FMO DATABASE

FMODB ID: 66K7Z

Calculation Name: 3FHV-A-Xray372

Preferred Name:

Target Type:

Ligand Name: d-arginine

ligand 3-letter code: DAR

PDB ID: 3FHV

Chain ID: A

ChEMBL ID:

UniProt ID: Q8Z1L1

Base Structure: X-ray

Registration Date: 2023-06-19

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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1194038.297303
FMO2-HF: Nuclear repulsion	1139657.698635
FMO2-HF: Total energy	-54380.598668
FMO2-MP2: Total energy	-54535.09527

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:32:ALA)

Summations of interaction energy for fragment #1(A:32:ALA)

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.
-4.032	-4.2	15.782	-6.932	-8.679	-0.038

Interaction energy analysis for fragmet #1(A:32:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.001

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	34	THR	0	0.025	0.006	3.792	-2.039	-0.699	0.000	-0.562	-0.777	0.002
4	A	35	GLU	-1	-0.825	-0.884	2.060	-1.988	-5.129	11.850	-4.723	-3.986	-0.034
5	A	36	LEU	0	-0.011	0.008	3.830	0.489	0.883	0.000	-0.151	-0.244	0.000
6	A	37	THR	0	0.011	0.002	5.386	0.491	0.575	-0.001	-0.004	-0.078	0.000
7	A	38	ASN	0	-0.012	-0.001	7.563	0.297	0.297	0.000	0.000	0.000	0.000
8	A	39	TYR	0	0.045	0.028	5.224	0.236	0.236	0.000	0.000	0.000	0.000
9	A	40	GLN	0	0.041	0.011	9.312	0.001	0.001	0.000	0.000	0.000	0.000
10	A	41	THR	0	-0.029	-0.029	11.455	0.092	0.092	0.000	0.000	0.000	0.000
11	A	42	LEU	0	0.031	0.033	12.615	0.046	0.046	0.000	0.000	0.000	0.000
12	A	43	ALA	0	0.022	0.020	13.651	0.045	0.045	0.000	0.000	0.000	0.000
13	A	44	THR	0	-0.016	-0.011	15.515	0.043	0.043	0.000	0.000	0.000	0.000
14	A	45	ASN	0	-0.032	-0.025	16.795	0.039	0.039	0.000	0.000	0.000	0.000
15	A	46	THR	0	-0.021	-0.015	17.469	0.021	0.021	0.000	0.000	0.000	0.000
16	A	47	ILE	0	-0.019	-0.007	18.905	0.018	0.018	0.000	0.000	0.000	0.000
17	A	48	GLY	0	-0.034	-0.019	21.500	0.014	0.014	0.000	0.000	0.000	0.000
18	A	49	MET	0	-0.004	-0.005	22.820	0.012	0.012	0.000	0.000	0.000	0.000
19	A	50	MET	0	-0.044	-0.029	23.265	0.008	0.008	0.000	0.000	0.000	0.000
20	A	51	LYS	1	0.921	0.961	24.844	0.099	0.099	0.000	0.000	0.000	0.000
21	A	52	GLY	0	0.004	0.014	27.899	0.006	0.006	0.000	0.000	0.000	0.000
22	A	53	VAL	0	-0.077	-0.009	27.927	0.004	0.004	0.000	0.000	0.000	0.000
23	A	54	ASP	-1	-0.817	-0.904	30.600	-0.068	-0.068	0.000	0.000	0.000	0.000
24	A	55	GLY	0	-0.034	-0.016	33.738	0.003	0.003	0.000	0.000	0.000	0.000
25	A	56	TYR	0	-0.058	-0.033	30.334	0.002	0.002	0.000	0.000	0.000	0.000
26	A	57	ALA	0	0.064	0.028	29.280	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	58	PHE	0	-0.016	-0.009	25.621	0.002	0.002	0.000	0.000	0.000	0.000
28	A	59	THR	0	0.040	0.014	27.867	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	60	SER	0	0.017	-0.003	25.785	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	61	GLY	0	0.070	0.021	21.537	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	62	ALA	0	-0.003	0.010	21.796	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	63	LYS	1	0.998	1.009	23.409	0.078	0.078	0.000	0.000	0.000	0.000
33	A	64	MET	0	0.005	0.018	21.345	0.002	0.002	0.000	0.000	0.000	0.000
34	A	65	THR	0	0.026	-0.002	18.000	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	66	ASP	-1	-0.791	-0.885	20.423	-0.083	-0.083	0.000	0.000	0.000	0.000
36	A	67	THR	0	-0.019	-0.018	22.946	0.010	0.010	0.000	0.000	0.000	0.000
37	A	68	LEU	0	0.000	-0.004	18.402	0.006	0.006	0.000	0.000	0.000	0.000
38	A	69	ILE	0	-0.068	-0.028	18.399	0.004	0.004	0.000	0.000	0.000	0.000
39	A	70	GLN	0	-0.083	-0.032	20.560	0.017	0.017	0.000	0.000	0.000	0.000
40	A	71	ALA	0	-0.034	-0.007	22.773	0.010	0.010	0.000	0.000	0.000	0.000
41	A	72	GLY	0	-0.014	0.000	20.585	0.006	0.006	0.000	0.000	0.000	0.000
42	A	73	ALA	0	-0.043	-0.020	18.194	0.001	0.001	0.000	0.000	0.000	0.000
43	A	74	ALA	0	0.038	-0.009	14.823	-0.033	-0.033	0.000	0.000	0.000	0.000
44	A	75	LYS	1	0.968	0.990	14.976	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	76	GLY	0	-0.008	-0.002	11.570	0.030	0.030	0.000	0.000	0.000	0.000
46	A	77	MET	0	-0.047	0.002	10.018	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	78	THR	0	0.014	0.016	11.852	0.068	0.068	0.000	0.000	0.000	0.000
48	A	79	VAL	0	0.024	0.010	14.003	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	80	SER	0	-0.029	-0.010	17.542	0.018	0.018	0.000	0.000	0.000	0.000
50	A	81	GLY	0	0.011	0.018	20.306	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	82	ASP	-1	-0.828	-0.939	23.296	-0.040	-0.040	0.000	0.000	0.000	0.000
52	A	83	PRO	0	-0.022	-0.014	23.509	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	84	ALA	0	-0.002	0.005	25.618	0.001	0.001	0.000	0.000	0.000	0.000
54	A	85	SER	0	-0.020	-0.013	28.702	0.005	0.005	0.000	0.000	0.000	0.000
55	A	86	GLY	0	-0.041	0.001	27.495	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	87	SER	0	-0.053	-0.038	25.862	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	88	ALA	0	-0.031	-0.001	21.889	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	89	THR	0	-0.002	-0.007	19.083	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	90	LEU	0	0.013	-0.002	13.585	0.009	0.009	0.000	0.000	0.000	0.000
60	A	91	TRP	0	-0.008	-0.006	13.446	-0.020	-0.020	0.000	0.000	0.000	0.000
61	A	92	ASN	0	-0.004	-0.022	7.793	0.018	0.018	0.000	0.000	0.000	0.000
62	A	93	SER	0	-0.021	-0.066	5.283	0.126	0.126	0.000	0.000	0.000	0.000
63	A	94	TRP	0	-0.014	-0.011	3.308	-0.299	0.045	0.019	-0.078	-0.285	0.000
64	A	95	GLY	0	0.005	0.023	9.990	0.045	0.045	0.000	0.000	0.000	0.000
65	A	96	GLY	0	-0.036	-0.011	11.604	0.031	0.031	0.000	0.000	0.000	0.000
66	A	97	GLN	0	-0.032	-0.030	12.505	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	98	ILE	0	-0.034	-0.011	9.857	-0.047	-0.047	0.000	0.000	0.000	0.000
68	A	99	VAL	0	-0.038	-0.018	13.566	0.038	0.038	0.000	0.000	0.000	0.000
69	A	100	VAL	0	0.009	0.005	15.778	-0.027	-0.027	0.000	0.000	0.000	0.000
70	A	101	ALA	0	0.015	-0.015	17.783	0.025	0.025	0.000	0.000	0.000	0.000
71	A	102	PRO	0	-0.014	0.001	20.901	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	103	ASP	-1	-0.967	-0.988	22.322	-0.162	-0.162	0.000	0.000	0.000	0.000
73	A	104	THR	0	-0.022	-0.014	24.171	0.008	0.008	0.000	0.000	0.000	0.000
74	A	105	ALA	0	-0.020	-0.006	27.438	0.003	0.003	0.000	0.000	0.000	0.000
75	A	106	GLY	0	0.001	-0.008	28.888	0.006	0.006	0.000	0.000	0.000	0.000
76	A	107	GLY	0	0.033	0.017	32.406	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	108	THR	0	-0.097	-0.052	34.091	0.003	0.003	0.000	0.000	0.000	0.000
78	A	109	GLY	0	0.038	0.008	35.498	0.003	0.003	0.000	0.000	0.000	0.000
79	A	110	PHE	0	-0.016	0.016	28.195	0.001	0.001	0.000	0.000	0.000	0.000
80	A	111	ASN	0	-0.038	-0.033	27.893	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	112	ASN	0	0.021	0.015	27.094	0.001	0.001	0.000	0.000	0.000	0.000
82	A	113	GLY	0	0.093	0.052	23.231	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	114	PHE	0	-0.069	-0.039	16.868	0.008	0.008	0.000	0.000	0.000	0.000
84	A	115	THR	0	-0.047	-0.023	17.205	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	116	ILE	0	0.014	0.008	11.941	0.012	0.012	0.000	0.000	0.000	0.000
86	A	117	THR	0	0.009	0.008	13.272	-0.035	-0.035	0.000	0.000	0.000	0.000
87	A	118	THR	0	-0.036	-0.024	8.065	0.040	0.040	0.000	0.000	0.000	0.000
88	A	119	ASN	0	0.007	-0.018	11.137	0.003	0.003	0.000	0.000	0.000	0.000
89	A	120	LYS	1	0.979	0.988	11.132	0.168	0.168	0.000	0.000	0.000	0.000
90	A	121	VAL	0	-0.005	0.018	5.995	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	122	PRO	0	0.040	-0.003	6.495	0.047	0.047	0.000	0.000	0.000	0.000
92	A	123	GLN	0	-0.014	0.002	7.173	-0.143	-0.143	0.000	0.000	0.000	0.000
93	A	124	SER	0	0.050	0.021	6.024	-0.158	-0.158	0.000	0.000	0.000	0.000
94	A	125	ALA	0	0.011	-0.002	2.692	-0.766	-0.253	0.297	-0.267	-0.542	0.001
95	A	126	CYS	0	-0.094	-0.020	3.564	-0.184	-0.133	-0.002	0.100	-0.149	0.000
96	A	127	VAL	0	0.060	0.042	6.741	-0.025	-0.025	0.000	0.000	0.000	0.000
97	A	128	SER	0	-0.046	-0.013	2.538	-0.915	-0.770	1.863	-0.729	-1.279	-0.007
98	A	129	ILE	0	0.011	0.000	2.459	-0.546	-0.465	1.757	-0.506	-1.331	0.000
99	A	130	SER	0	-0.005	-0.010	4.635	0.209	0.230	-0.001	-0.012	-0.008	0.000
100	A	131	THR	0	-0.042	-0.031	7.362	0.084	0.084	0.000	0.000	0.000	0.000
101	A	132	GLY	0	0.006	0.004	6.615	0.148	0.148	0.000	0.000	0.000	0.000
102	A	133	MET	0	-0.006	-0.009	7.577	0.127	0.127	0.000	0.000	0.000	0.000
103	A	134	SER	0	-0.044	-0.001	9.769	0.117	0.117	0.000	0.000	0.000	0.000
104	A	135	ARG	1	0.916	0.943	10.324	0.372	0.372	0.000	0.000	0.000	0.000
105	A	136	SER	0	-0.061	-0.014	10.823	0.061	0.061	0.000	0.000	0.000	0.000
106	A	137	GLY	0	0.017	0.007	12.713	0.045	0.045	0.000	0.000	0.000	0.000
107	A	138	GLY	0	-0.006	0.008	14.692	0.027	0.027	0.000	0.000	0.000	0.000
108	A	139	THR	0	-0.050	-0.013	13.244	0.022	0.022	0.000	0.000	0.000	0.000
109	A	140	SER	0	-0.022	-0.013	16.386	0.023	0.023	0.000	0.000	0.000	0.000
110	A	141	GLY	0	0.036	0.016	17.242	0.022	0.022	0.000	0.000	0.000	0.000
111	A	142	ILE	0	-0.055	-0.008	11.697	-0.028	-0.028	0.000	0.000	0.000	0.000
112	A	143	LYS	1	0.920	0.957	14.188	0.252	0.252	0.000	0.000	0.000	0.000
113	A	144	ILE	0	0.033	0.015	11.534	-0.057	-0.057	0.000	0.000	0.000	0.000
114	A	145	ASN	0	0.031	0.000	13.834	0.032	0.032	0.000	0.000	0.000	0.000
115	A	146	GLY	0	-0.026	-0.011	16.128	0.005	0.005	0.000	0.000	0.000	0.000
116	A	147	ASN	0	-0.029	0.000	17.057	0.038	0.038	0.000	0.000	0.000	0.000
117	A	148	ASN	0	0.001	-0.010	17.159	-0.044	-0.044	0.000	0.000	0.000	0.000
118	A	149	HIS	1	0.860	0.920	15.589	0.293	0.293	0.000	0.000	0.000	0.000
119	A	150	THR	0	0.051	0.012	18.287	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	151	ASP	-1	-0.888	-0.931	19.417	-0.194	-0.194	0.000	0.000	0.000	0.000
121	A	152	ALA	0	-0.037	-0.022	16.643	0.000	0.000	0.000	0.000	0.000	0.000
122	A	153	LYS	1	0.944	0.978	15.873	0.143	0.143	0.000	0.000	0.000	0.000
123	A	154	VAL	0	-0.010	-0.021	11.752	0.010	0.010	0.000	0.000	0.000	0.000
124	A	155	THR	0	0.013	0.000	12.729	-0.034	-0.034	0.000	0.000	0.000	0.000
125	A	156	ALA	0	0.042	0.006	11.294	-0.034	-0.034	0.000	0.000	0.000	0.000
126	A	157	GLU	-1	-0.896	-0.947	12.251	-0.199	-0.199	0.000	0.000	0.000	0.000
127	A	158	ILE	0	-0.023	0.003	15.048	0.007	0.007	0.000	0.000	0.000	0.000
128	A	159	ALA	0	0.039	0.017	10.210	0.002	0.002	0.000	0.000	0.000	0.000
129	A	160	SER	0	-0.070	-0.052	12.177	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	161	SER	0	-0.057	-0.014	13.063	0.020	0.020	0.000	0.000	0.000	0.000
131	A	162	GLU	-1	-0.773	-0.893	14.652	-0.264	-0.264	0.000	0.000	0.000	0.000
132	A	164	THR	0	0.031	-0.014	12.456	0.022	0.022	0.000	0.000	0.000	0.000
133	A	165	ALA	0	-0.004	-0.011	12.651	-0.033	-0.033	0.000	0.000	0.000	0.000
134	A	166	ASP	-1	-0.812	-0.891	10.868	-0.335	-0.335	0.000	0.000	0.000	0.000
135	A	167	ASN	0	-0.004	0.000	13.723	0.033	0.033	0.000	0.000	0.000	0.000
136	A	168	GLY	0	-0.010	-0.009	16.915	0.005	0.005	0.000	0.000	0.000	0.000
137	A	169	ARG	1	0.963	0.971	13.830	0.038	0.038	0.000	0.000	0.000	0.000
138	A	170	THR	0	-0.041	-0.016	13.013	-0.018	-0.018	0.000	0.000	0.000	0.000
139	A	171	GLY	0	0.061	0.040	10.823	0.003	0.003	0.000	0.000	0.000	0.000
140	A	172	THR	0	-0.062	-0.036	11.729	0.015	0.015	0.000	0.000	0.000	0.000
141	A	173	ASN	0	0.003	0.042	10.127	0.042	0.042	0.000	0.000	0.000	0.000
142	A	174	THR	0	-0.005	0.008	11.520	-0.023	-0.023	0.000	0.000	0.000	0.000
143	A	175	LEU	0	-0.029	-0.009	7.174	0.003	0.003	0.000	0.000	0.000	0.000
144	A	176	VAL	0	-0.005	-0.008	11.384	0.014	0.014	0.000	0.000	0.000	0.000
145	A	177	PHE	0	-0.003	0.001	7.872	-0.017	-0.017	0.000	0.000	0.000	0.000
146	A	178	ASN	0	0.047	0.011	13.867	0.011	0.011	0.000	0.000	0.000	0.000
147	A	179	TYR	0	0.028	-0.012	13.581	-0.038	-0.038	0.000	0.000	0.000	0.000
148	A	180	ASN	0	0.061	0.028	19.377	0.012	0.012	0.000	0.000	0.000	0.000
149	A	181	GLY	0	-0.009	0.022	22.751	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:32:ALA)