FMO DATABASE

FMODB ID: 85N8Y

Calculation Name: 3A7M-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A7M

Chain ID: B

ChEMBL ID:

UniProt ID: P0A1N2

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	OptHSide
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	117
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-787887.160341
FMO2-HF: Nuclear repulsion	741538.387069
FMO2-HF: Total energy	-46348.773272
FMO2-MP2: Total energy	-46484.458683

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(B:2:THR)

Summations of interaction energy for fragment #1(B: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.
-25.796	-20.975	11.999	-7.237	-9.583	0.053

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.099 / q_NPA : 0.048

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	B	4	THR	0	-0.028	-0.021	1.938	-14.341	-12.513	8.224	-4.902	-5.150	0.038
4	B	5	VAL	0	0.028	0.017	1.981	-7.509	-5.229	3.774	-2.192	-3.861	0.015
5	B	6	GLU	-1	-0.900	-0.943	3.883	-3.396	-2.683	0.001	-0.143	-0.572	0.000
6	B	7	PHE	0	-0.048	-0.023	5.809	0.164	0.164	0.000	0.000	0.000	0.000
7	B	8	ILE	0	0.027	-0.002	6.288	-0.237	-0.237	0.000	0.000	0.000	0.000
8	B	9	ASN	0	-0.017	-0.014	7.819	-0.130	-0.130	0.000	0.000	0.000	0.000
9	B	10	ARG	1	0.959	0.993	7.887	0.351	0.351	0.000	0.000	0.000	0.000
10	B	11	TRP	0	0.074	0.015	11.641	0.000	0.000	0.000	0.000	0.000	0.000
11	B	12	GLN	0	-0.033	-0.004	10.784	-0.105	-0.105	0.000	0.000	0.000	0.000
12	B	13	ARG	1	0.917	0.948	13.462	0.286	0.286	0.000	0.000	0.000	0.000
13	B	14	ILE	0	-0.007	0.005	15.250	0.011	0.011	0.000	0.000	0.000	0.000
14	B	15	ALA	0	0.039	0.024	17.264	0.008	0.008	0.000	0.000	0.000	0.000
15	B	16	LEU	0	-0.033	-0.001	16.362	0.005	0.005	0.000	0.000	0.000	0.000
16	B	17	LEU	0	0.005	-0.005	19.544	0.011	0.011	0.000	0.000	0.000	0.000
17	B	18	SER	0	0.021	0.021	21.728	0.015	0.015	0.000	0.000	0.000	0.000
18	B	19	GLN	0	-0.020	-0.024	22.875	0.015	0.015	0.000	0.000	0.000	0.000
19	B	20	SER	0	-0.091	-0.037	23.614	0.000	0.000	0.000	0.000	0.000	0.000
20	B	21	LEU	0	0.047	0.004	25.409	0.004	0.004	0.000	0.000	0.000	0.000
21	B	22	LEU	0	-0.003	0.005	27.644	0.007	0.007	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.832	-0.909	27.272	-0.080	-0.080	0.000	0.000	0.000	0.000
23	B	24	LEU	0	-0.108	-0.038	28.528	0.003	0.003	0.000	0.000	0.000	0.000
24	B	25	ALA	0	-0.006	0.011	31.827	0.003	0.003	0.000	0.000	0.000	0.000
25	B	26	GLN	0	-0.056	-0.038	31.971	0.000	0.000	0.000	0.000	0.000	0.000
26	B	27	ARG	1	0.741	0.869	29.843	0.076	0.076	0.000	0.000	0.000	0.000
27	B	28	GLY	0	0.029	0.011	35.780	0.003	0.003	0.000	0.000	0.000	0.000
28	B	29	GLU	-1	-0.867	-0.919	33.664	-0.064	-0.064	0.000	0.000	0.000	0.000
29	B	30	TRP	0	0.093	0.018	34.447	-0.002	-0.002	0.000	0.000	0.000	0.000
30	B	31	ASP	-1	-0.918	-0.958	35.554	-0.052	-0.052	0.000	0.000	0.000	0.000
31	B	32	LEU	0	0.004	0.004	31.890	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	33	LEU	0	0.002	0.014	30.331	-0.003	-0.003	0.000	0.000	0.000	0.000
33	B	34	LEU	0	-0.010	-0.017	31.033	-0.001	-0.001	0.000	0.000	0.000	0.000
34	B	35	GLN	0	-0.053	-0.028	31.252	-0.003	-0.003	0.000	0.000	0.000	0.000
35	B	36	GLN	0	-0.031	-0.027	25.917	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	37	GLU	-1	-0.893	-0.935	26.612	-0.057	-0.057	0.000	0.000	0.000	0.000
37	B	38	VAL	0	0.078	0.038	27.098	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	39	SER	0	-0.043	-0.018	23.805	-0.003	-0.003	0.000	0.000	0.000	0.000
39	B	40	TYR	0	-0.033	-0.041	22.290	-0.012	-0.012	0.000	0.000	0.000	0.000
40	B	41	LEU	0	0.032	0.023	22.772	0.003	0.003	0.000	0.000	0.000	0.000
41	B	42	GLN	0	0.013	-0.003	23.376	-0.007	-0.007	0.000	0.000	0.000	0.000
42	B	43	SER	0	-0.133	-0.051	19.103	-0.031	-0.031	0.000	0.000	0.000	0.000
43	B	44	ILE	0	0.001	-0.010	18.831	-0.006	-0.006	0.000	0.000	0.000	0.000
44	B	45	GLU	-1	-0.872	-0.940	19.673	-0.037	-0.037	0.000	0.000	0.000	0.000
45	B	46	THR	0	0.004	-0.003	16.324	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	47	VAL	0	-0.082	-0.057	13.934	-0.013	-0.013	0.000	0.000	0.000	0.000
47	B	48	MET	0	-0.046	-0.019	15.381	0.062	0.062	0.000	0.000	0.000	0.000
48	B	49	GLU	-1	-0.871	-0.893	17.821	-0.080	-0.080	0.000	0.000	0.000	0.000
49	B	50	LYS	1	0.770	0.879	12.561	0.166	0.166	0.000	0.000	0.000	0.000
50	B	51	GLN	0	0.008	0.009	11.763	0.088	0.088	0.000	0.000	0.000	0.000
51	B	52	THR	0	-0.030	-0.017	10.646	0.008	0.008	0.000	0.000	0.000	0.000
52	B	53	PRO	0	-0.028	-0.014	6.184	0.014	0.014	0.000	0.000	0.000	0.000
53	B	54	PRO	0	0.058	0.023	6.422	-0.011	-0.011	0.000	0.000	0.000	0.000
54	B	55	GLY	0	-0.009	0.005	7.169	-0.132	-0.132	0.000	0.000	0.000	0.000
55	B	56	ILE	0	-0.042	-0.013	8.137	0.270	0.270	0.000	0.000	0.000	0.000
56	B	57	THR	0	0.059	0.025	8.847	-0.311	-0.311	0.000	0.000	0.000	0.000
57	B	58	ARG	1	0.874	0.903	11.361	-0.311	-0.311	0.000	0.000	0.000	0.000
58	B	59	SER	0	0.029	0.014	11.739	-0.032	-0.032	0.000	0.000	0.000	0.000
59	B	60	ILE	0	0.018	0.010	6.291	-0.037	-0.037	0.000	0.000	0.000	0.000
60	B	61	GLN	0	0.002	-0.005	10.596	-0.110	-0.110	0.000	0.000	0.000	0.000
61	B	62	ASP	-1	-0.805	-0.884	13.210	0.226	0.226	0.000	0.000	0.000	0.000
62	B	63	MET	0	-0.021	0.002	10.778	-0.054	-0.054	0.000	0.000	0.000	0.000
63	B	64	VAL	0	-0.009	-0.008	10.802	-0.067	-0.067	0.000	0.000	0.000	0.000
64	B	65	ALA	0	0.021	0.010	13.609	-0.071	-0.071	0.000	0.000	0.000	0.000
65	B	66	GLY	0	-0.013	-0.002	16.820	-0.040	-0.040	0.000	0.000	0.000	0.000
66	B	67	TYR	0	0.054	0.031	12.771	-0.047	-0.047	0.000	0.000	0.000	0.000
67	B	68	ILE	0	0.010	0.020	16.376	-0.026	-0.026	0.000	0.000	0.000	0.000
68	B	69	LYS	1	0.928	0.972	19.239	-0.157	-0.157	0.000	0.000	0.000	0.000
69	B	70	GLN	0	0.061	0.031	20.569	-0.018	-0.018	0.000	0.000	0.000	0.000
70	B	71	THR	0	-0.024	-0.034	19.968	-0.017	-0.017	0.000	0.000	0.000	0.000
71	B	72	LEU	0	-0.029	-0.027	22.565	-0.006	-0.006	0.000	0.000	0.000	0.000
72	B	73	ASP	-1	-0.912	-0.958	24.999	0.032	0.032	0.000	0.000	0.000	0.000
73	B	74	ASN	0	-0.050	-0.038	23.912	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	75	GLU	-1	-0.879	-0.922	26.443	-0.029	-0.029	0.000	0.000	0.000	0.000
75	B	76	GLN	0	-0.039	-0.020	28.312	0.004	0.004	0.000	0.000	0.000	0.000
76	B	77	LEU	0	-0.025	-0.010	29.706	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	78	LEU	0	0.035	0.020	29.456	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	79	LYS	1	0.982	0.988	32.327	0.000	0.000	0.000	0.000	0.000	0.000
79	B	80	GLY	0	-0.007	0.008	34.440	0.001	0.001	0.000	0.000	0.000	0.000
80	B	81	LEU	0	0.028	0.002	33.923	0.000	0.000	0.000	0.000	0.000	0.000
81	B	82	LEU	0	-0.008	-0.009	33.602	-0.001	-0.001	0.000	0.000	0.000	0.000
82	B	83	GLN	0	-0.080	-0.040	37.617	0.000	0.000	0.000	0.000	0.000	0.000
83	B	84	GLN	0	0.022	0.015	40.009	0.000	0.000	0.000	0.000	0.000	0.000
84	B	85	ARG	1	0.873	0.931	40.390	0.028	0.028	0.000	0.000	0.000	0.000
85	B	86	LEU	0	-0.005	-0.004	41.547	0.000	0.000	0.000	0.000	0.000	0.000
86	B	87	ASP	-1	-0.865	-0.921	43.240	-0.009	-0.009	0.000	0.000	0.000	0.000
87	B	88	GLU	-1	-0.881	-0.939	44.409	-0.022	-0.022	0.000	0.000	0.000	0.000
88	B	89	LEU	0	-0.007	-0.002	43.845	0.000	0.000	0.000	0.000	0.000	0.000
89	B	90	SER	0	-0.044	-0.026	46.626	0.000	0.000	0.000	0.000	0.000	0.000
90	B	91	SER	0	-0.044	-0.014	49.112	0.002	0.002	0.000	0.000	0.000	0.000
91	B	92	LEU	0	-0.063	-0.037	50.477	0.001	0.001	0.000	0.000	0.000	0.000
92	B	93	ILE	0	-0.019	-0.010	50.072	0.001	0.001	0.000	0.000	0.000	0.000
93	B	94	GLY	0	0.021	0.020	53.935	0.001	0.001	0.000	0.000	0.000	0.000
94	B	95	GLN	0	0.062	0.019	55.965	0.001	0.001	0.000	0.000	0.000	0.000
95	B	96	SER	0	0.031	0.028	57.520	0.001	0.001	0.000	0.000	0.000	0.000
96	B	97	THR	0	0.064	0.063	59.248	-0.001	-0.001	0.000	0.000	0.000	0.000
97	B	98	ARG	1	0.834	0.889	60.975	0.011	0.011	0.000	0.000	0.000	0.000
98	B	99	GLN	0	0.112	0.055	61.163	0.001	0.001	0.000	0.000	0.000	0.000
99	B	100	LYS	1	1.011	1.022	63.466	0.010	0.010	0.000	0.000	0.000	0.000
100	B	101	SER	0	0.023	0.013	66.217	0.000	0.000	0.000	0.000	0.000	0.000
101	B	102	LEU	0	0.024	0.013	64.261	0.000	0.000	0.000	0.000	0.000	0.000
102	B	103	ASN	0	-0.034	-0.037	65.461	0.000	0.000	0.000	0.000	0.000	0.000
103	B	104	ASN	0	-0.084	-0.046	68.395	0.000	0.000	0.000	0.000	0.000	0.000
104	B	105	ALA	0	-0.045	-0.032	70.537	0.000	0.000	0.000	0.000	0.000	0.000
105	B	106	TYR	0	0.022	0.023	70.126	0.000	0.000	0.000	0.000	0.000	0.000
106	B	107	GLY	0	0.032	0.024	72.128	0.000	0.000	0.000	0.000	0.000	0.000
107	B	108	ARG	1	0.923	0.951	73.944	0.008	0.008	0.000	0.000	0.000	0.000
108	B	109	LEU	0	0.012	0.014	75.024	0.000	0.000	0.000	0.000	0.000	0.000
109	B	110	SER	0	-0.022	-0.040	74.343	0.000	0.000	0.000	0.000	0.000	0.000
110	B	111	GLY	0	-0.036	0.006	76.961	0.000	0.000	0.000	0.000	0.000	0.000
111	B	112	MET	0	-0.055	-0.019	79.796	0.000	0.000	0.000	0.000	0.000	0.000
112	B	113	LEU	0	0.015	-0.006	82.726	0.000	0.000	0.000	0.000	0.000	0.000
113	B	114	LEU	0	-0.024	-0.017	86.195	0.000	0.000	0.000	0.000	0.000	0.000
114	B	115	VAL	0	-0.054	-0.018	83.154	0.000	0.000	0.000	0.000	0.000	0.000
115	B	116	PRO	0	0.000	0.012	86.585	0.000	0.000	0.000	0.000	0.000	0.000
116	B	117	ASP	-1	-0.893	-0.954	87.190	-0.009	-0.009	0.000	0.000	0.000	0.000
117	B	118	ALA	0	-0.053	-0.014	88.186	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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