FMO DATABASE

FMODB ID: MNZVZ

Calculation Name: 4D70-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4D70

Chain ID: A

ChEMBL ID:

UniProt ID: Q8XNW0

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	160
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1617515.153276
FMO2-HF: Nuclear repulsion	1554528.907708
FMO2-HF: Total energy	-62986.245568
FMO2-MP2: Total energy	-63171.452686

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:28:SER)

Summations of interaction energy for fragment #1(A:28: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.
-34.751	-26.076	8.524	-8.316	-8.882	-0.038

Interaction energy analysis for fragmet #1(A:28:SER)

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 : -0.001

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	30	VAL	0	0.049	0.007	3.793	-2.322	-0.256	-0.016	-0.999	-1.051	0.005
4	A	31	GLU	-1	-0.792	-0.826	2.148	-28.140	-23.085	8.429	-6.723	-6.760	-0.047
5	A	32	LYS	1	0.869	0.911	3.261	-4.314	-3.103	0.113	-0.513	-0.811	0.004
6	A	33	LYS	1	0.938	0.976	4.802	-2.875	-2.741	0.000	-0.036	-0.099	0.000
7	A	34	THR	0	0.025	0.004	7.234	-0.601	-0.601	0.000	0.000	0.000	0.000
8	A	35	LEU	0	-0.041	-0.018	6.142	-0.395	-0.395	0.000	0.000	0.000	0.000
9	A	36	GLU	-1	-0.879	-0.944	8.412	0.209	0.209	0.000	0.000	0.000	0.000
10	A	37	GLU	-1	-0.848	-0.932	10.630	0.724	0.724	0.000	0.000	0.000	0.000
11	A	38	PHE	0	-0.032	-0.001	12.200	-0.117	-0.117	0.000	0.000	0.000	0.000
12	A	39	LYS	1	0.939	0.971	9.804	-0.113	-0.113	0.000	0.000	0.000	0.000
13	A	40	GLU	-1	-0.951	-0.972	14.646	0.373	0.373	0.000	0.000	0.000	0.000
14	A	41	LYS	1	0.943	0.967	16.578	-0.336	-0.336	0.000	0.000	0.000	0.000
15	A	42	PHE	0	-0.044	-0.016	15.664	-0.027	-0.027	0.000	0.000	0.000	0.000
16	A	43	ASN	0	-0.081	-0.038	19.947	-0.041	-0.041	0.000	0.000	0.000	0.000
17	A	44	TYR	0	0.000	0.017	20.539	0.006	0.006	0.000	0.000	0.000	0.000
18	A	45	SER	0	-0.040	-0.033	24.062	-0.020	-0.020	0.000	0.000	0.000	0.000
19	A	46	GLU	-1	-0.890	-0.974	26.473	0.032	0.032	0.000	0.000	0.000	0.000
20	A	47	GLU	-1	-0.912	-0.957	27.920	0.073	0.073	0.000	0.000	0.000	0.000
21	A	48	GLU	-1	-0.888	-0.935	25.067	0.134	0.134	0.000	0.000	0.000	0.000
22	A	49	LYS	1	0.867	0.954	22.441	-0.035	-0.035	0.000	0.000	0.000	0.000
23	A	50	LYS	1	0.966	0.987	24.200	-0.042	-0.042	0.000	0.000	0.000	0.000
24	A	51	LYS	1	0.955	0.970	26.380	-0.108	-0.108	0.000	0.000	0.000	0.000
25	A	52	THR	0	-0.074	-0.039	20.832	0.014	0.014	0.000	0.000	0.000	0.000
26	A	53	LEU	0	-0.028	0.006	21.843	0.007	0.007	0.000	0.000	0.000	0.000
27	A	54	GLU	-1	-0.959	-0.970	23.072	0.092	0.092	0.000	0.000	0.000	0.000
28	A	55	GLU	-1	-0.966	-1.019	22.895	0.193	0.193	0.000	0.000	0.000	0.000
29	A	56	ILE	0	-0.060	0.001	17.872	0.031	0.031	0.000	0.000	0.000	0.000
30	A	57	LYS	1	0.922	0.953	18.219	-0.285	-0.285	0.000	0.000	0.000	0.000
31	A	58	ASN	0	-0.011	-0.013	15.660	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	59	GLY	0	-0.063	-0.037	11.779	0.062	0.062	0.000	0.000	0.000	0.000
33	A	60	ASP	-1	-0.844	-0.909	11.604	0.518	0.518	0.000	0.000	0.000	0.000
34	A	61	GLY	0	-0.052	-0.034	12.192	-0.075	-0.075	0.000	0.000	0.000	0.000
35	A	62	ILE	0	-0.028	-0.022	12.903	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	63	ALA	0	0.003	-0.007	14.108	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	64	LEU	0	-0.053	-0.009	11.478	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	65	ILE	0	0.007	0.000	10.864	0.028	0.028	0.000	0.000	0.000	0.000
39	A	66	ASP	-1	-0.857	-0.910	11.799	-0.634	-0.634	0.000	0.000	0.000	0.000
40	A	67	ILE	0	0.018	0.002	13.731	0.074	0.074	0.000	0.000	0.000	0.000
41	A	68	GLU	-1	-0.864	-0.948	15.072	-0.535	-0.535	0.000	0.000	0.000	0.000
42	A	69	LYS	1	0.789	0.897	16.974	0.318	0.318	0.000	0.000	0.000	0.000
43	A	70	ILE	0	-0.045	-0.028	13.984	0.015	0.015	0.000	0.000	0.000	0.000
44	A	71	GLY	0	-0.041	-0.006	12.762	-0.117	-0.117	0.000	0.000	0.000	0.000
45	A	72	VAL	0	-0.004	0.011	9.638	-0.211	-0.211	0.000	0.000	0.000	0.000
46	A	73	HIS	1	0.794	0.866	9.077	0.963	0.963	0.000	0.000	0.000	0.000
47	A	74	THR	0	-0.073	-0.066	5.167	0.404	0.404	0.000	0.000	0.000	0.000
48	A	75	VAL	0	-0.012	-0.001	7.017	0.335	0.335	0.000	0.000	0.000	0.000
49	A	76	ILE	0	-0.038	-0.012	8.926	-0.257	-0.257	0.000	0.000	0.000	0.000
50	A	77	ALA	0	0.017	0.010	9.780	0.132	0.132	0.000	0.000	0.000	0.000
51	A	78	GLU	-1	-0.776	-0.880	11.617	-0.021	-0.021	0.000	0.000	0.000	0.000
52	A	79	GLY	0	0.025	0.022	14.247	0.084	0.084	0.000	0.000	0.000	0.000
53	A	80	SER	0	-0.086	-0.057	14.079	-0.040	-0.040	0.000	0.000	0.000	0.000
54	A	81	THR	0	0.044	0.017	15.208	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	82	LEU	0	0.013	-0.025	13.608	0.007	0.007	0.000	0.000	0.000	0.000
56	A	83	ASP	-1	-0.900	-0.943	12.091	0.572	0.572	0.000	0.000	0.000	0.000
57	A	84	VAL	0	-0.031	-0.002	10.607	0.216	0.216	0.000	0.000	0.000	0.000
58	A	85	LEU	0	-0.023	-0.020	8.849	0.124	0.124	0.000	0.000	0.000	0.000
59	A	86	GLU	-1	-1.049	-1.013	8.032	0.698	0.698	0.000	0.000	0.000	0.000
60	A	87	ASN	0	-0.047	-0.034	4.742	1.585	1.714	-0.001	-0.006	-0.122	0.000
61	A	88	ASN	0	-0.011	-0.003	4.026	-1.383	-1.303	-0.001	-0.039	-0.039	0.000
62	A	89	ILE	0	-0.015	0.006	6.430	0.096	0.096	0.000	0.000	0.000	0.000
63	A	90	GLY	0	0.020	0.018	9.193	0.151	0.151	0.000	0.000	0.000	0.000
64	A	91	HIS	1	0.828	0.903	12.224	-0.040	-0.040	0.000	0.000	0.000	0.000
65	A	92	PHE	0	-0.002	-0.022	15.775	0.045	0.045	0.000	0.000	0.000	0.000
66	A	93	GLU	-1	-0.764	-0.867	18.509	0.071	0.071	0.000	0.000	0.000	0.000
67	A	94	ASN	0	-0.067	-0.030	20.733	0.009	0.009	0.000	0.000	0.000	0.000
68	A	95	THR	0	-0.069	-0.041	20.871	-0.018	-0.018	0.000	0.000	0.000	0.000
69	A	96	ALA	0	0.042	0.025	22.896	0.011	0.011	0.000	0.000	0.000	0.000
70	A	97	MET	0	0.023	0.012	19.589	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	98	PRO	0	-0.016	-0.021	19.009	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	99	GLY	0	0.032	0.014	21.769	0.015	0.015	0.000	0.000	0.000	0.000
73	A	100	GLU	-1	-0.905	-0.955	25.014	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	101	ASN	0	-0.059	-0.033	27.131	-0.015	-0.015	0.000	0.000	0.000	0.000
75	A	102	GLY	0	0.006	0.014	27.943	0.008	0.008	0.000	0.000	0.000	0.000
76	A	103	ASN	0	-0.036	-0.001	23.721	-0.028	-0.028	0.000	0.000	0.000	0.000
77	A	104	PHE	0	0.044	0.040	16.415	0.000	0.000	0.000	0.000	0.000	0.000
78	A	105	SER	0	0.011	0.004	19.647	-0.033	-0.033	0.000	0.000	0.000	0.000
79	A	106	ILE	0	-0.014	-0.008	13.578	0.017	0.017	0.000	0.000	0.000	0.000
80	A	107	ALA	0	0.004	0.007	14.055	-0.016	-0.016	0.000	0.000	0.000	0.000
81	A	108	GLY	0	0.031	-0.010	11.061	-0.069	-0.069	0.000	0.000	0.000	0.000
82	A	109	HIS	0	-0.090	-0.058	11.713	-0.106	-0.106	0.000	0.000	0.000	0.000
83	A	110	ARG	1	0.987	1.010	10.698	-0.335	-0.335	0.000	0.000	0.000	0.000
84	A	111	ASN	0	-0.024	-0.014	13.073	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	112	THR	0	-0.019	-0.015	16.649	-0.032	-0.032	0.000	0.000	0.000	0.000
86	A	113	ILE	0	-0.012	-0.005	11.384	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	114	ASN	0	0.053	0.036	12.230	0.068	0.068	0.000	0.000	0.000	0.000
88	A	115	ASN	0	0.101	0.047	5.388	-0.290	-0.290	0.000	0.000	0.000	0.000
89	A	116	GLU	-1	-0.853	-0.940	6.340	-1.245	-1.245	0.000	0.000	0.000	0.000
90	A	117	VAL	0	-0.038	-0.019	6.368	0.232	0.232	0.000	0.000	0.000	0.000
91	A	118	PHE	0	-0.007	-0.019	8.129	0.313	0.313	0.000	0.000	0.000	0.000
92	A	119	ARG	1	0.913	0.972	10.013	1.440	1.440	0.000	0.000	0.000	0.000
93	A	120	ASN	0	-0.036	-0.025	12.632	0.191	0.191	0.000	0.000	0.000	0.000
94	A	121	ILE	0	0.027	0.014	15.089	0.056	0.056	0.000	0.000	0.000	0.000
95	A	122	ASP	-1	-0.924	-0.961	16.578	-0.429	-0.429	0.000	0.000	0.000	0.000
96	A	123	LYS	1	0.905	0.950	18.047	0.565	0.565	0.000	0.000	0.000	0.000
97	A	124	LEU	0	-0.048	-0.008	16.931	0.019	0.019	0.000	0.000	0.000	0.000
98	A	125	GLN	0	-0.028	-0.023	20.836	0.019	0.019	0.000	0.000	0.000	0.000
99	A	126	VAL	0	0.008	-0.005	24.276	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	127	GLY	0	-0.022	-0.012	26.521	0.004	0.004	0.000	0.000	0.000	0.000
101	A	128	ASP	-1	-0.841	-0.897	21.405	-0.331	-0.331	0.000	0.000	0.000	0.000
102	A	129	GLU	-1	-0.923	-0.979	21.502	-0.218	-0.218	0.000	0.000	0.000	0.000
103	A	130	ILE	0	-0.068	-0.036	16.665	-0.059	-0.059	0.000	0.000	0.000	0.000
104	A	131	LYS	1	0.956	0.987	17.672	0.322	0.322	0.000	0.000	0.000	0.000
105	A	132	ILE	0	-0.003	-0.004	16.030	-0.052	-0.052	0.000	0.000	0.000	0.000
106	A	133	THR	0	-0.007	0.009	16.530	0.040	0.040	0.000	0.000	0.000	0.000
107	A	134	THR	0	0.095	0.037	16.865	0.006	0.006	0.000	0.000	0.000	0.000
108	A	135	LEU	0	-0.015	-0.025	18.016	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	136	THR	0	-0.055	-0.060	20.644	0.010	0.010	0.000	0.000	0.000	0.000
110	A	137	ASP	-1	-0.862	-0.876	22.465	-0.042	-0.042	0.000	0.000	0.000	0.000
111	A	138	ILE	0	-0.050	-0.028	20.248	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	139	PHE	0	0.002	-0.004	21.214	0.008	0.008	0.000	0.000	0.000	0.000
113	A	140	GLN	0	0.027	0.006	21.217	-0.045	-0.045	0.000	0.000	0.000	0.000
114	A	141	TYR	0	0.050	0.023	21.098	0.024	0.024	0.000	0.000	0.000	0.000
115	A	142	GLU	-1	-0.884	-0.944	22.731	-0.201	-0.201	0.000	0.000	0.000	0.000
116	A	143	ILE	0	-0.050	-0.021	20.408	0.017	0.017	0.000	0.000	0.000	0.000
117	A	144	ASN	0	-0.004	-0.024	24.573	0.001	0.001	0.000	0.000	0.000	0.000
118	A	145	GLU	-1	-0.910	-0.945	26.295	-0.132	-0.132	0.000	0.000	0.000	0.000
119	A	146	ILE	0	-0.025	-0.014	23.215	-0.020	-0.020	0.000	0.000	0.000	0.000
120	A	147	PHE	0	-0.012	0.002	24.701	0.015	0.015	0.000	0.000	0.000	0.000
121	A	148	VAL	0	-0.008	-0.001	24.377	-0.021	-0.021	0.000	0.000	0.000	0.000
122	A	149	THR	0	-0.013	-0.041	24.642	0.018	0.018	0.000	0.000	0.000	0.000
123	A	150	SER	0	0.007	0.007	25.336	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	151	PRO	0	-0.024	-0.039	22.877	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	152	SER	0	-0.041	-0.015	24.231	0.010	0.010	0.000	0.000	0.000	0.000
126	A	153	ASP	-1	-0.824	-0.871	26.485	-0.090	-0.090	0.000	0.000	0.000	0.000
127	A	154	THR	0	0.050	0.002	25.710	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	155	ASP	-1	-0.846	-0.914	26.657	-0.061	-0.061	0.000	0.000	0.000	0.000
129	A	156	VAL	0	-0.073	-0.026	23.020	-0.005	-0.005	0.000	0.000	0.000	0.000
130	A	157	LEU	0	0.017	0.008	21.009	-0.015	-0.015	0.000	0.000	0.000	0.000
131	A	158	ASN	0	-0.032	0.006	24.704	0.015	0.015	0.000	0.000	0.000	0.000
132	A	159	GLN	0	-0.029	-0.027	24.618	-0.009	-0.009	0.000	0.000	0.000	0.000
133	A	160	ASN	0	0.055	0.031	28.947	0.015	0.015	0.000	0.000	0.000	0.000
134	A	161	LEU	0	-0.032	-0.043	30.300	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	162	ASP	-1	-0.940	-0.957	32.570	-0.054	-0.054	0.000	0.000	0.000	0.000
136	A	163	GLU	-1	-0.962	-0.964	31.036	-0.097	-0.097	0.000	0.000	0.000	0.000
137	A	164	LYS	1	0.889	0.945	27.692	0.068	0.068	0.000	0.000	0.000	0.000
138	A	165	THR	0	-0.046	-0.022	25.953	-0.013	-0.013	0.000	0.000	0.000	0.000
139	A	166	MET	0	-0.007	0.005	17.418	0.004	0.004	0.000	0.000	0.000	0.000
140	A	167	THR	0	-0.003	-0.030	20.602	0.000	0.000	0.000	0.000	0.000	0.000
141	A	168	ILE	0	-0.023	0.001	15.104	-0.015	-0.015	0.000	0.000	0.000	0.000
142	A	169	VAL	0	0.045	0.030	16.867	0.017	0.017	0.000	0.000	0.000	0.000
143	A	170	THR	0	-0.016	-0.010	13.855	-0.043	-0.043	0.000	0.000	0.000	0.000
144	A	171	CYS	0	-0.039	-0.012	16.184	0.084	0.084	0.000	0.000	0.000	0.000
145	A	172	THR	0	0.056	0.012	18.129	-0.044	-0.044	0.000	0.000	0.000	0.000
146	A	173	ASN	0	-0.037	-0.017	20.683	0.026	0.026	0.000	0.000	0.000	0.000
147	A	174	ARG	1	0.921	0.947	20.815	0.166	0.166	0.000	0.000	0.000	0.000
148	A	175	GLY	0	0.041	0.015	19.550	0.023	0.023	0.000	0.000	0.000	0.000
149	A	176	LYS	1	0.884	0.952	20.421	0.129	0.129	0.000	0.000	0.000	0.000
150	A	177	ASP	-1	-0.817	-0.890	22.976	-0.127	-0.127	0.000	0.000	0.000	0.000
151	A	178	ARG	1	0.854	0.922	19.580	0.131	0.131	0.000	0.000	0.000	0.000
152	A	179	TYR	0	0.007	-0.003	19.260	0.031	0.031	0.000	0.000	0.000	0.000
153	A	180	ILE	0	-0.008	-0.006	19.649	-0.028	-0.028	0.000	0.000	0.000	0.000
154	A	181	VAL	0	0.018	0.012	19.480	0.006	0.006	0.000	0.000	0.000	0.000
155	A	182	LYS	1	0.867	0.930	21.192	0.145	0.145	0.000	0.000	0.000	0.000
156	A	183	ALA	0	0.044	0.020	22.507	-0.008	-0.008	0.000	0.000	0.000	0.000
157	A	184	LYS	1	0.958	0.991	24.417	0.152	0.152	0.000	0.000	0.000	0.000
158	A	185	LEU	0	-0.013	-0.004	24.910	-0.013	-0.013	0.000	0.000	0.000	0.000
159	A	186	ILE	0	-0.019	-0.014	26.165	0.013	0.013	0.000	0.000	0.000	0.000
160	A	187	GLY	0	-0.022	0.002	26.027	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:28:SER)