FMO DATABASE

FMODB ID: KGVY3

Calculation Name: 3FFM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FFM

Chain ID: A

ChEMBL ID:

UniProt ID: O95257

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	OptHSide
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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1256141.860434
FMO2-HF: Nuclear repulsion	1200615.998358
FMO2-HF: Total energy	-55525.862076
FMO2-MP2: Total energy	-55684.640305

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:15:SER)

Summations of interaction energy for fragment #1(A:15: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.
-3.439	1.948	1.504	-2.901	-3.988	0.011

Interaction energy analysis for fragmet #1(A:15:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.034

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	17	ALA	0	0.041	0.020	3.775	-0.371	2.067	-0.015	-1.422	-1.000	0.008
4	A	18	ARG	1	0.837	0.899	6.506	0.740	0.740	0.000	0.000	0.000	0.000
5	A	19	MET	0	0.024	0.021	2.472	-0.657	0.063	0.481	-0.339	-0.861	-0.003
6	A	20	GLN	0	-0.088	-0.049	2.743	-1.658	0.476	1.039	-1.133	-2.040	0.006
7	A	21	GLY	0	-0.008	-0.016	4.974	-0.573	-0.478	-0.001	-0.007	-0.087	0.000
8	A	22	ALA	0	0.055	0.034	7.318	-0.118	-0.118	0.000	0.000	0.000	0.000
9	A	23	GLY	0	0.066	0.031	7.229	-0.141	-0.141	0.000	0.000	0.000	0.000
10	A	24	LYS	1	0.867	0.929	6.284	-2.082	-2.082	0.000	0.000	0.000	0.000
11	A	25	ALA	0	0.022	0.026	10.746	-0.120	-0.120	0.000	0.000	0.000	0.000
12	A	26	LEU	0	0.071	0.034	11.982	-0.073	-0.073	0.000	0.000	0.000	0.000
13	A	27	HIS	0	-0.040	-0.026	12.581	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	28	GLU	-1	-0.856	-0.939	13.875	0.332	0.332	0.000	0.000	0.000	0.000
15	A	29	LEU	0	0.014	0.011	16.370	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	30	LEU	0	0.010	0.014	15.968	-0.033	-0.033	0.000	0.000	0.000	0.000
17	A	31	LEU	0	-0.034	-0.014	18.350	-0.036	-0.036	0.000	0.000	0.000	0.000
18	A	32	SER	0	-0.071	-0.042	20.650	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	33	ALA	0	0.101	0.046	22.123	-0.022	-0.022	0.000	0.000	0.000	0.000
20	A	34	GLN	0	-0.009	-0.019	23.368	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	35	ARG	1	0.874	0.942	21.738	-0.213	-0.213	0.000	0.000	0.000	0.000
22	A	36	GLN	0	-0.069	-0.035	25.795	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	37	GLY	0	-0.013	0.010	28.283	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	38	CYS	0	-0.053	-0.010	26.107	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	39	LEU	0	-0.011	0.004	21.689	0.006	0.006	0.000	0.000	0.000	0.000
26	A	40	THR	0	-0.007	-0.001	25.681	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	41	ALA	0	0.006	-0.013	25.185	0.013	0.013	0.000	0.000	0.000	0.000
28	A	42	GLY	0	0.070	0.043	25.232	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	43	VAL	0	-0.028	-0.018	26.016	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	44	TYR	0	-0.028	-0.010	28.034	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	45	GLU	-1	-0.768	-0.885	29.865	0.095	0.095	0.000	0.000	0.000	0.000
32	A	46	SER	0	0.015	-0.005	26.484	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	47	ALA	0	0.019	0.002	28.745	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	48	LYS	1	0.765	0.873	31.245	-0.100	-0.100	0.000	0.000	0.000	0.000
35	A	49	VAL	0	0.028	0.016	29.672	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	50	LEU	0	0.005	0.008	27.388	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	51	ASN	0	-0.066	-0.035	31.440	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	52	VAL	0	-0.126	-0.059	34.829	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	53	ASP	-1	-0.911	-0.947	33.762	0.069	0.069	0.000	0.000	0.000	0.000
40	A	54	PRO	0	0.010	0.010	30.769	0.006	0.006	0.000	0.000	0.000	0.000
41	A	55	ASP	-1	-0.923	-0.957	30.021	0.060	0.060	0.000	0.000	0.000	0.000
42	A	56	ASN	0	-0.024	-0.015	30.214	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	57	VAL	0	-0.063	-0.022	24.965	0.011	0.011	0.000	0.000	0.000	0.000
44	A	58	THR	0	-0.032	-0.035	23.485	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	59	PHE	0	-0.006	-0.019	14.903	0.016	0.016	0.000	0.000	0.000	0.000
46	A	60	CYS	0	-0.024	-0.001	19.826	0.000	0.000	0.000	0.000	0.000	0.000
47	A	61	VAL	0	0.004	0.003	15.728	0.022	0.022	0.000	0.000	0.000	0.000
48	A	62	LEU	0	0.009	0.005	17.704	-0.018	-0.018	0.000	0.000	0.000	0.000
49	A	63	ALA	0	-0.025	-0.029	17.083	0.043	0.043	0.000	0.000	0.000	0.000
50	A	64	ALA	0	0.018	-0.007	17.695	-0.036	-0.036	0.000	0.000	0.000	0.000
51	A	65	GLY	0	-0.002	-0.006	17.482	0.043	0.043	0.000	0.000	0.000	0.000
52	A	66	GLU	-1	-0.922	-0.964	18.221	0.246	0.246	0.000	0.000	0.000	0.000
53	A	67	GLU	-1	-0.971	-0.977	20.631	0.157	0.157	0.000	0.000	0.000	0.000
54	A	68	ASP	-1	-0.817	-0.886	22.086	0.199	0.199	0.000	0.000	0.000	0.000
55	A	69	GLU	-1	-0.995	-0.989	22.178	0.154	0.154	0.000	0.000	0.000	0.000
56	A	70	GLY	0	-0.018	-0.016	24.231	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	71	ASP	-1	-0.882	-0.930	26.693	0.114	0.114	0.000	0.000	0.000	0.000
58	A	72	ILE	0	-0.020	-0.037	27.588	0.002	0.002	0.000	0.000	0.000	0.000
59	A	73	ALA	0	-0.007	-0.008	29.593	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	74	LEU	0	0.026	0.022	23.800	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	75	GLN	0	0.030	0.016	22.626	0.003	0.003	0.000	0.000	0.000	0.000
62	A	76	ILE	0	-0.040	-0.007	26.219	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	77	HIS	0	0.025	0.010	27.303	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	78	PHE	0	0.004	0.001	21.849	0.001	0.001	0.000	0.000	0.000	0.000
65	A	79	THR	0	-0.027	-0.017	24.306	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	80	LEU	0	-0.046	-0.025	26.115	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	81	ILE	0	0.025	0.010	23.556	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	82	GLN	0	0.017	0.008	21.457	0.007	0.007	0.000	0.000	0.000	0.000
69	A	83	ALA	0	-0.029	-0.017	23.854	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	84	PHE	0	0.027	0.007	27.046	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	85	CYS	0	-0.012	-0.016	22.930	0.000	0.000	0.000	0.000	0.000	0.000
72	A	86	CYS	0	-0.085	-0.029	22.854	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	87	GLU	-1	-0.945	-0.964	24.690	0.032	0.032	0.000	0.000	0.000	0.000
74	A	88	ASN	0	-0.101	-0.048	27.418	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	89	ASP	-1	-0.932	-0.950	24.651	0.040	0.040	0.000	0.000	0.000	0.000
76	A	90	ILE	0	-0.056	-0.025	22.502	0.007	0.007	0.000	0.000	0.000	0.000
77	A	91	ASP	-1	-0.777	-0.878	17.997	0.102	0.102	0.000	0.000	0.000	0.000
78	A	92	ILE	0	-0.013	-0.020	18.459	0.016	0.016	0.000	0.000	0.000	0.000
79	A	93	VAL	0	-0.025	-0.011	13.195	0.003	0.003	0.000	0.000	0.000	0.000
80	A	94	ARG	1	0.879	0.940	12.563	-0.249	-0.249	0.000	0.000	0.000	0.000
81	A	95	VAL	0	-0.030	-0.026	12.190	0.075	0.075	0.000	0.000	0.000	0.000
82	A	96	GLY	0	0.047	0.014	12.392	-0.058	-0.058	0.000	0.000	0.000	0.000
83	A	97	ASP	-1	-0.873	-0.914	12.165	0.534	0.534	0.000	0.000	0.000	0.000
84	A	98	VAL	0	0.074	0.026	14.125	0.014	0.014	0.000	0.000	0.000	0.000
85	A	99	GLN	0	0.012	0.007	15.522	-0.052	-0.052	0.000	0.000	0.000	0.000
86	A	100	ARG	1	0.845	0.922	12.204	-0.647	-0.647	0.000	0.000	0.000	0.000
87	A	101	LEU	0	0.014	-0.014	15.648	0.003	0.003	0.000	0.000	0.000	0.000
88	A	102	ALA	0	-0.001	-0.008	17.104	-0.030	-0.030	0.000	0.000	0.000	0.000
89	A	103	ALA	0	-0.038	-0.011	17.865	-0.022	-0.022	0.000	0.000	0.000	0.000
90	A	104	ILE	0	-0.098	-0.036	15.293	-0.015	-0.015	0.000	0.000	0.000	0.000
91	A	105	VAL	0	0.017	-0.008	18.662	-0.030	-0.030	0.000	0.000	0.000	0.000
92	A	106	GLY	0	0.028	0.041	21.460	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	107	ALA	0	-0.084	-0.037	22.805	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	108	GLY	0	-0.046	-0.027	24.520	-0.014	-0.014	0.000	0.000	0.000	0.000
95	A	109	GLU	-1	-0.970	-0.986	28.188	0.129	0.129	0.000	0.000	0.000	0.000
96	A	110	GLU	-1	-0.876	-0.943	25.645	0.195	0.195	0.000	0.000	0.000	0.000
97	A	111	ALA	0	-0.039	-0.015	30.042	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	112	GLY	0	-0.053	-0.042	31.565	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	113	ALA	0	0.066	0.021	26.890	0.006	0.006	0.000	0.000	0.000	0.000
100	A	114	PRO	0	-0.039	-0.020	25.203	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	115	GLY	0	-0.016	0.007	26.579	0.008	0.008	0.000	0.000	0.000	0.000
102	A	116	ASP	-1	-0.833	-0.904	26.090	0.167	0.167	0.000	0.000	0.000	0.000
103	A	117	LEU	0	0.019	0.019	21.451	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	118	HIS	1	0.788	0.868	21.287	-0.172	-0.172	0.000	0.000	0.000	0.000
105	A	119	CYS	0	-0.032	-0.012	21.615	0.004	0.004	0.000	0.000	0.000	0.000
106	A	120	ILE	0	-0.029	0.004	20.178	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	121	LEU	0	0.028	0.018	21.754	0.004	0.004	0.000	0.000	0.000	0.000
108	A	122	ILE	0	-0.001	-0.003	20.309	0.009	0.009	0.000	0.000	0.000	0.000
109	A	123	SER	0	0.059	0.030	23.943	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	124	ASN	0	-0.042	-0.023	26.734	0.014	0.014	0.000	0.000	0.000	0.000
111	A	125	PRO	0	-0.034	-0.028	27.659	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	126	ASN	0	-0.103	-0.041	30.844	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	127	GLU	-1	-0.894	-0.947	31.810	0.053	0.053	0.000	0.000	0.000	0.000
114	A	128	ASP	-1	-0.936	-0.959	32.736	0.054	0.054	0.000	0.000	0.000	0.000
115	A	129	ALA	0	0.030	0.013	27.960	0.006	0.006	0.000	0.000	0.000	0.000
116	A	130	TRP	0	0.082	0.036	23.141	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	131	LYS	1	0.925	0.970	24.646	-0.029	-0.029	0.000	0.000	0.000	0.000
118	A	132	ASP	-1	-0.825	-0.924	20.437	0.179	0.179	0.000	0.000	0.000	0.000
119	A	133	PRO	0	-0.014	-0.027	19.073	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	134	ALA	0	-0.018	-0.015	16.243	0.004	0.004	0.000	0.000	0.000	0.000
121	A	135	LEU	0	0.037	0.018	16.177	0.027	0.027	0.000	0.000	0.000	0.000
122	A	136	GLU	-1	-0.936	-0.961	18.209	0.043	0.043	0.000	0.000	0.000	0.000
123	A	137	LYS	1	0.745	0.870	12.281	-0.362	-0.362	0.000	0.000	0.000	0.000
124	A	138	LEU	0	-0.035	-0.019	12.042	0.000	0.000	0.000	0.000	0.000	0.000
125	A	139	SER	0	0.041	0.027	14.482	-0.021	-0.021	0.000	0.000	0.000	0.000
126	A	140	LEU	0	0.009	0.014	14.988	-0.024	-0.024	0.000	0.000	0.000	0.000
127	A	141	PHE	0	-0.013	-0.008	7.321	-0.014	-0.014	0.000	0.000	0.000	0.000
128	A	142	CYS	0	-0.020	-0.024	12.669	-0.022	-0.022	0.000	0.000	0.000	0.000
129	A	143	GLU	-1	-0.928	-0.943	14.960	-0.053	-0.053	0.000	0.000	0.000	0.000
130	A	144	GLU	-1	-0.865	-0.928	12.185	-0.185	-0.185	0.000	0.000	0.000	0.000
131	A	145	SER	0	-0.037	-0.027	11.813	-0.037	-0.037	0.000	0.000	0.000	0.000
132	A	146	ARG	1	0.881	0.942	13.964	-0.067	-0.067	0.000	0.000	0.000	0.000
133	A	147	SER	0	-0.036	-0.012	17.122	-0.005	-0.005	0.000	0.000	0.000	0.000
134	A	148	VAL	0	-0.120	-0.052	13.923	-0.016	-0.016	0.000	0.000	0.000	0.000
135	A	149	ASN	0	-0.069	-0.036	17.355	0.010	0.010	0.000	0.000	0.000	0.000
136	A	150	ASP	-1	-0.857	-0.930	12.807	0.110	0.110	0.000	0.000	0.000	0.000
137	A	151	TRP	0	0.002	-0.029	15.978	0.008	0.008	0.000	0.000	0.000	0.000
138	A	152	VAL	0	0.023	0.034	16.427	0.010	0.010	0.000	0.000	0.000	0.000
139	A	153	PRO	0	-0.013	0.021	11.205	0.023	0.023	0.000	0.000	0.000	0.000
140	A	154	SER	0	-0.001	-0.011	9.304	0.013	0.013	0.000	0.000	0.000	0.000
141	A	155	ILE	0	-0.009	-0.004	7.931	0.029	0.029	0.000	0.000	0.000	0.000
142	A	156	THR	0	-0.043	-0.022	5.432	-0.201	-0.201	0.000	0.000	0.000	0.000
143	A	157	LEU	0	0.019	0.009	7.320	0.429	0.429	0.000	0.000	0.000	0.000
144	A	158	PRO	0	-0.061	-0.013	7.974	0.216	0.216	0.000	0.000	0.000	0.000
145	A	159	GLU	-1	-0.865	-0.931	8.953	0.585	0.585	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:15:SER)