FMO DATABASE

FMODB ID: R56M8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1194884.133063
FMO2-HF: Nuclear repulsion	1140502.715203
FMO2-HF: Total energy	-54381.417861
FMO2-MP2: Total energy	-54535.815417

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.
-8.94	-2.887	7.032	-4.826	-8.258	-0.031

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 : 0.036 / q_NPA : 0.010

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	0.031	0.022	3.637	-1.586	-0.143	-0.003	-0.670	-0.770	0.001
4	A	35	GLU	-1	-0.820	-0.882	2.400	-5.929	-4.163	3.279	-2.193	-2.852	-0.025
5	A	36	LEU	0	-0.005	0.007	3.802	0.653	1.021	0.000	-0.131	-0.236	0.000
6	A	37	THR	0	0.004	-0.011	5.620	0.673	0.673	0.000	0.000	0.000	0.000
7	A	38	ASN	0	-0.034	-0.013	7.598	0.381	0.381	0.000	0.000	0.000	0.000
8	A	39	TYR	0	0.009	-0.008	4.996	0.139	0.139	0.000	0.000	0.000	0.000
9	A	40	GLN	0	0.038	0.012	9.641	0.060	0.060	0.000	0.000	0.000	0.000
10	A	41	THR	0	-0.037	-0.024	11.683	0.112	0.112	0.000	0.000	0.000	0.000
11	A	42	LEU	0	0.033	0.023	12.618	0.059	0.059	0.000	0.000	0.000	0.000
12	A	43	ALA	0	0.017	0.019	13.673	0.056	0.056	0.000	0.000	0.000	0.000
13	A	44	THR	0	-0.021	-0.020	15.555	0.055	0.055	0.000	0.000	0.000	0.000
14	A	45	ASN	0	-0.032	-0.034	16.668	0.050	0.050	0.000	0.000	0.000	0.000
15	A	46	THR	0	-0.026	-0.020	17.391	0.027	0.027	0.000	0.000	0.000	0.000
16	A	47	ILE	0	-0.024	-0.018	18.799	0.024	0.024	0.000	0.000	0.000	0.000
17	A	48	GLY	0	-0.026	-0.008	21.491	0.019	0.019	0.000	0.000	0.000	0.000
18	A	49	MET	0	-0.006	-0.004	22.757	0.013	0.013	0.000	0.000	0.000	0.000
19	A	50	MET	0	-0.033	-0.028	23.003	0.010	0.010	0.000	0.000	0.000	0.000
20	A	51	LYS	1	0.898	0.958	24.799	0.133	0.133	0.000	0.000	0.000	0.000
21	A	52	GLY	0	0.017	0.020	28.191	0.009	0.009	0.000	0.000	0.000	0.000
22	A	53	VAL	0	-0.093	-0.029	27.864	0.002	0.002	0.000	0.000	0.000	0.000
23	A	54	ASP	-1	-0.807	-0.907	30.769	-0.087	-0.087	0.000	0.000	0.000	0.000
24	A	55	GLY	0	-0.044	-0.021	33.917	0.004	0.004	0.000	0.000	0.000	0.000
25	A	56	TYR	0	-0.052	-0.027	30.614	0.000	0.000	0.000	0.000	0.000	0.000
26	A	57	ALA	0	0.067	0.034	29.243	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	58	PHE	0	-0.010	-0.006	25.789	0.002	0.002	0.000	0.000	0.000	0.000
28	A	59	THR	0	0.043	0.015	27.756	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	60	SER	0	-0.003	-0.007	25.569	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	61	GLY	0	0.066	0.022	21.184	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	62	ALA	0	-0.010	0.014	21.127	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	63	LYS	1	0.893	0.935	22.669	0.108	0.108	0.000	0.000	0.000	0.000
33	A	64	MET	0	0.005	0.027	20.897	0.004	0.004	0.000	0.000	0.000	0.000
34	A	65	THR	0	0.016	-0.010	17.221	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	66	ASP	-1	-0.759	-0.857	19.781	-0.126	-0.126	0.000	0.000	0.000	0.000
36	A	67	THR	0	-0.010	-0.022	22.323	0.008	0.008	0.000	0.000	0.000	0.000
37	A	68	LEU	0	0.011	0.001	18.164	0.006	0.006	0.000	0.000	0.000	0.000
38	A	69	ILE	0	-0.058	-0.024	17.947	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	70	GLN	0	-0.107	-0.063	20.343	0.017	0.017	0.000	0.000	0.000	0.000
40	A	71	ALA	0	-0.020	-0.004	22.414	0.010	0.010	0.000	0.000	0.000	0.000
41	A	72	GLY	0	-0.008	0.003	20.592	0.005	0.005	0.000	0.000	0.000	0.000
42	A	73	ALA	0	-0.027	-0.014	18.535	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	74	ALA	0	0.040	0.007	14.747	-0.038	-0.038	0.000	0.000	0.000	0.000
44	A	75	LYS	1	0.955	0.983	14.584	0.067	0.067	0.000	0.000	0.000	0.000
45	A	76	GLY	0	-0.012	0.000	12.026	0.045	0.045	0.000	0.000	0.000	0.000
46	A	77	MET	0	-0.039	0.006	9.603	-0.091	-0.091	0.000	0.000	0.000	0.000
47	A	78	THR	0	-0.001	0.009	11.759	0.092	0.092	0.000	0.000	0.000	0.000
48	A	79	VAL	0	0.013	-0.002	13.808	-0.027	-0.027	0.000	0.000	0.000	0.000
49	A	80	SER	0	-0.033	-0.024	17.164	0.025	0.025	0.000	0.000	0.000	0.000
50	A	81	GLY	0	0.010	0.023	19.907	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	82	ASP	-1	-0.797	-0.890	22.735	-0.069	-0.069	0.000	0.000	0.000	0.000
52	A	83	PRO	0	-0.005	-0.007	23.395	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	84	ALA	0	0.025	0.024	25.431	0.002	0.002	0.000	0.000	0.000	0.000
54	A	85	SER	0	-0.041	-0.038	28.877	0.005	0.005	0.000	0.000	0.000	0.000
55	A	86	GLY	0	-0.051	-0.007	27.346	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	87	SER	0	-0.018	-0.026	25.672	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	88	ALA	0	-0.026	-0.002	21.283	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	89	THR	0	0.001	-0.006	18.580	-0.011	-0.011	0.000	0.000	0.000	0.000
59	A	90	LEU	0	0.016	0.005	13.217	0.009	0.009	0.000	0.000	0.000	0.000
60	A	91	TRP	0	-0.018	-0.016	12.649	-0.015	-0.015	0.000	0.000	0.000	0.000
61	A	92	ASN	0	0.019	-0.001	7.043	0.028	0.028	0.000	0.000	0.000	0.000
62	A	93	SER	0	-0.017	-0.056	5.682	0.153	0.153	0.000	0.000	0.000	0.000
63	A	94	TRP	0	-0.007	-0.008	2.483	-0.591	-0.068	0.484	-0.270	-0.737	0.001
64	A	95	GLY	0	0.007	0.020	9.775	0.043	0.043	0.000	0.000	0.000	0.000
65	A	96	GLY	0	-0.048	-0.018	11.049	0.039	0.039	0.000	0.000	0.000	0.000
66	A	97	GLN	0	-0.009	-0.003	11.721	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	98	ILE	0	-0.037	-0.028	9.220	-0.049	-0.049	0.000	0.000	0.000	0.000
68	A	99	VAL	0	-0.033	-0.022	12.973	0.050	0.050	0.000	0.000	0.000	0.000
69	A	100	VAL	0	0.016	0.016	15.400	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	101	ALA	0	0.026	-0.008	17.395	0.030	0.030	0.000	0.000	0.000	0.000
71	A	102	PRO	0	0.008	0.011	20.547	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	103	ASP	-1	-0.886	-0.941	22.188	-0.192	-0.192	0.000	0.000	0.000	0.000
73	A	104	THR	0	-0.043	-0.032	24.040	0.011	0.011	0.000	0.000	0.000	0.000
74	A	105	ALA	0	-0.033	-0.013	27.287	0.006	0.006	0.000	0.000	0.000	0.000
75	A	106	GLY	0	0.041	0.009	28.931	0.006	0.006	0.000	0.000	0.000	0.000
76	A	107	GLY	0	0.023	0.017	32.587	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	108	THR	0	-0.084	-0.038	34.359	0.003	0.003	0.000	0.000	0.000	0.000
78	A	109	GLY	0	0.041	0.017	35.836	0.005	0.005	0.000	0.000	0.000	0.000
79	A	110	PHE	0	-0.030	0.002	28.301	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	111	ASN	0	-0.043	-0.028	27.842	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	112	ASN	0	-0.002	0.002	27.524	0.003	0.003	0.000	0.000	0.000	0.000
82	A	113	GLY	0	0.070	0.041	23.640	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	114	PHE	0	-0.084	-0.042	17.047	0.007	0.007	0.000	0.000	0.000	0.000
84	A	115	THR	0	-0.032	-0.011	17.327	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	116	ILE	0	0.015	0.007	11.907	0.012	0.012	0.000	0.000	0.000	0.000
86	A	117	THR	0	0.034	0.023	13.227	-0.039	-0.039	0.000	0.000	0.000	0.000
87	A	118	THR	0	0.003	0.001	8.059	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	119	ASN	0	-0.016	-0.012	11.089	0.016	0.016	0.000	0.000	0.000	0.000
89	A	120	LYS	1	0.981	0.981	10.459	0.175	0.175	0.000	0.000	0.000	0.000
90	A	121	VAL	0	-0.005	0.018	5.477	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	122	PRO	0	0.039	0.002	5.893	0.050	0.050	0.000	0.000	0.000	0.000
92	A	123	GLN	0	-0.014	-0.002	6.557	-0.188	-0.188	0.000	0.000	0.000	0.000
93	A	124	SER	0	0.039	0.014	5.942	-0.204	-0.204	0.000	0.000	0.000	0.000
94	A	125	ALA	0	0.016	0.021	2.593	-1.060	-0.525	0.751	-0.456	-0.830	0.001
95	A	126	CYS	0	-0.077	-0.017	3.384	-0.345	-0.432	0.003	0.293	-0.209	-0.001
96	A	127	VAL	0	0.061	0.046	6.551	-0.063	-0.063	0.000	0.000	0.000	0.000
97	A	128	SER	0	-0.046	-0.023	2.782	-2.370	-0.982	0.566	-0.795	-1.158	-0.008
98	A	129	ILE	0	-0.010	-0.005	2.304	-0.347	-0.264	1.953	-0.591	-1.446	0.000
99	A	130	SER	0	-0.008	-0.023	4.533	0.376	0.410	-0.001	-0.013	-0.020	0.000
100	A	131	THR	0	-0.035	-0.034	7.576	0.148	0.148	0.000	0.000	0.000	0.000
101	A	132	GLY	0	-0.006	-0.001	7.017	0.192	0.192	0.000	0.000	0.000	0.000
102	A	133	MET	0	-0.012	-0.016	7.934	0.168	0.168	0.000	0.000	0.000	0.000
103	A	134	SER	0	-0.048	-0.023	10.045	0.124	0.124	0.000	0.000	0.000	0.000
104	A	135	ARG	1	0.920	0.946	9.496	0.291	0.291	0.000	0.000	0.000	0.000
105	A	136	SER	0	-0.032	-0.010	11.469	0.054	0.054	0.000	0.000	0.000	0.000
106	A	137	GLY	0	-0.020	0.000	13.290	0.034	0.034	0.000	0.000	0.000	0.000
107	A	138	GLY	0	0.000	0.009	15.053	0.027	0.027	0.000	0.000	0.000	0.000
108	A	139	THR	0	-0.037	-0.021	13.376	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	140	SER	0	-0.057	-0.039	16.654	0.036	0.036	0.000	0.000	0.000	0.000
110	A	141	GLY	0	0.050	0.032	17.511	0.026	0.026	0.000	0.000	0.000	0.000
111	A	142	ILE	0	-0.060	-0.011	11.777	-0.037	-0.037	0.000	0.000	0.000	0.000
112	A	143	LYS	1	0.869	0.940	14.061	0.306	0.306	0.000	0.000	0.000	0.000
113	A	144	ILE	0	0.028	0.016	11.219	-0.071	-0.071	0.000	0.000	0.000	0.000
114	A	145	ASN	0	0.007	-0.012	13.622	0.040	0.040	0.000	0.000	0.000	0.000
115	A	146	GLY	0	0.004	0.012	15.918	0.006	0.006	0.000	0.000	0.000	0.000
116	A	147	ASN	0	-0.048	-0.015	16.530	0.044	0.044	0.000	0.000	0.000	0.000
117	A	148	ASN	0	0.017	-0.012	17.017	-0.051	-0.051	0.000	0.000	0.000	0.000
118	A	149	HIS	1	0.874	0.923	15.948	0.299	0.299	0.000	0.000	0.000	0.000
119	A	150	THR	0	0.058	0.010	18.149	-0.020	-0.020	0.000	0.000	0.000	0.000
120	A	151	ASP	-1	-0.899	-0.947	19.475	-0.204	-0.204	0.000	0.000	0.000	0.000
121	A	152	ALA	0	-0.015	-0.003	16.546	0.003	0.003	0.000	0.000	0.000	0.000
122	A	153	LYS	1	0.946	1.003	15.610	0.118	0.118	0.000	0.000	0.000	0.000
123	A	154	VAL	0	-0.013	-0.016	11.133	0.006	0.006	0.000	0.000	0.000	0.000
124	A	155	THR	0	-0.033	-0.045	13.018	-0.020	-0.020	0.000	0.000	0.000	0.000
125	A	156	ALA	0	0.032	0.007	11.413	-0.045	-0.045	0.000	0.000	0.000	0.000
126	A	157	GLU	-1	-0.833	-0.891	12.436	-0.173	-0.173	0.000	0.000	0.000	0.000
127	A	158	ILE	0	-0.011	0.002	14.831	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	159	ALA	0	0.055	0.022	10.017	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	160	SER	0	-0.067	-0.056	12.119	-0.018	-0.018	0.000	0.000	0.000	0.000
130	A	161	SER	0	-0.028	0.000	13.074	0.032	0.032	0.000	0.000	0.000	0.000
131	A	162	GLU	-1	-0.838	-0.900	14.113	-0.280	-0.280	0.000	0.000	0.000	0.000
132	A	164	THR	0	0.043	0.015	12.287	0.034	0.034	0.000	0.000	0.000	0.000
133	A	165	ALA	0	0.029	0.009	12.419	-0.037	-0.037	0.000	0.000	0.000	0.000
134	A	166	ASP	-1	-0.777	-0.865	10.079	-0.348	-0.348	0.000	0.000	0.000	0.000
135	A	167	ASN	0	0.035	0.014	13.394	0.043	0.043	0.000	0.000	0.000	0.000
136	A	168	GLY	0	-0.001	0.003	16.413	0.006	0.006	0.000	0.000	0.000	0.000
137	A	169	ARG	1	0.925	0.947	13.172	0.059	0.059	0.000	0.000	0.000	0.000
138	A	170	THR	0	-0.061	-0.016	12.490	-0.016	-0.016	0.000	0.000	0.000	0.000
139	A	171	GLY	0	0.030	0.018	10.174	0.009	0.009	0.000	0.000	0.000	0.000
140	A	172	THR	0	-0.045	-0.041	11.106	-0.002	-0.002	0.000	0.000	0.000	0.000
141	A	173	ASN	0	-0.022	0.007	9.841	0.036	0.036	0.000	0.000	0.000	0.000
142	A	174	THR	0	-0.018	-0.009	11.369	-0.022	-0.022	0.000	0.000	0.000	0.000
143	A	175	LEU	0	-0.021	-0.006	7.247	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	176	VAL	0	-0.012	-0.014	11.367	0.019	0.019	0.000	0.000	0.000	0.000
145	A	177	PHE	0	0.010	0.008	8.165	-0.028	-0.028	0.000	0.000	0.000	0.000
146	A	178	ASN	0	0.011	-0.016	14.136	0.003	0.003	0.000	0.000	0.000	0.000
147	A	179	TYR	0	0.017	0.001	13.317	-0.030	-0.030	0.000	0.000	0.000	0.000
148	A	180	ASN	0	0.035	0.024	19.637	0.016	0.016	0.000	0.000	0.000	0.000
149	A	181	GLY	0	0.012	0.015	22.843	-0.006	-0.006	0.000	0.000	0.000	0.000

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