FMO DATABASE

FMODB ID: 3QV6L

Calculation Name: 1RM1-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RM1

Chain ID: C

ChEMBL ID:

UniProt ID: P32774

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	119
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-894642.039923
FMO2-HF: Nuclear repulsion	845745.897466
FMO2-HF: Total energy	-48896.142457
FMO2-MP2: Total energy	-49038.803959

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(C:2:SER)

Summations of interaction energy for fragment #1(C:2: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.
-21.889	-23.978	17.731	-6.659	-8.984	-0.064

Interaction energy analysis for fragmet #1(C:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.028

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	C	4	ALA	0	0.041	0.016	3.864	0.167	1.495	-0.016	-0.615	-0.697	0.000
4	C	5	GLU	-1	-0.909	-0.914	6.274	-0.605	-0.605	0.000	0.000	0.000	0.000
5	C	6	ALA	0	0.053	0.022	5.559	0.224	0.224	0.000	0.000	0.000	0.000
6	C	7	SER	0	0.021	0.000	4.359	-0.267	-0.176	-0.001	-0.017	-0.073	0.000
7	C	8	ARG	1	0.938	0.974	6.486	0.001	0.001	0.000	0.000	0.000	0.000
8	C	9	VAL	0	-0.020	-0.013	9.902	0.055	0.055	0.000	0.000	0.000	0.000
9	C	10	TYR	0	-0.031	-0.048	8.603	0.130	0.130	0.000	0.000	0.000	0.000
10	C	11	GLU	-1	-0.822	-0.884	8.966	0.910	0.910	0.000	0.000	0.000	0.000
11	C	12	ILE	0	-0.027	-0.014	11.944	0.016	0.016	0.000	0.000	0.000	0.000
12	C	13	ILE	0	-0.002	0.019	13.628	0.006	0.006	0.000	0.000	0.000	0.000
13	C	14	VAL	0	-0.010	0.000	13.743	0.017	0.017	0.000	0.000	0.000	0.000
14	C	15	GLU	-1	-0.814	-0.904	16.344	0.149	0.149	0.000	0.000	0.000	0.000
15	C	16	SER	0	-0.072	-0.042	18.211	0.001	0.001	0.000	0.000	0.000	0.000
16	C	17	VAL	0	0.004	-0.002	19.392	0.001	0.001	0.000	0.000	0.000	0.000
17	C	18	VAL	0	0.006	0.002	20.163	0.005	0.005	0.000	0.000	0.000	0.000
18	C	19	ASN	0	-0.059	-0.036	21.915	0.013	0.013	0.000	0.000	0.000	0.000
19	C	20	GLU	-1	-0.950	-0.966	24.017	-0.059	-0.059	0.000	0.000	0.000	0.000
20	C	21	VAL	0	-0.020	-0.008	24.667	0.001	0.001	0.000	0.000	0.000	0.000
21	C	22	ARG	1	0.806	0.874	25.508	-0.031	-0.031	0.000	0.000	0.000	0.000
22	C	23	GLU	-1	-0.934	-0.959	28.693	-0.024	-0.024	0.000	0.000	0.000	0.000
23	C	24	ASP	-1	-0.889	-0.951	29.441	-0.068	-0.068	0.000	0.000	0.000	0.000
24	C	25	PHE	0	-0.062	-0.041	26.563	0.000	0.000	0.000	0.000	0.000	0.000
25	C	26	GLU	-1	-0.909	-0.959	31.334	0.013	0.013	0.000	0.000	0.000	0.000
26	C	27	ASN	0	-0.107	-0.047	34.229	-0.003	-0.003	0.000	0.000	0.000	0.000
27	C	28	ALA	0	-0.035	-0.015	33.688	0.000	0.000	0.000	0.000	0.000	0.000
28	C	29	GLY	0	-0.049	-0.016	35.797	0.000	0.000	0.000	0.000	0.000	0.000
29	C	30	ILE	0	-0.084	-0.038	30.586	0.004	0.004	0.000	0.000	0.000	0.000
30	C	31	ASP	-1	-0.794	-0.877	31.478	0.027	0.027	0.000	0.000	0.000	0.000
31	C	32	GLU	-1	-0.729	-0.845	26.868	0.048	0.048	0.000	0.000	0.000	0.000
32	C	33	GLN	0	-0.094	-0.047	26.295	0.013	0.013	0.000	0.000	0.000	0.000
33	C	34	THR	0	-0.019	-0.045	26.804	0.003	0.003	0.000	0.000	0.000	0.000
34	C	35	LEU	0	-0.038	0.000	24.770	-0.008	-0.008	0.000	0.000	0.000	0.000
35	C	36	GLN	0	-0.017	-0.034	22.490	0.013	0.013	0.000	0.000	0.000	0.000
36	C	37	ASP	-1	-0.827	-0.897	22.073	0.084	0.084	0.000	0.000	0.000	0.000
37	C	38	LEU	0	-0.037	-0.006	21.700	-0.006	-0.006	0.000	0.000	0.000	0.000
38	C	39	LYS	1	0.825	0.912	17.756	-0.143	-0.143	0.000	0.000	0.000	0.000
39	C	40	ASN	0	-0.037	-0.030	17.717	0.026	0.026	0.000	0.000	0.000	0.000
40	C	41	ILE	0	-0.050	-0.029	17.805	0.014	0.014	0.000	0.000	0.000	0.000
41	C	42	TRP	0	0.008	0.008	15.015	0.003	0.003	0.000	0.000	0.000	0.000
42	C	43	GLN	0	0.024	0.006	13.357	-0.031	-0.031	0.000	0.000	0.000	0.000
43	C	44	LYS	1	0.887	0.947	12.669	-0.039	-0.039	0.000	0.000	0.000	0.000
44	C	45	LYS	1	0.843	0.897	13.751	0.141	0.141	0.000	0.000	0.000	0.000
45	C	46	LEU	0	0.013	0.024	9.816	-0.094	-0.094	0.000	0.000	0.000	0.000
46	C	47	THR	0	0.029	-0.005	9.234	-0.186	-0.186	0.000	0.000	0.000	0.000
47	C	48	GLU	-1	-0.849	-0.910	10.000	-0.046	-0.046	0.000	0.000	0.000	0.000
48	C	49	THR	0	-0.086	-0.050	9.329	-0.127	-0.127	0.000	0.000	0.000	0.000
49	C	50	LYS	1	0.821	0.913	5.955	-0.112	-0.112	0.000	0.000	0.000	0.000
50	C	51	VAL	0	0.033	0.040	4.476	-0.399	-0.257	-0.001	-0.007	-0.134	0.000
51	C	52	THR	0	0.011	-0.006	1.967	-8.248	-9.662	9.417	-4.047	-3.956	-0.030
52	C	53	THR	0	0.001	0.018	2.243	2.929	2.348	0.767	1.151	-1.337	-0.002
53	C	54	PHE	0	0.002	0.002	4.380	-0.233	-0.189	-0.001	-0.009	-0.034	0.000
54	C	55	SER	0	-0.073	-0.071	7.505	0.100	0.100	0.000	0.000	0.000	0.000
55	C	56	TRP	0	0.065	0.022	10.625	0.007	0.007	0.000	0.000	0.000	0.000
56	C	57	ASP	-1	-0.781	-0.871	7.372	1.271	1.271	0.000	0.000	0.000	0.000
57	C	58	ASN	0	-0.075	-0.044	11.029	-0.046	-0.046	0.000	0.000	0.000	0.000
58	C	59	GLN	0	-0.058	-0.019	13.601	-0.088	-0.088	0.000	0.000	0.000	0.000
59	C	60	PHE	0	-0.044	-0.027	13.220	-0.097	-0.097	0.000	0.000	0.000	0.000
60	C	61	ASN	0	-0.017	0.007	13.413	0.034	0.034	0.000	0.000	0.000	0.000
61	C	228	ASP	-1	-0.818	-0.915	31.372	-0.186	-0.186	0.000	0.000	0.000	0.000
62	C	229	TYR	0	-0.127	-0.076	32.765	-0.008	-0.008	0.000	0.000	0.000	0.000
63	C	230	LEU	0	-0.075	-0.031	34.354	0.002	0.002	0.000	0.000	0.000	0.000
64	C	231	ILE	0	-0.011	-0.010	29.030	-0.009	-0.009	0.000	0.000	0.000	0.000
65	C	232	SER	0	-0.029	-0.017	26.861	0.013	0.013	0.000	0.000	0.000	0.000
66	C	233	GLU	-1	-0.861	-0.902	26.872	-0.301	-0.301	0.000	0.000	0.000	0.000
67	C	234	GLY	0	-0.043	-0.032	25.711	-0.023	-0.023	0.000	0.000	0.000	0.000
68	C	235	GLU	-1	-1.002	-0.999	21.026	-0.395	-0.395	0.000	0.000	0.000	0.000
69	C	236	GLH	0	-0.091	-0.067	21.479	0.017	0.017	0.000	0.000	0.000	0.000
70	C	237	ASP	-1	-0.884	-0.914	18.567	-0.466	-0.466	0.000	0.000	0.000	0.000
71	C	238	GLY	0	0.021	-0.004	16.249	0.052	0.052	0.000	0.000	0.000	0.000
72	C	239	PRO	0	-0.072	-0.041	11.345	-0.083	-0.083	0.000	0.000	0.000	0.000
73	C	240	ASP	-1	-0.832	-0.889	10.866	-1.056	-1.056	0.000	0.000	0.000	0.000
74	C	241	GLU	-1	-0.841	-0.913	13.108	-0.637	-0.637	0.000	0.000	0.000	0.000
75	C	242	ASN	0	-0.044	-0.020	11.917	-0.305	-0.305	0.000	0.000	0.000	0.000
76	C	243	LEU	0	0.021	0.029	13.767	0.070	0.070	0.000	0.000	0.000	0.000
77	C	244	MET	0	-0.039	-0.033	13.239	-0.113	-0.113	0.000	0.000	0.000	0.000
78	C	245	LEU	0	0.001	0.011	15.023	0.113	0.113	0.000	0.000	0.000	0.000
79	C	246	CYS	0	-0.027	-0.015	16.025	-0.049	-0.049	0.000	0.000	0.000	0.000
80	C	247	LEU	0	0.028	0.033	18.466	0.050	0.050	0.000	0.000	0.000	0.000
81	C	248	TYR	0	-0.019	-0.024	21.286	-0.029	-0.029	0.000	0.000	0.000	0.000
82	C	249	ASP	-1	-0.836	-0.885	23.999	-0.252	-0.252	0.000	0.000	0.000	0.000
83	C	250	LYS	1	0.905	0.950	26.470	0.231	0.231	0.000	0.000	0.000	0.000
84	C	251	VAL	0	0.069	0.039	25.958	-0.022	-0.022	0.000	0.000	0.000	0.000
85	C	252	THR	0	-0.040	-0.039	28.312	0.028	0.028	0.000	0.000	0.000	0.000
86	C	253	ARG	1	0.927	0.971	29.760	0.178	0.178	0.000	0.000	0.000	0.000
87	C	254	THR	0	-0.042	-0.024	32.206	0.019	0.019	0.000	0.000	0.000	0.000
88	C	255	LYS	1	0.922	0.956	34.224	0.135	0.135	0.000	0.000	0.000	0.000
89	C	256	ALA	0	0.095	0.059	32.714	0.000	0.000	0.000	0.000	0.000	0.000
90	C	257	ARG	1	0.882	0.955	29.815	0.179	0.179	0.000	0.000	0.000	0.000
91	C	258	TRP	0	0.043	0.001	27.013	0.019	0.019	0.000	0.000	0.000	0.000
92	C	259	LYS	1	0.804	0.880	25.907	0.246	0.246	0.000	0.000	0.000	0.000
93	C	260	CYS	0	-0.028	-0.006	23.289	0.034	0.034	0.000	0.000	0.000	0.000
94	C	261	SER	0	0.001	0.007	22.930	-0.013	-0.013	0.000	0.000	0.000	0.000
95	C	262	LEU	0	0.041	0.004	18.390	0.029	0.029	0.000	0.000	0.000	0.000
96	C	263	LYS	1	0.847	0.910	19.247	0.282	0.282	0.000	0.000	0.000	0.000
97	C	264	ASP	-1	-0.838	-0.911	17.655	-0.356	-0.356	0.000	0.000	0.000	0.000
98	C	265	GLY	0	0.019	0.002	15.570	0.036	0.036	0.000	0.000	0.000	0.000
99	C	266	VAL	0	-0.006	0.000	9.948	-0.060	-0.060	0.000	0.000	0.000	0.000
100	C	267	VAL	0	-0.045	-0.029	9.944	0.171	0.171	0.000	0.000	0.000	0.000
101	C	268	THR	0	0.035	0.018	8.508	-0.305	-0.305	0.000	0.000	0.000	0.000
102	C	269	ILE	0	-0.064	-0.044	7.981	0.382	0.382	0.000	0.000	0.000	0.000
103	C	270	ASN	0	-0.013	-0.026	7.311	-0.470	-0.470	0.000	0.000	0.000	0.000
104	C	271	ARG	1	0.810	0.873	6.864	0.509	0.509	0.000	0.000	0.000	0.000
105	C	272	ASN	0	-0.022	0.007	1.819	-13.216	-15.215	7.568	-3.086	-2.484	-0.032
106	C	273	ASP	-1	-0.738	-0.830	4.033	-0.868	-0.753	-0.001	-0.013	-0.101	0.000
107	C	274	TYR	0	-0.095	-0.059	4.566	-1.216	-1.031	-0.001	-0.016	-0.168	0.000
108	C	275	THR	0	-0.022	-0.038	7.225	0.288	0.288	0.000	0.000	0.000	0.000
109	C	276	PHE	0	0.007	-0.008	10.344	-0.019	-0.019	0.000	0.000	0.000	0.000
110	C	277	GLN	0	-0.030	-0.005	13.292	0.092	0.092	0.000	0.000	0.000	0.000
111	C	278	LYS	1	0.813	0.872	16.690	0.386	0.386	0.000	0.000	0.000	0.000
112	C	279	ALA	0	0.043	0.039	15.862	-0.056	-0.056	0.000	0.000	0.000	0.000
113	C	280	GLN	0	-0.030	-0.024	17.757	0.074	0.074	0.000	0.000	0.000	0.000
114	C	281	VAL	0	0.042	0.027	18.770	-0.041	-0.041	0.000	0.000	0.000	0.000
115	C	282	GLU	-1	-0.831	-0.905	21.037	-0.239	-0.239	0.000	0.000	0.000	0.000
116	C	283	ALA	0	0.039	0.030	22.994	-0.018	-0.018	0.000	0.000	0.000	0.000
117	C	284	GLU	-1	-0.879	-0.947	25.015	-0.191	-0.191	0.000	0.000	0.000	0.000
118	C	285	TRP	0	-0.023	-0.001	28.191	-0.001	-0.001	0.000	0.000	0.000	0.000
119	C	286	VAL	0	0.017	0.007	29.728	0.013	0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:2:SER)