FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 5R97Z

Calculation Name: 3C5R-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3C5R

Chain ID: A

ChEMBL ID:

UniProt ID: Q99728

Base Structure: X-ray

Registration Date: 2025-07-11

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 OptHSide
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 234
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1040779.41964
FMO2-HF: Nuclear repulsion 993093.709582
FMO2-HF: Total energy -47685.710058
FMO2-MP2: Total energy -47826.64955


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


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


Summations of interaction energy for fragment #1(A:-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.
-2.0842.2021.472-1.804-3.952-0.005
Interaction energy analysis for fragmet #1(A:-2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.007
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   
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].
3A-1PHE0-0.0970.0812.580-2.406-0.3201.484-0.962-2.607-0.008
4A0THR00.010-0.1113.802-0.8840.906-0.015-0.750-1.0250.003
5A0THR00.0310.1133.752-0.2270.0180.004-0.054-0.1940.000
6A425ASN00.070-0.0406.0290.0230.0230.0000.0000.0000.000
7A425ASN0-0.1090.03410.4340.0310.0310.0000.0000.0000.000
8A426HIS00.092-0.0669.227-0.087-0.0870.0000.0000.0000.000
9A426HIS0-0.0430.07813.262-0.035-0.0350.0000.0000.0000.000
10A427ARG00.007-0.12111.5350.0380.0380.0000.0000.0000.000
11A427ARG10.7840.98812.5710.2870.2870.0000.0000.0000.000
12A428GLY00.042-0.0827.3800.1260.1260.0000.0000.0000.000
13A429GLU00.090-0.0347.4100.1570.1570.0000.0000.0000.000
14A429GLU-1-0.834-0.7239.959-0.285-0.2850.0000.0000.0000.000
15A430THR00.036-0.0755.392-0.497-0.509-0.002-0.0050.0180.000
16A430THR0-0.0310.0563.670-0.0500.1270.001-0.033-0.1440.000
17A431LEU00.139-0.0856.1210.1770.1770.0000.0000.0000.000
18A431LEU0-0.0790.1227.827-0.022-0.0220.0000.0000.0000.000
19A432LEU00.109-0.1067.413-0.024-0.0240.0000.0000.0000.000
20A432LEU0-0.0440.1358.0250.0230.0230.0000.0000.0000.000
21A433HIS00.047-0.1108.6170.0500.0500.0000.0000.0000.000
22A433HIS0-0.0160.1327.719-0.112-0.1120.0000.0000.0000.000
23A434ILE00.134-0.03710.3570.0400.0400.0000.0000.0000.000
24A434ILE0-0.1240.07110.086-0.008-0.0080.0000.0000.0000.000
25A435ALA00.084-0.11911.893-0.005-0.0050.0000.0000.0000.000
26A435ALA0-0.0480.11212.6190.0030.0030.0000.0000.0000.000
27A436SER0-0.001-0.11913.105-0.004-0.0040.0000.0000.0000.000
28A436SER0-0.0560.06812.6550.0300.0300.0000.0000.0000.000
29A437ILE00.105-0.07314.6220.0210.0210.0000.0000.0000.000
30A437ILE0-0.1300.08513.978-0.009-0.0090.0000.0000.0000.000
31A438LYS00.010-0.11416.3560.0050.0050.0000.0000.0000.000
32A438LYS10.8611.05115.7820.1560.1560.0000.0000.0000.000
33A439GLY00.026-0.07017.6480.0000.0000.0000.0000.0000.000
34A440ASP00.140-0.00117.4130.0070.0070.0000.0000.0000.000
35A440ASP-1-0.998-0.80316.459-0.041-0.0410.0000.0000.0000.000
36A441ILE00.104-0.08516.9230.0140.0140.0000.0000.0000.000
37A441ILE0-0.0830.08820.2790.0010.0010.0000.0000.0000.000
38A442PRO00.010-0.10717.9100.0210.0210.0000.0000.0000.000
39A443SER00.0300.03214.8280.0230.0230.0000.0000.0000.000
40A443SER0-0.0730.01713.748-0.014-0.0140.0000.0000.0000.000
41A444VAL00.087-0.09613.3200.0230.0230.0000.0000.0000.000
42A444VAL0-0.0840.10713.8770.0030.0030.0000.0000.0000.000
43A445GLU00.118-0.09413.8600.0690.0690.0000.0000.0000.000
44A445GLU-1-1.011-0.86018.0000.1110.1110.0000.0000.0000.000
45A446TYR00.112-0.09014.8390.0460.0460.0000.0000.0000.000
46A446TYR0-0.1250.07312.161-0.021-0.0210.0000.0000.0000.000
47A447LEU00.057-0.09010.6830.0130.0130.0000.0000.0000.000
48A447LEU0-0.0800.0828.396-0.014-0.0140.0000.0000.0000.000
49A448LEU00.082-0.10110.8030.1270.1270.0000.0000.0000.000
50A448LEU0-0.0870.09111.4420.0020.0020.0000.0000.0000.000
51A449GLN00.054-0.11512.8230.0610.0610.0000.0000.0000.000
52A449GLN0-0.0880.08715.440-0.021-0.0210.0000.0000.0000.000
53A450ASN0-0.006-0.08811.808-0.002-0.0020.0000.0000.0000.000
54A450ASN0-0.1580.04511.131-0.040-0.0400.0000.0000.0000.000
55A451GLY00.012-0.1009.8650.0010.0010.0000.0000.0000.000
56A452SER0-0.001-0.0086.8840.3020.3020.0000.0000.0000.000
57A452SER0-0.0690.0527.349-0.062-0.0620.0000.0000.0000.000
58A453ASP00.096-0.1096.855-0.369-0.3690.0000.0000.0000.000
59A453ASP-1-0.925-0.7987.3051.4681.4680.0000.0000.0000.000
60A454PRO0-0.051-0.1187.9290.1850.1850.0000.0000.0000.000
61A455ASN00.0410.00110.391-0.161-0.1610.0000.0000.0000.000
62A455ASN0-0.1450.06211.496-0.131-0.1310.0000.0000.0000.000
63A456VAL00.119-0.1177.2160.1430.1430.0000.0000.0000.000
64A456VAL0-0.0860.1225.1710.0600.0600.0000.0000.0000.000
65A457LYS00.062-0.1218.265-0.212-0.2120.0000.0000.0000.000
66A457LYS10.8131.03410.000-0.377-0.3770.0000.0000.0000.000
67A458ASP00.012-0.0677.9790.0980.0980.0000.0000.0000.000
68A458ASP-1-0.838-0.83010.5010.0060.0060.0000.0000.0000.000
69A459HIS00.104-0.0879.7410.0780.0780.0000.0000.0000.000
70A459HIS0-0.1310.0688.2160.0780.0780.0000.0000.0000.000
71A460ALA00.115-0.09111.4920.0320.0320.0000.0000.0000.000
72A460ALA0-0.1160.09415.053-0.004-0.0040.0000.0000.0000.000
73A461GLY0-0.036-0.13612.9970.0130.0130.0000.0000.0000.000
74A462TRP00.040-0.04513.7840.0740.0740.0000.0000.0000.000
75A462TRP0-0.0680.12613.745-0.002-0.0020.0000.0000.0000.000
76A463THR0-0.008-0.07611.6390.0300.0300.0000.0000.0000.000
77A463THR0-0.0290.05512.4370.0020.0020.0000.0000.0000.000
78A464PRO00.030-0.0929.858-0.090-0.0900.0000.0000.0000.000
79A465LEU00.1580.02512.644-0.067-0.0670.0000.0000.0000.000
80A465LEU0-0.0820.11215.6150.0060.0060.0000.0000.0000.000
81A466HIS00.067-0.09715.692-0.036-0.0360.0000.0000.0000.000
82A466HIS0-0.0950.09716.0890.0330.0330.0000.0000.0000.000
83A467GLU00.079-0.08815.610-0.024-0.0240.0000.0000.0000.000
84A467GLU-1-0.935-0.84413.8570.0280.0280.0000.0000.0000.000
85A468ALA00.157-0.05716.742-0.038-0.0380.0000.0000.0000.000
86A468ALA0-0.0770.08617.0180.0050.0050.0000.0000.0000.000
87A469CYS00.062-0.14918.505-0.021-0.0210.0000.0000.0000.000
88A469CYS0-0.1820.08219.5050.0030.0030.0000.0000.0000.000
89A470ASN00.140-0.02320.406-0.010-0.0100.0000.0000.0000.000
90A470ASN0-0.1540.03720.360-0.012-0.0120.0000.0000.0000.000
91A471HIS0-0.015-0.11920.832-0.010-0.0100.0000.0000.0000.000
92A471HIS0-0.1410.05418.797-0.020-0.0200.0000.0000.0000.000
93A472GLY00.063-0.08522.240-0.009-0.0090.0000.0000.0000.000
94A473HIS00.0790.01220.941-0.006-0.0060.0000.0000.0000.000
95A473HIS0-0.1350.09519.4040.0070.0070.0000.0000.0000.000
96A474LEU00.207-0.08821.3690.0220.0220.0000.0000.0000.000
97A474LEU0-0.0900.11025.151-0.001-0.0010.0000.0000.0000.000
98A475LYS00.073-0.09922.7280.0180.0180.0000.0000.0000.000
99A475LYS10.8201.04321.722-0.136-0.1360.0000.0000.0000.000
100A476VAL00.079-0.09818.5150.0170.0170.0000.0000.0000.000
101A476VAL0-0.0440.11716.379-0.001-0.0010.0000.0000.0000.000
102A477VAL00.086-0.10817.9940.0390.0390.0000.0000.0000.000
103A477VAL0-0.0890.10819.8890.0000.0000.0000.0000.0000.000
104A478GLU00.118-0.09019.4390.0350.0350.0000.0000.0000.000
105A478GLU-1-0.953-0.83522.4490.1320.1320.0000.0000.0000.000
106A479LEU00.042-0.10318.2680.0150.0150.0000.0000.0000.000
107A479LEU0-0.1010.09317.349-0.001-0.0010.0000.0000.0000.000
108A480LEU00.158-0.04315.4690.0330.0330.0000.0000.0000.000
109A480LEU0-0.0950.08313.1060.0100.0100.0000.0000.0000.000
110A481LEU00.043-0.11416.3440.0630.0630.0000.0000.0000.000
111A481LEU0-0.0950.08219.430-0.006-0.0060.0000.0000.0000.000
112A482GLN00.049-0.10819.1970.0170.0170.0000.0000.0000.000
113A482GLN0-0.1170.07419.8030.0000.0000.0000.0000.0000.000
114A483HIS0-0.028-0.10315.580-0.015-0.0150.0000.0000.0000.000
115A483HIS0-0.1410.06614.619-0.003-0.0030.0000.0000.0000.000
116A484LYS00.077-0.06014.9020.0800.0800.0000.0000.0000.000
117A484LYS10.8471.02915.741-0.376-0.3760.0000.0000.0000.000
118A485ALA00.182-0.08414.7720.0740.0740.0000.0000.0000.000
119A485ALA0-0.0640.10614.844-0.008-0.0080.0000.0000.0000.000
120A486LEU00.077-0.12115.681-0.069-0.0690.0000.0000.0000.000
121A486LEU0-0.1200.10915.704-0.008-0.0080.0000.0000.0000.000
122A487VAL00.144-0.10517.8150.0060.0060.0000.0000.0000.000
123A487VAL0-0.0900.13121.6480.0000.0000.0000.0000.0000.000
124A488ASN00.035-0.09020.620-0.018-0.0180.0000.0000.0000.000
125A488ASN0-0.1320.04922.331-0.014-0.0140.0000.0000.0000.000
126A489THR00.038-0.09617.079-0.030-0.0300.0000.0000.0000.000
127A489THR0-0.0380.08215.0020.0220.0220.0000.0000.0000.000
128A490THR00.069-0.05818.492-0.020-0.0200.0000.0000.0000.000
129A490THR0-0.0500.08219.3660.0110.0110.0000.0000.0000.000
130A491GLY00.024-0.08516.3570.0500.0500.0000.0000.0000.000
131A492TYR00.1550.01717.321-0.004-0.0040.0000.0000.0000.000
132A492TYR0-0.1050.10517.541-0.009-0.0090.0000.0000.0000.000
133A493GLN00.000-0.11818.6600.0050.0050.0000.0000.0000.000
134A493GLN0-0.0330.11022.056-0.013-0.0130.0000.0000.0000.000
135A494ASN00.115-0.03520.540-0.007-0.0070.0000.0000.0000.000
136A494ASN0-0.1290.03420.7690.0080.0080.0000.0000.0000.000
137A495ASP00.192-0.10921.5390.0070.0070.0000.0000.0000.000
138A495ASP-1-0.890-0.76221.6480.0830.0830.0000.0000.0000.000
139A496SER0-0.001-0.08320.5210.0270.0270.0000.0000.0000.000
140A496SER0-0.0200.05323.026-0.001-0.0010.0000.0000.0000.000
141A497PRO00.031-0.10018.740-0.022-0.0220.0000.0000.0000.000
142A498LEU00.1590.02221.269-0.014-0.0140.0000.0000.0000.000
143A498LEU0-0.1000.10725.3800.0010.0010.0000.0000.0000.000
144A499HIS00.015-0.10624.639-0.013-0.0130.0000.0000.0000.000
145A499HIS0-0.0710.09324.3110.0120.0120.0000.0000.0000.000
146A500ASP00.093-0.07222.243-0.016-0.0160.0000.0000.0000.000
147A500ASP-1-0.887-0.79220.6100.1060.1060.0000.0000.0000.000
148A501ALA00.141-0.07223.764-0.014-0.0140.0000.0000.0000.000
149A501ALA0-0.0720.08224.3470.0030.0030.0000.0000.0000.000
150A502ALA00.063-0.11925.529-0.010-0.0100.0000.0000.0000.000
151A502ALA0-0.0980.08828.6780.0010.0010.0000.0000.0000.000
152A503LYS00.118-0.06327.490-0.007-0.0070.0000.0000.0000.000
153A503LYS10.6590.94923.637-0.070-0.0700.0000.0000.0000.000
154A504ASN00.014-0.08926.698-0.008-0.0080.0000.0000.0000.000
155A504ASN0-0.1470.04224.8650.0000.0000.0000.0000.0000.000
156A505GLY00.015-0.11728.105-0.004-0.0040.0000.0000.0000.000
157A506HIS00.0590.00427.373-0.005-0.0050.0000.0000.0000.000
158A506HIS0-0.1160.11725.4750.0020.0020.0000.0000.0000.000
159A507VAL00.167-0.10128.6460.0110.0110.0000.0000.0000.000
160A507VAL0-0.0670.09932.8380.0000.0000.0000.0000.0000.000
161A508ASP00.016-0.12529.7440.0060.0060.0000.0000.0000.000
162A508ASP-1-0.855-0.80628.3770.0730.0730.0000.0000.0000.000
163A509ILE00.118-0.10525.5160.0070.0070.0000.0000.0000.000
164A509ILE0-0.0800.11923.2520.0020.0020.0000.0000.0000.000
165A510VAL00.100-0.10226.2820.0160.0160.0000.0000.0000.000
166A510VAL0-0.0890.11828.006-0.001-0.0010.0000.0000.0000.000
167A511LYS00.038-0.11728.3970.0080.0080.0000.0000.0000.000
168A511LYS10.8611.05330.630-0.073-0.0730.0000.0000.0000.000
169A512LEU00.124-0.07826.3550.0010.0010.0000.0000.0000.000
170A512LEU0-0.0840.11823.610-0.001-0.0010.0000.0000.0000.000
171A513LEU00.089-0.08424.5320.0120.0120.0000.0000.0000.000
172A513LEU0-0.0680.09521.7270.0010.0010.0000.0000.0000.000
173A514LEU00.087-0.10425.4270.0170.0170.0000.0000.0000.000
174A514LEU0-0.1030.09129.256-0.002-0.0020.0000.0000.0000.000
175A515SER0-0.041-0.07528.6830.0030.0030.0000.0000.0000.000
176A515SER0-0.0620.03927.650-0.002-0.0020.0000.0000.0000.000
177A516TYR00.036-0.10724.630-0.005-0.0050.0000.0000.0000.000
178A516TYR0-0.0820.10822.7510.0090.0090.0000.0000.0000.000
179A517GLY0-0.004-0.12425.3220.0170.0170.0000.0000.0000.000
180A518ALA00.085-0.01425.1620.0090.0090.0000.0000.0000.000
181A518ALA0-0.0690.11225.067-0.001-0.0010.0000.0000.0000.000
182A519SER00.032-0.11026.056-0.014-0.0140.0000.0000.0000.000
183A519SER0-0.0810.07726.690-0.001-0.0010.0000.0000.0000.000
184A520ARG00.163-0.05128.1600.0000.0000.0000.0000.0000.000
185A520ARG10.7561.02031.877-0.085-0.0850.0000.0000.0000.000
186A521ASN0-0.036-0.09430.836-0.004-0.0040.0000.0000.0000.000
187A521ASN0-0.1290.02733.070-0.005-0.0050.0000.0000.0000.000
188A522ALA00.206-0.07226.999-0.008-0.0080.0000.0000.0000.000
189A522ALA0-0.0430.11526.1830.0030.0030.0000.0000.0000.000
190A523VAL0-0.041-0.14727.816-0.005-0.0050.0000.0000.0000.000
191A523VAL0-0.0680.11428.357-0.001-0.0010.0000.0000.0000.000
192A524ASN00.175-0.03925.0900.0140.0140.0000.0000.0000.000
193A524ASN0-0.1060.05525.052-0.005-0.0050.0000.0000.0000.000
194A525ILE00.016-0.13125.2100.0000.0000.0000.0000.0000.000
195A525ILE0-0.0810.08223.6630.0000.0000.0000.0000.0000.000
196A526PHE0-0.007-0.10426.519-0.004-0.0040.0000.0000.0000.000
197A526PHE0-0.0910.08326.466-0.001-0.0010.0000.0000.0000.000
198A527GLY0-0.010-0.10729.268-0.005-0.0050.0000.0000.0000.000
199A528LEU00.082-0.00930.0560.0000.0000.0000.0000.0000.000
200A528LEU0-0.0900.11630.309-0.001-0.0010.0000.0000.0000.000
201A529ARG00.040-0.10729.3800.0100.0100.0000.0000.0000.000
202A529ARG10.8851.06231.959-0.074-0.0740.0000.0000.0000.000
203A530PRO0-0.012-0.09927.643-0.007-0.0070.0000.0000.0000.000
204A531VAL00.1310.03629.919-0.004-0.0040.0000.0000.0000.000
205A531VAL0-0.0860.08634.2110.0010.0010.0000.0000.0000.000
206A532ASP00.037-0.09233.084-0.004-0.0040.0000.0000.0000.000
207A532ASP-1-0.926-0.83232.8210.0610.0610.0000.0000.0000.000
208A533TYR00.001-0.11030.902-0.006-0.0060.0000.0000.0000.000
209A533TYR0-0.1040.08329.2830.0030.0030.0000.0000.0000.000
210A534THR00.129-0.05032.436-0.003-0.0030.0000.0000.0000.000
211A534THR0-0.0730.04733.049-0.001-0.0010.0000.0000.0000.000
212A535ASP00.089-0.10234.6870.0020.0020.0000.0000.0000.000
213A535ASP-1-0.907-0.79938.7580.0300.0300.0000.0000.0000.000
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215A536ASP-1-0.855-0.82135.8340.0430.0430.0000.0000.0000.000
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