FMO DATABASE

FMODB ID: 1NK3Z

Calculation Name: 3SO6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SO6

Chain ID: A

ChEMBL ID:

UniProt ID: D3ZAR1

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	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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1221512.516484
FMO2-HF: Nuclear repulsion	1167647.3951
FMO2-HF: Total energy	-53865.121385
FMO2-MP2: Total energy	-54020.156017

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:42:MET)

Summations of interaction energy for fragment #1(A:42:MET)

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.
-19.485	-9.982	20.528	-8.337	-21.689	-0.048

Interaction energy analysis for fragmet #1(A:42:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.009

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	44	GLY	0	-0.022	-0.016	2.541	-4.862	-2.581	1.576	-1.710	-2.147	-0.011
4	A	45	MET	0	0.034	0.030	3.157	0.939	1.578	0.018	-0.107	-0.550	0.000
5	A	46	VAL	0	0.013	-0.001	5.108	0.234	0.284	-0.001	-0.001	-0.047	0.000
6	A	47	PHE	0	0.001	-0.005	5.664	0.141	0.141	0.000	0.000	0.000	0.000
7	A	48	SER	0	-0.011	-0.003	10.702	0.057	0.057	0.000	0.000	0.000	0.000
8	A	49	LEU	0	-0.060	-0.035	11.731	0.032	0.032	0.000	0.000	0.000	0.000
9	A	50	LYS	1	0.932	0.959	15.916	0.257	0.257	0.000	0.000	0.000	0.000
10	A	51	TYR	0	0.005	0.001	17.264	0.002	0.002	0.000	0.000	0.000	0.000
11	A	52	LEU	0	-0.058	-0.045	18.821	0.017	0.017	0.000	0.000	0.000	0.000
12	A	53	GLY	0	0.019	0.019	20.132	0.017	0.017	0.000	0.000	0.000	0.000
13	A	54	MET	0	0.007	-0.004	19.842	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	55	THR	0	-0.065	-0.022	21.443	0.008	0.008	0.000	0.000	0.000	0.000
15	A	56	LEU	0	0.077	0.052	22.086	0.000	0.000	0.000	0.000	0.000	0.000
16	A	57	VAL	0	-0.034	-0.028	20.352	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	58	GLU	-1	-0.877	-0.937	23.745	0.006	0.006	0.000	0.000	0.000	0.000
18	A	59	ARG	1	0.875	0.915	23.252	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	60	PRO	0	0.054	0.041	18.501	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	61	LYS	1	0.886	0.920	14.778	-0.219	-0.219	0.000	0.000	0.000	0.000
21	A	62	GLY	0	0.076	0.047	18.321	0.000	0.000	0.000	0.000	0.000	0.000
22	A	63	GLU	-1	-0.814	-0.892	19.484	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	64	GLU	-1	-0.726	-0.856	20.438	0.002	0.002	0.000	0.000	0.000	0.000
24	A	65	LEU	0	-0.061	-0.013	20.999	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	66	SER	0	-0.023	-0.016	17.640	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	67	ALA	0	0.052	0.028	19.620	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	68	ALA	0	-0.027	-0.016	22.151	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	69	ALA	0	-0.006	0.001	20.788	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	70	VAL	0	0.035	0.009	18.585	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	71	LYS	1	0.892	0.945	21.536	0.055	0.055	0.000	0.000	0.000	0.000
31	A	72	ARG	1	0.919	0.959	25.091	0.038	0.038	0.000	0.000	0.000	0.000
32	A	73	ILE	0	0.000	0.026	20.167	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	74	VAL	0	-0.007	-0.017	22.196	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	75	ALA	0	-0.029	-0.009	24.684	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	76	THR	0	0.008	-0.011	26.741	0.003	0.003	0.000	0.000	0.000	0.000
36	A	77	ALA	0	-0.002	-0.003	24.627	0.000	0.000	0.000	0.000	0.000	0.000
37	A	78	LYS	1	0.865	0.945	26.451	0.107	0.107	0.000	0.000	0.000	0.000
38	A	79	ALA	0	0.022	0.019	29.302	0.002	0.002	0.000	0.000	0.000	0.000
39	A	80	SER	0	-0.048	-0.027	28.979	0.003	0.003	0.000	0.000	0.000	0.000
40	A	81	GLY	0	0.027	0.018	31.185	0.002	0.002	0.000	0.000	0.000	0.000
41	A	82	LYS	1	0.927	0.970	29.722	0.085	0.085	0.000	0.000	0.000	0.000
42	A	83	LYS	1	0.904	0.943	27.509	0.115	0.115	0.000	0.000	0.000	0.000
43	A	84	LEU	0	0.014	0.009	21.777	0.001	0.001	0.000	0.000	0.000	0.000
44	A	85	GLN	0	0.005	0.002	21.088	0.001	0.001	0.000	0.000	0.000	0.000
45	A	86	LYS	1	0.922	0.955	19.789	0.188	0.188	0.000	0.000	0.000	0.000
46	A	87	VAL	0	0.043	0.030	14.827	0.013	0.013	0.000	0.000	0.000	0.000
47	A	88	THR	0	-0.004	0.002	12.033	-0.038	-0.038	0.000	0.000	0.000	0.000
48	A	89	LEU	0	0.007	0.015	8.799	0.042	0.042	0.000	0.000	0.000	0.000
49	A	90	LYS	1	0.812	0.886	6.526	1.520	1.520	0.000	0.000	0.000	0.000
50	A	91	VAL	0	0.003	0.012	2.565	-0.156	0.350	0.282	-0.160	-0.627	0.001
51	A	92	SER	0	-0.005	-0.010	2.487	-4.266	-2.729	1.538	-1.289	-1.786	-0.010
52	A	93	PRO	0	0.053	0.010	2.383	-0.627	-1.737	6.725	-1.219	-4.395	0.006
53	A	94	ARG	1	0.903	0.957	4.940	-1.205	-1.009	0.009	-0.104	-0.101	0.001
54	A	95	GLY	0	0.028	0.019	6.863	-0.140	-0.140	0.000	0.000	0.000	0.000
55	A	96	ILE	0	-0.055	-0.016	6.554	-0.171	-0.171	0.000	0.000	0.000	0.000
56	A	97	ILE	0	-0.005	0.004	8.352	0.096	0.096	0.000	0.000	0.000	0.000
57	A	98	LEU	0	0.007	0.006	10.525	-0.124	-0.124	0.000	0.000	0.000	0.000
58	A	99	THR	0	0.025	0.004	13.307	0.039	0.039	0.000	0.000	0.000	0.000
59	A	100	ASP	-1	-0.727	-0.841	15.732	-0.230	-0.230	0.000	0.000	0.000	0.000
60	A	101	SER	0	-0.039	-0.039	17.529	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	102	LEU	0	-0.070	-0.022	18.953	0.003	0.003	0.000	0.000	0.000	0.000
62	A	103	THR	0	-0.007	-0.024	21.915	0.011	0.011	0.000	0.000	0.000	0.000
63	A	104	SER	0	-0.026	-0.008	18.531	0.002	0.002	0.000	0.000	0.000	0.000
64	A	105	GLN	0	-0.021	0.001	18.544	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	106	LEU	0	-0.025	-0.018	14.754	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	107	ILE	0	-0.028	-0.010	16.973	0.024	0.024	0.000	0.000	0.000	0.000
67	A	108	GLU	-1	-0.780	-0.892	15.351	-0.045	-0.045	0.000	0.000	0.000	0.000
68	A	109	ASN	0	-0.050	-0.029	11.958	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	110	VAL	0	0.034	0.038	11.248	0.052	0.052	0.000	0.000	0.000	0.000
70	A	111	SER	0	0.020	0.005	10.650	0.063	0.063	0.000	0.000	0.000	0.000
71	A	112	ILE	0	0.040	-0.010	6.635	-0.073	-0.073	0.000	0.000	0.000	0.000
72	A	113	TYR	0	-0.008	-0.007	9.991	-0.024	-0.024	0.000	0.000	0.000	0.000
73	A	114	ARG	1	0.763	0.874	13.383	-0.056	-0.056	0.000	0.000	0.000	0.000
74	A	115	ILE	0	-0.066	-0.023	8.686	-0.055	-0.055	0.000	0.000	0.000	0.000
75	A	116	SER	0	0.003	-0.008	12.164	0.066	0.066	0.000	0.000	0.000	0.000
76	A	117	TYR	0	-0.010	-0.009	13.164	0.037	0.037	0.000	0.000	0.000	0.000
77	A	118	CYS	0	-0.009	-0.004	9.808	-0.026	-0.026	0.000	0.000	0.000	0.000
78	A	119	THR	0	-0.023	-0.008	12.006	0.027	0.027	0.000	0.000	0.000	0.000
79	A	120	ALA	0	0.032	0.019	13.444	-0.053	-0.053	0.000	0.000	0.000	0.000
80	A	121	ASP	-1	-0.805	-0.915	14.885	-0.075	-0.075	0.000	0.000	0.000	0.000
81	A	122	LYS	1	0.846	0.910	18.476	0.030	0.030	0.000	0.000	0.000	0.000
82	A	123	MET	0	-0.045	-0.008	21.385	0.008	0.008	0.000	0.000	0.000	0.000
83	A	124	HIS	0	-0.049	-0.036	21.574	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	125	ASP	-1	-0.726	-0.836	19.890	-0.187	-0.187	0.000	0.000	0.000	0.000
85	A	126	LYS	1	0.853	0.929	18.477	0.175	0.175	0.000	0.000	0.000	0.000
86	A	127	VAL	0	-0.027	-0.012	17.358	-0.031	-0.031	0.000	0.000	0.000	0.000
87	A	128	PHE	0	0.034	0.027	9.485	-0.011	-0.011	0.000	0.000	0.000	0.000
88	A	129	ALA	0	-0.007	-0.015	13.547	0.013	0.013	0.000	0.000	0.000	0.000
89	A	130	TYR	0	0.033	0.016	11.257	-0.022	-0.022	0.000	0.000	0.000	0.000
90	A	131	ILE	0	0.000	-0.002	13.270	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	132	ALA	0	0.017	0.003	13.860	0.033	0.033	0.000	0.000	0.000	0.000
92	A	133	GLN	0	0.022	0.036	15.704	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	134	SER	0	0.008	-0.006	17.914	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	135	GLN	0	-0.030	-0.013	17.570	0.025	0.025	0.000	0.000	0.000	0.000
95	A	136	GLN	0	0.022	0.009	20.706	0.012	0.012	0.000	0.000	0.000	0.000
96	A	137	ASN	0	-0.001	0.009	23.885	0.000	0.000	0.000	0.000	0.000	0.000
97	A	138	GLU	-1	-0.877	-0.942	23.535	0.055	0.055	0.000	0.000	0.000	0.000
98	A	139	SER	0	-0.060	-0.026	23.874	0.002	0.002	0.000	0.000	0.000	0.000
99	A	140	LEU	0	0.016	0.000	19.947	0.007	0.007	0.000	0.000	0.000	0.000
100	A	141	GLU	-1	-0.802	-0.878	18.836	-0.048	-0.048	0.000	0.000	0.000	0.000
101	A	142	CYS	0	-0.098	-0.051	17.139	0.000	0.000	0.000	0.000	0.000	0.000
102	A	143	HIS	0	0.059	0.027	15.536	-0.029	-0.029	0.000	0.000	0.000	0.000
103	A	144	ALA	0	0.020	-0.001	15.753	-0.013	-0.013	0.000	0.000	0.000	0.000
104	A	145	PHE	0	0.036	0.008	13.812	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	146	LEU	0	-0.016	0.003	16.193	-0.008	-0.008	0.000	0.000	0.000	0.000
106	A	147	CYS	0	-0.004	0.020	14.623	-0.043	-0.043	0.000	0.000	0.000	0.000
107	A	148	THR	0	0.018	-0.010	17.073	0.035	0.035	0.000	0.000	0.000	0.000
108	A	149	LYS	1	0.890	0.913	17.894	0.314	0.314	0.000	0.000	0.000	0.000
109	A	150	ARG	1	0.918	0.929	16.958	0.136	0.136	0.000	0.000	0.000	0.000
110	A	151	LYN	0	0.115	0.074	15.345	-0.008	-0.008	0.000	0.000	0.000	0.000
111	A	152	VAL	0	-0.034	-0.008	12.679	-0.050	-0.050	0.000	0.000	0.000	0.000
112	A	153	ALA	0	0.068	0.032	11.772	-0.087	-0.087	0.000	0.000	0.000	0.000
113	A	154	GLN	0	0.017	0.006	11.590	-0.040	-0.040	0.000	0.000	0.000	0.000
114	A	155	ALA	0	0.025	0.021	9.264	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	156	VAL	0	-0.003	0.019	7.369	-0.228	-0.228	0.000	0.000	0.000	0.000
116	A	157	THR	0	0.020	-0.013	6.598	-0.138	-0.138	0.000	0.000	0.000	0.000
117	A	158	LEU	0	-0.004	-0.004	7.510	0.101	0.101	0.000	0.000	0.000	0.000
118	A	159	THR	0	-0.031	-0.026	2.374	0.121	-0.133	1.859	-0.320	-1.284	0.000
119	A	160	VAL	0	-0.009	-0.012	2.538	-2.404	-1.400	1.068	-0.796	-1.276	-0.013
120	A	161	ALA	0	0.010	0.010	4.845	0.540	0.626	-0.001	-0.003	-0.082	0.000
121	A	162	GLN	0	-0.015	-0.009	2.550	-5.579	-3.215	3.767	-1.881	-4.251	-0.016
122	A	163	ALA	0	0.021	0.003	2.378	-0.129	1.613	2.921	-1.823	-2.840	-0.005
123	A	164	PHE	0	0.002	-0.015	3.695	0.663	-0.710	0.054	1.675	-0.355	-0.001
124	A	165	LYS	1	0.847	0.910	6.692	-0.786	-0.786	0.000	0.000	0.000	0.000
125	A	166	VAL	0	0.036	0.010	2.521	-1.930	-0.566	0.711	-0.472	-1.603	0.001
126	A	167	ALA	0	-0.013	-0.003	5.642	-0.627	-0.627	0.000	0.000	0.000	0.000
127	A	168	PHE	0	-0.007	0.002	7.500	-0.373	-0.373	0.000	0.000	0.000	0.000
128	A	169	GLU	-1	-0.786	-0.878	7.809	0.492	0.492	0.000	0.000	0.000	0.000
129	A	170	PHE	0	-0.014	-0.018	4.101	-0.287	-0.148	-0.001	-0.012	-0.126	0.000
130	A	171	TRP	0	-0.020	-0.004	9.520	-0.074	-0.074	0.000	0.000	0.000	0.000
131	A	172	GLN	0	0.003	0.001	12.681	-0.042	-0.042	0.000	0.000	0.000	0.000
132	A	173	VAL	0	-0.055	-0.014	11.292	-0.041	-0.041	0.000	0.000	0.000	0.000
133	A	174	SER	0	-0.031	-0.011	14.165	-0.029	-0.029	0.000	0.000	0.000	0.000
134	A	175	LEU	0	-0.024	-0.002	10.691	-0.027	-0.027	0.000	0.000	0.000	0.000
135	A	176	VAL	0	0.006	-0.011	11.524	0.044	0.044	0.000	0.000	0.000	0.000
136	A	177	PRO	0	0.016	0.017	6.869	-0.042	-0.042	0.000	0.000	0.000	0.000
137	A	178	ARG	1	0.957	0.988	3.759	-0.573	-0.241	0.003	-0.115	-0.219	-0.001

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Interactive mode: IFIE and PIEDA for fragment #1(A:42:MET)