FMO DATABASE

FMODB ID: N268Q

Calculation Name: 3N3F-A-Xray540

Preferred Name: Collagen

Target Type: PROTEIN COMPLEX GROUP

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3N3F

Chain ID: A

ChEMBL ID: CHEMBL2364188

UniProt ID: P39059

Base Structure: X-ray

Registration Date: 2025-07-08

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	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-278644.286011
FMO2-HF: Nuclear repulsion	256840.662756
FMO2-HF: Total energy	-21803.623256
FMO2-MP2: Total energy	-21867.069303

3D Structure Molmil

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:1:ASN)

Summations of interaction energy for fragment #1(A:1:ASN)

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.
-10.82	-16.518	19.075	-7.923	-5.453	0.048

Interaction energy analysis for fragmet #1(A:1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.175 / q_NPA : 0.077

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].
4	A	2	LEU	0	-0.115	0.058	3.023	0.549	-0.135	0.031	1.156	-0.503	0.002
5	A	3	VAL	0	0.103	-0.100	3.804	0.187	2.047	-0.027	-1.076	-0.757	0.001
6	A	3	VAL	0	-0.067	0.124	7.631	-0.116	-0.116	0.000	0.000	0.000	0.000
7	A	4	THR	0	0.064	-0.039	6.787	-0.559	-0.559	0.000	0.000	0.000	0.000
8	A	4	THR	0	-0.048	0.048	7.215	-0.168	-0.168	0.000	0.000	0.000	0.000
9	A	5	ALA	0	0.100	-0.098	8.679	0.049	0.049	0.000	0.000	0.000	0.000
10	A	5	ALA	0	-0.100	0.088	12.620	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	6	PHE	0	-0.014	-0.124	12.112	-0.010	-0.010	0.000	0.000	0.000	0.000
12	A	6	PHE	0	-0.038	0.125	10.702	0.010	0.010	0.000	0.000	0.000	0.000
13	A	7	SER	0	0.035	-0.059	14.989	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	7	SER	0	-0.009	0.055	19.820	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	8	ASN	0	0.122	-0.040	18.443	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	8	ASN	0	-0.033	0.081	20.555	0.024	0.024	0.000	0.000	0.000	0.000
17	A	9	MET	0	0.190	-0.071	17.380	0.065	0.065	0.000	0.000	0.000	0.000
18	A	9	MET	0	-0.065	0.114	17.745	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	10	ASP	0	0.061	-0.116	17.758	0.071	0.071	0.000	0.000	0.000	0.000
20	A	10	ASP	-1	-0.967	-0.825	21.586	0.320	0.320	0.000	0.000	0.000	0.000
21	A	11	ASP	0	0.128	-0.084	18.102	0.000	0.000	0.000	0.000	0.000	0.000
22	A	11	ASP	-1	-0.911	-0.824	16.962	0.485	0.485	0.000	0.000	0.000	0.000
23	A	12	MET	0	0.127	-0.103	14.173	0.016	0.016	0.000	0.000	0.000	0.000
24	A	12	MET	0	-0.127	0.084	12.564	0.061	0.061	0.000	0.000	0.000	0.000
25	A	13	LEU	0	-0.024	-0.152	14.336	0.102	0.102	0.000	0.000	0.000	0.000
26	A	13	LEU	0	-0.084	0.116	16.634	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	14	GLN	0	0.075	-0.089	16.761	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	14	GLN	0	-0.141	0.086	17.936	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	15	LYS	0	-0.023	-0.123	13.939	-0.084	-0.084	0.000	0.000	0.000	0.000
30	A	15	LYS	1	0.818	1.030	13.136	-0.462	-0.462	0.000	0.000	0.000	0.000
31	A	16	ALA	0	0.217	-0.088	11.805	0.207	0.207	0.000	0.000	0.000	0.000
32	A	16	ALA	0	-0.047	0.124	12.885	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	17	HIS	0	-0.020	-0.104	10.437	0.213	0.213	0.000	0.000	0.000	0.000
34	A	17	HIS	0	-0.074	0.093	12.657	0.020	0.020	0.000	0.000	0.000	0.000
35	A	18	LEU	0	0.060	-0.111	10.030	-0.101	-0.101	0.000	0.000	0.000	0.000
36	A	18	LEU	0	-0.053	0.105	10.606	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	19	VAL	0	0.048	-0.109	6.433	0.073	0.073	0.000	0.000	0.000	0.000
38	A	19	VAL	0	-0.096	0.092	5.974	0.092	0.092	0.000	0.000	0.000	0.000
39	A	20	ILE	0	0.099	-0.114	3.744	-0.471	-0.413	0.001	-0.011	-0.048	0.000
40	A	20	ILE	0	-0.056	0.127	2.727	-0.633	-0.213	0.103	-0.191	-0.332	0.000
41	A	21	GLU	0	0.098	-0.119	4.457	1.602	1.717	-0.002	-0.011	-0.103	0.000
42	A	21	GLU	-1	-1.001	-0.832	7.055	0.421	0.421	0.000	0.000	0.000	0.000
43	A	22	GLY	0	-0.033	-0.133	4.212	-0.530	-0.333	-0.001	-0.038	-0.157	0.000
44	A	23	THR	0	-0.010	0.016	3.211	-1.967	-1.190	0.037	-0.299	-0.515	0.002
45	A	23	THR	0	-0.049	0.033	1.839	-6.503	-15.241	18.915	-7.250	-2.926	0.042
46	A	24	PHE	0	0.039	-0.101	3.779	-1.982	-1.685	0.018	-0.203	-0.112	0.001
47	A	24	PHE	0	-0.102	0.094	6.304	-0.127	-0.127	0.000	0.000	0.000	0.000
48	A	25	ILE	0	0.085	-0.118	7.118	0.512	0.512	0.000	0.000	0.000	0.000
49	A	25	ILE	0	-0.069	0.090	8.418	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	26	TYR	0	0.137	-0.053	9.893	-0.190	-0.190	0.000	0.000	0.000	0.000
51	A	26	TYR	0	-0.102	0.082	12.523	-0.034	-0.034	0.000	0.000	0.000	0.000
52	A	27	LEU	0	0.034	-0.119	13.001	0.054	0.054	0.000	0.000	0.000	0.000
53	A	27	LEU	0	-0.104	0.099	14.532	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	28	ARG	0	0.112	-0.074	16.200	-0.043	-0.043	0.000	0.000	0.000	0.000
55	A	28	ARG	1	0.833	1.026	15.962	-0.403	-0.403	0.000	0.000	0.000	0.000
56	A	29	ASP	0	0.103	-0.088	18.424	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	29	ASP	-1	-1.016	-0.869	21.368	0.287	0.287	0.000	0.000	0.000	0.000
58	A	30	SER	0	0.025	-0.067	20.332	-0.037	-0.037	0.000	0.000	0.000	0.000
59	A	30	SER	0	-0.066	0.046	20.025	0.015	0.015	0.000	0.000	0.000	0.000
60	A	31	THR	0	-0.082	-0.064	18.692	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	31	THR	0	-0.007	0.032	20.123	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	32	GLU	0	0.122	-0.084	17.582	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	32	GLU	-1	-0.906	-0.786	17.777	0.370	0.370	0.000	0.000	0.000	0.000
64	A	33	PHE	0	0.111	-0.099	13.593	0.048	0.048	0.000	0.000	0.000	0.000
65	A	33	PHE	0	-0.112	0.106	10.148	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	34	PHE	0	0.063	-0.088	12.120	-0.139	-0.139	0.000	0.000	0.000	0.000
67	A	34	PHE	0	-0.028	0.095	12.358	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	35	ILE	0	0.083	-0.112	8.538	0.258	0.258	0.000	0.000	0.000	0.000
69	A	35	ILE	0	-0.096	0.120	8.609	-0.058	-0.058	0.000	0.000	0.000	0.000
70	A	36	ARG	0	0.135	-0.090	7.375	-0.533	-0.533	0.000	0.000	0.000	0.000
71	A	36	ARG	1	0.702	1.028	6.692	-1.117	-1.117	0.000	0.000	0.000	0.000
72	A	37	VAL	0	0.026	-0.087	7.301	0.202	0.202	0.000	0.000	0.000	0.000
73	A	37	VAL	0	-0.085	0.063	9.468	-0.050	-0.050	0.000	0.000	0.000	0.000
74	A	38	ARG	0	0.212	-0.084	9.739	0.066	0.066	0.000	0.000	0.000	0.000
75	A	38	ARG	1	0.810	1.083	12.075	-0.282	-0.282	0.000	0.000	0.000	0.000
76	A	39	ASP	0	-0.055	-0.152	12.082	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	39	ASP	-1	-0.962	-0.821	15.953	0.331	0.331	0.000	0.000	0.000	0.000
78	A	40	GLY	0	0.053	-0.100	12.767	-0.066	-0.066	0.000	0.000	0.000	0.000
79	A	41	TRP	0	0.049	-0.015	11.663	0.176	0.176	0.000	0.000	0.000	0.000
80	A	41	TRP	0	-0.003	0.124	10.903	-0.059	-0.059	0.000	0.000	0.000	0.000
81	A	42	LYS	0	0.044	-0.093	12.362	-0.125	-0.125	0.000	0.000	0.000	0.000
82	A	42	LYS	1	0.893	1.070	12.934	-0.417	-0.417	0.000	0.000	0.000	0.000
83	A	43	LYS	0	0.137	-0.097	13.158	0.129	0.129	0.000	0.000	0.000	0.000
84	A	43	LYS	1	0.776	1.020	16.900	-0.379	-0.379	0.000	0.000	0.000	0.000
85	A	44	LEU	0	0.028	-0.134	14.348	-0.055	-0.055	0.000	0.000	0.000	0.000
86	A	44	LEU	0	-0.091	0.115	11.706	0.010	0.010	0.000	0.000	0.000	0.000
87	A	45	GLN	0	0.080	-0.107	15.305	0.000	0.000	0.000	0.000	0.000	0.000
88	A	45	GLN	0	-0.106	0.092	18.847	0.009	0.009	0.000	0.000	0.000	0.000
89	A	46	LEU	0	0.046	-0.137	18.862	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	46	LEU	0	-0.052	0.130	16.267	0.007	0.007	0.000	0.000	0.000	0.000
91	A	47	GLY	0	-0.021	-0.095	19.927	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	48	GLU	0	0.160	-0.004	23.219	0.021	0.021	0.000	0.000	0.000	0.000
93	A	48	GLU	-1	-1.041	-0.847	27.434	0.152	0.152	0.000	0.000	0.000	0.000
94	A	49	LEU	0	0.121	-0.121	24.633	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	49	LEU	0	-0.102	0.122	23.979	0.001	0.001	0.000	0.000	0.000	0.000
96	A	50	ILE	0	0.064	-0.116	25.156	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	50	ILE	0	-0.091	0.115	24.598	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	51	PRO	0	-0.069	-0.131	26.545	0.000	0.000	0.000	0.000	0.000	0.000
99	A	52	ILE	0	0.092	-0.001	28.531	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	52	ILE	0	-0.052	0.108	25.541	0.000	0.000	0.000	0.000	0.000	0.000
101	A	53	PRO	0	-0.064	-0.112	29.110	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	54	ALA	0	-0.016	-0.016	32.317	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	54	ALA	0	0.043	0.040	36.400	0.000	0.000	0.000	0.000	0.000	0.000

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