FMO DATABASE

FMODB ID: MVNVZ

Calculation Name: 1A0K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1A0K

Chain ID: A

ChEMBL ID:

UniProt ID: Q42449

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:

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1105907.579496
FMO2-HF: Nuclear repulsion	1056018.674783
FMO2-HF: Total energy	-49888.904713
FMO2-MP2: Total energy	-50033.448914

3D Structure Molmil

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:SER)

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

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.
-17.299	-13.446	10.503	-6.275	-8.082	0.009

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.016

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	GLN	0	-0.030	-0.032	2.427	-3.676	0.135	0.489	-2.055	-2.245	0.008
4	A	5	SER	0	0.060	0.033	2.070	-12.809	-13.574	9.990	-4.092	-5.133	0.000
5	A	6	TYR	0	-0.001	0.016	3.477	-1.252	-0.539	0.025	-0.122	-0.617	0.001
6	A	7	VAL	0	-0.019	-0.015	5.266	0.627	0.721	-0.001	-0.006	-0.087	0.000
7	A	8	ASP	-1	-0.870	-0.960	6.933	1.316	1.316	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.884	-0.938	6.425	-0.486	-0.486	0.000	0.000	0.000	0.000
9	A	10	HIS	0	-0.046	-0.020	6.282	-0.008	-0.008	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.051	-0.028	9.413	0.246	0.246	0.000	0.000	0.000	0.000
11	A	12	MET	0	-0.106	-0.038	11.025	0.119	0.119	0.000	0.000	0.000	0.000
12	A	13	CYS	0	0.003	0.016	12.087	0.112	0.112	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.875	-0.962	13.679	-0.089	-0.089	0.000	0.000	0.000	0.000
14	A	15	VAL	0	-0.080	-0.034	17.481	-0.034	-0.034	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-1.013	-1.026	19.505	-0.113	-0.113	0.000	0.000	0.000	0.000
16	A	17	GLY	0	0.016	0.022	21.446	0.018	0.018	0.000	0.000	0.000	0.000
17	A	18	ASN	0	0.018	0.025	21.720	0.041	0.041	0.000	0.000	0.000	0.000
18	A	19	HIS	1	0.912	0.957	16.447	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.015	-0.008	14.845	0.029	0.029	0.000	0.000	0.000	0.000
20	A	21	THR	0	-0.089	-0.065	17.864	0.046	0.046	0.000	0.000	0.000	0.000
21	A	22	ALA	0	-0.041	-0.031	16.033	0.056	0.056	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.020	0.006	12.734	-0.063	-0.063	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.008	-0.004	11.371	0.137	0.137	0.000	0.000	0.000	0.000
24	A	25	ILE	0	0.019	0.027	7.745	-0.142	-0.142	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.002	0.002	10.868	0.115	0.115	0.000	0.000	0.000	0.000
26	A	27	GLY	0	0.097	0.040	13.271	-0.117	-0.117	0.000	0.000	0.000	0.000
27	A	28	GLN	0	-0.047	-0.039	14.224	0.119	0.119	0.000	0.000	0.000	0.000
28	A	29	ASP	-1	-0.914	-0.935	16.267	-0.174	-0.174	0.000	0.000	0.000	0.000
29	A	30	GLY	0	-0.031	-0.027	17.513	0.038	0.038	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.040	-0.027	13.782	0.018	0.018	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.017	-0.003	10.710	-0.097	-0.097	0.000	0.000	0.000	0.000
32	A	33	TRP	0	-0.049	-0.008	7.590	0.020	0.020	0.000	0.000	0.000	0.000
33	A	34	ALA	0	0.024	0.009	5.891	0.205	0.205	0.000	0.000	0.000	0.000
34	A	35	GLN	0	-0.021	-0.005	7.853	-0.296	-0.296	0.000	0.000	0.000	0.000
35	A	36	SER	0	0.056	0.045	10.367	0.200	0.200	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.001	-0.026	12.352	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.939	0.964	15.023	-0.122	-0.122	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.004	0.009	15.098	-0.048	-0.048	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.013	0.017	17.100	0.031	0.031	0.000	0.000	0.000	0.000
40	A	41	GLN	0	-0.007	0.003	18.743	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	42	LEU	0	0.005	-0.001	19.056	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	43	LYS	1	0.916	0.964	21.690	0.035	0.035	0.000	0.000	0.000	0.000
43	A	44	PRO	0	0.048	0.015	23.596	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	45	GLN	0	0.096	0.029	24.709	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.817	-0.905	24.361	-0.067	-0.067	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.017	0.012	19.473	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	48	ASP	-1	-0.919	-0.960	22.995	-0.140	-0.140	0.000	0.000	0.000	0.000
48	A	49	GLY	0	-0.013	-0.006	25.910	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.002	-0.006	21.759	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	51	LYS	1	0.883	0.940	21.124	0.200	0.200	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.922	0.977	24.685	0.121	0.121	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.838	-0.930	27.256	-0.174	-0.174	0.000	0.000	0.000	0.000
53	A	54	PHE	0	-0.051	-0.031	21.282	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.988	-0.989	25.931	-0.232	-0.232	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.957	-0.973	28.860	-0.115	-0.115	0.000	0.000	0.000	0.000
56	A	57	PRO	0	0.020	0.004	29.612	0.005	0.005	0.000	0.000	0.000	0.000
57	A	58	GLY	0	-0.035	-0.018	31.346	0.011	0.011	0.000	0.000	0.000	0.000
58	A	59	PHE	0	0.001	0.002	30.837	0.014	0.014	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.029	-0.030	27.300	0.012	0.012	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.038	-0.011	32.045	0.008	0.008	0.000	0.000	0.000	0.000
61	A	62	PRO	0	-0.035	-0.011	34.226	0.007	0.007	0.000	0.000	0.000	0.000
62	A	63	THR	0	0.003	-0.004	33.237	0.006	0.006	0.000	0.000	0.000	0.000
63	A	64	GLY	0	-0.074	-0.029	32.719	0.009	0.009	0.000	0.000	0.000	0.000
64	A	65	LEU	0	0.042	0.032	24.967	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	66	PHE	0	-0.030	-0.035	28.140	0.009	0.009	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.016	0.009	21.940	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.030	0.014	24.221	0.010	0.010	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.117	-0.061	24.689	0.014	0.014	0.000	0.000	0.000	0.000
69	A	70	GLU	-1	-0.922	-0.951	26.738	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.940	0.961	28.431	0.057	0.057	0.000	0.000	0.000	0.000
71	A	72	TYR	0	-0.024	-0.002	25.296	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	73	MET	0	-0.054	-0.032	29.824	0.002	0.002	0.000	0.000	0.000	0.000
73	A	74	VAL	0	0.051	0.020	29.538	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.022	-0.007	28.465	0.010	0.010	0.000	0.000	0.000	0.000
75	A	76	GLN	0	-0.003	-0.006	29.822	-0.011	-0.011	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.012	0.007	26.848	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.953	-0.974	24.789	-0.308	-0.308	0.000	0.000	0.000	0.000
78	A	79	GLN	0	0.024	0.000	26.272	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.027	0.026	25.870	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	81	ALA	0	-0.002	0.010	22.239	-0.026	-0.026	0.000	0.000	0.000	0.000
81	A	82	VAL	0	-0.058	-0.041	20.884	-0.041	-0.041	0.000	0.000	0.000	0.000
82	A	83	ILE	0	0.035	0.041	22.749	0.034	0.034	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.799	0.876	23.247	0.264	0.264	0.000	0.000	0.000	0.000
84	A	85	GLY	0	0.039	0.015	25.384	0.016	0.016	0.000	0.000	0.000	0.000
85	A	86	LYS	1	0.863	0.940	26.572	0.096	0.096	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.926	0.970	28.316	0.053	0.053	0.000	0.000	0.000	0.000
87	A	88	GLY	0	-0.002	0.009	29.964	0.004	0.004	0.000	0.000	0.000	0.000
88	A	89	PRO	0	0.002	-0.017	30.439	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	90	GLY	0	0.104	0.060	26.851	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	91	GLY	0	-0.053	-0.034	25.163	0.001	0.001	0.000	0.000	0.000	0.000
91	A	92	VAL	0	-0.035	-0.003	20.686	0.003	0.003	0.000	0.000	0.000	0.000
92	A	93	THR	0	-0.003	-0.008	19.609	0.022	0.022	0.000	0.000	0.000	0.000
93	A	94	ILE	0	-0.029	-0.018	18.839	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	95	LYS	1	0.910	0.970	16.474	0.586	0.586	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.959	0.992	17.188	0.284	0.284	0.000	0.000	0.000	0.000
96	A	97	THR	0	-0.023	-0.036	13.294	0.018	0.018	0.000	0.000	0.000	0.000
97	A	98	ASN	0	-0.019	-0.027	15.713	0.129	0.129	0.000	0.000	0.000	0.000
98	A	99	GLN	0	-0.005	-0.004	12.682	-0.023	-0.023	0.000	0.000	0.000	0.000
99	A	100	ALA	0	-0.028	-0.007	12.193	0.047	0.047	0.000	0.000	0.000	0.000
100	A	101	LEU	0	-0.005	0.010	14.296	0.073	0.073	0.000	0.000	0.000	0.000
101	A	102	VAL	0	0.007	0.008	12.212	-0.028	-0.028	0.000	0.000	0.000	0.000
102	A	103	PHE	0	0.012	-0.009	14.443	0.088	0.088	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.027	-0.005	15.281	-0.029	-0.029	0.000	0.000	0.000	0.000
104	A	105	PHE	0	0.007	0.007	17.355	0.018	0.018	0.000	0.000	0.000	0.000
105	A	106	TYR	0	0.027	-0.004	19.745	0.009	0.009	0.000	0.000	0.000	0.000
106	A	107	ASP	-1	-0.830	-0.899	22.074	-0.040	-0.040	0.000	0.000	0.000	0.000
107	A	108	GLU	-1	-0.945	-0.959	24.837	-0.059	-0.059	0.000	0.000	0.000	0.000
108	A	109	PRO	0	-0.034	-0.023	26.071	0.012	0.012	0.000	0.000	0.000	0.000
109	A	110	MET	0	-0.022	0.019	18.580	-0.011	-0.011	0.000	0.000	0.000	0.000
110	A	111	THR	0	0.006	-0.016	24.489	0.000	0.000	0.000	0.000	0.000	0.000
111	A	112	GLY	0	0.027	0.006	23.732	-0.018	-0.018	0.000	0.000	0.000	0.000
112	A	113	GLY	0	0.003	0.005	23.515	-0.024	-0.024	0.000	0.000	0.000	0.000
113	A	114	GLN	0	0.060	0.022	21.331	-0.023	-0.023	0.000	0.000	0.000	0.000
114	A	115	CYS	0	0.007	0.027	19.213	-0.040	-0.040	0.000	0.000	0.000	0.000
115	A	116	ASN	0	0.014	-0.003	18.698	-0.050	-0.050	0.000	0.000	0.000	0.000
116	A	117	LEU	0	-0.012	0.007	18.610	-0.052	-0.052	0.000	0.000	0.000	0.000
117	A	118	VAL	0	-0.003	-0.010	14.315	-0.068	-0.068	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.022	0.008	14.114	-0.134	-0.134	0.000	0.000	0.000	0.000
119	A	120	GLU	-1	-0.830	-0.922	15.003	-0.476	-0.476	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.932	0.982	12.948	0.694	0.694	0.000	0.000	0.000	0.000
121	A	122	LEU	0	-0.039	-0.002	8.232	-0.086	-0.086	0.000	0.000	0.000	0.000
122	A	123	GLY	0	0.004	-0.018	11.925	-0.134	-0.134	0.000	0.000	0.000	0.000
123	A	124	ASP	-1	-0.837	-0.933	14.135	-0.605	-0.605	0.000	0.000	0.000	0.000
124	A	125	TYR	0	0.004	0.019	6.840	0.205	0.205	0.000	0.000	0.000	0.000
125	A	126	LEU	0	-0.024	-0.014	7.915	-0.104	-0.104	0.000	0.000	0.000	0.000
126	A	127	ILE	0	-0.081	-0.043	11.112	0.088	0.088	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.938	-0.954	13.816	-0.659	-0.659	0.000	0.000	0.000	0.000
128	A	129	SER	0	-0.102	-0.048	10.206	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.954	-0.981	12.154	-0.580	-0.580	0.000	0.000	0.000	0.000
130	A	131	LEU	0	-0.038	0.026	8.331	0.052	0.052	0.000	0.000	0.000	0.000

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