FMO DATABASE

FMODB ID: 2NGJR

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	OptAll
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	-1618762.349687
FMO2-HF: Nuclear repulsion	1555774.460828
FMO2-HF: Total energy	-62987.888859
FMO2-MP2: Total energy	-63173.206098

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.
-43.47	-44.001	23.03	-11.889	-10.61	-0.059

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 : -0.004 / q_NPA : -0.027

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	0.054	0.024	3.897	-1.593	0.259	-0.015	-0.932	-0.906	0.003
4	A	31	GLU	-1	-0.779	-0.810	1.775	-36.625	-41.190	22.080	-9.809	-7.706	-0.072
5	A	32	LYS	1	0.838	0.905	2.753	-5.439	-3.636	0.939	-0.980	-1.761	0.009
6	A	33	LYS	1	0.801	0.874	4.177	-2.965	-2.620	0.027	-0.162	-0.210	0.001
7	A	34	THR	0	0.052	0.014	6.970	-0.441	-0.441	0.000	0.000	0.000	0.000
8	A	35	LEU	0	-0.034	-0.009	5.457	-0.237	-0.237	0.000	0.000	0.000	0.000
9	A	36	GLU	-1	-0.795	-0.872	7.724	1.059	1.059	0.000	0.000	0.000	0.000
10	A	37	GLU	-1	-0.747	-0.859	10.153	0.627	0.627	0.000	0.000	0.000	0.000
11	A	38	PHE	0	-0.023	-0.009	11.261	-0.123	-0.123	0.000	0.000	0.000	0.000
12	A	39	LYS	1	0.837	0.902	8.881	-0.666	-0.666	0.000	0.000	0.000	0.000
13	A	40	GLU	-1	-0.972	-0.980	14.150	0.432	0.432	0.000	0.000	0.000	0.000
14	A	41	LYS	1	0.851	0.909	15.254	-0.239	-0.239	0.000	0.000	0.000	0.000
15	A	42	PHE	0	-0.042	-0.015	15.260	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	43	ASN	0	-0.099	-0.050	18.825	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	44	TYR	0	-0.014	0.011	19.112	0.001	0.001	0.000	0.000	0.000	0.000
18	A	45	SER	0	-0.026	-0.047	23.439	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	46	GLU	-1	-0.809	-0.916	26.038	0.036	0.036	0.000	0.000	0.000	0.000
20	A	47	GLU	-1	-0.799	-0.875	27.093	0.043	0.043	0.000	0.000	0.000	0.000
21	A	48	GLU	-1	-0.870	-0.900	24.674	0.122	0.122	0.000	0.000	0.000	0.000
22	A	49	LYS	1	0.825	0.904	22.171	-0.033	-0.033	0.000	0.000	0.000	0.000
23	A	50	LYS	1	0.848	0.920	23.048	-0.041	-0.041	0.000	0.000	0.000	0.000
24	A	51	LYS	1	0.830	0.911	25.088	-0.075	-0.075	0.000	0.000	0.000	0.000
25	A	52	THR	0	-0.061	-0.027	19.867	0.019	0.019	0.000	0.000	0.000	0.000
26	A	53	LEU	0	-0.016	0.007	20.579	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	54	GLU	-1	-0.873	-0.955	22.966	0.039	0.039	0.000	0.000	0.000	0.000
28	A	55	GLU	-1	-0.892	-0.957	23.328	0.149	0.149	0.000	0.000	0.000	0.000
29	A	56	ILE	0	0.022	0.038	18.069	0.028	0.028	0.000	0.000	0.000	0.000
30	A	57	LYS	1	0.777	0.870	18.382	-0.164	-0.164	0.000	0.000	0.000	0.000
31	A	58	ASN	0	-0.041	-0.028	16.228	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	59	GLY	0	-0.037	-0.016	12.150	0.060	0.060	0.000	0.000	0.000	0.000
33	A	60	ASP	-1	-0.855	-0.904	11.855	0.288	0.288	0.000	0.000	0.000	0.000
34	A	61	GLY	0	0.001	0.005	12.054	-0.092	-0.092	0.000	0.000	0.000	0.000
35	A	62	ILE	0	-0.010	-0.019	12.636	0.040	0.040	0.000	0.000	0.000	0.000
36	A	63	ALA	0	0.006	-0.004	13.548	0.012	0.012	0.000	0.000	0.000	0.000
37	A	64	LEU	0	-0.043	-0.011	10.640	-0.048	-0.048	0.000	0.000	0.000	0.000
38	A	65	ILE	0	-0.021	-0.019	10.659	0.028	0.028	0.000	0.000	0.000	0.000
39	A	66	ASP	-1	-0.753	-0.853	11.283	-0.679	-0.679	0.000	0.000	0.000	0.000
40	A	67	ILE	0	-0.002	-0.010	13.355	0.075	0.075	0.000	0.000	0.000	0.000
41	A	68	GLU	-1	-0.764	-0.881	14.757	-0.509	-0.509	0.000	0.000	0.000	0.000
42	A	69	LYS	1	0.745	0.864	16.405	0.357	0.357	0.000	0.000	0.000	0.000
43	A	70	ILE	0	-0.037	-0.020	13.792	0.018	0.018	0.000	0.000	0.000	0.000
44	A	71	GLY	0	-0.031	-0.009	12.298	-0.135	-0.135	0.000	0.000	0.000	0.000
45	A	72	VAL	0	-0.030	-0.004	9.552	-0.158	-0.158	0.000	0.000	0.000	0.000
46	A	73	HIS	1	0.782	0.870	8.572	0.925	0.925	0.000	0.000	0.000	0.000
47	A	74	THR	0	-0.042	-0.038	4.810	0.793	0.793	0.000	0.000	0.000	0.000
48	A	75	VAL	0	-0.007	0.003	6.448	0.456	0.456	0.000	0.000	0.000	0.000
49	A	76	ILE	0	-0.018	-0.005	8.712	-0.406	-0.406	0.000	0.000	0.000	0.000
50	A	77	ALA	0	0.002	0.001	10.143	0.176	0.176	0.000	0.000	0.000	0.000
51	A	78	GLU	-1	-0.777	-0.866	11.830	-0.183	-0.183	0.000	0.000	0.000	0.000
52	A	79	GLY	0	0.001	-0.014	14.350	0.058	0.058	0.000	0.000	0.000	0.000
53	A	80	SER	0	-0.078	-0.071	14.336	-0.066	-0.066	0.000	0.000	0.000	0.000
54	A	81	THR	0	-0.020	-0.031	15.805	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	82	LEU	0	0.012	-0.014	13.864	-0.011	-0.011	0.000	0.000	0.000	0.000
56	A	83	ASP	-1	-0.824	-0.889	12.509	0.219	0.219	0.000	0.000	0.000	0.000
57	A	84	VAL	0	0.008	0.014	10.594	0.177	0.177	0.000	0.000	0.000	0.000
58	A	85	LEU	0	-0.006	0.001	8.982	-0.021	-0.021	0.000	0.000	0.000	0.000
59	A	86	GLU	-1	-0.934	-0.942	8.359	0.299	0.299	0.000	0.000	0.000	0.000
60	A	87	ASN	0	-0.075	-0.051	5.214	1.071	1.071	0.000	0.000	0.000	0.000
61	A	88	ASN	0	-0.007	-0.020	4.713	-0.557	-0.523	-0.001	-0.006	-0.027	0.000
62	A	89	ILE	0	-0.022	0.010	6.432	0.117	0.117	0.000	0.000	0.000	0.000
63	A	90	GLY	0	0.028	0.022	8.971	0.172	0.172	0.000	0.000	0.000	0.000
64	A	91	HIS	1	0.838	0.887	12.155	0.112	0.112	0.000	0.000	0.000	0.000
65	A	92	PHE	0	-0.001	-0.013	15.831	0.040	0.040	0.000	0.000	0.000	0.000
66	A	93	GLU	-1	-0.709	-0.813	18.584	-0.075	-0.075	0.000	0.000	0.000	0.000
67	A	94	ASN	0	-0.089	-0.037	20.762	0.018	0.018	0.000	0.000	0.000	0.000
68	A	95	THR	0	-0.059	-0.044	21.007	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	96	ALA	0	0.049	0.030	22.769	0.006	0.006	0.000	0.000	0.000	0.000
70	A	97	MET	0	0.032	0.010	19.243	-0.039	-0.039	0.000	0.000	0.000	0.000
71	A	98	PRO	0	-0.013	-0.018	18.470	-0.005	-0.005	0.000	0.000	0.000	0.000
72	A	99	GLY	0	0.030	0.019	21.354	0.024	0.024	0.000	0.000	0.000	0.000
73	A	100	GLU	-1	-0.885	-0.929	24.788	-0.071	-0.071	0.000	0.000	0.000	0.000
74	A	101	ASN	0	-0.069	-0.043	26.860	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	102	GLY	0	0.014	0.019	27.758	0.006	0.006	0.000	0.000	0.000	0.000
76	A	103	ASN	0	-0.023	0.009	23.434	-0.032	-0.032	0.000	0.000	0.000	0.000
77	A	104	PHE	0	0.049	0.037	16.020	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	105	SER	0	-0.001	0.004	19.682	-0.038	-0.038	0.000	0.000	0.000	0.000
79	A	106	ILE	0	-0.020	-0.009	13.591	0.009	0.009	0.000	0.000	0.000	0.000
80	A	107	ALA	0	-0.007	0.001	13.870	0.006	0.006	0.000	0.000	0.000	0.000
81	A	108	GLY	0	0.054	0.009	10.653	-0.128	-0.128	0.000	0.000	0.000	0.000
82	A	109	HIS	0	-0.069	-0.046	11.281	-0.098	-0.098	0.000	0.000	0.000	0.000
83	A	110	ARG	1	0.843	0.913	11.303	-0.169	-0.169	0.000	0.000	0.000	0.000
84	A	111	ASN	0	0.009	-0.008	13.240	0.008	0.008	0.000	0.000	0.000	0.000
85	A	112	THR	0	-0.024	-0.018	16.678	-0.017	-0.017	0.000	0.000	0.000	0.000
86	A	113	ILE	0	-0.016	-0.004	11.933	-0.014	-0.014	0.000	0.000	0.000	0.000
87	A	114	ASN	0	0.053	0.023	12.337	0.035	0.035	0.000	0.000	0.000	0.000
88	A	115	ASN	0	0.069	0.033	4.846	-0.351	-0.351	0.000	0.000	0.000	0.000
89	A	116	GLU	-1	-0.800	-0.906	6.176	-1.290	-1.290	0.000	0.000	0.000	0.000
90	A	117	VAL	0	-0.023	0.001	6.085	0.317	0.317	0.000	0.000	0.000	0.000
91	A	118	PHE	0	0.048	0.012	7.982	0.383	0.383	0.000	0.000	0.000	0.000
92	A	119	ARG	1	0.806	0.900	9.692	1.502	1.502	0.000	0.000	0.000	0.000
93	A	120	ASN	0	-0.005	-0.006	12.580	0.214	0.214	0.000	0.000	0.000	0.000
94	A	121	ILE	0	0.037	0.030	14.839	0.067	0.067	0.000	0.000	0.000	0.000
95	A	122	ASP	-1	-0.849	-0.910	16.544	-0.487	-0.487	0.000	0.000	0.000	0.000
96	A	123	LYS	1	0.785	0.872	16.967	0.623	0.623	0.000	0.000	0.000	0.000
97	A	124	LEU	0	-0.026	0.001	16.787	0.012	0.012	0.000	0.000	0.000	0.000
98	A	125	GLN	0	-0.011	-0.010	20.874	0.018	0.018	0.000	0.000	0.000	0.000
99	A	126	VAL	0	0.007	0.002	24.392	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	127	GLY	0	-0.007	0.002	26.522	0.011	0.011	0.000	0.000	0.000	0.000
101	A	128	ASP	-1	-0.806	-0.883	21.210	-0.370	-0.370	0.000	0.000	0.000	0.000
102	A	129	GLU	-1	-0.885	-0.950	21.315	-0.247	-0.247	0.000	0.000	0.000	0.000
103	A	130	ILE	0	-0.041	-0.023	16.513	-0.061	-0.061	0.000	0.000	0.000	0.000
104	A	131	LYS	1	0.820	0.900	16.082	0.389	0.389	0.000	0.000	0.000	0.000
105	A	132	ILE	0	0.015	0.002	15.837	-0.080	-0.080	0.000	0.000	0.000	0.000
106	A	133	THR	0	-0.062	-0.028	16.204	0.050	0.050	0.000	0.000	0.000	0.000
107	A	134	THR	0	0.078	0.034	16.407	-0.009	-0.009	0.000	0.000	0.000	0.000
108	A	135	LEU	0	-0.005	-0.010	17.244	0.010	0.010	0.000	0.000	0.000	0.000
109	A	136	THR	0	-0.054	-0.060	20.104	0.022	0.022	0.000	0.000	0.000	0.000
110	A	137	ASP	-1	-0.842	-0.873	21.936	-0.068	-0.068	0.000	0.000	0.000	0.000
111	A	138	ILE	0	-0.039	-0.021	20.063	-0.012	-0.012	0.000	0.000	0.000	0.000
112	A	139	PHE	0	0.003	0.004	20.862	0.010	0.010	0.000	0.000	0.000	0.000
113	A	140	GLN	0	-0.021	-0.009	20.846	-0.043	-0.043	0.000	0.000	0.000	0.000
114	A	141	TYR	0	0.060	0.016	20.801	0.027	0.027	0.000	0.000	0.000	0.000
115	A	142	GLU	-1	-0.811	-0.881	22.406	-0.222	-0.222	0.000	0.000	0.000	0.000
116	A	143	ILE	0	-0.015	-0.017	19.932	0.007	0.007	0.000	0.000	0.000	0.000
117	A	144	ASN	0	0.013	-0.007	24.216	0.008	0.008	0.000	0.000	0.000	0.000
118	A	145	GLU	-1	-0.910	-0.969	25.798	-0.184	-0.184	0.000	0.000	0.000	0.000
119	A	146	ILE	0	-0.018	-0.002	22.591	-0.026	-0.026	0.000	0.000	0.000	0.000
120	A	147	PHE	0	-0.036	-0.003	24.316	0.021	0.021	0.000	0.000	0.000	0.000
121	A	148	VAL	0	-0.026	-0.022	23.660	-0.030	-0.030	0.000	0.000	0.000	0.000
122	A	149	THR	0	-0.036	-0.039	24.395	0.026	0.026	0.000	0.000	0.000	0.000
123	A	150	SER	0	0.027	0.023	25.092	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	151	PRO	0	-0.005	-0.032	22.958	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	152	SER	0	-0.024	-0.011	24.166	0.004	0.004	0.000	0.000	0.000	0.000
126	A	153	ASP	-1	-0.840	-0.883	25.942	-0.159	-0.159	0.000	0.000	0.000	0.000
127	A	154	THR	0	0.038	-0.004	25.227	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	155	ASP	-1	-0.871	-0.925	26.360	-0.122	-0.122	0.000	0.000	0.000	0.000
129	A	156	VAL	0	-0.031	-0.011	22.716	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	157	LEU	0	0.013	0.014	20.908	-0.017	-0.017	0.000	0.000	0.000	0.000
131	A	158	ASN	0	-0.045	0.006	24.576	0.016	0.016	0.000	0.000	0.000	0.000
132	A	159	GLN	0	-0.036	-0.038	24.328	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	160	ASN	0	0.004	-0.016	28.793	0.020	0.020	0.000	0.000	0.000	0.000
134	A	161	LEU	0	-0.002	-0.010	30.188	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	162	ASP	-1	-0.953	-0.958	32.397	-0.081	-0.081	0.000	0.000	0.000	0.000
136	A	163	GLU	-1	-0.901	-0.923	30.574	-0.139	-0.139	0.000	0.000	0.000	0.000
137	A	164	LYS	1	0.849	0.903	27.695	0.110	0.110	0.000	0.000	0.000	0.000
138	A	165	THR	0	-0.027	-0.014	25.612	-0.012	-0.012	0.000	0.000	0.000	0.000
139	A	166	MET	0	-0.032	-0.002	17.089	0.000	0.000	0.000	0.000	0.000	0.000
140	A	167	THR	0	0.011	-0.024	20.354	0.011	0.011	0.000	0.000	0.000	0.000
141	A	168	ILE	0	-0.019	0.002	14.662	-0.031	-0.031	0.000	0.000	0.000	0.000
142	A	169	VAL	0	0.032	0.024	16.583	0.031	0.031	0.000	0.000	0.000	0.000
143	A	170	THR	0	-0.020	-0.013	13.756	-0.088	-0.088	0.000	0.000	0.000	0.000
144	A	171	CYS	0	-0.038	-0.007	16.042	0.100	0.100	0.000	0.000	0.000	0.000
145	A	172	THR	0	0.064	0.023	17.938	-0.041	-0.041	0.000	0.000	0.000	0.000
146	A	173	ASN	0	-0.008	-0.001	20.635	0.031	0.031	0.000	0.000	0.000	0.000
147	A	174	ARG	1	0.906	0.933	20.922	0.208	0.208	0.000	0.000	0.000	0.000
148	A	175	GLY	0	0.075	0.046	19.668	0.019	0.019	0.000	0.000	0.000	0.000
149	A	176	LYS	1	0.814	0.918	20.568	0.184	0.184	0.000	0.000	0.000	0.000
150	A	177	ASP	-1	-0.793	-0.883	23.148	-0.184	-0.184	0.000	0.000	0.000	0.000
151	A	178	ARG	1	0.806	0.883	19.133	0.232	0.232	0.000	0.000	0.000	0.000
152	A	179	TYR	0	-0.014	-0.011	18.667	0.052	0.052	0.000	0.000	0.000	0.000
153	A	180	ILE	0	-0.002	0.005	19.332	-0.044	-0.044	0.000	0.000	0.000	0.000
154	A	181	VAL	0	0.016	0.007	19.046	0.014	0.014	0.000	0.000	0.000	0.000
155	A	182	LYS	1	0.856	0.923	20.795	0.217	0.217	0.000	0.000	0.000	0.000
156	A	183	ALA	0	0.026	0.012	22.187	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	184	LYS	1	0.854	0.929	24.076	0.187	0.187	0.000	0.000	0.000	0.000
158	A	185	LEU	0	-0.025	-0.012	24.299	-0.012	-0.012	0.000	0.000	0.000	0.000
159	A	186	ILE	0	-0.060	-0.037	25.627	0.016	0.016	0.000	0.000	0.000	0.000
160	A	187	GLY	0	-0.024	0.000	25.446	0.007	0.007	0.000	0.000	0.000	0.000

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