FMO DATABASE

FMODB ID: 6YK8Z

Calculation Name: 1F46-A-Xray372

Preferred Name: Cell division protein zipA

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1F46

Chain ID: A

ChEMBL ID: CHEMBL3954

UniProt ID: P77173

Base Structure: X-ray

Registration Date: 2023-09-23

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1244915.052026
FMO2-HF: Nuclear repulsion	1189469.791002
FMO2-HF: Total energy	-55445.261024
FMO2-MP2: Total energy	-55603.539943

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:6:ARG)

Summations of interaction energy for fragment #1(A:6:ARG)

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.
-204.919	-191.959	10.297	-10.216	-13.042	-0.108

Interaction energy analysis for fragmet #1(A:6:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.887 / q_NPA : 0.931

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	8	GLU	-1	-0.896	-0.940	3.226	-30.798	-28.264	0.000	-1.183	-1.351	0.002
4	A	9	ALA	0	-0.005	0.001	2.690	-9.307	-8.125	0.142	-0.406	-0.917	-0.003
5	A	10	VAL	0	0.019	0.022	4.732	4.908	4.966	-0.001	-0.011	-0.047	0.000
6	A	11	ILE	0	-0.049	-0.025	7.024	-2.351	-2.351	0.000	0.000	0.000	0.000
7	A	12	ILE	0	0.032	0.007	9.262	2.735	2.735	0.000	0.000	0.000	0.000
8	A	13	MET	0	-0.012	0.032	12.037	-0.722	-0.722	0.000	0.000	0.000	0.000
9	A	14	ASN	0	-0.017	-0.011	15.055	0.861	0.861	0.000	0.000	0.000	0.000
10	A	15	VAL	0	0.043	0.047	18.320	-0.110	-0.110	0.000	0.000	0.000	0.000
11	A	16	ALA	0	-0.027	-0.016	21.611	0.136	0.136	0.000	0.000	0.000	0.000
12	A	17	ALA	0	0.077	0.043	23.418	0.218	0.218	0.000	0.000	0.000	0.000
13	A	18	HIS	0	-0.001	0.006	25.720	-0.500	-0.500	0.000	0.000	0.000	0.000
14	A	19	HIS	0	0.017	-0.003	25.760	0.002	0.002	0.000	0.000	0.000	0.000
15	A	20	GLY	0	-0.023	-0.010	27.378	0.299	0.299	0.000	0.000	0.000	0.000
16	A	21	SER	0	-0.093	-0.040	29.832	0.406	0.406	0.000	0.000	0.000	0.000
17	A	22	GLU	-1	-0.862	-0.935	29.401	-10.649	-10.649	0.000	0.000	0.000	0.000
18	A	23	LEU	0	-0.020	-0.004	26.260	0.244	0.244	0.000	0.000	0.000	0.000
19	A	24	ASN	0	0.042	0.016	30.656	0.100	0.100	0.000	0.000	0.000	0.000
20	A	25	GLY	0	0.079	0.021	32.018	-0.204	-0.204	0.000	0.000	0.000	0.000
21	A	26	GLU	-1	-0.893	-0.956	32.804	-8.283	-8.283	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.024	-0.007	33.400	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	28	LEU	0	0.025	0.010	26.666	-0.205	-0.205	0.000	0.000	0.000	0.000
24	A	29	LEU	0	-0.022	-0.001	29.888	-0.316	-0.316	0.000	0.000	0.000	0.000
25	A	30	ASN	0	0.006	0.002	31.317	-0.101	-0.101	0.000	0.000	0.000	0.000
26	A	31	SER	0	0.012	-0.001	29.277	-0.193	-0.193	0.000	0.000	0.000	0.000
27	A	32	ILE	0	-0.044	-0.022	25.992	-0.364	-0.364	0.000	0.000	0.000	0.000
28	A	33	GLN	0	0.046	0.000	27.788	-0.515	-0.515	0.000	0.000	0.000	0.000
29	A	34	GLN	0	-0.051	-0.009	30.424	0.065	0.065	0.000	0.000	0.000	0.000
30	A	35	ALA	0	-0.037	-0.011	25.491	-0.072	-0.072	0.000	0.000	0.000	0.000
31	A	36	GLY	0	-0.051	-0.025	26.128	-0.428	-0.428	0.000	0.000	0.000	0.000
32	A	37	PHE	0	-0.096	-0.048	20.888	-0.393	-0.393	0.000	0.000	0.000	0.000
33	A	38	ILE	0	0.033	0.012	26.015	0.482	0.482	0.000	0.000	0.000	0.000
34	A	39	PHE	0	-0.020	-0.014	26.413	-0.471	-0.471	0.000	0.000	0.000	0.000
35	A	40	GLY	0	0.033	0.005	26.718	0.268	0.268	0.000	0.000	0.000	0.000
36	A	41	ASP	-1	-0.886	-0.936	23.406	-11.877	-11.877	0.000	0.000	0.000	0.000
37	A	42	MET	0	-0.049	-0.042	21.547	-0.266	-0.266	0.000	0.000	0.000	0.000
38	A	43	ASN	0	0.010	0.020	24.702	0.041	0.041	0.000	0.000	0.000	0.000
39	A	44	ILE	0	0.000	0.003	20.194	-0.078	-0.078	0.000	0.000	0.000	0.000
40	A	45	TYR	0	0.036	0.021	23.639	0.353	0.353	0.000	0.000	0.000	0.000
41	A	46	HIS	1	0.822	0.894	20.193	12.791	12.791	0.000	0.000	0.000	0.000
42	A	47	ARG	1	0.996	1.036	21.136	13.131	13.131	0.000	0.000	0.000	0.000
43	A	48	HIS	0	0.039	0.014	21.597	-0.640	-0.640	0.000	0.000	0.000	0.000
44	A	49	LEU	0	-0.018	-0.010	22.886	0.155	0.155	0.000	0.000	0.000	0.000
45	A	50	SER	0	-0.049	-0.051	24.696	0.031	0.031	0.000	0.000	0.000	0.000
46	A	51	PRO	0	0.002	-0.007	28.174	-0.165	-0.165	0.000	0.000	0.000	0.000
47	A	52	ASP	-1	-0.832	-0.856	30.824	-9.837	-9.837	0.000	0.000	0.000	0.000
48	A	53	GLY	0	0.002	-0.002	27.841	0.058	0.058	0.000	0.000	0.000	0.000
49	A	54	SER	0	-0.041	-0.028	27.953	-0.227	-0.227	0.000	0.000	0.000	0.000
50	A	55	GLY	0	-0.006	-0.007	25.296	-0.226	-0.226	0.000	0.000	0.000	0.000
51	A	56	PRO	0	-0.025	-0.020	19.623	-0.044	-0.044	0.000	0.000	0.000	0.000
52	A	57	ALA	0	0.007	0.009	19.489	0.144	0.144	0.000	0.000	0.000	0.000
53	A	58	LEU	0	-0.045	-0.035	17.923	-0.777	-0.777	0.000	0.000	0.000	0.000
54	A	59	PHE	0	0.011	-0.015	15.935	-1.245	-1.245	0.000	0.000	0.000	0.000
55	A	60	SER	0	-0.030	-0.007	16.901	1.372	1.372	0.000	0.000	0.000	0.000
56	A	61	LEU	0	0.007	0.012	18.180	-0.875	-0.875	0.000	0.000	0.000	0.000
57	A	62	ALA	0	0.036	0.018	19.709	0.633	0.633	0.000	0.000	0.000	0.000
58	A	63	ASN	0	0.056	0.030	21.443	-0.346	-0.346	0.000	0.000	0.000	0.000
59	A	64	MET	0	-0.058	-0.008	19.583	-0.300	-0.300	0.000	0.000	0.000	0.000
60	A	65	VAL	0	-0.041	0.004	22.899	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	66	LYS	1	0.956	0.979	23.674	11.617	11.617	0.000	0.000	0.000	0.000
62	A	67	PRO	0	-0.020	-0.024	25.021	0.391	0.391	0.000	0.000	0.000	0.000
63	A	68	GLY	0	0.033	0.009	22.714	-0.411	-0.411	0.000	0.000	0.000	0.000
64	A	69	THR	0	-0.036	-0.001	23.676	-0.302	-0.302	0.000	0.000	0.000	0.000
65	A	70	PHE	0	-0.011	-0.020	24.170	0.001	0.001	0.000	0.000	0.000	0.000
66	A	71	ASP	-1	-0.854	-0.922	28.892	-8.913	-8.913	0.000	0.000	0.000	0.000
67	A	72	PRO	0	-0.068	-0.048	31.175	0.097	0.097	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.927	-0.954	33.482	-8.008	-8.008	0.000	0.000	0.000	0.000
69	A	74	MET	0	-0.084	-0.025	34.044	0.183	0.183	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.913	0.944	36.709	7.966	7.966	0.000	0.000	0.000	0.000
71	A	76	ASP	-1	-0.960	-0.974	38.502	-7.875	-7.875	0.000	0.000	0.000	0.000
72	A	77	PHE	0	0.010	0.034	30.901	-0.106	-0.106	0.000	0.000	0.000	0.000
73	A	78	THR	0	-0.047	-0.053	32.417	0.092	0.092	0.000	0.000	0.000	0.000
74	A	79	THR	0	0.019	-0.001	26.589	-0.175	-0.175	0.000	0.000	0.000	0.000
75	A	80	PRO	0	0.011	0.008	24.958	-0.047	-0.047	0.000	0.000	0.000	0.000
76	A	81	GLY	0	0.057	0.008	23.636	-0.278	-0.278	0.000	0.000	0.000	0.000
77	A	82	VAL	0	-0.025	0.002	21.928	0.157	0.157	0.000	0.000	0.000	0.000
78	A	83	THR	0	-0.039	-0.035	16.012	-0.293	-0.293	0.000	0.000	0.000	0.000
79	A	84	ILE	0	-0.007	-0.006	16.984	0.393	0.393	0.000	0.000	0.000	0.000
80	A	85	PHE	0	-0.020	-0.020	12.851	-1.354	-1.354	0.000	0.000	0.000	0.000
81	A	86	MET	0	0.027	0.003	11.511	1.812	1.812	0.000	0.000	0.000	0.000
82	A	87	GLN	0	-0.025	0.010	8.060	-1.411	-1.411	0.000	0.000	0.000	0.000
83	A	88	VAL	0	-0.049	-0.004	6.240	1.583	1.583	0.000	0.000	0.000	0.000
84	A	89	PRO	0	0.021	-0.014	6.779	-2.961	-2.961	0.000	0.000	0.000	0.000
85	A	90	SER	0	0.009	-0.010	9.329	0.960	0.960	0.000	0.000	0.000	0.000
86	A	91	TYR	0	-0.038	-0.039	13.048	0.451	0.451	0.000	0.000	0.000	0.000
87	A	92	GLY	0	0.034	0.033	13.658	0.793	0.793	0.000	0.000	0.000	0.000
88	A	93	ASP	-1	-0.885	-0.936	14.690	-15.718	-15.718	0.000	0.000	0.000	0.000
89	A	94	GLU	-1	-0.753	-0.891	10.041	-22.089	-22.089	0.000	0.000	0.000	0.000
90	A	95	LEU	0	-0.017	-0.012	11.524	-0.053	-0.053	0.000	0.000	0.000	0.000
91	A	96	GLN	0	-0.070	-0.032	14.107	1.211	1.211	0.000	0.000	0.000	0.000
92	A	97	LEU	0	0.049	0.026	15.253	0.621	0.621	0.000	0.000	0.000	0.000
93	A	98	PHE	0	0.016	0.010	12.792	0.249	0.249	0.000	0.000	0.000	0.000
94	A	99	LYS	1	0.929	0.965	14.886	14.907	14.907	0.000	0.000	0.000	0.000
95	A	100	LEU	0	0.011	0.008	17.944	0.599	0.599	0.000	0.000	0.000	0.000
96	A	101	MET	0	-0.010	0.018	13.224	0.505	0.505	0.000	0.000	0.000	0.000
97	A	102	LEU	0	0.008	-0.010	17.036	0.420	0.420	0.000	0.000	0.000	0.000
98	A	103	GLN	0	-0.025	-0.022	18.883	0.610	0.610	0.000	0.000	0.000	0.000
99	A	104	SER	0	-0.007	-0.011	21.399	0.772	0.772	0.000	0.000	0.000	0.000
100	A	105	ALA	0	-0.016	-0.007	19.748	0.459	0.459	0.000	0.000	0.000	0.000
101	A	106	GLN	0	-0.080	-0.057	21.898	-0.233	-0.233	0.000	0.000	0.000	0.000
102	A	107	HIS	0	0.031	0.016	24.247	0.437	0.437	0.000	0.000	0.000	0.000
103	A	108	ILE	0	0.027	0.017	23.741	0.315	0.315	0.000	0.000	0.000	0.000
104	A	109	ALA	0	-0.039	-0.026	24.341	0.350	0.350	0.000	0.000	0.000	0.000
105	A	110	ASP	-1	-0.862	-0.921	26.422	-11.245	-11.245	0.000	0.000	0.000	0.000
106	A	111	GLU	-1	-0.964	-0.985	29.469	-9.932	-9.932	0.000	0.000	0.000	0.000
107	A	112	VAL	0	-0.078	-0.038	27.758	0.344	0.344	0.000	0.000	0.000	0.000
108	A	113	GLY	0	-0.010	0.009	30.567	0.166	0.166	0.000	0.000	0.000	0.000
109	A	114	GLY	0	-0.039	-0.021	26.689	0.034	0.034	0.000	0.000	0.000	0.000
110	A	115	VAL	0	-0.043	-0.027	22.278	-0.010	-0.010	0.000	0.000	0.000	0.000
111	A	116	VAL	0	0.031	0.021	18.652	-0.388	-0.388	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.070	-0.037	17.495	-0.090	-0.090	0.000	0.000	0.000	0.000
113	A	118	ASP	-1	-0.732	-0.881	12.484	-23.084	-23.084	0.000	0.000	0.000	0.000
114	A	119	ASP	-1	-0.850	-0.932	8.422	-30.646	-30.646	0.000	0.000	0.000	0.000
115	A	120	GLN	0	-0.113	-0.052	8.819	1.645	1.645	0.000	0.000	0.000	0.000
116	A	121	ARG	1	0.913	0.955	12.569	18.630	18.630	0.000	0.000	0.000	0.000
117	A	122	ARG	1	0.884	0.937	10.895	24.350	24.350	0.000	0.000	0.000	0.000
118	A	123	MET	0	0.037	0.021	16.767	-0.203	-0.203	0.000	0.000	0.000	0.000
119	A	124	MET	0	0.000	0.020	14.596	-1.192	-1.192	0.000	0.000	0.000	0.000
120	A	125	THR	0	0.047	0.029	15.446	0.584	0.584	0.000	0.000	0.000	0.000
121	A	126	PRO	0	0.035	-0.005	16.276	-0.943	-0.943	0.000	0.000	0.000	0.000
122	A	127	GLN	0	-0.019	-0.001	11.494	1.229	1.229	0.000	0.000	0.000	0.000
123	A	128	LYS	1	0.904	0.968	8.392	30.082	30.082	0.000	0.000	0.000	0.000
124	A	129	LEU	0	0.010	0.010	11.789	-1.726	-1.726	0.000	0.000	0.000	0.000
125	A	130	ARG	1	0.791	0.869	12.307	22.434	22.434	0.000	0.000	0.000	0.000
126	A	131	GLU	-1	-0.859	-0.936	8.002	-31.351	-31.351	0.000	0.000	0.000	0.000
127	A	132	TYR	0	-0.023	-0.041	7.645	-3.916	-3.916	0.000	0.000	0.000	0.000
128	A	133	GLN	0	0.014	0.004	8.717	-1.684	-1.684	0.000	0.000	0.000	0.000
129	A	134	ASP	-1	-0.780	-0.894	7.630	-28.277	-28.277	0.000	0.000	0.000	0.000
130	A	135	ILE	0	0.032	0.035	2.887	-3.859	-2.455	0.356	-0.332	-1.429	0.001
131	A	136	ILE	0	-0.003	0.002	4.800	-2.354	-2.227	-0.001	-0.003	-0.123	0.000
132	A	137	ARG	1	0.833	0.896	7.374	26.984	26.984	0.000	0.000	0.000	0.000
133	A	138	GLU	-1	-0.855	-0.917	2.163	-114.922	-108.212	9.543	-8.028	-8.225	-0.107
134	A	139	VAL	0	-0.009	0.002	2.688	0.463	1.181	0.258	-0.200	-0.776	-0.001
135	A	140	LYS	1	0.809	0.902	4.808	26.828	26.850	-0.001	-0.006	-0.015	0.000
136	A	141	ASP	-1	-0.942	-0.969	7.496	-25.136	-25.136	0.000	0.000	0.000	0.000
137	A	142	ALA	0	-0.007	0.007	3.735	2.120	2.325	0.001	-0.047	-0.159	0.000
138	A	143	ASN	0	-0.141	-0.077	5.670	3.693	3.693	0.000	0.000	0.000	0.000
139	A	144	ALA	0	-0.035	-0.001	8.594	2.217	2.217	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ARG)