FMO DATABASE

FMODB ID: YV8M2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1218595.922888
FMO2-HF: Nuclear repulsion	1164732.071449
FMO2-HF: Total energy	-53863.851439
FMO2-MP2: Total energy	-54019.113436

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.
-21.734	-9.985	17.896	-8.397	-21.25	-0.045

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 : -0.053 / q_NPA : -0.011

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	-0.039	-0.047	2.478	-5.135	-2.704	1.601	-1.785	-2.248	-0.014
4	A	45	MET	0	-0.040	-0.009	2.915	0.270	1.015	0.096	-0.136	-0.705	0.000
5	A	46	VAL	0	0.027	0.012	5.122	0.335	0.379	-0.001	0.000	-0.042	0.000
6	A	47	PHE	0	-0.011	-0.004	5.942	0.089	0.089	0.000	0.000	0.000	0.000
7	A	48	SER	0	0.009	0.009	10.713	0.083	0.083	0.000	0.000	0.000	0.000
8	A	49	LEU	0	-0.036	-0.017	11.818	0.024	0.024	0.000	0.000	0.000	0.000
9	A	50	LYS	1	0.929	0.960	15.870	0.223	0.223	0.000	0.000	0.000	0.000
10	A	51	TYR	0	-0.005	-0.010	17.671	-0.008	-0.008	0.000	0.000	0.000	0.000
11	A	52	LEU	0	-0.065	-0.046	19.238	0.012	0.012	0.000	0.000	0.000	0.000
12	A	53	GLY	0	0.028	0.015	20.309	0.012	0.012	0.000	0.000	0.000	0.000
13	A	54	MET	0	-0.002	0.012	20.200	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	55	THR	0	-0.061	-0.015	21.767	0.004	0.004	0.000	0.000	0.000	0.000
15	A	56	LEU	0	0.092	0.054	22.386	0.002	0.002	0.000	0.000	0.000	0.000
16	A	57	VAL	0	-0.069	-0.049	20.589	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	58	GLU	-1	-0.858	-0.937	23.904	0.028	0.028	0.000	0.000	0.000	0.000
18	A	59	ARG	1	0.873	0.926	23.610	-0.032	-0.032	0.000	0.000	0.000	0.000
19	A	60	PRO	0	0.054	0.031	18.678	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	61	LYS	1	0.876	0.937	15.391	-0.236	-0.236	0.000	0.000	0.000	0.000
21	A	62	GLY	0	0.078	0.040	18.377	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	63	GLU	-1	-0.926	-0.962	19.625	-0.037	-0.037	0.000	0.000	0.000	0.000
23	A	64	GLU	-1	-0.794	-0.895	20.470	0.021	0.021	0.000	0.000	0.000	0.000
24	A	65	LEU	0	-0.085	-0.026	21.234	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	66	SER	0	0.043	0.002	18.160	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	67	ALA	0	0.007	0.024	20.088	-0.015	-0.015	0.000	0.000	0.000	0.000
27	A	68	ALA	0	-0.024	-0.011	22.391	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	69	ALA	0	-0.002	-0.007	21.193	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	70	VAL	0	0.069	0.032	18.892	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	71	LYS	1	0.914	0.962	21.855	0.040	0.040	0.000	0.000	0.000	0.000
31	A	72	ARG	1	0.893	0.947	25.189	0.017	0.017	0.000	0.000	0.000	0.000
32	A	73	ILE	0	-0.009	0.008	20.540	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	74	VAL	0	-0.017	-0.017	22.671	-0.007	-0.007	0.000	0.000	0.000	0.000
34	A	75	ALA	0	-0.042	-0.018	25.036	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	76	THR	0	0.021	0.009	27.290	0.002	0.002	0.000	0.000	0.000	0.000
36	A	77	ALA	0	0.030	0.017	25.086	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	78	LYS	1	0.879	0.938	27.219	0.086	0.086	0.000	0.000	0.000	0.000
38	A	79	ALA	0	0.004	0.013	29.577	0.001	0.001	0.000	0.000	0.000	0.000
39	A	80	SER	0	-0.039	-0.020	29.180	0.002	0.002	0.000	0.000	0.000	0.000
40	A	81	GLY	0	0.025	0.015	31.641	0.003	0.003	0.000	0.000	0.000	0.000
41	A	82	LYS	1	0.935	0.974	29.736	0.070	0.070	0.000	0.000	0.000	0.000
42	A	83	LYS	1	0.903	0.948	27.397	0.105	0.105	0.000	0.000	0.000	0.000
43	A	84	LEU	0	0.014	0.001	22.225	0.001	0.001	0.000	0.000	0.000	0.000
44	A	85	GLN	0	-0.010	-0.002	21.195	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	86	LYS	1	0.925	0.955	19.758	0.180	0.180	0.000	0.000	0.000	0.000
46	A	87	VAL	0	0.046	0.031	14.823	0.015	0.015	0.000	0.000	0.000	0.000
47	A	88	THR	0	-0.034	-0.015	12.072	-0.044	-0.044	0.000	0.000	0.000	0.000
48	A	89	LEU	0	0.004	0.005	9.188	0.047	0.047	0.000	0.000	0.000	0.000
49	A	90	LYS	1	0.922	0.966	7.067	1.162	1.162	0.000	0.000	0.000	0.000
50	A	91	VAL	0	0.011	0.003	2.545	-0.173	0.274	0.372	-0.141	-0.678	0.001
51	A	92	SER	0	0.005	-0.002	2.860	-3.795	-2.355	0.900	-1.051	-1.289	-0.003
52	A	93	PRO	0	0.069	0.018	2.313	-1.415	-2.176	6.105	-1.208	-4.137	0.009
53	A	94	ARG	1	0.895	0.951	4.904	-1.416	-1.266	0.006	-0.077	-0.079	0.000
54	A	95	GLY	0	0.012	0.012	7.052	-0.243	-0.243	0.000	0.000	0.000	0.000
55	A	96	ILE	0	-0.032	-0.003	6.914	-0.037	-0.037	0.000	0.000	0.000	0.000
56	A	97	ILE	0	-0.020	-0.002	8.830	0.041	0.041	0.000	0.000	0.000	0.000
57	A	98	LEU	0	0.016	0.015	11.115	-0.116	-0.116	0.000	0.000	0.000	0.000
58	A	99	THR	0	0.026	0.006	13.725	0.030	0.030	0.000	0.000	0.000	0.000
59	A	100	ASP	-1	-0.726	-0.825	16.079	-0.191	-0.191	0.000	0.000	0.000	0.000
60	A	101	SER	0	-0.033	-0.050	17.265	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	102	LEU	0	-0.065	-0.015	18.954	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	103	THR	0	0.008	-0.028	22.221	0.003	0.003	0.000	0.000	0.000	0.000
63	A	104	SER	0	-0.050	-0.011	18.501	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	105	GLN	0	0.019	0.014	18.947	0.003	0.003	0.000	0.000	0.000	0.000
65	A	106	LEU	0	-0.061	-0.043	15.493	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	107	ILE	0	-0.017	0.002	17.301	0.013	0.013	0.000	0.000	0.000	0.000
67	A	108	GLU	-1	-0.789	-0.891	16.223	0.026	0.026	0.000	0.000	0.000	0.000
68	A	109	ASN	0	-0.040	-0.013	12.472	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	110	VAL	0	0.013	0.013	11.758	0.033	0.033	0.000	0.000	0.000	0.000
70	A	111	SER	0	0.009	-0.003	11.190	0.105	0.105	0.000	0.000	0.000	0.000
71	A	112	ILE	0	0.068	0.008	6.774	-0.087	-0.087	0.000	0.000	0.000	0.000
72	A	113	TYR	0	-0.022	-0.020	10.390	-0.028	-0.028	0.000	0.000	0.000	0.000
73	A	114	ARG	1	0.781	0.888	13.686	-0.131	-0.131	0.000	0.000	0.000	0.000
74	A	115	ILE	0	-0.031	0.005	9.261	-0.060	-0.060	0.000	0.000	0.000	0.000
75	A	116	SER	0	-0.070	-0.040	12.719	0.061	0.061	0.000	0.000	0.000	0.000
76	A	117	TYR	0	0.054	0.010	13.209	0.034	0.034	0.000	0.000	0.000	0.000
77	A	118	CYS	0	-0.061	-0.025	9.474	-0.051	-0.051	0.000	0.000	0.000	0.000
78	A	119	THR	0	0.003	0.004	11.987	0.012	0.012	0.000	0.000	0.000	0.000
79	A	120	ALA	0	0.040	0.028	13.390	-0.043	-0.043	0.000	0.000	0.000	0.000
80	A	121	ASP	-1	-0.858	-0.941	14.731	-0.060	-0.060	0.000	0.000	0.000	0.000
81	A	122	LYS	1	1.037	1.016	18.403	0.037	0.037	0.000	0.000	0.000	0.000
82	A	123	MET	0	-0.056	-0.024	21.218	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	124	HIS	0	-0.023	-0.019	21.716	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	125	ASP	-1	-0.845	-0.919	19.583	-0.168	-0.168	0.000	0.000	0.000	0.000
85	A	126	LYS	1	0.863	0.927	18.413	0.143	0.143	0.000	0.000	0.000	0.000
86	A	127	VAL	0	-0.031	-0.024	17.404	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	128	PHE	0	0.038	0.031	9.450	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	129	ALA	0	0.015	-0.005	13.778	0.008	0.008	0.000	0.000	0.000	0.000
89	A	130	TYR	0	0.025	0.011	11.339	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	131	ILE	0	0.005	-0.002	13.411	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	132	ALA	0	-0.002	-0.015	14.242	0.044	0.044	0.000	0.000	0.000	0.000
92	A	133	GLN	0	0.036	0.040	16.070	-0.038	-0.038	0.000	0.000	0.000	0.000
93	A	134	SER	0	0.017	0.013	18.294	0.012	0.012	0.000	0.000	0.000	0.000
94	A	135	GLN	0	-0.010	-0.019	19.370	0.006	0.006	0.000	0.000	0.000	0.000
95	A	136	GLN	0	-0.016	-0.015	20.919	0.007	0.007	0.000	0.000	0.000	0.000
96	A	137	ASN	0	0.000	0.007	23.998	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	138	GLU	-1	-0.890	-0.952	23.726	0.077	0.077	0.000	0.000	0.000	0.000
98	A	139	SER	0	-0.049	0.006	24.177	0.000	0.000	0.000	0.000	0.000	0.000
99	A	140	LEU	0	0.022	-0.001	20.280	0.012	0.012	0.000	0.000	0.000	0.000
100	A	141	GLU	-1	-0.819	-0.900	19.208	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	142	CYS	0	-0.114	-0.054	17.371	0.003	0.003	0.000	0.000	0.000	0.000
102	A	143	HIS	0	0.072	0.042	15.604	-0.032	-0.032	0.000	0.000	0.000	0.000
103	A	144	ALA	0	0.008	-0.008	15.757	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	145	PHE	0	0.038	0.012	14.111	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	146	LEU	0	-0.016	-0.008	16.599	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	147	CYS	0	-0.019	0.010	14.625	-0.042	-0.042	0.000	0.000	0.000	0.000
107	A	148	THR	0	0.004	-0.016	17.082	0.028	0.028	0.000	0.000	0.000	0.000
108	A	149	LYS	1	0.920	0.946	17.985	0.294	0.294	0.000	0.000	0.000	0.000
109	A	150	ARG	1	1.076	1.047	17.152	0.161	0.161	0.000	0.000	0.000	0.000
110	A	151	LYN	0	0.045	0.008	15.683	0.002	0.002	0.000	0.000	0.000	0.000
111	A	152	VAL	0	-0.024	-0.003	12.940	-0.048	-0.048	0.000	0.000	0.000	0.000
112	A	153	ALA	0	0.066	0.040	12.087	-0.072	-0.072	0.000	0.000	0.000	0.000
113	A	154	GLN	0	0.007	-0.001	11.837	-0.039	-0.039	0.000	0.000	0.000	0.000
114	A	155	ALA	0	0.012	0.017	9.343	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	156	VAL	0	0.001	0.012	7.587	-0.239	-0.239	0.000	0.000	0.000	0.000
116	A	157	THR	0	0.019	-0.016	6.798	-0.124	-0.124	0.000	0.000	0.000	0.000
117	A	158	LEU	0	0.013	0.011	7.503	0.095	0.095	0.000	0.000	0.000	0.000
118	A	159	THR	0	-0.026	-0.023	2.591	-0.395	-0.063	0.848	-0.201	-0.980	0.000
119	A	160	VAL	0	-0.014	-0.023	2.527	-2.449	-1.475	1.127	-0.808	-1.293	-0.013
120	A	161	ALA	0	0.012	0.022	4.725	0.553	0.652	-0.001	-0.003	-0.095	0.000
121	A	162	GLN	0	0.012	-0.005	2.695	-5.816	-2.427	3.929	-2.249	-5.069	-0.022
122	A	163	ALA	0	0.023	0.011	2.489	0.269	2.154	2.207	-1.566	-2.526	-0.003
123	A	164	PHE	0	-0.002	-0.010	3.662	0.315	-0.765	0.052	1.356	-0.329	-0.001
124	A	165	LYS	1	0.891	0.954	6.858	-0.740	-0.740	0.000	0.000	0.000	0.000
125	A	166	VAL	0	0.037	0.018	2.400	-1.839	-0.489	0.656	-0.492	-1.514	0.001
126	A	167	ALA	0	-0.028	-0.022	5.493	-0.673	-0.673	0.000	0.000	0.000	0.000
127	A	168	PHE	0	-0.012	-0.006	7.707	-0.367	-0.367	0.000	0.000	0.000	0.000
128	A	169	GLU	-1	-0.812	-0.910	8.109	0.391	0.391	0.000	0.000	0.000	0.000
129	A	170	PHE	0	-0.036	-0.032	4.440	-0.240	-0.146	-0.001	-0.005	-0.087	0.000
130	A	171	TRP	0	-0.037	-0.018	9.917	-0.082	-0.082	0.000	0.000	0.000	0.000
131	A	172	GLN	0	-0.001	0.000	12.916	-0.041	-0.041	0.000	0.000	0.000	0.000
132	A	173	VAL	0	-0.041	-0.006	11.746	-0.042	-0.042	0.000	0.000	0.000	0.000
133	A	174	SER	0	-0.032	-0.004	14.610	-0.027	-0.027	0.000	0.000	0.000	0.000
134	A	175	LEU	0	-0.012	0.003	10.669	-0.029	-0.029	0.000	0.000	0.000	0.000
135	A	176	VAL	0	-0.014	-0.019	11.055	0.046	0.046	0.000	0.000	0.000	0.000
136	A	177	PRO	0	0.017	0.022	7.353	-0.035	-0.035	0.000	0.000	0.000	0.000
137	A	178	ARG	1	0.986	0.986	4.275	-0.254	-0.044	0.000	-0.031	-0.179	0.000

Top

Graph

Manual

About

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