FMO DATABASE

FMODB ID: 8551Y

Calculation Name: 5MSM-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5MSM

Chain ID: B

ChEMBL ID:

UniProt ID: P49956

Base Structure: X-ray

Registration Date: 2023-06-21

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1037357.289209
FMO2-HF: Nuclear repulsion	983986.095052
FMO2-HF: Total energy	-53371.194157
FMO2-MP2: Total energy	-53523.897936

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(B:2:PRO)

Summations of interaction energy for fragment #1(B:2:PRO)

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.
-1.061	0.85	-0.017	-0.985	-0.908	0

Interaction energy analysis for fragmet #1(B:2:PRO)

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 : -0.004

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].
3	B	4	VAL	0	-0.037	-0.010	3.879	-0.253	1.658	-0.017	-0.985	-0.908
4	B	5	ASP	-1	-0.896	-0.931	6.321	-0.668	-0.668	0.000	0.000	0.000
5	B	6	ILE	0	-0.027	-0.024	9.910	-0.020	-0.020	0.000	0.000	0.000
6	B	7	ASP	-1	-0.812	-0.877	12.368	-0.169	-0.169	0.000	0.000	0.000
7	B	8	ALA	0	0.039	0.001	15.067	-0.012	-0.012	0.000	0.000	0.000
8	B	9	SER	0	-0.054	-0.036	18.536	0.034	0.034	0.000	0.000	0.000
9	B	10	GLN	0	0.058	0.024	20.415	0.032	0.032	0.000	0.000	0.000
10	B	11	TRP	0	0.020	0.005	21.262	0.012	0.012	0.000	0.000	0.000
11	B	12	GLN	0	0.009	0.007	21.114	0.028	0.028	0.000	0.000	0.000
12	B	13	LYS	1	0.980	0.994	24.596	0.120	0.120	0.000	0.000	0.000
13	B	14	LEU	0	-0.039	-0.012	24.523	0.014	0.014	0.000	0.000	0.000
14	B	15	THR	0	-0.002	-0.011	26.160	0.007	0.007	0.000	0.000	0.000
15	B	16	GLN	0	-0.028	-0.021	28.684	0.008	0.008	0.000	0.000	0.000
16	B	17	SER	0	-0.095	-0.045	30.291	0.010	0.010	0.000	0.000	0.000
17	B	18	ARG	1	0.810	0.912	29.792	0.113	0.113	0.000	0.000	0.000
18	B	19	GLU	-1	-0.734	-0.852	33.725	-0.092	-0.092	0.000	0.000	0.000
19	B	20	LYS	1	0.815	0.901	35.263	0.093	0.093	0.000	0.000	0.000
20	B	21	GLN	0	-0.003	-0.023	29.509	-0.010	-0.010	0.000	0.000	0.000
21	B	22	THR	0	-0.035	-0.014	34.850	0.004	0.004	0.000	0.000	0.000
22	B	23	THR	0	-0.006	-0.001	34.185	0.000	0.000	0.000	0.000	0.000
23	B	24	VAL	0	0.007	0.007	35.833	0.000	0.000	0.000	0.000	0.000
24	B	25	ILE	0	-0.008	0.003	32.441	-0.003	-0.003	0.000	0.000	0.000
25	B	26	THR	0	-0.015	-0.029	27.999	0.008	0.008	0.000	0.000	0.000
26	B	27	PRO	0	0.025	0.009	30.035	0.004	0.004	0.000	0.000	0.000
27	B	28	LEU	0	-0.041	-0.033	25.302	0.009	0.009	0.000	0.000	0.000
28	B	29	GLY	0	-0.030	0.010	29.201	0.002	0.002	0.000	0.000	0.000
29	B	30	MET	0	-0.026	0.001	24.712	-0.004	-0.004	0.000	0.000	0.000
30	B	31	MET	0	-0.007	-0.023	28.894	0.008	0.008	0.000	0.000	0.000
31	B	32	MET	0	0.034	0.025	26.795	-0.010	-0.010	0.000	0.000	0.000
32	B	33	LEU	0	0.007	0.001	29.484	0.010	0.010	0.000	0.000	0.000
33	B	34	GLU	-1	-0.791	-0.889	30.290	-0.164	-0.164	0.000	0.000	0.000
34	B	35	ILE	0	0.035	-0.003	32.052	0.010	0.010	0.000	0.000	0.000
35	B	36	GLN	0	-0.011	0.004	33.278	-0.012	-0.012	0.000	0.000	0.000
36	B	37	GLY	0	-0.010	-0.017	34.327	0.007	0.007	0.000	0.000	0.000
37	B	38	GLU	-1	-0.899	-0.935	31.679	-0.131	-0.131	0.000	0.000	0.000
38	B	39	LEU	0	-0.030	-0.010	33.220	0.008	0.008	0.000	0.000	0.000
39	B	40	GLU	-1	-0.851	-0.913	34.400	-0.091	-0.091	0.000	0.000	0.000
40	B	41	LEU	0	-0.033	-0.002	32.946	0.007	0.007	0.000	0.000	0.000
41	B	42	PRO	0	-0.026	-0.027	36.207	0.000	0.000	0.000	0.000	0.000
42	B	43	LYS	1	0.856	0.898	34.205	0.086	0.086	0.000	0.000	0.000
43	B	44	ASP	-1	-0.782	-0.848	34.833	-0.058	-0.058	0.000	0.000	0.000
44	B	45	PHE	0	0.027	-0.001	33.034	0.003	0.003	0.000	0.000	0.000
45	B	46	ALA	0	0.047	0.040	37.064	0.003	0.003	0.000	0.000	0.000
46	B	47	SER	0	-0.060	-0.083	38.776	0.005	0.005	0.000	0.000	0.000
47	B	48	LEU	0	-0.061	-0.020	40.421	0.003	0.003	0.000	0.000	0.000
48	B	49	ALA	0	0.052	0.024	40.160	0.002	0.002	0.000	0.000	0.000
49	B	50	ARG	1	0.881	0.929	39.982	0.048	0.048	0.000	0.000	0.000
50	B	51	ARG	1	0.903	0.959	44.706	0.045	0.045	0.000	0.000	0.000
51	B	52	ASP	-1	-0.788	-0.870	44.422	-0.053	-0.053	0.000	0.000	0.000
52	B	53	SER	0	-0.024	-0.013	46.603	0.003	0.003	0.000	0.000	0.000
53	B	54	PRO	0	0.032	0.015	48.517	-0.002	-0.002	0.000	0.000	0.000
54	B	55	ASN	0	-0.026	-0.018	49.879	-0.001	-0.001	0.000	0.000	0.000
55	B	56	GLU	-1	-0.800	-0.877	47.135	-0.054	-0.054	0.000	0.000	0.000
56	B	57	GLY	0	0.037	0.031	45.363	-0.003	-0.003	0.000	0.000	0.000
57	B	58	ARG	1	0.749	0.861	42.276	0.059	0.059	0.000	0.000	0.000
58	B	59	PHE	0	0.014	-0.001	38.160	-0.004	-0.004	0.000	0.000	0.000
59	B	60	SER	0	-0.028	0.000	38.479	0.002	0.002	0.000	0.000	0.000
60	B	61	GLU	-1	-0.887	-0.945	35.664	-0.059	-0.059	0.000	0.000	0.000
61	B	62	GLN	0	-0.095	-0.062	33.706	0.000	0.000	0.000	0.000	0.000
62	B	63	ASP	-1	-0.911	-0.952	29.585	-0.082	-0.082	0.000	0.000	0.000
63	B	64	GLY	0	0.029	0.037	30.892	-0.003	-0.003	0.000	0.000	0.000
64	B	65	GLU	-1	-0.964	-0.971	27.679	-0.112	-0.112	0.000	0.000	0.000
65	B	66	THR	0	-0.062	-0.046	32.132	0.005	0.005	0.000	0.000	0.000
66	B	67	LEU	0	0.029	0.018	32.091	-0.004	-0.004	0.000	0.000	0.000
67	B	68	ILE	0	-0.010	-0.011	34.986	0.005	0.005	0.000	0.000	0.000
68	B	69	ARG	1	0.855	0.918	36.911	0.058	0.058	0.000	0.000	0.000
69	B	70	PHE	0	0.008	-0.009	34.503	0.005	0.005	0.000	0.000	0.000
70	B	71	GLY	0	0.031	0.003	39.346	0.002	0.002	0.000	0.000	0.000
71	B	72	SER	0	-0.082	-0.036	40.789	0.002	0.002	0.000	0.000	0.000
72	B	73	LEU	0	0.006	0.009	36.921	0.000	0.000	0.000	0.000	0.000
73	B	74	GLN	0	-0.026	-0.008	40.963	0.003	0.003	0.000	0.000	0.000
74	B	75	ILE	0	-0.001	-0.018	38.861	-0.003	-0.003	0.000	0.000	0.000
75	B	76	ASP	-1	-0.843	-0.905	42.885	-0.067	-0.067	0.000	0.000	0.000
76	B	77	GLY	0	-0.011	0.008	44.247	0.003	0.003	0.000	0.000	0.000
77	B	78	GLU	-1	-0.850	-0.908	41.212	-0.096	-0.096	0.000	0.000	0.000
78	B	79	ARG	1	0.909	0.952	41.508	0.065	0.065	0.000	0.000	0.000
79	B	80	ALA	0	0.065	0.032	40.571	0.000	0.000	0.000	0.000	0.000
80	B	81	THR	0	-0.083	-0.055	42.472	0.004	0.004	0.000	0.000	0.000
81	B	82	LEU	0	0.024	0.030	37.891	-0.001	-0.001	0.000	0.000	0.000
82	B	83	PHE	0	-0.019	-0.010	41.858	0.002	0.002	0.000	0.000	0.000
83	B	84	VAL	0	0.046	0.020	39.883	-0.002	-0.002	0.000	0.000	0.000
84	B	85	GLY	0	0.038	0.011	42.153	0.004	0.004	0.000	0.000	0.000
85	B	86	LYS	1	0.820	0.886	43.852	0.054	0.054	0.000	0.000	0.000
86	B	87	LYS	1	0.946	0.969	46.730	0.054	0.054	0.000	0.000	0.000
87	B	88	GLN	0	0.018	0.028	42.487	-0.001	-0.001	0.000	0.000	0.000
88	B	89	ARG	1	0.897	0.938	45.283	0.060	0.060	0.000	0.000	0.000
89	B	90	LEU	0	0.030	0.026	39.204	0.001	0.001	0.000	0.000	0.000
90	B	91	LEU	0	-0.002	-0.012	43.132	0.001	0.001	0.000	0.000	0.000
91	B	92	GLY	0	0.055	0.019	40.148	-0.003	-0.003	0.000	0.000	0.000
92	B	93	LYS	1	0.805	0.894	38.747	0.106	0.106	0.000	0.000	0.000
93	B	94	VAL	0	0.021	0.007	36.478	-0.007	-0.007	0.000	0.000	0.000
94	B	95	THR	0	-0.043	-0.030	33.609	0.005	0.005	0.000	0.000	0.000
95	B	96	LYS	1	0.915	0.948	32.782	0.131	0.131	0.000	0.000	0.000
96	B	97	LEU	0	-0.068	-0.031	26.757	0.003	0.003	0.000	0.000	0.000
97	B	98	ASP	-1	-0.885	-0.942	28.754	-0.184	-0.184	0.000	0.000	0.000
98	B	99	VAL	0	0.012	0.006	23.339	-0.003	-0.003	0.000	0.000	0.000
99	B	100	PRO	0	-0.064	-0.043	24.965	-0.002	-0.002	0.000	0.000	0.000
100	B	101	MET	0	0.014	0.019	20.662	-0.022	-0.022	0.000	0.000	0.000
101	B	102	GLY	0	0.000	-0.005	19.611	0.020	0.020	0.000	0.000	0.000
102	B	103	ILE	0	-0.009	0.003	19.155	-0.026	-0.026	0.000	0.000	0.000
103	B	104	MET	0	-0.011	-0.014	14.615	-0.018	-0.018	0.000	0.000	0.000
104	B	105	HIS	0	0.027	0.025	15.562	-0.015	-0.015	0.000	0.000	0.000
105	B	106	PHE	0	0.047	0.004	9.631	-0.051	-0.051	0.000	0.000	0.000
106	B	107	ASN	0	-0.007	0.002	11.899	0.054	0.054	0.000	0.000	0.000
107	B	108	SER	0	0.070	0.007	9.341	-0.003	-0.003	0.000	0.000	0.000
108	B	109	LYS	1	0.869	0.946	9.604	0.078	0.078	0.000	0.000	0.000
109	B	110	ASP	-1	-0.815	-0.885	10.122	-0.030	-0.030	0.000	0.000	0.000
110	B	111	ASN	0	-0.054	-0.027	4.833	-0.134	-0.134	0.000	0.000	0.000
111	B	112	LYS	1	0.896	0.939	6.158	0.029	0.029	0.000	0.000	0.000
112	B	113	VAL	0	-0.006	-0.005	8.746	0.013	0.013	0.000	0.000	0.000
113	B	114	GLU	-1	-0.945	-0.961	11.099	-0.218	-0.218	0.000	0.000	0.000
114	B	115	LEU	0	-0.035	-0.018	14.782	-0.011	-0.011	0.000	0.000	0.000
115	B	116	VAL	0	0.003	-0.004	17.632	0.032	0.032	0.000	0.000	0.000
116	B	117	ASP	-1	-0.720	-0.870	20.482	-0.153	-0.153	0.000	0.000	0.000
117	B	118	VAL	0	-0.067	-0.022	21.785	-0.026	-0.026	0.000	0.000	0.000
118	B	119	MET	0	0.009	0.032	24.017	0.025	0.025	0.000	0.000	0.000
119	B	120	LYS	1	0.962	0.967	26.365	0.166	0.166	0.000	0.000	0.000
120	B	121	TYR	0	0.017	0.007	29.173	0.008	0.008	0.000	0.000	0.000
121	B	122	LYS	1	0.893	0.948	29.417	0.157	0.157	0.000	0.000	0.000
122	B	123	VAL	0	-0.029	-0.003	32.082	0.008	0.008	0.000	0.000	0.000
123	B	124	ILE	0	-0.034	-0.012	32.978	-0.005	-0.005	0.000	0.000	0.000
124	B	125	PHE	0	0.008	0.001	35.470	0.008	0.008	0.000	0.000	0.000
125	B	126	LYS	1	0.848	0.924	33.188	0.126	0.126	0.000	0.000	0.000
126	B	127	ASP	-1	-0.863	-0.930	38.482	-0.085	-0.085	0.000	0.000	0.000
127	B	128	ARG	1	0.945	0.972	41.517	0.070	0.070	0.000	0.000	0.000
128	B	129	PRO	0	-0.006	-0.010	41.426	0.002	0.002	0.000	0.000	0.000
129	B	130	LEU	0	-0.003	0.015	44.132	0.003	0.003	0.000	0.000	0.000
130	B	131	PRO	0	0.040	0.015	47.474	-0.001	-0.001	0.000	0.000	0.000
131	B	132	ILE	0	0.022	0.013	48.381	-0.001	-0.001	0.000	0.000	0.000
132	B	133	MET	0	0.007	0.015	50.484	0.002	0.002	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:PRO)