FMO DATABASE

FMODB ID: QVLRY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1257460.472487
FMO2-HF: Nuclear repulsion	1201935.391574
FMO2-HF: Total energy	-55525.080913
FMO2-MP2: Total energy	-55683.985979

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.
-3.613	1.168	2.712	-3.098	-4.397	0.015

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 : 0.058 / 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	0.032	0.019	3.800	0.428	2.907	-0.013	-1.467	-0.999	0.008
4	A	18	ARG	1	0.809	0.877	6.402	0.501	0.501	0.000	0.000	0.000	0.000
5	A	19	MET	0	0.031	0.020	2.537	-0.773	-0.038	0.390	-0.324	-0.802	-0.002
6	A	20	GLN	0	-0.082	-0.047	2.568	-2.484	-1.040	2.336	-1.286	-2.495	0.009
7	A	21	GLY	0	-0.023	-0.024	4.667	-1.049	-0.926	-0.001	-0.021	-0.101	0.000
8	A	22	ALA	0	0.047	0.033	7.451	-0.233	-0.233	0.000	0.000	0.000	0.000
9	A	23	GLY	0	0.063	0.026	7.336	-0.233	-0.233	0.000	0.000	0.000	0.000
10	A	24	LYS	1	0.864	0.923	6.408	-1.920	-1.920	0.000	0.000	0.000	0.000
11	A	25	ALA	0	0.038	0.036	10.560	-0.144	-0.144	0.000	0.000	0.000	0.000
12	A	26	LEU	0	0.059	0.027	12.050	-0.091	-0.091	0.000	0.000	0.000	0.000
13	A	27	HIS	0	-0.044	-0.025	12.426	-0.073	-0.073	0.000	0.000	0.000	0.000
14	A	28	GLU	-1	-0.962	-1.004	14.092	0.367	0.367	0.000	0.000	0.000	0.000
15	A	29	LEU	0	0.009	0.009	16.214	-0.047	-0.047	0.000	0.000	0.000	0.000
16	A	30	LEU	0	-0.005	0.005	15.908	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	31	LEU	0	-0.029	-0.013	18.062	-0.043	-0.043	0.000	0.000	0.000	0.000
18	A	32	SER	0	-0.073	-0.039	20.505	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	33	ALA	0	0.117	0.050	21.981	-0.025	-0.025	0.000	0.000	0.000	0.000
20	A	34	GLN	0	-0.014	-0.026	23.264	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	35	ARG	1	0.866	0.935	21.644	-0.229	-0.229	0.000	0.000	0.000	0.000
22	A	36	GLN	0	-0.072	-0.037	25.444	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	37	GLY	0	-0.010	0.012	28.163	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	38	CYS	0	-0.040	0.006	26.280	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	39	LEU	0	-0.013	0.001	21.849	0.008	0.008	0.000	0.000	0.000	0.000
26	A	40	THR	0	-0.021	-0.008	25.737	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	41	ALA	0	0.017	-0.015	25.209	0.015	0.015	0.000	0.000	0.000	0.000
28	A	42	GLY	0	0.065	0.042	25.230	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	43	VAL	0	-0.035	-0.029	26.067	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	44	TYR	0	-0.035	-0.018	28.007	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	45	GLU	-1	-0.857	-0.948	29.781	0.109	0.109	0.000	0.000	0.000	0.000
32	A	46	SER	0	0.025	0.004	26.459	0.000	0.000	0.000	0.000	0.000	0.000
33	A	47	ALA	0	0.023	0.006	28.745	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	48	LYS	1	0.857	0.938	31.232	-0.108	-0.108	0.000	0.000	0.000	0.000
35	A	49	VAL	0	0.027	0.017	29.793	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	50	LEU	0	-0.004	0.003	27.389	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	51	ASN	0	-0.042	-0.029	31.446	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	52	VAL	0	-0.149	-0.064	34.841	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	53	ASP	-1	-0.895	-0.939	33.603	0.088	0.088	0.000	0.000	0.000	0.000
40	A	54	PRO	0	-0.008	0.005	30.795	0.007	0.007	0.000	0.000	0.000	0.000
41	A	55	ASP	-1	-0.915	-0.956	30.057	0.085	0.085	0.000	0.000	0.000	0.000
42	A	56	ASN	0	-0.028	-0.017	30.281	0.001	0.001	0.000	0.000	0.000	0.000
43	A	57	VAL	0	-0.055	-0.018	24.932	0.013	0.013	0.000	0.000	0.000	0.000
44	A	58	THR	0	-0.027	-0.037	23.538	0.002	0.002	0.000	0.000	0.000	0.000
45	A	59	PHE	0	-0.003	-0.024	14.938	0.024	0.024	0.000	0.000	0.000	0.000
46	A	60	CYS	0	-0.017	0.003	19.855	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	61	VAL	0	0.006	0.009	16.069	0.031	0.031	0.000	0.000	0.000	0.000
48	A	62	LEU	0	-0.004	-0.002	17.678	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	63	ALA	0	-0.020	-0.025	17.040	0.048	0.048	0.000	0.000	0.000	0.000
50	A	64	ALA	0	0.007	-0.012	17.765	-0.038	-0.038	0.000	0.000	0.000	0.000
51	A	65	GLY	0	-0.009	-0.009	17.591	0.043	0.043	0.000	0.000	0.000	0.000
52	A	66	GLU	-1	-0.919	-0.960	18.136	0.230	0.230	0.000	0.000	0.000	0.000
53	A	67	GLU	-1	-0.953	-0.968	20.735	0.148	0.148	0.000	0.000	0.000	0.000
54	A	68	ASP	-1	-0.841	-0.907	22.248	0.203	0.203	0.000	0.000	0.000	0.000
55	A	69	GLU	-1	-0.991	-0.986	22.279	0.157	0.157	0.000	0.000	0.000	0.000
56	A	70	GLY	0	-0.026	-0.023	24.382	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	71	ASP	-1	-0.896	-0.945	26.748	0.124	0.124	0.000	0.000	0.000	0.000
58	A	72	ILE	0	-0.022	-0.033	27.705	0.003	0.003	0.000	0.000	0.000	0.000
59	A	73	ALA	0	-0.006	-0.010	29.558	0.000	0.000	0.000	0.000	0.000	0.000
60	A	74	LEU	0	0.030	0.032	23.896	0.000	0.000	0.000	0.000	0.000	0.000
61	A	75	GLN	0	0.038	0.017	22.225	0.004	0.004	0.000	0.000	0.000	0.000
62	A	76	ILE	0	-0.033	-0.003	26.124	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	77	HIS	0	0.016	0.006	27.148	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	78	PHE	0	0.012	0.006	21.845	0.003	0.003	0.000	0.000	0.000	0.000
65	A	79	THR	0	-0.024	-0.015	24.243	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	80	LEU	0	-0.050	-0.028	26.039	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	81	ILE	0	0.014	0.009	23.574	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	82	GLN	0	0.013	0.002	21.637	0.010	0.010	0.000	0.000	0.000	0.000
69	A	83	ALA	0	-0.040	-0.025	23.809	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	84	PHE	0	0.027	0.007	27.000	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	85	CYS	0	0.005	-0.006	22.915	0.002	0.002	0.000	0.000	0.000	0.000
72	A	86	CYS	0	-0.090	-0.036	22.693	0.001	0.001	0.000	0.000	0.000	0.000
73	A	87	GLU	-1	-0.929	-0.956	24.672	0.061	0.061	0.000	0.000	0.000	0.000
74	A	88	ASN	0	-0.073	-0.031	27.444	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	89	ASP	-1	-0.965	-0.962	24.697	0.083	0.083	0.000	0.000	0.000	0.000
76	A	90	ILE	0	-0.052	-0.021	22.381	0.009	0.009	0.000	0.000	0.000	0.000
77	A	91	ASP	-1	-0.844	-0.941	18.036	0.189	0.189	0.000	0.000	0.000	0.000
78	A	92	ILE	0	-0.008	-0.024	18.458	0.012	0.012	0.000	0.000	0.000	0.000
79	A	93	VAL	0	-0.030	-0.012	13.184	0.014	0.014	0.000	0.000	0.000	0.000
80	A	94	ARG	1	0.892	0.938	13.186	-0.328	-0.328	0.000	0.000	0.000	0.000
81	A	95	VAL	0	-0.022	-0.024	12.298	0.089	0.089	0.000	0.000	0.000	0.000
82	A	96	GLY	0	0.043	0.012	12.482	-0.063	-0.063	0.000	0.000	0.000	0.000
83	A	97	ASP	-1	-0.844	-0.897	12.116	0.527	0.527	0.000	0.000	0.000	0.000
84	A	98	VAL	0	0.068	0.021	14.145	0.015	0.015	0.000	0.000	0.000	0.000
85	A	99	GLN	0	-0.019	-0.012	15.559	-0.048	-0.048	0.000	0.000	0.000	0.000
86	A	100	ARG	1	0.861	0.939	12.363	-0.611	-0.611	0.000	0.000	0.000	0.000
87	A	101	LEU	0	0.014	-0.010	15.725	0.006	0.006	0.000	0.000	0.000	0.000
88	A	102	ALA	0	0.006	-0.007	17.197	-0.027	-0.027	0.000	0.000	0.000	0.000
89	A	103	ALA	0	-0.038	-0.010	17.978	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	104	ILE	0	-0.104	-0.041	14.931	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	105	VAL	0	0.033	0.005	18.706	-0.025	-0.025	0.000	0.000	0.000	0.000
92	A	106	GLY	0	0.037	0.041	21.482	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	107	ALA	0	-0.083	-0.036	22.898	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	108	GLY	0	-0.058	-0.038	24.548	-0.015	-0.015	0.000	0.000	0.000	0.000
95	A	109	GLU	-1	-0.970	-0.986	28.205	0.126	0.126	0.000	0.000	0.000	0.000
96	A	110	GLU	-1	-0.877	-0.935	25.614	0.196	0.196	0.000	0.000	0.000	0.000
97	A	111	ALA	0	-0.020	-0.004	30.120	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	112	GLY	0	-0.055	-0.043	31.705	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	113	ALA	0	0.050	0.007	27.016	0.005	0.005	0.000	0.000	0.000	0.000
100	A	114	PRO	0	-0.029	-0.012	25.285	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	115	GLY	0	-0.019	0.003	26.580	0.008	0.008	0.000	0.000	0.000	0.000
102	A	116	ASP	-1	-0.839	-0.912	25.884	0.180	0.180	0.000	0.000	0.000	0.000
103	A	117	LEU	0	0.021	0.019	21.414	0.000	0.000	0.000	0.000	0.000	0.000
104	A	118	HIS	1	0.822	0.900	21.263	-0.179	-0.179	0.000	0.000	0.000	0.000
105	A	119	CYS	0	-0.019	-0.005	21.575	0.009	0.009	0.000	0.000	0.000	0.000
106	A	120	ILE	0	-0.030	0.011	20.392	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	121	LEU	0	0.018	0.011	21.768	0.009	0.009	0.000	0.000	0.000	0.000
108	A	122	ILE	0	-0.008	0.002	20.575	0.007	0.007	0.000	0.000	0.000	0.000
109	A	123	SER	0	0.031	0.016	23.997	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	124	ASN	0	-0.010	-0.013	26.812	0.012	0.012	0.000	0.000	0.000	0.000
111	A	125	PRO	0	-0.026	-0.017	27.696	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	126	ASN	0	-0.076	-0.029	30.937	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	127	GLU	-1	-0.890	-0.937	31.898	0.070	0.070	0.000	0.000	0.000	0.000
114	A	128	ASP	-1	-0.973	-0.979	32.819	0.080	0.080	0.000	0.000	0.000	0.000
115	A	129	ALA	0	0.000	-0.012	28.025	0.007	0.007	0.000	0.000	0.000	0.000
116	A	130	TRP	0	0.060	0.032	22.901	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	131	LYS	1	0.912	0.962	24.757	-0.064	-0.064	0.000	0.000	0.000	0.000
118	A	132	ASP	-1	-0.823	-0.929	20.769	0.226	0.226	0.000	0.000	0.000	0.000
119	A	133	PRO	0	-0.031	-0.026	18.889	0.004	0.004	0.000	0.000	0.000	0.000
120	A	134	ALA	0	-0.007	-0.004	16.219	0.016	0.016	0.000	0.000	0.000	0.000
121	A	135	LEU	0	0.049	0.020	16.291	0.043	0.043	0.000	0.000	0.000	0.000
122	A	136	GLU	-1	-0.916	-0.956	18.306	0.127	0.127	0.000	0.000	0.000	0.000
123	A	137	LYS	1	0.875	0.942	12.015	-0.421	-0.421	0.000	0.000	0.000	0.000
124	A	138	LEU	0	-0.040	-0.027	12.273	0.029	0.029	0.000	0.000	0.000	0.000
125	A	139	SER	0	0.067	0.060	14.569	-0.014	-0.014	0.000	0.000	0.000	0.000
126	A	140	LEU	0	0.017	0.009	15.018	-0.021	-0.021	0.000	0.000	0.000	0.000
127	A	141	PHE	0	-0.041	-0.018	7.569	0.015	0.015	0.000	0.000	0.000	0.000
128	A	142	CYS	0	0.000	-0.010	12.731	-0.020	-0.020	0.000	0.000	0.000	0.000
129	A	143	GLU	-1	-0.939	-0.950	14.986	0.022	0.022	0.000	0.000	0.000	0.000
130	A	144	GLU	-1	-0.851	-0.924	12.235	0.028	0.028	0.000	0.000	0.000	0.000
131	A	145	SER	0	-0.015	-0.011	11.599	-0.027	-0.027	0.000	0.000	0.000	0.000
132	A	146	ARG	1	0.938	0.986	13.943	-0.149	-0.149	0.000	0.000	0.000	0.000
133	A	147	SER	0	-0.041	-0.013	17.041	-0.018	-0.018	0.000	0.000	0.000	0.000
134	A	148	VAL	0	-0.113	-0.047	13.899	-0.024	-0.024	0.000	0.000	0.000	0.000
135	A	149	ASN	0	-0.061	-0.034	17.300	0.005	0.005	0.000	0.000	0.000	0.000
136	A	150	ASP	-1	-0.912	-0.949	12.705	0.201	0.201	0.000	0.000	0.000	0.000
137	A	151	TRP	0	0.002	-0.031	15.933	0.017	0.017	0.000	0.000	0.000	0.000
138	A	152	VAL	0	0.020	0.034	16.383	0.010	0.010	0.000	0.000	0.000	0.000
139	A	153	PRO	0	0.000	0.028	11.225	0.021	0.021	0.000	0.000	0.000	0.000
140	A	154	SER	0	0.008	-0.007	9.253	0.001	0.001	0.000	0.000	0.000	0.000
141	A	155	ILE	0	0.002	0.003	7.929	0.089	0.089	0.000	0.000	0.000	0.000
142	A	156	THR	0	-0.066	-0.030	5.420	-0.140	-0.140	0.000	0.000	0.000	0.000
143	A	157	LEU	0	0.011	0.002	7.324	0.445	0.445	0.000	0.000	0.000	0.000
144	A	158	PRO	0	-0.070	-0.014	8.053	0.177	0.177	0.000	0.000	0.000	0.000
145	A	159	GLU	-1	-0.862	-0.934	9.015	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)