FMO DATABASE

FMODB ID: 9Y5Y2

Calculation Name: 3FHV-A-Xray312

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	150
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1199331.940108
FMO2-HF: Nuclear repulsion	1144800.241265
FMO2-HF: Total energy	-54531.698843
FMO2-MP2: Total energy	-54686.614683

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:31:ACE )

Summations of interaction energy for fragment #1(A:31:ACE )

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.
0.675	1.802	-0.002	-0.563	-0.562	-0.001

Interaction energy analysis for fragmet #1(A:31:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.012

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	33	GLY	0	0.027	0.021	3.636	0.796	1.905	-0.002	-0.553	-0.554	-0.001
4	A	34	THR	0	0.028	0.009	5.720	0.261	0.261	0.000	0.000	0.000	0.000
5	A	35	GLU	-1	-0.820	-0.881	5.710	-2.104	-2.104	0.000	0.000	0.000	0.000
6	A	36	LEU	0	-0.005	0.010	7.890	0.220	0.220	0.000	0.000	0.000	0.000
7	A	37	THR	0	0.007	0.000	9.743	0.192	0.192	0.000	0.000	0.000	0.000
8	A	38	ASN	0	-0.013	-0.002	11.248	0.155	0.155	0.000	0.000	0.000	0.000
9	A	39	TYR	0	0.047	0.029	10.646	0.103	0.103	0.000	0.000	0.000	0.000
10	A	40	GLN	0	0.044	0.013	12.987	0.031	0.031	0.000	0.000	0.000	0.000
11	A	41	THR	0	-0.029	-0.030	15.354	0.043	0.043	0.000	0.000	0.000	0.000
12	A	42	LEU	0	0.029	0.031	17.073	0.027	0.027	0.000	0.000	0.000	0.000
13	A	43	ALA	0	0.028	0.024	18.524	0.027	0.027	0.000	0.000	0.000	0.000
14	A	44	THR	0	-0.018	-0.011	20.043	0.028	0.028	0.000	0.000	0.000	0.000
15	A	45	ASN	0	-0.036	-0.028	20.639	0.029	0.029	0.000	0.000	0.000	0.000
16	A	46	THR	0	-0.022	-0.016	22.439	0.013	0.013	0.000	0.000	0.000	0.000
17	A	47	ILE	0	-0.012	-0.002	23.564	0.013	0.013	0.000	0.000	0.000	0.000
18	A	48	GLY	0	-0.036	-0.020	26.087	0.011	0.011	0.000	0.000	0.000	0.000
19	A	49	MET	0	-0.007	-0.007	27.451	0.007	0.007	0.000	0.000	0.000	0.000
20	A	50	MET	0	-0.039	-0.027	28.392	0.006	0.006	0.000	0.000	0.000	0.000
21	A	51	LYS	1	0.920	0.962	29.379	0.077	0.077	0.000	0.000	0.000	0.000
22	A	52	GLY	0	0.002	0.014	32.734	0.005	0.005	0.000	0.000	0.000	0.000
23	A	53	VAL	0	-0.079	-0.011	32.928	0.002	0.002	0.000	0.000	0.000	0.000
24	A	54	ASP	-1	-0.816	-0.903	35.633	-0.056	-0.056	0.000	0.000	0.000	0.000
25	A	55	GLY	0	-0.038	-0.018	38.874	0.002	0.002	0.000	0.000	0.000	0.000
26	A	56	TYR	0	-0.062	-0.034	35.404	0.001	0.001	0.000	0.000	0.000	0.000
27	A	57	ALA	0	0.065	0.029	34.705	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	58	PHE	0	-0.017	-0.010	30.908	0.000	0.000	0.000	0.000	0.000	0.000
29	A	59	THR	0	0.039	0.015	33.193	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	60	SER	0	0.016	-0.004	31.057	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	61	GLY	0	0.078	0.024	26.744	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	62	ALA	0	-0.008	0.008	26.858	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	63	LYS	1	0.996	1.007	28.298	0.086	0.086	0.000	0.000	0.000	0.000
34	A	64	MET	0	0.011	0.021	26.543	0.001	0.001	0.000	0.000	0.000	0.000
35	A	65	THR	0	0.021	-0.003	22.773	-0.010	-0.010	0.000	0.000	0.000	0.000
36	A	66	ASP	-1	-0.792	-0.886	25.178	-0.112	-0.112	0.000	0.000	0.000	0.000
37	A	67	THR	0	-0.017	-0.017	27.480	0.007	0.007	0.000	0.000	0.000	0.000
38	A	68	LEU	0	0.001	-0.003	23.389	0.003	0.003	0.000	0.000	0.000	0.000
39	A	69	ILE	0	-0.064	-0.026	22.465	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	70	GLN	0	-0.087	-0.034	24.565	0.008	0.008	0.000	0.000	0.000	0.000
41	A	71	ALA	0	-0.036	-0.008	26.819	0.007	0.007	0.000	0.000	0.000	0.000
42	A	72	GLY	0	-0.017	-0.001	23.927	0.004	0.004	0.000	0.000	0.000	0.000
43	A	73	ALA	0	-0.043	-0.020	22.279	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	74	ALA	0	0.041	-0.008	18.689	-0.020	-0.020	0.000	0.000	0.000	0.000
45	A	75	LYS	1	0.964	0.989	18.277	0.110	0.110	0.000	0.000	0.000	0.000
46	A	76	GLY	0	-0.008	-0.003	14.492	0.007	0.007	0.000	0.000	0.000	0.000
47	A	77	MET	0	-0.047	0.002	13.595	-0.070	-0.070	0.000	0.000	0.000	0.000
48	A	78	THR	0	0.014	0.016	14.957	0.051	0.051	0.000	0.000	0.000	0.000
49	A	79	VAL	0	0.028	0.012	17.215	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	80	SER	0	-0.034	-0.013	20.919	0.011	0.011	0.000	0.000	0.000	0.000
51	A	81	GLY	0	0.011	0.019	23.592	0.002	0.002	0.000	0.000	0.000	0.000
52	A	82	ASP	-1	-0.829	-0.942	26.749	-0.083	-0.083	0.000	0.000	0.000	0.000
53	A	83	PRO	0	-0.020	-0.013	26.799	0.004	0.004	0.000	0.000	0.000	0.000
54	A	84	ALA	0	-0.005	0.005	29.153	0.004	0.004	0.000	0.000	0.000	0.000
55	A	85	SER	0	-0.022	-0.014	32.248	0.007	0.007	0.000	0.000	0.000	0.000
56	A	86	GLY	0	-0.043	0.000	31.591	0.002	0.002	0.000	0.000	0.000	0.000
57	A	87	SER	0	-0.052	-0.038	30.134	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	88	ALA	0	-0.036	-0.003	25.587	-0.005	-0.005	0.000	0.000	0.000	0.000
59	A	89	THR	0	0.004	-0.006	23.130	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	90	LEU	0	0.014	-0.002	17.925	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	91	TRP	0	-0.010	-0.007	16.920	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	92	ASN	0	-0.002	-0.021	11.885	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	93	SER	0	-0.024	-0.067	8.366	0.161	0.161	0.000	0.000	0.000	0.000
64	A	94	TRP	0	-0.010	-0.009	5.881	0.120	0.120	0.000	0.000	0.000	0.000
65	A	95	GLY	0	0.002	0.021	12.020	0.075	0.075	0.000	0.000	0.000	0.000
66	A	96	GLY	0	-0.039	-0.013	14.682	0.054	0.054	0.000	0.000	0.000	0.000
67	A	97	GLN	0	-0.030	-0.031	16.392	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	98	ILE	0	-0.033	-0.009	14.359	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	99	VAL	0	-0.037	-0.019	18.407	0.028	0.028	0.000	0.000	0.000	0.000
70	A	100	VAL	0	0.004	0.004	21.053	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	101	ALA	0	0.008	-0.020	23.103	0.015	0.015	0.000	0.000	0.000	0.000
72	A	102	PRO	0	-0.018	-0.002	26.318	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	103	ASP	-1	-0.941	-0.973	27.821	-0.115	-0.115	0.000	0.000	0.000	0.000
74	A	104	THR	0	-0.027	-0.016	29.680	0.007	0.007	0.000	0.000	0.000	0.000
75	A	105	ALA	0	-0.020	-0.004	32.920	0.003	0.003	0.000	0.000	0.000	0.000
76	A	106	GLY	0	-0.007	-0.013	34.388	0.003	0.003	0.000	0.000	0.000	0.000
77	A	107	GLY	0	0.039	0.020	37.895	0.000	0.000	0.000	0.000	0.000	0.000
78	A	108	THR	0	-0.106	-0.056	39.487	0.003	0.003	0.000	0.000	0.000	0.000
79	A	109	GLY	0	0.035	0.007	40.861	0.003	0.003	0.000	0.000	0.000	0.000
80	A	110	PHE	0	-0.020	0.012	33.175	0.000	0.000	0.000	0.000	0.000	0.000
81	A	111	ASN	0	-0.043	-0.037	33.212	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	112	ASN	0	0.025	0.018	32.468	0.001	0.001	0.000	0.000	0.000	0.000
83	A	113	GLY	0	0.117	0.067	28.562	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	114	PHE	0	-0.081	-0.048	22.186	0.001	0.001	0.000	0.000	0.000	0.000
85	A	115	THR	0	-0.029	-0.011	22.694	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	116	ILE	0	0.003	0.002	17.331	0.000	0.000	0.000	0.000	0.000	0.000
87	A	117	THR	0	0.006	0.009	18.769	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	118	THR	0	-0.031	-0.024	13.332	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	119	ASN	0	0.000	-0.021	16.005	0.012	0.012	0.000	0.000	0.000	0.000
90	A	120	LYS	1	0.979	0.987	14.996	0.196	0.196	0.000	0.000	0.000	0.000
91	A	121	VAL	0	-0.003	0.019	9.803	-0.054	-0.054	0.000	0.000	0.000	0.000
92	A	122	PRO	0	0.037	-0.006	8.205	0.094	0.094	0.000	0.000	0.000	0.000
93	A	123	GLN	0	-0.025	-0.001	9.665	-0.137	-0.137	0.000	0.000	0.000	0.000
94	A	124	SER	0	0.042	0.013	5.213	-0.116	-0.116	0.000	0.000	0.000	0.000
95	A	125	ALA	0	0.016	0.004	5.748	-0.131	-0.131	0.000	0.000	0.000	0.000
96	A	163	CYS	0	-0.100	-0.020	6.608	0.115	0.115	0.000	0.000	0.000	0.000
97	A	127	VAL	0	0.061	0.042	8.787	0.079	0.079	0.000	0.000	0.000	0.000
98	A	128	SER	0	-0.018	-0.002	4.464	0.145	0.163	0.000	-0.010	-0.008	0.000
99	A	129	ILE	0	0.017	0.001	7.119	0.134	0.134	0.000	0.000	0.000	0.000
100	A	130	SER	0	-0.015	-0.013	8.969	0.178	0.178	0.000	0.000	0.000	0.000
101	A	131	THR	0	-0.036	-0.029	9.944	0.086	0.086	0.000	0.000	0.000	0.000
102	A	132	GLY	0	-0.002	-0.001	10.125	0.072	0.072	0.000	0.000	0.000	0.000
103	A	133	MET	0	-0.003	-0.009	10.992	0.047	0.047	0.000	0.000	0.000	0.000
104	A	134	SER	0	-0.040	0.003	13.893	0.050	0.050	0.000	0.000	0.000	0.000
105	A	135	ARG	1	0.911	0.940	11.303	0.023	0.023	0.000	0.000	0.000	0.000
106	A	136	SER	0	-0.068	-0.018	14.341	0.019	0.019	0.000	0.000	0.000	0.000
107	A	137	GLY	0	0.017	0.006	16.073	0.015	0.015	0.000	0.000	0.000	0.000
108	A	138	GLY	0	-0.014	0.003	18.588	0.009	0.009	0.000	0.000	0.000	0.000
109	A	139	THR	0	-0.054	-0.015	17.968	0.006	0.006	0.000	0.000	0.000	0.000
110	A	140	SER	0	-0.002	-0.001	20.903	0.014	0.014	0.000	0.000	0.000	0.000
111	A	141	GLY	0	0.044	0.022	21.771	0.010	0.010	0.000	0.000	0.000	0.000
112	A	142	ILE	0	-0.061	-0.013	15.883	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	143	LYS	1	0.923	0.958	19.020	0.171	0.171	0.000	0.000	0.000	0.000
114	A	144	ILE	0	0.027	0.011	14.810	-0.046	-0.046	0.000	0.000	0.000	0.000
115	A	145	ASN	0	0.026	-0.002	17.285	0.016	0.016	0.000	0.000	0.000	0.000
116	A	146	GLY	0	-0.028	-0.011	20.235	0.006	0.006	0.000	0.000	0.000	0.000
117	A	147	ASN	0	-0.035	-0.004	20.433	0.030	0.030	0.000	0.000	0.000	0.000
118	A	148	ASN	0	0.009	-0.005	21.233	-0.026	-0.026	0.000	0.000	0.000	0.000
119	A	149	HIS	1	0.853	0.915	19.228	0.158	0.158	0.000	0.000	0.000	0.000
120	A	150	THR	0	0.066	0.021	22.372	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	151	ASP	-1	-0.892	-0.931	23.114	-0.087	-0.087	0.000	0.000	0.000	0.000
122	A	152	ALA	0	-0.029	-0.017	20.735	0.003	0.003	0.000	0.000	0.000	0.000
123	A	153	LYS	1	0.939	0.975	19.468	0.042	0.042	0.000	0.000	0.000	0.000
124	A	154	VAL	0	-0.009	-0.021	15.058	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	155	THR	0	0.007	-0.004	15.672	-0.007	-0.007	0.000	0.000	0.000	0.000
126	A	156	ALA	0	0.043	0.005	12.735	-0.025	-0.025	0.000	0.000	0.000	0.000
127	A	157	GLU	-1	-0.898	-0.947	13.794	-0.014	-0.014	0.000	0.000	0.000	0.000
128	A	158	ILE	0	-0.023	0.004	16.947	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	159	ALA	0	0.037	0.017	12.805	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	160	SER	0	-0.066	-0.051	13.531	-0.016	-0.016	0.000	0.000	0.000	0.000
131	A	161	SER	0	-0.062	-0.016	14.415	0.001	0.001	0.000	0.000	0.000	0.000
132	A	162	GLU	-1	-0.773	-0.894	17.440	-0.156	-0.156	0.000	0.000	0.000	0.000
133	A	164	THR	0	0.031	-0.014	15.164	0.028	0.028	0.000	0.000	0.000	0.000
134	A	165	ALA	0	-0.006	-0.013	14.537	-0.041	-0.041	0.000	0.000	0.000	0.000
135	A	166	ASP	-1	-0.814	-0.890	11.328	-0.400	-0.400	0.000	0.000	0.000	0.000
136	A	167	ASN	0	-0.004	-0.001	14.643	0.051	0.051	0.000	0.000	0.000	0.000
137	A	168	GLY	0	-0.012	-0.010	17.171	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	169	ARG	1	0.961	0.971	13.499	0.133	0.133	0.000	0.000	0.000	0.000
139	A	170	THR	0	-0.041	-0.016	13.325	-0.053	-0.053	0.000	0.000	0.000	0.000
140	A	171	GLY	0	0.062	0.040	12.923	0.020	0.020	0.000	0.000	0.000	0.000
141	A	172	THR	0	-0.062	-0.036	13.621	0.026	0.026	0.000	0.000	0.000	0.000
142	A	173	ASN	0	0.000	0.041	12.838	0.075	0.075	0.000	0.000	0.000	0.000
143	A	174	THR	0	-0.004	0.007	15.399	-0.041	-0.041	0.000	0.000	0.000	0.000
144	A	175	LEU	0	-0.030	-0.010	11.810	0.016	0.016	0.000	0.000	0.000	0.000
145	A	176	VAL	0	-0.004	-0.007	16.386	0.002	0.002	0.000	0.000	0.000	0.000
146	A	177	PHE	0	-0.013	-0.006	13.244	0.001	0.001	0.000	0.000	0.000	0.000
147	A	178	ASN	0	0.075	0.024	19.170	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	179	TYR	0	0.008	-0.024	18.476	-0.019	-0.019	0.000	0.000	0.000	0.000
149	A	180	ASN	0	0.015	0.003	24.456	0.006	0.006	0.000	0.000	0.000	0.000
150	A	181	GLY	-1	-0.925	-0.934	27.779	-0.106	-0.106	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:31:ACE )