FMO DATABASE

FMODB ID: V5KN1

Calculation Name: 3SOK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SOK

Chain ID: A

ChEMBL ID:

UniProt ID: P02975

Base Structure: X-ray

Registration Date: 2023-06-22

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	150
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1199766.986963
FMO2-HF: Nuclear repulsion	1143672.20046
FMO2-HF: Total energy	-56094.786503
FMO2-MP2: Total energy	-56259.820254

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:1:PHE)

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

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.
-11.604	-4.237	10.123	-6.496	-10.994	-0.028

Interaction energy analysis for fragmet #1(A:1:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / 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	3	LEU	0	0.058	0.020	2.357	-5.336	-2.633	2.050	-2.010	-2.744	-0.016
4	A	4	ILE	0	0.058	0.017	4.408	0.407	0.572	-0.001	-0.005	-0.158	0.000
5	A	5	GLU	-1	-0.841	-0.913	2.314	-5.475	-3.087	3.424	-2.766	-3.046	-0.027
6	A	6	LEU	0	0.004	0.008	2.283	-2.168	-0.285	4.644	-1.646	-4.881	0.015
7	A	7	MET	0	-0.048	-0.034	4.130	0.323	0.551	0.006	-0.069	-0.165	0.000
8	A	8	ILE	0	0.017	0.007	7.350	0.262	0.262	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.005	-0.004	5.352	0.168	0.168	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.004	-0.011	7.167	0.077	0.077	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.022	0.004	9.756	0.005	0.005	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.033	-0.009	11.375	0.040	0.040	0.000	0.000	0.000	0.000
13	A	13	ILE	0	0.008	0.000	10.120	0.021	0.021	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.005	0.009	13.448	0.007	0.007	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.013	0.003	15.519	0.003	0.003	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.029	-0.013	15.066	0.009	0.009	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.017	0.009	17.565	0.007	0.007	0.000	0.000	0.000	0.000
18	A	18	ALA	0	-0.015	0.005	19.324	0.003	0.003	0.000	0.000	0.000	0.000
19	A	19	PHE	0	-0.013	-0.007	21.786	0.003	0.003	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.000	0.001	20.912	0.004	0.004	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.006	-0.001	19.216	0.004	0.004	0.000	0.000	0.000	0.000
22	A	22	PRO	0	-0.008	-0.005	23.375	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.049	0.035	26.255	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.013	-0.012	24.221	0.004	0.004	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.001	-0.021	25.755	0.004	0.004	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.800	-0.897	28.327	-0.023	-0.023	0.000	0.000	0.000	0.000
27	A	27	TYR	0	-0.058	-0.033	28.249	0.002	0.002	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.006	0.014	27.507	0.002	0.002	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.029	-0.017	30.755	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.984	1.000	32.358	0.014	0.014	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.051	-0.020	32.955	0.001	0.001	0.000	0.000	0.000	0.000
32	A	32	GLN	0	0.032	0.010	32.179	0.000	0.000	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.031	0.018	36.236	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.007	0.014	38.546	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.749	-0.860	39.791	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.014	0.002	41.508	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.000	0.004	43.941	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.006	0.009	43.144	0.001	0.001	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.014	-0.009	44.499	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.027	0.014	47.444	0.000	0.000	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.906	-0.964	48.652	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.020	-0.002	49.790	0.000	0.000	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.031	-0.018	51.360	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.887	0.957	52.694	0.004	0.004	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.017	0.003	55.986	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.928	0.962	53.227	0.005	0.005	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.027	0.000	56.080	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.005	-0.012	59.939	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.880	-0.938	62.077	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	50	HIS	1	0.739	0.865	59.718	0.005	0.005	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.024	-0.002	63.077	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.980	-0.964	65.913	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.063	-0.030	68.070	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.123	-0.060	69.088	0.000	0.000	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.918	-0.960	65.814	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	56	CYS	0	-0.068	-0.013	59.495	0.000	0.000	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.909	0.952	59.376	0.008	0.008	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.076	0.019	61.627	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.939	-0.955	61.801	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.059	-0.037	60.555	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	ASN	0	0.009	-0.005	62.623	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	PRO	0	-0.021	-0.020	64.800	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.007	-0.005	65.821	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	SER	0	0.010	0.005	66.619	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.012	0.023	63.713	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.020	0.004	62.078	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.000	0.010	56.614	0.000	0.000	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.048	0.034	58.693	0.000	0.000	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.038	0.006	57.185	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.855	-0.905	52.325	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.913	-0.963	49.653	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.905	0.977	45.305	0.008	0.008	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.065	0.043	43.691	0.001	0.001	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.878	0.930	34.793	0.007	0.007	0.000	0.000	0.000	0.000
75	A	75	TYR	0	-0.057	-0.072	34.342	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.014	0.010	39.843	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.008	0.024	43.472	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.016	-0.003	47.136	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.023	0.003	49.529	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.041	-0.013	53.132	0.000	0.000	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.900	-0.961	56.194	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	82	GLY	0	-0.064	-0.035	58.114	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.910	-0.941	60.600	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.003	-0.024	64.288	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.003	-0.007	65.571	0.000	0.000	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.950	0.961	67.618	0.005	0.005	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.939	-0.951	70.523	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.039	0.001	66.132	0.000	0.000	0.000	0.000	0.000	0.000
89	A	89	LYS	1	0.920	0.954	68.092	0.004	0.004	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.112	-0.075	66.830	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.003	-0.020	62.312	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	ASP	-1	-0.918	-0.951	59.823	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	93	GLU	-1	-0.825	-0.896	61.632	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.918	0.945	57.833	0.009	0.009	0.000	0.000	0.000	0.000
95	A	95	ASN	0	0.045	0.006	60.499	0.000	0.000	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.039	0.025	61.808	0.000	0.000	0.000	0.000	0.000	0.000
97	A	98	LYS	1	0.909	0.950	55.227	0.010	0.010	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.022	-0.002	50.646	0.000	0.000	0.000	0.000	0.000	0.000
99	A	100	VAL	0	-0.002	-0.007	50.545	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	101	ILE	0	0.003	0.015	44.952	0.000	0.000	0.000	0.000	0.000	0.000
101	A	102	THR	0	-0.009	-0.006	45.424	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	103	TYR	0	0.015	-0.028	40.425	0.001	0.001	0.000	0.000	0.000	0.000
103	A	104	GLY	0	-0.008	-0.007	40.151	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	105	GLN	0	-0.013	-0.007	41.088	0.000	0.000	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.041	0.036	42.427	0.001	0.001	0.000	0.000	0.000	0.000
106	A	107	THR	0	-0.042	-0.054	41.356	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	108	ALA	0	-0.091	-0.035	36.544	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	GLY	0	0.011	0.013	37.720	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.887	-0.963	37.679	-0.019	-0.019	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.866	0.949	33.334	0.015	0.015	0.000	0.000	0.000	0.000
111	A	112	ILE	0	-0.028	-0.009	33.720	0.002	0.002	0.000	0.000	0.000	0.000
112	A	113	SER	0	-0.003	0.000	31.990	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	114	LYS	1	1.017	0.988	30.205	0.032	0.032	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.074	-0.046	31.369	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	ILE	0	-0.005	0.006	35.023	0.000	0.000	0.000	0.000	0.000	0.000
116	A	117	VAL	0	-0.002	0.010	36.769	0.001	0.001	0.000	0.000	0.000	0.000
117	A	118	GLY	0	-0.011	-0.011	38.878	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	119	LYS	1	0.896	0.975	40.032	0.021	0.021	0.000	0.000	0.000	0.000
119	A	120	LYS	1	0.976	0.983	43.091	0.014	0.014	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.004	0.009	44.448	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	122	VAL	0	0.009	0.013	46.911	0.001	0.001	0.000	0.000	0.000	0.000
122	A	123	LEU	0	-0.024	-0.016	48.160	0.000	0.000	0.000	0.000	0.000	0.000
123	A	124	ASP	-1	-0.798	-0.888	51.980	-0.009	-0.009	0.000	0.000	0.000	0.000
124	A	125	GLN	0	0.000	-0.008	55.282	0.000	0.000	0.000	0.000	0.000	0.000
125	A	126	PHE	0	-0.041	-0.018	55.610	0.000	0.000	0.000	0.000	0.000	0.000
126	A	127	VAL	0	0.041	0.027	59.697	0.000	0.000	0.000	0.000	0.000	0.000
127	A	128	ASN	0	-0.005	-0.003	58.217	0.000	0.000	0.000	0.000	0.000	0.000
128	A	129	GLY	0	0.020	0.018	58.650	0.000	0.000	0.000	0.000	0.000	0.000
129	A	130	SER	0	-0.075	-0.048	55.158	0.000	0.000	0.000	0.000	0.000	0.000
130	A	131	TYR	0	-0.010	-0.023	51.105	0.000	0.000	0.000	0.000	0.000	0.000
131	A	132	LYS	1	0.892	0.952	51.417	0.007	0.007	0.000	0.000	0.000	0.000
132	A	133	TYR	0	-0.004	-0.017	48.134	0.000	0.000	0.000	0.000	0.000	0.000
133	A	134	ASN	0	-0.004	0.005	50.658	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.937	-0.969	50.239	-0.014	-0.014	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.017	-0.004	50.748	0.000	0.000	0.000	0.000	0.000	0.000
136	A	137	GLU	-1	-0.859	-0.935	52.133	-0.011	-0.011	0.000	0.000	0.000	0.000
137	A	138	THR	0	-0.120	-0.065	46.218	0.000	0.000	0.000	0.000	0.000	0.000
138	A	139	ASP	-1	-0.861	-0.932	44.638	-0.019	-0.019	0.000	0.000	0.000	0.000
139	A	140	LEU	0	-0.121	-0.056	39.946	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-0.881	-0.952	38.308	-0.023	-0.023	0.000	0.000	0.000	0.000
141	A	142	LEU	0	0.109	0.046	41.101	0.001	0.001	0.000	0.000	0.000	0.000
142	A	143	LYS	1	0.791	0.890	33.720	0.027	0.027	0.000	0.000	0.000	0.000
143	A	144	PHE	0	-0.073	-0.050	34.210	0.001	0.001	0.000	0.000	0.000	0.000
144	A	145	ILE	0	0.027	0.039	38.793	0.001	0.001	0.000	0.000	0.000	0.000
145	A	146	PRO	0	0.023	0.016	41.523	0.000	0.000	0.000	0.000	0.000	0.000
146	A	147	ASN	0	0.042	-0.019	40.317	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	148	ALA	0	-0.013	0.005	44.025	0.000	0.000	0.000	0.000	0.000	0.000
148	A	149	VAL	0	0.033	0.029	46.438	0.000	0.000	0.000	0.000	0.000	0.000
149	A	150	LYS	1	0.878	0.955	41.600	0.012	0.012	0.000	0.000	0.000	0.000
150	A	151	ASN	0	-0.026	0.001	48.276	0.000	0.000	0.000	0.000	0.000	0.000

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