FMO DATABASE

FMODB ID: 6NM4Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1244718.730381
FMO2-HF: Nuclear repulsion	1189833.356347
FMO2-HF: Total energy	-54885.374034
FMO2-MP2: Total energy	-55043.623313

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.
-7.659	-1.784	2.983	-2.365	-6.492	-0.004

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 : 0.040 / 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].	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	1.022	0.987	3.836	-2.067	-0.494	-0.002	-0.629	-0.942	0.001
4	A	8	PHE	0	0.035	0.034	2.524	-1.143	0.607	0.496	-0.670	-1.575	-0.002
5	A	9	ALA	0	0.019	-0.004	4.401	0.777	0.995	-0.001	-0.030	-0.187	0.000
6	A	10	ASP	-1	-0.924	-0.960	6.912	-0.232	-0.232	0.000	0.000	0.000	0.000
7	A	11	LEU	0	-0.014	-0.010	7.441	0.216	0.216	0.000	0.000	0.000	0.000
8	A	12	ARG	1	0.809	0.915	7.317	1.190	1.190	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.950	-0.966	9.788	-0.276	-0.276	0.000	0.000	0.000	0.000
10	A	14	ARG	1	0.963	0.993	11.987	0.493	0.493	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.898	0.940	12.912	0.641	0.641	0.000	0.000	0.000	0.000
12	A	16	ALA	0	0.006	0.019	11.498	0.079	0.079	0.000	0.000	0.000	0.000
13	A	17	TYR	0	0.005	-0.024	11.426	-0.138	-0.138	0.000	0.000	0.000	0.000
14	A	18	ALA	0	0.006	-0.008	11.936	-0.068	-0.068	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.879	-0.966	12.212	-0.433	-0.433	0.000	0.000	0.000	0.000
16	A	20	ILE	0	-0.075	-0.024	6.343	-0.127	-0.127	0.000	0.000	0.000	0.000
17	A	21	VAL	0	-0.015	-0.017	7.274	-0.358	-0.358	0.000	0.000	0.000	0.000
18	A	22	ASP	-1	-0.926	-0.918	9.599	-0.376	-0.376	0.000	0.000	0.000	0.000
19	A	23	ALA	0	-0.043	-0.027	7.948	0.158	0.158	0.000	0.000	0.000	0.000
20	A	24	LEU	0	0.016	0.004	3.678	-0.431	-0.247	0.003	-0.027	-0.160	0.000
21	A	25	PRO	0	-0.026	-0.020	7.672	0.142	0.142	0.000	0.000	0.000	0.000
22	A	26	TYR	0	0.097	0.009	6.825	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	27	VAL	0	0.035	0.030	12.202	0.054	0.054	0.000	0.000	0.000	0.000
24	A	28	LYS	1	0.808	0.916	12.319	0.520	0.520	0.000	0.000	0.000	0.000
25	A	29	LEU	0	-0.054	0.012	14.113	0.043	0.043	0.000	0.000	0.000	0.000
26	A	30	MET	0	-0.017	-0.013	15.885	0.044	0.044	0.000	0.000	0.000	0.000
27	A	31	GLY	0	0.009	0.027	16.492	-0.037	-0.037	0.000	0.000	0.000	0.000
28	A	32	THR	0	-0.066	-0.069	14.192	0.028	0.028	0.000	0.000	0.000	0.000
29	A	33	SER	0	-0.001	0.028	16.008	-0.033	-0.033	0.000	0.000	0.000	0.000
30	A	34	MET	0	-0.030	-0.034	9.283	-0.049	-0.049	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.007	0.002	14.886	0.002	0.002	0.000	0.000	0.000	0.000
32	A	36	GLU	-1	-0.895	-0.941	16.145	-0.451	-0.451	0.000	0.000	0.000	0.000
33	A	37	ASH	0	-0.194	-0.124	17.837	0.046	0.046	0.000	0.000	0.000	0.000
34	A	38	GLU	-1	-0.900	-0.968	21.197	-0.208	-0.208	0.000	0.000	0.000	0.000
35	A	39	GLN	0	-0.049	-0.021	22.028	0.024	0.024	0.000	0.000	0.000	0.000
36	A	40	GLY	0	0.033	-0.007	21.182	0.006	0.006	0.000	0.000	0.000	0.000
37	A	41	GLU	-1	-0.801	-0.833	15.685	-0.353	-0.353	0.000	0.000	0.000	0.000
38	A	42	LEU	0	0.016	0.024	11.083	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.839	0.911	15.210	0.315	0.315	0.000	0.000	0.000	0.000
40	A	44	PHE	0	-0.017	-0.027	10.736	-0.040	-0.040	0.000	0.000	0.000	0.000
41	A	45	GLU	-1	-0.908	-0.963	16.430	-0.236	-0.236	0.000	0.000	0.000	0.000
42	A	46	LEU	0	0.079	0.039	17.998	-0.034	-0.034	0.000	0.000	0.000	0.000
43	A	47	PRO	0	-0.032	0.013	20.036	0.022	0.022	0.000	0.000	0.000	0.000
44	A	48	PHE	0	-0.037	-0.037	22.721	0.010	0.010	0.000	0.000	0.000	0.000
45	A	49	LEU	0	0.035	0.010	24.802	0.012	0.012	0.000	0.000	0.000	0.000
46	A	50	GLN	0	0.025	0.124	25.543	0.011	0.011	0.000	0.000	0.000	0.000
47	A	59	PRO	0	0.006	-0.026	23.179	0.006	0.006	0.000	0.000	0.000	0.000
48	A	60	ALA	0	-0.135	-0.107	24.161	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	61	LEU	0	0.094	0.025	21.450	0.001	0.001	0.000	0.000	0.000	0.000
50	A	62	HIS	0	0.069	0.022	24.499	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	63	GLY	0	-0.060	-0.021	25.877	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	64	GLY	0	0.016	-0.002	25.520	0.002	0.002	0.000	0.000	0.000	0.000
53	A	65	LEU	0	-0.023	-0.010	21.824	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	66	ILE	0	0.074	0.016	19.272	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	67	GLY	0	-0.008	-0.008	17.643	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	68	GLY	0	0.066	0.036	14.504	-0.011	-0.011	0.000	0.000	0.000	0.000
57	A	69	PHE	0	0.054	0.045	13.126	-0.052	-0.052	0.000	0.000	0.000	0.000
58	A	70	MET	0	-0.025	-0.009	13.367	-0.063	-0.063	0.000	0.000	0.000	0.000
59	A	71	GLU	-1	-0.916	-0.956	11.332	-0.214	-0.214	0.000	0.000	0.000	0.000
60	A	72	SER	0	-0.022	-0.053	8.942	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	73	ALA	0	-0.015	0.014	8.837	-0.161	-0.161	0.000	0.000	0.000	0.000
62	A	74	ALA	0	0.045	0.009	10.681	-0.050	-0.050	0.000	0.000	0.000	0.000
63	A	75	MET	0	-0.059	-0.022	4.908	0.136	0.136	0.000	0.000	0.000	0.000
64	A	76	ILE	0	-0.006	-0.020	6.220	-0.093	-0.093	0.000	0.000	0.000	0.000
65	A	77	HIS	0	0.025	0.005	7.241	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	78	LEU	0	-0.006	-0.009	8.469	0.055	0.055	0.000	0.000	0.000	0.000
67	A	79	MET	0	-0.062	-0.025	2.367	-0.937	-0.635	1.404	-0.233	-1.473	-0.001
68	A	80	TRP	0	-0.014	0.001	6.831	-0.177	-0.177	0.000	0.000	0.000	0.000
69	A	81	ASN	0	-0.049	-0.055	8.674	0.012	0.012	0.000	0.000	0.000	0.000
70	A	82	ARG	1	0.917	0.989	9.564	0.167	0.167	0.000	0.000	0.000	0.000
71	A	83	GLU	-1	-0.850	-0.917	9.467	-0.387	-0.387	0.000	0.000	0.000	0.000
72	A	84	SER	0	-0.039	-0.015	3.847	-0.090	0.096	-0.001	-0.024	-0.161	0.000
73	A	85	LEU	0	-0.083	-0.030	4.466	-0.838	-0.765	-0.001	-0.023	-0.049	0.000
74	A	86	GLU	-1	-0.931	-0.980	3.759	-0.197	0.233	0.023	-0.146	-0.307	0.000
75	A	87	ALA	0	0.000	0.004	2.782	-1.111	-0.063	1.042	-0.605	-1.485	-0.002
76	A	88	PRO	0	-0.049	-0.013	4.390	-0.683	-0.572	0.020	0.022	-0.153	0.000
77	A	89	LYS	1	0.995	0.987	7.289	-0.489	-0.489	0.000	0.000	0.000	0.000
78	A	90	ILE	0	0.026	0.033	9.981	-0.054	-0.054	0.000	0.000	0.000	0.000
79	A	91	VAL	0	-0.080	-0.034	11.878	0.033	0.033	0.000	0.000	0.000	0.000
80	A	92	ASP	-1	-0.875	-0.928	15.617	-0.043	-0.043	0.000	0.000	0.000	0.000
81	A	93	PHE	0	0.080	0.015	15.291	-0.020	-0.020	0.000	0.000	0.000	0.000
82	A	94	SER	0	-0.045	-0.008	17.344	0.012	0.012	0.000	0.000	0.000	0.000
83	A	95	LEU	0	-0.017	-0.016	19.421	-0.018	-0.018	0.000	0.000	0.000	0.000
84	A	96	ASP	-1	-0.904	-0.931	21.742	-0.084	-0.084	0.000	0.000	0.000	0.000
85	A	97	TYR	0	0.007	-0.003	21.926	-0.017	-0.017	0.000	0.000	0.000	0.000
86	A	98	LEU	0	-0.031	-0.022	26.554	0.010	0.010	0.000	0.000	0.000	0.000
87	A	99	ARG	1	0.854	0.923	28.729	0.117	0.117	0.000	0.000	0.000	0.000
88	A	100	PRO	0	0.022	0.016	28.968	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	101	GLY	0	0.026	0.023	27.960	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	102	ARG	1	0.869	0.908	28.801	0.137	0.137	0.000	0.000	0.000	0.000
91	A	103	PRO	0	0.025	0.017	29.067	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	104	GLN	0	0.000	-0.004	29.065	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	105	THR	0	0.022	0.013	23.309	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	106	LEU	0	-0.071	-0.039	20.999	0.015	0.015	0.000	0.000	0.000	0.000
95	A	107	PHE	0	0.020	0.017	21.037	-0.024	-0.024	0.000	0.000	0.000	0.000
96	A	108	ALA	0	0.018	-0.008	17.359	0.018	0.018	0.000	0.000	0.000	0.000
97	A	109	GLN	0	0.049	0.046	17.201	-0.039	-0.039	0.000	0.000	0.000	0.000
98	A	110	CYS	0	-0.015	-0.009	14.408	0.020	0.020	0.000	0.000	0.000	0.000
99	A	111	GLU	-1	-0.876	-0.924	16.588	-0.177	-0.177	0.000	0.000	0.000	0.000
100	A	112	ILE	0	-0.034	-0.027	13.205	0.016	0.016	0.000	0.000	0.000	0.000
101	A	113	THR	0	0.028	0.024	17.392	0.012	0.012	0.000	0.000	0.000	0.000
102	A	114	LYS	1	0.943	0.982	19.706	0.045	0.045	0.000	0.000	0.000	0.000
103	A	115	GLN	0	0.006	-0.026	15.234	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	116	GLY	0	-0.007	0.009	18.743	0.003	0.003	0.000	0.000	0.000	0.000
105	A	117	LYS	1	0.992	0.999	18.449	-0.050	-0.050	0.000	0.000	0.000	0.000
106	A	118	ARG	1	0.879	0.919	15.088	-0.132	-0.132	0.000	0.000	0.000	0.000
107	A	119	VAL	0	0.002	0.023	15.587	0.024	0.024	0.000	0.000	0.000	0.000
108	A	120	ALA	0	0.022	0.028	13.425	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	121	HIS	0	-0.037	-0.026	15.349	0.023	0.023	0.000	0.000	0.000	0.000
110	A	122	VAL	0	0.023	0.016	12.741	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	123	LEU	0	-0.006	0.009	16.174	0.020	0.020	0.000	0.000	0.000	0.000
112	A	124	ILE	0	0.042	0.017	15.084	-0.024	-0.024	0.000	0.000	0.000	0.000
113	A	125	GLU	-1	-0.870	-0.927	18.110	-0.157	-0.157	0.000	0.000	0.000	0.000
114	A	126	ALA	0	0.063	0.017	20.362	-0.025	-0.025	0.000	0.000	0.000	0.000
115	A	127	TRP	0	-0.020	-0.002	21.160	0.021	0.021	0.000	0.000	0.000	0.000
116	A	128	GLN	0	0.009	0.022	24.525	0.001	0.001	0.000	0.000	0.000	0.000
117	A	129	ASP	-1	-0.888	-0.932	27.140	-0.128	-0.128	0.000	0.000	0.000	0.000
118	A	130	ASP	-1	-0.733	-0.863	30.145	-0.116	-0.116	0.000	0.000	0.000	0.000
119	A	131	ARG	1	0.813	0.906	21.566	0.206	0.206	0.000	0.000	0.000	0.000
120	A	132	SER	0	-0.079	-0.045	27.755	0.002	0.002	0.000	0.000	0.000	0.000
121	A	133	LYS	1	0.847	0.914	30.379	0.101	0.101	0.000	0.000	0.000	0.000
122	A	134	PRO	0	0.020	0.013	25.501	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	135	VAL	0	-0.023	-0.016	25.023	0.011	0.011	0.000	0.000	0.000	0.000
124	A	136	ALA	0	0.014	-0.006	22.614	0.010	0.010	0.000	0.000	0.000	0.000
125	A	137	VAL	0	-0.002	0.018	22.095	-0.013	-0.013	0.000	0.000	0.000	0.000
126	A	138	ALA	0	0.011	0.002	18.042	0.011	0.011	0.000	0.000	0.000	0.000
127	A	139	ARG	1	0.931	0.957	18.404	0.113	0.113	0.000	0.000	0.000	0.000
128	A	140	ALA	0	0.058	0.043	13.998	0.006	0.006	0.000	0.000	0.000	0.000
129	A	141	HIS	1	0.776	0.888	15.780	0.053	0.053	0.000	0.000	0.000	0.000
130	A	142	PHE	0	0.101	0.038	8.914	0.014	0.014	0.000	0.000	0.000	0.000
131	A	143	LEU	0	-0.035	-0.024	12.389	-0.015	-0.015	0.000	0.000	0.000	0.000
132	A	144	LEU	0	0.004	-0.020	10.405	0.079	0.079	0.000	0.000	0.000	0.000
133	A	145	THR	0	-0.017	-0.045	10.632	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	146	ASN	0	0.004	0.033	11.915	0.020	0.020	0.000	0.000	0.000	0.000
135	A	147	LEU	0	0.011	0.018	12.532	0.015	0.015	0.000	0.000	0.000	0.000
136	A	148	GLU	-1	-0.937	-0.973	14.292	-0.074	-0.074	0.000	0.000	0.000	0.000

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