FMO DATABASE

FMODB ID: 6N9KZ

Calculation Name: 2D7V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D7V

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KMK9

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:

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1283804.516854
FMO2-HF: Nuclear repulsion	1224055.046754
FMO2-HF: Total energy	-59749.4701
FMO2-MP2: Total energy	-59923.374656

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:7:SER)

Summations of interaction energy for fragment #1(A:7: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.
-0.571	1.407	0	-1.028	-0.951	0.003

Interaction energy analysis for fragmet #1(A:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.005

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].	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	9	SER	0	-0.006	0.003	3.693	0.765	2.743	-1.028	-0.951	0.003
4	A	10	GLU	-1	-0.966	-0.973	6.325	-0.684	-0.684	0.000	0.000	0.000
5	A	11	HIS	0	-0.008	-0.015	7.264	0.438	0.438	0.000	0.000	0.000
6	A	12	SER	0	-0.067	-0.042	12.432	-0.019	-0.019	0.000	0.000	0.000
7	A	13	ALA	0	0.042	-0.003	16.282	0.001	0.001	0.000	0.000	0.000
8	A	14	ILE	0	-0.025	-0.003	19.328	0.001	0.001	0.000	0.000	0.000
9	A	15	VAL	0	0.019	0.015	22.648	0.013	0.013	0.000	0.000	0.000
10	A	16	THR	0	-0.053	-0.039	25.010	0.017	0.017	0.000	0.000	0.000
11	A	17	TRP	0	0.029	0.015	28.725	0.002	0.002	0.000	0.000	0.000
12	A	18	LYS	1	0.921	0.953	32.160	0.084	0.084	0.000	0.000	0.000
13	A	19	ARG	1	0.852	0.934	35.569	0.065	0.065	0.000	0.000	0.000
14	A	20	LYS	1	0.882	0.942	36.288	0.085	0.085	0.000	0.000	0.000
15	A	21	ASP	-1	-0.837	-0.914	41.458	-0.053	-0.053	0.000	0.000	0.000
16	A	22	SER	0	-0.014	-0.026	44.892	0.000	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.824	-0.892	40.487	-0.081	-0.081	0.000	0.000	0.000
18	A	24	ALA	0	0.046	0.024	44.672	0.000	0.000	0.000	0.000	0.000
19	A	25	PHE	0	-0.025	0.003	37.786	-0.001	-0.001	0.000	0.000	0.000
20	A	26	THR	0	-0.018	-0.031	42.968	-0.004	-0.004	0.000	0.000	0.000
21	A	27	ASP	-1	-0.817	-0.912	44.752	-0.073	-0.073	0.000	0.000	0.000
22	A	28	ASN	0	-0.031	-0.007	40.890	-0.005	-0.005	0.000	0.000	0.000
23	A	29	GLN	0	0.006	0.000	42.395	-0.006	-0.006	0.000	0.000	0.000
24	A	30	TYR	0	-0.017	0.012	36.622	0.000	0.000	0.000	0.000	0.000
25	A	31	SER	0	0.056	0.034	37.850	-0.006	-0.006	0.000	0.000	0.000
26	A	32	ARG	1	0.800	0.859	33.902	0.104	0.104	0.000	0.000	0.000
27	A	33	ALA	0	0.018	0.031	32.960	-0.010	-0.010	0.000	0.000	0.000
28	A	34	HIS	0	-0.126	-0.068	27.890	-0.006	-0.006	0.000	0.000	0.000
29	A	35	THR	0	-0.045	-0.022	27.940	0.007	0.007	0.000	0.000	0.000
30	A	36	TRP	0	-0.009	-0.011	22.593	-0.016	-0.016	0.000	0.000	0.000
31	A	37	GLU	-1	-0.793	-0.870	22.930	-0.074	-0.074	0.000	0.000	0.000
32	A	38	PHE	0	0.006	0.004	17.551	-0.025	-0.025	0.000	0.000	0.000
33	A	39	ASP	-1	-0.807	-0.880	15.730	-0.151	-0.151	0.000	0.000	0.000
34	A	40	GLY	0	-0.041	-0.013	17.754	0.038	0.038	0.000	0.000	0.000
35	A	41	GLY	0	-0.008	-0.002	18.719	0.011	0.011	0.000	0.000	0.000
36	A	42	SER	0	-0.037	-0.010	20.938	0.005	0.005	0.000	0.000	0.000
37	A	43	LYS	1	0.819	0.869	22.721	0.069	0.069	0.000	0.000	0.000
38	A	44	ILE	0	-0.003	0.002	21.822	0.007	0.007	0.000	0.000	0.000
39	A	45	LEU	0	-0.010	-0.002	26.042	-0.003	-0.003	0.000	0.000	0.000
40	A	46	ALA	0	0.049	0.028	26.688	-0.005	-0.005	0.000	0.000	0.000
41	A	47	SER	0	0.002	-0.019	28.776	0.019	0.019	0.000	0.000	0.000
42	A	48	ALA	0	0.001	0.001	29.710	-0.015	-0.015	0.000	0.000	0.000
43	A	49	SER	0	0.022	-0.007	30.335	0.012	0.012	0.000	0.000	0.000
44	A	50	PRO	0	0.049	0.016	32.053	0.005	0.005	0.000	0.000	0.000
45	A	51	HIS	0	-0.048	-0.018	32.140	0.011	0.011	0.000	0.000	0.000
46	A	52	VAL	0	-0.087	-0.040	32.326	0.000	0.000	0.000	0.000	0.000
47	A	53	VAL	0	-0.016	-0.010	35.356	0.003	0.003	0.000	0.000	0.000
48	A	54	PRO	0	0.023	0.043	37.229	-0.002	-0.002	0.000	0.000	0.000
49	A	55	VAL	0	0.058	0.053	38.301	0.000	0.000	0.000	0.000	0.000
50	A	56	PRO	0	-0.061	-0.034	40.388	0.003	0.003	0.000	0.000	0.000
51	A	57	LEU	0	-0.029	-0.013	39.583	0.000	0.000	0.000	0.000	0.000
52	A	58	SER	0	-0.056	-0.035	35.072	-0.003	-0.003	0.000	0.000	0.000
53	A	59	VAL	0	0.005	-0.025	34.923	0.008	0.008	0.000	0.000	0.000
54	A	60	GLU	-1	-0.860	-0.945	34.044	-0.095	-0.095	0.000	0.000	0.000
55	A	61	ALA	0	-0.063	-0.021	33.614	-0.003	-0.003	0.000	0.000	0.000
56	A	62	ASN	0	-0.097	-0.043	30.679	0.006	0.006	0.000	0.000	0.000
57	A	63	VAL	0	0.022	0.030	24.655	-0.002	-0.002	0.000	0.000	0.000
58	A	64	ASP	-1	-0.759	-0.855	27.779	-0.184	-0.184	0.000	0.000	0.000
59	A	65	PRO	0	0.008	-0.023	24.285	-0.017	-0.017	0.000	0.000	0.000
60	A	66	GLU	-1	-0.899	-0.958	23.561	-0.248	-0.248	0.000	0.000	0.000
61	A	67	GLU	-1	-0.863	-0.938	24.479	-0.184	-0.184	0.000	0.000	0.000
62	A	68	ALA	0	-0.014	-0.009	21.095	-0.015	-0.015	0.000	0.000	0.000
63	A	69	PHE	0	-0.023	-0.009	19.762	-0.043	-0.043	0.000	0.000	0.000
64	A	70	VAL	0	0.005	-0.004	19.695	-0.032	-0.032	0.000	0.000	0.000
65	A	71	ALA	0	0.005	0.005	20.648	-0.012	-0.012	0.000	0.000	0.000
66	A	72	ALA	0	-0.010	-0.006	15.866	-0.016	-0.016	0.000	0.000	0.000
67	A	73	LEU	0	0.001	-0.003	15.666	-0.057	-0.057	0.000	0.000	0.000
68	A	74	SER	0	-0.041	-0.039	16.821	-0.007	-0.007	0.000	0.000	0.000
69	A	75	SER	0	-0.007	-0.008	16.123	0.006	0.006	0.000	0.000	0.000
70	A	76	CYS	0	-0.018	-0.001	11.290	-0.071	-0.071	0.000	0.000	0.000
71	A	77	HIS	0	0.086	0.068	12.890	0.015	0.015	0.000	0.000	0.000
72	A	78	MET	0	-0.011	-0.006	15.422	0.047	0.047	0.000	0.000	0.000
73	A	79	LEU	0	-0.001	-0.006	12.094	0.052	0.052	0.000	0.000	0.000
74	A	80	VAL	0	0.022	0.025	9.979	0.073	0.073	0.000	0.000	0.000
75	A	81	PHE	0	0.049	0.013	12.579	0.100	0.100	0.000	0.000	0.000
76	A	82	LEU	0	0.010	0.003	16.304	0.050	0.050	0.000	0.000	0.000
77	A	83	SER	0	-0.047	-0.022	12.567	0.075	0.075	0.000	0.000	0.000
78	A	84	ILE	0	-0.013	-0.010	14.193	0.065	0.065	0.000	0.000	0.000
79	A	85	ALA	0	0.027	0.000	16.303	0.028	0.028	0.000	0.000	0.000
80	A	86	ALA	0	0.006	0.011	17.020	0.019	0.019	0.000	0.000	0.000
81	A	87	LYS	1	0.894	0.943	11.084	-0.110	-0.110	0.000	0.000	0.000
82	A	88	GLN	0	-0.069	-0.023	17.991	0.002	0.002	0.000	0.000	0.000
83	A	89	ARG	1	0.902	0.961	21.221	-0.070	-0.070	0.000	0.000	0.000
84	A	90	TYR	0	0.000	0.005	22.368	-0.005	-0.005	0.000	0.000	0.000
85	A	91	LEU	0	0.006	0.011	23.219	-0.002	-0.002	0.000	0.000	0.000
86	A	92	VAL	0	-0.021	-0.023	22.146	-0.008	-0.008	0.000	0.000	0.000
87	A	93	GLU	-1	-0.866	-0.889	24.656	-0.005	-0.005	0.000	0.000	0.000
88	A	94	SER	0	-0.012	-0.013	24.934	-0.003	-0.003	0.000	0.000	0.000
89	A	95	TYR	0	0.066	0.018	20.046	0.002	0.002	0.000	0.000	0.000
90	A	96	THR	0	-0.039	-0.028	23.800	0.002	0.002	0.000	0.000	0.000
91	A	97	ASP	-1	-0.730	-0.844	21.934	-0.215	-0.215	0.000	0.000	0.000
92	A	98	ASN	0	-0.019	0.012	24.934	-0.002	-0.002	0.000	0.000	0.000
93	A	99	ALA	0	0.026	0.021	23.547	0.006	0.006	0.000	0.000	0.000
94	A	100	VAL	0	-0.019	-0.003	25.604	0.011	0.011	0.000	0.000	0.000
95	A	101	GLY	0	0.036	0.013	26.074	-0.016	-0.016	0.000	0.000	0.000
96	A	102	ILE	0	-0.038	-0.015	26.749	0.016	0.016	0.000	0.000	0.000
97	A	103	LEU	0	0.037	0.017	28.635	-0.011	-0.011	0.000	0.000	0.000
98	A	104	GLY	0	0.031	0.012	30.506	0.013	0.013	0.000	0.000	0.000
99	A	105	LYS	1	0.819	0.908	31.396	0.138	0.138	0.000	0.000	0.000
100	A	106	ASN	0	0.078	0.033	26.624	0.019	0.019	0.000	0.000	0.000
101	A	107	SER	0	0.028	0.003	28.761	0.008	0.008	0.000	0.000	0.000
102	A	108	LYS	1	0.828	0.904	25.139	0.273	0.273	0.000	0.000	0.000
103	A	109	GLY	0	0.044	0.032	31.396	0.006	0.006	0.000	0.000	0.000
104	A	110	LYS	1	0.925	0.960	28.282	0.221	0.221	0.000	0.000	0.000
105	A	111	THR	0	0.036	-0.001	30.583	-0.004	-0.004	0.000	0.000	0.000
106	A	112	SER	0	-0.008	0.005	26.268	-0.011	-0.011	0.000	0.000	0.000
107	A	113	VAL	0	0.078	0.042	24.139	0.019	0.019	0.000	0.000	0.000
108	A	114	THR	0	-0.072	-0.013	24.818	-0.017	-0.017	0.000	0.000	0.000
109	A	115	LYS	1	0.848	0.903	25.560	0.171	0.171	0.000	0.000	0.000
110	A	116	VAL	0	-0.007	-0.012	21.759	0.003	0.003	0.000	0.000	0.000
111	A	117	VAL	0	-0.018	0.009	24.124	-0.005	-0.005	0.000	0.000	0.000
112	A	118	LEU	0	0.017	0.010	19.058	0.006	0.006	0.000	0.000	0.000
113	A	119	ARG	1	0.844	0.914	23.723	0.156	0.156	0.000	0.000	0.000
114	A	120	PRO	0	-0.021	-0.003	22.218	0.011	0.011	0.000	0.000	0.000
115	A	121	GLN	0	0.026	0.022	24.733	0.014	0.014	0.000	0.000	0.000
116	A	122	VAL	0	-0.042	-0.038	23.255	-0.007	-0.007	0.000	0.000	0.000
117	A	123	VAL	0	-0.002	0.018	26.252	0.008	0.008	0.000	0.000	0.000
118	A	124	PHE	0	0.063	0.018	23.807	0.002	0.002	0.000	0.000	0.000
119	A	125	SER	0	-0.054	-0.065	28.497	0.002	0.002	0.000	0.000	0.000
120	A	126	GLY	0	0.046	0.014	29.865	0.003	0.003	0.000	0.000	0.000
121	A	127	THR	0	-0.034	-0.030	31.661	-0.004	-0.004	0.000	0.000	0.000
122	A	128	SER	0	-0.033	-0.022	27.025	0.003	0.003	0.000	0.000	0.000
123	A	129	LYS	1	0.874	0.944	28.007	0.009	0.009	0.000	0.000	0.000
124	A	130	PRO	0	0.002	0.022	25.229	0.005	0.005	0.000	0.000	0.000
125	A	131	THR	0	0.002	-0.006	27.509	-0.004	-0.004	0.000	0.000	0.000
126	A	132	LEU	0	0.048	0.016	28.006	-0.005	-0.005	0.000	0.000	0.000
127	A	133	GLN	0	0.103	0.035	27.638	-0.009	-0.009	0.000	0.000	0.000
128	A	134	GLN	0	-0.025	0.003	24.866	-0.004	-0.004	0.000	0.000	0.000
129	A	135	LEU	0	0.036	0.011	23.378	-0.008	-0.008	0.000	0.000	0.000
130	A	136	GLU	-1	-0.904	-0.961	23.111	-0.098	-0.098	0.000	0.000	0.000
131	A	137	LYS	1	0.969	0.985	20.921	0.028	0.028	0.000	0.000	0.000
132	A	138	MET	0	-0.046	-0.007	19.043	-0.007	-0.007	0.000	0.000	0.000
133	A	139	HIS	1	0.862	0.914	18.087	0.142	0.142	0.000	0.000	0.000
134	A	140	HIS	0	-0.056	-0.015	18.669	-0.029	-0.029	0.000	0.000	0.000
135	A	141	LEU	0	0.013	0.006	15.371	-0.029	-0.029	0.000	0.000	0.000
136	A	142	ALA	0	-0.026	-0.017	14.109	-0.050	-0.050	0.000	0.000	0.000
137	A	143	HIS	0	-0.013	0.000	14.137	-0.087	-0.087	0.000	0.000	0.000
138	A	144	GLU	-1	-0.846	-0.928	14.323	-0.276	-0.276	0.000	0.000	0.000
139	A	145	ASN	0	-0.073	-0.041	9.856	-0.068	-0.068	0.000	0.000	0.000
140	A	146	CYS	0	-0.038	0.015	9.645	-0.219	-0.219	0.000	0.000	0.000
141	A	147	PHE	0	0.051	0.014	5.386	-0.172	-0.172	0.000	0.000	0.000
142	A	148	ILE	0	0.025	0.014	9.781	0.037	0.037	0.000	0.000	0.000
143	A	149	ALA	0	0.054	0.004	13.159	0.067	0.067	0.000	0.000	0.000
144	A	150	ASN	0	-0.113	-0.063	11.247	0.093	0.093	0.000	0.000	0.000
145	A	151	SER	0	-0.047	-0.022	11.877	-0.075	-0.075	0.000	0.000	0.000
146	A	152	VAL	0	-0.062	-0.027	14.366	0.055	0.055	0.000	0.000	0.000
147	A	153	GLU	-1	-0.829	-0.901	18.160	-0.271	-0.271	0.000	0.000	0.000
148	A	154	THR	0	-0.062	-0.027	20.914	0.018	0.018	0.000	0.000	0.000
149	A	155	GLU	-1	-0.786	-0.873	21.483	-0.208	-0.208	0.000	0.000	0.000
150	A	156	VAL	0	-0.004	0.001	18.765	0.015	0.015	0.000	0.000	0.000
151	A	157	VAL	0	-0.006	0.003	21.619	0.002	0.002	0.000	0.000	0.000
152	A	158	THR	0	-0.016	-0.027	21.485	-0.013	-0.013	0.000	0.000	0.000
153	A	159	GLU	-1	-0.909	-0.950	23.901	-0.122	-0.122	0.000	0.000	0.000
154	A	160	ILE	0	-0.022	-0.021	24.138	-0.002	-0.002	0.000	0.000	0.000
155	A	161	ILE	0	-0.038	-0.009	26.839	0.013	0.013	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)