FMO DATABASE

FMODB ID: MNN4Z

Calculation Name: 5SV2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5SV2

Chain ID: A

ChEMBL ID:

UniProt ID: P9WF91

Base Structure: X-ray

Registration Date: 2023-09-21

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	135
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1233120.005035
FMO2-HF: Nuclear repulsion	1179572.07556
FMO2-HF: Total energy	-53547.929475
FMO2-MP2: Total energy	-53706.344131

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:2:THR)

Summations of interaction energy for fragment #1(A:2:THR)

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.
-1.847	0.146	2.061	-1.57	-2.485	-0.001

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.026

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	4	ARG	1	0.914	0.952	3.719	-0.355	1.150	-0.012	-0.660	-0.833	0.004
4	A	5	TYR	0	-0.002	-0.012	5.599	0.668	0.668	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.011	-0.002	9.004	-0.154	-0.154	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.025	-0.006	12.411	0.046	0.046	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.039	0.022	14.143	-0.029	-0.029	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.999	0.995	17.729	-0.069	-0.069	0.000	0.000	0.000	0.000
9	A	10	SER	0	-0.073	-0.018	20.353	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	11	ALA	0	0.071	0.040	16.446	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.037	0.015	17.826	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	13	TYR	0	-0.066	-0.044	18.680	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.882	0.935	20.701	-0.087	-0.087	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.035	0.023	18.189	0.005	0.005	0.000	0.000	0.000	0.000
15	A	16	HIS	0	-0.012	0.002	19.317	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.032	-0.014	21.938	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	18	PRO	0	0.040	0.013	20.726	0.007	0.007	0.000	0.000	0.000	0.000
18	A	19	ALA	0	0.031	0.015	19.089	0.002	0.002	0.000	0.000	0.000	0.000
19	A	20	VAL	0	0.008	0.005	17.000	0.022	0.022	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.905	0.936	15.949	0.025	0.025	0.000	0.000	0.000	0.000
21	A	22	HIS	0	-0.033	-0.008	15.291	-0.016	-0.016	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.846	0.925	7.144	-0.813	-0.813	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.010	-0.029	11.317	0.041	0.041	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.822	-0.887	11.598	-0.075	-0.075	0.000	0.000	0.000	0.000
25	A	26	PRO	0	0.040	0.021	9.800	-0.059	-0.059	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.055	-0.025	6.099	-0.049	-0.049	0.000	0.000	0.000	0.000
27	A	28	MET	0	-0.042	-0.009	7.575	-0.263	-0.263	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.921	-0.954	10.067	-0.295	-0.295	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.876	0.940	5.327	0.385	0.385	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.052	0.041	6.087	-0.493	-0.493	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.061	-0.037	2.147	-1.486	-0.998	2.073	-0.910	-1.652	-0.005
32	A	33	LEU	0	-0.006	0.007	5.589	0.452	0.452	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.039	0.016	9.127	-0.105	-0.105	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.846	0.926	11.213	0.187	0.187	0.000	0.000	0.000	0.000
35	A	36	CYS	0	0.041	0.027	14.994	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.061	0.024	17.805	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.034	0.011	20.947	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	39	THR	0	0.041	0.011	17.304	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.800	-0.897	19.026	-0.048	-0.048	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.029	-0.010	21.235	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.861	-0.931	20.604	0.067	0.067	0.000	0.000	0.000	0.000
42	A	43	PHE	0	0.003	-0.011	20.551	0.000	0.000	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.029	0.021	23.037	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	45	VAL	0	-0.031	-0.019	26.032	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.090	-0.044	25.186	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.025	-0.002	27.654	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	48	ARG	1	0.955	0.965	28.173	0.004	0.004	0.000	0.000	0.000	0.000
48	A	49	SER	0	0.004	-0.003	32.078	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	50	ARG	1	1.007	1.001	32.113	0.015	0.015	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.877	-0.948	31.544	-0.035	-0.035	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.817	-0.903	28.703	-0.024	-0.024	0.000	0.000	0.000	0.000
52	A	53	HIS	0	0.016	0.011	27.705	0.000	0.000	0.000	0.000	0.000	0.000
53	A	54	ARG	1	0.862	0.934	26.778	0.032	0.032	0.000	0.000	0.000	0.000
54	A	55	THR	0	0.011	0.010	25.402	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	56	LEU	0	0.011	0.007	23.393	-0.010	-0.010	0.000	0.000	0.000	0.000
56	A	57	GLY	0	-0.021	-0.009	21.975	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.042	-0.043	21.484	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	59	TYR	0	0.073	0.047	16.989	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.860	0.921	17.280	0.004	0.004	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.842	0.915	16.509	0.059	0.059	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.894	-0.928	16.672	-0.163	-0.163	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.037	-0.011	14.079	-0.039	-0.039	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.069	-0.042	11.822	-0.021	-0.021	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.904	-0.950	9.858	-0.428	-0.428	0.000	0.000	0.000	0.000
65	A	66	TYR	0	-0.059	-0.034	11.821	0.073	0.073	0.000	0.000	0.000	0.000
66	A	67	VAL	0	0.032	0.020	12.027	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	68	ASN	0	0.022	0.000	14.941	0.017	0.017	0.000	0.000	0.000	0.000
68	A	69	THR	0	-0.023	-0.014	18.120	0.019	0.019	0.000	0.000	0.000	0.000
69	A	70	PRO	0	-0.013	0.014	19.625	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.874	-0.948	22.616	0.059	0.059	0.000	0.000	0.000	0.000
71	A	72	THR	0	0.046	0.008	22.519	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.031	-0.012	21.439	0.005	0.005	0.000	0.000	0.000	0.000
73	A	74	TRP	0	-0.003	-0.001	24.078	0.003	0.003	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.038	0.018	27.657	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.808	0.886	20.422	-0.149	-0.149	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.007	-0.011	24.856	0.004	0.004	0.000	0.000	0.000	0.000
77	A	78	TRP	0	-0.016	-0.003	25.649	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.855	-0.929	25.923	0.102	0.102	0.000	0.000	0.000	0.000
79	A	80	ILE	0	-0.020	-0.010	21.613	0.000	0.000	0.000	0.000	0.000	0.000
80	A	81	GLN	0	-0.019	-0.020	25.811	-0.003	-0.003	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.933	-0.958	28.727	0.063	0.063	0.000	0.000	0.000	0.000
82	A	83	ALA	0	-0.004	-0.003	27.010	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.073	-0.041	25.320	0.000	0.000	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.038	-0.043	29.123	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.885	-0.928	32.851	0.057	0.057	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.871	0.929	28.039	-0.093	-0.093	0.000	0.000	0.000	0.000
87	A	88	GLY	0	0.006	0.011	33.019	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	89	PHE	0	0.004	-0.010	28.290	0.000	0.000	0.000	0.000	0.000	0.000
89	A	90	HIS	0	0.042	0.039	29.713	0.004	0.004	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.908	0.954	31.146	-0.049	-0.049	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.026	-0.017	29.380	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.018	0.013	24.914	0.001	0.001	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.940	0.971	26.254	-0.076	-0.076	0.000	0.000	0.000	0.000
94	A	95	ILE	0	0.093	0.035	26.077	0.006	0.006	0.000	0.000	0.000	0.000
95	A	96	PRO	0	-0.004	-0.030	24.935	0.005	0.005	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.852	-0.921	21.832	0.101	0.101	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.009	0.009	21.220	0.015	0.015	0.000	0.000	0.000	0.000
98	A	99	ILE	0	-0.016	-0.002	21.964	0.009	0.009	0.000	0.000	0.000	0.000
99	A	100	ILE	0	-0.024	-0.012	17.420	0.007	0.007	0.000	0.000	0.000	0.000
100	A	101	ALA	0	0.000	0.007	17.279	0.019	0.019	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.054	0.035	17.299	0.025	0.025	0.000	0.000	0.000	0.000
102	A	103	VAL	0	-0.028	-0.022	16.121	0.008	0.008	0.000	0.000	0.000	0.000
103	A	104	ALA	0	-0.002	-0.008	13.020	0.008	0.008	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.807	-0.876	13.199	0.254	0.254	0.000	0.000	0.000	0.000
105	A	106	HIS	0	-0.038	-0.017	14.906	0.023	0.023	0.000	0.000	0.000	0.000
106	A	107	HIS	0	-0.099	-0.060	12.212	0.013	0.013	0.000	0.000	0.000	0.000
107	A	108	GLY	0	0.000	0.023	11.015	0.069	0.069	0.000	0.000	0.000	0.000
108	A	109	ILE	0	-0.074	-0.030	7.961	0.201	0.201	0.000	0.000	0.000	0.000
109	A	110	PRO	0	-0.009	-0.009	7.020	-0.130	-0.130	0.000	0.000	0.000	0.000
110	A	111	VAL	0	0.006	0.014	9.927	-0.066	-0.066	0.000	0.000	0.000	0.000
111	A	112	MET	0	-0.030	0.007	9.492	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	113	HIS	0	0.026	0.011	12.985	-0.082	-0.082	0.000	0.000	0.000	0.000
113	A	114	TYR	0	-0.051	-0.041	16.642	0.005	0.005	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.871	-0.953	19.595	0.081	0.081	0.000	0.000	0.000	0.000
115	A	116	GLN	0	0.064	0.029	20.576	0.016	0.016	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.862	-0.944	22.237	0.101	0.101	0.000	0.000	0.000	0.000
117	A	118	PHE	0	-0.023	-0.023	17.460	0.003	0.003	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.874	-0.931	17.314	0.231	0.231	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.834	0.924	19.739	-0.101	-0.101	0.000	0.000	0.000	0.000
120	A	121	ILE	0	0.019	0.012	19.578	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.044	0.035	16.860	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.066	-0.025	18.690	0.002	0.002	0.000	0.000	0.000	0.000
123	A	124	ILE	0	-0.062	-0.026	21.452	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	125	THR	0	-0.005	-0.031	18.186	0.002	0.002	0.000	0.000	0.000	0.000
125	A	126	ARG	1	0.844	0.925	17.679	-0.168	-0.168	0.000	0.000	0.000	0.000
126	A	127	GLN	0	0.003	0.031	14.327	0.003	0.003	0.000	0.000	0.000	0.000
127	A	128	PRO	0	0.012	0.001	9.747	-0.026	-0.026	0.000	0.000	0.000	0.000
128	A	129	VAL	0	-0.008	-0.014	11.886	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.812	-0.901	8.866	0.778	0.778	0.000	0.000	0.000	0.000
130	A	131	TRP	0	-0.058	-0.021	12.566	-0.031	-0.031	0.000	0.000	0.000	0.000
131	A	132	VAL	0	-0.004	-0.012	13.430	0.030	0.030	0.000	0.000	0.000	0.000
132	A	133	VAL	0	-0.016	-0.019	14.030	0.012	0.012	0.000	0.000	0.000	0.000
133	A	134	ALA	0	0.023	0.009	16.397	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	135	PRO	0	0.002	0.010	18.140	-0.016	-0.016	0.000	0.000	0.000	0.000
135	A	136	GLY	0	-0.013	-0.004	21.093	-0.016	-0.016	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)