FMO DATABASE

FMODB ID: Z6JZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1246430.151214
FMO2-HF: Nuclear repulsion	1191543.402799
FMO2-HF: Total energy	-54886.748416
FMO2-MP2: Total energy	-55044.852437

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.
-8.084	-2.614	3.854	-2.486	-6.836	-0.006

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 : 0.001

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	1.015	0.989	3.869	-2.287	-0.748	0.000	-0.620	-0.919	0.001
4	A	8	PHE	0	0.017	0.026	2.721	-1.653	0.398	0.513	-0.795	-1.770	-0.003
5	A	9	ALA	0	0.024	0.001	4.465	0.799	1.009	-0.001	-0.024	-0.184	0.000
6	A	10	ASP	-1	-0.921	-0.965	6.773	-0.197	-0.197	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.010	-0.008	7.656	0.276	0.276	0.000	0.000	0.000	0.000
8	A	12	ARG	1	0.774	0.894	6.664	1.722	1.722	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.924	-0.948	9.590	-0.388	-0.388	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.943	0.981	11.986	0.583	0.583	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.816	0.891	12.845	0.776	0.776	0.000	0.000	0.000	0.000
12	A	16	ALA	0	0.009	0.019	11.760	0.099	0.099	0.000	0.000	0.000	0.000
13	A	17	TYR	0	0.018	-0.012	11.740	-0.138	-0.138	0.000	0.000	0.000	0.000
14	A	18	ALA	0	0.006	-0.008	12.126	-0.056	-0.056	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.897	-0.960	12.185	-0.405	-0.405	0.000	0.000	0.000	0.000
16	A	20	ILE	0	-0.077	-0.023	6.323	-0.066	-0.066	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.007	-0.019	7.190	-0.320	-0.320	0.000	0.000	0.000	0.000
18	A	22	ASP	-1	-0.875	-0.924	9.453	-0.243	-0.243	0.000	0.000	0.000	0.000
19	A	23	ALA	0	-0.051	-0.018	8.105	0.171	0.171	0.000	0.000	0.000	0.000
20	A	24	LEU	0	0.012	0.005	3.770	-0.315	-0.150	0.001	-0.023	-0.143	0.000
21	A	25	PRO	0	-0.011	-0.009	7.904	0.092	0.092	0.000	0.000	0.000	0.000
22	A	26	TYR	0	0.078	0.007	7.002	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	27	VAL	0	0.023	0.022	12.310	0.036	0.036	0.000	0.000	0.000	0.000
24	A	28	LYS	1	0.780	0.902	12.733	0.399	0.399	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.036	0.018	14.581	0.042	0.042	0.000	0.000	0.000	0.000
26	A	30	MET	0	-0.041	-0.020	16.004	0.032	0.032	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.020	0.028	16.565	-0.031	-0.031	0.000	0.000	0.000	0.000
28	A	32	THR	0	-0.069	-0.067	13.878	0.020	0.020	0.000	0.000	0.000	0.000
29	A	33	SER	0	-0.006	0.020	15.964	-0.030	-0.030	0.000	0.000	0.000	0.000
30	A	34	MET	0	-0.028	-0.029	9.349	-0.041	-0.041	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.008	0.005	15.148	0.004	0.004	0.000	0.000	0.000	0.000
32	A	36	GLU	-1	-0.785	-0.878	14.855	-0.665	-0.665	0.000	0.000	0.000	0.000
33	A	37	ASH	0	-0.107	-0.047	17.750	0.053	0.053	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.891	-0.954	20.989	-0.266	-0.266	0.000	0.000	0.000	0.000
35	A	39	GLN	0	-0.040	-0.012	21.345	0.028	0.028	0.000	0.000	0.000	0.000
36	A	40	GLY	0	0.036	0.005	20.888	0.003	0.003	0.000	0.000	0.000	0.000
37	A	41	GLU	-1	-0.859	-0.913	15.373	-0.455	-0.455	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.013	-0.001	10.848	0.022	0.022	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.869	0.929	15.039	0.365	0.365	0.000	0.000	0.000	0.000
40	A	44	PHE	0	-0.004	-0.018	10.863	-0.036	-0.036	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.850	-0.934	16.580	-0.240	-0.240	0.000	0.000	0.000	0.000
42	A	46	LEU	0	0.047	0.035	18.065	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	47	PRO	0	0.001	0.021	20.093	0.021	0.021	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.045	-0.037	22.771	0.014	0.014	0.000	0.000	0.000	0.000
45	A	49	LEU	0	0.010	0.010	24.976	0.010	0.010	0.000	0.000	0.000	0.000
46	A	50	GLN	0	0.045	0.177	25.584	0.012	0.012	0.000	0.000	0.000	0.000
47	A	59	PRO	0	0.028	-0.018	23.236	0.006	0.006	0.000	0.000	0.000	0.000
48	A	60	ALA	0	-0.122	-0.137	24.261	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	61	LEU	0	0.060	0.003	21.402	0.006	0.006	0.000	0.000	0.000	0.000
50	A	62	HIS	0	0.069	0.022	24.713	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	63	GLY	0	-0.050	-0.018	26.143	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	64	GLY	0	0.012	-0.003	25.740	0.000	0.000	0.000	0.000	0.000	0.000
53	A	65	LEU	0	-0.011	-0.007	22.096	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	66	ILE	0	0.068	0.016	19.395	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	67	GLY	0	-0.009	0.000	17.810	-0.027	-0.027	0.000	0.000	0.000	0.000
56	A	68	GLY	0	0.061	0.032	14.724	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	69	PHE	0	0.029	0.012	13.326	-0.049	-0.049	0.000	0.000	0.000	0.000
58	A	70	MET	0	-0.003	-0.002	13.499	-0.075	-0.075	0.000	0.000	0.000	0.000
59	A	71	GLU	-1	-0.914	-0.957	11.578	-0.179	-0.179	0.000	0.000	0.000	0.000
60	A	72	SER	0	-0.013	-0.028	9.177	-0.035	-0.035	0.000	0.000	0.000	0.000
61	A	73	ALA	0	-0.009	0.012	8.900	-0.200	-0.200	0.000	0.000	0.000	0.000
62	A	74	ALA	0	0.051	0.013	10.635	-0.091	-0.091	0.000	0.000	0.000	0.000
63	A	75	MET	0	-0.052	-0.021	5.319	0.098	0.098	0.000	0.000	0.000	0.000
64	A	76	ILE	0	0.001	-0.021	6.132	-0.221	-0.221	0.000	0.000	0.000	0.000
65	A	77	HIS	0	0.035	0.006	7.166	-0.100	-0.100	0.000	0.000	0.000	0.000
66	A	78	LEU	0	-0.018	-0.012	8.215	0.037	0.037	0.000	0.000	0.000	0.000
67	A	79	MET	0	-0.050	-0.018	2.499	-0.962	-1.201	2.252	-0.297	-1.716	-0.002
68	A	80	TRP	0	-0.046	-0.018	6.218	-0.285	-0.285	0.000	0.000	0.000	0.000
69	A	81	ASN	0	-0.038	-0.044	8.219	0.052	0.052	0.000	0.000	0.000	0.000
70	A	82	ARG	1	0.850	0.942	9.017	0.438	0.438	0.000	0.000	0.000	0.000
71	A	83	GLU	-1	-0.788	-0.877	8.715	-0.694	-0.694	0.000	0.000	0.000	0.000
72	A	84	SER	0	-0.020	-0.003	3.939	-0.425	-0.230	-0.001	-0.031	-0.163	0.000
73	A	85	LEU	0	-0.091	-0.038	4.837	-0.599	-0.560	-0.001	-0.013	-0.024	0.000
74	A	86	GLU	-1	-0.843	-0.927	3.827	0.409	0.793	0.031	-0.136	-0.278	0.000
75	A	87	ALA	0	0.012	0.012	2.689	-1.496	-0.518	1.041	-0.560	-1.459	-0.002
76	A	88	PRO	0	-0.049	-0.013	4.211	-0.507	-0.359	0.019	0.013	-0.180	0.000
77	A	89	LYS	1	0.903	0.933	7.179	-0.819	-0.819	0.000	0.000	0.000	0.000
78	A	90	ILE	0	0.007	0.023	9.881	-0.084	-0.084	0.000	0.000	0.000	0.000
79	A	91	VAL	0	-0.064	-0.027	11.833	0.047	0.047	0.000	0.000	0.000	0.000
80	A	92	ASP	-1	-0.858	-0.910	15.566	-0.046	-0.046	0.000	0.000	0.000	0.000
81	A	93	PHE	0	0.078	0.022	15.047	-0.029	-0.029	0.000	0.000	0.000	0.000
82	A	94	SER	0	-0.048	-0.011	17.364	0.017	0.017	0.000	0.000	0.000	0.000
83	A	95	LEU	0	-0.001	-0.012	19.644	-0.022	-0.022	0.000	0.000	0.000	0.000
84	A	96	ASP	-1	-0.828	-0.888	21.800	-0.095	-0.095	0.000	0.000	0.000	0.000
85	A	97	TYR	0	0.024	-0.001	22.489	-0.019	-0.019	0.000	0.000	0.000	0.000
86	A	98	LEU	0	-0.042	-0.027	26.647	0.011	0.011	0.000	0.000	0.000	0.000
87	A	99	ARG	1	0.862	0.931	28.811	0.126	0.126	0.000	0.000	0.000	0.000
88	A	100	PRO	0	0.031	0.016	29.077	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	101	GLY	0	0.017	0.020	28.104	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	102	ARG	1	0.879	0.916	28.942	0.144	0.144	0.000	0.000	0.000	0.000
91	A	103	PRO	0	0.031	0.018	29.220	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	104	GLN	0	-0.053	-0.047	29.098	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	105	THR	0	-0.017	-0.011	23.510	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	106	LEU	0	-0.063	-0.038	21.158	0.012	0.012	0.000	0.000	0.000	0.000
95	A	107	PHE	0	-0.009	0.009	21.087	-0.025	-0.025	0.000	0.000	0.000	0.000
96	A	108	ALA	0	0.021	-0.006	17.460	0.021	0.021	0.000	0.000	0.000	0.000
97	A	109	GLN	0	0.014	0.024	17.125	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	110	CYS	0	-0.036	-0.015	14.299	0.025	0.025	0.000	0.000	0.000	0.000
99	A	111	GLU	-1	-0.850	-0.907	16.462	-0.234	-0.234	0.000	0.000	0.000	0.000
100	A	112	ILE	0	-0.039	-0.030	13.005	0.015	0.015	0.000	0.000	0.000	0.000
101	A	113	THR	0	0.013	0.018	17.144	0.017	0.017	0.000	0.000	0.000	0.000
102	A	114	LYS	1	0.937	0.976	19.469	0.093	0.093	0.000	0.000	0.000	0.000
103	A	115	GLN	0	0.021	-0.018	14.457	-0.032	-0.032	0.000	0.000	0.000	0.000
104	A	116	GLY	0	-0.005	0.011	18.426	0.004	0.004	0.000	0.000	0.000	0.000
105	A	117	LYS	1	0.883	0.942	17.988	0.009	0.009	0.000	0.000	0.000	0.000
106	A	118	ARG	1	0.890	0.920	14.976	-0.109	-0.109	0.000	0.000	0.000	0.000
107	A	119	VAL	0	-0.006	0.018	15.312	0.026	0.026	0.000	0.000	0.000	0.000
108	A	120	ALA	0	0.015	0.027	13.172	-0.015	-0.015	0.000	0.000	0.000	0.000
109	A	121	HIS	0	-0.003	-0.005	15.134	0.039	0.039	0.000	0.000	0.000	0.000
110	A	122	VAL	0	0.013	0.003	12.523	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	123	LEU	0	-0.006	0.018	16.005	0.031	0.031	0.000	0.000	0.000	0.000
112	A	124	ILE	0	0.036	0.008	14.898	-0.034	-0.034	0.000	0.000	0.000	0.000
113	A	125	GLU	-1	-0.811	-0.856	18.051	-0.189	-0.189	0.000	0.000	0.000	0.000
114	A	126	ALA	0	0.053	0.013	20.356	-0.028	-0.028	0.000	0.000	0.000	0.000
115	A	127	TRP	0	-0.017	-0.006	21.221	0.024	0.024	0.000	0.000	0.000	0.000
116	A	128	GLN	0	0.016	0.023	24.573	0.000	0.000	0.000	0.000	0.000	0.000
117	A	129	ASP	-1	-0.853	-0.908	27.191	-0.140	-0.140	0.000	0.000	0.000	0.000
118	A	130	ASP	-1	-0.748	-0.856	30.146	-0.130	-0.130	0.000	0.000	0.000	0.000
119	A	131	ARG	1	0.768	0.852	21.495	0.254	0.254	0.000	0.000	0.000	0.000
120	A	132	SER	0	-0.045	-0.041	27.715	0.002	0.002	0.000	0.000	0.000	0.000
121	A	133	LYS	1	0.797	0.889	30.338	0.120	0.120	0.000	0.000	0.000	0.000
122	A	134	PRO	0	0.018	0.008	25.535	0.001	0.001	0.000	0.000	0.000	0.000
123	A	135	VAL	0	-0.019	-0.011	25.072	0.013	0.013	0.000	0.000	0.000	0.000
124	A	136	ALA	0	0.009	-0.008	22.673	0.013	0.013	0.000	0.000	0.000	0.000
125	A	137	VAL	0	-0.009	0.012	22.069	-0.017	-0.017	0.000	0.000	0.000	0.000
126	A	138	ALA	0	0.008	0.001	18.018	0.015	0.015	0.000	0.000	0.000	0.000
127	A	139	ARG	1	0.830	0.903	18.352	0.118	0.118	0.000	0.000	0.000	0.000
128	A	140	ALA	0	0.048	0.039	13.925	0.015	0.015	0.000	0.000	0.000	0.000
129	A	141	HIS	1	0.746	0.856	15.673	0.067	0.067	0.000	0.000	0.000	0.000
130	A	142	PHE	0	0.097	0.036	8.768	0.013	0.013	0.000	0.000	0.000	0.000
131	A	143	LEU	0	-0.024	-0.017	12.235	-0.022	-0.022	0.000	0.000	0.000	0.000
132	A	144	LEU	0	0.002	-0.018	10.258	0.074	0.074	0.000	0.000	0.000	0.000
133	A	145	THR	0	-0.014	-0.013	10.497	0.031	0.031	0.000	0.000	0.000	0.000
134	A	146	ASN	0	0.016	0.029	12.104	0.031	0.031	0.000	0.000	0.000	0.000
135	A	147	LEU	0	0.043	0.029	12.508	0.038	0.038	0.000	0.000	0.000	0.000
136	A	148	GLU	-1	-0.875	-0.953	13.812	-0.175	-0.175	0.000	0.000	0.000	0.000

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