36.776	0.001	0.001	0.000	0.000	0.000	0.000
139	A	166	SER	0	0.014	-0.007	37.312	0.002	0.002	0.000	0.000	0.000	0.000
140	A	167	GLU	-1	-0.835	-0.935	34.424	-0.058	-0.058	0.000	0.000	0.000	0.000
141	A	168	ALA	0	0.000	0.008	33.173	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	169	ALA	0	0.046	0.025	32.774	-0.002	-0.002	0.000	0.000	0.000	0.000
143	A	170	MET	0	-0.046	-0.001	30.695	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	171	ILE	0	-0.021	-0.010	28.123	-0.008	-0.008	0.000	0.000	0.000	0.000
145	A	172	GLU	-1	-0.928	-0.960	27.859	-0.039	-0.039	0.000	0.000	0.000	0.000
146	A	173	GLU	-1	-0.877	-0.931	27.938	-0.071	-0.071	0.000	0.000	0.000	0.000
147	A	174	LEU	0	-0.034	-0.009	23.803	-0.008	-0.008	0.000	0.000	0.000	0.000
148	A	175	ALA	0	0.025	0.004	23.573	-0.014	-0.014	0.000	0.000	0.000	0.000
149	A	176	GLU	-1	-0.870	-0.933	22.892	-0.042	-0.042	0.000	0.000	0.000	0.000
150	A	177	ASP	-1	-0.815	-0.878	22.722	-0.159	-0.159	0.000	0.000	0.000	0.000
151	A	178	VAL	0	-0.027	-0.019	18.526	-0.020	-0.020	0.000	0.000	0.000	0.000
152	A	179	LEU	0	0.042	0.024	18.422	-0.021	-0.021	0.000	0.000	0.000	0.000
153	A	180	ARG	1	0.838	0.921	18.167	0.071	0.071	0.000	0.000	0.000	0.000
154	A	181	LYS	1	0.850	0.925	16.827	0.176	0.176	0.000	0.000	0.000	0.000
155	A	182	THR	0	-0.074	-0.042	13.966	-0.051	-0.051	0.000	0.000	0.000	0.000
156	A	183	MET	0	-0.025	-0.018	13.526	0.032	0.032	0.000	0.000	0.000	0.000
157	A	184	THR	0	-0.066	-0.041	12.738	0.035	0.035	0.000	0.000	0.000	0.000
158	A	185	PRO	0	-0.045	-0.014	8.491	-0.121	-0.121	0.000	0.000	0.000	0.000

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