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: 9MQN2

Calculation Name: 3D33-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3D33

Chain ID: A

ChEMBL ID:

UniProt ID: A6KX32

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 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 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -666573.92369
FMO2-HF: Nuclear repulsion 629601.000213
FMO2-HF: Total energy -36972.923477
FMO2-MP2: Total energy -37079.94669


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:34:PRO)


Summations of interaction energy for fragment #1(A:34: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.
-6.413-3.0680.127-1.743-1.731-0.003
Interaction energy analysis for fragmet #1(A:34:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.035
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].
3A35VAL0-0.0660.1093.977-0.0540.4910.003-0.185-0.3640.000
4A36LYS00.112-0.0823.041-4.091-1.2910.124-1.558-1.367-0.003
5A36LYS10.7821.0236.4181.7681.7680.0000.0000.0000.000
6A37ASP00.073-0.1315.7450.4880.4880.0000.0000.0000.000
7A37ASP-1-0.947-0.8137.047-1.208-1.2080.0000.0000.0000.000
8A38VAL0-0.001-0.1247.792-0.059-0.0590.0000.0000.0000.000
9A38VAL0-0.1350.06810.6710.0080.0080.0000.0000.0000.000
10A39GLU00.196-0.09411.4590.0800.0800.0000.0000.0000.000
11A39GLU-1-1.035-0.82712.601-0.662-0.6620.0000.0000.0000.000
12A40LEU0-0.011-0.13813.3790.0180.0180.0000.0000.0000.000
13A40LEU0-0.1030.07615.0000.0150.0150.0000.0000.0000.000
14A41ASP00.114-0.11716.6900.0110.0110.0000.0000.0000.000
15A41ASP-1-0.993-0.82119.327-0.403-0.4030.0000.0000.0000.000
16A42GLY0-0.025-0.11220.0120.0070.0070.0000.0000.0000.000
17A43ARG00.0980.00423.3140.0050.0050.0000.0000.0000.000
18A43ARG10.6850.95626.7540.1570.1570.0000.0000.0000.000
19A44TRP00.111-0.11023.5530.0010.0010.0000.0000.0000.000
20A44TRP0-0.0660.12123.012-0.014-0.0140.0000.0000.0000.000
21A45ASP00.063-0.10224.960-0.002-0.0020.0000.0000.0000.000
22A45ASP-1-0.898-0.80129.006-0.152-0.1520.0000.0000.0000.000
23A46ASP0-0.112-0.15427.407-0.009-0.0090.0000.0000.0000.000
24A46ASP-1-0.814-0.87029.749-0.106-0.1060.0000.0000.0000.000
25A54ASN00.1380.04418.8010.0010.0010.0000.0000.0000.000
26A54ASN0-0.1380.02715.983-0.017-0.0170.0000.0000.0000.000
27A55CYS00.102-0.10118.8510.0320.0320.0000.0000.0000.000
28A55CYS0-0.0990.12817.8640.0050.0050.0000.0000.0000.000
29A56PRO0-0.020-0.10417.679-0.020-0.0200.0000.0000.0000.000
30A57ILE00.036-0.03017.5330.0110.0110.0000.0000.0000.000
31A57ILE0-0.0120.13917.087-0.003-0.0030.0000.0000.0000.000
32A58THR00.045-0.06112.857-0.006-0.0060.0000.0000.0000.000
33A58THR0-0.0320.07111.815-0.008-0.0080.0000.0000.0000.000
34A59VAL00.108-0.10212.2760.0790.0790.0000.0000.0000.000
35A59VAL0-0.0800.11712.4960.0060.0060.0000.0000.0000.000
36A60PHE00.050-0.0708.060-0.047-0.0470.0000.0000.0000.000
37A60PHE0-0.0800.0837.1570.0790.0790.0000.0000.0000.000
38A61THR0-0.001-0.1038.3450.3570.3570.0000.0000.0000.000
39A61THR0-0.0060.0808.8260.0880.0880.0000.0000.0000.000
40A62ASP00.095-0.1236.878-1.118-1.1180.0000.0000.0000.000
41A62ASP-1-0.996-0.8226.237-1.054-1.0540.0000.0000.0000.000
42A63GLY00.018-0.1027.4680.5400.5400.0000.0000.0000.000
43A64TYR0-0.025-0.0129.475-0.180-0.1800.0000.0000.0000.000
44A64TYR0-0.1080.04913.3730.0410.0410.0000.0000.0000.000
45A65LEU00.193-0.10111.7830.1300.1300.0000.0000.0000.000
46A65LEU0-0.1100.11711.7870.0270.0270.0000.0000.0000.000
47A66LEU00.130-0.08311.333-0.239-0.2390.0000.0000.0000.000
48A66LEU0-0.1030.09613.6550.0150.0150.0000.0000.0000.000
49A67THR0-0.007-0.11912.1170.1430.1430.0000.0000.0000.000
50A67THR0-0.0470.07411.3810.0690.0690.0000.0000.0000.000
51A68LEU00.115-0.07112.712-0.130-0.1300.0000.0000.0000.000
52A68LEU0-0.0690.10316.3720.0060.0060.0000.0000.0000.000
53A69LYS00.069-0.08714.7830.0560.0560.0000.0000.0000.000
54A69LYS10.8471.04811.7370.2150.2150.0000.0000.0000.000
55A70ASN00.162-0.08715.877-0.041-0.0410.0000.0000.0000.000
56A70ASN0-0.0810.10019.8950.0050.0050.0000.0000.0000.000
57A71ALA00.093-0.09418.5940.0260.0260.0000.0000.0000.000
58A71ALA0-0.1050.08117.530-0.001-0.0010.0000.0000.0000.000
59A72SER0-0.083-0.11319.2960.0290.0290.0000.0000.0000.000
60A72SER0-0.0130.06822.481-0.001-0.0010.0000.0000.0000.000
61A73PRO0-0.051-0.13322.276-0.005-0.0050.0000.0000.0000.000
62A74ASP00.0790.01224.6340.0150.0150.0000.0000.0000.000
63A74ASP-1-0.840-0.76226.370-0.154-0.1540.0000.0000.0000.000
64A75ARG00.108-0.05927.3520.0090.0090.0000.0000.0000.000
65A75ARG10.6040.90526.6740.1570.1570.0000.0000.0000.000
66A76ASP00.148-0.09427.381-0.011-0.0110.0000.0000.0000.000
67A76ASP-1-0.958-0.82530.367-0.118-0.1180.0000.0000.0000.000
68A77MET00.018-0.10825.0230.0010.0010.0000.0000.0000.000
69A77MET0-0.0860.08721.275-0.007-0.0070.0000.0000.0000.000
70A78THR00.036-0.09925.9860.0110.0110.0000.0000.0000.000
71A78THR0-0.0810.05326.9780.0030.0030.0000.0000.0000.000
72A79ILE00.080-0.06422.255-0.010-0.0100.0000.0000.0000.000
73A79ILE0-0.0820.08319.782-0.007-0.0070.0000.0000.0000.000
74A80ARG00.122-0.08923.2220.0170.0170.0000.0000.0000.000
75A80ARG10.7491.01425.3260.2170.2170.0000.0000.0000.000
76A81ILE00.066-0.10321.694-0.022-0.0220.0000.0000.0000.000
77A81ILE0-0.1050.08719.086-0.007-0.0070.0000.0000.0000.000
78A82THR00.009-0.09722.6570.0270.0270.0000.0000.0000.000
79A82THR0-0.0300.06024.9650.0110.0110.0000.0000.0000.000
80A83ASP00.061-0.05123.412-0.040-0.0400.0000.0000.0000.000
81A83ASP-1-0.849-0.81624.556-0.261-0.2610.0000.0000.0000.000
82A84MET00.094-0.12323.7590.0330.0330.0000.0000.0000.000
83A84MET0-0.0890.12322.1650.0060.0060.0000.0000.0000.000
84A85ALA00.093-0.09325.2080.0120.0120.0000.0000.0000.000
85A85ALA0-0.1120.10626.3220.0020.0020.0000.0000.0000.000
86A86LYS0-0.055-0.17027.5750.0180.0180.0000.0000.0000.000
87A86LYS10.8541.04629.7920.1890.1890.0000.0000.0000.000
88A87GLY0-0.006-0.08228.3450.0160.0160.0000.0000.0000.000
89A88GLY0-0.036-0.02428.8380.0140.0140.0000.0000.0000.000
90A89VAL00.107-0.01826.986-0.027-0.0270.0000.0000.0000.000
91A89VAL0-0.0900.11926.8640.0020.0020.0000.0000.0000.000
92A90VAL0-0.008-0.12524.9150.0250.0250.0000.0000.0000.000
93A90VAL0-0.0840.10422.862-0.003-0.0030.0000.0000.0000.000
94A91TYR00.111-0.10123.6870.0140.0140.0000.0000.0000.000
95A91TYR0-0.0860.08922.655-0.009-0.0090.0000.0000.0000.000
96A92GLU00.060-0.10325.168-0.022-0.0220.0000.0000.0000.000
97A92GLU-1-0.897-0.78627.621-0.186-0.1860.0000.0000.0000.000
98A93ASN00.082-0.09225.4930.0160.0160.0000.0000.0000.000
99A93ASN0-0.1400.04823.8020.0140.0140.0000.0000.0000.000
100A94ASP00.137-0.07726.272-0.020-0.0200.0000.0000.0000.000
101A94ASP-1-0.966-0.80229.879-0.164-0.1640.0000.0000.0000.000
102A95ILE00.074-0.12425.5170.0150.0150.0000.0000.0000.000
103A95ILE0-0.1280.09422.968-0.005-0.0050.0000.0000.0000.000
104A96PRO0-0.009-0.11327.0530.0000.0000.0000.0000.0000.000
105A97GLU00.181-0.00327.437-0.011-0.0110.0000.0000.0000.000
106A97GLU-1-1.016-0.82428.287-0.098-0.0980.0000.0000.0000.000
107A98VAL00.036-0.08226.680-0.007-0.0070.0000.0000.0000.000
108A98VAL0-0.0880.08629.2850.0020.0020.0000.0000.0000.000
109A99GLN00.000-0.12725.4080.0100.0100.0000.0000.0000.000
110A99GLN0-0.0770.08125.438-0.007-0.0070.0000.0000.0000.000
111A100SER0-0.009-0.12523.308-0.015-0.0150.0000.0000.0000.000
112A100SER0-0.0420.07223.746-0.003-0.0030.0000.0000.0000.000
113A101ALA00.195-0.07020.876-0.030-0.0300.0000.0000.0000.000
114A101ALA0-0.0890.10320.6230.0060.0060.0000.0000.0000.000
115A102TYR00.082-0.09117.772-0.025-0.0250.0000.0000.0000.000
116A102TYR0-0.1630.04314.262-0.001-0.0010.0000.0000.0000.000
117A103ILE00.015-0.11417.5610.0430.0430.0000.0000.0000.000
118A103ILE0-0.0390.13418.982-0.004-0.0040.0000.0000.0000.000
119A104THR00.025-0.08216.017-0.065-0.0650.0000.0000.0000.000
120A104THR0-0.0330.07114.5460.0190.0190.0000.0000.0000.000
121A105ILE00.040-0.11416.1500.0680.0680.0000.0000.0000.000
122A105ILE0-0.0520.12317.518-0.003-0.0030.0000.0000.0000.000
123A106SER00.071-0.05216.216-0.085-0.0850.0000.0000.0000.000
124A106SER0-0.0460.05018.328-0.004-0.0040.0000.0000.0000.000
125A107ILE00.037-0.09816.2550.0650.0650.0000.0000.0000.000
126A107ILE0-0.0560.12113.373-0.001-0.0010.0000.0000.0000.000
127A108ALA00.161-0.08816.964-0.020-0.0200.0000.0000.0000.000
128A108ALA0-0.0730.10716.9060.0090.0090.0000.0000.0000.000
129A109ASN0-0.001-0.08017.7770.0090.0090.0000.0000.0000.000
130A109ASN0-0.1270.04721.9400.0030.0030.0000.0000.0000.000
131A110PHE00.063-0.13920.0540.0450.0450.0000.0000.0000.000
132A110PHE00.0110.15319.264-0.005-0.0050.0000.0000.0000.000
133A111PRO0-0.004-0.09720.447-0.016-0.0160.0000.0000.0000.000
134A112ALA00.1510.03319.193-0.039-0.0390.0000.0000.0000.000
135A112ALA0-0.1060.10219.5880.0050.0050.0000.0000.0000.000
136A113GLU00.063-0.10119.2120.0370.0370.0000.0000.0000.000
137A113GLU-1-0.949-0.84321.868-0.340-0.3400.0000.0000.0000.000
138A114GLU00.089-0.12818.823-0.072-0.0720.0000.0000.0000.000
139A114GLU-1-1.010-0.84318.424-0.516-0.5160.0000.0000.0000.000
140A115TYR00.032-0.13318.9370.0640.0640.0000.0000.0000.000
141A115TYR0-0.1260.06418.6940.0230.0230.0000.0000.0000.000
142A116LYS00.149-0.07219.077-0.067-0.0670.0000.0000.0000.000
143A116LYS10.7621.01222.0550.3010.3010.0000.0000.0000.000
144A117LEU00.067-0.12418.3380.0420.0420.0000.0000.0000.000
145A117LEU0-0.1130.10016.074-0.016-0.0160.0000.0000.0000.000
146A118GLU00.093-0.10519.839-0.023-0.0230.0000.0000.0000.000
147A118GLU-1-0.898-0.80323.475-0.264-0.2640.0000.0000.0000.000
148A119ILE00.046-0.09821.2100.0080.0080.0000.0000.0000.000
149A119ILE0-0.0800.10418.091-0.004-0.0040.0000.0000.0000.000
150A120THR00.029-0.09822.405-0.003-0.0030.0000.0000.0000.000
151A120THR0-0.0290.08725.9810.0010.0010.0000.0000.0000.000
152A121GLY00.008-0.09425.8800.0000.0000.0000.0000.0000.000
153A122THR0-0.004-0.01827.6730.0020.0020.0000.0000.0000.000
154A122THR0-0.0360.11230.7640.0020.0020.0000.0000.0000.000
155A123PRO0-0.008-0.11631.3430.0050.0050.0000.0000.0000.000
156A124SER00.0000.02630.7210.0000.0000.0000.0000.0000.000
157A124SER0-0.0390.04731.0060.0000.0000.0000.0000.0000.000
158A125GLY00.042-0.07826.6510.0010.0010.0000.0000.0000.000
159A126HIS00.1330.01225.2110.0030.0030.0000.0000.0000.000
160A126HIS0-0.1580.05225.203-0.001-0.0010.0000.0000.0000.000
161A127LEU00.086-0.08920.7970.0130.0130.0000.0000.0000.000
162A127LEU0-0.0880.10819.289-0.004-0.0040.0000.0000.0000.000
163A128THR00.022-0.10420.718-0.002-0.0020.0000.0000.0000.000
164A128THR0-0.0320.07621.0860.0120.0120.0000.0000.0000.000
165A129GLY00.076-0.03916.699-0.016-0.0160.0000.0000.0000.000
166A130TYR00.004-0.02216.2490.0490.0490.0000.0000.0000.000
167A130TYR0-0.0280.12117.5040.0240.0240.0000.0000.0000.000
168A131PHE00.053-0.09414.438-0.102-0.1020.0000.0000.0000.000
169A131PHE0-0.0760.08113.637-0.003-0.0030.0000.0000.0000.000
170A132THR00.074-0.09014.3270.1000.1000.0000.0000.0000.000
171A132THR0-0.0030.10414.833-0.028-0.0280.0000.0000.0000.000
172A133LYS00.104-0.09413.938-0.166-0.1660.0000.0000.0000.000
173A133LYS10.6771.00715.6730.4220.4220.0000.0000.0000.000
174A134GLU0-0.110-0.17014.4470.1120.1120.0000.0000.0000.000
175A134GLU-1-0.807-0.86713.542-0.511-0.5110.0000.0000.0000.000