FMO DATABASE

FMODB ID: ZYKLN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1193871.366798
FMO2-HF: Nuclear repulsion	1139490.140414
FMO2-HF: Total energy	-54381.226384
FMO2-MP2: Total energy	-54535.638618

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.
-6.313	-2.212	8.648	-5.191	-7.558	-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 : 0.027 / q_NPA : 0.007

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	0.026	0.010	3.792	-1.895	-0.525	-0.001	-0.577	-0.793	0.002
4	A	35	GLU	-1	-0.809	-0.878	2.220	-4.249	-3.608	5.649	-3.125	-3.165	-0.030
5	A	36	LEU	0	-0.007	0.008	3.874	0.578	0.962	0.000	-0.145	-0.239	0.000
6	A	37	THR	0	0.005	-0.006	5.427	0.604	0.604	0.000	0.000	0.000	0.000
7	A	38	ASN	0	-0.016	-0.006	7.502	0.326	0.326	0.000	0.000	0.000	0.000
8	A	39	TYR	0	0.004	-0.013	5.011	0.136	0.136	0.000	0.000	0.000	0.000
9	A	40	GLN	0	0.033	0.013	9.477	0.036	0.036	0.000	0.000	0.000	0.000
10	A	41	THR	0	-0.024	-0.023	11.495	0.101	0.101	0.000	0.000	0.000	0.000
11	A	42	LEU	0	0.025	0.030	12.656	0.051	0.051	0.000	0.000	0.000	0.000
12	A	43	ALA	0	0.023	0.017	13.694	0.048	0.048	0.000	0.000	0.000	0.000
13	A	44	THR	0	-0.028	-0.023	15.554	0.043	0.043	0.000	0.000	0.000	0.000
14	A	45	ASN	0	-0.034	-0.026	16.795	0.039	0.039	0.000	0.000	0.000	0.000
15	A	46	THR	0	-0.010	-0.013	17.518	0.023	0.023	0.000	0.000	0.000	0.000
16	A	47	ILE	0	-0.025	-0.010	18.890	0.019	0.019	0.000	0.000	0.000	0.000
17	A	48	GLY	0	-0.039	-0.019	21.540	0.015	0.015	0.000	0.000	0.000	0.000
18	A	49	MET	0	-0.010	-0.008	22.863	0.012	0.012	0.000	0.000	0.000	0.000
19	A	50	MET	0	-0.024	-0.019	23.160	0.008	0.008	0.000	0.000	0.000	0.000
20	A	51	LYS	1	0.918	0.963	24.817	0.111	0.111	0.000	0.000	0.000	0.000
21	A	52	GLY	0	0.005	0.017	27.939	0.006	0.006	0.000	0.000	0.000	0.000
22	A	53	VAL	0	-0.103	-0.029	28.027	0.004	0.004	0.000	0.000	0.000	0.000
23	A	54	ASP	-1	-0.819	-0.906	30.639	-0.070	-0.070	0.000	0.000	0.000	0.000
24	A	55	GLY	0	-0.041	-0.019	33.776	0.004	0.004	0.000	0.000	0.000	0.000
25	A	56	TYR	0	-0.055	-0.031	30.488	0.001	0.001	0.000	0.000	0.000	0.000
26	A	57	ALA	0	0.060	0.026	29.353	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	58	PHE	0	-0.004	0.001	25.870	0.002	0.002	0.000	0.000	0.000	0.000
28	A	59	THR	0	0.040	0.014	27.898	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	60	SER	0	0.009	-0.005	25.806	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	61	GLY	0	0.060	0.019	21.561	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	62	ALA	0	-0.007	0.012	21.826	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	63	LYS	1	0.931	0.963	23.436	0.075	0.075	0.000	0.000	0.000	0.000
33	A	64	MET	0	0.008	0.018	21.029	0.003	0.003	0.000	0.000	0.000	0.000
34	A	65	THR	0	0.025	-0.011	17.851	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	66	ASP	-1	-0.754	-0.860	20.458	-0.075	-0.075	0.000	0.000	0.000	0.000
36	A	67	THR	0	-0.020	-0.024	22.981	0.010	0.010	0.000	0.000	0.000	0.000
37	A	68	LEU	0	0.005	0.003	18.481	0.005	0.005	0.000	0.000	0.000	0.000
38	A	69	ILE	0	-0.061	-0.026	18.427	0.003	0.003	0.000	0.000	0.000	0.000
39	A	70	GLN	0	-0.091	-0.050	20.600	0.016	0.016	0.000	0.000	0.000	0.000
40	A	71	ALA	0	-0.031	-0.006	22.802	0.009	0.009	0.000	0.000	0.000	0.000
41	A	72	GLY	0	-0.018	-0.001	20.488	0.005	0.005	0.000	0.000	0.000	0.000
42	A	73	ALA	0	-0.046	-0.020	18.334	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	74	ALA	0	0.039	-0.010	14.886	-0.035	-0.035	0.000	0.000	0.000	0.000
44	A	75	LYS	1	0.969	0.992	14.886	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	76	GLY	0	-0.003	0.001	11.461	0.034	0.034	0.000	0.000	0.000	0.000
46	A	77	MET	0	-0.042	0.006	10.054	-0.037	-0.037	0.000	0.000	0.000	0.000
47	A	78	THR	0	0.008	0.013	11.772	0.067	0.067	0.000	0.000	0.000	0.000
48	A	79	VAL	0	0.021	0.004	13.944	-0.029	-0.029	0.000	0.000	0.000	0.000
49	A	80	SER	0	-0.026	-0.022	17.483	0.020	0.020	0.000	0.000	0.000	0.000
50	A	81	GLY	0	0.010	0.024	20.261	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	82	ASP	-1	-0.801	-0.909	23.262	-0.028	-0.028	0.000	0.000	0.000	0.000
52	A	83	PRO	0	-0.003	-0.003	23.281	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	84	ALA	0	-0.003	0.014	25.557	0.000	0.000	0.000	0.000	0.000	0.000
54	A	85	SER	0	-0.030	-0.037	28.682	0.003	0.003	0.000	0.000	0.000	0.000
55	A	86	GLY	0	-0.061	-0.012	27.539	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	87	SER	0	-0.051	-0.038	25.884	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	88	ALA	0	-0.023	0.013	21.835	0.000	0.000	0.000	0.000	0.000	0.000
58	A	89	THR	0	0.007	-0.002	19.143	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	90	LEU	0	0.012	-0.004	13.672	0.010	0.010	0.000	0.000	0.000	0.000
60	A	91	TRP	0	-0.022	-0.017	13.469	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	92	ASN	0	-0.004	-0.023	7.832	0.017	0.017	0.000	0.000	0.000	0.000
62	A	93	SER	0	-0.010	-0.063	5.456	0.085	0.085	0.000	0.000	0.000	0.000
63	A	94	TRP	0	-0.012	-0.012	3.135	-0.398	0.017	0.048	-0.099	-0.363	0.001
64	A	95	GLY	0	0.004	0.020	10.027	0.033	0.033	0.000	0.000	0.000	0.000
65	A	96	GLY	0	-0.036	-0.008	11.608	0.022	0.022	0.000	0.000	0.000	0.000
66	A	97	GLN	0	-0.016	-0.011	12.519	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	98	ILE	0	-0.022	-0.010	9.821	-0.047	-0.047	0.000	0.000	0.000	0.000
68	A	99	VAL	0	-0.045	-0.022	13.590	0.038	0.038	0.000	0.000	0.000	0.000
69	A	100	VAL	0	0.020	0.015	15.702	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	101	ALA	0	0.007	-0.013	17.813	0.025	0.025	0.000	0.000	0.000	0.000
71	A	102	PRO	0	0.000	0.009	20.928	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	103	ASP	-1	-0.903	-0.956	22.272	-0.168	-0.168	0.000	0.000	0.000	0.000
73	A	104	THR	0	-0.041	-0.019	24.194	0.008	0.008	0.000	0.000	0.000	0.000
74	A	105	ALA	0	-0.032	-0.011	27.365	0.003	0.003	0.000	0.000	0.000	0.000
75	A	106	GLY	0	0.034	0.003	28.915	0.006	0.006	0.000	0.000	0.000	0.000
76	A	107	GLY	0	0.016	0.004	32.433	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	108	THR	0	-0.087	-0.041	34.117	0.002	0.002	0.000	0.000	0.000	0.000
78	A	109	GLY	0	0.040	0.007	35.520	0.003	0.003	0.000	0.000	0.000	0.000
79	A	110	PHE	0	-0.014	0.016	28.204	0.000	0.000	0.000	0.000	0.000	0.000
80	A	111	ASN	0	-0.020	-0.020	27.950	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	112	ASN	0	0.009	0.011	27.327	0.001	0.001	0.000	0.000	0.000	0.000
82	A	113	GLY	0	0.072	0.044	23.256	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	114	PHE	0	-0.070	-0.041	16.904	0.009	0.009	0.000	0.000	0.000	0.000
84	A	115	THR	0	-0.042	-0.019	17.312	-0.018	-0.018	0.000	0.000	0.000	0.000
85	A	116	ILE	0	0.023	0.013	12.103	0.012	0.012	0.000	0.000	0.000	0.000
86	A	117	THR	0	0.019	0.015	13.293	-0.035	-0.035	0.000	0.000	0.000	0.000
87	A	118	THR	0	0.007	0.014	8.028	0.015	0.015	0.000	0.000	0.000	0.000
88	A	119	ASN	0	-0.018	-0.027	11.151	0.001	0.001	0.000	0.000	0.000	0.000
89	A	120	LYS	1	0.980	0.992	11.132	0.138	0.138	0.000	0.000	0.000	0.000
90	A	121	VAL	0	-0.009	0.012	5.930	0.001	0.001	0.000	0.000	0.000	0.000
91	A	122	PRO	0	0.040	0.002	6.369	0.033	0.033	0.000	0.000	0.000	0.000
92	A	123	GLN	0	-0.030	-0.011	7.129	-0.146	-0.146	0.000	0.000	0.000	0.000
93	A	124	SER	0	0.038	0.015	6.126	-0.171	-0.171	0.000	0.000	0.000	0.000
94	A	125	ALA	0	0.016	0.006	2.709	-0.796	-0.279	0.289	-0.264	-0.541	0.000
95	A	126	CYS	0	-0.080	-0.008	3.561	-0.181	-0.123	-0.002	0.103	-0.159	0.000
96	A	127	VAL	0	0.063	0.051	6.786	-0.029	-0.029	0.000	0.000	0.000	0.000
97	A	128	SER	0	-0.032	-0.007	2.792	-1.167	-0.339	0.569	-0.493	-0.904	-0.004
98	A	129	ILE	0	-0.012	-0.008	2.356	-0.417	-0.544	2.097	-0.579	-1.392	0.000
99	A	130	SER	0	-0.004	-0.017	4.707	0.197	0.212	-0.001	-0.012	-0.002	0.000
100	A	131	THR	0	-0.036	-0.030	7.442	0.072	0.072	0.000	0.000	0.000	0.000
101	A	132	GLY	0	-0.013	-0.005	6.765	0.140	0.140	0.000	0.000	0.000	0.000
102	A	133	MET	0	-0.005	-0.010	7.714	0.137	0.137	0.000	0.000	0.000	0.000
103	A	134	SER	0	-0.057	-0.011	9.924	0.116	0.116	0.000	0.000	0.000	0.000
104	A	135	ARG	1	0.925	0.950	10.071	0.457	0.457	0.000	0.000	0.000	0.000
105	A	136	SER	0	-0.052	-0.010	11.177	0.053	0.053	0.000	0.000	0.000	0.000
106	A	137	GLY	0	0.013	0.003	12.897	0.049	0.049	0.000	0.000	0.000	0.000
107	A	138	GLY	0	-0.003	0.009	14.868	0.030	0.030	0.000	0.000	0.000	0.000
108	A	139	THR	0	-0.064	-0.021	13.250	0.017	0.017	0.000	0.000	0.000	0.000
109	A	140	SER	0	-0.034	-0.022	16.409	0.022	0.022	0.000	0.000	0.000	0.000
110	A	141	GLY	0	0.047	0.022	17.246	0.024	0.024	0.000	0.000	0.000	0.000
111	A	142	ILE	0	-0.042	-0.003	11.741	-0.028	-0.028	0.000	0.000	0.000	0.000
112	A	143	LYS	1	0.887	0.949	14.176	0.259	0.259	0.000	0.000	0.000	0.000
113	A	144	ILE	0	0.031	0.019	11.516	-0.055	-0.055	0.000	0.000	0.000	0.000
114	A	145	ASN	0	0.020	-0.003	13.824	0.031	0.031	0.000	0.000	0.000	0.000
115	A	146	GLY	0	-0.016	-0.002	16.116	0.004	0.004	0.000	0.000	0.000	0.000
116	A	147	ASN	0	-0.035	-0.006	16.887	0.038	0.038	0.000	0.000	0.000	0.000
117	A	148	ASN	0	0.009	-0.011	17.152	-0.044	-0.044	0.000	0.000	0.000	0.000
118	A	149	HIS	1	0.864	0.914	15.837	0.289	0.289	0.000	0.000	0.000	0.000
119	A	150	THR	0	0.054	0.015	18.345	-0.016	-0.016	0.000	0.000	0.000	0.000
120	A	151	ASP	-1	-0.894	-0.944	19.611	-0.204	-0.204	0.000	0.000	0.000	0.000
121	A	152	ALA	0	-0.041	-0.025	16.754	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	153	LYS	1	0.947	0.990	15.981	0.154	0.154	0.000	0.000	0.000	0.000
123	A	154	VAL	0	-0.008	-0.018	11.711	0.012	0.012	0.000	0.000	0.000	0.000
124	A	155	THR	0	-0.035	-0.046	12.772	-0.037	-0.037	0.000	0.000	0.000	0.000
125	A	156	ALA	0	0.048	0.012	11.252	-0.033	-0.033	0.000	0.000	0.000	0.000
126	A	157	GLU	-1	-0.851	-0.905	12.207	-0.231	-0.231	0.000	0.000	0.000	0.000
127	A	158	ILE	0	-0.022	0.002	15.036	0.008	0.008	0.000	0.000	0.000	0.000
128	A	159	ALA	0	0.048	0.021	10.147	0.005	0.005	0.000	0.000	0.000	0.000
129	A	160	SER	0	-0.067	-0.054	12.199	-0.006	-0.006	0.000	0.000	0.000	0.000
130	A	161	SER	0	-0.025	-0.001	13.002	0.029	0.029	0.000	0.000	0.000	0.000
131	A	162	GLU	-1	-0.814	-0.901	14.519	-0.266	-0.266	0.000	0.000	0.000	0.000
132	A	164	THR	0	0.036	-0.006	12.496	0.023	0.023	0.000	0.000	0.000	0.000
133	A	165	ALA	0	0.001	-0.009	12.627	-0.030	-0.030	0.000	0.000	0.000	0.000
134	A	166	ASP	-1	-0.788	-0.876	10.617	-0.302	-0.302	0.000	0.000	0.000	0.000
135	A	167	ASN	0	0.008	0.003	13.641	0.030	0.030	0.000	0.000	0.000	0.000
136	A	168	GLY	0	-0.010	-0.007	16.793	0.007	0.007	0.000	0.000	0.000	0.000
137	A	169	ARG	1	0.956	0.967	13.694	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	170	THR	0	-0.047	-0.019	12.863	-0.006	-0.006	0.000	0.000	0.000	0.000
139	A	171	GLY	0	0.058	0.041	10.715	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	172	THR	0	-0.066	-0.041	11.624	0.012	0.012	0.000	0.000	0.000	0.000
141	A	173	ASN	0	0.004	0.032	10.181	0.029	0.029	0.000	0.000	0.000	0.000
142	A	174	THR	0	-0.015	-0.005	11.510	-0.016	-0.016	0.000	0.000	0.000	0.000
143	A	175	LEU	0	-0.014	0.000	7.205	-0.003	-0.003	0.000	0.000	0.000	0.000
144	A	176	VAL	0	-0.009	-0.012	11.385	0.015	0.015	0.000	0.000	0.000	0.000
145	A	177	PHE	0	0.002	0.004	7.906	-0.021	-0.021	0.000	0.000	0.000	0.000
146	A	178	ASN	0	0.025	-0.008	13.887	0.013	0.013	0.000	0.000	0.000	0.000
147	A	179	TYR	0	0.031	-0.007	13.349	-0.036	-0.036	0.000	0.000	0.000	0.000
148	A	180	ASN	0	0.040	0.022	19.403	0.015	0.015	0.000	0.000	0.000	0.000
149	A	181	GLY	0	0.006	0.023	22.904	-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)