FMO DATABASE

FMODB ID: R9ZL8

Calculation Name: 4RMM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RMM

Chain ID: A

ChEMBL ID:

UniProt ID: Q7NVP2

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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1244446.563572
FMO2-HF: Nuclear repulsion	1189558.207571
FMO2-HF: Total energy	-54888.356001
FMO2-MP2: Total energy	-55046.36339

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:5:MET)

Summations of interaction energy for fragment #1(A:5:MET)

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.
-7.984	-3.193	5.092	-2.487	-7.398	-0.008

Interaction energy analysis for fragmet #1(A:5:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.002

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	7	ARG	1	0.994	0.984	3.858	-2.336	-0.622	-0.003	-0.752	-0.960	0.000
4	A	8	PHE	0	0.007	0.020	2.899	-1.533	0.288	0.313	-0.624	-1.511	-0.002
5	A	9	ALA	0	0.009	0.004	4.576	0.583	0.767	-0.001	-0.016	-0.167	0.000
6	A	10	ASP	-1	-0.858	-0.925	6.933	-0.156	-0.156	0.000	0.000	0.000	0.000
7	A	11	LEU	0	0.006	-0.005	8.144	0.153	0.153	0.000	0.000	0.000	0.000
8	A	12	ARG	1	0.808	0.915	6.117	1.981	1.981	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.933	-0.961	9.777	-0.396	-0.396	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.775	0.869	11.816	0.578	0.578	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.841	0.921	13.209	0.769	0.769	0.000	0.000	0.000	0.000
12	A	16	ALA	0	0.016	0.022	12.060	0.082	0.082	0.000	0.000	0.000	0.000
13	A	17	TYR	0	-0.016	-0.038	12.299	-0.075	-0.075	0.000	0.000	0.000	0.000
14	A	18	ALA	0	0.015	0.011	12.641	-0.038	-0.038	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.832	-0.922	12.188	-0.441	-0.441	0.000	0.000	0.000	0.000
16	A	20	ILE	0	-0.058	-0.025	6.575	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.002	-0.007	7.636	-0.280	-0.280	0.000	0.000	0.000	0.000
18	A	22	ASP	-1	-0.846	-0.907	10.068	-0.226	-0.226	0.000	0.000	0.000	0.000
19	A	23	ALA	0	-0.060	-0.023	7.950	0.127	0.127	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.019	-0.003	4.326	-0.148	-0.055	-0.001	-0.005	-0.087	0.000
21	A	25	PRO	0	0.007	-0.002	8.350	0.103	0.103	0.000	0.000	0.000	0.000
22	A	26	TYR	0	0.067	0.008	6.874	0.029	0.029	0.000	0.000	0.000	0.000
23	A	27	VAL	0	0.016	0.037	12.171	0.044	0.044	0.000	0.000	0.000	0.000
24	A	28	LYS	1	0.776	0.877	12.908	0.388	0.388	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.037	0.005	14.847	0.043	0.043	0.000	0.000	0.000	0.000
26	A	30	MET	0	-0.025	-0.013	16.454	0.026	0.026	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.026	0.026	17.034	-0.028	-0.028	0.000	0.000	0.000	0.000
28	A	32	THR	0	-0.068	-0.058	13.679	0.017	0.017	0.000	0.000	0.000	0.000
29	A	33	SER	0	-0.008	0.005	15.978	-0.033	-0.033	0.000	0.000	0.000	0.000
30	A	34	MET	0	-0.018	-0.011	9.553	-0.046	-0.046	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.027	0.016	15.209	0.017	0.017	0.000	0.000	0.000	0.000
32	A	36	GLU	-1	-0.745	-0.871	14.594	-0.726	-0.726	0.000	0.000	0.000	0.000
33	A	37	ASH	0	-0.058	-0.032	17.646	0.045	0.045	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.881	-0.937	21.107	-0.270	-0.270	0.000	0.000	0.000	0.000
35	A	39	GLN	0	-0.056	-0.026	21.461	0.013	0.013	0.000	0.000	0.000	0.000
36	A	40	GLY	0	0.004	0.004	20.564	0.016	0.016	0.000	0.000	0.000	0.000
37	A	41	GLU	-1	-0.845	-0.925	15.333	-0.474	-0.474	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.037	0.006	10.463	0.028	0.028	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.889	0.940	14.656	0.371	0.371	0.000	0.000	0.000	0.000
40	A	44	PHE	0	0.008	-0.006	10.962	-0.045	-0.045	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.825	-0.896	16.736	-0.238	-0.238	0.000	0.000	0.000	0.000
42	A	46	LEU	0	0.026	0.017	18.332	-0.029	-0.029	0.000	0.000	0.000	0.000
43	A	47	PRO	0	0.026	0.022	20.644	0.021	0.021	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.025	-0.008	23.168	0.015	0.015	0.000	0.000	0.000	0.000
45	A	49	LEU	0	-0.005	0.009	25.472	0.012	0.012	0.000	0.000	0.000	0.000
46	A	50	GLN	0	-0.012	-0.027	25.270	0.005	0.005	0.000	0.000	0.000	0.000
47	A	59	PRO	0	0.026	-0.008	23.375	0.006	0.006	0.000	0.000	0.000	0.000
48	A	60	ALA	0	-0.005	0.018	24.495	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	61	LEU	0	0.040	0.037	21.753	0.008	0.008	0.000	0.000	0.000	0.000
50	A	62	HIS	0	0.023	-0.001	24.497	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	63	GLY	0	-0.023	-0.013	26.685	0.000	0.000	0.000	0.000	0.000	0.000
52	A	64	GLY	0	-0.009	0.002	25.771	0.000	0.000	0.000	0.000	0.000	0.000
53	A	65	LEU	0	-0.003	-0.006	22.537	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	66	ILE	0	0.046	0.012	19.458	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	67	GLY	0	-0.005	-0.003	17.921	-0.029	-0.029	0.000	0.000	0.000	0.000
56	A	68	GLY	0	0.070	0.036	14.536	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	69	PHE	0	0.020	0.017	13.295	-0.064	-0.064	0.000	0.000	0.000	0.000
58	A	70	MET	0	0.010	0.000	13.797	-0.076	-0.076	0.000	0.000	0.000	0.000
59	A	71	GLU	-1	-0.912	-0.957	11.721	-0.232	-0.232	0.000	0.000	0.000	0.000
60	A	72	SER	0	-0.027	-0.038	9.380	-0.055	-0.055	0.000	0.000	0.000	0.000
61	A	73	ALA	0	-0.005	0.010	9.133	-0.202	-0.202	0.000	0.000	0.000	0.000
62	A	74	ALA	0	0.040	0.008	10.805	-0.100	-0.100	0.000	0.000	0.000	0.000
63	A	75	MET	0	-0.051	-0.017	5.307	0.038	0.038	0.000	0.000	0.000	0.000
64	A	76	ILE	0	0.006	-0.009	5.991	-0.293	-0.293	0.000	0.000	0.000	0.000
65	A	77	HIS	0	0.053	0.019	7.031	-0.132	-0.132	0.000	0.000	0.000	0.000
66	A	78	LEU	0	-0.046	-0.022	8.169	0.031	0.031	0.000	0.000	0.000	0.000
67	A	79	MET	0	-0.060	-0.028	2.505	-0.847	-1.739	3.252	-0.384	-1.975	-0.004
68	A	80	TRP	0	-0.055	-0.020	6.059	-0.232	-0.232	0.000	0.000	0.000	0.000
69	A	81	ASN	0	-0.038	-0.029	8.113	0.076	0.076	0.000	0.000	0.000	0.000
70	A	82	ARG	1	0.838	0.921	8.933	0.532	0.532	0.000	0.000	0.000	0.000
71	A	83	GLU	-1	-0.822	-0.901	8.375	-0.792	-0.792	0.000	0.000	0.000	0.000
72	A	84	SER	0	-0.011	-0.009	3.865	0.003	0.161	-0.001	-0.016	-0.141	0.000
73	A	85	LEU	0	-0.090	-0.034	4.298	-0.753	-0.634	-0.001	-0.028	-0.090	0.000
74	A	86	GLU	-1	-0.826	-0.924	3.682	0.549	1.055	0.076	-0.181	-0.401	0.000
75	A	87	ALA	0	0.042	0.028	2.835	-1.764	-0.730	1.424	-0.638	-1.820	-0.002
76	A	88	PRO	0	-0.033	-0.005	3.873	-0.281	-0.227	0.034	0.157	-0.246	0.000
77	A	89	LYS	1	0.816	0.893	7.090	-1.248	-1.248	0.000	0.000	0.000	0.000
78	A	90	ILE	0	0.009	0.014	9.624	-0.071	-0.071	0.000	0.000	0.000	0.000
79	A	91	VAL	0	-0.071	-0.033	11.443	0.061	0.061	0.000	0.000	0.000	0.000
80	A	92	ASP	-1	-0.841	-0.901	15.210	-0.070	-0.070	0.000	0.000	0.000	0.000
81	A	93	PHE	0	0.059	0.020	15.101	-0.035	-0.035	0.000	0.000	0.000	0.000
82	A	94	SER	0	-0.042	-0.010	17.271	0.025	0.025	0.000	0.000	0.000	0.000
83	A	95	LEU	0	0.002	-0.006	19.582	-0.025	-0.025	0.000	0.000	0.000	0.000
84	A	96	ASP	-1	-0.814	-0.873	21.667	-0.115	-0.115	0.000	0.000	0.000	0.000
85	A	97	TYR	0	0.039	-0.004	22.458	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	98	LEU	0	-0.026	-0.009	26.527	0.012	0.012	0.000	0.000	0.000	0.000
87	A	99	ARG	1	0.861	0.930	28.729	0.139	0.139	0.000	0.000	0.000	0.000
88	A	100	PRO	0	0.021	0.008	29.122	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	101	GLY	0	0.005	0.015	28.362	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	102	ARG	1	0.859	0.915	29.194	0.154	0.154	0.000	0.000	0.000	0.000
91	A	103	PRO	0	0.029	0.010	29.633	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	104	GLN	0	-0.045	-0.042	29.055	0.002	0.002	0.000	0.000	0.000	0.000
93	A	105	THR	0	-0.026	-0.043	23.530	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	106	LEU	0	-0.070	-0.038	21.898	0.016	0.016	0.000	0.000	0.000	0.000
95	A	107	PHE	0	-0.009	0.011	21.368	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	108	ALA	0	0.012	-0.003	17.717	0.022	0.022	0.000	0.000	0.000	0.000
97	A	109	GLN	0	-0.017	-0.004	17.124	0.003	0.003	0.000	0.000	0.000	0.000
98	A	110	CYS	0	-0.024	-0.008	14.451	0.020	0.020	0.000	0.000	0.000	0.000
99	A	111	GLU	-1	-0.784	-0.861	16.667	-0.248	-0.248	0.000	0.000	0.000	0.000
100	A	112	ILE	0	-0.016	-0.018	13.049	0.000	0.000	0.000	0.000	0.000	0.000
101	A	113	THR	0	-0.013	-0.015	16.929	0.022	0.022	0.000	0.000	0.000	0.000
102	A	114	LYS	1	0.877	0.940	18.886	0.144	0.144	0.000	0.000	0.000	0.000
103	A	115	GLN	0	0.032	0.006	13.736	-0.026	-0.026	0.000	0.000	0.000	0.000
104	A	116	GLY	0	0.025	0.020	17.751	0.007	0.007	0.000	0.000	0.000	0.000
105	A	117	LYS	1	0.856	0.911	17.349	0.051	0.051	0.000	0.000	0.000	0.000
106	A	118	ARG	1	0.889	0.937	14.580	-0.083	-0.083	0.000	0.000	0.000	0.000
107	A	119	VAL	0	0.019	0.010	15.196	0.024	0.024	0.000	0.000	0.000	0.000
108	A	120	ALA	0	0.021	0.029	13.083	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	121	HIS	0	-0.023	-0.015	15.215	0.042	0.042	0.000	0.000	0.000	0.000
110	A	122	VAL	0	0.005	-0.001	12.504	-0.020	-0.020	0.000	0.000	0.000	0.000
111	A	123	LEU	0	0.000	0.016	15.977	0.033	0.033	0.000	0.000	0.000	0.000
112	A	124	ILE	0	0.017	-0.012	15.076	-0.040	-0.040	0.000	0.000	0.000	0.000
113	A	125	GLU	-1	-0.813	-0.866	18.238	-0.206	-0.206	0.000	0.000	0.000	0.000
114	A	126	ALA	0	0.041	0.007	20.208	-0.031	-0.031	0.000	0.000	0.000	0.000
115	A	127	TRP	0	-0.026	-0.024	21.281	0.024	0.024	0.000	0.000	0.000	0.000
116	A	128	GLN	0	0.038	0.027	24.919	0.001	0.001	0.000	0.000	0.000	0.000
117	A	129	ASP	-1	-0.838	-0.898	27.640	-0.147	-0.147	0.000	0.000	0.000	0.000
118	A	130	ASP	-1	-0.780	-0.859	30.359	-0.140	-0.140	0.000	0.000	0.000	0.000
119	A	131	ARG	1	0.785	0.853	21.568	0.271	0.271	0.000	0.000	0.000	0.000
120	A	132	SER	0	-0.040	-0.040	28.088	0.003	0.003	0.000	0.000	0.000	0.000
121	A	133	LYS	1	0.776	0.869	30.501	0.129	0.129	0.000	0.000	0.000	0.000
122	A	134	PRO	0	0.010	0.014	25.620	0.002	0.002	0.000	0.000	0.000	0.000
123	A	135	VAL	0	-0.013	-0.001	25.285	0.013	0.013	0.000	0.000	0.000	0.000
124	A	136	ALA	0	-0.025	-0.015	22.891	0.012	0.012	0.000	0.000	0.000	0.000
125	A	137	VAL	0	0.011	0.011	22.003	-0.015	-0.015	0.000	0.000	0.000	0.000
126	A	138	ALA	0	0.002	0.004	18.213	0.016	0.016	0.000	0.000	0.000	0.000
127	A	139	ARG	1	0.813	0.890	18.448	0.134	0.134	0.000	0.000	0.000	0.000
128	A	140	ALA	0	0.038	0.029	13.885	0.016	0.016	0.000	0.000	0.000	0.000
129	A	141	HIS	1	0.763	0.860	15.291	0.111	0.111	0.000	0.000	0.000	0.000
130	A	142	PHE	0	0.083	0.036	8.594	0.008	0.008	0.000	0.000	0.000	0.000
131	A	143	LEU	0	-0.001	0.005	12.500	-0.019	-0.019	0.000	0.000	0.000	0.000
132	A	144	LEU	0	0.002	-0.001	10.060	0.055	0.055	0.000	0.000	0.000	0.000
133	A	145	THR	0	-0.012	-0.017	9.135	-0.038	-0.038	0.000	0.000	0.000	0.000
134	A	146	ASN	0	-0.004	-0.003	11.773	0.012	0.012	0.000	0.000	0.000	0.000
135	A	147	LEU	0	0.045	0.047	12.341	0.017	0.017	0.000	0.000	0.000	0.000
136	A	148	GLU	-1	-0.820	-0.900	13.690	-0.182	-0.182	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:MET)