FMO DATABASE

FMODB ID: J3919

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-894511.012732
FMO2-HF: Nuclear repulsion	845615.257614
FMO2-HF: Total energy	-48895.755117
FMO2-MP2: Total energy	-49038.463911

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.
-14.703	-10.9	7.134	-4.681	-6.255	-0.028

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 : 0.008 / q_NPA : -0.006

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

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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	0.036	0.017	3.817	0.828	2.145	-0.017	-0.607	-0.694	0.001
4	C	5	GLU	-1	-0.902	-0.929	6.062	0.109	0.109	0.000	0.000	0.000	0.000
5	C	6	ALA	0	0.072	0.030	5.777	0.082	0.082	0.000	0.000	0.000	0.000
6	C	7	SER	0	0.023	-0.003	4.898	0.515	0.578	-0.001	-0.001	-0.060	0.000
7	C	8	ARG	1	0.922	0.959	7.142	-0.416	-0.416	0.000	0.000	0.000	0.000
8	C	9	VAL	0	-0.028	-0.020	10.310	-0.059	-0.059	0.000	0.000	0.000	0.000
9	C	10	TYR	0	-0.034	-0.053	9.462	-0.047	-0.047	0.000	0.000	0.000	0.000
10	C	11	GLU	-1	-0.802	-0.867	9.381	0.635	0.635	0.000	0.000	0.000	0.000
11	C	12	ILE	0	-0.018	-0.014	12.877	-0.071	-0.071	0.000	0.000	0.000	0.000
12	C	13	ILE	0	-0.001	0.020	14.472	-0.044	-0.044	0.000	0.000	0.000	0.000
13	C	14	VAL	0	-0.002	0.005	14.783	-0.031	-0.031	0.000	0.000	0.000	0.000
14	C	15	GLU	-1	-0.836	-0.907	16.923	0.183	0.183	0.000	0.000	0.000	0.000
15	C	16	SER	0	-0.072	-0.053	19.031	-0.029	-0.029	0.000	0.000	0.000	0.000
16	C	17	VAL	0	-0.005	-0.004	20.366	-0.016	-0.016	0.000	0.000	0.000	0.000
17	C	18	VAL	0	0.001	-0.002	21.258	-0.011	-0.011	0.000	0.000	0.000	0.000
18	C	19	ASN	0	-0.052	-0.035	22.824	-0.013	-0.013	0.000	0.000	0.000	0.000
19	C	20	GLU	-1	-0.955	-0.969	25.022	0.044	0.044	0.000	0.000	0.000	0.000
20	C	21	VAL	0	0.006	0.013	25.759	-0.006	-0.006	0.000	0.000	0.000	0.000
21	C	22	ARG	1	0.782	0.869	25.803	-0.093	-0.093	0.000	0.000	0.000	0.000
22	C	23	GLU	-1	-0.931	-0.972	29.399	0.034	0.034	0.000	0.000	0.000	0.000
23	C	24	ASP	-1	-0.884	-0.949	30.830	0.036	0.036	0.000	0.000	0.000	0.000
24	C	25	PHE	0	-0.073	-0.046	27.370	0.000	0.000	0.000	0.000	0.000	0.000
25	C	26	GLU	-1	-0.920	-0.960	32.436	0.052	0.052	0.000	0.000	0.000	0.000
26	C	27	ASN	0	-0.108	-0.046	35.202	-0.005	-0.005	0.000	0.000	0.000	0.000
27	C	28	ALA	0	-0.020	-0.007	34.744	-0.003	-0.003	0.000	0.000	0.000	0.000
28	C	29	GLY	0	-0.065	-0.023	36.841	-0.001	-0.001	0.000	0.000	0.000	0.000
29	C	30	ILE	0	-0.070	-0.027	31.437	0.001	0.001	0.000	0.000	0.000	0.000
30	C	31	ASP	-1	-0.838	-0.923	32.577	0.069	0.069	0.000	0.000	0.000	0.000
31	C	32	GLU	-1	-0.701	-0.837	27.709	0.099	0.099	0.000	0.000	0.000	0.000
32	C	33	GLN	0	-0.081	-0.037	27.051	0.008	0.008	0.000	0.000	0.000	0.000
33	C	34	THR	0	0.012	0.004	27.777	0.008	0.008	0.000	0.000	0.000	0.000
34	C	35	LEU	0	-0.035	0.006	25.598	0.006	0.006	0.000	0.000	0.000	0.000
35	C	36	GLN	0	-0.041	-0.047	23.449	0.027	0.027	0.000	0.000	0.000	0.000
36	C	37	ASP	-1	-0.859	-0.921	22.991	0.134	0.134	0.000	0.000	0.000	0.000
37	C	38	LEU	0	-0.043	-0.010	22.408	0.013	0.013	0.000	0.000	0.000	0.000
38	C	39	LYS	1	0.851	0.917	18.670	-0.174	-0.174	0.000	0.000	0.000	0.000
39	C	40	ASN	0	-0.002	-0.004	18.526	0.048	0.048	0.000	0.000	0.000	0.000
40	C	41	ILE	0	-0.045	-0.028	18.271	0.028	0.028	0.000	0.000	0.000	0.000
41	C	42	TRP	0	-0.003	-0.002	16.241	0.016	0.016	0.000	0.000	0.000	0.000
42	C	43	GLN	0	0.020	0.001	14.386	0.017	0.017	0.000	0.000	0.000	0.000
43	C	44	LYS	1	0.869	0.939	13.426	-0.127	-0.127	0.000	0.000	0.000	0.000
44	C	45	LYS	1	0.821	0.895	14.041	-0.100	-0.100	0.000	0.000	0.000	0.000
45	C	46	LEU	0	0.029	0.021	10.935	-0.018	-0.018	0.000	0.000	0.000	0.000
46	C	47	THR	0	0.021	0.000	9.454	0.039	0.039	0.000	0.000	0.000	0.000
47	C	48	GLU	-1	-0.862	-0.913	9.906	0.187	0.187	0.000	0.000	0.000	0.000
48	C	49	THR	0	-0.100	-0.061	10.116	-0.075	-0.075	0.000	0.000	0.000	0.000
49	C	50	LYS	1	0.865	0.939	6.717	-0.476	-0.476	0.000	0.000	0.000	0.000
50	C	51	VAL	0	0.043	0.045	5.228	-0.373	-0.373	0.000	0.000	0.000	0.000
51	C	52	THR	0	-0.012	-0.030	2.657	2.626	3.920	1.577	-1.197	-1.673	0.001
52	C	53	THR	0	-0.036	0.008	2.840	-5.249	-3.959	0.323	-0.354	-1.259	0.000
53	C	54	PHE	0	0.011	0.005	4.570	0.115	0.149	-0.001	-0.006	-0.027	0.000
54	C	55	SER	0	-0.102	-0.080	7.884	-0.152	-0.152	0.000	0.000	0.000	0.000
55	C	56	TRP	0	0.070	0.019	10.469	-0.093	-0.093	0.000	0.000	0.000	0.000
56	C	57	ASP	-1	-0.767	-0.869	7.559	1.116	1.116	0.000	0.000	0.000	0.000
57	C	58	ASN	0	-0.074	-0.030	11.147	-0.045	-0.045	0.000	0.000	0.000	0.000
58	C	59	GLN	0	-0.058	-0.026	13.417	-0.063	-0.063	0.000	0.000	0.000	0.000
59	C	60	PHE	0	-0.071	-0.037	13.568	-0.058	-0.058	0.000	0.000	0.000	0.000
60	C	61	ASN	0	0.001	0.010	13.801	0.062	0.062	0.000	0.000	0.000	0.000
61	C	228	ASP	-1	-0.843	-0.929	31.896	-0.074	-0.074	0.000	0.000	0.000	0.000
62	C	229	TYR	0	-0.119	-0.069	33.217	-0.005	-0.005	0.000	0.000	0.000	0.000
63	C	230	LEU	0	-0.076	-0.037	34.610	0.002	0.002	0.000	0.000	0.000	0.000
64	C	231	ILE	0	-0.009	-0.013	29.194	-0.004	-0.004	0.000	0.000	0.000	0.000
65	C	232	SER	0	-0.011	-0.002	26.731	0.004	0.004	0.000	0.000	0.000	0.000
66	C	233	GLU	-1	-0.906	-0.936	27.030	-0.091	-0.091	0.000	0.000	0.000	0.000
67	C	234	GLY	0	-0.041	-0.036	25.817	-0.011	-0.011	0.000	0.000	0.000	0.000
68	C	235	GLU	-1	-0.993	-0.993	21.412	-0.164	-0.164	0.000	0.000	0.000	0.000
69	C	236	GLH	0	-0.052	-0.041	21.455	0.010	0.010	0.000	0.000	0.000	0.000
70	C	237	ASP	-1	-0.881	-0.911	18.892	-0.143	-0.143	0.000	0.000	0.000	0.000
71	C	238	GLY	0	0.020	-0.001	16.906	0.032	0.032	0.000	0.000	0.000	0.000
72	C	239	PRO	0	-0.085	-0.046	12.068	-0.035	-0.035	0.000	0.000	0.000	0.000
73	C	240	ASP	-1	-0.842	-0.904	11.648	-0.464	-0.464	0.000	0.000	0.000	0.000
74	C	241	GLU	-1	-0.864	-0.907	13.764	-0.253	-0.253	0.000	0.000	0.000	0.000
75	C	242	ASN	0	-0.046	-0.020	12.020	-0.135	-0.135	0.000	0.000	0.000	0.000
76	C	243	LEU	0	0.031	0.026	13.335	0.055	0.055	0.000	0.000	0.000	0.000
77	C	244	MET	0	-0.033	-0.023	13.490	-0.032	-0.032	0.000	0.000	0.000	0.000
78	C	245	LEU	0	0.021	0.027	15.226	0.042	0.042	0.000	0.000	0.000	0.000
79	C	246	CYS	0	-0.052	-0.030	16.377	-0.012	-0.012	0.000	0.000	0.000	0.000
80	C	247	LEU	0	0.037	0.039	18.812	0.015	0.015	0.000	0.000	0.000	0.000
81	C	248	TYR	0	-0.017	-0.026	21.556	-0.018	-0.018	0.000	0.000	0.000	0.000
82	C	249	ASP	-1	-0.828	-0.891	24.230	-0.096	-0.096	0.000	0.000	0.000	0.000
83	C	250	LYS	1	0.915	0.947	26.452	0.104	0.104	0.000	0.000	0.000	0.000
84	C	251	VAL	0	0.054	0.037	26.188	-0.010	-0.010	0.000	0.000	0.000	0.000
85	C	252	THR	0	-0.046	-0.025	28.579	0.012	0.012	0.000	0.000	0.000	0.000
86	C	253	ARG	1	0.930	0.969	29.952	0.080	0.080	0.000	0.000	0.000	0.000
87	C	254	THR	0	-0.006	0.005	32.305	0.010	0.010	0.000	0.000	0.000	0.000
88	C	255	LYS	1	0.897	0.939	34.115	0.067	0.067	0.000	0.000	0.000	0.000
89	C	256	ALA	0	0.100	0.054	32.591	0.001	0.001	0.000	0.000	0.000	0.000
90	C	257	ARG	1	0.905	0.965	29.832	0.095	0.095	0.000	0.000	0.000	0.000
91	C	258	TRP	0	0.027	0.000	27.134	0.010	0.010	0.000	0.000	0.000	0.000
92	C	259	LYS	1	0.788	0.875	25.787	0.133	0.133	0.000	0.000	0.000	0.000
93	C	260	CYS	0	-0.032	-0.022	22.806	0.016	0.016	0.000	0.000	0.000	0.000
94	C	261	SER	0	0.021	0.031	22.597	-0.011	-0.011	0.000	0.000	0.000	0.000
95	C	262	LEU	0	0.023	-0.007	18.637	0.015	0.015	0.000	0.000	0.000	0.000
96	C	263	LYS	1	0.861	0.907	19.215	0.089	0.089	0.000	0.000	0.000	0.000
97	C	264	ASP	-1	-0.853	-0.919	17.407	-0.093	-0.093	0.000	0.000	0.000	0.000
98	C	265	GLY	0	0.009	-0.008	15.698	0.016	0.016	0.000	0.000	0.000	0.000
99	C	266	VAL	0	0.008	0.011	10.461	-0.009	-0.009	0.000	0.000	0.000	0.000
100	C	267	VAL	0	-0.062	-0.043	9.797	0.012	0.012	0.000	0.000	0.000	0.000
101	C	268	THR	0	0.050	0.022	8.651	-0.099	-0.099	0.000	0.000	0.000	0.000
102	C	269	ILE	0	-0.071	-0.053	8.109	0.184	0.184	0.000	0.000	0.000	0.000
103	C	270	ASN	0	-0.019	-0.031	7.583	-0.313	-0.313	0.000	0.000	0.000	0.000
104	C	271	ARG	1	0.805	0.870	6.903	-0.010	-0.010	0.000	0.000	0.000	0.000
105	C	272	ASN	0	-0.005	0.015	1.899	-12.666	-13.100	5.255	-2.502	-2.319	-0.030
106	C	273	ASP	-1	-0.730	-0.812	4.446	0.176	0.248	-0.001	-0.005	-0.066	0.000
107	C	274	TYR	0	-0.112	-0.057	4.720	-0.491	-0.324	-0.001	-0.009	-0.157	0.000
108	C	275	THR	0	0.002	-0.017	7.294	0.168	0.168	0.000	0.000	0.000	0.000
109	C	276	PHE	0	-0.015	-0.012	10.557	-0.057	-0.057	0.000	0.000	0.000	0.000
110	C	277	GLN	0	-0.020	-0.004	13.477	0.042	0.042	0.000	0.000	0.000	0.000
111	C	278	LYS	1	0.852	0.903	16.733	0.165	0.165	0.000	0.000	0.000	0.000
112	C	279	ALA	0	0.047	0.042	16.044	-0.035	-0.035	0.000	0.000	0.000	0.000
113	C	280	GLN	0	-0.031	-0.019	17.816	0.042	0.042	0.000	0.000	0.000	0.000
114	C	281	VAL	0	0.025	0.016	19.279	-0.022	-0.022	0.000	0.000	0.000	0.000
115	C	282	GLU	-1	-0.823	-0.908	21.265	-0.133	-0.133	0.000	0.000	0.000	0.000
116	C	283	ALA	0	0.036	0.037	23.024	-0.008	-0.008	0.000	0.000	0.000	0.000
117	C	284	GLU	-1	-0.881	-0.960	24.710	-0.102	-0.102	0.000	0.000	0.000	0.000
118	C	285	TRP	0	-0.040	-0.011	28.124	0.000	0.000	0.000	0.000	0.000	0.000
119	C	286	VAL	0	0.028	0.009	29.531	0.007	0.007	0.000	0.000	0.000	0.000

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