FMO DATABASE

FMODB ID: 1NMYZ

Calculation Name: 5MDT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MDT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UTE3

Base Structure: X-ray

Registration Date: 2023-09-23

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1405897.070975
FMO2-HF: Nuclear repulsion	1348138.336184
FMO2-HF: Total energy	-57758.73479
FMO2-MP2: Total energy	-57928.160804

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: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.
-31.096	-24.156	13.516	-9.775	-10.68	-0.059

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 : -0.002 / q_NPA : -0.010

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	ILE	0	0.016	0.013	3.846	-3.503	-0.441	-0.033	-1.903	-1.127	0.003
4	A	5	ALA	0	0.028	0.020	6.320	-0.130	-0.130	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.916	-0.957	2.405	-14.620	-11.380	0.869	-1.918	-2.190	-0.024
6	A	7	PHE	0	-0.023	-0.014	5.266	-0.202	-0.137	-0.001	-0.003	-0.060	0.000
7	A	8	ASP	-1	-0.801	-0.910	7.350	-0.281	-0.281	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.051	0.038	8.910	0.038	0.038	0.000	0.000	0.000	0.000
9	A	10	ILE	0	-0.079	-0.050	6.750	0.077	0.077	0.000	0.000	0.000	0.000
10	A	11	LEU	0	-0.031	-0.019	10.632	0.106	0.106	0.000	0.000	0.000	0.000
11	A	12	ASP	-1	-0.853	-0.917	13.107	-0.243	-0.243	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.079	-0.038	13.078	0.038	0.038	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.101	-0.048	14.936	0.034	0.034	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.826	-0.884	16.690	-0.207	-0.207	0.000	0.000	0.000	0.000
15	A	16	HIS	0	-0.025	-0.015	17.884	0.057	0.057	0.000	0.000	0.000	0.000
16	A	17	SER	0	-0.113	-0.052	19.117	0.018	0.018	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.985	0.965	21.086	0.206	0.206	0.000	0.000	0.000	0.000
18	A	19	THR	0	-0.005	-0.011	22.884	0.005	0.005	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.072	0.063	19.903	0.010	0.010	0.000	0.000	0.000	0.000
20	A	21	ILE	0	0.004	-0.009	19.529	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	22	SER	0	-0.029	-0.019	16.079	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	23	GLY	0	0.058	0.030	16.056	-0.046	-0.046	0.000	0.000	0.000	0.000
23	A	24	SER	0	0.017	0.004	13.692	-0.054	-0.054	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.964	0.976	11.520	0.519	0.519	0.000	0.000	0.000	0.000
25	A	26	ILE	0	0.058	0.042	11.213	-0.131	-0.131	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.009	0.008	11.752	-0.078	-0.078	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.944	0.972	7.432	1.354	1.354	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.002	0.007	6.956	-0.441	-0.441	0.000	0.000	0.000	0.000
29	A	30	THR	0	0.023	0.016	7.825	-0.078	-0.078	0.000	0.000	0.000	0.000
30	A	31	ASN	0	0.001	0.015	5.521	0.376	0.376	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.002	0.010	2.077	0.299	-1.513	6.506	-2.005	-2.688	0.011
32	A	33	SER	0	-0.060	-0.032	3.931	-0.215	-0.065	0.000	-0.077	-0.072	0.000
33	A	34	MET	0	-0.045	-0.024	6.658	0.328	0.328	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.923	-0.963	2.090	-10.909	-10.035	4.568	-2.530	-2.913	-0.030
35	A	36	ASN	0	-0.033	-0.019	2.302	-4.723	-3.382	1.608	-1.339	-1.611	-0.019
36	A	37	VAL	0	0.064	0.045	5.346	0.113	0.133	-0.001	0.000	-0.019	0.000
37	A	38	SER	0	0.022	0.016	8.989	0.027	0.027	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.967	-0.986	7.981	0.192	0.192	0.000	0.000	0.000	0.000
39	A	40	ASN	0	-0.001	-0.010	10.014	-0.078	-0.078	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.012	0.001	11.249	-0.025	-0.025	0.000	0.000	0.000	0.000
41	A	42	GLN	0	0.003	0.008	10.345	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	43	PHE	0	0.036	0.014	4.826	0.032	0.032	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.003	0.001	10.690	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.012	0.006	14.155	0.014	0.014	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.025	-0.040	12.207	0.049	0.049	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.007	0.001	12.965	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	48	TYR	0	0.004	0.008	15.433	0.033	0.033	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.932	0.953	17.344	0.149	0.149	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.017	0.004	16.155	0.014	0.014	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.033	0.001	18.246	0.016	0.016	0.000	0.000	0.000	0.000
51	A	52	LYS	1	0.859	0.935	20.818	0.161	0.161	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.826	0.911	15.848	0.279	0.279	0.000	0.000	0.000	0.000
53	A	54	ALA	0	-0.007	0.015	20.738	0.006	0.006	0.000	0.000	0.000	0.000
54	A	55	PRO	0	0.047	0.022	22.587	0.020	0.020	0.000	0.000	0.000	0.000
55	A	56	VAL	0	0.049	0.017	25.249	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.042	-0.047	25.575	0.002	0.002	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.010	0.013	20.647	0.000	0.000	0.000	0.000	0.000	0.000
58	A	59	LYS	1	0.874	0.970	21.977	0.164	0.164	0.000	0.000	0.000	0.000
59	A	60	LEU	0	-0.008	0.000	23.007	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.030	0.011	20.469	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.007	0.001	18.313	-0.047	-0.047	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.027	0.014	18.545	-0.024	-0.024	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.017	-0.017	19.335	0.004	0.004	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.009	0.002	13.369	-0.035	-0.035	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.006	0.003	15.083	-0.044	-0.044	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.804	-0.877	16.881	-0.335	-0.335	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.050	-0.040	13.462	0.034	0.034	0.000	0.000	0.000	0.000
68	A	69	ILE	0	0.005	0.001	10.972	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	70	VAL	0	-0.006	0.007	13.440	0.023	0.023	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.831	0.883	16.473	0.372	0.372	0.000	0.000	0.000	0.000
71	A	72	SER	0	0.019	0.027	12.285	0.014	0.014	0.000	0.000	0.000	0.000
72	A	73	PHE	0	0.007	-0.012	10.153	0.029	0.029	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.007	0.006	14.330	0.035	0.035	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.949	-0.983	16.014	-0.245	-0.245	0.000	0.000	0.000	0.000
75	A	76	GLY	0	-0.025	-0.016	14.466	0.036	0.036	0.000	0.000	0.000	0.000
76	A	77	ALA	0	0.012	0.010	15.417	0.047	0.047	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.960	0.983	18.167	0.190	0.190	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.919	0.961	14.742	0.135	0.135	0.000	0.000	0.000	0.000
79	A	80	ASN	0	-0.078	-0.041	15.464	0.050	0.050	0.000	0.000	0.000	0.000
80	A	81	ASN	0	-0.057	-0.016	19.449	0.007	0.007	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.770	-0.837	17.570	-0.049	-0.049	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.006	-0.008	21.679	-0.016	-0.016	0.000	0.000	0.000	0.000
83	A	84	PHE	0	-0.001	-0.016	21.555	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.937	-0.974	23.401	-0.059	-0.059	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.063	-0.025	25.551	0.009	0.009	0.000	0.000	0.000	0.000
86	A	87	PRO	0	0.013	0.010	20.278	0.004	0.004	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.023	0.018	18.057	0.017	0.017	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.899	-0.958	17.570	-0.045	-0.045	0.000	0.000	0.000	0.000
89	A	90	ALA	0	-0.039	-0.026	14.359	-0.032	-0.032	0.000	0.000	0.000	0.000
90	A	91	SER	0	-0.005	-0.031	13.318	0.017	0.017	0.000	0.000	0.000	0.000
91	A	92	PHE	0	-0.009	-0.022	10.559	-0.045	-0.045	0.000	0.000	0.000	0.000
92	A	93	SER	0	0.006	-0.015	14.591	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.027	0.036	16.888	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	95	GLY	0	-0.002	-0.003	13.916	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	96	TRP	0	-0.040	-0.030	14.853	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	97	CYS	0	0.020	0.009	17.565	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	98	LYS	1	0.912	0.955	15.780	0.126	0.126	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.001	-0.007	16.100	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	100	ALA	0	-0.002	-0.008	18.028	0.006	0.006	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-0.955	-0.974	21.473	-0.096	-0.096	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.056	-0.015	17.828	0.009	0.009	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.019	-0.025	21.380	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.866	-0.935	23.203	-0.130	-0.130	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.023	-0.013	24.578	0.006	0.006	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.015	-0.008	19.758	0.001	0.001	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.014	0.008	24.328	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	108	ALA	0	-0.008	-0.001	26.954	0.006	0.006	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.856	-0.936	26.106	-0.161	-0.161	0.000	0.000	0.000	0.000
109	A	110	ALA	0	-0.005	-0.012	26.254	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	ILE	0	-0.047	-0.028	28.188	0.004	0.004	0.000	0.000	0.000	0.000
111	A	112	GLN	0	-0.057	-0.012	31.459	0.004	0.004	0.000	0.000	0.000	0.000
112	A	113	HIS	0	-0.012	-0.007	29.292	0.005	0.005	0.000	0.000	0.000	0.000
113	A	114	ALA	0	-0.033	-0.008	28.544	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	115	PRO	0	0.008	0.002	29.598	0.010	0.010	0.000	0.000	0.000	0.000
115	A	116	SER	0	0.104	0.036	32.199	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.030	-0.013	32.935	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	118	HIS	0	-0.027	-0.023	27.212	0.000	0.000	0.000	0.000	0.000	0.000
118	A	119	LEU	0	0.058	0.044	29.693	-0.010	-0.010	0.000	0.000	0.000	0.000
119	A	120	PRO	0	0.017	-0.004	31.343	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	121	LYS	1	0.870	0.932	27.476	0.186	0.186	0.000	0.000	0.000	0.000
121	A	122	ILE	0	0.074	0.040	26.455	-0.013	-0.013	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.016	0.010	28.035	0.000	0.000	0.000	0.000	0.000	0.000
123	A	124	LYS	1	0.931	0.959	28.353	0.162	0.162	0.000	0.000	0.000	0.000
124	A	125	LEU	0	0.000	0.017	22.648	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	126	CYS	0	-0.014	0.000	25.869	0.001	0.001	0.000	0.000	0.000	0.000
126	A	127	ASP	-1	-0.849	-0.913	28.216	-0.138	-0.138	0.000	0.000	0.000	0.000
127	A	128	ILE	0	-0.080	-0.039	22.974	0.004	0.004	0.000	0.000	0.000	0.000
128	A	129	TRP	0	-0.014	-0.034	21.286	0.011	0.011	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.820	-0.898	25.373	-0.112	-0.112	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.912	0.960	27.494	0.172	0.172	0.000	0.000	0.000	0.000
131	A	132	ALA	0	-0.036	-0.017	23.104	0.006	0.006	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.005	0.004	24.683	0.005	0.005	0.000	0.000	0.000	0.000
133	A	134	THR	0	-0.050	-0.025	20.875	0.004	0.004	0.000	0.000	0.000	0.000
134	A	135	PHE	0	0.015	0.001	21.335	0.000	0.000	0.000	0.000	0.000	0.000
135	A	136	PRO	0	0.064	0.030	25.925	0.003	0.003	0.000	0.000	0.000	0.000
136	A	137	PRO	0	0.059	0.008	29.434	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	138	GLU	-1	-0.862	-0.917	32.374	-0.073	-0.073	0.000	0.000	0.000	0.000
138	A	139	LYS	1	0.904	0.972	24.926	0.138	0.138	0.000	0.000	0.000	0.000
139	A	140	LEU	0	-0.010	-0.016	27.198	-0.005	-0.005	0.000	0.000	0.000	0.000
140	A	141	GLU	-1	-0.944	-0.956	30.767	-0.082	-0.082	0.000	0.000	0.000	0.000
141	A	142	SER	0	-0.008	-0.009	32.294	0.003	0.003	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.061	-0.032	27.116	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	144	ARG	1	0.815	0.885	31.491	0.123	0.123	0.000	0.000	0.000	0.000
144	A	145	SER	0	-0.004	0.006	33.806	0.002	0.002	0.000	0.000	0.000	0.000
145	A	146	LYS	1	1.001	0.998	32.731	0.101	0.101	0.000	0.000	0.000	0.000
146	A	147	LEU	0	-0.005	-0.009	29.930	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	148	LYS	1	0.888	0.936	34.314	0.107	0.107	0.000	0.000	0.000	0.000
148	A	149	ASP	-1	-0.888	-0.928	37.785	-0.082	-0.082	0.000	0.000	0.000	0.000
149	A	150	ALA	0	-0.016	-0.010	35.570	0.002	0.002	0.000	0.000	0.000	0.000
150	A	151	MET	0	-0.150	-0.072	35.433	-0.004	-0.004	0.000	0.000	0.000	0.000
151	A	152	ALA	0	0.010	0.016	38.609	0.002	0.002	0.000	0.000	0.000	0.000
152	A	153	LEU	0	-0.016	0.001	42.159	0.002	0.002	0.000	0.000	0.000	0.000

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