FMO DATABASE

FMODB ID: G6951

Calculation Name: 1N12-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1N12

Chain ID: A

ChEMBL ID:

UniProt ID: P08407

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:

Apendix: None

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1099535.639016
FMO2-HF: Nuclear repulsion	1047450.819648
FMO2-HF: Total energy	-52084.819368
FMO2-MP2: Total energy	-52235.014475

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:VAL)

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

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.
-5.475	-2.477	12.714	-4.832	-10.878	-0.025

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

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 : 0.009

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	14	ALA	0	0.032	0.007	3.062	-2.874	-0.049	0.148	-1.521	-1.451	-0.001
4	A	15	CYS	0	-0.076	-0.051	4.811	0.285	0.362	-0.002	-0.004	-0.070	0.000
5	A	16	THR	0	-0.014	-0.005	7.532	0.072	0.072	0.000	0.000	0.000	0.000
6	A	17	VAL	0	-0.015	-0.019	10.970	0.094	0.094	0.000	0.000	0.000	0.000
7	A	18	SER	0	-0.027	-0.002	13.305	0.059	0.059	0.000	0.000	0.000	0.000
8	A	19	ASN	0	-0.014	-0.012	16.969	-0.021	-0.021	0.000	0.000	0.000	0.000
9	A	20	THR	0	0.006	-0.002	19.640	0.029	0.029	0.000	0.000	0.000	0.000
10	A	21	THR	0	-0.012	-0.008	21.988	-0.001	-0.001	0.000	0.000	0.000	0.000
11	A	22	VAL	0	-0.037	-0.001	24.141	0.005	0.005	0.000	0.000	0.000	0.000
12	A	23	ASP	-1	-0.848	-0.928	26.777	-0.166	-0.166	0.000	0.000	0.000	0.000
13	A	24	TRP	0	-0.033	-0.049	27.747	-0.004	-0.004	0.000	0.000	0.000	0.000
14	A	25	GLN	0	-0.031	0.004	33.163	0.007	0.007	0.000	0.000	0.000	0.000
15	A	26	ASP	-1	-0.920	-0.952	36.112	-0.114	-0.114	0.000	0.000	0.000	0.000
16	A	27	VAL	0	-0.036	-0.028	35.572	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	28	GLU	-1	-0.928	-0.958	38.980	-0.091	-0.091	0.000	0.000	0.000	0.000
18	A	29	ILE	0	0.064	0.033	41.140	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	30	GLN	0	-0.008	-0.014	42.188	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	31	THR	0	-0.027	-0.025	41.259	0.000	0.000	0.000	0.000	0.000	0.000
21	A	32	LEU	0	-0.012	0.008	36.420	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	33	SER	0	0.001	0.004	37.215	0.006	0.006	0.000	0.000	0.000	0.000
23	A	34	GLN	0	-0.021	-0.006	36.856	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	35	ASN	0	-0.033	-0.039	35.035	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	36	GLY	0	0.028	0.002	32.795	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	37	ASN	0	-0.068	-0.047	33.849	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	38	HIS	0	0.026	0.010	33.246	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	39	GLU	-1	-0.914	-0.963	29.594	-0.180	-0.180	0.000	0.000	0.000	0.000
29	A	40	LYS	1	0.915	0.972	28.629	0.194	0.194	0.000	0.000	0.000	0.000
30	A	41	GLU	-1	-0.921	-0.960	25.968	-0.209	-0.209	0.000	0.000	0.000	0.000
31	A	42	PHE	0	-0.036	-0.025	20.263	0.003	0.003	0.000	0.000	0.000	0.000
32	A	43	THR	0	0.000	-0.007	20.509	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	44	VAL	0	0.020	0.013	15.663	0.000	0.000	0.000	0.000	0.000	0.000
34	A	45	ASN	0	0.036	0.040	16.440	-0.009	-0.009	0.000	0.000	0.000	0.000
35	A	46	MET	0	0.013	-0.011	11.194	-0.089	-0.089	0.000	0.000	0.000	0.000
36	A	47	ARG	1	0.900	0.958	11.487	0.415	0.415	0.000	0.000	0.000	0.000
37	A	49	PRO	0	0.022	0.000	6.783	0.131	0.131	0.000	0.000	0.000	0.000
38	A	50	TYR	0	0.022	0.019	2.344	-0.926	-2.132	10.315	-2.082	-7.027	-0.008
39	A	51	ASN	0	-0.064	-0.051	4.951	-0.462	-0.407	-0.001	-0.004	-0.049	0.000
40	A	52	LEU	0	0.042	0.038	5.543	0.152	0.152	0.000	0.000	0.000	0.000
41	A	53	GLY	0	0.012	0.013	5.595	-0.269	-0.269	0.000	0.000	0.000	0.000
42	A	54	THR	0	-0.017	-0.039	7.425	0.083	0.083	0.000	0.000	0.000	0.000
43	A	55	MET	0	0.015	0.021	7.141	-0.203	-0.203	0.000	0.000	0.000	0.000
44	A	56	LYS	1	0.901	0.955	7.762	0.908	0.908	0.000	0.000	0.000	0.000
45	A	57	VAL	0	0.028	0.003	8.797	-0.237	-0.237	0.000	0.000	0.000	0.000
46	A	58	THR	0	0.000	0.005	11.337	0.112	0.112	0.000	0.000	0.000	0.000
47	A	59	ILE	0	0.016	0.009	13.346	-0.043	-0.043	0.000	0.000	0.000	0.000
48	A	60	THR	0	0.013	0.005	16.336	0.046	0.046	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.056	0.021	18.672	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	62	THR	0	-0.009	-0.004	22.053	0.006	0.006	0.000	0.000	0.000	0.000
51	A	63	ASN	0	0.027	0.029	24.569	0.024	0.024	0.000	0.000	0.000	0.000
52	A	64	THR	0	-0.030	-0.010	24.071	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	65	TYR	0	0.046	0.006	27.489	0.017	0.017	0.000	0.000	0.000	0.000
54	A	66	ASN	0	-0.008	-0.004	29.001	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	67	ASN	0	-0.021	-0.011	23.489	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	68	ALA	0	0.020	0.035	25.322	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	69	ILE	0	0.001	-0.012	22.936	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	70	LEU	0	-0.028	-0.014	26.798	0.011	0.011	0.000	0.000	0.000	0.000
59	A	71	VAL	0	-0.029	-0.015	30.045	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	72	GLN	0	0.025	0.009	31.102	0.007	0.007	0.000	0.000	0.000	0.000
61	A	73	ASN	0	-0.033	-0.025	33.521	0.004	0.004	0.000	0.000	0.000	0.000
62	A	74	THR	0	0.079	0.043	35.224	0.003	0.003	0.000	0.000	0.000	0.000
63	A	75	SER	0	0.034	0.015	37.875	0.006	0.006	0.000	0.000	0.000	0.000
64	A	76	ASN	0	-0.036	-0.017	40.369	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	77	THR	0	-0.046	-0.008	40.405	0.004	0.004	0.000	0.000	0.000	0.000
66	A	78	SER	0	0.021	-0.002	38.087	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	79	SER	0	-0.014	0.002	36.075	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	80	ASP	-1	-0.917	-0.969	36.042	-0.115	-0.115	0.000	0.000	0.000	0.000
69	A	81	GLY	0	0.039	0.008	36.019	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	82	LEU	0	0.006	0.006	33.282	0.000	0.000	0.000	0.000	0.000	0.000
71	A	83	LEU	0	-0.050	-0.021	30.936	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	84	VAL	0	0.043	0.026	26.106	0.004	0.004	0.000	0.000	0.000	0.000
73	A	85	TYR	0	-0.001	0.003	26.648	-0.015	-0.015	0.000	0.000	0.000	0.000
74	A	86	LEU	0	0.015	0.001	20.841	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	87	TYR	0	0.014	-0.002	23.122	0.012	0.012	0.000	0.000	0.000	0.000
76	A	88	ASN	0	0.047	0.025	17.614	-0.029	-0.029	0.000	0.000	0.000	0.000
77	A	89	SER	0	-0.016	-0.044	20.257	0.028	0.028	0.000	0.000	0.000	0.000
78	A	90	ASN	0	-0.028	-0.022	20.944	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	91	ALA	0	0.013	-0.003	22.515	0.016	0.016	0.000	0.000	0.000	0.000
80	A	92	GLY	0	-0.040	-0.026	24.094	0.013	0.013	0.000	0.000	0.000	0.000
81	A	93	ASN	0	0.037	0.046	26.050	0.009	0.009	0.000	0.000	0.000	0.000
82	A	94	ILE	0	0.018	0.030	25.563	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	95	GLY	0	0.010	-0.005	23.707	0.012	0.012	0.000	0.000	0.000	0.000
84	A	96	THR	0	-0.016	-0.022	21.625	0.007	0.007	0.000	0.000	0.000	0.000
85	A	97	ALA	0	0.016	0.006	22.817	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	98	ILE	0	-0.030	-0.012	18.633	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	99	THR	0	0.001	0.019	20.228	0.030	0.030	0.000	0.000	0.000	0.000
88	A	100	LEU	0	-0.012	-0.026	19.135	-0.047	-0.047	0.000	0.000	0.000	0.000
89	A	101	GLY	0	-0.016	-0.017	17.003	0.022	0.022	0.000	0.000	0.000	0.000
90	A	102	THR	0	-0.067	-0.021	15.706	-0.011	-0.011	0.000	0.000	0.000	0.000
91	A	103	PRO	0	-0.020	-0.012	11.487	-0.022	-0.022	0.000	0.000	0.000	0.000
92	A	104	PHE	0	0.021	0.010	13.397	0.081	0.081	0.000	0.000	0.000	0.000
93	A	105	THR	0	0.019	-0.001	11.690	-0.089	-0.089	0.000	0.000	0.000	0.000
94	A	106	PRO	0	-0.031	-0.017	12.580	0.071	0.071	0.000	0.000	0.000	0.000
95	A	107	GLY	0	0.050	0.024	15.549	0.002	0.002	0.000	0.000	0.000	0.000
96	A	108	LYS	1	0.928	0.976	18.239	0.266	0.266	0.000	0.000	0.000	0.000
97	A	109	ILE	0	-0.016	-0.015	12.413	-0.039	-0.039	0.000	0.000	0.000	0.000
98	A	110	THR	0	0.019	0.008	16.443	0.042	0.042	0.000	0.000	0.000	0.000
99	A	111	GLY	0	0.041	0.024	16.453	-0.039	-0.039	0.000	0.000	0.000	0.000
100	A	112	ASN	0	0.014	-0.010	15.326	-0.057	-0.057	0.000	0.000	0.000	0.000
101	A	113	ASN	0	-0.012	-0.002	14.687	0.013	0.013	0.000	0.000	0.000	0.000
102	A	114	ALA	0	0.033	0.000	11.237	-0.038	-0.038	0.000	0.000	0.000	0.000
103	A	115	ASP	-1	-0.887	-0.913	12.177	-0.445	-0.445	0.000	0.000	0.000	0.000
104	A	116	LYS	1	0.872	0.952	11.007	0.486	0.486	0.000	0.000	0.000	0.000
105	A	117	THR	0	0.023	-0.006	14.301	-0.018	-0.018	0.000	0.000	0.000	0.000
106	A	118	ILE	0	-0.020	-0.005	13.992	0.012	0.012	0.000	0.000	0.000	0.000
107	A	119	SER	0	-0.030	-0.022	17.027	0.031	0.031	0.000	0.000	0.000	0.000
108	A	120	LEU	0	-0.022	0.025	17.470	-0.020	-0.020	0.000	0.000	0.000	0.000
109	A	121	HIS	0	0.035	0.023	21.348	0.010	0.010	0.000	0.000	0.000	0.000
110	A	122	ALA	0	-0.018	-0.008	24.290	-0.017	-0.017	0.000	0.000	0.000	0.000
111	A	123	LYS	1	0.903	0.968	26.537	0.179	0.179	0.000	0.000	0.000	0.000
112	A	124	LEU	0	0.039	0.027	29.692	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	125	GLY	0	0.051	0.027	32.356	0.008	0.008	0.000	0.000	0.000	0.000
114	A	126	TYR	0	-0.071	-0.022	34.295	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	127	LYS	1	0.884	0.965	34.427	0.129	0.129	0.000	0.000	0.000	0.000
116	A	128	GLY	0	0.061	0.030	36.948	0.002	0.002	0.000	0.000	0.000	0.000
117	A	129	ASN	0	-0.027	-0.029	40.603	0.000	0.000	0.000	0.000	0.000	0.000
118	A	130	MET	0	0.051	0.025	42.361	0.000	0.000	0.000	0.000	0.000	0.000
119	A	131	GLN	0	-0.005	-0.019	43.477	0.000	0.000	0.000	0.000	0.000	0.000
120	A	132	ASN	0	0.006	0.019	43.509	0.005	0.005	0.000	0.000	0.000	0.000
121	A	133	LEU	0	-0.015	0.013	38.793	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	134	ILE	0	-0.034	-0.012	40.814	0.005	0.005	0.000	0.000	0.000	0.000
123	A	135	ALA	0	-0.013	-0.001	40.693	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	136	GLY	0	0.025	0.007	41.026	0.002	0.002	0.000	0.000	0.000	0.000
125	A	137	PRO	0	-0.022	-0.017	37.016	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	138	PHE	0	0.034	0.029	31.376	0.000	0.000	0.000	0.000	0.000	0.000
127	A	139	SER	0	-0.009	-0.013	29.857	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	140	ALA	0	0.003	-0.001	27.512	0.005	0.005	0.000	0.000	0.000	0.000
129	A	141	THR	0	-0.011	-0.004	22.872	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	142	ALA	0	0.011	0.003	20.303	0.009	0.009	0.000	0.000	0.000	0.000
131	A	143	THR	0	-0.021	-0.001	15.117	-0.014	-0.014	0.000	0.000	0.000	0.000
132	A	144	LEU	0	-0.003	-0.002	12.641	0.000	0.000	0.000	0.000	0.000	0.000
133	A	145	VAL	0	-0.001	0.009	9.656	-0.053	-0.053	0.000	0.000	0.000	0.000
134	A	146	ALA	0	0.053	0.001	8.537	0.121	0.121	0.000	0.000	0.000	0.000
135	A	147	SER	0	0.040	0.022	3.094	-0.512	-0.236	0.035	-0.080	-0.231	0.000
136	A	148	TYR	0	0.007	0.005	3.688	0.189	0.589	0.005	-0.085	-0.321	0.000
137	A	149	SER	0	0.008	0.032	2.409	-2.240	-1.669	2.214	-1.056	-1.729	-0.016

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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