FMO DATABASE

FMODB ID: VQ2N1

Calculation Name: 3M5B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M5B

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y2Y4

Base Structure: X-ray

Registration Date: 2023-09-20

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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-811917.194551
FMO2-HF: Nuclear repulsion	770850.682804
FMO2-HF: Total energy	-41066.511747
FMO2-MP2: Total energy	-41187.814893

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:5:PRO)

Summations of interaction energy for fragment #1(A:5:PRO)

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.
-5.769	0.157	1.577	-2.852	-4.652	-0.014

Interaction energy analysis for fragmet #1(A:5:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / 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	7	ARG	1	0.922	0.959	3.562	0.734	2.364	0.017	-0.737	-0.911	0.001
4	A	8	LEU	0	0.000	-0.002	5.135	0.545	0.617	-0.001	-0.007	-0.064	0.000
5	A	9	PRO	0	-0.031	-0.024	8.469	0.076	0.076	0.000	0.000	0.000	0.000
6	A	10	SER	0	0.025	0.012	11.106	0.103	0.103	0.000	0.000	0.000	0.000
7	A	11	PRO	0	-0.045	-0.021	13.924	0.010	0.010	0.000	0.000	0.000	0.000
8	A	12	TYR	0	0.040	0.023	17.244	0.038	0.038	0.000	0.000	0.000	0.000
9	A	13	GLY	0	0.040	0.031	17.053	0.028	0.028	0.000	0.000	0.000	0.000
10	A	14	SER	0	-0.045	-0.021	17.941	0.003	0.003	0.000	0.000	0.000	0.000
11	A	15	ASP	-1	-0.805	-0.881	21.333	-0.193	-0.193	0.000	0.000	0.000	0.000
12	A	16	ARG	1	0.968	0.966	23.474	0.154	0.154	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.055	-0.025	25.995	0.006	0.006	0.000	0.000	0.000	0.000
14	A	18	VAL	0	0.042	0.019	20.449	0.006	0.006	0.000	0.000	0.000	0.000
15	A	19	GLN	0	0.018	0.002	20.554	0.015	0.015	0.000	0.000	0.000	0.000
16	A	20	LEU	0	-0.074	-0.027	22.239	0.000	0.000	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.026	0.004	23.952	0.005	0.005	0.000	0.000	0.000	0.000
18	A	22	ALA	0	-0.009	-0.007	18.998	0.007	0.007	0.000	0.000	0.000	0.000
19	A	23	ARG	1	0.879	0.930	20.712	0.245	0.245	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.037	0.001	22.671	0.014	0.014	0.000	0.000	0.000	0.000
21	A	25	ARG	1	0.848	0.939	16.087	0.347	0.347	0.000	0.000	0.000	0.000
22	A	26	PRO	0	0.022	-0.004	23.128	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	27	ALA	0	0.019	-0.001	25.786	0.012	0.012	0.000	0.000	0.000	0.000
24	A	28	LEU	0	-0.015	-0.027	28.048	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	29	CYS	0	-0.075	0.007	25.965	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	30	ASP	-1	-0.763	-0.829	28.576	-0.120	-0.120	0.000	0.000	0.000	0.000
27	A	31	THR	0	-0.012	-0.022	27.065	0.009	0.009	0.000	0.000	0.000	0.000
28	A	32	LEU	0	-0.037	-0.013	26.123	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	33	ILE	0	0.051	0.029	23.200	0.008	0.008	0.000	0.000	0.000	0.000
30	A	34	THR	0	0.005	-0.018	24.097	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	35	VAL	0	0.007	-0.009	20.274	0.001	0.001	0.000	0.000	0.000	0.000
32	A	36	GLY	0	0.018	0.005	22.906	0.004	0.004	0.000	0.000	0.000	0.000
33	A	37	SER	0	-0.047	-0.030	23.924	0.008	0.008	0.000	0.000	0.000	0.000
34	A	38	GLN	0	-0.026	-0.002	18.510	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.795	-0.883	23.123	-0.087	-0.087	0.000	0.000	0.000	0.000
36	A	40	PHE	0	-0.010	-0.007	17.842	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	41	PRO	0	-0.025	-0.010	22.497	0.002	0.002	0.000	0.000	0.000	0.000
38	A	42	ALA	0	0.036	0.015	22.838	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	43	HIS	0	-0.005	0.003	24.481	0.003	0.003	0.000	0.000	0.000	0.000
40	A	44	SER	0	-0.026	-0.055	26.299	-0.011	-0.011	0.000	0.000	0.000	0.000
41	A	45	LEU	0	-0.003	-0.006	28.226	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	46	VAL	0	-0.008	-0.008	22.447	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	47	LEU	0	0.006	0.011	22.434	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	48	ALA	0	0.027	0.001	24.706	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	49	GLY	0	-0.074	-0.019	26.184	0.005	0.005	0.000	0.000	0.000	0.000
46	A	50	VAL	0	-0.050	-0.022	19.869	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	51	SER	0	-0.025	-0.037	23.164	0.004	0.004	0.000	0.000	0.000	0.000
48	A	52	GLN	0	0.031	0.013	25.069	0.005	0.005	0.000	0.000	0.000	0.000
49	A	53	GLN	0	-0.031	-0.015	25.989	0.002	0.002	0.000	0.000	0.000	0.000
50	A	54	LEU	0	0.023	0.007	21.560	0.008	0.008	0.000	0.000	0.000	0.000
51	A	55	GLY	0	-0.003	0.020	26.129	0.000	0.000	0.000	0.000	0.000	0.000
52	A	56	ARG	1	0.820	0.906	28.406	0.116	0.116	0.000	0.000	0.000	0.000
53	A	57	ARG	1	0.976	0.994	29.728	0.085	0.085	0.000	0.000	0.000	0.000
54	A	58	GLY	0	-0.018	-0.012	31.779	0.006	0.006	0.000	0.000	0.000	0.000
55	A	59	GLN	0	-0.048	-0.032	29.886	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	60	TRP	0	-0.060	-0.038	25.492	0.007	0.007	0.000	0.000	0.000	0.000
57	A	61	ALA	0	0.013	0.014	27.410	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	62	LEU	0	-0.012	0.005	22.156	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	63	GLY	0	0.033	-0.008	25.335	0.004	0.004	0.000	0.000	0.000	0.000
60	A	64	GLU	-1	-0.964	-0.970	23.959	-0.081	-0.081	0.000	0.000	0.000	0.000
61	A	65	GLY	0	-0.018	-0.012	22.395	0.000	0.000	0.000	0.000	0.000	0.000
62	A	66	ILE	0	-0.024	-0.008	18.045	0.003	0.003	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.001	-0.003	15.113	0.001	0.001	0.000	0.000	0.000	0.000
64	A	68	PRO	0	0.057	0.008	17.109	-0.026	-0.026	0.000	0.000	0.000	0.000
65	A	69	SER	0	0.025	0.025	11.282	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	70	THR	0	0.002	0.016	12.921	-0.038	-0.038	0.000	0.000	0.000	0.000
67	A	71	PHE	0	0.030	0.012	13.940	-0.047	-0.047	0.000	0.000	0.000	0.000
68	A	72	ALA	0	0.011	0.010	14.124	-0.023	-0.023	0.000	0.000	0.000	0.000
69	A	73	GLN	0	-0.042	-0.037	8.880	-0.028	-0.028	0.000	0.000	0.000	0.000
70	A	74	LEU	0	-0.004	0.004	11.980	-0.054	-0.054	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.004	0.000	14.645	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.017	-0.008	12.894	0.062	0.062	0.000	0.000	0.000	0.000
73	A	77	PHE	0	0.027	0.023	11.462	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.028	0.001	13.898	0.012	0.012	0.000	0.000	0.000	0.000
75	A	79	TYR	0	-0.039	-0.051	17.182	0.028	0.028	0.000	0.000	0.000	0.000
76	A	80	GLY	0	-0.020	-0.012	16.507	0.012	0.012	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.854	-0.909	12.109	-0.537	-0.537	0.000	0.000	0.000	0.000
78	A	82	SER	0	-0.044	-0.032	8.448	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	83	VAL	0	0.016	0.016	7.191	0.034	0.034	0.000	0.000	0.000	0.000
80	A	84	GLU	-1	-0.926	-0.976	2.361	-4.916	-3.702	0.663	-0.629	-1.248	-0.002
81	A	85	LEU	0	-0.018	0.005	2.863	-0.069	0.834	0.280	-0.335	-0.848	-0.002
82	A	86	GLN	0	0.046	0.012	2.946	-1.091	0.961	0.619	-1.136	-1.535	-0.011
83	A	87	PRO	0	0.003	-0.013	4.430	-0.496	-0.441	-0.001	-0.008	-0.046	0.000
84	A	88	GLY	0	-0.038	-0.012	6.742	-0.167	-0.167	0.000	0.000	0.000	0.000
85	A	89	GLU	-1	-0.812	-0.902	6.443	-0.248	-0.248	0.000	0.000	0.000	0.000
86	A	90	LEU	0	0.012	0.016	8.232	-0.060	-0.060	0.000	0.000	0.000	0.000
87	A	91	ARG	1	0.872	0.952	10.045	-0.102	-0.102	0.000	0.000	0.000	0.000
88	A	92	PRO	0	0.065	0.025	12.641	-0.023	-0.023	0.000	0.000	0.000	0.000
89	A	93	LEU	0	0.031	0.011	9.778	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	94	GLN	0	-0.041	-0.026	13.428	0.002	0.002	0.000	0.000	0.000	0.000
91	A	95	GLU	-1	-0.924	-0.978	15.398	-0.025	-0.025	0.000	0.000	0.000	0.000
92	A	96	ALA	0	0.022	0.004	16.373	0.010	0.010	0.000	0.000	0.000	0.000
93	A	97	ALA	0	-0.006	-0.010	16.036	0.004	0.004	0.000	0.000	0.000	0.000
94	A	98	ARG	1	0.901	0.963	18.055	0.108	0.108	0.000	0.000	0.000	0.000
95	A	99	ALA	0	-0.039	-0.013	20.946	0.010	0.010	0.000	0.000	0.000	0.000
96	A	100	LEU	0	0.009	0.019	19.997	0.009	0.009	0.000	0.000	0.000	0.000
97	A	101	GLY	0	0.069	0.052	22.902	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	102	VAL	0	-0.013	0.006	17.677	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	103	GLN	0	0.019	-0.008	18.628	-0.035	-0.035	0.000	0.000	0.000	0.000
100	A	104	SER	0	0.001	-0.015	17.988	-0.013	-0.013	0.000	0.000	0.000	0.000
101	A	105	LEU	0	0.026	0.020	12.038	-0.039	-0.039	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.806	-0.906	14.331	-0.200	-0.200	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.764	-0.877	15.959	-0.252	-0.252	0.000	0.000	0.000	0.000
104	A	108	ALA	0	-0.049	-0.019	12.260	-0.013	-0.013	0.000	0.000	0.000	0.000
105	A	109	CYS	0	-0.044	-0.026	11.369	-0.091	-0.091	0.000	0.000	0.000	0.000
106	A	110	TRP	0	-0.051	-0.024	12.447	0.032	0.032	0.000	0.000	0.000	0.000
107	A	111	ARG	1	0.829	0.880	14.146	0.359	0.359	0.000	0.000	0.000	0.000
108	A	112	ALA	0	-0.026	0.007	9.040	0.014	0.014	0.000	0.000	0.000	0.000
109	A	113	ARG	1	0.893	0.968	9.925	0.202	0.202	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:PRO)